U.S. patent application number 12/984939 was filed with the patent office on 2011-12-15 for delta3, fthma-070, tango85, tango77, spoil, neokine, tango129, and integrin alpha subunit protein and nucleic acid molecules and uses thereof.
This patent application is currently assigned to MILLENNIUM PHARMACEUTICALS, INC.. Invention is credited to David P. Gearing, Sean A. McCarthy.
Application Number | 20110306044 12/984939 |
Document ID | / |
Family ID | 46322225 |
Filed Date | 2011-12-15 |
United States Patent
Application |
20110306044 |
Kind Code |
A1 |
McCarthy; Sean A. ; et
al. |
December 15, 2011 |
DELTA3, FTHMA-070, TANGO85, TANGO77, SPOIL, NEOKINE, TANGO129, AND
INTEGRIN ALPHA SUBUNIT PROTEIN AND NUCLEIC ACID MOLECULES AND USES
THEREOF
Abstract
The invention provides novel Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 and A259 polypeptides, proteins,
and nucleic acid molecules. In addition to isolated, full-length
Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 and
A259 proteins, the invention further provides isolated Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 and A259
fusion proteins, antigenic peptides and anti-Delta3, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 and A259 antibodies. The
invention also provides Delta3, FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 and A259 nucleic acid molecules, recombinant
expression vectors containing a nucleic acid molecule of the
invention, host cells into which the expression vectors have been
introduced and non-human transgenic animals in which a Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene
has been introduced or disrupted. Diagnostic, screening and
therapeutic methods utilizing compositions of the invention are
also provided.
Inventors: |
McCarthy; Sean A.; (San
Diego, CA) ; Gearing; David P.; (Camberwell,
AU) |
Assignee: |
MILLENNIUM PHARMACEUTICALS,
INC.
Cambridge
MA
|
Family ID: |
46322225 |
Appl. No.: |
12/984939 |
Filed: |
January 5, 2011 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11974478 |
Oct 12, 2007 |
7897725 |
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12984939 |
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11175714 |
Jul 5, 2005 |
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11974478 |
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10417719 |
Apr 17, 2003 |
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11175714 |
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09568218 |
May 9, 2000 |
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10417719 |
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08872855 |
Jun 11, 1997 |
6121045 |
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09568218 |
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08832633 |
Apr 4, 1997 |
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Current U.S.
Class: |
435/6.11 ;
435/188; 435/320.1; 435/325; 435/375; 435/69.1; 435/7.92; 436/501;
530/324; 530/350; 530/387.3; 530/387.9; 530/391.3; 530/409;
536/23.5 |
Current CPC
Class: |
A61K 38/00 20130101;
C07K 2319/00 20130101; C12Q 1/6876 20130101; C07K 14/47 20130101;
C12Q 1/48 20130101 |
Class at
Publication: |
435/6.11 ;
536/23.5; 435/320.1; 435/325; 435/69.1; 436/501; 435/375; 530/350;
530/324; 530/387.9; 530/387.3; 435/7.92; 530/409; 530/391.3;
435/188 |
International
Class: |
G01N 33/566 20060101
G01N033/566; C12N 15/85 20060101 C12N015/85; C12N 5/10 20060101
C12N005/10; C12P 21/02 20060101 C12P021/02; C12N 5/071 20100101
C12N005/071; C12N 9/96 20060101 C12N009/96; C07K 14/47 20060101
C07K014/47; C07K 19/00 20060101 C07K019/00; C07K 16/18 20060101
C07K016/18; G01N 33/53 20060101 G01N033/53; C07K 1/107 20060101
C07K001/107; C12N 15/12 20060101 C12N015/12; C12Q 1/68 20060101
C12Q001/68 |
Claims
1-12. (canceled)
13. An isolated nucleic acid molecule selected from the group
consisting of: a) a nucleic acid molecule comprising a nucleotide
sequence which is at least 80% identical to the nucleotide sequence
of SEQ ID NO: 1 or SEQ ID NO:3; b) a nucleic acid molecule
comprising a fragment of at least 500 nucleotides of the nucleotide
sequence of SEQ ID NO:1 or SEQ ID NO:3; c) a nucleic acid molecule
which encodes a polypeptide comprising the amino acid sequence of
SEQ ID NO:2; d) a nucleic acid molecule which encodes a fragment of
a polypeptide comprising the amino acid sequence of SEQ ID NO:2,
wherein the fragment comprises at least 100 contiguous amino acids
of SEQ ID NO:2; and e) a nucleic acid molecule which encodes a
naturally occurring allelic variant of a polypeptide comprising the
amino acid sequence of SEQ ID NO:2, wherein the nucleic acid
molecule hybridizes to a nucleic acid molecule comprising SEQ ID
NO:1, 3, or a complement thereof, under stringent conditions.
14. The isolated nucleic acid molecule of claim 13, further
comprising a fragment of at least 1000 nucleotides of the
nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3.
15. The isolated nucleic acid molecule of claim 13, further
comprising a fragment of at least 1500 nucleotides of the
nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3.
16. The isolated nucleic acid molecule of claim 13, further
comprising a fragment of at least 2000 nucleotides of the
nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3.
17. The isolated nucleic acid molecule of claim 13, which encodes a
fragment of a polypeptide comprising the amino acid sequence of SEQ
ID NO:2, wherein the fragment comprises at least 100 contiguous
amino acids of SEQ ID NO:2.
18. The isolated nucleic acid molecule of claim 13, which encodes a
fragment of a polypeptide comprising the amino acid sequence of SEQ
ID NO:2, wherein the fragment comprises at least 200 contiguous
amino acids of SEQ ID NO:2.
19. The isolated nucleic acid molecule of claim 13, which is
selected from the group consisting of: a) a nucleic acid comprising
the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3; and b) a
nucleic acid molecule which encodes a polypeptide comprising the
amino acid sequence of SEQ ID NO:2.
20. The nucleic acid molecule of claim 13 further comprising vector
nucleic acid sequences.
21. The nucleic acid molecule of claim 13 further comprising
nucleic acid sequences encoding a heterologous polypeptide.
22. A host cell which contains the nucleic acid molecule of claim
13.
23. The host cell of claim 22 which is a mammalian host cell.
24. A non-human mammalian host cell containing the nucleic acid
molecule of claim 13.
25. An isolated polypeptide selected from the group consisting of:
a) a polypeptide which is encoded by a nucleic acid molecule
comprising a nucleotide sequence which is at least 80% identical to
a nucleic acid comprising the nucleotide sequence of SEQ ID NO:1,
SEQ ID NO:3, or a complement thereof; b) a naturally occurring
allelic variant of a polypeptide comprising the amino acid sequence
of SEQ ID NO:2, wherein the polypeptide is encoded by a nucleic
acid molecule which hybridizes to a nucleic acid molecule
comprising SEQ ID NO:1 or SEQ ID NO:3; and c) a fragment of a
polypeptide comprising the amino acid sequence of SEQ ID NO:2,
wherein the fragment comprises at least 100 contiguous amino acids
of SEQ ID NO:2.
26. The isolated polypeptide of claim 25, comprising a fragment
which comprises at least 100 contiguous amino acids of SEQ ID
NO:2.
27. The isolated polypeptide of claim 25, comprising a fragment
which comprises at least 200 contiguous amino acids of SEQ ID
NO:2.
28. The isolated polypeptide of claim 25, comprising a fragment
which comprises at least 500 contiguous amino acids of SEQ ID
NO:2.
29. The isolated polypeptide of claim 25, comprising a fragment
which is at least 90% homologous to the amino acid sequence of SEQ
ID NO:2.
30. The isolated polypeptide of claim 25, comprising a fragment
which is at least 95% homologous to the amino acid sequence of SEQ
ID NO:2.
31. The isolated polypeptide of claim 25, comprising the amino acid
sequence of SEQ ID NO:2.
32. The isolated polypeptide of claim 25 further comprising
heterologous amino acid sequences.
33. An antibody which selectively binds to a polypeptide of claim
25.
34. The antibody of claim 33, which is a monoclonal antibody.
35. The antibody of claim 34, comprising an immunologically active
portion selected from the group consisting of: a) an scFV fragment;
b) a dcFV fragment; c) an Fab fragment; and d) an F(ab').sub.2
fragment.
36. The antibody of claim 34, wherein the antibody is selected from
the group consisting of: a) a chimeric antibody; b) a humanized
antibody; c) a human antibody; d) a non-human antibody; and e) a
single chain antibody.
37. A method for producing a polypeptide selected from the group
consisting of: a) a polypeptide comprising the amino acid sequence
of SEQ ID NO:2; b) a polypeptide comprising a fragment of the amino
acid sequence of SEQ ID NO:2, wherein the fragment comprises at
least 100 contiguous amino acids of SEQ ID NO:2; c) a naturally
occurring allelic variant of a polypeptide comprising the amino
acid sequence of SEQ ID NO:2, or the amino acid sequence encoded by
the cDNA insert of the plasmid deposited with the ATCC as Accession
Number ______, wherein the polypeptide is encoded by a nucleic acid
molecule which hybridizes to a nucleic acid molecule comprising SEQ
ID NO:1, SEQ ID NO:3, or a complement thereof under stringent
conditions; comprising culturing the host cell of claim 22 under
conditions in which the nucleic acid molecule is expressed.
38. A method for detecting the presence of a polypeptide of claim
25 in a sample, comprising: contacting the sample with a compound
which selectively binds to a polypeptide of claim 25; and
determining whether the compound binds to the polypeptide in the
sample.
39. The method of claim 38, wherein the compound which binds to the
polypeptide is an antibody.
40. A kit comprising a compound which selectively binds to a
polypeptide of claim 25 and instructions for use.
41. A method for detecting the presence of a nucleic acid molecule
of claim 13 in a sample, comprising the steps of: contacting the
sample with a nucleic acid probe or primer which selectively
hybridizes to the nucleic acid molecule; and determining whether
the nucleic acid probe or primer binds to a nucleic acid molecule
in the sample.
42. The method of claim 41, wherein the sample comprises mRNA
molecules and is contacted with a nucleic acid probe.
43. A kit comprising a compound which selectively hybridizes to a
nucleic acid molecule of claim 13 and instructions for use.
44. A method for identifying a compound which binds to a
polypeptide of claim 25 comprising the steps of: contacting a
polypeptide, or a cell expressing a polypeptide of claim 25 with a
test compound; and determining whether the polypeptide binds to the
test compound.
45. The method of claim 44, wherein the binding of the test
compound to the polypeptide is detected by a method selected from
the group consisting of: a) detection of binding by direct
detecting of test compound/polypeptide binding; b) detection of
binding using a competition binding assay; and c) detection of
binding using an assay for Delta3-mediated signal transduction.
46. A method for modulating the activity of a polypeptide of claim
25 comprising contacting a polypeptide or a cell expressing a
polypeptide of claim 25 with a compound which binds to the
polypeptide in a sufficient concentration to modulate the activity
of the polypeptide.
47. A method for identifying a compound which modulates the
activity of a polypeptide of claim 25, comprising: contacting a
polypeptide of claim 25 with a test compound; and determining the
effect of the test compound on the activity of the polypeptide to
thereby identify a compound which modulates the activity of the
polypeptide.
48. An isolated antibody, or portion thereof, that specifically
binds to a polypeptide selected from the group consisting of: a)
the polypeptide comprising the amino acid sequence of SEQ ID NO:2;
b) the polypeptide encoded by the nucleic acid molecule of SEQ ID
NO: 1 or 3; and c) the polypeptide encoded by the nucleotide
sequence contained in the plasmid deposited with the ATCC as
Accession number 98348.
49. The antibody, or portion thereof, of claim 48, wherein said
antibody specifically binds to the polypeptide comprising the amino
acid sequence of SEQ ID NO:2.
50. The antibody, or portion thereof, of claim 48, wherein said
antibody specifically binds to the polypeptide encoded by the
nucleic acid molecule of SEQ ID NO: 1 or 3.
51. The antibody, or portion thereof, of claim 48, wherein said
antibody specifically binds to the polypeptide encoded by the
nucleotide sequence contained in the plasmid deposited with the
ATCC as Accession number 98348.
52. The antibody, or portion thereof, of claim 48, wherein said
antibody is selected from the group consisting of: i) a monoclonal
antibody; ii) a polyclonal antibody; iii) a bispecific antibody;
and iii) a chimeric antibody.
53. The antibody, or portion thereof, of claim 48, wherein said
portion is a F(ab) fragment or a F(ab').sub.2 fragment.
54. The antibody, or portion thereof, of claim 48, wherein said
antibody binds to amino acid residues 18-529 of SEQ ID NO:2.
55. The antibody, or portion thereof, of claim 48, wherein said
antibody is detectably labeled.
56. The antibody, or portion thereof, of claim 55, wherein the
detectable label is selected from the group consisting of: a) an
enzyme; b) a fluorescent material; c) a luminescent material; d) a
bioluminescent material; and e) a radioactive material.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 11/175,714, filed Jul. 5, 2005, pending.
[0002] U.S. patent application Ser. No. 11/175,714, filed Jul. 5,
2005, is a continuation-in-part of U.S. patent application Ser. No.
10/417,719, filed Apr. 17, 2003, now abandoned, which is a
continuation of U.S. patent application Ser. No. 09/568,218, filed
May 9, 2000, now abandoned, which is a continuation-in-part of U.S.
patent application Ser. No. 08/872,855, filed Jun. 11, 1997, now
U.S. Pat. No. 6,121,045, which is a continuation-in-part of U.S.
patent application Ser. No. 08/832,633, filed Apr. 4, 1997, now
abandoned.
[0003] U.S. patent application Ser. No. 11/175,714, filed Jul. 5,
2005, is also a continuation-in-part of U.S. patent application
Ser. No. 10/895,676, filed Jul. 21, 2004, now abandoned, which is a
continuation of U.S. patent application Ser. No. 10/105,934, filed
Mar. 25, 2002, now abandoned, which is a continuation of U.S.
patent application Ser. No. 09/862,972, filed May 22, 2001, now
abandoned, which is a continuation of U.S. patent application Ser.
No. 09/062,389, filed Apr. 17, 1998, now abandoned, which claims
the benefit of Provisional Application Ser. No. 60/062,017, filed
Oct. 10, 1997, now abandoned, and Provisional Application Ser. No.
60/044,746, filed Apr. 18, 1997, now abandoned.
[0004] U.S. patent application Ser. No. 11/175,714, filed Jul. 5,
2005, is also a continuation-in-part of U.S. patent application
Ser. No. 10/095,407, filed Mar. 11, 2002, now abandoned, which is a
continuation of U.S. patent application Ser. No. 09/451,828, filed
Nov. 30, 1999, now abandoned, which is a divisional of U.S. patent
application Ser. No. 09/128,155, filed Aug. 3, 1998, now U.S. Pat.
No. 6,117,654, which claims the benefit of Provisional Application
Ser. No. 60/091,650, filed Jul. 2, 1998, now abandoned, and
Provisional Application Ser. No. 60/054,646, filed Aug. 4, 1997,
now abandoned.
[0005] U.S. patent application Ser. No. 11/175,714, filed Jul. 5,
2005, is also a continuation-in-part of U.S. patent application
Ser. No. 10/126,560, filed Apr. 19, 2002, now abandoned, which is a
continuation-in-part of U.S. patent application Ser. No.
09/237,571, filed Jan. 26, 1999, now abandoned, which is a
continuation-in-part of U.S. patent application Ser. No.
09/013,810, filed Jan. 27, 1998, now U.S. Pat. No. 6,197,551.
[0006] U.S. patent application Ser. No. 11/175,714, filed Jul. 5,
2005, is also a continuation-in-part of U.S. patent application
Ser. No. 10/413,899, filed Apr. 14, 2003, now abandoned, which is a
divisional of U.S. patent application Ser. No. 09/940,240, filed
Aug. 27, 2001, now abandoned, which is a continuation of U.S.
patent application Ser. No. 09/248,239, filed Feb. 10, 1999, now
abandoned, which is a continuation-in-part of U.S. patent
application Ser. No. 09/023,664, filed Feb. 10, 1998, now
abandoned.
[0007] U.S. patent application Ser. No. 11/175,714, filed Jul. 5,
2005, is also a continuation-in-part of U.S. patent application
Ser. No. 10/105,150, filed Mar. 25, 2002, now abandoned, which is a
continuation of U.S. patent application Ser. No. 10/060,680, filed
Jan. 30, 2002, now abandoned, which is a continuation of U.S.
patent application Ser. No. 09/057,951, filed Jan. 8, 2001, now
abandoned.
[0008] U.S. patent application Ser. No. 11/175,714, filed Jul. 5,
2005, is also a continuation-in-part of U.S. patent application
Ser. No. 10/601,368, filed Jun. 23, 2003, now abandoned, which is a
continuation of U.S. patent application Ser. No. 09/572,003, filed
May 15, 2000, now abandoned, which is a continuation-in-part of
U.S. patent application Ser. No. 09/561,263, filed Apr. 27, 2000,
now abandoned, which is a continuation-in-part of U.S. patent
application Ser. No. 09/322,790, filed May 28, 1999, now
abandoned.
[0009] The entire contents of each of the above-listed patent
applications are incorporated herein by reference.
[0010] The contents of the Sequence Listing are submitted herewith
on compact disc in duplicate. Each duplicate disc has a copy of the
file "sequence listing.txt" which is incorporated herein by this
reference. This file is 961 kilobytes and was copied onto compact
disc on Oct. 12, 2007.
BACKGROUND OF THE INVENTION
[0011] There is considerable medical interest in secreted and
membrane-associated mammalian proteins. Many such proteins, for
example, cytokines, are important for inducing the growth or
differentiation of cells with which they interact or for triggering
one or more specific cellular responses.
[0012] The demonstrated clinical utility of several secreted
proteins in the treatment of human disease, for example,
erythropoietin, granulocyte-macrophage colony stimulating factor
(GM-CSF), human growth hormone, and various interleukins,
illustrates the importance of secreted proteins.
[0013] Many membrane-associated proteins are receptors which bind a
ligand(s) and transmit an intracellular signal. As such,
membrane-associated proteins can be used to identify (or design)
small molecules which act as agonists or antagonists of the
ligand.
SUMMARY OF THE INVENTION
[0014] The present invention is based, at least in part, on the
discovery of cDNA molecules which encode the TANGO 24 (DELTA3),
FTHMA-070, TANGO 85, TANGO 77, TANGO 80 (SPOIL), TANGO 112
(NEOKINE), TANGO 129 and A259 (INTEGRIN ALPHA SUBUNIT)
proteins.
Delta 3
[0015] The invention is based at least in part on the discovery of
a human gene encoding a novel Delta protein, and its mouse homolog,
each of which differs substantially from the previously described
Delta proteins. Accordingly, the novel Delta proteins of the
invention are referred to herein as Delta3 proteins. Thus, the
invention provides Delta3 proteins, and nucleic acids encoding
Delta3 proteins. An exemplary human Delta3 (hDelta3) is contained
in a plasmid which was deposited with the ATCC.RTM. on Mar. 5,
1997, and has been assigned ATCC.RTM. accession number 98348.
[0016] Based on Northern blot analysis of RNA prepared from a
number of human tissues, a 3.5 kb message was expressed in fetal
brain, lung, liver and kidney; and adult heart, placenta, lung,
skeletal muscle, kidney, pancreas, spleen, thymus, prostate,
testis, ovary, small intestine and colon. In addition, the hDelta3
gene was found to be expressed at relatively high levels in at
least some tumor cells (e.g., colon carcinoma) and its expression
can be up-regulated in response to various growth factors (e.g.,
bFGF and VEGF). Furthermore, the expression of hDelta3 was also
shown to increase in response to a signal-induced differentiation
of endothelial cells, indicating a role for hDelta3 in modulating
the growth and/or differentiation of cells, in particular
endothelial cells.
[0017] In situ hybridization of a panel of adult and embryonic
tissues using a probe complementary to mRNA of mDelta3 showed that
mDelta3 expression was most abundant and widespread during
embryogenesis. Strongest expression was observed in the eye during
all stages of embryogenesis tested, mDelta3 was also seen in the
developing lung, thymus and brown fat. In addition to the focal
expression seen above, a multi-focal, scattered pattern was seen
throughout the embryo. This signal pattern was more focused in the
cortical region of the kidney and outlining the intestinal tract.
Adult expression was highest in the ovary and the cortical regions
of the kidney and adrenal gland. The expression seen during
embryogenesis indicates that Delta3 has a role in cell growth
and/or differentiation.
[0018] As demonstrated herein, Delta3 encodes a Notch ligand. In
particular, data presented herein demonstrates that hDelta3 encodes
a Notch ligand, as it has been shown to block the differentiation
of C2C12 into myotubes in a similar fashion to other Notch ligands
(e.g., Jagged 1).
[0019] As described herein, the hDelta3 gene has been localized by
Southern blotting a membrane containing DNA from a panel of a
human/hamster mono-chromosomal somatic cell hybrids. The results
demonstrate that human Delta3 is located on human chromosome 15,
close to framework markers D15S1244 and D15S144, a chromosomal
region that has been associated with the neurological disease
Agenesis of the Corpus Callosum with Peripheral Neuropathy (ACCPN)
(Casaubon et al. (1996) Am J. Hum. Genet. 58:28). Accordingly,
polymorphisms in Delta3 are thought to be involved in this
neurological disease. As described further herein, Delta3 is also
likely to be involved in other neurological diseases as well as in
non-neurological diseases.
[0020] In one aspect, the invention features isolated Delta3
nucleic acid molecules, e.g., mammalian, such as human or mouse,
Delta3 nucleic acids. The disclosed molecules can be non-coding,
(e.g., probe, antisense or ribozyme molecules) or can encode a
functional Delta3 polypeptide, e.g., a polypeptide which can
modulate at least one activity of a Delta3 polypeptide. In one
embodiment, the nucleic acid molecules hybridize to the Delta3 gene
contained in the plasmid having American Type Culture Collection
(ATCC.RTM.) Accession Number 98348. In another embodiment, the
claimed nucleic acid is capable of hybridizing under stringent
conditions to the nucleotide sequence set forth in SEQ ID NOS: 1,
3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or the
nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, or to the complement
thereof.
[0021] In further embodiments, the nucleic acid molecule is a
Delta3 nucleic acid molecule that is at least about 50%, 55%, 60%,
70%, preferably 80%, more preferably 85%, and even more preferably
at least about 95% or 98% identical to the nucleic acids shown in
SEQ ID Nos: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45,
or the nucleotide sequence of the cDNA of a clone deposited with
the ATCC.RTM. as Accession Number 98348, or a complement
thereof.
[0022] In another embodiment, the nucleic acid molecule is a Delta3
nucleic acid that is at least about 50%, 55%, 60%, 65%, 70%,
preferably 80%, more preferably 85%, and even more preferably at
least about 95% or 98% identical to the nucleic acids shown in SEQ
ID NOS: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or
the nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348 or a complement thereof,
wherein such nucleic acid molecules encode polypeptides or proteins
that exhibit at least one structural and/or functional feature of a
polypeptide of the invention.
[0023] In another embodiment, the nucleic acid molecule encodes a
polypeptide that is at least about 55%, 60%, 70%, preferably 80%,
more preferably 85%, and even more preferably at least about 90,
95% or 98% identical to the polypeptide shown in SEQ ID NOS: 2, 25,
28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, or a complement thereof.
[0024] In another embodiment, the nucleic acid molecule encodes a
polypeptide that is at least about 55%, 60%, 70%, preferably 80%,
more preferably 85%, and even more preferably at least about 90,
95% or 98% identical to the polypeptide shown in SEQ ID NOS: 2, 25,
28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, or a complement thereof,
wherein such nucleic acid molecules encode polypeptides or proteins
that exhibit at least one structural and/or functional feature of a
polypeptide of the invention. In another embodiment, the nucleic
acid molecule encodes a polypeptide that is at least about 72%,
preferably 80%, more preferably 85%, and even more preferably at
least about 90 or 95% similar to the polypeptide shown in SEQ ID
NOS: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the hDelta
3 cDNA sequence contained in the plasmid having ATCC.RTM. Accession
Number 98348, or a complement thereof.
[0025] In another embodiment, the nucleic acid molecule encodes a
polypeptide that is at least about 72%, preferably 80%, more
preferably 85%, and even more preferably at least about 90 or 95%
similar to the polypeptide shown in SEQ ID NOS: 2, 25, 28, 30, 32,
34, 36, 38, 40, 42, 44 or 46, or the Delta 3 cDNA sequence
contained in the plasmid having ATCC.RTM. Accession Number 98348,
or a complement thereof, wherein such nucleic acid molecules encode
polypeptides or proteins that exhibit at least one structural
and/or functional feature of a polypeptide of the invention.
[0026] Also within the invention are nucleic acid molecules which
encode a fragment of a polypeptide having the amino acid sequence
of any of SEQ ID NOS: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or
46, the fragment including at least 15 (20, 25, 30, 35, 40, 45, 50,
55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150,
160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280,
290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410,
420, 440, 460, 475, 500, 525, 550, 575, 600, 625, 650, 675, or 685)
contiguous amino acids of any of SEQ ID NOS: 2, 25, 28, 30, 32, 34,
36, 38, 40, 42, 44 or 46, or the polypeptide encoded by the cDNA of
a clone deposited with the ATCC.RTM. as Accession Number 98348.
[0027] Also within the invention are nucleic acid molecules which
encode a fragment of a polypeptide having the amino acid sequence
of any of SEQ ID NOS: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or
46, the fragment including at least 15 (20, 25, 30, 35, 40, 45, 50,
55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150,
160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280,
290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410,
420, 440, 460, 475, 500, 525, 550, 575, 600, 625, 650, 675, or 685)
contiguous amino acids of any of SEQ ID NOS: 2, 25, 28, 30, 32, 34,
36, 38, 40, 42, 44 or 46, or the polypeptide encoded by the cDNA of
a clone deposited with the ATCC.RTM. as Accession Number 98348,
wherein the fragment exhibits at least one structural and/or
functional feature of a polypeptide of the invention.
[0028] The nucleic acids of the invention can comprise a nucleotide
sequence encoding at least one domain or motif of a Delta3 protein,
i.e., a domain or motif selected from the group consisting of an
amino-terminal signal peptide, a Delta-Serrated lag-2 (DSL) domain,
Epidermal Growth Factor (EGF)-like domain 1, EGF-like domain 2,
EGF-like domain 3, EGF-like domain 4, EGF-like domain 5, EGF-like
domain 6, EGF-like domain 7, EGF-like domain 8, a Delta3
extracellular domain, a transmembrane domain (TM), and a
cytoplasmic domain. Other nucleic acids of the invention encode
soluble Delta3 proteins, e.g., Delta3 proteins comprising at least
a portion, such as one or more domains, of the extracellular domain
of a Delta3 protein. A soluble Delta3 protein is a protein that is
soluble at standard physiological conditions, and includes, but is
not limited to a Delta3 protein that does not comprise a
transmembrane domain, e.g., an extracellular Delta3 domain. These
soluble polypeptides may or may not comprise a signal peptide.
Other such nucleic acids encode soluble fusion proteins comprising
Delta3 amino acid sequence and a heterologous amino acid sequence,
e.g., an immunoglobulin constant region.
[0029] The invention also provides probes and primers comprising
substantially purified oligonucleotides, which correspond to a
region of nucleotide sequence which hybridizes to at least about 6
consecutive nucleotides of the sequences set forth as SEQ ID NOs:
1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or the
nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, or a complement thereof, or
naturally-occurring mutants thereof. In preferred embodiments, the
probe/primer further includes a label group attached thereto, which
is capable of being detected.
[0030] The invention features nucleic acid molecules of at least
425, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000,
1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100,
2200, 2300, 2400, 2500, 2600, 2700, or 2800 nucleotides of the
nucleotide sequence of SEQ ID NO: 1, the nucleotide sequence of the
human Delta3 cDNA clone of ATCC.RTM. Accession NO: 98348, or a
complement thereof. The invention also features nucleic acid
molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350,
400, 450, 500, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050,
1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600,
1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050 or 2061
nucleotides of nucleic acids 1 to 2062 of SEQ ID NO:1, or a
complement thereof, wherein such nucleic acid molecules encode
polypeptides or proteins that exhibit at least one structural
and/or functional feature of a polypeptide of the invention.
[0031] The invention features nucleic acid molecules which include
a fragment of at least 340, 400, 450, 500, 550, 600, 650, 700, 750,
800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350,
1400, 1450, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850,
1900, 1950, 2000, 2050 or 2058 nucleotides of the nucleotide
sequence of SEQ ID NO:3, or a complement thereof. The invention
also features nucleic acid molecules comprising at least 25, 50,
100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 650, 700, 750,
800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350,
1400, 1450, 1500, 1550, 1600, 1650, 1700, or 1724 nucleotides of
nucleic acids 1 to 1725 of SEQ ID NO:3, or a complement
thereof.
[0032] The invention features nucleic acid molecules of at least
480, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050,
1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1450, 1500, 1550,
1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100,
2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100 or 3130
nucleotides of the nucleotide sequence of SEQ ID NO:24, the
nucleotide sequence of the mouse Delta3 cDNA, or a complement
thereof. The invention also features nucleic acid molecules
comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450,
500, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100,
1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, or 1529 nucleotides
of nucleic acids 1 to 1530 of SEQ ID NO:24, or a complement
thereof, wherein such nucleic acid molecules encode polypeptides or
proteins that exhibit at least one structural and/or functional
feature of a polypeptide of the invention.
[0033] The invention features nucleic acid molecules which include
a fragment of at least 415, 450, 500, 550, 600, 650, 700, 750, 800,
850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350,
1400, 1450, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850,
1900, 1950, 2000, 2050, 2100 nucleotides of the nucleotide sequence
of SEQ ID NO: 26, or a complement thereof. The invention also
features nucleic acid molecules comprising at least 25, 50, 100,
150, 200, 250, 300, 350, 400, 450, 500, 600, 650, 700, 750, 800,
850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350,
1400, 1450, 1500 or 1529 nucleotides of nucleic acids 1 to 1530 of
SEQ ID NO: 3, or a complement thereof.
[0034] Another aspect of the invention provides vectors, e.g.,
recombinant expression vectors, comprising a nucleic acid molecule
of the invention. In another embodiment the invention provides host
cells containing such a vector. The invention also provides methods
for producing a polypeptide of the invention by culturing, in a
suitable medium, a host cell of the invention containing a
recombinant expression vector encoding a polypeptide of the
invention such that the polypeptide of the invention is
produced.
[0035] For expression, the subject Delta3 nucleic acids can include
a mammalian transcriptional regulatory sequence, e.g., at least one
of a transcriptional promoter (e.g., for constitutive expression or
inducible expression) or transcriptional enhancer sequence, the
regulatory sequence is operably linked to the Delta3 gene sequence.
Such regulatory sequences in conjunction with Delta3 nucleic acid
molecules can be useful in vectors for gene expression. This
invention also describes host cells transfected with said
expression vectors whether prokaryotic or eukaryotic, also in vitro
(e.g., cell culture) and in vivo (e.g., transgenic) methods for
producing Delta3 proteins by employing said expression vectors. In
a preferred embodiment, the Delta3 nucleic acids are cloned into a
mammalian expression vector, and transfected into mammalian cells.
The use of mammalian cells increases the likelihood of proper
protein folding and post-translational modification of the
expressed proteins.
[0036] The invention also features nucleic acid molecules that
hybridize under stringent conditions to a nucleic acid molecule
comprising the nucleotide sequence of any of SEQ ID NOS: 1, 3, 24,
26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45 of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348, or a
complement thereof, wherein preferably such nucleic acid molecules
encode polypeptides or proteins that exhibit at least one
structural and/or functional feature of a polypeptide of the
invention. In other embodiments, the nucleic acid molecules are at
least 485 (500, 550, 600, 650, 700, 800, 900, 1000, 1100, 1200,
1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300,
2400, 2500, 2600, 2700, or 2800) nucleotides in length and
hybridize under stringent conditions to a nucleic acid molecule
comprising the nucleotide sequence of any of SEQ ID NOS: 1, 3, 24,
26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45 of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348, or a
complement thereof.
[0037] In preferred embodiments, the isolated nucleic acid
molecules encode a cytoplasmic, transmembrane, or extracellular
domain of a polypeptide of the invention.
[0038] The invention includes nucleic acid molecules which encode
an allelic variant of a polypeptide comprising the amino acid
sequence of any of SEQ ID NOS: 2, 25, 28, 30, 32, 34, 36, 38, 40,
42, 44 or 46, or an amino acid sequence encoded by the cDNA of a
clone deposited with the ATCC.RTM. as Accession Number 98348, or a
complement thereof, wherein the nucleic acid molecule hybridizes
under stringent conditions to a nucleic acid molecule having a
nucleic acid sequence encoding any of SEQ ID NOS:1, 3, 24, 26, 27,
29, 31, 33, 35, 37, 39, 41, 43 or 45, or the nucleotide sequence of
the cDNA of a clone deposited with the ATCC.RTM. as Accession
Number 98348, or a complement thereof.
[0039] The invention includes nucleic acid molecules which encode
an allelic variant of a polypeptide comprising the amino acid
sequence of any of SEQ ID NOS: 2, 25, 28, 30, 32, 34, 36, 38, 40,
42, 44 or 46, or an amino acid sequence encoded by the cDNA of a
clone deposited with the ATCC.RTM. as Accession Number 98348, or a
complement thereof, wherein the nucleic acid molecule hybridizes
under stringent conditions to a nucleic acid molecule having a
nucleic acid sequence encoding a polypeptide having any of the
amino acid sequences shown in SEQ ID NOS: 2, 25, 28, 30, 32, 34,
36, 38, 40, 42, 44 or 46, or the amino acid sequence encoded by the
cDNA of a clone deposited with the ATCC.RTM. as Accession Number
98348, or a complement thereof, wherein such nucleic acid molecules
encode polypeptides or proteins that exhibit at least one
structural and/or functional feature of a polypeptide of the
invention.
[0040] In one embodiment of a nucleotide sequence of human Delta3,
the nucleotide at position 455 is a guanine (G) (SEQ ID NO: 1). In
this embodiment, the amino acid at position 40 is glutamate (E)
(SEQ ID NO: 2). In another embodiment of a nucleotide sequence of
human Delta3, the nucleotide at position 455 is a cytosine (C) (SEQ
ID NO: 27). In this embodiment, the amino acid at position 40 is
glutamine (Q) (SEQ ID NO: 28). In another embodiment of a
nucleotide sequence of human Delta3, the nucleotide at position 455
is a thymidine (T) (SEQ ID NO: 29). In this embodiment, the amino
acid at position 40 is a stop codon (SEQ ID NO: 30). In another
embodiment of a nucleotide sequence of human Delta3, the nucleotide
at position 455 is a adenine (A) (SEQ ID NO: 31). In this
embodiment, the amino acid at position 40 is lysine (K) (SEQ ID NO:
32).
[0041] In another embodiment, the invention provides an isolated
nucleic acid molecule which is antisense to the coding strand of a
nucleic acid of the invention.
[0042] In another aspect, the invention features isolated Delta3
polypeptides, preferably substantially pure preparations, e.g., of
plasma-purified or recombinantly produced Delta3 polypeptides.
Preferred proteins and polypeptides possess at least one biological
activity of the corresponding naturally-occurring human
polypeptide. Such an activity can be a direct activity, such as an
association with or an enzymatic activity on a second protein or an
indirect activity, such as a cellular signaling activity mediated
by interaction of the protein with a second protein. Thus, such
activities include, for example, ones related to Delta3's function
as a Notch ligand. Delta3 activities include, e.g., (1) the ability
to form protein-protein interactions with proteins in the signaling
pathway of the naturally-occurring polypeptide; (2) the ability to
bind a ligand of the naturally-occurring polypeptide; (3) the
ability to bind to an intracellular target of the
naturally-occurring polypeptide; (4) the ability to modulate
cellular proliferation; (5) the ability to modulate cellular
differentiation; (6) the ability to modulate chemotaxis and/or
migration; and/or (7) the ability to modulate cell death; (8)
maintenance of energy homeostasis (e.g., regulating the balance or
imbalance between energy storage and energy expenditure, for
example, increasing or decreasing energy expenditure; (9)
regulation of adaptive thermogenesis (e.g., regulation of the
biogenesis of mitochondria, regulation of the expression of
mitochondrial enzymes, regulation of expression of uncoupling
proteins; (10) regulation of adiposity; (11) modulation of the
efficiency of energy storage; (12) regulation of appetite; (13)
expansion/reduction of fat mass; (14) regulation of vasculogenesis
(blood vessel formation); (15) regulation of tumor angiogenesis;
(16) regulation of wound healing; (17) expansion/reduction of tumor
mass; (18) the ability to modulate development, differentiation,
proliferation and/or activity of immune cells (e.g., leukocytes and
macrophages), endothelial cells and smooth muscle cells; (19) the
ability to modulate the host immune response; (20) the ability to
modulate the development of organs, tissues and/or cells of the
embryo and/or fetus; (21) the ability to modulate cell-cell
interactions and/or cell-extracellular matrix interactions; (22)
the ability to modulate atherosclerosis, e.g., the initiation and
progression of atherosclerosis; (23) the ability to modulate
atherogenesis; (24) the ability to modulate inflammatory functions
e.g., by modulating leukocyte adhesion to extracellular matrix
and/or endothelial cells; (25) the ability to form, e.g.,
stabilize, promote, facilitate, inhibit, or disrupt, cell to cell
and cell to blood product interaction, e.g., between leukocytes and
platelets or leukocytes and vascular endothelial cells; (26)
ability to modulate development, differentiation and activity of
skeletal muscle cells and tissue; and (27) ability to act in stem
cell preservation.
[0043] In certain embodiments, the subject polypeptides are capable
of modulating an activity of a Delta3 polypeptide, e.g., cell
growth and/or differentiation or induction of apoptosis. In other
embodiments, the subject Delta3 polypeptides can modulate
neurogenesis (e.g., by inhibiting Notch expressing cells from
becoming committed to a neural fate). In addition, Delta3
polypeptides which specifically antagonize the activity of a native
Delta3 polypeptide, such as may be provided by truncation mutants
or other dominant negative mutants, are also specifically provided
herein.
[0044] In one embodiment, a polypeptide of the invention has an
amino acid sequence sufficiently identical to an identified domain
of a polypeptide of the invention. As used herein, the term
"sufficiently identical" refers to a first amino acid or nucleotide
sequence which contains a sufficient or minimum number of identical
or equivalent (e.g., with a similar side chain) amino acid residues
or nucleotides to a second amino acid or nucleotide sequence such
that the first and second amino acid or nucleotide sequences have a
common structural domain and/or common functional activity. For
example, amino acid or nucleotide sequences which contain a common
structural domain having about 65% identity, preferably 75%
identity, more preferably 85%, 95%, or 98% identity.
[0045] In one embodiment, the polypeptide is identical to a Delta3
protein represented in SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38,
40, 42, 44 or 46, or the amino acid sequence encoded by the cDNA of
a clone deposited with the ATCC.RTM. as Accession Number 98348.
Preferably, a Delta3 polypeptide has an amino acid sequence, which
is at least about 55%, 60%, 70%, preferably at least about 80%,
more preferably at least about 90%, and even more preferably at
least about 95% or 98% identical to the polypeptide represented by
SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the
amino acid sequence encoded by the cDNA of a clone deposited with
the ATCC.RTM. as Accession Number 98348.
[0046] Also within the invention are isolated polypeptides or
proteins having an amino acid sequence that is at least about 55%,
preferably 65%, 75%, 85%, 95%, or 98% identical to the amino acid
sequence of any of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40,
42, 44 or 46, or the amino acid sequence encoded by the cDNA of a
clone deposited with the ATCC.RTM. as Accession Number 98348,
wherein the polypeptides or proteins also exhibit at least one
structural and/or functional feature of a polypeptide of the
invention.
[0047] Also within the invention are isolated polypeptides or
proteins which preferably are encoded by a nucleic acid molecule
having a nucleotide sequence that is at least about 55%, more
preferably 60%, 65%, 75%, 85%, or 95% identical the nucleic acid
sequence encoding any of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38,
40, 42, 44 or 46, wherein the polypeptides or proteins preferably
also exhibit at least one structural and/or functional feature of a
polypeptide of the invention, and isolated polypeptides or proteins
which are encoded by a nucleic acid molecule having a nucleotide
sequence which hybridizes under stringent hybridization conditions
to a nucleic acid molecule having the sequence of any of SEQ ID
NOs:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or a
complement thereof, or the non-coding strand of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348.
[0048] In a preferred embodiment, the Delta3 polypeptide is encoded
by a nucleic acid which hybridizes in high stringency conditions
with a nucleic acid sequence represented in one of SEQ ID NOs: 1,
3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45 or with the
nucleic acid contained in the plasmid having ATCC.RTM. Accession
NO: 98348.
[0049] The subject Delta3 proteins also include modified proteins,
which are resistant to post-translational modification, as for
example, due to mutations which alter modification sites (such as
tyrosine, threonine, serine or asparagine residues), or which
prevent glycosylation of the protein, or which prevent interaction
of the protein with intracellular proteins involved in signal
transduction.
[0050] The Delta3 polypeptide can comprise a full-length protein,
such as represented in SEQ ID NO: 2, 25, 28, 30, 32, 34, 36, 38,
40, 42, 44 or 46, or it can comprise a fragment corresponding to
one or more particular motifs/domains (e.g., an extracellular
domain, a DSL domain or an EGF-like domain, all of which are
described below), or to other sizes, e.g., at least 5, 10, 25, 50,
100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or 650 amino
acids in length.
[0051] The polypeptides of the invention can comprise at least one
domain or motif of a Delta3 protein, i.e., a domain or motif
selected from the group consisting of an amino-terminal signal
peptide, a Delta-Serrated lag-2 (DSL) domain, Epidermal Growth
Factor (EGF)-like domain 1, EGF-like domain 2, EGF-like domain 3,
EGF-like domain 4, EGF-like domain 5, EGF-like domain 6, EGF-like
domain 7, EGF-like domain 8, a Delta3 extracellular domain, a
transmembrane domain (TM), and a cytoplasmic domain. Other
polypeptides comprise soluble Delta3 proteins, e.g., Delta3
proteins comprising at least a portion, such as one or more
domains, of the extracellular domain of a Delta3 protein. A soluble
Delta3 protein is a protein that is soluble at physiological
conditions, and includes but is not limited to a Delta3 protein
that does not comprise a transmembrane domain, e.g., an
extracellular Delta3 domain. These soluble polypeptides may or may
not comprise a signal peptide. Other such polypeptides comprise
soluble fusion proteins comprising Delta3 amino acid sequence and a
heterologous amino acid sequence, e.g., an immunoglobulin constant
region.
[0052] In one embodiment, the isolated polypeptide of the invention
lacks both a transmembrane and a cytoplasmic domain. In another
embodiment, the polypeptide lacks both a transmembrane domain and a
cytoplasmic domain and is soluble under physiological
conditions.
[0053] Also within the invention are polypeptides which are allelic
variants of a polypeptide that includes the amino acid sequence of
any of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46,
or an amino acid sequence encoded by the cDNA of a clone deposited
with the ATCC.RTM. as Accession Number 98348, wherein the
polypeptide is encoded by a nucleic acid molecule which hybridizes
under stringent conditions to a nucleic acid molecule having the
sequence of any of SEQ ID NOs:1, 3, 24, 26, 27, 29, 31, 33, 35, 37,
39, 41, 43 or 45, or the nucleotide sequence of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348, or a
complement thereof.
[0054] Also within the invention are polypeptides which are allelic
variants of a polypeptide that includes the amino acid sequence of
any of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46,
or an amino acid sequence encoded by the cDNA of a clone deposited
with the ATCC.RTM. as Accession Number 98348, wherein the
polypeptide is encoded by a nucleic acid molecule which hybridizes
under stringent conditions to a nucleic acid molecule having the
sequence of any of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35,
37, 39, 41, 43 or 45, or the nucleotide sequence of the cDNA of a
clone deposited with the ATCC.RTM. as Accession Number 98348, or a
complement thereof, wherein such nucleic acid molecules encode
polypeptides or proteins that exhibit at least one structural
and/or functional feature of a polypeptide of the invention.
[0055] Another aspect of the invention features fusion proteins
comprising a Delta3 amino acid sequence. For instance, the Delta3
protein can be provided as a recombinant fusion protein which
includes a second polypeptide portion, e.g., a second polypeptide
having an amino acid sequence unrelated (heterologous) to the
Delta3 polypeptide, (e.g., the second polypeptide portion is
glutathione-S-transferase, an enzymatic sequence such as alkaline
phosphatase or an epitope tag).
[0056] Fusion proteins of the invention include, for example,
Delta3 immunoglobulin (Delta3-Ig) fusion proteins. For example, a
Delta3 fusion protein can comprise the extracellular portion of a
Delta3 protein fused to the constant region of an immunoglobulin
molecule. Preferred extracellular portions comprise at least one
domain selected from the group consisting of a signal peptide, a
DSL domain, and the eight EGF-like domains of a Delta3 protein. An
even more preferred extracellular domain comprises an amino acid
sequence from amino acid 1 to amino acid 529 of SEQ ID NO: 2 or
from amino acid 1 to 530 of SEQ ID NO: 25. Yet other preferred
Delta3 fusion proteins comprise a portion of a Delta3 protein that
is sufficient for binding to a second protein, such as the DSL
domain to a second protein which is, for example, a Notch
protein.
[0057] Yet another aspect of the present invention concerns an
immunogen comprising a Delta3 polypeptide in an immunogenic
preparation, the immunogen being capable of eliciting an immune
response specific for a Delta3 polypeptide, e.g., a humoral
response, an antibody response and/or cellular response. In
preferred embodiments, the immunogen comprises an antigenic
determinant, e.g., a unique determinant, from the protein
represented by SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42,
44 or 46, or the amino acid sequence encoded by the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348.
[0058] A still further aspect of the present invention features
antibodies and antibody preparations specifically reactive with an
epitope of the Delta3 protein. In preferred embodiments, the
antibody specifically binds to an epitope of a polypeptide shown in
SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the
amino acid sequence encoded by the cDNA of a clone deposited with
the ATCC.RTM. as Accession Number 98348.
[0059] In yet a further aspect, the invention provides
substantially purified antibodies or fragments thereof, including
human or non-human antibodies or fragments thereof, which
antibodies or fragments specifically bind to a polypeptide
comprising an amino acid sequence selected from the group
consisting of: the amino acid sequence of SEQ ID NOs: 2, 25, 28,
30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid sequence
encoded by the cDNA insert of the plasmid deposited with the
ATCC.RTM. as Accession Number 98348; a fragment of at least 15
amino acid residues of the amino acid sequence of SEQ ID NOs: 2,
25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348; an amino acid sequence which
is at least 95% identical to the amino acid sequence of SEQ ID NOs:
2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348 wherein the percent identity is
determined using the ALIGN program of the GCG software package with
a PAM120 weight residue table, a gap length penalty of 12, and a
gap penalty of 4; and an amino acid sequence which is encoded by a
nucleic acid molecule which hybridizes to the nucleic acid molecule
consisting of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39,
41, 43 or 45, or the nucleotide sequence of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348, under
conditions of hybridization of 6.times.SSC at 45.quadrature.C. and
washing in 0.2.times.SSC, 0.1% SDS at 65.quadrature.C. In various
embodiments, the substantially purified antibodies of the
invention, or fragments thereof, can be human, non-human, chimeric
and/or humanized antibodies.
[0060] In another aspect, the invention provides human or non-human
antibodies or fragments thereof, which antibodies or fragments
specifically bind to a polypeptide comprising an amino acid
sequence selected from the group consisting of: the amino acid
sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, or the amino acid sequence encoded by the cDNA insert of the
plasmid deposited with the ATCC.RTM. as Accession Number 98348; a
fragment of at least 15 amino acid residues of the amino acid
sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, or the amino acid sequence encoded by the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348; an amino
acid sequence which is at least 95% identical to the amino acid
sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, or the amino acid sequence encoded by the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348 wherein the
percent identity is determined using the ALIGN program of the GCG
software package with a PAM120 weight residue table, a gap length
penalty of 12, and a gap penalty of 4; and an amino acid sequence
which is encoded by a nucleic acid molecule which hybridizes to the
nucleic acid molecule consisting of SEQ ID NOs: 1, 3, 24, 26, 27,
29, 31, 33, 35, 37, 39, 41, 43 or 45, or the nucleotide sequence of
the cDNA of a clone deposited with the ATCC.RTM. as Accession
Number 98348, under conditions of hybridization of 6.times.SSC at
45.degree. C. and washing in 0.2.times.SSC, 0.1% SDS at 65.degree.
C. With respect to non-human antibodies, such antibodies can be
goat, mouse, sheep, horse, chicken, rabbit, or rat antibodies.
Alternatively, the non-human antibodies of the invention can be
chimeric and/or humanized antibodies. In addition, the human and
non-human antibodies of the invention can be polyclonal antibodies
or monoclonal antibodies.
[0061] In still a further aspect, the invention provides monoclonal
antibodies or fragments thereof, which antibodies or fragments
specifically bind to a polypeptide comprising an amino acid
sequence selected from the group consisting of: the amino acid
sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, or the amino acid sequence encoded by the cDNA insert of the
plasmid deposited with the ATCC.RTM. as Accession Number 98348; a
fragment of at least 15 amino acid residues of the amino acid
sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46; an amino acid sequence which is at least 95% identical to
the amino acid sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36,
38, 40, 42, 44 or 46, or the amino acid sequence encoded by the
cDNA of a clone deposited with the ATCC.RTM. as Accession Number
98348, wherein the percent identity is determined using the ALIGN
program of the GCG software package with a PAM120 weight residue
table, a gap length penalty of 12, and a gap penalty of 4; and an
amino acid sequence which is encoded by a nucleic acid molecule
which hybridizes to the nucleic acid molecule consisting of SEQ ID
NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or the
nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, under conditions of
hybridization of 6.times.SSC at 45.degree. C. and washing in
0.2.times.SSC, 0.1% SDS at 65.degree. C. The monoclonal antibodies
can be human, humanized, chimeric and/or non-human antibodies.
[0062] In a particularly preferred embodiment, the substantially
purified antibodies or fragments thereof, the human and non-human
antibodies or fragments thereof, and/or monoclonal antibodies or
fragments thereof, of the invention specifically bind to an
extracellular domain of the amino acid sequence of SEQ ID NOs: 2,
25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348. Preferably, the extracellular
domain to which the antibody, or fragment thereof, binds comprises
amino acid residues 1-529 of SEQ ID NO: 2 of human Delta3, or amino
acid residues 1-530 of SEQ ID NO: 25 of murine Delta3.
[0063] Any of the antibodies of the invention can be conjugated to
a therapeutic moiety or to a detectable substance. Non-limiting
examples of detectable substances that can be conjugated to the
antibodies of the invention are an enzyme, a prosthetic group, a
fluorescent material, a luminescent material, a bioluminescent
material, and a radioactive material.
[0064] The invention also provides a kit containing an antibody of
the invention and instructions for use. Such kits can also comprise
an antibody of the invention conjugated to a detectable substance
and instructions for use. Still another aspect of the invention is
a pharmaceutical composition comprising an antibody of the
invention and a pharmaceutically acceptable carrier. In preferred
embodiments, the pharmaceutical composition contains an antibody of
the invention, a therapeutic moiety, and a pharmaceutically
acceptable carrier.
[0065] In addition, the polypeptides of the invention or
biologically active portions thereof, or antibodies of the
invention, can be incorporated into pharmaceutical compositions,
which optionally include pharmaceutically acceptable carriers.
[0066] The invention also features transgenic non-human animals
which include (and preferably express) a heterologous form of a
Delta3 gene described herein, or which misexpress (e.g., do not
express) an endogenous Delta3 gene (e.g., an animal in which
expression of one or more of the subject Delta3 proteins is
disrupted). Such a transgenic animal can serve as an animal model
for studying cellular or tissue disorders comprising mutated or
mis-expressed Delta3 alleles or for use in drug screening. For
example, the transgenic animals of the invention can be used as an
animal model to study a neurological disease, e.g., ACCPN.
Alternatively, such a transgenic animal can be useful for
expressing recombinant polypeptides, and for generating cells,
e.g., cell lines that can, for example, be utilized as part of
screening techniques.
[0067] In another aspect, the invention provides a method for
identifying a compound that binds to or modulates the activity of a
polypeptide of the invention. In general, such methods entail
measuring a biological activity of the polypeptide in the presence
and absence of a test compound and identifying those compounds
which alter the activity of the polypeptide.
[0068] The invention also features methods for identifying a
compound which modulates the expression of a polypeptide or nucleic
acid of the invention by measuring the expression of the
polypeptide or nucleic acid in the presence and absence of the
compound.
[0069] In one embodiment, the invention provides assays, e.g., for
screening test compounds to identify agonists, or alternatively,
antagonists, of a Delta3 activity. For example, the test compound
may positively or negatively influence an interaction between a
Delta3 protein and a Delta3 target molecule, for example, a Notch
protein. An exemplary method includes the steps of (i) combining a
Delta3 polypeptide or active fragment thereof, with a Delta3 target
molecule, e.g., Notch, and a test compound, e.g., under conditions
wherein, but for the test compound, the Delta3 protein and target
molecule are able to interact; and (ii) detecting the formation of
a complex which includes the Delta3 protein and the target molecule
either by directly quantitating the complex, by measuring inductive
effects of the Delta3 protein, or, in the instance of a substrate,
measuring the conversion to product. A statistically significant
change, such as a decrease, in the interaction of the Delta3 and
target molecule in the presence of a test compound (relative to
what is detected in the absence of the test compound) is indicative
of a modulation (e.g., suppression or potentiation of the
interaction between the Delta3 protein and the target
molecule).
[0070] The invention provides yet other methods for identifying
compounds which modulate a Delta activity. For example, a compound
that interacts with a Delta3 protein can be identified by
contacting a Delta3 protein with a test compound. Either the test
compound or the Delta3 protein can be labeled. Optionally, the
non-labeled compound or Delta3 protein can be attached to a solid
phase support. Binding of the test compound to the Delta3 protein
can then be determined, e.g by measuring the amount of label. Such
a Delta3 binding molecule can be an agonist or an antagonist. In
one embodiment, an agonist of a Delta3 activity is identified by
contacting a cell having a Delta3 protein with a test compound and
measuring a Delta3 activity, e.g., expression of a gene which is
regulated by binding of a protein, e.g., a Notch protein, to
Delta3. An increased expression of the gene when the cell is
incubated with the test compound relative to incubation in the
absence of the test compound indicates that the test compound is a
Delta3 agonist. The gene that is monitored can also be a reporter
gene transfected to a cell, the reporter gene being under the
control of a promoter of a gene which is regulated by Delta3.
[0071] In another aspect, the invention provides methods for
modulating activity of a polypeptide of the invention comprising
contacting a cell with an agent that modulates (inhibits or
stimulates) the activity or expression of a polypeptide of the
invention such that activity or expression in the cell is
modulated. In one embodiment, the agent is an antibody that
specifically binds to a polypeptide of the invention.
[0072] In another embodiment, the agent modulates expression of a
polypeptide of the invention by modulating transcription, splicing,
or translation of an mRNA encoding a polypeptide of the invention.
In yet another embodiment, the agent is a nucleic acid molecule
having a nucleotide sequence that is antisense to the coding strand
of an mRNA encoding a polypeptide of the invention.
[0073] Yet another aspect of the present invention concerns methods
for treating diseases or conditions that are caused or contributed
to by an aberrant Delta3 expression, level, or activity, e.g.,
aberrant cell proliferation, degeneration or differentiation, in a
subject, by administering to the subject an effective amount of a
modulator (e.g., an agonist or antagonist) of a Delta3 activity. In
one embodiment, an agonist or antagonist can modulate Delta3
protein levels, by, e.g., modulating expression of a Delta3 gene. A
modulator can, for example, be a protein of the invention, or,
alternatively, a nucleic acid of the invention. In other
embodiments, the modulator is a peptide, antibody, peptidomimetic,
or other small organic molecule. For example, administration of a
therapeutic comprised of a Delta3 agonist can be useful for
promoting the tissue regeneration or repair needed to effectively
treat a nerve injury, neurodegenerative disease, or
neurodevelopmental disorder including but not limited to peripheral
neuropathies, e.g., ACCPN, stroke, dementia, Alzheimer's disease,
Parkinson's disease, Huntington's chorea, amylotrophic lateral
sclerosis, and the like, as well as spinocerebellar
degenerations.
[0074] Alternatively, administration of a Delta3 antagonist may be
to effectively treat a neoplastic or hyperplastic disease,
particularly of endothelial tissue.
[0075] Additionally, Delta3 agonists or antagonists may be used to
treat various hematologic abnormalities such as neutropenia seen in
patients undergoing chemotherapy, or immunodeficiency disorders
such as AIDS. Delta3 nucleic acids, polypeptides or modulators
thereof can also be utilized in treating or ameliorating a symptom
of obesity and/or disorders that accompany or are exacerbated by an
obese state, such as cardiovascular and circulatory disorders,
metabolic abnormalities typical of obesity, such as
hyperinsulinemia, insulin resistance, diabetes, including
non-insulin dependent diabetes mellitus (NIDDM), insulin dependent
diabetes mellitus (IDDM), and maturity onset diabetes of the young
(MODY), disorders of energy homeostasis, disorders associated with
lipid metabolism, such as cachexia, disorders associated with
abnormal vasculogenesis (e.g., cancers, including, but not limited
to, cancers of the epithelia (e.g., carcinomas of the pancreas,
stomach, liver, secretory glands (e.g., adenocarcinoma), bladder,
lung, breast, skin (e.g., fibromatosis or malignant melanoma),
reproductive tract including prostate gland, ovary, cervix and
uterus); cancers of the hematopoietic and immune system (e.g.,
leukemias and lymphomas); cancers of the central nervous, brain
system and eye (e.g., gliomas, neuroblastoma and retinoblastoma);
and cancers of connective tissues, bone, muscles and vasculature
(e.g., hemangiomas and sarcomas)), disorders related to fetal
development, in particular, disorders involving development of lung
and kidney, lung-related disorders, atherosclerosis, e.g., the
initiation and progression of atherosclerosis; and
inflammatory-related disorders, e.g., asthma, allergy, and
autoimmune disorders, neurological disorders, including
developmental, cognitive and personality-related disorders, renal
disorders, adrenal gland-related disorders; and disorders relating
to skeletal muscle, such as dystrophic disorders.
[0076] The invention also provides methods for treating diseases or
conditions associated with one or more specific Delta alleles,
e.g., mutant allele, comprising administering to the subject an
effective amount of a therapeutic compound. In one embodiment, the
therapeutic compound is capable of compensating for the effect of
the specific Delta allele. In another embodiment, the therapeutic
compound is capable of modulating a Delta3 activity. In a one
embodiment, the Delta allele is a Delta3 allele. For example, in
one embodiment, the disease or condition is a neurological disease,
e.g., ACCPN.
[0077] A further aspect of the present invention provides a method
for determining whether a subject is at risk for developing a
disease or condition, which is caused by or contributed to by an
aberrant Delta3 activity, e.g. aberrant cell proliferation,
degeneration or differentiation. In one embodiment, the disease or
condition is a neurological disease, e.g., ACCPN. The method
includes detecting, in a tissue of the subject, the presence or
absence of a genetic lesion characterized by at least one of (i) a
mutation of a gene encoding a Delta3 protein, e.g., as shown in SEQ
ID Nos: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or
the nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, or a homolog thereof; or (ii)
the mis-expression of a Delta3 gene. In one embodiments, detecting
the genetic lesion includes ascertaining the existence of at least
one of the following: a deletion of one or more nucleotides from a
Delta3 gene; an addition of one or more nucleotides to the gene, a
substitution of one or more nucleotides of the gene, a gross
chromosomal rearrangement of the gene; an alteration in the level
of a messenger RNA transcript of the gene; the presence of a
non-wild type splicing pattern of a messenger RNA transcript of the
gene; and/or a non-wild type level of the protein.
[0078] In a preferred embodiment, the invention provides a method
for determining whether a subject has or is at risk of developing a
disease or condition associated with a specific Delta3 allele,
comprising determining the identity of a Delta3 allele in the
subject. In an even more preferred embodiment, the disease or
condition is a neurological disease, e.g., ACCPN. In another
preferred embodiment, the disease is a vascular disorder. In
another preferred embodiment, the disease is a neoplastic disorder.
In another preferred embodiment the disease is a hematologic
disorder. In another preferred embodiment the disease is an
immunodeficiency disorder.
[0079] For example, detecting the genetic lesion or determining the
identity of a Delta allele, e.g., a Delta3 allele, can include: (i)
providing a probe/primer comprised of an oligonucleotide which
hybridizes to a sense or antisense sequence of a Delta3 gene or
naturally-occurring mutants thereof, or 5' or 3' flanking sequences
naturally associated with the Delta3 gene; (ii) contacting the
probe/primer with an appropriate nucleic acid containing sample;
and (iii) detecting, by hybridization of the probe/primer to the
nucleic acid, the presence or absence of the genetic lesion, e.g.,
by utilizing the probe/primer to determine the nucleotide sequence
of the Delta3 gene and, optionally, of the flanking nucleic acid
sequences. For instance, the primer can be employed in a polymerase
chain reaction (PCR) or in a ligation chain reaction (LCR).
[0080] In another diagnostic method of the invention, at least a
portion of a Delta3 gene of a subject is sequenced and the
nucleotide sequence is compared to that of a wild-type Delta3 gene,
to determine the presence of a genetic lesion. Another preferred
diagnostic method of the invention is single strand conformation
polymorphism (SSCP) which detects differences in electrophoretic
mobility between mutant and wild-type nucleic acids.
[0081] In alternate embodiments, the diagnostic methods comprise
determining the level of a Delta3 protein in an immunoassay using
an antibody which is specifically immunoreactive with a wildtype or
mutant Delta3 protein.
[0082] In another aspect, the present invention provides methods
for detecting the presence of the activity or expression of a
polypeptide of the invention in a biological sample by contacting
the biological sample with an agent capable of detecting an
indicator of activity such that the presence of activity is
detected in the biological sample.
[0083] The present invention also provides diagnostic assays for
identifying the presence or absence of a genetic lesion or mutation
characterized by at least one of: (i) aberrant modification or
mutation of a gene encoding a polypeptide of the invention, (ii)
mis-regulation of a gene encoding a polypeptide of the invention,
and (iii) aberrant post-translational modification of a polypeptide
of the invention wherein a wild-type form of the gene encodes a
polypeptide having the activity of the polypeptide of the
invention.
[0084] Other features and advantages of the invention will be
apparent from the following detailed description and claims.
FTHMA-070 and TANGO85
[0085] The present invention is based, at least in part, on the
discovery of a gene encoding FTHMA-070, a protein having homology
to tumor necrosis factor (TNF) receptor and on the discovery of a
gene encoding T85 (also referred to as FMHB-SD4 or FMHB-6D4).
[0086] The FTHMA-070 cDNA described below (SEQ ID NO:53) has a 1203
nucleotide open reading frame (nucleotides 73-1275 of SEQ ID NO:53;
SEQ ID NO:55) which encodes a 403 amino acid protein (SEQ ID
NO:54). This protein includes a predicted signal sequence of about
21 amino acids (from amino acid 1 to about amino acid 21 of SEQ ID
NO:54) and a predicted mature protein of about 382 amino acids
(from about amino acid 22 to amino acid 403 of SEQ ID NO:54; SEQ ID
NO:56).
[0087] The T85 cDNA described below (SEQ ID NO:57) has a 2259
nucleotide open reading frame (nucleotides 958-3216 of SEQ ID
NO:57; SEQ ID NO:59) which encodes a 753 amino acid protein (SEQ ID
NO:58). This protein includes a predicted signal sequence of about
20 amino acids (from amino acid 1 to about amino acid 20 of SEQ ID
NO:58) and a predicted mature protein of about 733 amino acids
(from about amino acid 21 to amino acid 753 of SEQ ID NO:58; SEQ ID
NO:60).
[0088] The nucleic acid and polypeptide molecules of the present
invention are useful as modulating agents in regulating a variety
of cellular processes. Accordingly, in one aspect, this invention
provides isolated nucleic acid molecules encoding FTHMA-070
proteins or biologically active portions thereof, as well as
nucleic acid fragments suitable as primers or hybridization probes
for the detection of FTHMA-070-encoding nucleic acids. In another
aspect, this invention provides isolated nucleic acid molecules
encoding T85 proteins or biologically active portions thereof, as
well as nucleic acid fragments suitable as primers or hybridization
probes for the detection of T85-encoding nucleic acids.
[0089] The invention features a nucleic acid molecule which is at
least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the
nucleotide sequence shown in SEQ ID NO:53, or SEQ ID NO:55, or a
complement thereof. The invention features a nucleic acid molecule
which includes a fragment of at least 300 (325, 350, 375, 400, 425,
450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides
of the nucleotide sequence shown in SEQ ID NO:53, or SEQ ID NO:55,
or a complement thereof.
[0090] The invention also features a nucleic acid molecule which
includes a nucleotide sequence encoding a protein having an amino
acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, or
98%) identical to the amino acid sequence of SEQ ID NO:54, SEQ ID
NO:56. In a preferred embodiment, a FTHMA-070 nucleic acid molecule
has the nucleotide sequence shown SEQ ID NO:53, or SEQ ID
NO:55.
[0091] Also within the invention is a nucleic acid molecule which
encodes a fragment of a polypeptide having the amino acid sequence
of SEQ ID NO:54 or SEQ ID NO:56, the fragment including at least 15
(25, 30, 50, 100, 150, 300, or 400) contiguous amino acids of SEQ
ID NO:54 or SEQ ID NO:56.
[0092] The invention includes a nucleic acid molecule which encodes
a naturally occurring allelic variant of a polypeptide comprising
the amino acid sequence of SEQ ID NO:54 or SEQ ID NO:56, wherein
the nucleic acid molecule hybridizes to a nucleic acid molecule
comprising SEQ ID NO:53 or SEQ ID NO:55 under stringent
conditions.
[0093] Also within the invention are: an isolated FTHMA-070 protein
having an amino acid sequence that is at least about 65%,
preferably 75%, 85%, 95%, or 98% identical to the amino acid
sequence of SEQ ID NO:56 (mature human FTHMA-070) or the amino acid
sequence of SEQ ID NO:54 (immature human FTHMA-070).
[0094] Also within the invention are: an isolated FTHMA-070 protein
which is encoded by a nucleic acid molecule having a nucleotide
sequence that is at least about 65%, preferably 75%, 85%, or 95%
identical to SEQ ID NO:55; and an isolated FTHMA-070 protein which
is encoded by a nucleic acid molecule having a nucleotide sequence
which hybridizes under stringent hybridization conditions to a
nucleic acid molecule having the nucleotide sequence of SEQ ID
NO:55.
[0095] Also within the invention is a polypeptide which is a
naturally occurring allelic variant of a polypeptide that includes
the amino acid sequence of SEQ ID NO:54 or SEQ ID NO:56, wherein
the polypeptide is encoded by a nucleic acid molecule which
hybridizes to a nucleic acid molecule comprising SEQ ID NO:53 or
SEQ ID NO:55 under stringent conditions.
[0096] Another embodiment of the invention features FTHMA-070
nucleic acid molecules which specifically detect FTHMA-070 nucleic
acid molecules. For example, in one embodiment, a FTHMA-070 nucleic
acid molecule hybridizes under stringent conditions to a nucleic
acid molecule comprising the nucleotide sequence of SEQ ID NO:53,
SEQ ID NO:55, or a complement thereof. In another embodiment, the
FTHMA-070 nucleic acid molecule is at least 300 (325, 350, 375,
400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1200)
nucleotides in length and hybridizes under stringent conditions to
a nucleic acid molecule comprising the nucleotide sequence shown in
SEQ ID NO:53 or SEQ ID NO:55, or a complement thereof. In another
embodiment, the invention provides an isolated nucleic acid
molecule which is antisense to the coding strand of a FTHMA-070
nucleic acid.
[0097] Another aspect of the invention provides a vector, e.g., a
recombinant expression vector, comprising a FTHMA-070 nucleic acid
molecule of the invention. In another embodiment the invention
provides a host cell containing such a vector. The invention also
provides a method for producing FTHMA-070 protein by culturing, in
a suitable medium, a host cell of the invention containing a
recombinant expression vector such that a FTHMA-070 protein is
produced.
[0098] Another aspect of this invention features isolated or
recombinant FTHMA-070 proteins and polypeptides. Preferred
FTHMA-070 proteins and polypeptides possess at least one biological
activity possessed by naturally occurring human FTHMA-070, e.g.,
the ability to form protein:protein interactions with other
proteins.
[0099] The FTHMA-070 proteins of the present invention, or
biologically active portions thereof, can be operatively linked to
a non-FTHMA-070 polypeptide (e.g., heterologous amino acid
sequences) to form FTHMA-070 fusion proteins. The invention further
features antibodies that specifically bind FTHMA-070 proteins, such
as monoclonal or polyclonal antibodies. In addition, the FTHMA-070
proteins or biologically active portions thereof can be
incorporated into pharmaceutical compositions, which optionally
include pharmaceutically acceptable carriers.
[0100] In another aspect, the present invention provides a method
for detecting the presence of FTHMA-070 activity or expression in a
biological sample by contacting the biological sample with an agent
capable of detecting an indicator of FTHMA-070 activity such that
the presence of FTHMA-070 activity is detected in the biological
sample.
[0101] In another aspect, the invention provides a method for
modulating FTHMA-070 activity comprising contacting a cell with an
agent that modulates (inhibits or stimulates) FTHMA-070 activity or
expression such that FTHMA-070 activity or expression in the cell
is modulated. In one embodiment, the agent is an antibody that
specifically binds to FTHMA-070 protein. In another embodiment, the
agent modulates expression of FTHMA-070 by modulating transcription
of a FTHMA-070 gene, splicing of a FTHMA-070 mRNA, or translation
of a FTHMA-070 mRNA. In yet another embodiment, the agent is a
nucleic acid molecule having a nucleotide sequence that is
antisense to the coding strand of the FTHMA-070 mRNA or the
FTHMA-070 gene.
[0102] In one embodiment, the methods of the present invention are
used to treat a subject having a disorder characterized by aberrant
FTHMA-070 protein or nucleic acid expression or activity by
administering an agent which is a FTHMA-070 modulator to the
subject. In one embodiment, the FTHMA-070 modulator is a FTHMA-070
protein. In another embodiment the FTHMA-070 modulator is a
FTHMA-070 nucleic acid molecule. In other embodiments, the
FTHMA-070 modulator is a peptide, peptidomimetic, or other small
molecule.
[0103] The present invention also provides a diagnostic assay for
identifying the presence or absence of a genetic lesion or mutation
characterized by at least one of: (i) aberrant modification or
mutation of a gene encoding a FTHMA-070 protein; (ii)
mis-regulation of a gene encoding a FTHMA-070 protein; and (iii)
aberrant post-translational modification of a FTHMA-070 protein,
wherein a wild-type form of the gene encodes a protein with a
FTHMA-070 activity.
[0104] In another aspect, the invention provides a method for
identifying a compound that binds to or modulates the activity of a
FTHMA-070 protein. In general, such methods entail measuring a
biological activity of a FTHMA-070 protein in the presence and
absence of a test compound and identifying those compounds which
alter the activity of the FTHMA-070 protein.
[0105] The invention also features methods for identifying a
compound which modulates the expression of FTHMA-070 by measuring
the expression of FTHMA-070 in the presence and absence of a
compound.
[0106] The invention features a nucleic acid molecule which is at
least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the
nucleotide sequence shown in SEQ ID NO:57, or SEQ ID NO:59, or a
complement thereof. The invention features a nucleic acid molecule
which includes a fragment of at least 300 (325, 350, 375, 400, 425,
450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides
of the nucleotide sequence shown in SEQ ID NO:57, or SEQ ID NO:59,
or a complement thereof.
[0107] The invention also features a nucleic acid molecule which
includes a nucleotide sequence encoding a protein having an amino
acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, or
98%) identical to the amino acid sequence of SEQ ID NO:58 or SEQ ID
NO:60. In a preferred embodiment, a T85 nucleic acid molecule has
the nucleotide sequence shown SEQ ID NO:57, or SEQ ID NO:59.
[0108] Also within the invention is a nucleic acid molecule which
encodes a fragment of a polypeptide having the amino acid sequence
of SEQ ID NO:58 or SEQ ID NO:60, the fragment including at least 15
(25, 30, 50, 100, 150, 300, or 400) contiguous amino acids of SEQ
ID NO:58 or SEQ ID NO:60.
[0109] The invention includes a nucleic acid molecule which encodes
a naturally occurring allelic variant of a polypeptide comprising
the amino acid sequence of SEQ ID NO:58 or SEQ ID NO:60, wherein
the nucleic acid molecule hybridizes to a nucleic acid molecule
comprising SEQ ID NO:57 or SEQ ID NO:59 under stringent
conditions.
[0110] Also within the invention are: an isolated T85 protein
having an amino acid sequence that is at least about 65%,
preferably 75%, 85%, 95%, or 98% identical to the amino acid
sequence of SEQ ID NO:60 (mature human T85) or the amino acid
sequence of SEQ ID NO:58 (immature human T85); and an isolated T85
protein having an amino acid sequence that is at least about 85%,
95%, or 98% identical to one or more of the fibronectin type III
domains and Ig superfamily domains described herein.
[0111] Also within the invention are: an isolated T85 protein which
is encoded by a nucleic acid molecule having a nucleotide sequence
that is at least about 65%, preferably 75%, 85%, or 95% identical
to SEQ ID NO:59; an isolated T85 protein which is encoded by a
nucleic acid molecule having a nucleotide sequence at least about
65% preferably 75%, 85%, or 95% identical a fibronectin III or Ig
superfamily domain encoding portion of SEQ ID NO:57; and an
isolated T85 protein which is encoded by a nucleic acid molecule
having a nucleotide sequence which hybridizes under stringent
hybridization conditions to a nucleic acid molecule having the
nucleotide sequence of SEQ ID NO:59.
[0112] Also within the invention is a polypeptide which is a
naturally occurring allelic variant of a polypeptide that includes
the amino acid sequence of SEQ ID NO:58 or SEQ ID NO:60, wherein
the polypeptide is encoded by a nucleic acid molecule which
hybridizes to a nucleic acid molecule comprising SEQ ID NO:57 or
SEQ ID NO:59 under stringent conditions.
[0113] Another embodiment of the invention features T85 nucleic
acid molecules which specifically detect T85 nucleic acid
molecules. For example, in one embodiment, a T85 nucleic acid
molecule hybridizes under stringent conditions to a nucleic acid
molecule comprising the nucleotide sequence of SEQ ID NO:57 or SEQ
ID NO:59, or a complement thereof. In another embodiment, the T85
nucleic acid molecule is at least 300 (325, 350, 375, 400, 425,
450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides
in length and hybridizes under stringent conditions to a nucleic
acid molecule comprising the nucleotide sequence shown in SEQ ID
NO:57 or SEQ ID NO:59, or a complement thereof. In a preferred
embodiment, an isolated T85 nucleic acid molecule comprises a
nucleotide sequence of SEQ ID NO:57 which encodes a fibronectin
type III domain, or a complement thereof. In another preferred
embodiment, an isolated T85 nucleic acid molecule comprises a
nucleotide of SEQ ID NO:57 which encodes an Ig superfamily domain,
or a complement thereof. In another embodiment, the invention
provides an isolated nucleic acid molecule which is antisense to
the coding strand of a T85 nucleic acid.
[0114] Another aspect of the invention provides a vector, e.g., a
recombinant expression vector, comprising a T85 nucleic acid
molecule of the invention. In another embodiment the invention
provides a host cell containing such a vector. The invention also
provides a method for producing T85 protein by culturing, in a
suitable medium, a host cell of the invention containing a
recombinant expression vector such that a T85 protein is
produced.
[0115] Another aspect of this invention features isolated or
recombinant T85 proteins and polypeptides. Preferred T85 proteins
and polypeptides possess at least one biological activity possessed
by naturally occurring human T85, e.g., the ability to form
protein:protein interactions with other proteins.
[0116] The T85 proteins of the present invention, or biologically
active portions thereof, can be operatively linked to a non-T85
polypeptide (e.g., heterologous amino acid sequences) to form T85
fusion proteins. The invention further features antibodies that
specifically bind T85 proteins, such as monoclonal or polyclonal
antibodies. In addition, the T85 proteins or biologically active
portions thereof can be incorporated into pharmaceutical
compositions, which optionally include pharmaceutically acceptable
carriers.
[0117] In another aspect, the present invention provides a method
for detecting the presence of T85 activity or expression in a
biological sample by contacting the biological sample with an agent
capable of detecting an indicator of T85 activity such that the
presence of T85 activity is detected in the biological sample.
[0118] In another aspect, the invention provides a method for
modulating T85 activity comprising contacting a cell with an agent
that modulates (inhibits or stimulates) T85 activity or expression
such that T85 activity or expression in the cell is modulated. In
one embodiment, the agent is an antibody that specifically binds to
T85 protein. In another embodiment, the agent modulates expression
of T85 by modulating transcription of a T85 gene, splicing of a T85
mRNA, or translation of a T85 mRNA. In yet another embodiment, the
agent is a nucleic acid molecule having a nucleotide sequence that
is antisense to the coding strand of the T85 mRNA or the T85
gene.
[0119] In one embodiment, the methods of the present invention are
used to treat a subject having a disorder characterized by aberrant
T85 protein or nucleic acid expression or activity by administering
an agent which is a T85 modulator to the subject. In one
embodiment, the T85 modulator is a T85 protein. In another
embodiment the T85 modulator is a T85 nucleic acid molecule. In
other embodiments, the T85 modulator is a peptide, peptidomimetic,
or other small molecule.
[0120] The present invention also provides a diagnostic assay for
identifying the presence or absence of a genetic lesion or mutation
characterized by at least one of: (i) aberrant modification or
mutation of a gene encoding a T85 protein; (ii) mis-regulation of a
gene encoding a T85 protein; and (iii) aberrant post-translational
modification of a T85 protein, wherein a wild-type form of the gene
encodes a protein with a T85 activity.
[0121] In another aspect, the invention provides a method for
identifying a compound that binds to or modulates the activity of a
T85 protein. In general, such methods entail measuring a biological
activity of a T85 protein in the presence and absence of a test
compound and identifying those compounds which alter the activity
of the T85 protein.
[0122] The invention also features methods for identifying a
compound which modulates the expression of T85 by measuring the
expression of T85 in the presence and absence of a compound.
TANGO 77
[0123] The present invention is based, at least in part, on the
discovery of a gene encoding Tango-77, a secreted protein that is
predicted to be a member of the cytokine superfamily. The Tango-77
cDNA described below (SEQ ID NO:71) has three possible open reading
frames. The first potential open reading frame encompasses 534
nucleotides extending from nucleotide 356 to nucleotide 889 of SEQ
ID NO:71 (SEQ ID NO:73) and encodes a 178 amino acid protein (SEQ
ID NO:72). This protein may include a predicted signal sequence of
about 63 amino acids (from about amino acid 1 to about amino acid
63 of SEQ ID NO:72 (SEQ ID NO:74) and a predicted mature protein of
about 115 amino acids (from about amino acid 64 to amino acid 178
of SEQ ID NO:72 (SEQ ID NO:75)).
[0124] The second potential open reading frame encompasses 498
nucleotides extending from nucleotide 389 to nucleotide 889 of SEQ
ID NO:71 (SEQ ID NO:76) and encodes a 167 amino acid protein (SEQ
ID NO:77). This protein may include a predicted signal sequence of
about 52 amino acids (from about amino acid 1 to about amino acid
52 of SEQ ID NO:77 (SEQ ID NO:78)) and a predicted mature protein
of about 115 amino acids (from about amino acid 52 to amino acid
167 of SEQ ID NO:77 (SEQ ID NO:79)).
[0125] The third potential open reading frame encompasses 408
nucleotides extending from nucleotide 481 to nucleotide 889 of SEQ
ID NO:71 (SEQ ID NO:80) and encodes a 136 amino acid protein (SEQ
ID NO:81). This protein includes a predicted signal sequence of
about 21 amino acids (from about amino acid 1 to about amino acid
21 of SEQ ID NO:81 (SEQ ID NO:82)) and a predicted mature protein
of about 115 amino acids (from about amino acid 22 to amino acid
136 of SEQ ID NO:81 (SEQ ID NO:83)).
[0126] As used herein, the terms "Tango-77", "Tango-77 protein",
"Tango-77 polypeptide" and the like, can refer and polypeptide
produced by the cDNA of SEQ ID NO:71 including any and all of the
Tango-77 gene products described above.
[0127] Tango-77 is expected to inhibit inflammation and play a
functional role similar to that of secreted IL-1ra. For example, it
is expected that Tango-77 may bind to the IL-1 receptor, thus
blocking receptor activation by inhibiting the binding of
IL-1.alpha. and IL-1.beta. to the receptor. Alternatively, Tango-77
may inhibit inflammation through another pathway, for example, by
binding to a novel receptor. Accordingly, Tango-77 may be useful as
a modulating agent in regulating a variety of cellular processes
including acute and chronic inflammation, e.g., asthma, chronic
myelogenous leukemia, rheumatoid arthritis, psoriasis and
inflammatory bowel disease.
[0128] In one aspect, the invention provides isolated nucleic acid
molecules encoding Tango-77 or biologically active portions
thereof, as well as nucleic acid fragments suitable as primers or
hybridization probes for the detection of Tango-77.
[0129] The invention encompasses methods of diagnosing and treating
patients who are suffering from a disorder associated with an
abnormal level (undesirably high or undesirably low) of
inflammation, abnormal activity of the IL-1 receptor complex, or
abnormal activity of IL-1, by administering a compound that
modulates the expression of Tango-77 (at the DNA, mRNA or protein
level, e.g., by altering mRNA splicing) or by altering the activity
of Tango-77. Examples of such compounds include small molecules,
antisense nucleic acid molecules, ribozymes, and polypeptides.
[0130] The invention features a nucleic acid molecule which is at
least 45% (e.g., 55%, 65%, 75%, 85%, 95%, or 98%) identical to the
nucleotide sequence shown in SEQ ID NO:71, SEQ ID NO:73, SEQ ID
NO:76, SEQ ID NO:80, the nucleotide sequence of the cDNA insert of
the plasmid deposited with ATCC as Accession Number (the "cDNA of
ATCC 98807"), or a complement thereof.
[0131] The invention features a nucleic acid molecule which
includes a fragment of at least 100 (e.g., 250, 325, 350, 375, 400,
425, 450, 500, 550, 600, 650, 700, 800, 900, or 989) nucleotides of
the nucleotide sequence shown in SEQ ID NO:71, SEQ ID NO:73, SEQ ID
NO:76, SEQ ID NO:80, the nucleotide sequence of the cDNA ATCC
98807, or a complement thereof.
[0132] The invention also features a nucleic acid molecule which
includes a nucleotide sequence encoding a protein having an amino
acid sequence that is at least 45% (55%, 65%, 75%, 85%, 95%, or
98%) identical to the amino acid sequence of SEQ ID NO:72, SEQ ID
NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, or
the amino acid sequence encoded by the cDNA of ATCC 98807.
[0133] In a preferred embodiment, a Tango-77 nucleic acid molecule
has the nucleotide sequence shown in SEQ ID NO:71, SEQ ID NO:73,
SEQ ID NO:76, SEQ ID NO:80 or the nucleotide sequence of the cDNA
of ATCC 98807.
[0134] Also within the invention is a nucleic acid molecule which
encodes a fragment of a polypeptide having the amino acid sequence
of SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:77, SEQ ID
NO:78, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:82, SEQ ID NO:83,
wherein the fragment includes at least 15 (e.g., 25, 30, 50, 100,
150, or 178) contiguous amino acids of SEQ ID NO:72, SEQ ID NO:74,
SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:79, SEQ ID
NO:81, SEQ ID NO:82, SEQ ID NO:83, or the polypeptide encoded by
the cDNA of ATCC Accession Number 98807.
[0135] The invention includes a nucleic acid molecule which encodes
a naturally occurring allelic variant of a polypeptide comprising
the amino acid sequence of SEQ ID NO:72, SEQ ID NO:74, SEQ ID
NO:75, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:81, SEQ
ID NO:82, SEQ ID NO:83, or an amino acid sequence encoded by the
cDNA of ATCC Accession Number 98807, wherein the nucleic acid
molecule hybridizes to a nucleic acid molecule comprising SEQ ID
NO:71, SEQ ID NO:73, SEQ ID NO:76, SEQ ID NO:80, or a complement
thereof under stringent conditions.
[0136] Also within the invention are: an isolated Tango-77 protein
having an amino acid sequence that is at least about 45%,
preferably 65%, 75%, 85%, 95%, or 98% identical to the amino acid
sequence of SEQ ID NO:75, SEQ ID NO:79 or SEQ ID NO:83 (mature
human Tango-77), or the amino acid sequence of SEQ ID NO:72, SEQ ID
NO:77 or SEQ ID NO:81 (immature human Tango-77).
[0137] Also within the invention are: an isolated Tango-77 protein
which is encoded by a nucleic acid molecule having a nucleotide
sequence that is at least about 65%, preferably 75%, 85%, or 95%
identical to SEQ ID NO:73, SEQ ID NO:76, SEQ ID NO:80 or the cDNA
of ATCC 98807; and an isolated Tango-77 protein which is encoded by
a nucleic acid molecule having a nucleotide sequence which
hybridizes under stringent hybridization conditions to a nucleic
acid molecule having the nucleotide sequence of SEQ ID NO:73, SEQ
ID NO:76, SEQ ID NO:80, the non-coding strand of the cDNA of ATCC
98807, or the complement thereof.
[0138] Also within the invention is a polypeptide which is a
naturally occurring allelic variant of a polypeptide that includes
the amino acid sequence of SEQ ID NO:72, SEQ ID NO:74, SEQ ID
NO:75, SEQ ID NO:77, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:81, SEQ
ID NO:82, SEQ ID NO:83, or an amino acid sequence encoded by the
cDNA insert of the plasmid deposited with ATCC as Accession Number
98807, wherein the polypeptide is encoded by a nucleic acid
molecule which hybridizes to a nucleic acid molecule comprising SEQ
ID NO:71, SEQ ID NO:73, SEQ ID NO:76, SEQ ID NO:80 or the
complement thereof under stringent conditions.
[0139] Another embodiment of the invention features Tango-77
nucleic acid molecules which specifically detect Tango-77 nucleic
acid molecules relative to nucleic acid molecules encoding other
members of the cytokine superfamily. For example, in one
embodiment, a Tango-77 nucleic acid molecule hybridizes under
stringent conditions to a nucleic acid molecule comprising the
nucleotide sequence of SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:76,
SEQ ID NO:80, the cDNA of ATCC 98807, or a complement thereof. In
another embodiment, the Tango-77 nucleic acid molecule is at least
300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800,
900, or 989) nucleotides in length and hybridizes under stringent
conditions to a nucleic acid molecule comprising the nucleotide
sequence shown in SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:76, SEQ ID
NO:80, the cDNA of ATCC 98807, or a complement thereof. In yet
another embodiment, the invention provides an isolated nucleic acid
molecule which is antisense to the coding strand of a Tango-77
nucleic acid.
[0140] Another aspect of the invention provides a vector, e.g., a
recombinant expression vector, comprising a Tango-77 nucleic acid
molecule of the invention. In another embodiment, the invention
provides a host cell containing such a vector. The invention also
provides a method for producing Tango-77 protein by culturing, in a
suitable medium, a host cell of the invention containing a
recombinant expression vector such that a Tango-77 protein is
produced.
[0141] Another aspect of this invention features isolated or
recombinant Tango-77 proteins and polypeptides. Preferred Tango-77
proteins and polypeptides possess at least one biological activity
possessed by naturally occurring human Tango-77, e.g., (i) the
ability to interact with proteins in the Tango-77 signalling
pathway (ii) the ability to interact with a Tango-77 ligand or
receptor; or (iii) the ability to interact with an intracellular
target protein, (iv) the ability to interact with a protein
involved in inflammation and (v) the ability to bind the IL-1
receptor. Other activities include the induction and suppression of
polypeptide interleukins, cytokines and growth factors.
[0142] The Tango-77 proteins of the present invention, or
biologically active portions thereof, can be operably linked to a
non-Tango-77 polypeptide (e.g., heterologous amino acid sequences)
to form Tango-77 fusion proteins. The invention further features
antibodies that specifically bind Tango-77 proteins, such as
monoclonal or polyclonal antibodies. In addition, the Tango-77
proteins or biologically active portions thereof can be
incorporated into pharmaceutical compositions, which optionally
include pharmaceutically acceptable carriers.
[0143] In another aspect, the present invention provides a method
for detecting the presence of Tango-77 activity or expression in a
biological sample by contacting the biological sample with an agent
capable of detecting an indicator of Tango-77 activity or
expression such that the presence of Tango-77 activity or
expression is detected in the biological sample.
[0144] In another aspect, the invention provides a method for
modulating Tango-77 activity comprising contacting a cell with an
agent that modulates (inhibits or stimulates)
[0145] Tango-77 activity or expression such that Tango-77 activity
or expression in the cell is modulated. In one embodiment, the
agent is an antibody that specifically binds to Tango-77 protein.
In another embodiment, the agent modulates expression of Tango-77
by modulating transcription of a Tango-77 gene, splicing of a
Tango-77 mRNA, or translation of a Tango-77 mRNA. In yet another
embodiment, the agent is a nucleic acid molecule having a
nucleotide sequence that is antisense to the coding strand of the
Tango-77 mRNA or the Tango-77 gene.
[0146] In one embodiment, the methods of the present invention are
used to treat a subject having a disorder characterized by aberrant
Tango-77 protein activity or nucleic acid expression by
administering an agent which is a Tango-77 modulator to the
subject. In one embodiment, the Tango-77 modulator is a Tango-77
protein. In another embodiment, the Tango-77 modulator is a
Tango-77 nucleic acid molecule. In other embodiments, the Tango-77
modulator is a peptide, peptidomimetic, or other small molecule. In
a preferred embodiment, the disorder characterized by aberrant
Tango-77 protein or nucleic acid expression can include chronic and
acute inflammation.
[0147] The present invention also provides a diagnostic assay for
identifying the presence or absence of a genetic lesion or mutation
characterized by at least one of: (i) aberrant modification or
mutation of a gene encoding a Tango-77 protein; (ii) mis-regulation
of a gene encoding a Tango-77 protein; and (iii) aberrant
post-translational modification of a Tango-77 protein, wherein a
wild-type form of the gene encodes a protein with a Tango-77
activity.
[0148] In another aspect, the invention provides a method for
identifying a compound that binds to or modulates the activity of a
Tango-77 protein. In general, such methods entail measuring a
biological activity of a Tango-77 protein in the presence and
absence of a test compound and identifying those compounds which
alter the activity of the Tango-77 protein.
[0149] The invention also features methods for identifying a
compound which modulates the expression of Tango-77 by measuring
the expression of Tango-77 in the presence and absence of a
compound.
SPOIL
[0150] The present invention is based, at least in part, on the
discovery of novel nucleic acid molecules which encode a novel
family of proteins having homology to IL-1 receptor antagonist
(IL-1ra) molecules, referred to herein as SPOIL nucleic acid and
protein molecules. The SPOIL molecules of the present invention are
useful as modulating agents in regulating a variety of cellular
processes. Accordingly, in one aspect, this invention provides
isolated nucleic acid molecules encoding SPOIL proteins and
biologically active portions thereof, as well as nucleic acid
fragments suitable as primers or hybridization probes for the
detection of SPOIL-encoding nucleic acids. In one embodiment, an
isolated nucleic acid molecule of the present invention preferably
encodes a SPOIL protein which includes an interleukin-1 (IL-1)
signature domain.
[0151] In another embodiment, an isolated nucleic acid molecule of
the present invention preferably encodes a SPOIL protein which
includes a SPOIL signature motif. In another embodiment, an
isolated nucleic acid molecule of the present invention preferably
encodes a SPOIL protein which includes a SPOIL unique domain. In
another embodiment, an isolated nucleic acid molecule of the
present invention preferably encodes a SPOIL protein which includes
a SPOIL C-terminal unique domain. In another embodiment, an
isolated nucleic acid molecule of the present invention preferably
encodes a SPOIL protein which includes a signal sequence and/or is
secreted. In yet another embodiment, an isolated nucleic acid
molecule of the present invention preferably encodes a SPOIL
protein which lacks a signal sequence and/or is intracellular. In
another embodiment, the nucleic acid molecule is a naturally
occurring nucleotide sequence.
[0152] In another embodiment, a nucleic acid molecule of the
invention has 65% identity with the nucleotide sequence shown in
SEQ ID NO:89, SEQ ID NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA
insert of the plasmid deposited with ATCC as Accession Number
98883, the DNA insert of the plasmid deposited with ATCC as
Accession Number 98984 or a complement thereof and, preferably,
encodes a SPOIL protein. In yet another embodiment, the isolated
nucleic acid molecule has 65% identity with the nucleotide sequence
shown in SEQ ID NO:91, SEQ ID NO:103, SEQ ID NO:106, SEQ ID NO:114,
or a complement thereof and, preferably, encodes a SPOIL protein.
In a preferred embodiment, an isolated nucleic acid molecule
encodes the amino acid sequence of a mammalian protein, (e.g., a
human or mouse SPOIL protein.)
[0153] In another embodiment, the isolated nucleic acid molecule
includes a nucleotide sequence encoding a protein having an amino
acid sequence sufficiently homologous to the amino acid sequence of
SEQ ID NO:90; SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the
amino acid sequence encoded by the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the DNA insert of
the plasmid deposited with ATCC as Accession Number 98984 and,
preferably, encodes a SPOIL protein. In a preferred embodiment, the
nucleic acid molecule has the nucleotide sequence shown in SEQ ID
NO:91, SEQ ID NO:103, SEQ ID NO:106, or SEQ ID NO:114. In another
preferred embodiment, the nucleic acid molecule has the nucleotide
sequence shown in SEQ ID NO:89, SEQ ID NO:101, SEQ ID NO:104, SEQ
ID NO:112, the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984.
[0154] Another embodiment of the invention features isolated
nucleic acid molecules which hybridize under stringent conditions
to a nucleic acid molecule consisting of nucleotides 135-428 or
nucleotides 495-746 of SEQ ID NO:89. In yet another preferred
embodiment, the isolated nucleic acid molecules hybridize under
stringent conditions to a nucleic acid molecule consisting of
nucleotides 1-280, 123-260, or nucleotides 390-1291 of SEQ ID
NO:101. In yet another preferred embodiment, the isolated nucleic
acid molecules hybridize under stringent conditions to a nucleic
acid molecule consisting of nucleotides 1-371, 98-721, or
nucleotides 481-1377 of SEQ ID NO:104. In yet another preferred
embodiment, the isolated nucleic acid molecules hybridize under
stringent conditions to a nucleic acid molecule consisting of
nucleotides 225-365, 96-575, or nucleotides 495-838 of SEQ ID
NO:112. In another embodiment, the nucleic acid molecule is at
least 300 nucleotides in length. In another embodiment, the nucleic
acid molecule is at least 300 nucleotides in length and hybridizes
under stringent conditions to a nucleic acid molecule comprising
the nucleotide sequence shown in SEQ ID NO:89, SEQ ID NO:101, SEQ
ID NO:104, SEQ ID NO:112, the DNA insert of the plasmid deposited
with ATCC as Accession Number 98883, or the DNA insert of the
plasmid deposited with ATCC as Accession Number 98984, or a
complement thereof. In yet another embodiment, the nucleic acid
molecule is at least 300 nucleotides in length and encodes a SPOIL
protein or portion thereof, preferably a biologically active
portion thereof.
[0155] In a preferred embodiment, an isolated nucleic acid molecule
comprises nucleotides 135-428 of SEQ ID NO:89, or a complement
thereof. In another embodiment, the nucleic acid molecule further
comprises nucleotides 1-134 of SEQ ID NO:89. In yet another
embodiment, the nucleic acid molecule further comprises nucleotides
429-746 of SEQ ID NO:89.
[0156] In another preferred embodiment, an isolated nucleic acid
molecule comprises nucleotides 124-630 of SEQ ID NO:101, or a
complement thereof. In another embodiment, the nucleic acid
molecule further comprises nucleotides 1-123 of SEQ ID NO:101. In
yet another embodiment, the nucleic acid molecule further comprises
nucleotides 631-1291 of SEQ ID NO:101.
[0157] In another preferred embodiment, an isolated nucleic acid
molecule comprises nucleotides 98-721 of SEQ ID NO:104, or a
complement thereof. In another embodiment, the nucleic acid
molecule further comprises nucleotides 1-97 of SEQ ID NO:104. In
yet another embodiment, the nucleic acid molecule further comprises
nucleotides 722-1377 of SEQ ID NO:104.
[0158] In another preferred embodiment, an isolated nucleic acid
molecule comprises nucleotides 96-575 of SEQ ID NO:112, or a
complement thereof. In another embodiment, the nucleic acid
molecule further comprises nucleotides 1-95 of SEQ ID NO:112. In
yet another embodiment, the nucleic acid molecule further comprises
nucleotides 576-838 of SEQ ID NO:112.
[0159] Another embodiment the invention provides an isolated
nucleic acid molecule which is antisense to the coding strand of a
SPOIL nucleic acid.
[0160] Another aspect of the invention provides a vector comprising
a nucleic acid molecule of the invention, preferably a SPOIL
nucleic acid molecule. In certain embodiments, the vector is a
recombinant expression vector. In another embodiment, the invention
provides a host cell containing a vector of the invention. The
invention also provides a method for producing SPOIL protein by
culturing in a suitable medium, a host cell of the invention
containing a recombinant expression vector such that SPOIL protein
is produced.
[0161] Another aspect of this invention features isolated or
recombinant proteins and polypeptides, preferably SPOIL proteins or
polypeptides. In one embodiment, an isolated protein, preferably a
SPOIL protein, has a SPOIL signature motif. In another embodiment,
an isolated protein, preferably a SPOIL protein, has an IL-1
signature domain. In another embodiment, an isolated protein,
preferably a SPOIL protein, has a SPOIL unique domain. In another
embodiment, an isolated protein, preferably a SPOIL protein, has a
SPOIL C-terminal unique domain. In another embodiment, an isolated
protein, preferably a SPOIL protein, has a combination of two or
more of the above-stated domains and/or motifs. In yet another
embodiment, an isolated protein, preferably a SPOIL protein, has a
signal sequence and/or is secreted. In yet another embodiment, an
isolated protein, preferably a SPOIL protein, lacks a signal
sequence and/or is intracellular. In another embodiment, an
isolated protein, preferably a SPOIL protein, has an amino acid
sequence sufficiently homologous to the amino acid sequence of SEQ
ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98883, or the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98984. This invention further features isolated
proteins, preferably SPOIL proteins, having an amino acid sequence
at least about 45% identical to a SPOIL unique domain amino acid
sequence. This invention further features isolated proteins,
preferably SPOIL proteins, having an amino acid sequence at least
about 45% identical to a SPOIL C-terminal unique domain amino acid
sequence.
[0162] In another embodiment, the invention features fragments of
the protein having the amino acid sequence of SEQ ID NO:90, SEQ ID
NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984, wherein the fragment comprises at least 15 contiguous amino
acids of the amino acid sequence of SEQ ID NO:90, SEQ ID NO:102,
SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence encoded by
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98883, or the amino acid sequence encoded by the DNA insert
of the plasmid deposited with ATCC as Accession Number 98984. In a
preferred embodiment, the protein has the amino acid sequence of
SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, or SEQ ID NO:113.
[0163] Another embodiment of the invention features an isolated
protein, preferably a SPOIL protein, having an amino acid sequence
at least about 60% identical to the amino acid sequence of SEQ ID
NO:90, SEQ ID NO:102, SEQ ID NO:105, or SEQ ID NO:113, the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98883, or the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98984. Another embodiment of the invention
features an isolated protein, preferably a SPOIL protein, having an
amino acid sequence at least about 85% identical to the amino acid
sequence of SEQ ID NO:102 or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984. Yet another embodiment of the invention features isolated
proteins, preferably SPOIL proteins, which are encoded by nucleic
acid molecules having a nucleotide sequence at least about 60%
identical to a nucleotide sequence of SEQ ID NO:89, SEQ ID NO:91,
SEQ ID NO:101, SEQ ID NO:103; SEQ ID NO:104, SEQ ID NO:106, SEQ ID
NO:112, SEQ ID NO:114, the DNA insert of the plasmid deposited with
ATCC as Accession Number 98883, or the DNA insert of the plasmid
deposited with ATCC as Accession Number 98984, or a complement
thereof.
[0164] This invention further features isolated proteins,
preferably SPOIL proteins, which are encoded by nucleic acid
molecules having a nucleotide sequence which hybridizes under
stringent hybridization conditions to the complement of a nucleic
acid molecule comprising the nucleotide sequence of SEQ ID NO:89,
SEQ ID NO:91, SEQ ID NO:101, SEQ ID NO:103; SEQ ID NO:104, SEQ ID
NO:106, SEQ ID NO:112, or SEQ ID NO:114.
[0165] The proteins of the present invention, preferably SPOIL
proteins, or portions thereof (e.g., biologically active portions
thereof), can be operatively linked to a non-SPOIL polypeptide to
form fusion proteins, preferably SPOIL fusion proteins. The
invention further features antibodies that specifically bind SPOIL
proteins, such as monoclonal or polyclonal antibodies. In addition,
the proteins of the invention or biologically active portions
thereof can be incorporated into pharmaceutical compositions, which
optionally include pharmaceutically acceptable carriers.
[0166] In another aspect, the present invention provides a method
for detecting the presence of SPOIL activity or expression in a
biological sample by contacting the biological sample with an agent
capable of detecting an indicator of SPOIL activity such that the
presence of SPOIL activity is detected in the biological
sample.
[0167] In another aspect, the invention provides a method for
modulating SPOIL activity comprising contacting a cell capable of
expressing SPOIL with an agent that modulates SPOIL activity such
that SPOIL activity in the cell is modulated. In one embodiment,
the agent inhibits SPOIL activity. In another embodiment, the agent
stimulates SPOIL activity. In one embodiment, the agent is an
antibody that specifically binds to SPOIL protein. In another
embodiment, the agent modulates expression of SPOIL by modulating
transcription of a SPOIL gene or translation of a SPOIL mRNA. In
yet another embodiment, the agent is a nucleic acid molecule having
a nucleotide sequence that is antisense to the coding strand of the
SPOIL mRNA or the SPOIL gene.
[0168] In another aspect, the invention provides a method for
modulating IL-1 activity comprising contacting a cell capable of
expressing and/or responding to IL-1 with an agent that modulates
SPOIL activity such that IL-1 activity in the cell is modulated. In
one embodiment, an agent inhibits or reduces IL-1 activity. Thus,
in one embodiment, the SPOIL agent is a protein of the invention,
preferably a SPOIL protein or a biologically active portion thereof
which functions as an IL-1 receptor antagonist. In another
embodiment, a SPOIL agent stimulates IL-1 activity. Thus, in
another embodiment, the SPOIL agent is a protein of the invention,
preferably a SPOIL protein, SPOIL variant, or biologically active
portion thereof which functions as an IL-1 receptor agonist.
[0169] In another embodiment, the SPOIL agent is a protein of the
invention, preferably a SPOIL protein or a biologically active
portion thereof, which modulates an anti-inflammatory cytokine
(e.g., soluble TNF-Receptor p55 (sTNFRp55), sTNFRp75 and IL-1
receptor antagonist (IL-1Ra)). In yet another embodiment, the SPOIL
agent is a protein of the invention, preferably a SPOIL protein,
SPOIL variant, or biologically active portion thereof, which
modulates a pro-inflammatory cytokine (e.g., tumor necrosis factor
(TNF-.alpha.), interleukin-6 (IL-6) and interleukin-1b
(IL-1b)).
[0170] In one embodiment, the methods of the present invention are
used to treat a subject having a disorder characterized by aberrant
SPOIL and/or IL-1 expression by administering an agent which is a
SPOIL modulator to the subject. In one embodiment, the SPOIL agent
is a SPOIL protein or SPOIL variant. In yet another embodiment, the
SPOIL agent is a peptide, peptidomimetic, or other small molecule.
In a preferred embodiment, the disorder characterized by aberrant
SPOIL and/or IL-1 expression is a bone metabolism disorder, a
proinflammatory disorder, or an immune disorder.
[0171] The present invention also provides a diagnostic assay for
identifying the presence or absence of a genetic alteration
characterized by at least one of (i) aberrant modification or
mutation of a gene encoding a SPOIL protein; (ii) mis-regulation of
said gene; and (iii) aberrant post-translational modification of a
SPOIL protein, wherein a wild-type form of said gene encodes an
protein with a SPOIL activity.
[0172] In another aspect, the invention provides a method for
identifying a compound that binds to or modulates the activity of a
SPOIL protein, by providing an indicator composition comprising an
a SPOIL protein having SPOIL activity, contacting the indicator
composition with a test compound, and determining the effect of the
test compound on SPOIL activity in the indicator composition to
identify a compound that modulates the activity of a SPOIL
protein.
NEOKINE
[0173] The present invention is based, at least in part, on the
discovery of nucleic acid molecules which encode a novel family of
secreted proteins, referred to herein as the Neokine family of
proteins ("NEOKINES" or "NEOKINE proteins") which are ligands for a
previously-identified putative G protein-coupled receptor termed
"RDC1" also referred to herein as the "NEOKINE receptor". The
NEOKINE molecules of the present invention are useful as modulating
agents in regulating a variety of cellular processes. Accordingly,
in one aspect, this invention provides isolated nucleic acid
molecules encoding NEOKINE proteins or biologically active portions
thereof, as well as nucleic acid fragments suitable as primers or
hybridization probes for the detection of NEOKINE-encoding nucleic
acids.
[0174] In one embodiment, a NEOKINE nucleic acid molecule is 60%
homologous to the nucleotide sequence shown in SEQ ID NO:115, SEQ
ID NO:117, the nucleotide sequence of the DNA insert of the plasmid
deposited with ATCC as Accession Number 98751, or complement
thereof. In another embodiment, a NEOKINE nucleic acid molecule is
60% homologous to the nucleotide sequence shown in SEQ ID NO:118,
SEQ ID NO:120, or a complement thereof. In yet another embodiment,
a NEOKINE nucleic acid molecule is 60% homologous to the nucleotide
sequence shown in SEQ ID NO:121 or SEQ ID NO:123. In yet another
embodiment, a NEOKINE nucleic acid molecule is 60% homologous to
the nucleotide sequence shown in SEQ ID NO:124. In a preferred
embodiment, an isolated NEOKINE nucleic acid molecule has the
nucleotide sequence shown SEQ ID NO:117, or a complement thereof.
In another embodiment, a NEOKINE nucleic acid molecule further
comprises nucleotides 1-96 of SEQ ID NO:115. In another embodiment,
a NEOKINE nucleic acid molecule further comprises nucleotides
394-1564 of SEQ ID NO:115. In another preferred embodiment, an
isolated NEOKINE nucleic acid molecule has the nucleotide sequence
shown in SEQ ID NO:115.
[0175] In another preferred embodiment, an isolated NEOKINE nucleic
acid molecule has the nucleotide sequence shown SEQ ID NO:120, or a
complement thereof. In another embodiment, a NEOKINE nucleic acid
molecule further comprises nucleotides 1-211 of SEQ ID NO:118. In
another embodiment, a NEOKINE nucleic acid molecule further
comprises nucleotides 509-1656 of SEQ ID NO:118. In another
preferred embodiment, an isolated NEOKINE nucleic acid molecule has
the nucleotide sequence shown in SEQ ID NO:118.
[0176] In another preferred embodiment, an isolated NEOKINE nucleic
acid molecule has the nucleotide sequence shown SEQ ID NO:123, or a
complement thereof. In another embodiment, a NEOKINE nucleic acid
molecule further comprises nucleotides 235-1372 of SEQ ID NO:121.
In another preferred embodiment, an isolated NEOKINE nucleic acid
molecule has the nucleotide sequence shown in SEQ ID NO:121.
[0177] In another preferred embodiment, an isolated NEOKINE nucleic
acid molecule has the nucleotide sequence shown SEQ ID NO:136, or a
complement thereof. In another embodiment, a NEOKINE nucleic acid
molecule further comprises nucleotides 285-1458 of SEQ ID NO:124.
In another preferred embodiment, an isolated NEOKINE nucleic acid
molecule has the nucleotide sequence shown in SEQ ID NO:124.
[0178] In another preferred embodiment, an isolated NEOKINE nucleic
acid molecule is of human origin and has the nucleotide sequence of
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98751, or a complement thereof. In another embodiment, an
isolated NEOKINE nucleic acid molecule is of rat origin. In another
embodiment, an isolated NEOKINE nucleic acid molecule is of macaque
origin.
[0179] In another embodiment, a NEOKINE nucleic acid molecule
includes a nucleotide sequence encoding a protein having an amino
acid sequence sufficiently homologous to the amino acid sequence of
SEQ ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125. In
another preferred embodiment, a NEOKINE nucleic acid molecule
includes a nucleotide sequence encoding a protein having an amino
acid sequence at least 60% homologous to the amino acid sequence of
SEQ ID NO:116. In yet another preferred embodiment, a NEOKINE
nucleic acid molecule includes a nucleotide sequence encoding a
protein having an amino acid sequence at least 60% homologous to
the amino acid sequence of SEQ ID NO:119. In yet another preferred
embodiment, a NEOKINE nucleic acid molecule includes a nucleotide
sequence encoding a protein having an amino acid sequence at least
60% homologous to the amino acid sequence of SEQ ID NO:122. In yet
another preferred embodiment, a NEOKINE nucleic acid molecule
includes a nucleotide sequence encoding a protein having an amino
acid sequence at least 60% homologous to the amino acid sequence of
SEQ ID NO:125.
[0180] In another embodiment, an isolated nucleic acid molecule of
the present invention encodes a NEOKINE protein which includes a
NEOKINE CXC signature motif. In another embodiment, an isolated
nucleic acid molecule of the present invention encodes a NEOKINE
protein which includes a NEOKINE CXC signature motif and a signal
sequence and is secreted. In yet another embodiment, a NEOKINE
nucleic acid molecule encodes a NEOKINE protein and is a naturally
occurring nucleotide sequence.
[0181] Another embodiment of the invention features NEOKINE nucleic
acid molecules which specifically detect NEOKINE nucleic acid
molecules relative to nucleic acid molecules encoding non-NEOKINE
proteins. For example, in one embodiment, a NEOKINE nucleic acid
molecule is at least 650 nucleotides in length and hybridizes under
stringent conditions to a nucleic acid molecule comprising the
nucleotide sequence shown in SEQ ID NO:115, SEQ ID NO:118, SEQ ID
NO:121, or SEQ ID NO:124, or a complement thereof.
[0182] Another embodiment of the invention provides an isolated
nucleic acid molecule which is antisense to the coding strand of a
NEOKINE nucleic acid.
[0183] Another aspect of the invention provides a vector comprising
a NEOKINE nucleic acid molecule. In certain embodiments, the vector
is a recombinant expression vector. In another embodiment, the
invention provides a host cell containing a vector of the
invention. The invention also provides a method for producing a
NEOKINE protein by culturing in a suitable medium, a host cell of
the invention containing a recombinant expression vector such that
a NEOKINE protein is produced.
[0184] Another aspect of this invention features isolated or
recombinant NEOKINE proteins and polypeptides. In one embodiment,
an isolated NEOKINE protein includes a NEOKINE CXC signature motif
and is secreted. In another embodiment, an isolated NEOKINE protein
includes a NEOKINE CXC signature motif and a signal sequence, and
is secreted. In another embodiment, an isolated NEOKINE protein has
an amino acid sequence sufficiently homologous to the amino acid
sequence of SEQ ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID
NO:125. In a preferred embodiment, a NEOKINE protein has an amino
acid sequence at least about 60% homologous to the amino acid
sequence of SEQ ID NO:116. In another preferred embodiment, a
NEOKINE protein has an amino acid sequence at least about 60%
homologous to the amino acid sequence of SEQ ID NO:119. In another
preferred embodiment, a NEOKINE protein has an amino acid sequence
at least about 60% homologous to the amino acid sequence of SEQ ID
NO:122. In another preferred embodiment, a NEOKINE protein has an
amino acid sequence at least about 60% homologous to the amino acid
sequence of SEQ ID NO:125. In another embodiment, a NEOKINE protein
has the amino acid sequence of SEQ ID NO:116, SEQ ID NO:119, SEQ ID
NO:122, or SEQ ID NO:125.
[0185] Another embodiment of the invention features an isolated
NEOKINE protein which is encoded by a nucleic acid molecule having
a nucleotide sequence at least about 60% homologous to a nucleotide
sequence of SEQ ID NO:115, or a complement thereof. Another
embodiment of the invention features an isolated NEOKINE protein
which is encoded by a nucleic acid molecule having a nucleotide
sequence at least about 60% homologous to a nucleotide sequence of
SEQ ID NO:118, or a complement thereof. Another embodiment of the
invention features an isolated NEOKINE protein which is encoded by
a nucleic acid molecule having a nucleotide sequence at least about
60% homologous to a nucleotide sequence of SEQ ID NO:121, or a
complement thereof. Another embodiment of the invention features an
isolated NEOKINE protein which is encoded by a nucleic acid
molecule having a nucleotide sequence at least about 60% homologous
to a nucleotide sequence of SEQ ID NO:124, or a complement thereof.
This invention further features an isolated NEOKINE protein which
is encoded by a nucleic acid molecule having a nucleotide sequence
which hybridizes under stringent hybridization conditions to a
nucleic acid molecule comprising the nucleotide sequence of SEQ ID
NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or a
complement thereof.
[0186] The NEOKINE proteins of the present invention, or
biologically active portions thereof, can be operatively linked to
a non-NEOKINE polypeptide to form NEOKINE fusion proteins. The
invention further features antibodies that specifically bind
NEOKINE proteins, such as monoclonal or polyclonal antibodies. In
addition, the NEOKINE proteins or biologically active portions
thereof can be incorporated into pharmaceutical compositions, which
optionally include pharmaceutically acceptable carriers.
[0187] In another aspect, the present invention provides a method
for detecting NEOKINE expression in a biological sample by
contacting the biological sample with an agent capable of detecting
a NEOKINE nucleic acid molecule, protein or polypeptide such that
the presence of a NEOKINE nucleic acid molecule, protein or
polypeptide is detected in the biological sample.
[0188] In another aspect, the present invention provides a method
for detecting the presence of NEOKINE activity in a biological
sample by contacting the biological sample with an agent capable of
detecting an indicator of NEOKINE activity such that the presence
of NEOKINE activity is detected in the biological sample.
[0189] In another aspect, the invention provides a method for
modulating NEOKINE activity comprising contacting the cell with an
agent that modulates NEOKINE activity such that NEOKINE activity in
the cell is modulated. In one embodiment, the agent inhibits
NEOKINE activity. In another embodiment, the agent stimulates
NEOKINE activity. In one embodiment, the agent is an antibody that
specifically binds to a NEOKINE protein. In another embodiment, the
agent modulates expression of NEOKINE by modulating transcription
of a NEOKINE gene or translation of a NEOKINE mRNA. In yet another
embodiment, the agent is a nucleic acid molecule having a
nucleotide sequence that is antisense to the coding strand of a
NEOKINE mRNA or a NEOKINE gene.
[0190] In one embodiment, the methods of the present invention are
used to treat a subject having a disorder characterized by aberrant
NEOKINE protein or nucleic acid expression or activity by
administering an agent which is a NEOKINE modulator to the subject.
In one embodiment, the NEOKINE modulator is a NEOKINE protein. In
another embodiment the NEOKINE modulator is a NEOKINE nucleic acid
molecule. In yet another embodiment, the NEOKINE modulator is a
peptide, peptidomimetic, or other small molecule. In a preferred
embodiment, the disorder characterized by aberrant NEOKINE protein
or nucleic acid expression is a developmental, differentiative,
proliferative disorder, an immunological disorder, or cell
death.
[0191] The present invention also provides a diagnostic assay for
identifying the presence or absence of a genetic alteration
characterized by at least one of (i) aberrant modification or
mutation of a gene encoding a NEOKINE protein; (ii) mis-regulation
of said gene; and (iii) aberrant post-translational modification of
a NEOKINE protein, wherein a wild-type form of said gene encodes an
protein with a NEOKINE activity.
[0192] The present invention also provides methods for identifying
compounds which modulate binding of NEOKINE to the NEOKINE receptor
and methods for identifying compounds which modulate the activity
of the NEOKINE receptor (e.g., cell-based as well as in vitro
screening assays).
TANGO 129
[0193] The present invention is based, at least in part, on the
discovery of a gene encoding T129, a transmembrane protein that is
predicted to be a member of the TNF receptor superfamily. The T129
cDNA described below (SEQ ID NO:137) has a 1290 nucleotide open
reading frame (nucleotides 99-1388 of SEQ ID NO:137; SEQ ID NO:139)
which encodes a 430 amino acid protein (SEQ ID NO:138). This
protein includes a predicted signal sequence of about 22 amino
acids (from amino acid 1 to about amino acid 22 of SEQ ID NO:138)
and a predicted mature protein of about 408 amino acids (from about
amino acid 23 to amino acid 430 of SEQ ID NO:138; SEQ ID NO:140).
T129 protein possesses a Tumor Necrosis Factor Receptor/Nerve
Growth Factor Receptor ("TNFR/NGFR") cysteine-rich region domain
(amino acids 51-90; SEQ ID NO:142). T129 is predicted to have one
transmembrane domain (TM) which extends from about amino acid 163
(extracellular end) to about amino acid 186 (cytoplasmic end) of
SEQ ID NO:138.
[0194] The T129 molecules of the present invention are useful as
modulating agents in regulating a variety of cellular processes.
Accordingly, in one aspect, this invention provides isolated
nucleic acid molecules encoding T129 proteins or biologically
active portions thereof, as well as nucleic acid fragments suitable
as primers or hybridization probes for the detection of
T129-encoding nucleic acids.
[0195] The invention features a nucleic acid molecule which is at
least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the
nucleotide sequence shown in SEQ ID NO:137, or SEQ ID NO:139, or a
complement thereof. The invention features a nucleic acid molecule
which includes a fragment of at least 300 (325, 350, 375, 400, 425,
450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides
of the nucleotide sequence shown in SEQ ID NO:137, or SEQ ID
NO:139, or a complement thereof.
[0196] The invention also features a nucleic acid molecule which
includes a nucleotide sequence encoding a protein having an amino
acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, or
98%) identical to the amino acid sequence of SEQ ID NO:138, SEQ ID
NO:140. In a preferred embodiment, a T129 nucleic acid molecule has
the nucleotide sequence shown SEQ ID NO:137, or SEQ ID NO:139.
[0197] Also within the invention is a nucleic acid molecule which
encodes a fragment of a polypeptide having the amino acid sequence
of SEQ ID NO:138 or SEQ ID NO:140, the fragment including at least
15 (25, 30, 50, 100, 150, 300, or 400) contiguous amino acids of
SEQ ID NO:138 or SEQ ID NO:140.
[0198] The invention includes a nucleic acid molecule which encodes
a naturally occurring allelic variant of a polypeptide comprising
the amino acid sequence of SEQ ID NO:138 or SEQ ID NO:140, wherein
the nucleic acid molecule hybridizes to a nucleic acid molecule
comprising SEQ ID NO:137 or SEQ ID NO:139 under stringent
conditions.
[0199] Also within the invention are: an isolated T129 protein
having an amino acid sequence that is at least about 65%,
preferably 75%, 85%, 95%, or 98% identical to the amino acid
sequence of SEQ ID NO:140 (mature human T129) or the amino acid
sequence of SEQ ID NO:138 (immature human T129); and an isolated
T129 protein having an amino acid sequence that is at least about
85%, 95%, or 98% identical to the TNFR/NGFR cysteine-rich domain of
SEQ ID NO:138 (e.g., about amino acid residues 51 to 90 of SEQ ID
NO:138; SEQ ID NO:142).
[0200] Also within the invention are: an isolated T129 protein
which is encoded by a nucleic acid molecule having a nucleotide
sequence that is at least about 65%, preferably 75%, 85%, or 95%
identical to SEQ ID NO:139; an isolated T129 protein which is
encoded by a nucleic acid molecule having a nucleotide sequence at
least about 65% preferably 75%, 85%, or 95% identical the TNFR/NGFR
cysteine-rich domain encoding portion of SEQ ID NO:137 (e.g., about
nucleotides 248 to 368 of SEQ ID NO:137); and an isolated T129
protein which is encoded by a nucleic acid molecule having a
nucleotide sequence which hybridizes under stringent hybridization
conditions to a nucleic acid molecule having the nucleotide
sequence of SEQ ID NO:139.
[0201] Also within the invention is a polypeptide which is a
naturally occurring allelic variant of a polypeptide that includes
the amino acid sequence of SEQ ID NO:138 or SEQ ID NO:140, wherein
the polypeptide is encoded by a nucleic acid molecule which
hybridizes to a nucleic acid molecule comprising SEQ ID NO:137 or
SEQ ID NO:139 under stringent conditions.
[0202] Another embodiment of the invention features T129 nucleic
acid molecules which specifically detect T129 nucleic acid
molecules relative to nucleic acid molecules encoding other members
of the TNF receptor superfamily. For example, in one embodiment, a
T129 nucleic acid molecule hybridizes under stringent conditions to
a nucleic acid molecule comprising the nucleotide sequence of SEQ
ID NO:137, SEQ ID NO:139, or a complement thereof. In another
embodiment, the T129 nucleic acid molecule is at least 300 (325,
350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000,
or 1290) nucleotides in length and hybridizes under stringent
conditions to a nucleic acid molecule comprising the nucleotide
sequence shown in SEQ ID NO:137, SEQ ID NO:139, or a complement
thereof. In a preferred embodiment, an isolated T129 nucleic acid
molecule comprises nucleotides 248 to 368 of SEQ ID NO:137,
encoding the TNFR/NGFR cysteine-rich domain of T129, or a
complement thereof. In another embodiment, the invention provides
an isolated nucleic acid molecule which is antisense to the coding
strand of a T129 nucleic acid.
[0203] Another aspect of the invention provides a vector, e.g., a
recombinant expression vector, comprising a T129 nucleic acid
molecule of the invention. In another embodiment the invention
provides a host cell containing such a vector. The invention also
provides a method for producing T129 protein by culturing, in a
suitable medium, a host cell of the invention containing a
recombinant expression vector such that a T129 protein is
produced.
[0204] Another aspect of this invention features isolated or
recombinant T129 proteins and polypeptides. Preferred T129 proteins
and polypeptides possess at least one biological activity possessed
by naturally occurring human T129, e.g., (1) the ability to form
protein:protein interactions with proteins in the T129 signalling
pathway; (2) the ability to bind T129 ligand; (3) the ability to
bind to an intracellular target. Other activities include: (1)
modulation of cellular proliferation and (2) modulation of cellular
differentiation. In one embodiment, an isolated T129 protein has a
TNFR/NGFR cysteine-rich domain and lacks both a transmembrane and a
cytoplasmic domain. In another embodiment the T129 polypeptide
lacks both a transmembrane domain and a cytoplasmic domain and is
soluble under physiological conditions.
[0205] The T129 proteins of the present invention, or biologically
active portions thereof, can be operatively linked to a non-T129
polypeptide (e.g., heterologous amino acid sequences) to form T129
fusion proteins. The invention further features antibodies that
specifically bind T129 proteins, such as monoclonal or polyclonal
antibodies. In addition, the T129 proteins or biologically active
portions thereof can be incorporated into pharmaceutical
compositions, which optionally include pharmaceutically acceptable
carriers.
[0206] In another aspect, the present invention provides a method
for detecting the presence of T129 activity or expression in a
biological sample by contacting the biological sample with an agent
capable of detecting an indicator of T129 activity such that the
presence of T129 activity is detected in the biological sample.
[0207] In another aspect, the invention provides a method for
modulating T129 activity comprising contacting a cell with an agent
that modulates (inhibits or stimulates) T129 activity or expression
such that T129 activity or expression in the cell is modulated. In
one embodiment, the agent is an antibody that specifically binds to
T129 protein. In another embodiment, the agent modulates expression
of T129 by modulating transcription of a T129 gene, splicing of a
T129 mRNA, or translation of a T129 mRNA. In yet another
embodiment, the agent is a nucleic acid molecule having a
nucleotide sequence that is antisense to the coding strand of the
T129 mRNA or the T129 gene.
[0208] In one embodiment, the methods of the present invention are
used to treat a subject having a disorder characterized by aberrant
T129 protein or nucleic acid expression or activity by
administering an agent which is a T129 modulator to the subject. In
one embodiment, the T129 modulator is a T129 protein. In another
embodiment the T129 modulator is a T129 nucleic acid molecule. In
other embodiments, the T129 modulator is a peptide, peptidomimetic,
or other small molecule. In a preferred embodiment, the disorder
characterized by aberrant T129 protein or nucleic acid expression
is a proliferative or differentiative disorder, particularly of the
immune system. The present invention also provides a diagnostic
assay for identifying the presence or absence of a genetic lesion
or mutation characterized by at least one of: (i) aberrant
modification or mutation of a gene encoding a T129 protein; (ii)
mis-regulation of a gene encoding a T129 protein; and (iii)
aberrant post-translational modification of a T129 protein, wherein
a wild-type form of the gene encodes a protein with a T129
activity.
[0209] In another aspect, the invention provides a method for
identifying a compound that binds to or modulates the activity of a
T129 protein. In general, such methods entail measuring a
biological activity of a T129 protein in the presence and absence
of a test compound and identifying those compounds which alter the
activity of the T129 protein.
[0210] The invention also features methods for identifying a
compound which modulates the expression of T129 by measuring the
expression of T129 in the presence and absence of a compound.
A259 (Integrin Alpha Subunit)
[0211] This invention provides novel human and murine nucleic acid
molecules which encode proteins referred to herein as A259
proteins, which are novel integrin .alpha. subunits. These
proteins, fragments, derivatives, and variants thereof are
collectively referred to herein as "polypeptides of the invention"
or "proteins of the invention". Nucleic acid molecules encoding the
polypeptides or proteins of the invention are collectively referred
to as "nucleic acids of the invention".
[0212] The A259 proteins are homologous to the .alpha. subunits of
the integrin family, and in particular, to the .alpha.10 and
.alpha.1 subunits of the integrin family.
[0213] The nucleic acids and polypeptides of the present invention
are useful as modulating agents in regulating a variety of cellular
processes. Accordingly, in one aspect, this invention provides
isolated nucleic acid molecules encoding a polypeptide of the
invention or a biologically active portion thereof. The present
invention also provides nucleic acid molecules which are suitable
for use as primers or hybridization probes for the detection of
nucleic acids encoding a polypeptide of the invention.
[0214] The invention features nucleic acid molecules which are at
least 47% (or 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or
98%) identical to the nucleotide sequence of SEQ ID NO:145, SEQ ID
NO:163, the nucleotide sequence of the cDNA insert of a clone
deposited with ATCC as Accession Number 207190 or 207191, or a
complement thereof.
[0215] The invention features nucleic acid molecules which are at
least 56% (or 57%, 58%, 59%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,
95%, or 98%) identical to the nucleotide sequence of SEQ ID NO:146,
SEQ ID NO:164, the nucleotide sequence of the cDNA insert of a
clone deposited with ATCC as Accession Number 207190 or 207191, or
a complement thereof.
[0216] The invention features nucleic acid molecules which include
a fragment of at least 390 (400, 500, 600, 800, 1000, 1250, 1500,
1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250,
4500, 4750, 5000, 5025, or 5042) nucleotides of the nucleotide
sequence of SEQ ID NO:145, SEQ ID NO:163, the nucleotide sequence
of the cDNA of ATCC Accession Number 207190 or 207191, or a
complement thereof.
[0217] The invention also features nucleic acid molecules which
include a nucleotide sequence encoding a protein having an amino
acid sequence that is at least 44% (or 45%, 50%, 55%, 60%, 65%,
75%, 85%, 95%, or 98%) identical to the amino acid sequence of SEQ
ID NO:147, SEQ ID NO:165, the amino acid sequence encoded by the
cDNA of ATCC Accession Number 207190 or 207191, or a complement
thereof.
[0218] In preferred embodiments, the nucleic acid molecules have
the nucleotide sequence of SEQ ID NO:145, 146, 163, 164, or the
nucleotide sequence of the cDNA of ATCC Accession Number 207190 or
207191.
[0219] Also within the invention are nucleic acid molecules which
encode a fragment of a polypeptide having the amino acid sequence
of SEQ ID NO:147, SEQ ID NO:165, or a fragment including at least
15 (25, 30, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500,
550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100,
1150, 1170, 1180, or 1188) contiguous amino acids of SEQ ID NO:147,
SEQ ID NO:165, or the amino acid sequence encoded by the cDNA of
ATCC Accession Number 207190 or 207191.
[0220] The invention includes nucleic acid molecules which encode a
naturally occurring allelic variant of a polypeptide comprising the
amino acid sequence of SEQ ID NO:147, SEQ ID NO:165, or the amino
acid sequence encoded by the cDNA of ATCC Accession Number 207190
or 207191, wherein the nucleic acid molecule hybridizes to a
nucleic acid molecule consisting of a nucleic acid sequence
encoding SEQ ID NO:147, SEQ ID NO:165, the amino acid sequence
encoded by the cDNA of ATCC Accession Number 207190 or 207191, or a
complement thereof under stringent conditions.
[0221] Also within the invention are isolated polypeptides or
proteins having an amino acid sequence that is at least about 44%,
preferably 45%, 50%, 55%, 60%, 65%, 75%, 85%, 95%, or 98% identical
to the amino acid sequence of SEQ ID NO:147, SEQ ID NO:165, or the
amino acid sequence encoded by the cDNA of ATCC Accession Number
207190 or 207191.
[0222] Also within the invention are isolated polypeptides or
proteins which are encoded by a nucleic acid molecule having a
nucleotide sequence that is at least about 56%, preferably 57%,
58%, 59%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98% identical
to the nucleic acid sequence encoding SEQ ID NO:147, SEQ ID NO:165,
and isolated polypeptides or proteins which are encoded by a
nucleic acid molecule having a nucleotide sequence which hybridizes
under stringent hybridization conditions to a nucleic acid molecule
having the nucleotide sequence of SEQ ID NO:145, 146, 163, or 164,
a complement thereof, or the non-coding strand of the cDNA of ATCC
Accession Number 207190 or 207191.
[0223] Also within the invention are polypeptides which are
naturally occurring allelic variants of a polypeptide that includes
the amino acid sequence of SEQ ID NO:147, or the amino acid
sequence encoded by the cDNA of ATCC Accession Number 207190 or
207191, wherein the polypeptide is encoded by a nucleic acid
molecule which hybridizes to a nucleic acid molecule having the
sequence of SEQ ID NO:145, 146, 163, 164, or a complement thereof
under stringent conditions.
[0224] The invention also features nucleic acid molecules that
hybridize under stringent conditions to a nucleic acid molecule
having the nucleotide sequence of SEQ ID NO:145, 146, 163, or 164,
the cDNA of ATCC Accession Number 207190 or 207191, or a complement
thereof. In other embodiments, the nucleic acid molecules are at
least 390 (400, 500, 600, 800, 1000, 1250, 1500, 1750, 2000, 2250,
2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, 4750, 5000,
5025, or 5042) nucleotides in length and hybridize under stringent
conditions to a nucleic acid molecule comprising the nucleotide
sequence of SEQ ID NO:145, 146, 163, or 164, the cDNA of ATCC
Accession Number 207190 or 207191, or a complement thereof.
[0225] In one embodiment, the invention provides an isolated
nucleic acid molecule which is antisense to the coding strand of a
nucleic acid of the invention.
[0226] Another aspect of the invention provides vectors, e.g.,
recombinant expression vectors, comprising a nucleic acid molecule
of the invention. In another embodiment, the invention provides
host cells containing such a vector or a nucleic acid molecule of
the invention. The invention also provides methods for producing a
polypeptide of the invention by culturing, in a suitable medium, a
host cell of the invention containing a recombinant expression
vector such that a polypeptide is produced.
[0227] Another aspect of this invention features isolated or
recombinant proteins and polypeptides of the invention. Preferred
proteins and polypeptides possess at least one biological activity
possessed by the corresponding naturally-occurring human
polypeptide. An activity, a biological activity, or a functional
activity of a polypeptide or nucleic acid of the invention refers
to an activity exerted by a protein, polypeptide or nucleic acid
molecule of the invention on a responsive cell as determined in
vivo, or in vitro, according to standard techniques. Such
activities can be a direct activity, such as an association with or
an enzymatic activity on a second protein, or an indirect activity,
such as a cellular signaling activity mediated by interaction of
the protein with a second protein.
[0228] A259 biological activities include, e.g., (1) the ability to
form protein-protein interactions with proteins in the signaling
pathway of the naturally-occurring polypeptide; (2) the ability to
bind a ligand of the naturally-occurring polypeptide; (3) the
ability to interact with an A259 ligand; and (4) the ability to
modulate function, survival, morphology, migration, proliferation
and/or differentiation of cells, e.g., of tissues in which it is
expressed (e.g., osteoblasts, bone marrow, neural tissue).
[0229] A259 biological activities also include, e.g., (1) the
ability to modulate, e.g., stabilize, protein-protein interactions
(e.g., homophilic and/or heterophilic), and protein-ligand
interactions, e.g., in receptor-ligand recognition; (2) ability to
modulate signalling pathways; (3) ability to modulate cell-cell
interactions, e.g., by acting as a cell-cell adhesion molecule, or
by acting as a receptor for cell-cell adhesion molecules; (4) the
ability to modulate interactions between cells and proteins (e.g.,
extracellular matrix proteins, e.g., collagens, fibrinogens,
laminins, and fibronectin), e.g., by acting as a cell surface
receptor; (5) the ability to interact, e.g., noncovalently
interact, with an integrin .beta. subunit; and (6) the ability to
exhibit an activity of an integrin .alpha.10 or an integrin
.alpha.1 subunit.
[0230] Still other A259 biological activities include, e.g., (1)
the ability to modulate, e.g., initiate, an immune response, e.g.,
an inflammatory response; (2) the ability to modulate, e.g.,
initiate wound healing, e.g., by modulating platelet aggregation or
by modulating fibroblast attachment to wound sites during wound
contraction; and (3) the ability to stimulate fibrogenesis.
[0231] In one embodiment, a polypeptide of the invention has an
amino acid sequence sufficiently identical to an identified domain
of a polypeptide of the invention. As used herein, the term
"sufficiently identical" refers to a first amino acid or nucleotide
sequence which contains a sufficient or minimum number of identical
or equivalent (e.g., with a similar side chain) amino acid residues
or nucleotides to a second amino acid or nucleotide sequence such
that the first and second amino acid or nucleotide sequences have a
common structural domain and/or common functional activity. For
example, amino acid or nucleotide sequences which contain a common
structural domain having about 60% identity, preferably 65%
identity, more preferably 75%, 85%, 95%, 98% or more identity are
defined herein as sufficiently identical.
[0232] In one embodiment, an A259 protein includes at least one or
more of the following domains: a signal sequence, an extracellular
domain, a repeat domain, an I domain, an intergrin alpha repeat
domain, a transmembrane domain, and a cytoplasmic domain. In yet
another embodiment, an A259 protein includes an extracellular
domain and one or more repeat domains, and or one or more integrin
alpha repeat domains, and is a soluble protein. In still another
embodiment, an A259 protein includes an extracellular domain, one
or more repeat domains, a transmembrane domain, a cytoplasmic
domain, and is a receptor protein.
[0233] The polypeptides of the present invention, or biologically
active portions thereof, can be operably linked to a heterologous
amino acid sequence to form fusion proteins. The invention further
features antibodies that specifically bind a polypeptide of the
invention such as monoclonal or polyclonal antibodies. In addition,
the polypeptides of the invention or biologically active portions
thereof can be incorporated into pharmaceutical compositions, which
optionally include pharmaceutically acceptable carriers.
[0234] In another aspect, the present invention provides methods
for detecting the presence of the activity or expression of a
polypeptide of the invention in a biological sample by contacting
the biological sample with an agent capable of detecting an
indicator of activity such that the presence of activity is
detected in the biological sample.
[0235] In another aspect, the invention provides methods for
modulating activity of a polypeptide of the invention comprising
contacting a cell with an agent that modulates (inhibits or
stimulates) the activity or expression of a polypeptide of the
invention such that activity or expression in the cell is
modulated. In one embodiment, the agent is an antibody that
specifically binds to a polypeptide of the invention.
[0236] In another embodiment, the agent modulates expression of a
polypeptide of the invention by modulating transcription, splicing,
or translation of an mRNA encoding a polypeptide of the invention.
In yet another embodiment, the agent is a nucleic acid molecule
having a nucleotide sequence that is antisense to the coding strand
of an mRNA encoding a polypeptide of the invention.
[0237] The present invention also provides methods to treat a
subject having a disorder characterized by aberrant activity of a
polypeptide of the invention or aberrant expression of a nucleic
acid of the invention by administering an agent which is a
modulator of the activity of a polypeptide of the invention or a
modulator of the expression of a nucleic acid of the invention to
the subject. In one embodiment, the modulator is a protein of the
invention. In another embodiment, the modulator is a nucleic acid
of the invention. In other embodiments, the modulator is a peptide,
peptidomimetic, or other small molecule.
[0238] The present invention also provides diagnostic assays for
identifying the presence or absence of a genetic lesion or mutation
characterized by at least one of: (i) aberrant modification or
mutation of a gene encoding a polypeptide of the invention, (ii)
mis-regulation of a gene encoding a polypeptide of the invention,
and (iii) aberrant post-translational modification of the invention
wherein a wild-type form of the gene encodes a protein having the
activity of the polypeptide of the invention.
[0239] In another aspect, the invention provides a method for
identifying a compound that binds to or modulates the activity of a
polypeptide of the invention. In general, such methods entail
measuring a biological activity of the polypeptide in the presence
and absence of a test compound and identifying those compounds
which alter the activity of the polypeptide.
[0240] The invention also features methods for identifying a
compound which modulates the expression of a polypeptide or nucleic
acid of the invention by measuring the expression of the
polypeptide or nucleic acid in the presence and absence of the
compound
BRIEF DESCRIPTION OF THE DRAWINGS
[0241] FIG. 1 is a series of sequence comparisons between portions
of the amino acid sequence of T85 and a fibronectin type III domain
(PF00041) and an Ig superfamily domain (PF00047) derived from a
hidden Markov model.
[0242] FIGS. 2A-D depict a comparison of the amino acid sequence of
T85 and human Robo protein.
[0243] FIG. 3 depicts an alignment of an amino acid sequence of
Tango-77 (T77; SEQ ID NO:2) with IL4RA (SEQ ID NO:14), and
IL-1.beta. (SEQ ID NO:15).
[0244] FIG. 4 depicts an alignment of the amino acid sequence of
murine SPOIL-I (also referred to as murine or mTANGO 080-1)
(corresponding amino acids 1 to 98 of SEQ ID NO:2), murine IL-1ra
(Swissprot.TM. Accession Number P25085) (SEQ ID NO:10), murine
IL-1.alpha. (Swissprot.TM. Accession Number P01582) (SEQ ID NO:11)
and murine IL-1.beta. (Swissprot.TM. Accession Number P10749) (SEQ
ID NO:12).
[0245] FIGS. 5A-D depict pairwise alignments of SPOIL amino acid
sequences of the present invention. FIG. 5A depicts an alignment of
human SPOIL-I with human SPOIL-II. FIG. 5B depicts an alignment of
murine SPOIL-I with murine SPOIL-II. FIG. 5C depicts an alignment
human SPOIL-I with murine SPOIL-I. FIG. 5D depicts an alignment of
human SPOIL-II with murine SPOIL-II. The alignments were generated
using the ALIGN algorithm (Myers and Miller (1989) CABIOS). Gap
penalties were set at -12/-4 and a PAM120 residue weight matrix was
used.
[0246] FIG. 6 depicts a multiple sequence alignment of the amino
acid sequence of murine SPOIL-I (corresponding to SEQ ID NO:2), the
amino acid sequence of murine SPOIL-II (corresponding to SEQ ID
NO:25), the amino acid sequence of human SPOIL-I (corresponding to
SEQ ID NO:14), and the amino acid sequence of human SPOIL-II
(corresponding to SEQ ID NO:18). Asterisks indicate amino acid
residues that are conserved between SPOIL family members.
[0247] FIG. 7 depicts a multiple sequence alignment of the amino
acid sequence of murine IL-1.alpha. (Swissprot.TM. Accession Number
P01582) (SEQ ID NO:11), murine IL-1.beta. (Swissprot.TM. Accession
Number P10749) (SEQ ID NO:12), murine IL-1ra (Swissprot.TM.
Accession Number P25085) (SEQ ID NO:10), the amino acid sequence of
murine SPOIL-I (also referred to as murine or mTANGO 080-I)
(corresponding amino acids 1 to 98 of SEQ ID NO:2), the amino acid
sequence of murine SPOIL-II (also referred to as murine or mTANGO
080-II (corresponding amino acids 1 to 160 of SEQ ID NO:25), the
amino acid sequence of human SPOIL-I (corresponding nucleotides 1
to 169 of SEQ ID NO:14), and the amino acid sequence of human
SPOIL-II (corresponding to nucleotides 1 to 208 of SEQ ID NO:16).
Asterisks indicate amino acid residues that are conserved between
SPOIL proteins and IL-1ra.
[0248] FIG. 8 is a diagram depicting the relationship between the
NEOKINE proteins of the instant invention. The figure depicts the
functional domains of the NEOKINE family members, human NEOKINE-1
(SEQ ID NO:2), mouse NEOKINE-1 (SEQ ID NO:5), rat NEOKINE-1 (SEQ ID
NO:8), and macaque NEOKINE-1 (SEQ ID NO:21). The NEOKINE CXC
signature motifs are indicated in italics. The conserved cysteine
residues are indicated with asterisks.
[0249] FIG. 9 is a hydropathy plot of T129. The location of the
predicted transmembrane (TM), cytoplasmic (IN), and extracellular
(OUT) domains are indicated as are the position of cysteines (cys;
vertical bars immediately below the plot). Relative hydrophilicity
is shown above the dotted line, and relative hydrophobicity is
shown below the dotted line.
[0250] FIG. 10 depicts a hydropathy plot of human A259. Relatively
hydrophobic regions of the protein are above the dashed horizontal
line, and relatively hydrophilic regions of the protein are below
the dashed horizontal line. The cysteine residues (cys) and
potential N-glycosylation sites (Ngly) are indicated by short
vertical lines just below the hydropathy trace. The dashed vertical
line separates the signal sequence (amino acids 1 to 22 of SEQ ID
NO:3; SEQ ID NO:5) on the left from the mature protein (amino acids
23 to 1188 of SEQ ID NO:3; SEQ ID NO:4) on the right. Thicker gray
horizontal bars below the dashed horizontal line indicate
extracellular ("out"), transmembrane ("TM"), and intracellular
("in") regions of the molecule.
[0251] FIG. 11 depicts a hydropathy plot of murine A259. Relatively
hydrophobic regions of the protein are above the dashed horizontal
line, and relatively hydrophilic regions of the protein are below
the dashed horizontal line. The cysteine residues (cys) and
potential N-glycosylation sites (Ngly) are indicated by short
vertical lines just below the hydropathy trace. The dashed vertical
line separates the signal sequence (amino acids 1 to 22 of SEQ ID
NO:21; SEQ ID NO:23) on the left from the mature protein (amino
acids 23 to 1188 of SEQ ID NO:21; SEQ ID NO:22) on the right.
Thicker gray horizontal bars below the dashed horizontal line
indicate extracellular ("out"), transmembrane ("TM"), and
intracellular ("in") regions of the molecule.
[0252] FIG. 12A depicts an alignment of amino acids 37-90 of human
A259 (SEQ ID NO:35) with a consensus integrin alpha repeat domain
derived from a hidden Markov model (SEQ ID NO:40).
[0253] FIG. 12B depicts an alignment of amino acids 421-472 of
human A259 (SEQ ID NO:36) with a consensus integrin alpha repeat
domain derived from a hidden Markov model (SEQ ID NO:40).
[0254] FIG. 12C depicts an alignment of amino acids 476-532 of
human A259 (SEQ ID NO:37) with a consensus integrin alpha repeat
domain derived from a hidden Markov model (SEQ ID NO:40).
[0255] FIG. 12D depicts an alignment of amino acids 538-593 of
human A259 (SEQ ID NO:38) with a consensus integrin alpha repeat
domain derived from a hidden Markov model (SEQ ID NO:40).
[0256] FIG. 12E depicts an alignment of amino acids 600-654 of
human A259 (SEQ ID NO:39) with a consensus integrin alpha repeat
domain derived from a hidden Markov model (SEQ ID NO:40).
[0257] FIG. 13A is a graph depicting the results of an analysis of
A259 expression in three normal liver clinical samples (A, B, and
C) and eight liver fibrosis clinical samples (D, E, F, G, H, I, J,
and K).
[0258] FIG. 13B is a graph depicting the results an analysis of
human A259 expression in a variety of cells: heart (A), lung (B),
liver (C), passaged stellate cells (D), quiescent stellate cells
(E), srellate cells (F) stellate/F BS cells (G), NHDF fibroblasts
(H); TGF-treated NHDF fibroblasts (I); NHLF fibroblasts (J); and
TGF-treated NHLF fibroblasts (K).
DETAILED DESCRIPTION OF THE INVENTION
Delta 3
[0259] Notch, first identified in Drosophila, is the founding
member of a family of transmembrane receptor proteins that mediate
cell responses to intrinsic and/or extrinsic developmental cues.
The cellular response to Notch signaling can be differentiation,
proliferation and/or apoptosis depending on the specific
developmental program. Defects in the Notch signaling pathway may
be involved in neurological, vascular and hematologic diseases.
[0260] Analysis of gene expression patterns for Notch and its
ligands has indicated that Notch signaling may have a role in
hematopoiesis (Milner and Bigas (1999) Blood 93:2431). Notch-1 was
also shown to be involved in determination of T-cell education and
fate in the thymus (Robey (1999) An Rev Immunol 17:283).
Furthermore, a subset of human T-cell leukemia patients harbor a
translocation involving the Notch 1 gene which results in a
constitutively active Notch protein (Ellisen et al. (1991) Cell
66:649). Compelling evidence that the Notch signaling pathway is
involved in B-cell development is seen in B-cell malignancies
induced by Epstein-Barr virus (EBV). EBNA2, the transforming
protein of EBV, transactivates cellular genes by direct interaction
with a primary component of the Notch pathway (Henkel et al. (1994)
Science 265:92).
[0261] It has recently been shown that the human Notch3 gene,
located on chromosome 19, is mutated in CADASIL patients (Joutel et
al., (1996) Nature 383: 707-710). CADASIL causes a type of stroke
and dementia whose key features include recurrent subcortical
ischemic events, progressive vascular dementia, craniofacial
paralysis, migraine and mood disorders with severe depression
(Chabriat et al., (1995) Lancet 346: 934-939). Pathological
examination reveals multiple small, deep cerebral infarcts, a
leukoencephalopathy and a non-atherosclerotic, non-amyloid
angiopathy involving mainly the small cerebral arteries (Baudrimont
et al., (1993) Stroke 24: 122-125). Severe alterations of vascular
smooth muscle cells are evident on ultrastructural analysis
(Ruchoux et al., (1995) Acta. Neuropathol. 89:500-512). Therefore,
disruption of the Notch signaling pathway appears to be responsible
for CADASIL stroke and dementia. Defects in the Notch signaling
pathway may also be involved in other neurological diseases, e.g.,
Alzheimer's disease.
[0262] The Notch signaling pathway comprises Notch proteins, which
are membrane proteins, and proteins interacting with Notch
proteins, termed Delta proteins. The product of the Delta gene,
acting as a ligand, and that of the Notch gene, acting as a
receptor, are key components in a lateral-inhibition signaling
pathway that regulates the detailed patterning of many different
tissues in Drosophila (Vassin et al., (1987) EMBO J. 6:3431-3440;
Kopczynski et al., (1988) Genes Dev. 2:1723-1735; Fehon et al.,
(1990) Cell 61:523-534; Artavanis-Tsakonas et al., (1991) Trends,
Genet. Sci. 7:403-407; Heitzler et al., (1991) Cell 64: 1083-1092;
Greenwald et al., (1992) Cell 68: 271-281; Fortini et al., (1993)
Cell 75: 124501247; and Muskavitch (1994) Devl. Biol. 166:415-430).
During neurogenesis in particular, neural precursors, by expressing
Delta, inhibit neighboring Notch-expressing cells from becoming
committed to a neural fate. Mutations leading to a failure of
lateral inhibition cause an overproduction of neurons, giving rise
to a phenotype termed the "neurogenic phenotype" in Drosophila. For
example, loss of Notch 1 leads to somite defects and embryonic
death in mice, whereas constitutively active mutant forms of Notch
1 appear to inhibit cell differentiation in Xenopus and in cultured
mammalian cells (Swiatek et al. (1994) Genes Dev. 8:707; Conlon et
al. (1995) J. Development 121:1533; Lopan et al. (1994) Development
120:2385; and Nye et al. (1994) Development 120:2421). Furthermore,
loss of Dll1 function in mice leads to excessive neuronal
differentiation, resulting in severe patterning defects in the
paraxial mesoderm and a hyperplastic central nervous system (CNS)
(Hrabe de Angelis et al. (1997) Nature 386:717). Thus, the Notch
signaling pathway, in particular Delta proteins, mediate lateral
inhibition during neurogenesis so that only a limited proportion of
cells having the potential to become neurons will in fact
differentiate into neurons.
[0263] The Notch family of proteins are transmembrane receptors
containing several conserved peptide motifs. The extracellular
domains contain many tandemly repeated copies of an epidermal
growth factor (EGF) like motif. The intracellular domains contain
six copies of another conserved motif, termed the Cdc10/ankyrin
repeat.
[0264] A protein interacting with Notch was first discovered in
Drosophila and has been called Delta protein. This protein encodes
a transmembrane protein ligand, which contains tandem arrays of
epidermal growth factor-like repeats in the extracellular domain.
The Delta and Notch proteins can directly bind to each other and
specific EGF-like domains are sufficient and necessary for this
binding (Fehon et al., (1990) Cell 61:523-534; Rebay et al., (1991)
Cell 67:687-699; and Lieber et al., (1992) Neuron 9: 847-859).
[0265] It is also possible that soluble forms of the protein also
exist. Such soluble isoforms can arise through variable splicing of
the Delta3 gene or alternatively as a result of proteolysis of a
membranous isoform. In fact, a splice variant of a chicken Delta
protein have been described in PCT Publication No. WO 97/01571
(Jan. 16, 1997). Furthermore, the human Delta-like polypeptide Dlk
is a soluble protein (Jansen et al. (1994) Eur. J. Biochem.
225:83-92).
[0266] In addition to the Drosophila Delta protein, a chick Delta
ortholog, C-Delta protein (Henrique et al., (1995) Nature 375:
787-790 and GenBank Accession No. U26590) two Xenopus orthologs,
X-Delta-1 and X-Delta-2 (Chitnis et al., (1995) Nature 375:761-766
and GenBank Accession Nos. L42229 and U70843), a mouse ortholog
(GenBank Accession No. X80903), a delta-like human gene 1(Dlk)
(Bettenhausen et al., (1995) Development 121:2407-2418) a rat
ortholog (GenBank Accession No. U78889), and a Zebrafish ortholog
(GenBank Accession No. Y11760) have been identified.
[0267] The present invention is based at least in part on the
discovery of a novel gene encoding a human Delta protein referred
to herein as "hDelta3" polypeptide, and the mouse equivalent
referred to herein as "mDelta3". An exemplary hDelta3 has been
deposited with the ATCC.RTM. on Mar. 5, 1997 and has been assigned
ATCC.RTM. GenBank Accession Number 98348. The human Delta3 gene
maps to human chromosome 15.
[0268] The DNA sequence of human Delta3 including 5' and 3'
non-coding sequences is shown in SEQ ID NO:1, the coding sequence
is shown in SEQ ID NO:3, and the deduced amino acid sequence of the
human Delta3 protein is shown in SEQ ID NO: 2. The DNA sequence of
mouse Delta3 including 5' and 3' non-coding sequences is shown in
SEQ ID NO:24 and the coding sequence is shown in SEQ ID NO:26. The
deduced amino acid sequence of the mouse Delta3 protein is shown in
SEQ ID NO:25.
[0269] Human Delta3 is expressed in endothelial cells and in fact
was cloned from a human microvascular endothelial cell library.
Northern blot analysis of RNA prepared from a number of different
human tissues, indicate that a 3.5 kb Delta3 mRNA transcript is
present in fetal brain, lung, liver and kidney, and adult heart,
placenta, lung, skeletal muscle, kidney, pancreas, spleen, thymus,
prostate, testis, ovary, small intestine and colon. Low levels of
Delta3 mRNA were also detected in adult brain and adult liver.
However, no Delta3 mRNA was detected in peripheral blood
leukocytes. These results indicate that Delta3 is expressed in a
tissue-specific manner. Further, expression in human microvascular
endothelial cells was found to be up-regulated (about 2-3 fold) in
cells that had been stimulated with certain growth factors (e.g.,
basic fibroblast growth factor (bFGF) or vascular endothelial
growth factor (VEGF)). In addition, strong expression of human
Delta3 was observed in the colorectal carcinoma cell line, SW480.
Furthermore, expression of hDelta3 has been shown to be induced in
response to proliferation and differentiation signals (See
Examples). Thus, the Delta3 gene, in particular, the hDelta3 gene,
is a gene whose expression in a cell changes with the state of
proliferative and/or differentiative state of cells.
[0270] In situ hybridization was performed on a wide range of
murine adult and embryonic tissues using a probe complementary to
mRNA of mDelta3. Expression was most abundant and widespread during
embryogenesis. Strongest expression was observed in the eye of all
the embryonic ages tested. Signal in a pattern suggestive of
neuronal expression was not observed in any other tissues making
the expression in the eye unique. Ubiquitous expression was also
detected in lung, thymus and brown fat during embryogenesis. A
multifocal, scattered signal was also observed throughout the
embryo. This signal pattern was more focused in the cortical region
of the kidney and outlining the intestinal tract. Adult expression
was highest in the ovary and the cortical regions of the kidney and
adrenal gland. This is consistent with Delta3's role as a regulator
of cell growth and/or differentiation.
[0271] As predicted from the nucleotide sequence of the nucleic
acid encoding hDelta3, the novel, full-length hDelta3 polypeptide
comprises 685 amino acids and is similar and structure to Delta
proteins obtained from other organisms (discussed below). An amino
acid sequence analysis of Delta3 proteins predicts that the protein
comprises at least the structural domains described herein. First,
human and mouse Delta3 have a signal peptide, corresponding to
amino acid 1 to amino acid 16, amino acid 1 to amino acid 17, amino
acid 1 to amino acid 18, amino acid 1 to amino acid 19 or amino
acid 1 to amino acid 20 of SEQ ID NOs: 2 or 25. The signal sequence
is normally cleaved during processing of the mature protein. In
such embodiments of the invention, the domains and the mature
protein resulting from cleavage of such signal peptides are also
included herein. For example, the cleavage of a signal sequence
consisting of amino acids 1 to 17 results in an extracellular
domain consisting of amino acids 18 to 529 of SEQ ID No. 2 and the
mature Delta3 polypeptide corresponding to amino acids 18 to 685 of
SEQ ID NO: 2.
[0272] Second, human and mouse Delta3 have protein interaction
domains such as a Delta Serrated lag-2 (DSL) motif corresponding to
amino acid 173 to amino acid 217 of SEQ ID NO: 2 and amino acid 174
to amino acid 218 of SEQ ID NO: 25, as well as eight epidermal
growth factor (EGF)-like repeats.
[0273] In addition, Delta3 proteins have a transmembrane domain,
i.e., in human Delta3 the transmembrane domain corresponds to about
amino acid 530 to about amino acid 553 of SEQ ID NO: 2, and in
mouse Delta3, amino acid 531 to amino acid 554 of SEQ ID NO: 25.
Delta3 proteins have also have a cytoplasmic domain corresponding
to about amino acid 554 to about amino acid 685 of SEQ ID NO: 2 or
amino acid 555 to amino acid 686 of SEQ ID NO: 25. Accordingly,
sequence analysis for conserved domains of Delta3 amino acid
sequence shows that the protein is likely a transmembrane protein
having an extracellular domain corresponding to about amino acid 1
to about amino acid 529 of SEQ ID NO:2, about amino acid 18 to
about amino acid 529 of SEQ ID NO: 2, amino acid 1 to about amino
acid 530 of SEQ ID NO: 25, or amino acid 18 to 530 of SEQ ID NO:
25, said extracellular domain comprising a DSL motif and eight
EGF-like domains. The Delta3 protein further comprises a
transmembrane domain and a cytoplasmic domain.
[0274] Human Delta3 protein is similar in structure and in sequence
to the Delta proteins identified in Drosophila, Xenopus, zebrafish,
chicken, rat, mouse, rat, and human. Applicants have aligned known
Delta proteins with the Delta3 protein of the present invention.
This alignment contains the following Delta proteins: a mouse
Delta1 protein (m-delta1), rat Delta-1 protein (r-delta1), a human
Delta-1 protein (h-delta1), a Xenopus Delta1 protein (x-delta1), a
chicken Delta1 protein (c-delta1), a zebrafish Delta1 protein
(z-delta1), a second Xenopus Delta protein (x-delta2), as well as
the human Delta3 protein (h-delta3), and a Drosophila Delta1
protein (d-delta). The amino acid sequence of h-delta1 is the amino
acid sequence published in PCT Publication WO 97/01571 (Jan. 16,
1997) which is incomplete and contains numerous errors, as stated
in the application. Since the amino acid sequence alignment has
been done using the pileup computer program (GCG Package), the
order of the amino acid sequences reflects the relative identity
between the different Delta proteins. Accordingly, the Drosophila
protein, which corresponds to the bottom sequence in the alignment
is most distant from the other Delta proteins.
[0275] The alignment shows that hDelta3, which is listed second to
the last, is the second most distant Delta protein from the
previously identified mouse, rat, human, Xenopus, zebrafish, and
chicken delta protein. Accordingly, hDelta3 protein is
significantly different from the previously described human Delta
protein, as well as the Delta proteins from the other species.
Interestingly, the hDelta3 protein has an amino acid sequence which
is equally distant from both Xenopus proteins, i.e., Delta1 and
Delta2, suggesting that hDelta3 does not correspond to either of
the Xenopus Delta proteins. Therefore, the newly isolated
polypeptide has been termed hDelta3 and the previously identified
mouse, rat, human, zebrafish, and Xenopus Delta proteins are termed
Delta1 proteins herein and the two Xenopus proteins are termed
Delta1 and Delta2 proteins. The difference between hDelta3 protein
and previously isolated Delta proteins can also be visualized by
comparing the percentage similarity or identity between hDelta3 and
the previously identified Delta1 and Delta2 proteins on one hand
(Table I), and the percent similarity or identity of a Delta1
protein with the other Delta1 and Delta2 proteins (Table II).
[0276] A hallmark of Notch ligands such as Jagged-1, is the ability
to block the differentiation of the C2C12 cell line from myoblasts
into myotubes when co-cultured with NIH3T3 cells under low
mitogenic conditions. When C2C12 cells were co-cultured with NIH3T3
cells, which were engineered to express hDelta3, differentiation of
C2C12 cells from myoblasts to myotubes was blocked in a similar
fashion as has been described for other Notch ligands such as
Jagged-1. Therefore, the hDelta3 gene is likely to encode a
polypeptide which functions as a bona fide Notch ligand. Indeed,
the data presented in Section 5.6, below, indicates that hDelta3 is
a bona fide Notch ligand.
[0277] Table I indicates the percent similarity and identity
between human Delta3, the Delta1 disclosed in PCT Publication No.
WO 97/01571 (Jan. 16, 1997) and non-human Delta1 proteins. Since
the amino acid sequence of the human Delta1 protein that is
disclosed in PCT Publication No. WO 97/01571 (Jan. 16, 1997) is
incomplete, the percentage similarity and identity was determined
using a portion of the human Delta1 amino acid sequence which seems
most reliable. The portion of the amino acid sequence used
corresponds to amino acids 214-370 of the human Delta1 amino acid
sequence shown in FIG. 11 of the PCT Publication No. WO 97/01571
(Jan. 16, 1997).
TABLE-US-00001 TABLE I Percentage similarity between the amino acid
sequence of human Delta3 (SEQ ID NO: 2) and that of the various
Delta proteins Accession % % GenBank NO: SEQ ID NO: identity
similarity Human Delta1 N.A. (SEQ ID NO: 6) 50 66 Mouse Delta1
X80903 (SEQ ID NO: 4) 53 70 rat Delta1 U78889 (SEQ ID NO: 5) 54 70
chicken Delta1 U26590 (SEQ ID NO: 8) 52 68 Xenopus Delta1 L42229
(SEQ ID NO: 7) 51 68 zebrafish Delta1 Y11760 (SEQ ID NO: 9) 48 67
Xenopus Delta2 U70843 (SEQ ID NO: 10) 47 65 Drosophila AA142228
(SEQ ID NO: 11) 40 58 Delta1 hDelta-like (dlk) U15979 33 55
[0278] Table II indicates the percent similarity and identity
between human Delta1 disclosed in PCT Publication No. WO 97/01571
(1997) and non-human Delta1 proteins. Since the amino acid sequence
of the human Delta1 protein that is disclosed in PCT Publication
No. WO 97/01571 (1997) is incomplete, the percentage similarity and
identity was determined using a portion of the human Delta1 amino
acid sequence which seems most reliable. The portion of the amino
acid sequence used corresponds to amino acids 214-370 of the human
Delta1 amino acid sequence shown in FIG. 11 of the PCT
application.
TABLE-US-00002 TABLE II Percentage similarity between human Delta1
and the various non-human Delta1 or Delta2 proteins % % similarity
GenBank Accession SEQ ID NO: identity NO: Human Delta1 N.A. (SEQ ID
NO: 6) 100 100 mouseDelta1 X80903 (SEQ ID NO: 4) 86 95 rat Delta1
U78889 (SEQ ID NO: 5) 88 94 chicken Delta1 U26590 (SEQ ID NO: 8) 85
89 Xenopus Delta1 L42229 (SEQ ID NO: 7) 78 84 zebrafish Delta1
Y11760 (SEQ ID NO: 9) 69 80 Xenopus Delta2 U70843 (SEQ ID NO: 10)
57 70 Drosophila AA142228 (SEQ ID NO: 11) 45 62 Delta1 hDelta-like
(dlk) U15979 37 55
[0279] Accordingly, Table I indicates that hDelta3 is only
approximately 66% similar to the human Delta1 protein;
approximately 70% similar to the mouse Delta1 protein;
approximately 70% similar to the rat Delta1 protein; approximately
68% similar to the chick Delta1 protein; approximately 68% similar
to the Xenopus Delta1 protein, approximately 70% similar to the
Xenopus Delta2 protein and approximately 58% similar to the
Drosophila Delta1 protein. However, as shown in Table II, the
human-Delta1 protein is very similar to the mouse, rat, chick,
Xenopus, zebrafish, and Drosophila Delta1 and the Xenopus Delta2
proteins. In addition, mouse and rat Delta1 proteins are about 95%
similar. Thus, the amino acid sequence of the orthologs of the
Delta1 protein share greater similarity and identity with each
other than with the human Delta3 protein of the invention,
indicating that at least two families of Delta proteins exist.
[0280] The difference between the newly isolated hDelta3 protein
and the previously identified Delta1 and Delta2 proteins can also
be seen by creating a phylogenic tree using the Growtree Phylogram
computer program (GCG Package). The result of this analysis,
indicates that h-Delta3 is on a different "branch" in the
phylogenic tree from the other Delta proteins, thus confirming that
hDelta3 protein is more distant from the other Delta1 and Delta2
proteins than they are distant from each other. According to the
analysis, and as predicted by the sequence alignment, only the
Drosophila Delta protein is more distantly related to the
previously identified mouse, rat, Xenopus, chicken, zebrafish and
human Delta proteins than hDelta3. Thus, the newly isolated hDelta3
protein is a member of a different subspecies of the family of
Delta proteins.
[0281] Notwithstanding that each animal species is likely to have
at least two or three members (e.g., Delta1, Delta 2, and Delta3),
the DSL region, the eight EGF repeats and the TM appear to be
highly conserved throughout species. However, these domains of the
hDelta3 protein differ more from the corresponding domains in the
other Delta proteins than the corresponding domains in the other
Delta differ from one another.
[0282] A comparison of human and mouse Delta3 shows that they are
86.6% identical and 88.2% similar. The polypeptides were aligned
with the BLAST program using Blosum62, gap weight 12 and length
weight 4. One gap was introduced at amino acid position twenty one
due to an extra codon present in mouse Delta3. The skilled artisan
will appreciate that the domains identified in hDelta3 protein of
the present invention are also present in corresponding positions
in mouse Delta3.
[0283] Furthermore, as set forth in the examples presented below,
Delta3 has been localized to human chromosome 15 in a region close
to the framework markers D15S1244 and D15S144. Interestingly, the
region on chromosome 15 that is flanked by the markers D15S1040 and
D15S118 has been shown to be genetically linked with the disease
called Agenesis of the Corpus Callosum with Peripheral Neuropathy
(ACCPN) (Casaubon et al. (1996) Am J. Hum. Genet. 58:28). No
specific gene has so far been linked to this disease. Accordingly,
since Delta3 is localized to a chromosomal region genetically
linked to ACCPN and Delta3 is a member of the Notch signaling
pathway, defects in which have been associated with a number of
neurological diseases or conditions, Delta3 is likely to be the
gene involved in ACCPN.
[0284] ACCPN, which is also termed Andermann syndrome (MIM 218000),
is an autosomal recessive disorder that occurs with a high
prevalence in the French Canadian population in the Charlevoix and
Saguenay-Lac St Jean region in Quebec. The disease is characterized
by a progressive peripheral neuropathy caused by axonal
degeneration and a central nervous system (CNS) malformation
characterized by the absence of hypoplasia of the corpus callosum.
The disorder appears early in life, is progressive and results in
death in the third decade of life of the subject.
[0285] Accordingly, certain aspects of the present invention relate
to Delta3 proteins, nucleic acid molecules encoding Delta3
proteins, antibodies immunoreactive with Delta3 proteins, and
preparations of such compositions. In addition, drug discovery
assays are provided for identifying agents that modulate the
biological function of Delta proteins, e.g., Delta3 proteins (i.e.
agonists or antagonists), such as by binding to Delta3 or by
altering the interaction of Delta3 with either downstream or
upstream elements in the Delta/Notch signal transduction pathway by
altering the interaction between Delta3 and a Delta3 binding
protein. Such agents can be useful therapeutically, for example, to
alter cell growth and/or differentiation or induction of apoptosis.
Moreover, the present invention provides diagnostic and therapeutic
assays and reagents for detecting and treating disorders involving
an aberrant Delta3 activity, for example, aberrant expression (or
loss thereof) of Delta3 gene or which are associated with a
specific Delta allele, e.g., a Delta3 allele.
[0286] The term "activity," for the purposes herein refers to an
activity exerted by a polypeptide of the invention on a responsive
cell as determined, in vivo or in vitro, according to standard
techniques. An activity can refer to an effector or antigenic
function that is directly or indirectly performed by a Delta3
polypeptide (whether in its native or denatured conformation), or
by any subsequence thereof. Effector functions include, for
example, receptor binding or activation, induction of
differentiation, mitogenic or growth promoting activity, induction
of apoptosis, signal transduction, immune modulation, DNA
regulatory functions and the like, whether presently known or
inherent. Antigenic functions include possession of an epitope or
antigenic site that is capable of binding antibodies raised against
a naturally-occurring or denatured Delta3 polypeptide or fragment
thereof. Accordingly, an activity of a Delta3 protein can be
binding to a receptor, such as Notch. An activity of a Delta3
protein can also be modulation of cell proliferation and/or
differentiation, or cell death in a target cell having an
appropriate receptor. A target cell can be, e.g., a neural cell, an
endothelial cell, or a cancer cell.
[0287] The term "aberrant Delta3 activity" or "abnormal Delta3
activity" is intended to encompass an activity of Delta3 which
differs from the same Delta3 expression or activity in a healthy
subject. An aberrant Delta3 activity can result, e.g., from a
mutation in the protein, which results, e.g., in lower or higher
binding affinity to a receptor. An aberrant Delta3 activity can
also result from a lower or higher level of Delta3 on cells, which
can result, e.g., from aberrant transcription, splicing, or
translation of the Delta3 gene. For example, an aberrant Delta3
activity can result from an abnormal promoter activity. An aberrant
Delta3 activity can also result from an aberrant signalling through
the cytoplasmic domain of the Delta3 protein, such that, e.g., an
aberrant signal is transduced. Aberrant signalling can result from
a mutation in the cytoplasmic domain of Delta3 or, alternatively,
from the contact with an abnormal cytoplasmic protein. An aberrant
Delta3 activity can also result from contact of a Delta3 protein
with an aberrant receptor, e.g., abnormal Notch protein.
[0288] The term "allele", which is used interchangeably herein with
"allelic variant" refers to alternative forms of a gene, nucleic
acid or portions thereof, as well as to a polypeptide encoded by
said gene, nucleic acid, or portion thereof. Nucleic acid alleles
occupy the same locus or position on homologous chromosomes. When a
subject has two identical alleles of a gene, the subject is said to
be homozygous for the gene or allele. When a subject has two
different alleles of a gene, the subject is said to be heterozygous
for the gene. Alleles of a specific gene can differ from each other
in a single nucleotide, or several nucleotides, and can include
substitutions, deletions, and insertions of nucleotides. An allele
of a gene can also be a form of a gene containing a mutation.
[0289] The term "allelic variant of a polymorphic region of a
Delta3 gene" refers to a region of a Delta gene having one of
several nucleotide sequences found in that region of the gene in
other individuals, as well as to polypeptides encoded by nucleic
acid molecules comprising said sequences.
[0290] The term "agonist", as used herein, is meant to refer to an
agent that upregulates (e.g., potentiates or supplements) Delta3
expression, levels and/or activity. It is to be understood that a
Delta3 agonist can include a compound which increases signaling
from a Delta3 protein, e.g., a compound bound to Delta3, such as a
stimulatory form of a toporythmic protein or a small molecule. A
Delta3 agonist can also, for example, be a compound which modulates
the expression or activity of a protein which is located upstream
or downstream of Delta3 and or which interacts with Delta3.
[0291] "Antagonist" as used herein is meant to refer to an agent
that downregulates (e.g., suppresses or inhibits) Delta3
expression, levels and/or activity. A Delta3 antagonist can, for
example, be a compound which decreases signalling from a Delta3
protein, e.g., a compound binding to Delta3 such as an inhibitory
form of a toporythmic protein, or a small molecule. A Delta3
antagonist can include compounds that inhibit the interaction
between a Delta3 protein and another molecule, e.g., a toporythmic
protein. A Delta3 antagonist can also be a compound which modulates
the expression or activity of a protein which is located upstream
or downstream of Delta3 and/or which interacts with Delta3.
[0292] The term "antibody" as used herein refers to immunoglobulin
molecules and immunologically active portions of immunoglobulin
molecules, i.e., molecules that contain an antigen biding site
which specifically binds an antigen, such as a polypeptide of the
invention, e.g., an epitope of a polypeptide of the invention. A
molecule
[0293] The term "antibody" as used herein refers to immunoglobulin
molecules and immunologically active portions of immunoglobulin
molecules, i.e., molecules that contain an antigen binding site
which specifically binds an antigen, such as a polypeptide of the
invention, e.g., an epitope of a polypeptide of the invention. A
molecule which specifically binds to a given polypeptide of the
invention is a molecule which binds the polypeptide, but does not
substantially bind other molecules in a sample, e.g., a biological
sample, which naturally contains the polypeptide. Examples of
immunologically active portions of immunoglobulin molecules include
F(ab) and F(ab').sub.2 fragments which can be generated by treating
the antibody with an enzyme such as pepsin. The invention provides
polyclonal and monoclonal antibodies. The term "monoclonal
antibody" or "monoclonal antibody composition", as used herein,
refers to a population of antibody molecules that contain only one
species of an antigen binding site capable of immunoreacting with a
particular epitope.
[0294] "Cells," "host cells" or "recombinant host cells" are terms
used interchangeably herein. It is understood that such terms refer
not only to the particular subject cell but to the progeny or
potential progeny of such a cell. Because certain modifications may
occur in succeeding generations due to either mutation or
environmental influences, such progeny may not, in fact, be
identical to the parent cell, but are still included within the
scope of the term as used herein.
[0295] "Complementary" sequences as used herein refer to sequences
which have sufficient complementarity to be able to hybridize,
forming a stable duplex.
[0296] A "delivery complex" shall mean a targeting means (e.g., a
molecule that results in higher affinity binding of a gene,
protein, polypeptide or peptide to a target cell surface and/or
increased cellular uptake by a target cell). Examples of targeting
means include: sterols (e.g., cholesterol), lipids (e.g., a
cationic lipid, virosome or liposome), viruses (e.g., adenovirus,
adeno-associated virus, and retrovirus) or target cell specific
binding agents (e.g., ligands recognized by target cell specific
receptors). Preferred complexes are sufficiently stable in vivo to
prevent significant uncoupling prior to internalization by the
target cell. However, the complex is cleavable under appropriate
conditions within the cell so that the gene, protein, polypeptide
or peptide is released in a functional form.
[0297] As is well known, genes for a particular polypeptide may
exist in single or multiple copies within the genome of an
individual. Such duplicate genes may be identical or may have
certain modifications, including nucleotide substitutions,
additions or deletions, which all still code for polypeptides
having substantially the same activity. The term "DNA sequence
encoding a Delta3 polypeptide" may thus refer to one or more genes
within a particular individual. Moreover, certain differences in
nucleotide sequences may exist between individual organisms, which
are called alleles. Such allelic differences may or may not result
in differences in amino acid sequence of the encoded polypeptide
yet still encode a protein with the same biological activity.
[0298] The term "Delta3 therapeutic" refers to various compositions
of Delta3 modulators (e.g., agonists or antagonists), such as
polypeptides, antibodies, peptidomimetics, small molecules and
nucleic acids which are capable of mimicking or potentiating
(agonizing) or inhibiting suppressing (antagonizing) Delta3
expression, levels, or activity, e.g., which are capable of
agonizing or antagonizing the effects of a naturally-occurring
Delta3 protein.
[0299] The terms "Delta3 polypeptide" and "Delta3 protein" are
intended to encompass, e.g., Delta3 polypeptides which have at
least one activity of a native Delta3 polypeptide, or can, e.g.,
antagonize or agonize at least one biological activity of a native
Delta3 polypeptide.
[0300] A "fusion protein" is a fusion of a first amino acid
sequence encoding one of the subject Delta3 polypeptides with a
second, heterologous amino acid sequence. In general, a fusion
protein can be represented by the general formula X-Delta3-Y,
wherein Delta3 represents a portion of the protein which is derived
from one of the Delta3 proteins of the invention, and X and Y are
independently absent or represent amino acid sequences which are
heterologous to (that is, not related to) one of the Delta3
sequences in an organism, including naturally-occurring mutants.
Among the Delta3 fusion protein is a Delta3-Ig fusion protein.
[0301] As used herein, the term "gene" or "recombinant gene", as
applied to Delta3, refers to a nucleic acid molecule comprising an
open reading frame encoding one of the Delta3 polypeptides of the
present invention. In one embodiment, these terms relate to a cDNa
sequence including, but not limited to a nucelci acid sequence
obtained via reverse transcription of an mRNA molecule.
[0302] The term "growth state" of a cell refers to the
proliferative state of a cell as well as to its differentiative
state. Accordingly, the term refers to the phase of the cell cycle
in which the cell is, e.g., G0, G1, G2, prophase, metaphase, or
telophase, as well as to its state of differentiation, e.g.,
undiffereniated, partially differentiated, or fully differentiated.
Without wanting to be limited, differentiation of a cell is usually
accompanied by a decrease in the proliferative rate of a cell.
[0303] "Homology" or "identity" or "similarity" refers to sequence
similarity between two peptides or between two nucleic acid
molecules. Homology can be determined by comparing a position in
each sequence which may be aligned for purposes of comparison. When
a position in the compared sequence is occupied by the same base or
amino acid, then the molecules are identical at that position. A
degree of homology or similarity or identity between nucleic acid
sequences is a function of the number of identical or matching
nucleotides at positions shared by the nucleic acid sequences. A
degree of identity of amino acid sequences is a function of the
number of identical amino acids at positions shared by the amino
acid sequences. Likewise, a degree of identity of nucleic acid
sequences is a function of the number of identical nucleic acids at
positions shared by the nucleic acid sequences.
[0304] Furthermore, a degree of homology or similarity of amino
acid sequences is a function of the number of conserved amino acids
at positions shared by the amino acid sequences. A sequence which
is "unrelated" or "non-homologous" with one of the hDelta3
sequences of the present invention typically is a sequence which
shares less than 40% identity, though preferably less than 25%
identity with one of the hDelta3 sequences of the present
invention.
[0305] To determine the percent identity of two amino acid
sequences or of two nucleic acids, the sequences are aligned for
optimal comparison purposes (e.g., gaps can be introduced in the
sequence of a first amino acid or nucleic acid sequence for optimal
alignment with a second amino or nucleic acid sequence). The amino
acid residues or nucleotides at corresponding amino acid positions
or nucleotide positions are then compared. When a position in the
first sequence is occupied by the same amino acid residue or
nucleotide as the corresponding position in the second sequence,
then the molecules are identical at that position. The percent
identity between the two sequences is a function of the number of
identical positions shared by the sequences (i.e., % identity=# of
identical positions/total # of positions (e.g., overlapping
positions).times.100). In one embodiment the two sequences are the
same length. In another embodiment, the mouse Delta3 polypeptide is
one amino acid longer than human Delta3.
[0306] Preferably, the determination of percent identity between
two sequences is accomplished using a mathematical algorithm. A
preferred, non-limiting example of a mathematical algorithm
utilized for the comparison of two sequences is the algorithm of
Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264-2268,
modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci.
USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST
and XBLAST programs of Altschul, et al. (1990) J. Mol. Biol.
215:403-410. BLAST nucleotide searches can be performed with the
NBLAST program, score=100, wordlength=12 to obtain nucleotide
sequences homologous to a nucleic acid molecules of the invention.
BLAST protein searches can be performed with the XBLAST program,
score=50, wordlength=3 to obtain amino acid sequences homologous to
a protein molecules of the invention. To obtain gapped alignments
for comparison purposes, Gapped BLAST can be utilized as described
in Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402.
Alternatively, PSI-Blast can be used to perform an iterated search
which detects distant relationships between molecules. Id. When
utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default
parameters of the respective programs (e.g., XBLAST and NBLAST) can
be used. Another preferred, non-limiting example of a mathematical
algorithm utilized for the comparison of sequences is the algorithm
of Myers and Miller, (1988) CABIOS 4:11-17. Such an algorithm is
incorporated into the ALIGN program (version 2.0) which is part of
the GCG sequence alignment software package. When utilizing the
ALIGN program for comparing amino acid sequences, a PAM120 weight
residue table, a gap length penalty of 12, and a gap penalty of 4
can be used.
[0307] As used herein, the term "hybridizes under stringent
conditions" is intended to describe conditions for hybridization
and washing under which nucleotide sequences at least 60% (65%,
70%, preferably 75% or more) identical to each other typically
remain hybridized to each other. Such stringent conditions are
known to those skilled in the art and can be found in Current
Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989),
6.3.1-6.3.6, which describes aqueous and non-aqueous methods,
either of which can be used. Another preferred, non-limiting
example of stringent hybridization conditions are hybridization in
6.times. sodium chloride/sodium citrate (SSC) at about 45_C,
followed by one or more washes in 2.0.times.SSC at 50.degree. C.
(low stringency) or 0.2.times.SSC, 0.1% SDS at 50-65_C (high
stringency). Another preferred example of stringent hybridization
conditions are hybridization in 6.times. sodium
chloride/sodiumcitrate (SSC) at about 45.quadrature.C., followed by
one or more washes in 0.2.times.SSC, 0.1% SDS at 50.quadrature.C.
Another example of stringent hybridization conditions are
hybridization in 6.times. sodium chloride/sodium citrate (SSC) at
about 45.quadrature.C., followed by one or more washes in
0.2.times.SSC, 0.1% SDS at 55.quadrature.C. A further example of
stringent hybridization conditions are hybridizationin 6.times.
sodium chloride/sodium citrate (SSC) at about 45.quadrature.C.,
followed by one or more washes in 0.2.times.SSC, 0.1% SDS at
60.quadrature.C. Preferably, stringent hybridization conditions are
hybridization in 6.times. sodium chloride/sodium citrate (SSC) at
about 45.quadrature.C., followed by one or more washes in
0.2.times.SSC, 0.1% SDS at 65.quadrature.C. Particularly preferred
stringency conditions (and the conditions that should be used if
the practitioner is uncertain about what conditions should be
applied to determine if a molecule is within a hybridization
limitation of the invention) are 0.5M Sodium Phosphate, 7% SDS at
65.quadrature.C., followed by one or more washes at 0.2.times.SSC,
1% SDS at 65.quadrature.C. In one embodiment, an isolated nucleic
acid molecule of the invention that hybridizes under stringent
conditions to the sequence of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31,
33, 35, 37, 39, 41, 43 or 45, or complement thereof, corresponds to
a naturally-occurring nucleic acid molecule.
[0308] The term "interact" as used herein is meant to include
detectable interactions between molecules, such as can be detected
using, for example, a yeast two hybrid assay. The term interact is
also meant to include "binding" interactions between molecules.
Interactions may be, e.g., protein-protein, protein-nucleic acid,
protein-small molecule, or nucleic acid-small molecule in
nature.
[0309] The term "modulation" as used herein refers to both
upregulation, i.e., stimulation, and downregulation, e.g.,
suppression, of a response.
[0310] The term "mutated gene" refers to an allelic form of a gene,
which is capable of altering the phenotype of a subject having the
mutated gene relative to a subject which does not have the mutated
gene. If a subject must be homozygous for this mutation to have an
altered phenotype, the mutation is said to be recessive. If one
copy of the mutated gene is sufficient to alter the genotype of the
subject, the mutation is said to be dominant. If a subject has one
copy of the mutated gene and has a phenotype that is intermediate
between that of a homozygous and that of a heterozygous (for that
gene) subject, the mutation is said to be co-dominant. As used
herein, a "naturally-occurring" nucleic acid molecule refers to an
RNA or DNA molecule having a nucleotide sequence that occurs in
nature (e.g., encodes a natural protein).
[0311] The "non-human animals" of the invention include mammalians
such as rodents, non-human primates, sheep, dog, cow, chickens,
amphibians, reptiles, etc. Preferred non-human animals are selected
from the rodent family including rat and mouse, most preferably
mouse, though transgenic amphibians, such as members of the Xenopus
genus, and transgenic chickens can also provide important tools for
understanding and identifying agents which can affect, for example,
embryogenesis and tissue formation. The term "chimeric animal" is
used herein to refer to animals in which the recombinant gene is
found, or in which the recombinant is expressed in some but not all
cells of the animal. The term "tissue-specific chimeric animal"
indicates that one of the recombinant Delta3 genes is present
and/or expressed or disrupted in some tissues but not others.
[0312] As used herein, the term "nucleic acid molecule" is intended
to include DNA molecules and RNA molecules (e.g., mRNA) and analogs
of the DNA or RNA generated using nucleotide analogs. The nucleic
acid molecule can be single-stranded or double-stranded, but
preferably is double-stranded DNA. An "isolated" nucleic acid
molecule is one which is separated from other nucleic acid
molecules which are present in the natural source of the nucleic
acid molecule. Preferably, an "isolated" nucleic acid molecule is
free of sequences (preferably protein encoding sequences) which
naturally flank the nucleic acid (i.e., sequences located at the 5'
and 3' ends of the nucleic acid) in the genomic DNA of the organism
from which the nucleic acid is derived. In other embodiments, the
"isolated" nucleic acid is free of intron sequences. For example,
in various embodiments, the isolated nucleic acid molecule
preferably includes no more than 10 kilobases (kb), and more
preferably, contains less than about 5 kB, 4 kB, 3 kB, 2 kB, 1 kB,
0.5 kB or 0.1 kB of nucleotide sequences which naturally flank the
nucleic acid molecule in genomic DNA of the cell from which the
nucleic acid is derived. Moreover, an "isolated" nucleic acid
molecule, such as a cDNA molecule, can be substantially free of
other cellular material, viral material, or culture medium when
produced by recombinant techniques, or substantially free of
chemical precursors or other chemicals when chemically
synthesized.
[0313] The terms "protein", "polypeptide" and "peptide" are used
interchangably herein. The term "substantially free of other
cellular proteins" (also referred to herein as "contaminating
proteins") or "substantially pure or purified preparations" are
defined as encompassing preparations of Delta3 polypeptides having
less than about 20% (by dry weight) contaminating protein, and
preferably having less than about 5% contaminating protein.
Functional forms of the subject polypeptides can be prepared, for
the first time, as purified or isolated preparations by using a
cloned gene as described herein. By "purified" or "isolated," it is
meant, when referring to a protein of the invention, that the
indicated molecule is present in the substantial absence of other
biological macromolecules, such as other proteins. The term
"purified" or "isolated" as used herein preferably means at least
80% by dry weight, more preferably in the range of 95-99% by
weight, and most preferably at least 99.8% by weight, of biological
macromolecules of the same type present (but water, buffers, and
other small molecules, especially molecules having a molecular
weight of less than about 5000, can be present). The term "pure" or
"isolated" as used herein preferably has the same numerical limits
as "purified" or "isolated" immediately above. "Isolated" and
"purified" do not encompass either natural materials in their
native state or natural materials that have been separated into
components (e.g., in an acrylamide gel) but not obtained either as
pure (e.g., lacking contaminating proteins, or chromatography
reagents such as denaturing agents and polymers, e.g., acrylamide
or agarose) substances or solutions. In preferred embodiments,
purified or isolated Delta3 preparations will lack any
contaminating proteins from the same animal from which Delta3 is
normally produced, as can be accomplished by recombinant expression
of, for example, a human Delta3 protein in a non-human cell.
[0314] As used herein, the term "tissue-specific promoter" means a
DNA sequence that serves as a promoter, i.e., regulates expression
of a selected DNA sequence operably linked to the promoter, and
which effects expression of the selected DNA sequence in specific
cells of a tissue, such as cells of cardiac, hepatic or pancreatic
origin, neuronal cells, or immune cells. The term also covers
so-called "leaky" promoters, which regulate expression of a
selected DNA primarily in one tissue, but cause expression in other
tissues as well.
[0315] "Transcriptional regulatory sequence" is a generic term used
throughout the specification to refer to DNA sequences, such as
initiation signals, enhancers, and promoters, which induce or
control transcription of protein coding sequences with which they
are operably linked. In certain embodiments, transcription of one
of the recombinant Delta3 genes is under the control of a promoter
sequence (or other transcriptional regulatory sequence) which
controls the expression of the recombinant gene in a cell-type in
which expression is intended. It will also be understood that the
recombinant gene can be under the control of transcriptional
regulatory sequences which are the same or which are different from
those sequences which control transcription of the
naturally-occurring forms of Delta3 proteins.
[0316] As used herein, the term "transfection" means the
introduction of a nucleic acid, e.g., an expression vector, into a
recipient cell by nucleic acid-mediated gene transfer.
"Transformation", as used herein, refers to a process in which a
cell's genotype is changed as a result of the cellular uptake of
exogenous DNA or RNA, and, for example, the transformed cell
expresses a recombinant form of a Delta3 polypeptide or, in the
case of anti-sense expression from the transferred gene, the
expression of a naturally-occurring form of the Delta3 protein is
disrupted.
[0317] As used herein, the term "transgene" means a nucleic acid
sequence (encoding, e.g., one of the Delta3 polypeptides, or an
antisense transcript thereto), which is partly or entirely
heterologous, i.e., foreign, to the transgenic animal or cell into
which it is introduced, or, is homologous to an endogenous gene of
the transgenic animal or cell into which it is introduced, but
which is designed to be inserted, or is inserted, into the animal's
genome in such a way as to alter the genome of the cell into which
it is inserted (e.g., it is inserted at a location which differs
from that of the natural gene or its insertion results in a
knockout). A transgene can include one or more transcriptional
regulatory sequences and any other nucleic acid, such as introns,
that may be necessary for optimal expression of a selected nucleic
acid.
[0318] A "transgenic animal" refers to any non-human animal,
preferably a non-human mammal, bird or an amphibian, in which one
or more of the cells of the animal contain heterologous nucleic
acid ("transgene") introduced by way of human intervention, such as
by transgenic techniques well known in the art. The nucleic acid is
introduced into the cell, directly or indirectly by introduction
into a precursor of the cell, by way of deliberate genetic
manipulation, such as by microinjection or by infection with a
recombinant virus. The term genetic manipulation does not include
classical cross-breeding, or in vitro fertilization, but rather is
directed to the introduction of a recombinant DNA molecule. This
molecule may be integrated within a chromosome, or it may be
extrachromosomally replicating DNA. In the typical transgenic
animals described herein, the transgene causes cells to express a
recombinant form of one of the Delta3 proteins, e.g., either
agonistic or antagonistic forms. However, transgenic animals in
which the recombinant Delta3 gene is silent are also contemplated,
as for example, the FLP or CRE recombinase dependent constructs
described below. Moreover, "transgenic animal" also includes those
recombinant animals in which gene disruption of one or more Delta3
genes is caused by human intervention, including both recombination
and antisense techniques. A "homologous recombinant animal" is a
non-human animal, preferably a mammal, more preferably a mouse, in
which an endogenous gene has been altered by homologous
recombination between the endogenous gene and an exogenous DNA
molecule introduced into a cell of the animal, e.g., an embryonic
cell of the animal, prior to development of the animal.
[0319] As used herein, the term "vector" refers to a nucleic acid
molecule capable of transporting another nucleic acid to which it
has been linked. One type of preferred vector is an episome, i.e.,
a nucleic acid capable of extra-chromosomal replication. Preferred
vectors are those capable of autonomous replication and/expression
of nucleic acids to which they are linked. Vectors capable of
directing the expression of genes to which they are operatively
linked are referred to herein as "expression vectors". In general,
expression vectors of utility in recombinant DNA techniques are
often in the form of "plasmids" which refer generally to circular
double stranded DNA loops which, in their vector form are not bound
to the chromosome. However, the invention is intended to include
such other forms of expression vectors which serve equivalent
functions and which become known in the art subsequently
hereto.
[0320] The term "treating" as used herein is intended to encompass
curing as well as ameliorating at least one symptom of the
condition or disease.
[0321] The percent identity between two sequences can be determined
using techniques similar to those described above, with or without
allowing gaps. In calculating percent identity, typically only
exact matches are counted.
FTHMA-070 and T85
[0322] The present invention is based, in part, on the discovery of
a cDNA molecule encoding human FTHMA-070, a member of the TNF
receptor superfamily.
[0323] A nucleotide sequence encoding a human FTHMA-070 protein is
shown in SEQ ID NO:53 and SEQ ID NO:55 (open reading frame only). A
predicted amino acid sequence of FTHMA-070 protein is also shown in
SEQ ID NO:54.
[0324] The FTHMA-070 cDNA of SEQ ID NO:53, which is approximately
2133 nucleotides long including untranslated regions, encodes a 401
amino acid protein.
[0325] Human FTHMA-070 is one member of a family of molecules (the
"FTHMA-070 family") having certain conserved structural and
functional features. The term "family" when referring to the
protein and nucleic acid molecules of the invention is intended to
mean two or more proteins or nucleic acid molecules having a common
structural domain and having sufficient amino acid or nucleotide
sequence identity as defined herein. Such family members can be
naturally occurring and can be from either the same or different
species. For example, a family can contain a first protein of human
origin and a homologue of that protein of murine origin, as well as
a second, distinct protein of human origin and a murine homologue
of that protein. Members of a family may also have common
functional characteristics.
[0326] As used interchangeably herein a "FTHMA-070 activity",
"biological activity of FTHMA-070" or "functional activity of
FTHMA-070", refers to an activity exerted by a FTHMA-070 protein,
polypeptide or nucleic acid molecule on a FTHMA-070 responsive cell
as determined in vivo, or in vitro, according to standard
techniques. A FTHMA-070 activity can be a direct activity, such as
an association with or an enzymatic activity on a second protein or
an indirect activity.
[0327] Accordingly, another embodiment of the invention features
isolated FTHMA-070 proteins and polypeptides having a FTHMA-070
activity.
[0328] Yet another embodiment of the invention features FTHMA-070
molecules which contain a signal sequence. Generally, a signal
sequence (or signal peptide) is a peptide containing about 20 amino
acids which occurs at the extreme N-terminal end of secretory and
integral membrane proteins and which contains large numbers of
hydrophobic amino acid residues and serves to direct a protein
containing such a sequence to a lipid bilayer.
[0329] The present invention is also based, in part, on the
discovery of a cDNA molecule encoding human T85, a protein which
appears to be a secreted (non-membrane bound) form of human Robo
protein, a protein which is a nerve axon guidance receptor.
[0330] A nucleotide sequence encoding a human T85 protein is shown
in SEQ ID NO:57 and SEQ ID NO:59 (open reading frame only). A
predicted amino acid sequence of FTHMA-070 protein is also shown in
SEQ ID NO:58.
[0331] The FTHMA-070 cDNA of SEQ ID NO:57, which is approximately
4291 nucleotides long including untranslated regions, encodes a 753
amino acid protein. Human T85 is one member of a family of
molecules (the "T85 family") having certain conserved structural
and functional features. The term "family" when referring to the
protein and nucleic acid molecules of the invention is intended to
mean two or more proteins or nucleic acid molecules having a common
structural domain and having sufficient amino acid or nucleotide
sequence identity as defined herein. Such family members can be
naturally occurring and can be from either the same or different
species. For example, a family can contain a first protein of human
origin and a homologue of that protein of murine origin, as well as
a second, distinct protein of human origin and a murine homologue
of that protein. Members of a family may also have common
functional characteristics.
[0332] In one embodiment, a T85 protein includes a fibronectin type
III domain having at least about 65%, preferably at least about
75%, and more preferably about 85%, 95%, or 98% amino acid sequence
identity to a fibronectin type III domain of SEQ ID NO:61, or
62.
[0333] In one embodiment, a T85 protein includes an Ig superfamily
domain having at least about 65%, preferably at least about 75%,
and more preferably about 85%, 95%, or 98% amino acid sequence
identity to an Ig superfamily domain of SEQ ID NO:63, 64, 65, 66,
or 67.
[0334] Preferred T85 polypeptides of the present invention have an
amino acid sequence sufficiently identical to a sequence identity
to a fibronectin type III domain of SEQ ID NO:61 or 62 or an Ig
superfamily domain of SEQ ID NO:63, 64, 65, 66, or 67. As used
herein, the term "sufficiently identical" refers to a first amino
acid or nucleotide sequence which contains a sufficient or minimum
number of identical or equivalent (e.g., an amino acid residue
which has a similar side chain) amino acid residues or nucleotides
to a second amino acid or nucleotide sequence such that the first
and second amino acid or nucleotide sequences have a common
structural domain and/or common functional activity. For example,
amino acid or nucleotide sequences which contain a common
structural domain having about 65% identity, preferably 75%
identity, more preferably 85%, 95%, or 98% identity are defined
herein as sufficiently identical.
[0335] As used interchangeably herein a "T85 activity", "biological
activity of T85" or "functional activity of T85", refers to an
activity exerted by a T85 protein, polypeptide or nucleic acid
molecule on a T85 responsive cell as determined in vivo, or in
vitro, according to standard techniques. A T85 activity can be a
direct activity, such as an association with or an enzymatic
activity on a second protein.
[0336] Accordingly, another embodiment of the invention features
isolated T85 proteins and polypeptides having a T85 activity.
[0337] Yet another embodiment of the invention features T85
molecules which contain a signal sequence. Generally, a signal
sequence (or signal peptide) is a peptide containing about 20 amino
acids which occurs at the extreme N-terminal end of secretory and
integral membrane proteins and which contains large numbers of
hydrophobic amino acid residues and serves to direct a protein
containing such a sequence to a lipid bilayer.
TANGO 77
[0338] The polypeptide cytokine interleukin-1 (IL-1) is a critical
mediator of inflammatory and overall immune response. To date,
three members of the IL-1 family, IL-1.alpha., IL-1.beta. and
IL-1ra (Interleukin-1 receptor antagonist) have been isolated and
cloned. IL-1.alpha. and IL-1.beta. are proinflammatory cytokines
which elicit biological responses, whereas IL-1ra is an antagonist
of IL-1.alpha. and IL-18 activity. Two distinct cell-surface
receptors have been identified for these ligands, the type 1 IL-1
receptor (IL-1RtI) and type II IL-1 receptor (IL-1RtII). Recent
results suggest that the IL-1 RtI is the receptor responsible for
transducing a signal and producing biological effects.
[0339] While inflammation is an important homeostatic mechanism,
aberrant inflammation has the potential for inducing damage to the
host. Elevated IL-1 levels are known to be associated with a number
of diseases particularly autoimmune diseases and inflammatory
disorders. Since II-1ra is a naturally occurring inhibitor of IL-1,
IL-1ra can be used to limit the aberrant and potentially
deleterious effects of IL-1. In experimental animals, pretreatment
with IL-1ra has been shown to prevent death resulting from
lipopolysaccharide-induced sepsis. The relative absence of IL-1ra
has also been suggested to play a role in human inflammatory bowel
disease.
[0340] The present invention is based on the discovery of a cDNA
molecule encoding human Tango-77, a member of the cytokine
superfamily. The cDNA molecule encoding human Tango-77 has three
possible open reading frames. The three possible nucleotide open
reading frames for human Tango-77 protein are shown in SEQ ID
NO:73, SEQ ID NO:76 and SEQ ID NO:80. The predicted amino acid
sequence for the three possible Tango-77 immature proteins are
shown in SEQ ID NO:72, SEQ ID NO:77 or SEQ ID NO:81 and three
possible mature proteins are shown in SEQ ID NO:75, SEQ ID NO:79
and SEQ ID NO:83.
[0341] The Tango-77 cDNA of SEQ ID NO:71, which is approximately
989 nucleotides long including untranslated regions, encodes a
protein amino acid having a molecular weight of approximately 19
kDa, 18 kDa, or 14.9 KDa (excluding post-translational
modifications) and the possible mature form of the protein has a
molecular weight of 13 kDa. A plasmid containing a cDNA encoding
human Tango-77 (with the cDNA insert name of Of fthx077) was
deposited with American Type Culture Collection (ATCC), 10801
University Boulevard, Manassas, Va. 20110-2209 on Jul. 2, 1998 and
assigned Accession Number 98807. This deposit will be maintained
under the terms of the Budapest Treaty on the International
Recognition of the Deposit of Microorganisms for the Purposes of
Patent Procedure. This deposit was made merely as a convenience for
those of skill in the art and is not an admission that a deposit is
required under 35 U.S.C. .sctn.112.
[0342] Human Tango-77 is one member of a family of molecules (the
"Tango-77 family") having certain conserved structural and
functional features. The term "family," when referring to the
protein and nucleic acid molecules of the invention, is intended to
mean two or more proteins or nucleic acid molecules having a common
structural domain and having sufficient amino acid or nucleotide
sequence identity as defined herein. Such family members can be
naturally occurring and can be from either the same or different
species. For example, a family can contain a first protein of human
origin and a homologue of that protein of murine origin, as well as
a second, distinct protein of human origin and a murine homologue
of that protein. Members of a family may also have common
functional characteristics.
[0343] As used interchangeably herein a "Tango-77 activity",
"biological activity of Tango-77" or "functional activity of
Tango-77", refers to an activity exerted by a Tango-77 protein,
polypeptide or nucleic acid molecule on a Tango-77 responsive cell
as determined in vivo, or in vitro, according to standard
techniques. A Tango-77 activity can be a direct activity, such as
an association with a second protein, or an indirect activity, such
as a cellular signaling activity mediated by interaction of the
Tango-77 protein with a second protein. In a preferred embodiment,
a Tango-77 activity includes at least one or more of the following
activities: (i) the ability to interact with proteins in the
Tango-77 signalling pathway (ii) the ability to interact with a
Tango-77 ligand or receptor; or (iii) the ability to interact with
an intracellular target protein, (iv) the ability to interact with
a protein involved in inflammation, and (v) the ability to bind the
IL-1 receptor.
[0344] Accordingly, another embodiment of the invention features
isolated Tango-77 proteins and polypeptides having a Tango-77
activity.
[0345] Yet another embodiment of the invention features Tango-77
molecules which contain a signal sequence. Generally, a signal
sequence (or signal peptide) is a peptide containing about 21 to 63
amino acids which occurs at the extreme N-terminal end of a
secretory protein. The native Tango-77 signal sequence (SEQ ID
NO:74, SEQ ID NO:78, or SEQ ID NO:82) can be removed and replaced
with a signal sequence from another protein. In certain host cells
(e.g., mammalian host cells), expression and/or secretion of
Tango-77 can be increased through use of a heterologous signal
sequence. For example, the gp67 secretory sequence of the
baculovirus envelope protein can be used as a heterologous signal
sequence. Alternatively, the native Tango-77 signal sequence can
itself be used as a heterologous signal sequence in expression
systems, e.g., to facilitate the secretion of a protein of
interest.
SPOIL
[0346] Interleukin-1 (IL-1) is a multifunctional cytokine which
comprises a family of two polypeptides, IL-1.alpha. and IL-1.beta.,
with a wide spectrum of activities. IL-1.alpha. and IL-1.beta. have
been found to possess inflammatory, metabolic, physiologic,
hematopoeitic and immunologic properties. Although both forms of
IL-1 are distinct gene products, they recognize the same cell
surface receptors (i.e. IL-1 receptors, IL-1RtI and IL-1RtII).
[0347] Besides skin keratinocytes, some epithelial cells and
certain cells in the central nervous system, significant amounts of
mRNA encoding IL-1 are not observed in most other healthy cells.
However, IL-1 production is dramatically increased by a variety of
cells in response to infection, microbial toxins, inflammatory
agents, products of activated lymphocytes, complement and clotting
components. In addition, IL-1 has been recognized as a prototype of
proinflammatory cytokines in that it induces the expression of a
variety of genes and the synthesis of several proteins that in
turn, induce acute and chronic inflammation. Thus, circulating IL-1
has been implicated in various disease states including sepsis,
rheumatoid arthritis, stroke and diabetes. Dinarello (1991) Blood
77(8):1627-1652.
[0348] In addition, IL-1 has been shown to regulate bone
reabsorption and bone formation with its major activity in bone
metabolism being osteoclast activation. See Gowen et al. (1983)
Nature 306:378-380. In fact, IL-1 has been reported to be a potent
stimulator of bone reabsorption and has also been reported to
increase prostaglandin synthesis in bone. Lorenzo et al. (1987)
Endocrinology 121:1164-1170.
[0349] A naturally-occurring, secreted inhibitor of IL-1 which
specifically inhibits IL-1 activity has also been identified.
Carter et al. (1990) Nature 344:633. This protein, called IL-1
receptor antagonist protein (IL-1ra), has been shown to compete
with the binding of IL-1 to its surface receptors. Thus,
significant interest has arisen in administering IL-1ra to block
the activity of IL-1 in various diseases including septic shock
(Ohlsson et al. (1990) Nature 348:550-556), immune complex-induced
colitis (Cominelli (1990) J. Clin. Invest. 86:972-979), acute
myelogenous leukemia (Rambaldi et al. (1990) Blood 76:114-120) and
osteoporosis (Pacifici et al. (1993) J. Clin. Endocrinol. Metab.
77:1135-1141). Further research has indicated that the secreted
form of IL-1ra is, in fact, a member of a family of IL-1ra
proteins, at least three of which are intracellular proteins
(Haskill et al. (1991) Proc. Natl. Acad. Sci. USA 88:3681-3685;
Muzio et al. (1995) J. Exp. Med. 182:623-628; and Weissbach et al.
(1998) Biochem. Biophys. Res. Comm. 244:91-95. The family members
are alternatively spliced isoforms of the IL-ra gene which consists
of at least seven exons. A truncated form of the fourth exon is
produced as a result of an internal splice acceptor site, resulting
in the secreted isoform.
[0350] The present invention is based on the discovery of novel
molecules having homology to members of the IL-1 receptor
antagonist (IL-1ra) family, referred to herein as SPOIL protein and
nucleic acid molecules. The SPOIL proteins and nucleic acid
molecules comprise a family of molecules having certain conserved
structural and functional features. The term "family" when
referring to the protein and nucleic acid molecules of the
invention is intended to mean two or more protein or nucleic acid
molecules having a common structural domain and having sufficient
amino acid or nucleotide sequence identity as defined herein. Such
family members can be naturally occurring and can be from either
the same or different species. For example, a family can contain a
first protein of human origin, as well as other, distinct proteins
of human origin or alternatively, can contain homologues of
non-human origin (e.g., mouse). Members of a family may also have
common functional characteristics.
[0351] For example, an isolated protein of the invention,
preferably a SPOIL protein, is identified based on the presence of
at least one "IL-1 signature domain" in the protein or
corresponding nucleic acid molecule. As used herein, the term "IL-1
signature domain" refers to a protein domain which contains a
conserved motif of a SPOIL protein member (or IL-1ra or IL-1 family
member) and is at least about 10-30 amino acid residues, preferably
about 15-25 amino acid residues, more preferably about 17-24 amino
acid residues, more preferably 19-23 amino acid residues, and more
preferably 21-22 amino acid residues in length. An IL-1 signature
domain includes the following amino acid motif:
Xaa.sub.1-Xaa.sub.2-S-Xaa.sub.3-Xaa.sub.4-Xaa.sub.5-P-Xaa.sub.6-Xaa.sub.7-
-Xaa.sub.9-Xaa.sub.9-Xaa.sub.10-Xaa.sub.n-Xaa.sub.11, wherein
Xaa.sub.1, Xaa.sub.2, Xaa.sub.4, Xaa.sub.5, Xaa.sub.6, Xaa.sub.7,
and Xaa.sub.n represents any amino acid residue; Xaa.sub.3 is
alanine (A), serine (S), leucine (L) or valine (V); Xaa.sub.9 is
phenylalanine (F), tyrosine (Y), leucine (L), isoleucine (I) or
valine (V); Xaa.sub.9 is either leucine (L) or isoleucine (I);
Xaa.sub.10 is serine (S), cysteine (C) or alanine (A); Xaa.sub.11
is leucine (L), isoleucine (I), valine (V) or methionine (M); and n
is about 5-25 amino acid residues, more preferably about 6-18 amino
acid residues, and more preferably about 6-15 amino acid residues
(SEQ ID NO:107). In one embodiment, an IL-1 signature domain
includes the following amino acid motif:
L-Xaa.sub.1-S-V-Xaa.sub.2-Xaa.sub.3-P-Xaa.sub.4-Xaa.sub.5-Xaa.sub.n-I,
wherein Xaa represents any amino acid, and n is about 5-25 amino
acid residues, more preferably about 6-18 amino acid residues, and
more preferably about 6-15 amino acid residues (SEQ ID NO:108).
Preferably, the IL-1 signature domain includes the following amino
acid sequence:
L-Xaa.sub.1-S-V-Xaa.sub.2-Xaa.sub.3-P-Xaa.sub.4-Xaa.sub.5-Xaa.sub.n-I,
wherein Xaa.sub.1 is either threonine (T) or glutamic acid (E);
Xaa.sub.2 is either alanine (A) or glutamic acid (E); and Xaa.sub.5
is either tryptophan (W) or leucine (L) (SEQ ID NO:111). In another
embodiment, an IL-1 signature domain includes the following amino
acid sequence motif:
F-Xaa.sub.1-S-A-Xaa.sub.2-Xaa.sub.3-P-Xaa.sub.4-Xaa.sub.5-Xaa.sub.n-L,
wherein Xaa represents any amino acid, and n is about 5-25 amino
acid residues, more preferably about 6-18 amino acid residues, and
more preferably about 6-15 amino acid residues (SEQ ID NO:94).
Preferably, the IL-1 signature domain includes the following amino
acid sequence:
F-Xaa.sub.1-S-A-Xaa.sub.2-Xaa.sub.3-P-Xaa.sub.4-Xaa.sub.5-Xaa.sub.n-L,
wherein Xaa.sub.1 is either threonine (T) or glutamic acid (E);
Xaa.sub.2 is either alanine (A) or glutamic acid (E); and Xaa.sub.5
is either tryptophan (W) or leucine (L) (SEQ ID NO:95). In yet
another embodiment, the IL-1 signature domain is at least about
10-30 amino acid residues in length, preferably 15-25 amino acid
residues in length, preferably 17-24 amino acid residues, 19-23
amino acid residues or more preferably 21-22 amino acid residues in
length and has at least about 30-60% identity, preferably at least
about 35-55% identity, more preferably at least about 40-50%
identity, and more preferably at least about 46-49% identity with
an IL-1 signature domain of a protein of the invention having an
amino acid sequence as set forth in SEQ ID NO:90 (e.g., amino acid
residues 58-80), SEQ ID NO:102 (e.g., amino acid residues 130-151),
SEQ ID NO:105 (e.g., amino acid residues 169-190), or SEQ ID NO:113
(e.g., amino acid residues 120-142).
[0352] In a preferred embodiment, a protein of the invention,
preferably a SPOIL protein, contains an IL-1 signature domain of
SEQ ID NO:90 (e.g., amino acid residues 58-80), SEQ ID NO:102
(e.g., amino acid residues 130-151), SEQ ID NO:105 (e.g., amino
acid residues 169-190), or SEQ ID NO:113 (e.g., amino acid residues
120-142).
[0353] In another embodiment of the invention, a SPOIL protein is
identified based on the presence of at least one "SPOIL signature
motif" in the protein or corresponding nucleic acid molecule. As
used herein, the term "SPOIL signature motif" includes an amino
acid sequence which contains amino acid residues that are conserved
among SPOIL family members. In one embodiment, a SPOIL signature
motif, referred to herein as a "short SPOIL signature motif",
includes an amino acid sequence at least about 35-55 amino acid
residues, preferably about 38-50 amino acid residues, more
preferably about 40-48 amino acid residues, more preferably 42-46
amino acid residues, and more preferably 44 amino acid residues in
length and having the following amino acid sequence:
Q-Xaa.sub.1-Xaa.sub.2-E-Xaa.sub.3-Xaa.sub.4-1-M-Xaa.sub.5-Xaa.sub.6-Y-Xaa-
.sub.7-Xaa.sub.8-Xaa.sub.9-E-P-V-K-Xaa.sub.10-Xaa.sub.11-L-F-Y-Xaa.sub.12--
Xaa.sub.13-K-Xaa.sub.14-G-Xaa.sub.15-T-S-T-Xaa.sub.16-E-S-Xaa.sub.17-A-F-P-
-Xaa.sub.18-W-F-1-A, wherein Xaa.sub.1-18 is any amino acid (set
forth in SEQ ID NO:109). Accordingly, preferred proteins include
the conserved amino acid residues of the above-recited SPOIL
signature motif. Proteins including at least 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, or 43 conserved amino acid residues
of the above-recited SPOIL signature motif are also considered to
be within the scope of the present invention.
[0354] In another embodiment, a SPOIL signature motif, referred to
herein as a "long SPOIL signature motif" includes an amino acid
sequence of at least about 58-78 amino acid residues, preferably
about 61-74 amino acid residues, more preferably about 63-72 amino
acid residues, more preferably 65-70 amino acid residues, and more
preferably 67-68 amino acid residues in length and having the
following amino acid sequence:
Q-Xaa.sub.1-Xaa.sub.2-E-Xaa.sub.3-Xaa.sub.4-1-M-Xaa.sub.5-Xaa.sub.6-Y-Xaa-
.sub.7-Xaa.sub.8-Xaa.sub.9-E-P-V-K-Xaa.sub.10-Xaa.sub.11-L-F-Y-Xaa.sub.12--
Xaa.sub.13-K-Xaa.sub.14-G-Xaa.sub.15-T-S-T-Xaa.sub.16-E-S-Xaa.sub.17-A-F-P-
-Xaa.sub.18-W-F-1-A-Xaa.sub.19-Xaa.sub.20-Xaa.sub.21-Xaa.sub.22-Xaa.sub.23-
-Xaa.sub.24-Xaa.sub.25-P-Xaa.sub.26-1-L-T-Xaa.sub.27-E-L-G-Xaa.sub.28-Xaa.-
sub.29-Xaa.sub.30-Xaa.sub.31-T-Xaa.sub.32-F-E, wherein Xaa.sub.1-24
and 26-32 is any amino acid Xaa.sub.25 is no amino acid or any
amino acid (set forth in SEQ ID NO:110). A preferred protein
includes the conserved amino acid residues of the above-recited
SPOIL signature motif. Proteins including at least 56, 57, 58, 59,
60, 61, 62, 63, 64, 65, or 66 conserved amino acid residues of the
above-recited SPOIL signature motif are also considered to be
within the scope of the present invention.
[0355] Table III depicts the conserved amino acid residues of the
SPOIL signature motifs set forth in SEQ ID NO:109 and SEQ ID
NO:110. The conserved amino acid residues are numbered according to
their position in the SPOIL signature motif as well as by their
relative amino acid position in each of murine SPOIL-I, murine
SPOIL-II, human SPOIL-I and human SPOIL-II. As used herein, the
amino acid residues in each of the SPOIL proteins "correspond to"
the relative amino acid residues in a SPOIL signature motif.
TABLE-US-00003 TABLE III corre- corre- corre- corre- Residue in
sponding sponding sponding sponding SPOIL residue in residue in
residue in residue in signature motif muSPOIL-I muSPOIL-II
huSPOIL-I huSPOIL-II Gln1 Gln26 Gln88 Gln98 Gln137 Glu4 Glu29 Glu91
Glu101 Glu140 Ile7 Ile32 Ile94 Ile104 Ile143 Met8 Met33 Met95
Met105 Met144 Tyr11 Tyr36 Tyr98 Tyr108 Tyr147 Glu15 Glu40 Glu102
Glu112 Glu151 Pro16 Pro41 Pro103 Pro113 Pro152 Val17 Val42 Val104
Val114 Val153 Lys18 Lys43 Lys105 Lys115 Lys154 Leu21 Leu46 Leu108
Leu118 Leu157 Phe22 Phe47 Phe109 Phe119 Phe158 Tyr23 Tyr48 Tyr110
Tyr120 Tyr159 Lys26 Lys51 Lys113 Lys123 Lys162 Gly28 Gly53 Gly115
Gly125 Gly164 Thr30 Thr55 Thr117 Thr127 Thr166 Ser31 Ser56 Ser118
Ser128 Ser167 Thr32 Thr57 Thr119 Thr129 Thr168 Glu34 Glu59 Glu121
Glu131 Glu170 Ser35 Ser60 Ser122 Ser132 Ser171 Ala37 Ala62 Ala124
Ala134 Ala173 Phe38 Phe63 Phe125 Phe135 Phe174 Pro39 Pro64 Pro126
Pro136 Pro175 Trp41 Trp66 Trp128 Trp138 Trp177 Phe42 Phe67 Phe129
Phe139 Phe178 Ile43 Ile68 Ile130 Ile140 Ile179 Ala44 Ala69 Ala131
Ala141 Ala180 Pro51 Pro77 Pro139 Pro148 Pro187 Ile53 Ile79 Ile141
Ile150 Ile189 Leu54 Leu80 Leu142 Leu151 Leu190 Thr55 Thr81 Thr143
Thr152 Thr191 Glu57 Glu83 Glu145 Glu154 Glu193 Leu58 Leu84 Leu146
Leu155 Leu194 Gly59 Gly85 Gly147 Gly156 Gly195 Thr64 Thr90 Thr152
Thr161 Thr200 Phe66 Phe92 Phe154 Phe163 Phe202 Glu67 Glu93 Glu155
Glu164 Glu203
[0356] Another embodiment of the invention features proteins having
a "SPOIL unique domain". As used herein, a "SPOIL unique domain" is
at least about 134-150 amino acid residues in length and has at
least about 45-50% identity with amino acid residues 66-206 of SEQ
ID NO:105. In another embodiment, the SPOIL unique domain is at
least about 136-148 amino acid residues, preferably about 138-146
amino acid residues, more preferably 140-144 amino acid residues,
and more preferably 141, 142, or 143 amino acid residues in length
and has at least about 55-60%, preferably about 65-70%, and more
preferably about 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 100%
identity with amino acid residues 66-206 of SEQ ID NO:105. In a
preferred embodiment, the SPOIL unique domain is from about amino
acid residues 66-206 of human SPOIL-II shown in SEQ ID NO:105. In
another preferred embodiment, the SPOIL unique domain is from about
amino acid residues 27-167 of human SPOIL-I shown in SEQ ID NO:102.
In yet another preferred embodiment, the SPOIL unique domain is
from about amino acid residues 17-158 of murine SPOIL-II shown in
SEQ ID NO:113.
[0357] Another embodiment of the invention features proteins having
a "SPOIL C-terminal unique domain". As used herein, a "SPOIL
C-terminal unique domain" is at least about 58-78 amino acid
residues in length and has at least about 45-50% identity with
amino acid residues 137-203 of SEQ ID NO:105. In another
embodiment, the SPOIL C-terminal unique domain is at least about
61-74 amino acid residues, preferably about 63-72 amino acid
residues, more preferably 65-70 amino acid residues, and more
preferably 67-68 amino acid residues in length and has about
55-60%, preferably about 65-70%, and more preferably about 75%,
80%, 85%, 90%, 95%, 98%, 99%, or 100% identity with amino acid
residues 137-203 of SEQ ID NO:105. In one embodiment, the
C-terminal unique domain is located within the C-terminal 70 amino
acids of the full-length protein, preferably within the C-terminal
80 amino acid residues of the protein, more preferably within the
C-terminal 90 amino acid residues of the protein, and even more
preferably within the C-terminal 100, 120, 140, 160 or 180 amino
acid residues of the full-length protein. In a preferred
embodiment, the SPOIL C-terminal unique domain is from about amino
acid residues 137-203 of human SPOIL-II shown in SEQ ID NO:105. In
another preferred embodiment, the SPOIL C-terminal unique domain is
from about amino acid residues 98-164 of human SPOIL-I shown in SEQ
ID NO:102. In another preferred embodiment, the SPOIL C-terminal
unique domain is from about amino acid residues 26-93 of murine
SPOIL-I shown in SEQ ID NO:90. In yet another preferred embodiment,
the SPOIL C-terminal unique domain is from about amino acid
residues 88-155 of murine SPOIL-II shown in SEQ ID NO:113.
[0358] Another embodiment of the invention features a protein of
the invention, preferably a SPOIL protein, which contain a signal
sequence. As used herein, a "signal sequence" refers to a peptide
containing about 17 amino acids which occurs at the N-terminus of
secretory proteins and which contains a large number of hydrophobic
amino acid residues. For example, a signal sequence contains at
least about 13-22 amino acid residues, preferably about 15-20 amino
acid residues, more preferably about 16-19 amino acid residues, and
more preferably about 17 amino acid residues, and has at least
about 35-65%, preferably about 38-50%, and more preferably about
40-45% hydrophobic amino acid residues (e.g., Valine, Leucine,
Isoleucine or Phenylalanine). Such a "signal sequence", also
referred to in the art as a "signal peptide", serves to direct a
protein containing such a sequence to a lipid bilayer. For example,
in one embodiment, a SPOIL protein contains a signal sequence
containing about amino acids 1-17 of SEQ ID NO:90.
[0359] In yet another embodiment, a protein of the invention,
preferably a SPOIL protein, encodes a mature protein. As used
herein, the term "mature protein" refers to a protein of the
invention, preferably a SPOIL protein, from which the signal
peptide has been cleaved. In an exemplary embodiment, a mature
SPOIL protein contains amino acid residues 1 to 81 of SEQ ID NO:93.
In a preferred embodiment, a SPOIL protein is a mature SPOIL
protein which includes an IL-1 signature domain. In yet another
embodiment, a SPOIL protein is a mature protein which includes a
SPOIL signature motif and/or a SPOIL C-terminal unique domain.
[0360] Preferred proteins of the present invention, preferably
SPOIL proteins, have an amino acid sequence sufficiently homologous
to the amino acid sequence of SEQ ID NO:90; SEQ ID NO:93; SEQ ID
NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984. As used herein, the term "sufficiently homologous" refers to
a first amino acid or nucleotide sequence which contains a
sufficient or minimum number of identical or equivalent (e.g., an
amino acid residue which has a similar side chain) amino acid
residues or nucleotides to a second amino acid or nucleotide
sequence such that the first and second amino acid or nucleotide
sequences share common structural domains or motifs and/or a common
functional activity. For example, amino acid or nucleotide
sequences which share common structural domains have at least 45%
or 50% identity, preferably 60% identity, more preferably 70%-80%,
and even more preferably 90-95% identity across the amino acid
sequences of the domains and contain at least one and preferably
two structural domains or motifs, are defined herein as
sufficiently homologous. Furthermore, amino acid or nucleotide
sequences which share at least 45% or 50%, preferably 60%, more
preferably 70-80%, or 90-95% identity and share a common functional
activity are defined herein as sufficiently homologous.
[0361] As used interchangeably herein a "SPOIL activity",
"biological activity of SPOIL" or "functional activity of SPOIL",
refers to an activity exerted by a SPOIL protein, polypeptide or
nucleic acid molecule on a SPOIL responsive cell as determined in
vivo, or in vitro, according to standard techniques. In one
embodiment, a SPOIL activity is a direct activity, such as an
association with a target protein, preferably a SPOIL target
molecule (e.g., a cell-surface or internalized IL-1 or SPOIL
receptor). In another embodiment, a SPOIL activity is an indirect
activity, such as inhibiting the synthesis or activity of a second
protein (e.g., a protein of a signal pathway). In a preferred
embodiment, a SPOIL activity is at least one or more of the
following activities: (i) interaction of a SPOIL protein in the
extracellular milieu with a protein molecule on the surface of the
same cell which secreted the SPOIL protein molecule (e.g., a SPOIL
receptor or IL-1 receptor); (ii) interaction of a SPOIL protein in
the extracellular milieu with a protein molecule on the surface of
a different cell from that which secreted the SPOIL protein
molecule (e.g., a SPOIL receptor or IL-1 receptor); (iii) complex
formation between a SPOIL protein and a cell-surface receptor; (iv)
interaction of a SPOIL protein with a target molecule in the
extracellular milieu (e.g., a soluble target molecule); (v)
interaction of the SPOIL protein with an intracellular target
molecule (e.g., interaction with an internalized or endocytosed
receptor or ligand-coupled receptor); and (vi) complex formation
with at least one, preferably two or more, intracellular target
molecules.
[0362] In yet another preferred embodiment, a SPOIL activity is at
least one or more of the following activities: (1) modulating, for
example, antagonizing a signal transduction pathway (e.g., an
IL-1-dependent or SPOIL-dependent pathway; (2) modulating cytokine
production and/or secretion (e.g., production and/or secretion of a
proinflammatory cytokine); (3) modulating lymphokine production
and/or secretion; (4) modulating production of adhesion molecules
and/or cellular adhesion; (5) modulating expression or activity of
nuclear transcription factors; (6) modulating secretion of IL-1;
(7) competing with IL-1 to bind an IL-1 receptor; (8) competing
with a SPOIL protein (e.g., a SPOIL-I or SPOIL-II family member) to
bind a SPOIL receptor; (9) modulating nuclear translocation of
internalized IL-1 or SPOIL receptor or ligand-complexed receptor;
(10) modulating cell proliferation, development or differentiation,
for example, IL-1-stimulated or a SPOIL protein-stimulated
proliferation, development or differentiation (e.g., of an
epithelial cell, for example, a squamous epithelial cell of the
esophagus, or of a skin cell, e.g., a keratinocyte); (11)
modulating cell proliferation, development or differentiation of an
osteogenic cell (e.g., of an osteoclast precursor cell, osteoclast
and/or osteoblast); (12) modulating function of an osteogenic cell
(e.g., osteoblast and/or osteoclast function); (13) modulating bone
formation, bone metabolism and/or bone homeostasis (e.g.,
inhibiting bone resorption); (14) modulating cellular immune
responses; (15) modulating cytokine-mediated proinflammatory
actions (e.g., inhibiting acute phase protein synthesis by
hepatocytes, fever, and/or prostaglandin synthesis, for example
PGE.sub.2 synthesis); and (16) promoting and/or potentiating wound
healing.
[0363] The present invention is based, at least in part, on the
discovery of a family of SPOIL proteins (e.g., SPOIL-I and SPOIL-II
proteins) sharing certain conserved structural features (e.g., a
SPOIL signature motif, an IL-1 signature domain, a SPOIL C-terminal
unique domain). Moreover, it has been discovered that SPOIL
proteins exist as multiple isoforms, presumably due to alternative
splicing of one or more common genes. For example, SPOIL proteins
having internal inserted amino acid segments have been identified
(e.g., human SPOIL-II includes a segment of at least 40 amino acid
residues not appearing in human SPOIL-I). SPOIL proteins have also
been identified which may function as both secreted and
intracellular molecules (e.g., murine SPOIL-I has a signal sequence
which is not found in murine SPOIL-II). Therefore, additional SPOIL
family members can be identified based on the nucleotide and amino
acid sequence information provided herein which, e.g., via
alternative splicing of genomic SPOIL sequences, have unique
combinations of the structural features defined herein. For
example, secreted isoforms of human SPOIL can be identified which
include all, or a portion of the amino acid sequences set forth as
SEQ ID NOs:102 and 105.
[0364] Moreover, SPOIL family members can be identified based on
unique nucleotide and/or amino acid sequences found in one SPOIL
family member as compared to a second SPOIL family member. For
example, a comparison between the nucleotide sequences of murine
SPOIL-I (SEQ ID NO:89) and murine SPOIL-II (SEQ ID NO:112) reveals
that murine SPOIL-II includes a fragment from nucleotides 225 to
364 that is absent from murine SPOIL-I (SEQ ID NO:89). Moreover, a
comparison of the amino acid sequences of murine SPOIL-I (SEQ ID
NO:90) and murine SPOIL-II (SEQ ID NO:113) reveals that murine
SPOIL-II includes a fragment from amino acids 1 to 90 that is
absent from murine SPOIL-I. Accordingly, one embodiment of the
present invention includes an isolated nucleic acid molecule
including nucleotides 225 to 364 of SEQ ID NO:112. In another
embodiment, an isolated nucleic acid molecule of the present
invention includes at least 30 contiguous nucleotides of SEQ ID
NO:112 from nucleotides 225 to 364. In another embodiment, an
isolated nucleic acid molecule of the present invention includes at
least 20-140, 30-130, 40-120, 50-110, 60-100, 70, 80, or 90
contiguous nucleotides of SEQ ID NO:112 from nucleotides 225 to
364. In yet another embodiment, an isolated nucleic acid molecule
of the present invention has at least about 50% identity to
nucleotides 225 to 364 of SEQ ID NO:112. In yet another embodiment,
an isolated nucleic acid molecule has at least 50% identity to at
least 30 contiguous nucleotides of SEQ ID NO:112 from nucleotides
224 to 364. In yet another embodiment, an isolated nucleic acid
molecule of the invention hybridizes under stringent conditions to
nucleotides 225 to 364 of SEQ ID NO:112. In yet another embodiment,
an isolated nucleic acid molecule hybridizes under stringent
conditions to at least 30 contiguous nucleotides of SEQ ID NO:112
from nucleotides 225 to 364.
[0365] Another embodiment of the present invention pertains to a
polypeptide including amino acids 1 to 90 of SEQ ID NO:113. In yet
another embodiment, the polypeptide includes at least 30 contiguous
amino acids of SEQ ID NO:113 from amino acids 1 to 90 of SEQ ID
NO:113. In yet another embodiment, the polypeptide includes at
least 10-90, 20-80, 30-70, 40, 50 or 60 contiguous amino acids of
SEQ ID NO:113 from amino acids 1 to 90. Yet another embodiment of
the invention pertains to a polypeptide having at least 50%
identity to amino acids 1 to 90 of SEQ ID NO:113. In yet another
embodiment, the polypeptide has at least 50% identity to at least
10-90, 20-80, 30-70, 40, 50 or 60 contiguous amino acids of SEQ ID
NO:113 from amino acids 1 to 90. Yet another embodiment of the
present invention features isolated nucleic acid molecules encoding
any of the polypeptides described herein.
[0366] Likewise, a comparison between the nucleic acid sequences of
human SPOIL-I (SEQ ID NO:101) and human SPOIL-II (SEQ ID NO:104)
reveals that human SPOIL-II includes a fragment from nucleotides
153 to 269 that is absent from human SPOIL-I (SEQ ID NO:101).
Moreover, a comparison of the amino acid sequences of human SPOIL-I
(SEQ ID NO:102) and human SPOIL-II (SEQ ID NO:105) reveals that
human SPOIL-II includes a fragment from amino acids 19 to 58 that
is absent from human SPOIL-I. Accordingly, one embodiment of the
present invention includes an isolated nucleic acid molecule
including nucleotides 153 to 269 of SEQ ID NO:112. In another
embodiment, an isolated nucleic acid molecule of the present
invention includes at least 30 contiguous nucleotides of SEQ ID
NO:112 from nucleotides 153 to 269. In another embodiment, an
isolated nucleic acid molecule of the present invention includes at
least 20-140, 30-130, 40-120, 50-110, 60-100, 70, 80, or 90
contiguous nucleotides of SEQ ID NO:104 from nucleotides 153 to
269. In yet another embodiment, an isolated nucleic acid molecule
of the present invention has at least about 50% identity to
nucleotides 153 to 269 of SEQ ID NO:104. In yet another embodiment,
an isolated nucleic acid molecule has at least 50% identity to at
least 30 contiguous nucleotides of SEQ ID NO:104 from nucleotides
224 to 364. In yet another embodiment, an isolated nucleic acid
molecule of the invention hybridizes under stringent conditions to
nucleotides 153 to 269 of SEQ ID NO:104. In yet another embodiment,
an isolated nucleic acid molecule hybridizes under stringent
conditions to at least 30 contiguous nucleotides of SEQ ID NO:104
from nucleotides 153 to 269.
[0367] Another embodiment of the present invention includes a
polypeptide including amino acids 19 to 58 of SEQ ID NO:105. In yet
another embodiment, the invention features a polypeptide which
includes at least 30 contiguous amino acids of SEQ ID NO:105 from
amino acids 19 to 58 of SEQ ID NO:105. In yet another embodiment,
the polypeptide includes at least 10-90, 20-80, 30-70, 40, 50 or 60
contiguous amino acids of SEQ ID NO:105 from amino acids 19 to 58.
In yet another embodiment, the polypeptide has at least 50%
identity to amino acids 19 to 58 of SEQ ID NO:105. In yet another
embodiment, the polypeptide has at least 50% identity to at least
10-90, 20-80, 30-70, 40, 50 or 60 contiguous amino acids of SEQ ID
NO:105 from amino acids 19 to 58. Yet another embodiment of the
present invention features isolated nucleic acid molecules encoding
any of the polypeptides described herein.
[0368] Given the existence of both secreted and intracellular SPOIL
molecules (e.g., SPOIL-I and II isoforms) described herein, it will
be appreciated that the SPOIL molecules of the present invention
and modulators of SPOIL proteins are useful, for example, in
regulating cellular responses triggered by extracellular events
(e.g., by interaction of, for example, a cytokine (e.g., IL-1) or a
SPOIL protein with a cell surface receptor. For example, it is
known that unbalanced production of IL-1 is associated with the
pathogenesis of various inflammatory diseases. Accordingly, SPOIL
proteins and/or SPOIL modulators may be useful as therapeutic
agents in achieving homeostasis and ameliorating such
imbalances.
[0369] Likewise, it will be appreciated that the SPOIL molecules of
the present invention and modulators of SPOIL proteins are useful
in regulating cytokine (e.g., IL-1) and/or SPOIL protein dependent
intracellular responses (e.g., acting as intracellular antagonists
or agonists). For example, it is known that cytokines (e.g., IL-1)
are not secreted from certain cell types, for example, skin cells,
e.g., keratinocytes, and accordingly, there exist a discreet subset
of intracellular cytokine-dependent responses and a corresponding
set of intracellular SPOIL protein-dependent activities.
[0370] Moreover, SPOIL molecules of the present invention have been
found to be constitutively expressed, for example, in epithelial
cells, in particular in the squamous epithelium of the esophagus
and the epithelial lining of the mouth (e.g., murine SPOIL-II was
isolated from an esophageal cDNA library). In addition, expression
of SPOIL molecules can also be induced in certain cell types and
tissues. For example, the human SPOILs were isolated from a
stimulated keratinocyte library and human SPOIL-I was expressed in
keratinocytes induced with PMA, ionomycin, TNF and cyclohexamide.
In addition, human SPOIL-I was observed in monocytic cells
stimulated with LPS and expression of SPOIL-I was induced in the
kidneys of lippopolysaccharide (LPS)-injected mice. Furthermore,
expression has been correlated with certain proliferative
disorders. For example, human SPOIL-I was found to be expressed on
human esophageal tumor samples and overexpressed in squamous cell
carcinoma of the esophagus. It has further been demonstrated that a
secreted form of SPOIL (e.g., murine SPOIL-I), when expressed in
vivo, caused impairment of osteoclast differentiation and/or
function as well as evidence of impaired bone resorption (see
EXAMPLE 25).
[0371] Accordingly, in another embodiment of the invention, a SPOIL
molecule or preferably, a SPOIL modulator, is useful for
regulating, preventing and/or treating at least one or more of the
following diseases or disorders: (1) inflammatory diseases and
disorders including, but not limited to, inflammation, septic
shock, arthritis, intercolitis, and pneumonitis; (2) epithelial
cell and/or skin diseases and disorders including, but not limited
to proliferative disorders (e.g., skin cancers including, but not
limited to, melanoma, and Kaposi's sarcoma, and other epithelial
cancers including squamous cell carcinoma, esophageal cancer and
cancer of the mouth and/or throat); (3) bone-related and/or bone
resorption disorders including, but not limited to osteoporosis,
Paget's disease, osteoarthritis, degenerative arthritis,
osteogenesis imperfecta, fibrous displasia, hypophosphatasia, bone
sarcoma, myeloma bone disorder (e.g., osteolytic bone lesions) and
hypercalcemia; and (4) diseases and disorders that involve the
bowel and are characterized by the production of inflammation and
at times, ulceration in the small or large bowel, including but not
limited to, inflammatory bowl disease (IBD) (e.g., Crohn's disease,
irritable bowel syndrome (IBS) and ulcerative colitis). Moreover,
it will be appreciated that the SPOIL molecules and SPOIL
modulators are useful for the following purposes: (1) regulation of
bone mass (e.g., increase bone mass and/or inhibit bone loss); (2)
management of bone fragility (e.g., decrease bone fragility); and
(3) prevention and/or treatment of bone pain, bone deformities,
and/or bone fractures.
[0372] Another embodiment of the invention features isolated SPOIL
proteins and polypeptides having a conserved SPOIL structural
feature and a SPOIL activity, as defined herein. Preferred SPOIL
proteins have an IL-1 signature domain and a SPOIL activity. In one
embodiment, the SPOIL protein has a signal peptide, an IL-1
signature domain, and a SPOIL activity. In another preferred
embodiment, the SPOIL protein has a signal peptide, an IL-1
signature domain, a SPOIL activity, and an amino acid sequence
sufficiently homologous to an amino acid sequence of SEQ ID NO:90;
SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid
sequence encoded by the DNA insert of the plasmid deposited with
ATCC as Accession Number 98883, or the amino acid sequence encoded
by the DNA insert of the plasmid deposited with ATCC as Accession
Number 98984.
[0373] Another embodiment of the invention features isolated SPOIL
proteins and polypeptides having a SPOIL activity, a SPOIL
signature motif (short or long form) and/or SPOIL unique domain. In
another embodiment, the SPOIL protein has a SPOIL activity, a SPOIL
signature motif (short or long form) and/or SPOIL C-terminal unique
domain. In another preferred embodiment, the SPOIL protein has a
SPOIL activity, a SPOIL signature motif (short or long form) and/or
SPOIL C-terminal unique domain, and an amino acid sequence
sufficiently homologous to an amino acid sequence of SEQ ID NO:90;
SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid
sequence encoded by the DNA insert of the plasmid deposited with
ATCC as Accession Number 98883, or the amino acid sequence encoded
by the DNA insert of the plasmid deposited with ATCC as Accession
Number 98984. The above-described SPOIL proteins can further
include an IL-1 signature domain as described herein.
[0374] In a particularly preferred embodiment, the SPOIL protein
and nucleic acid molecules of the present invention are human SPOIL
molecules. A nucleotide sequence of the isolated human SPOIL-I cDNA
and the predicted amino acid sequence of the human SPOIL-I protein
are shown in SEQ ID NOs:101 and 102, respectively. In addition, the
nucleotide sequence corresponding to the coding region of the human
SPOIL-I cDNA (nucleotides 124 to 630) is represented as SEQ ID
NO:103.
[0375] The human SPOIL-I cDNA, which is approximately 1291
nucleotides in length, encodes a protein which is approximately 169
amino acid residues in length. A plasmid containing the full length
nucleotide sequence encoding human SPOIL-I (clone designation
Epjthkf 035f11) was deposited under the provisions of the Budapest
Treaty with the American Type Culture Collection (ATCC), presently
in Manassas, Va., on Sep. 11, 1998 and assigned Accession Number
98883. The human SPOIL-I protein contains an IL-1 signature domain,
which can be found, for example, from about amino acids 130 to 151
of SEQ ID NO:102 (Leu130 to Leu151 of the human SPOIL-I amino acid
sequence). The human SPOIL-I protein further contains a SPOIL
signature motif, which can be found, for example, from about amino
acids 98-141 (short) of from about 98-164 (long) of SEQ ID NO:102
(Gln98 to Ala141 or Gln98 to Glu164 of the human SPOIL-I amino acid
sequence). A SPOIL C-terminal unique domain can be found in the
human SPOIL-I protein, for example, from about amino acid residues
98-164 of SEQ ID NO:102 (Gln98 to Glu164 of the human SPOIL-I amino
acid sequence).
[0376] A nucleotide sequence of the isolated human SPOIL-II cDNA
and the predicted amino acid sequence of the human SPOIL-II protein
are shown in SEQ ID NOs:106 and 107, respectively. In addition, the
nucleotide sequence corresponding to the coding region of the human
SPOIL-II cDNA (nucleotides 98-721) is represented as SEQ ID
NO:106.
[0377] The human SPOIL-II cDNA, which is approximately 1377
nucleotides in length, encodes a protein which is approximately 208
amino acid residues in length. A plasmid containing the full length
nucleotide sequence encoding human SPOIL-II (clone designation
Epjthkf 074e01) was deposited under the provisions of the Budapest
Treaty with the American Type Culture Collection (ATCC), presently
in Manassas, Va., on Nov. 11, 1998 and assigned Accession Number
98984. The human SPOIL-II protein contains an IL-1 signature
domain, which can be found, for example, from about amino acids
169-190 of SEQ ID NO:102 (Leu169 to Leu190 of the human SPOIL-II
amino acid sequence). The human SPOIL-II protein further contains a
SPOIL signature motif, which can be found, for example, from about
amino acids 137-180 (short) of from about 137-203 (long) of SEQ ID
NO:105 (Gln137 to Ala180 or Gln137 to Glu203 of the human SPOIL-II
amino acid sequence). A SPOIL C-terminal unique domain can be found
in the human SPOIL-II protein, for example, from about amino acid
residues 137-203 of SEQ ID NO:105 (Gln137 to Glu203 of the human
SPOIL-II amino acid sequence), having 100% identity to the SPOIL
C-terminal unique domain of human SPOIL-I.
[0378] In another embodiment, the SPOIL protein and nucleic acid
molecules of the present invention are murine SPOIL molecules. A
nucleotide sequence of the isolated murine SPOIL-I cDNA and the
predicted amino acid sequence of the murine SPOIL-I protein are
shown in SEQ ID NOs:89 and 90, respectively. In addition, the
nucleotide sequences corresponding to the coding region of the
murine SPOIL-I cDNA (nucleotides 135-428) and the SPOIL-I cDNA
encoding the mature SPOIL-I protein are represented as SEQ ID NO:91
and SEQ ID NO:92, respectively.
[0379] The murine SPOIL-I cDNA (set forth in SEQ ID NO:89), which
is approximately 746 nucleotides in length, encodes a protein
having a molecular weight of approximately 10.96 kD (with signal
sequence) and 9.1 kD (without signal sequence) and which is
approximately 98 amino acid residues in length (SEQ ID NO:90). The
murine SPOIL-I protein contains an IL-1 signature domain as defined
herein, which can be found, for example, from about amino acids 58
to 80 of SEQ ID NO:90 and, for example, from about amino acids
41-63 of SEQ ID NO:93. The murine SPOIL-I protein further contains
a SPOIL signature motif, which can be found, for example, from
about amino acids 26-69 (short) of from about 26-93 (long) of SEQ
ID NO:90 (Gln26 to Ala69 or Gln26 to Glu93 of the murine SPOIL-I
amino acid sequence). A SPOIL C-terminal unique domain can be found
in the murine SPOIL-I protein, for example, from about amino acid
residues 26-93 of SEQ ID NO:105 (Gln26 to Glu93 of the murine
SPOIL-I amino acid sequence), having 52.2% identity to the SPOIL
C-terminal unique domain of human SPOIL-I. (Comparison can be made
using, for example, the Lipman-Pearson Algorithm (Lipman and
Pearson (1985) Science 227:1435-1441, with a K-tuple of 2, a Gap
Penalty of 4, and a Gap Weight Penalty of 12. In addition, the
murine SPOIL-I protein can contain a signal sequence. A signal
sequence can be found at least, for example, from about amino acids
1-17 of SEQ ID NO:90. The prediction of such a signal peptide can
be made, for example, utilizing the computer algorithm SignalP
(Henrik, et al. (1997) Protein Engineering 10:1-6).
[0380] The entire amino acid sequence of SEQ ID NO:90 was subcloned
into retroviral vector MSCVneo (Hawley, et al. (1994) Gene Therapy
1:136-138) and used for retroviral delivery. Bone marrow infected
with the retroviral vector expressing murine SPOIL-I was
transplanted into irradiated mice recipients. Bones removed from
these mouse recipients, histologically, appeared thicker than the
bones of control mice. In addition, spleen cells (i.e., a source of
osteoclast progenitors) which were removed from mice recipients and
were cultured on a bone marrow cell line, demonstrated reduced
osteoclast production than the spleen cells of control mice. These
experiments are discussed in further detail herein.
[0381] According to in situ analysis of mouse tissues, in the
tissues tested, SPOIL-I mRNA transcript is expressed almost
exclusively in the squamous cell epithelium of the esophagus and in
the epithelial lining of the mouth. Northern blot analysis of human
tissues confirms this pattern of SPOIL expression with transcripts
being detected in esophagus with expression also likely in the
trachea, among the tissues tested. In addition, SPOIL is also
present on human esophageal tumor samples and overexpressed in
moderately differentiated squamous cell carcinoma of the
esophagus.
[0382] A multiple sequence alignment of the amino acid sequences of
murine SPOIL-I with murine IL-1ra (Swiss-Prot.TM. Accession No.
P25085) (SEQ ID NO:98), as well as murine IL-1.alpha.
(Swiss-Prot.TM. Accession No. P01582) (SEQ ID NO:99) and murine
IL-1.beta. (Swiss-Prot.TM. Accession No. P10749) (SEQ ID NO:100)
was generated using MegAlign.TM. sequence alignment software (refer
to FIG. 4).
[0383] A nucleotide sequence of the isolated murine SPOIL-II cDNA
and the predicted amino acid sequence of the murine SPOIL-II
protein are shown in SEQ ID NOs:112 and 113, respectively. In
addition, the nucleotide sequences corresponding to the coding
region of the murine SPOIL-II cDNA (nucleotides 96-575) is
represented as SEQ ID NO:114.
[0384] The murine SPOIL-II cDNA (set forth in SEQ ID NO:112), which
is approximately 838 nucleotides in length, encodes a protein which
is approximately 160 amino acid residues in length (SEQ ID NO:113).
The murine SPOIL-II protein contains an IL-1 signature domain as
defined herein, which can be found, for example, from about amino
acids 120 to 142 of SEQ ID NO:113. The murine SPOIL-II protein
further contains a SPOIL signature motif, which can be found, for
example, from about amino acids 88-131 (short) of from about 88-155
(long) of SEQ ID NO:113 (Gln88 to Ala131 or Gln88 to Glu155 of the
murine SPOIL-II amino acid sequence). A SPOIL C-terminal unique
domain can be found in the murine SPOIL-II protein, for example,
from about amino acid residues 88-155 of SEQ ID NO:113 (Gln88 to
Glu155 of the murine SPOIL-II amino acid sequence), having 52.2%
identity to the SPOIL C-terminal unique domain of human
SPOIL-I.
[0385] A multiple sequence alignment of the amino acid sequences of
human SPOIL-I (corresponding to amino acid residues 1-169 of SEQ ID
NO:102), human SPOIL-II (corresponding to amino acid residues 1-208
of SEQ ID NO:105), murine SPOIL-I (corresponding to amino acid
residues 1-98 of SEQ ID NO:90), and murine SPOIL-II (corresponding
to amino acid residues 1-160 of SEQ ID NO:113) is shown in FIG.
6.
[0386] A multiple sequence alignment of the amino acid sequences of
murine SPOIL-I, murine SPOIL-II, human SPOIL-I, and human SPOIL-II
with murine IL-1ra (Swiss-Prot.TM. Accession No. P25085) (SEQ ID
NO:98), as well as murine (Swiss-Prot.TM. Accession No. P01582)
(SEQ ID NO:99) and murine IL-1.beta. (Swiss-Prot.TM. Accession No.
P10749) (SEQ ID NO:100) is shown in FIG. 7. (The alignments of
FIGS. 4, 6, and 7 were generated using MegAlign.TM. sequence
alignment software using the Clustal algorithm). The initial
pairwise alignment parameters are set to a K-tuple of 1, a GAP
penalty of 3, a window of 5, and diagonals saved set to =5. The
multiple alignment parameters are set at a GAP penalty of 10, and a
GAP length penalty of 10.)
NEOKINE
[0387] Cytokines are small peptide molecules produced by a variety
of cells that mediate a wide range of biological activities. Arai
et al. (1990) Annu. Rev. Biochem. 59:783 and Paul and Seder (1994)
Cell 76:241. Through a complex network, cytokines regulate
functions including cellular growth, inflammation, immunity,
differentiation and repair. Mosmann (1991) Curr. Opin. Immunol.
3:311. One superfamily of cytokines, termed the chemokine
superfamily, is a large group of more than 30 small proteins, many
of which play a role in the selective recruitment and activation of
leukocytes during inflammation. Wells and Peitsch (1997) J. Leukoc.
Biol. 61:5. The chemokine superfamily can be subdivided into two
groups based on the arrangement of the first two of four conserved
cysteines, which are either separated by one amino acid (CXC
chemokines) or adjacent (CC chemokines). Baggiolini et al. (1995)
Int. J. Immunopharmacol. 17:2. IL-8 and the other CXC chemokines
act preferentially on neutrophils, while the CC chemokines (MCP-1,
MCP-2, MCP-3, RANTES, MIP-1 alpha and MIP-1 beta) act on monocytes,
but not neutrophils, and have additional activities toward basophil
and eosinophil granulocytes, and T-lymphocytes. Baggiolini et al.,
supra.
[0388] The CXC chemokine family of cytokines display disparate
angiogenic activity depending upon the presence or absence of the
ELR motif, a structural amino acid motif previously found to be
important in receptor:ligand binding on neutrophils. CXC chemokines
containing the ELR motif are potent angiogenic factors, inducing
both in vitro endothelial chemotaxis and in vivo corneal
neovascularization. In contrast, the CXC chemokines that lack the
ELR motif including, PF4, IP-10, and MIG, not only fail to induce
significant in vitro endothelial cell chemotaxis or in vivo corneal
neovascularization, but are found to be potent angiostatic factors
in the presence of CXC chemokines containing the ELR motif.
Strieter et al. (1995) Shock 4:3. The CXC cytokines have a
signature pattern which spans the region that includes the four
conserved cysteine residues. A CXC-signature pattern has been
generated from the consensus of multiple CXC chemokines. The
signature pattern has been assigned Prosite Signature PS00471.
[0389] The present invention is based on the discovery of family of
molecules, referred to herein as NEOKINE protein and nucleic acid
molecules. The NEOKINEs are members of the non-ELR-CXC subfamily of
chemokines (a shortening of chemoattractant cytokines). The
CXC-chemokines display four highly conserved cysteine amino acid
residues, with the first two cysteines separated by one
non-conserved amino acid residue. The cloning of the NEOKINE family
of CXC chemokines revealed at least three atypical features which
distinguish them from previously characterized chemokines. These
are (1) the presence of approximately 5 residues between the third
and fourth conserved cysteine residues which are absent from other
CXC chemokines; (2) the fewest residues preceeding the predicted
amino terminus of the mature form of any naturally-occurring
chemokine; and (3) a general dissimilarity to all other chemokines
in the region between the second and third conserved cysteines.
Phylogenetic analysis of known chemokines (e.g., known CXC as well
as CC chemokines) further demonstrates that NEOKINE is unique from
other chemokines subfamilies identified to date although it is
clearly a related chemokine.
[0390] The family of NEOKINE chemokines described herein include
human, murine, rat and macaque NEOKINE-1. Upon comparison of the
sequences for each species orthologue, it was noticed that the
NEOKINE-1 chemokines displayed a remarkable degree of identity
between orthologues. For example, human NEOKINE-1 is 92% identical
at the amino acid level to murine NEOKINE-1 (as determined using a
Lipman-Pearson algorithm (Lipman and Pearson (1985) Science
227:1435-1441, Ktuple=2, Gap Penalty=4, Gap Length Penalty=12).
[0391] The present invention is also based on the discovery that
NEOKINE is the surrogate ligand for a previously-identified orphan
receptor known in the art as RDC1. RDC1 was first identified as one
of four orphan receptors cloned from a dog thyroid cDNA library
based on homology to the seven-transmembrane helice-containing
G-protein coupled receptors (Libert et al. (1989) Science
244:569-572). Three of these, RDC4, RDC7, and RDC8 have since been
identified as 5-HT.sub.1D, adenosine A.sub.1 and adenosine A.sub.2
receptors, respectively (Maenhaut et al. (1991) Biochem. Biophys.
Res. Commun. 173:1169-1178; Libert et al. (1991) EMBO J.
10:1677-1682; and Maenhaut et al. (1991) Biochem. Biophys. Res.
Commun. 180:1460-1468). A human orthologue of the fourth orphan,
termed GPRN1, was subsequently cloned which was initially proposed
to be the receptor for vasoactive intestinal peptide ("VIP")
(Sreedharan et al. (1991) Proc. Nat'l. Acad. Sci. USA
88:4986-4990). This finding has more recently been refuted (Nagata
et al. (1992) Trends Biochem. Sci. 13:102-103; and Cook et al.
(1992) FEBS Lett. 300:149-152), leaving the receptor orphaned.
Recent reports have characterized the tissue expression of
RDC1/GPRN1 receptor (Law and Rosenzweig (1994) Biochem. Biophys.
Res. Commun. 201:458-465) and have identified and characterized a
murine homologue of RDC1/GPRN1 (Heesen et al. (1998) Immunogenetics
47:364-370).
[0392] Sequence comparison of human and murine RDC1/GPRN1 reveals
that these orthologues exhibit remarkable sequence identity as is
the case with species orthologues of NEOKINE. Moreover,
phylogenetic analysis of chemokine receptors demonstrates that
RDC1/GPRN1 is a unique but distantly related member of the CXC
subfamily of chemokine receptors. Given the remarkable sequence
identity between species orthologues of NEOKINE and between
orthologues of RDC1/GPRN1, as well as the unique positions which
both NEOKINE and RDC1/GPRN1 fall on their respective phylogenetic
trees, it has been determined that the NEOKINE is the surrogate
ligand for the previously orphaned RDC1/GPRN1 receptor.
[0393] The term "family" when referring to the protein and nucleic
acid molecules of the invention is intended to mean two or more
proteins or nucleic acid molecules having a common structural
domain and having sufficient amino acid or nucleotide sequence
homology as defined herein. Such family members can be naturally
occurring and can be from either the same or different species. For
example, a family can contain a first protein of human origin, as
well as other, distinct proteins of human origin or alternatively,
can contain homologues of non-human origin. Members of a family may
also have common functional characteristics.
[0394] In one embodiment, the NEOKINE proteins of the present
invention are proteins having an amino acid sequence of about
75-125, preferably about 80-120, more preferably about 85-115, more
preferably about 90-110, and even more preferably about 95-105
amino acids containing 3-7, preferably 5-6, and more preferably 4
cysteine residues which are conserved between family members. In
another embodiment, a NEOKINE family member is identified based on
the presence of at least one "NEOKINE CXC signature motif" in the
protein or corresponding nucleic acid molecule. As used herein, the
term "NEOKINE CXC signature motif" refers to a protein domain
having an amino acid sequence of about 35-65, preferably about
40-60, more preferably about 45-55 amino acid residues, and even
more preferably at least about 48-50 amino acids containing 3-7,
preferably 5-6, and more preferably 4 cysteine residues which are
conserved between family members, the first three residues of the
NEOKINE CXC signature motif having the sequence C-X-C ("CXC"),
wherein X is any amino acid and C is cysteine. In a preferred
embodiment, a NEOKINE CXC signature motif has the pattern X
(0-2)-C-X-C-X (20-24)-C-X (17-24)-C-X (0-2) (SEQ ID NO:185),
wherein X is any amino acid and C is cysteine. In another preferred
embodiment, a NEOKINE CXC signature motif has the pattern X
(0-2)-C-X-C-X (23, 24)-C-X (20, 21)-C-X (2) (SEQ ID NO:186),
wherein X is any amino acid and C is cysteine. In another preferred
embodiment, a NEOKINE CXC signature motif has the pattern X
(0-2)-C-X-C-X (6,7)-[LIVMFY]-X (2)-[RKSEQ]-X-[LIVM]-X (2)-[LIVM]-X
(8)-C-X (4)-[LIVM] (2)-X (13,14)-C-[LIVM]-X (SEQ ID NO:187). In
another preferred embodiment, a NEOKINE CXC signature motif has the
pattern X (0, 1)-[RK]-C-[RK]-C-X(4)-P-X(4,
5)-[ED]-X(6)-[KR]-X(5)-C-[DE](2)-X[LIVMFY](4)-X (12,13)-H-C[LIVM]-H
(SEQ ID NO:188). The motifs described herein, are described
according to standard Prosite Signature designation (e.g., X (0-2)
designates any amino acid, n=0-2; X (6, 7) designates any amino
acid, n=6 or 7; and [LIVM] indicates any one of Leu, Ile, Val, or
Met. All amino acids are described using universal single letter
abbreviations according to these motifs. In a preferred embodiment,
the N-terminal amino acid of the NEOKINE CXC signature motif is the
N-terminal amino acid of the mature NEOKINE protein:
[0395] Accordingly, in one embodiment, a NEOKINE protein is human
NEOKINE-1 which contains a NEOKINE CXC signature motif containing
about amino acids 25-72 of SEQ ID NO:116 having the sequence CXC at
amino acid residues 25-27, and having 4 conserved cysteine residues
at the positions indicated in FIG. 8. In another embodiment, a
NEOKINE protein is murine NEOKINE-1 which contains a NEOKINE CXC
signature motif containing about amino acids 25-72 of SEQ ID NO:119
having the sequence CXC at amino acid residues 25-27, and having 4
conserved cysteine residues at the positions indicated in FIG. 8.
In another embodiment, a NEOKINE protein is rat NEOKINE-1 which
contains a NEOKINE CXC signature motif containing at least amino
acids 4-51 of SEQ ID NO:122, having 4 conserved cysteine residues
at the positions indicated in FIG. 8. In another embodiment, a
NEOKINE protein is macaque NEOKINE-1 which contains a NEOKINE CXC
signature motif containing at least amino acids 20-67 of SEQ ID
NO:135, having 4 conserved cysteine residues at the positions
indicated in FIG. 8.
[0396] In another embodiment of the invention, a NEOKINE protein
has at least one NEOKINE CXC signature motif and a signal sequence.
As used herein, a "signal sequence" refers to a peptide containing
about 20 amino acids which occurs at the N-terminus of secretory
and integral membrane proteins and which contains a majority of
hydrophobic amino acid residues. For example, a signal sequence
contains at least about 14-28 amino acid residues, preferably about
16-26 amino acid residues, more preferably about 18-24 amino acid
residues, and more preferably about 20-22 amino acid residues, and
has at least about 40-70%, preferably about 50-65%, and more
preferably about 55-60% hydrophobic amino acid residues (e.g.,
Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tyrosine,
Tryptophan, or Proline). Such a "signal sequence", also referred to
in the art as a "signal peptide", serves to direct a protein
containing such a sequence to a lipid bilayer. For example, in one
embodiment, a NEOKINE-1 protein contains a signal sequence of about
amino acids 1-22 of SEQ ID NO:116. In another embodiment, a
NEOKINE-2 protein contains a signal sequence of about amino acids
1-22 of SEQ ID NO:119. In another embodiment, a NEOKINE-2 protein
contains a signal sequence of about amino acids 1-17 of SEQ ID
NO:135.
[0397] Accordingly, one embodiment of the invention features a
NEOKINE protein having at least a NEOKINE CXC signature motif.
Another embodiment features a NEOKINE protein having at least a
NEOKINE CXC signature motif and a signal peptide.
[0398] Preferred NEOKINE molecules of the present invention have an
amino acid sequence sufficiently homologous to the amino acid
sequence of SEQ ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID
NO:125. As used herein, the term "sufficiently homologous" refers
to a first amino acid or nucleotide sequence which contains a
sufficient or minimum number of identical or equivalent (e.g., an
amino acid residue which has a similar side chain) amino acid
residues or nucleotides to a second amino acid or nucleotide
sequence such that the first and second amino acid or nucleotide
sequences share common structural domains and/or a common
functional activity. For example, amino acid or nucleotide
sequences which share common structural domains have at least about
50% homology, preferably 60% homology, more preferably 70%-80%, and
even more preferably 90-95% homology across the amino acid
sequences of the domains and contain at least one and preferably
two structural domains, are defined herein as sufficiently
homologous. Furthermore, amino acid or nucleotide sequences which
share at least 50%, preferably 60%, more preferably 70-80, or
90-95% homology and share a common functional activity are defined
herein as sufficiently homologous.
[0399] As used interchangeably herein, an "NEOKINE activity",
"biological activity of NEOKINE" or "functional activity of
NEOKINE", refers to an activity exerted by a NEOKINE protein,
polypeptide or nucleic acid molecule on a NEOKINE responsive cell
as determined in vivo, or in vitro, according to standard
techniques. In one embodiment, a NEOKINE activity is a direct
activity, such as an association with a NEOKINE-target molecule. As
used herein, a "target molecule" or "binding partner" is a molecule
with which a NEOKINE protein binds or interacts in nature, such
that NEOKINE-mediated function is achieved. A NEOKINE target
molecule can be a non-NEOKINE molecule or a NEOKINE protein or
polypeptide of the present invention. In an exemplary embodiment, a
NEOKINE target molecule is a carbohydrate molecule on the cell
membrane (e.g., heparan sulfate). In another exemplary embodiment,
a NEOKINE target molecule is a membrane-bound protein (e.g., a
"NEOKINE receptor").
[0400] In another embodiment, a NEOKINE target is a membrane-bound
chemokine receptor. In another embodiment, a NEOKINE target is an
protein molecule (e.g., a "NEOKINE binding partner"). In such an
exemplary embodiment, a NEOKINE binding partner can be an
non-NEOKINE protein or a second NEOKINE protein molecule of the
present invention. Alternatively, a NEOKINE activity is an indirect
activity, such as a cellular signaling activity mediated by
interaction of the NEOKINE protein with a second protein (e.g., a
NEOKINE receptor or a receptor specific for another chemokine).
[0401] In one embodiment, a NEOKINE activity is at least one or
more of the following activities: (i) interaction of a NEOKINE
protein with a membrane-bound NEOKINE receptor (e.g., RDC1); (ii)
interaction of a NEOKINE protein with a membrane-bound chemokine
receptor; (iii) indirect interaction of a NEOKINE protein with an
intracellular protein via a membrane-bound NEOKINE receptor (e.g.,
RDC1); (iv) indirect interaction of a NEOKINE protein with an
intracellular protein via a membrane-bound chemokine receptor; (v)
complex formation between a soluble NEOKINE protein and a NEOKINE
binding partner; (vi) inhibition of the interaction of chemokines
(e.g., pro-inflammatory chemokines) by binding to their cognate
receptors; (vii) inhibition of the binding of HIV to HIV
co-receptors; and (vii) inhibition of the binding of HIV to HIV
co-receptors wherein said binding induces subsequent infection of
susceptible cells.
[0402] In another embodiment, a NEOKINE activity is at least one or
more of the following activities: (1) modulation of cellular signal
transduction, either in vitro or in vivo; (2) regulation of gene
transcription in a cell expressing a NEOKINE receptor or a
chemokine receptor; (3) regulation of gene transcription, in a cell
expressing a NEOKINE receptor (e.g., RDC1) or a chemokine receptor,
wherein said cell is involved in angiogenesis or inflammation; (4)
regulation of angiogenesis; (5) regulation of angiogenesis, wherein
said regulation comprises inhibibition of angiogenesis; (6)
regulation of angiogenesis, wherein said regulation comprises
maintenance of angiostasis; (7) regulation of inflammation; (8)
inhibition of chemoattraction (e.g., neutrophil chemoattraction);
and (9) inhibition of pro-inflammatory chemokines by binding to
their cognate receptors.
[0403] In a preferred embodiment of the invention a NEOKINE or
NEOKINE modulator is useful for regulating, preventing and/or
treating at least one or more of the following proliferative
diseases or disorders: (1) cancers of the epithelia (e.g.,
carcinomas of the pancreas, stomach, liver, secretory glands (e.g.,
adenocarcinoma) bladder, lung, breast, skin (e.g., malignant
melanoma), reproductive tract including prostate gland, ovary,
cervix and uterus); (2) cancers of the hematopoietic and immune
system (e.g., leukemias and lymphomas); (3) cancers of the central
nervous, brain system and eye (e.g., gliomas, neuroblastoma and
retinoblastoma); and (4) cancers of connective tissues, bone,
muscles and vasculature (e.g., sarcomas).
[0404] In yet another embodiment of the invention, a NEOKINE or
NEOKINE modulator is useful for regulating, preventing and/or
treating at least one or more of the following diseases or
disorders: (1) inflammation; (2) psoriasis; (3) immune rejection
following skin graft; (4) immune rejection following kidney
transplant; (5) kidney inflammation in acute renal failure; (6)
brain inflammation following stroke or ischaemia; and (7) brain
inflammation following viral infection.
[0405] Accordingly, another embodiment of the invention features
isolated NEOKINE proteins and polypeptides having a NEOKINE
activity. Preferred NEOKINE proteins have at least one NEOKINE CXC
signature motif and a NEOKINE activity. In another preferred
embodiment, a NEOKINE protein further comprises a signal sequence.
In still another preferred embodiment, a NEOKINE protein has a
NEOKINE CXC signature motif, a NEOKINE activity, and an amino acid
sequence sufficiently homologous to an amino acid sequence of SEQ
ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125.
[0406] The human NEOKINE-1 cDNA, which is approximately 1564
nucleotides in length, encodes a protein which is approximately 99
amino acid residues in length. The human NEOKINE-1 protein contains
at least a NEOKINE CXC signature motif. A NEOKINE CXC signature
motif can be found at least, for example, from about amino acids
25-72 of SEQ ID NO:116. The human NEOKINE-1 protein is predicted to
be a secreted protein which further contains a signal sequence at
about amino acids 1-22 of SEQ ID NO:116. The prediction of such a
signal peptide can be made, for example, utilizing the computer
algorithm SIGNALP (Henrik, et al. (1997) Protein Engineering
10:1-6).
[0407] The murine NEOKINE-1 cDNA, which is approximately 1564
nucleotides in length, encodes approximately 99 amino acid residues
of the murine NEOKINE-1 protein. The murine NEOKINE-1 protein
contains a NEOKINE CXC signature motif. A NEOKINE CXC signature
motif can be found at least, for example, from about amino acids
25-72 of SEQ ID NO:119. The murine NEOKINE-1 protein is predicted
to be a secreted protein which further contains a signal sequence
at about amino acids 1-22 of SEQ ID NO:119.
[0408] The rat NEOKINE-1 cDNA, which is approximately 1372
nucleotides in length, encodes approximately 79 amino acid residues
of the rat NEOKINE-1 protein. The rat NEOKINE-1 protein contains a
NEOKINE CXC signature motif. A NEOKINE CXC signature motif
comprises at least about amino acids 4-51 of SEQ ID NO:122. The rat
NEOKINE-1 protein is predicted to be a secreted protein.
[0409] The macaque NEOKINE-1 cDNA, which is approximately 1458
nucleotides, encodes approximately 94 amino acid residues of the
macaque NEOKINE-1 protein. The macaque NEOKINE-1 protein contains a
NEOKINE CXC signature motif. A NEOKINE CXC signature motif
comprises at least about amino acids 20-67 of SEQ ID NO:135. The
macaque NEOKINE-1 protein is predicted to be a secreted protein
which further contains a signal sequence including at least amino
acids 1-17 of SEQ ID NO:135.
TANGO 129
[0410] Members of the tumor necrosis factor (TNF) superfamily and
their receptors, both of which are expressed on activated T cells
and elsewhere, are thought to play an important role in T-cell
activation and stimulation, cell proliferation and differentiation,
as well as apoptosis.
[0411] Proteins that are members of the TNF superfamily initiate
signal transduction by binding to receptors, members of the TNF
receptor (TNFR) superfamily, which lack intrinsic catalytic
activity. This is in marked contrast epidermal growth factor and
platelet-derived growth factor both of which bind to receptors
having an intracellular tyrosine kinase domain which causes
receptor autophosphorylation and initiates downstream
phosphorylation events.
[0412] Members of the TNFR superfamily carry out signal
transduction by interacting with members of the Janus or JAK family
of tyrosine kinases. In turn, JAK family members interact with STAT
(signal transducers and activators of transcription) family
members, a class of transcriptional activators.
[0413] The present invention is based on the discovery of a cDNA
molecule encoding human TANGO129 (T129), a member of the TNF
receptor superfamily.
[0414] A nucleotide sequence encoding a human T129 protein is shown
in SEQ ID NO:137; and SEQ ID NO:139 (open reading frame only). A
predicted amino acid sequence of T129 protein is also shown in SEQ
ID NO:138.
[0415] The T129 cDNA of SEQ ID NO:137, which is approximately 2570
nucleotides long including untranslated regions, encodes a protein
amino acid having a molecular weight of approximately 46 kDa
(excluding post-translational modifications).
[0416] Alignment of the TNFR/NGFR cysteine-rich domain of human
T129 protein (SEQ ID NO:142) with a TNFR/NGFR cysteine-rich domain
consensus derived from a hidden Markov model (PF00020; SEQ ID
NO:5), revealed some similarity.
[0417] An approximately 3.0 kb T129 mRNA transcript is expressed at
a moderate level in peripheral blood leukocytes, spleen, and
skeletal muscle. Lower levels of this transcript were observed in
heart, brain, and placenta. Human T129 is one member of a family of
molecules (the "T129 family") having certain conserved structural
and functional features. The term "family" when referring to the
protein and nucleic acid molecules of the invention is intended to
mean two or more proteins or nucleic acid molecules having a common
structural domain and having sufficient amino acid or nucleotide
sequence identity as defined herein. Such family members can be
naturally occurring and can be from either the same or different
species. For example, a family can contain a first protein of human
origin and a homologue of that protein of murine origin, as well as
a second, distinct protein of human origin and a murine homologue
of that protein. Members of a family may also have common
functional characteristics.
[0418] In one embodiment, a T129 protein includes a TNFR/NGFR
domain having at least about 65%, preferably at least about 75%,
and more preferably about 85%, 95%, or 98% amino acid sequence
identity to the TNFR/NGFR domain of SEQ ID NO:141.
[0419] Preferred T129 polypeptides of the present invention have an
amino acid sequence sufficiently identical to the TNFR/NGFR domain
amino acid sequence of SEQ ID NO:141. As used herein, the term
"sufficiently identical" refers to a first amino acid or nucleotide
sequence which contains a sufficient or minimum number of identical
or equivalent (e.g., an amino acid residue which has a similar side
chain) amino acid residues or nucleotides to a second amino acid or
nucleotide sequence such that the first and second amino acid or
nucleotide sequences have a common structural domain and/or common
functional activity. For example, amino acid or nucleotide
sequences which contain a common structural domain having about 65%
identity, preferably 75% identity, more preferably 85%, 95%, or 98%
identity are defined herein as sufficiently identical.
[0420] As used interchangeably herein a "T129 activity",
"biological activity of T129" or "functional activity of T129",
refers to an activity exerted by a T129 protein, polypeptide or
nucleic acid molecule on a T129 responsive cell as determined in
vivo, or in vitro, according to standard techniques. A T129
activity can be a direct activity, such as an association with or
an enzymatic activity on a second protein or an indirect activity,
such as a cellular signaling activity mediated by interaction of
the T129 protein with a second protein. In a preferred embodiment,
a T129 activity includes at least one or more of the following
activities: (i) interaction with proteins in the T129 signaling
pathway (ii) interaction with a T129 ligand; or (iii) interaction
with an intracellular target protein.
[0421] Accordingly, another embodiment of the invention features
isolated T129 proteins and polypeptides having a T129 activity.
[0422] Yet another embodiment of the invention features T129
molecules which contain a signal sequence. Generally, a signal
sequence (or signal peptide) is a peptide containing about 20 amino
acids which occurs at the extreme N-terminal end of secretory and
integral membrane proteins and which contains large numbers of
hydrophobic amino acid residues and serves to direct a protein
containing such a sequence to a lipid bilayer.
A259
[0423] The A259 proteins and nucleic acid molecules comprise a
family of molecules having certain conserved structural and
functional features. As used herein, the term "family" is intended
to mean two or more proteins or nucleic acid molecules having a
common structural domain and having sufficient amino acid or
nucleotide sequence identity as defined herein. Family members can
be from either the same or different species. For example, a family
can comprises two or more proteins of human origin, or can comprise
one or more proteins of human origin and one or more of non-human
origin. Members of the same family may also have common structural
domains.
[0424] For example, A259 proteins of the invention have signal
sequences. As used herein, a "signal sequence" includes a peptide
of at least about 15 or 20 amino acid residues in length which
occurs at the N-terminus of secretory and membrane-bound proteins
and which contains at least about 70% hydrophobic amino acid
residues such as alanine, leucine, isoleucine, phenylalanine,
proline, tyrosine, tryptophan, or valine. In a preferred
embodiment, a signal sequence contains at least about 10 to 40
amino acid residues, preferably about 15-30 amino acid residues,
more preferably about 22 amino acid residues, and has at least
about 60-80%, more preferably 65-75%, and more preferably at least
about 70% hydrophobic residues. A signal sequence serves to direct
a protein containing such a sequence to a lipid bilayer. Thus, in
one embodiment, an A259 protein contains a signal sequence at about
amino acids 1 to 22 of SEQ ID NO:147 (SEQ ID NO:149). The signal
sequence is cleaved during processing of the mature protein.
[0425] In another example, an A259 family member also includes one
or more of the following domains: (1) an extracellular domain; (2)
a transmembrane domain; and (3) a cytoplasmic domain. Thus, in one
embodiment, an A259 protein contains an extracellular domain at
about amino acids 1 to 1141 of SEQ ID NO:147 (SEQ ID NO:150). In
another embodiment, an A259 protein contains a transmembrane domain
at about amino acids 1142 to 1164 of SEQ ID NO:147 (SEQ ID NO:159).
In another embodiment, an A259 protein contains a cytoplasmic
domain at about amino acids 1165 to 1188 of SEQ ID NO:147 (SEQ ID
NO:160).
[0426] In one embodiment, the extracellular domain of A259 can
include an inserted domain ("I" domain). In another embodiment, the
I domain is located between integrin .alpha.-subunit repeat domains
2 and 3.
[0427] In a preferred embodiment, an A259 family member has the
amino acid sequence of SEQ ID NO:147 wherein the extracellular
domain is located at about amino acids 1 to 1141 (SEQ ID NO:150),
the I domain (SEQ ID NO:151) is located at about amino acid
positions 164 to 345, and the integrin .alpha.-subunit repeat
domains on either side of the I domain (integrin .alpha.-subunit
repeat domains 2 and 3) are located at amino acid positions 115 to
157 (SEQ ID NO:153) and 367 to 392 (SEQ ID NO:154),
respectively.
[0428] An A259 family member can include one or more integrin
.alpha.-subunit repeat domains within the extracellular domain. As
used herein, a "repeat domain" refers to one or more of seven
homologous protein domains that are conserved in integrin
.alpha.-subunit family members, which are about 10 to 65 residues,
preferably about 20 to 50 residues, more preferably about 25 to 45
amino acid residues, and most preferably about 26 to 43 residues,
in length, and which are about 10 to 50, preferably about 15 to 40,
more preferably about 20 to 35 amino acids apart from one
another.
[0429] A repeat domain typically has one of the two following
consensus sequences. The first repeat consensus sequence (type 1)
is: F-G-Xaa(n)-[G or A]-A-[P or L or Q] (SEQ ID NO:189), wherein F
is phenylalanine, G is glycine, Xaa is any amino acid, n is about
10 to 30 amino acid residues, preferably about 15 to 20 amino acid
residues, more preferably about 16 to 19 amino acid residues, A is
alanine, P is proline, L is leucine, and Q is glutamine. The second
repeat consensus sequence (type 2) is: [G or S]-[F or Y]-Xaa(n)-[G
or V or L]-[A or M]-[P or Y] (SEQ ID NO:190), wherein G is glycine,
S is serine, F is phenylalanine, Y is tyrosine, Xaa is any amino
acid, n is about 5 to 40 amino acid residues, preferably about 10
to 35 amino acid residues, more preferably about 14 to 33 amino
acid residues, V is valine, A is alanine, M is methionine, and P is
proline.
[0430] In one embodiment, an A259 family member includes one or
more repeat domains having an amino acid sequence that is at least
about 55%, preferably at least about 65%, more preferably at least
about 75%, yet more preferably at least about 85%, and most
preferably at least about 95% identical to amino acids 39 to 74,
and/or 115 to 157, and/or 367 to 392, and/or 421 to 455, and/or 478
to 516, and/or 540 to 575, and/or 602 to 640 of SEQ ID NO:147,
which are the repeat domains of A259 (these repeat domains are also
represented as SEQ ID NO:152, 153, 154, 155, 156, 157, and 158,
respectively). In another embodiment, an A259 family member
includes one or more repeat domains having an amino acid sequence
that is at least about 55%, preferably at least about 65%, more
preferably at least about 75%, yet more preferably at least about
85%, and most preferably at least about 95% identical to amino
acids 39 to 74, and/or 115 to 157, and/or 367 to 392, and/or 421 to
455, and/or 478 to 516, and/or 540 to 575, and/or 602 to 640 of SEQ
ID NO:147, which are the repeat domains of A259 (these repeat
domains are also represented as SEQ ID NO:152, 153, 154, 155, 156,
157, and 158, respectively), and has one or more repeat consensus
sequences described herein. In another embodiment, an A259 family
member includes one or more repeat domains having an amino acid
sequence that is at least about 55%, preferably at least about 65%,
more preferably at least about 75%, yet more preferably at least
about 85%, and most preferably at least about 95% identical to
amino acids 39 to 74, and/or 115 to 157, and/or 367 to 392, and/or
421 to 455, and/or 478 to 516, and/or 540 to 575, and/or 602 to 640
of SEQ ID NO:147, which are the repeat domains of A259 (these
repeat domains are also represented as SEQ ID NO:152, 153, 154,
155, 156, 157, and 158, respectively), has one or more I consensus
sequences described herein, and has at least one A259 biological
activity as described herein.
[0431] An A259 family member can also include an inserted, or I
domain (also called von Willebrand factor type A domain). As used
herein, an "I domain" refers to a domain that appears in only some
of the integrin .alpha. subunits, e.g., .alpha.1, .alpha.2,
.alpha.M, and .alpha.X, and that is inserted between the second and
third integrin .alpha.-subunit repeat domains. I domains prevent
the occurrence of proteolytic cleavage that separates integrin
.alpha. subunits into heavy and light fragments that are disulfide
linked. An I domain includes about 100 to 300 amino acid residues,
preferably about 150 to 200 amino acid residues, more preferably
about 160 to 190 amino acid residues, and most preferably about 182
amino acid residues.
[0432] An I domain typically has the following consensus sequence:
D-G-S-Xaa-S-Xaa(n1)-F-Xaa(n2)-Q-Y (SEQ ID NO:191), wherein D is
aspartic acid, G is glycine, S is serine, Xaa is any amino acid, n1
is about 5 to 15, preferably about 8 to 12, more preferably about 9
to 11 amino acid residues, F is phenylalanine, n2 is about 15 to
30, preferably 18 to 28, more preferably about 20 to 26 amino acid
residues, Q is glutamine, and Y is tyrosine.
[0433] In one embodiment, an A259 family member includes an I
domain having an amino acid sequence that is at least about 55%,
preferably at least about 65%, more preferably at least about 75%,
yet more preferably at least about 85%, and most preferably at
least about 95% identical to amino acids 164 to 345 of SEQ ID
NO:147, which is the I domain of A259 (this I domain is also
represented as SEQ ID NO:151). In another embodiment, an A259
family member includes an I domain having an amino acid sequence
that is at least about 55%, preferably at least about 65%, more
preferably at least about 75%, yet more preferably at least about
85%, and most preferably at least about 95% identical to amino
acids 164 to 345 of SEQ ID NO:147, which is the I domain of A259
(this I domain is also represented as SEQ ID NO:151), and an I
domain consensus sequence described herein. In another embodiment,
an A259 family member includes an I domain having an amino acid
sequence that is at least about 55%, preferably at least about 65%,
more preferably at least about 75%, yet more preferably at least
about 85%, and most preferably at least about 95% identical to
amino acids 164 to 345 of SEQ ID NO:147, which is the I domain of
A259 (this I domain is also represented as SEQ ID NO:151). In
another embodiment, an A259 family member includes an I domain
having an amino acid sequence that is at least about 55%,
preferably at least about 65%, more preferably at least about 75%,
yet more preferably at least about 85%, and most preferably at
least about 95% identical to amino acids 164 to 345 of SEQ ID
NO:147, which is the I domain of A259 (this I domain is also
represented as SEQ ID NO:151), has one or more I domain consensus
sequences described herein, and has at least one A259 biological
activity as described herein.
[0434] An A259 family member can also include a cytoplasmic domain.
The cytoplasmic domain typically includes about 10 to 40,
preferably about 20 to 30, more preferably about 22 to 28, still
more preferably about 22 to 26 amino acid residues in length. The
A259 cytoplasmic domain typically has the following consensus
sequence: [F or Y or W or S]-[R or K]-Xaa(n1)-G-F-F-Xaa(n2)-R (SEQ
ID NO:192), wherein F is phenylalanine, Y is tyrosine, W is
tryptophan, S is serine, R is arginine, K is lysine, Xaa is any
amino acid, n1 and n2 are 0 to 1, and G is glycine.
[0435] In a preferred embodiment, an A259 family member has the
amino acid sequence of SEQ ID NO:147 wherein the cytoplasmic domain
is located at about amino acids 1165 to 1188 (SEQ ID NO:160) and
the cytoplasmic domain consensus sequence is located from about
amino acid 1165 to 1170.
[0436] Various features of human and murine A259 are summarized
below.
Human A259
[0437] A cDNA encoding human A259 was identified by analyzing the
sequences of clones present in an LPS stimulated human primary
osteoblast cDNA library. This analysis led to the identification of
a clone, Atho002i17, encoding full-length human A259. The human
A259 cDNA of this clone is 5042 nucleotides long (SEQ ID NO:145).
The open reading frame of this cDNA, nucleotides 127 to 3690 of SEQ
ID NO:145 (SEQ ID NO:146), encodes a 1188 amino acid receptor
protein (SEQ ID NO:147).
[0438] The signal peptide prediction program SIGNALP (Nielsen et
al. (1997) Protein Engineering 10:1-6) predicted that human A259
includes a 22 amino acid signal peptide (amino acid 1 to about
amino acid 22 of SEQ ID NO:147; SEQ ID NO:149) preceding the mature
A259 protein (corresponding to about amino acid 23 to amino acid
1188 of SEQ ID NO:147) (SEQ ID NO:148). The human A259 protein
molecular weight is 133.5 kDa prior to the cleavage of the signal
peptide, 131.1 kDa after cleavage of the signal peptide.
[0439] Human A259 includes a extracellular domain (about amino
acids 1 to 1141 of SEQ ID NO:147; SEQ ID NO:150), an I domain (also
called a Von Willebrand Factor type A domain; about amino acids 164
to 345 of SEQ ID NO:147; SEQ ID NO:151), seven repeat domains
(about amino acids 39 to 74, 115 to 157, 367 to 392, 421 to 455,
478 to 516, 540 to 575, and 602 to 640 of SEQ ID NO:147 (SEQ ID
NO:152, 153, 154, 155, 156, 157, and 158, respectively)), a
transmembrane domain (about amino acids 1142 to 1164 of SEQ ID
NO:147; SEQ ID NO:159), and a cytoplasmic domain (about amino acids
1165 to 1188 of SEQ ID NO:147; SEQ ID NO:160).
[0440] A slightly different model of the integrin alpha repeat
domain identifies five integrin alpha repeat domains within human
A259 (about amino acids 37-90, 421-472, 476-532, 538-593, and
600-654 of SEQ ID NO:147 (SEQ ID NOS:179, 180, 181, 182, and 183,
respectively)). These domains were identified by homology searching
using consensus domains derived from hidden Markov models (HMMs).
HMMs can be used to do multiple sequence alignment and very
sensitive database searching, using statistical descriptions of a
sequence family's consensus. FIG. 12A depicts an alignment of amino
acids 37-90 of human A259 (SEQ ID NO:179) with a consensus integrin
alpha repeat domain derived from a hidden Markov model (SEQ ID
NO:184). FIG. 12B depicts an alignment of amino acids 421-472 of
human A259 (SEQ ID NO:180) with a consensus integrin alpha repeat
domain derived from a hidden Markov model (SEQ ID NO:184). FIG. 12C
depicts an alignment of amino acids 476-532 of human A259 (SEQ ID
NO:181) with a consensus integrin alpha repeat domain derived from
a hidden Markov model (SEQ ID NO:184). FIG. 12D depicts an
alignment of amino acids 538-593 of human A259 (SEQ ID NO:182) with
a consensus integrin alpha repeat domain derived from a hidden
Markov model (SEQ ID NO:184). FIG. 12E depicts an alignment of
amino acids 600-654 of human A259 (SEQ ID NO:183) with a consensus
integrin alpha repeat domain derived from a hidden Markov model
(SEQ ID NO:184).
[0441] Predicted N-glycosylation sites are found from amino acids
82 to 85, 95 to 98, 291 to 294, 331 to 334, 358 to 361, 449 to 452,
462 to 465, 528 to 531, 642 to 645, 694 to 697, 857 to 860, 894 to
897, 973 to 976, 1031 to 1034, 1039 to 1042 and 1059 to 1062 of SEQ
ID NO:147. A cAMP and cGMP-dependent protein kinase phosphorylation
site is found from amino acids 700 to 703 of SEQ ID NO:147.
[0442] Predicted protein kinase C phosphorylation sites are found
from amino acids 27 to 29, 97 to 99, 221 to 223, 287 to 289, 355 to
357, 434 to 436, 451 to 453, 530 to 532, 548 to 550, 587 to 589,
662 to 664, 703 to 705, 716 to 718, 770 to 772, 833 to 835, 938 to
940, 1092 to 1094, 1100 to 1102, 1171 to 1173 and 1183 to 1185 of
SEQ ID NO:147.
[0443] Predicted casein kinase II phosphorylation sites are found
from amino acids 161 to 164, 221 to 224, 230 to 233, 270 to 273,
287 to 290, 322 to 325, 485 to 488, 530 to 533, 548 to 551, 556 to
559, 593 to 596, 662 to 665, 696 to 669, 724 to 727, 753 to 756,
801 to 804, 938 to 941, 966 to 969, 974 to 977, 1046 to 1049, 1061
to 1064 and 1133 to 1136 of SEQ ID NO:147.
[0444] A predicted tyrosine kinase phosphorylation site is found
from amino acids 812 to 820 of SEQ ID NO:147.
[0445] Predicted N-myristoylation sites are found from amino acids
6 to 11, 35 to 40, 106 to 111, 236 to 241, 245 to 250, 257 to 262,
354 to 359, 363 to 368, 379 to 384, 422 to 427, 473 to 478, 481 to
486, 543 to 548, 625 to 630, 690 to 695, 725 to 730, 877 to 882,
930 to 935 and 1147 to 1152 of SEQ ID NO:147.
[0446] A predicted amidation site is found from amino acids 257 to
260 of SEQ ID NO:147. An immunoglobulin and major
histocompatibility complex proteins signature is found from amino
acids 74 to 80 of SEQ ID NO:147.
[0447] Human A259 is homologous to human integrin .alpha.10 (SEQ ID
NO:161; GenBank Accession Number AF074015), a .beta.1-associated
collagen binding integrin (Camper, Hellman, and Lundgren-Akerlund
(1998) Journal of Biol. Chem. 273, 32:20383-20389). The human A259
signal sequence is represented by amino acids 1 to 22 (and encoded
by nucleotides 127 to 192 of SEQ ID NO:145). The human .alpha.10
integrin signal sequence is represented by amino acids 1 to 22 (and
encoded by nucleotides 22 to 87 of SEQ ID NO:161). The human A259
extracellular domain sequence (SEQ ID NO:150) is represented by
amino acids 1 to 1141 (and encoded by nucleotides 127 to 3549 of
SEQ ID NO:145), and the human .alpha.10 extracellular domain
sequence is represented by amino acids 1 to 1098 (and encoded by
nucleotides 22 to 3381 of SEQ ID NO:161). The human A259 I domain
(SEQ ID NO:151) is represented by amino acids 164 to 345 (and
encoded by nucleotides 616 to 1161 of SEQ ID NO:145), and the human
.alpha.10 I domain is represented by amino acids 140 to 337 (and
encoded by nucleotides 505 to 1098 of SEQ ID NO:161). The human
A259 transmembrane domain (SEQ ID NO:159) is represented by amino
acids 1142 to 1164 (and encoded by nucleotides 3550 to 3618 of SEQ
ID NO:145), and the human .alpha.10 transmembrane domain is
represented by amino acids 1099 to 1123 (and encoded by nucleotides
3382 to 3456 of SEQ ID NO:161). The human A259 cytoplasmic domain
(SEQ ID NO:160) is represented by amino acids 1165 to 1188 (and
encoded by nucleotides 3619 to 3690 of SEQ ID NO:145), and the
human .alpha.10 cytoplasmic domain is represented by amino acids
1124 to 1145 (and encoded by nucleotides 3457 to 3522 of SEQ ID
NO:161).
[0448] Alignments have shown that there is an overall 46.3%
identity between the full length human A259 nucleic acid molecule
and the full length human .alpha.10 molecule, and a 43.0% identity
between the A259 amino acid sequence and the human .alpha.10 amino
acid sequence. There is also a 55.1% identity between the human
A259 and the human .alpha.10 open reading frames. There is also an
overall 37.6% amino acid identity, and a 41.5% full length nucleic
acid identity, between the full length human A259 nucleic acid
molecule and the full length human .alpha.1 (VLA-1 (very late
antigen-1) molecule.
[0449] Human A259 is homologous to murine A259. The human A259
signal sequence is represented by amino acids 1 to 22 (and encoded
by nucleotides 127 to 192 of SEQ ID NO:145). The murine A259 signal
sequence is represented by amino acids 1 to 22 (and encoded by
nucleotides 28 to 93 of SEQ ID NO:163). The human A259
extracellular domain sequence (SEQ ID NO:150) is represented by
amino acids 1 to 1141 (and encoded by nucleotides 127 to 3549 of
SEQ ID NO:145), and the murine A259 extracellular domain sequence
is represented by amino acids 1 to 1141 (and encoded by nucleotides
28 to 3450 of SEQ ID NO:163). The human A259 I domain (SEQ ID
NO:151) is represented by amino acids 164 to 345 (and encoded by
nucleotides 616 to 1161 of SEQ ID NO:145), and the murine A259 I
domain is represented by amino acids 164 to 345 (and encoded by
nucleotides 517 to 1062 of SEQ ID NO:163). The human A259 repeat
domains are represented by amino acids 39 to 74, 115 to 157, 367 to
392, 421 to 455, 478 to 516, 540 to 575, and 602 to 640 (and
encoded by nucleotides 244 to 348, 469 to 597, 1225 to 1302, 1387
to 1491, 1558 to 1674, 1744 to 1851, and 1930 to 2046,
respectively, of SEQ ID NO:145), and the murine A259 repeat domains
are represented by amino acids 39 to 74, 115 to 157, 367 to 392,
421 to 455, 478 to 516, 540 to 575, and 602 to 640 (and encoded by
nucleotides 145 to 249, 370 to 498, 1126 to 1203, 1288 to 1392,
1459 to 1575, 1645 to 1752, and 1831 to 1947, respectively, of SEQ
ID NO:163). The human A259 transmembrane domain (SEQ ID NO:159) is
represented by amino acids 1142 to 1164 (and encoded by nucleotides
3550 to 3618 of SEQ ID NO:145), and the murine A259 transmembrane
domain is represented by amino acids 1142 to 1164 (and encoded by
nucleotides 3283 to 3357 of SEQ ID NO:163). The human A259
cytoplasmic domain (SEQ ID NO:160) is represented by amino acids
1165 to 1188 (and encoded by nucleotides 3619 to 3690 of SEQ ID
NO:145), and the murine A259 cytoplasmic domain is represented by
amino acids 1165 to 1188 (and encoded by nucleotides 3358 to 3423
of SEQ ID NO:163).
[0450] Alignments show that there is an overall 78.4% identity
between the full length human A259 nucleic acid molecule and the
full length murine A259 molecule, and a 90.3% identity between the
A259 amino acid sequence and the murine A259 amino acid sequence.
There is also an 86.8% identity between the human and murine A259
open reading frames.
[0451] Clone Human I2, which encodes human A259, was deposited with
the American Type Culture Collection (10801 University Boulevard,
Manassas, Va. 20110-2209) on Apr. 2, 1999 and assigned Accession
Number 207190. This deposit will be maintained under the terms of
the Budapest Treaty on the International Recognition of the Deposit
of Microorganisms for the Purposes of Patent Procedure. This
deposit was made merely as a convenience for those of skill in the
art and is not an admission that a deposit is required under 35
U.S.C. 112.
[0452] FIG. 10 depicts a hydropathy plot of human A259. Relatively
hydrophobic regions of the protein are shown above the horizontal
line, and relatively hydrophilic regions of the protein are below
the horizontal line. The cysteine residues (cys) and predicted
N-glycosylation sites are indicated by short vertical lines just
below the hydropathy trace. The dashed vertical line separates the
signal sequence (amino acids 1 to 22 of SEQ ID NO:147; SEQ ID
NO:149) on the left from the mature protein (amino acids 23 to 1188
of SEQ ID NO:147; SEQ ID NO:148) on the right. The A259
transmembrane domain is indicated by the section of the plot under
which the number 6.4 can be seen, which represents a score assigned
to the predicted transmembrane domain. The extracellular domain
(SEQ ID NO:150) and cytoplasmic domain (SEQ ID NO:160) are
similarly indicated by gray horizontal bars, labeled as "out" and
"in", respectively.
[0453] An electronic survey of proprietary databases revealed that
A259 is found in abundantly in human and mouse osteoblast cDNA
libraries and also in human bone marrow and neuronal cDNA
libraries. In addition, in a Northern blot containing RNA from
human tissues, A259 was expressed as two messages, a 6 kb and a 4
kb message, in RNA from human osteoblasts. The sequence used to
probe this human Northern blot contained human A259 C-terminal and
3' untranslated regions. The expression level in human osteoblasts
did not change when stimulated with TNF-.alpha..
[0454] The expression of human A259 was measured in various
clinical liver samples taken from subjects not suffering from liver
fibrosis and from patients suffering from liver fibrosis using
TaqMan quantitative PCR. The results of this analysis are depicted
in FIG. 13A. Human A259 was expressed at a lower level in the
livers of patients not suffering from liver fibrosis (A, B, and C;
relative expression 0.13, 0.29, and 0.09, respectively) than in the
livers of patients suffering from liver fibrosis (D, E, F, G, H, I,
J, and K; relative expression 1.59, 0.50, 0.55, 1.56, 0.62, 0.93,
3.54, and 0.61, respectively).
[0455] The expression of human A259 was measured in various cells
using TaqMan quantitative PCR. The results of this analysis are
depicted in FIG. 13B. The cells tested were: heart (A; relative
expression 1.69), lung (B; relative expression 0.41), liver (C;
relative expression 0.10), passaged stellate cells (D; relative
expression 36.15), quiescent stellate cells (E; relative expression
0.15), stellate cells (F; relative expression 18.71); stellate/F BS
cells (G; relative expression 31.03), NHDF fibroblasts (H; relative
expression 0.71); TGF-treated NHDF fibroblasts (I; relative
expression 12.69); NHLF fibroblasts (J; relative expression 4.81);
and TGF-treated NHLF fibroblasts (K; relative expression
66.06).
[0456] Human A259 maps to human chromosome location hu15q22. The
flanking markers are AFM094YC1 and NIB1778. The nearby known
disease loci include: CLN6 (neuronal ceroid-lipofuscinosis) and
BBS4 (Bardet-Biedl Syndrome 4). The nearby known genes include: HDC
(histidine decarboxylase), LIPC (hepatic lipase), PKM2 (pyruvate
kinase 3), CLN6 (neuronal ceroid-lipofuscinosis), BBS4
(Bardet-Biedl Syndrome 4), and NMB (neuromedin B). The murine
syntenic chromosomal location is mo9. The known nearby loci
include: rc (rough coat), ash (ashen), flail (flailer), pml
(promyelotic leukemia), and sty (small thymus). The known nearby
genes include: hpl (hepatitic lipase).
Murine A259
[0457] A cDNA encoding human A259 was identified by analyzing the
sequences of clones present in a murine bone marrow cDNA library.
This analysis led to the identification of a clone, AtmMa113d1,
encoding full-length murine A259. The murine A259 cDNA of this
clone is 4858 nucleotides long (SEQ ID NO:163). The open reading
frame of this cDNA, nucleotides 28 to 3591 of SEQ ID NO:163 (SEQ ID
NO:164), encodes a 1188 amino acid receptor protein (SEQ ID
NO:165).
[0458] The signal peptide prediction program SIGNALP (Nielsen et
al. (1997) Protein Engineering 10:1-6) predicted that murine A259
includes a 22 amino acid signal peptide (amino acid 1 to about
amino acid 22 of SEQ ID NO:165) (SEQ ID NO:167) preceding the
mature A259 protein (corresponding to about amino acid 23 to amino
acid 1188 of SEQ ID NO:165) (SEQ ID NO:166). The mouse A259 protein
molecular weight is 133.1 kDa prior to the cleavage of the signal
peptide, 130.5 kDa after cleavage of the signal peptide.
[0459] Murine A259 includes a extracellular domain (about amino
acids 1 to 1141 of SEQ ID NO:165; SEQ ID NO:168), an I domain
(about amino acids 164 to 345 of SEQ ID NO:165; SEQ 169), seven
repeat domains (about amino acids 39 to 74, 115 to 157, 367 to 392,
421 to 455, 478 to 516, 540 to 575, and 602 to 640 of SEQ ID NO:165
(SEQ ID NO:170, 171, 172, 173, 174, 175, and 176, respectively)), a
transmembrane domain (about amino acids 1142 to 1164 of SEQ ID
NO:165; SEQ ID NO:177), and a cytoplasmic domain (about amino acids
1165 to 1188 of SEQ ID NO:165; SEQ ID NO:178).
[0460] Predicted N-glycosylation sites are found from amino acids
82 to 85, 95 to 98, 291 to 294, 331 to 334, 358 to 361, 449 to 452,
462 to 465, 528 to 531, 642 to 645, 694 to 697, 857 to 860, 894 to
897, 973 to 976, 1031 to 1034, 1039 to 1042 and 1059 to 1062 of SEQ
ID NO:165.
[0461] Predicted protein kinase C phosphorylation sites are found
from amino acids 51 to 53, 97 to 99, 221 to 223, 287 to 289, 355 to
357, 434 to 436, 451 to 453, 530 to 532, 569 to 571, 716 to 718,
770 to 772, 833 to 835, 1092 to 1094, 1100 to 1102 and 1171 to 1173
of SEQ ID NO:165.
[0462] Predicted casein kinase II phosphorylation sites are found
from amino acids 161 to 164, 221 to 224, 230 to 233, 270 to 273,
287 to 290, 322 to 325, 485 to 488, 530 to 533, 548 to 551, 556 to
559, 593 to 596, 696 to 669, 724 to 727, 753 to 756, 801 to 804,
859 to 862, 938 to 941, 966 to 969, 974 to 977, 1046 to 1049, 1061
to 1064 and 1133 to 1136 of SEQ ID NO:165.
[0463] A predicted tyrosine kinase phosphorylation site is found
from amino acids 812 to 820.
[0464] Predicted N-myristoylation sites are found from amino acids
6 to 11, 106 to 111, 236 to 241, 245 to 250, 257 to 262, 354 to
359, 363 to 368, 379 to 384, 477 to 482, 543 to 548, 625 to 630,
690 to 695, 725 to 730, 1030 to 1035 and 1147 to 1152 of SEQ ID
NO:165.
[0465] Predicted amidation site are found from amino acids 51 to 54
and 257 to 260 of SEQ ID NO:165.
[0466] Clone Mouse 12, which encodes murine A259, was deposited
with the American Type Culture Collection (10801 University
Boulevard, Manassas, Va. 20110-2209) on Apr. 2, 1999 and assigned
Accession Number 207191. This deposit will be maintained under the
terms of the Budapest Treaty on the International Recognition of
the Deposit of Microorganisms for the Purposes of Patent Procedure.
This deposit was made merely as a convenience for those of skill in
the art and is not an admission that a deposit is required under 35
U.S.C. 112.
[0467] FIG. 11 depicts a hydropathy plot of murine A259. Relatively
hydrophobic regions of the protein are shown above the horizontal
line, and relatively hydrophilic regions of the protein are below
the horizontal line. The cysteine residues (cys) and predicted
N-glycosylation sites are indicated by short vertical lines just
below the hydropathy trace. The dashed vertical line separates the
signal sequence (amino acids 1 to 22 of SEQ ID NO:165; SEQ ID
NO:167) on the left from the mature protein (amino acids 23 to 1188
of SEQ ID NO:165; SEQ ID NO:166) on the right. The A259
transmembrane domain is indicated by the section of the plot under
which the number 6.4 can be seen, which represents a score assigned
to the predicted transmembrane domain. The extracellular domain
(SEQ ID NO:168) and cytoplasmic domain (SEQ ID NO:178) are
similarly indicated by gray horizontal bars, labeled as "out" and
"in", respectively.
[0468] In situ data of A259 expression in mouse is summarized as
follows: During embryogenesis, E13.5 through postnatal day 1.5
tested, all developing bone structures have strong expression. The
signal is located mostly at the edge of the developing bones.
Beginning at E14.5 the bone marrow space can be seen and is
negative for expression. However, some large bones have signal in
the bone, not just at the edge. Signal is also observed in the
small intestine, diaphragm and to a lesser extent the muscle layer
under the skin. The diaphragm and intestine expression pattern is
suggestive of smooth muscle. The expression in these tissues is
strongest at E15.5 and E16.5 and decreases to almost background
levels by P1.5. Adult expression is observed in a small number of
tissues examined, including brain, submandibular gland, bladder,
colon, small intestine, liver, spleen, and placenta. The signal in
positive tissues is very weak in all but the mucosal epithelium of
the bladder which has the strongest expression. There is no
expression observed in the following tested tissues: spinal cord,
eye and harderian gland, white fat, brown fat, stomach, heart,
kidney, adrenal gland, thymus, lymph node, lung, pancreas, skeletal
muscle, and testes.
Uses of A259 Nucleic acids, Polypeptides, and Modulators
Thereof
[0469] As human A259 was originally found in a LPS stimulated human
primary osteoblast library, A259 nucleic acids, proteins, and
modulators thereof can be used to modulate the proliferation,
differentiation, and/or function of cells that form bone matrix,
e.g., osteoblasts and osteoclasts, and can be used to modulate the
formation of bone matrix. Thus A259 nucleic acids, proteins, and
modulators thereof can be used to treat cartilage and bone
associated diseases and disorders, and can play a role in bone
growth, formation, and remodeling. Examples of cartilage and bone
associated diseases and disorders include e.g., bone cancer,
achondroplasia, myeloma, fibrous dysplasia, scoliosis,
osteoarthritis, osteosarcoma, and osteoporosis.
[0470] As murine A259 was originally found in a bone marrow
library, A259 nucleic acids, proteins, and modulators thereof can
be used to modulate the proliferation, differentiation, and/or
function of cells that appear in the bone marrow, e.g., stem cells
(e.g., hematopoietic stem cells), and blood cells, e.g.,
erythrocytes, platelets, and leukocytes. Thus A259 nucleic acids,
proteins, and modulators thereof can be used to treat bone marrow,
blood, and hematopoietic associated diseases and disorders, e.g.,
acute myeloid leukemia, hemophilia, leukemia, anemia (e.g., sickle
cell anemia), and thalassemia.
[0471] As integrin family members play a role in immune response,
A259 nucleic acids, proteins, and modulators thereof can be used to
treat immune related disorders, e.g., immunodeficiency disorders
(e.g., HIV), viral disorders (e.g., infection by HSV), cell growth
disorders, e.g., cancers (e.g., carcinoma, lymphoma, e.g.,
follicular lymphoma), autoimmune disorders (e.g., arthritis, graft
rejection (e.g., allograft rejection), T cell autoimmune disorders
(e.g., AIDS)), and inflammatory disorders (e.g., bacterial or viral
infection, psoriasis, septicemia, cerebral malaria, inflammatory
bowel disease, arthritis (e.g., rheumatoid arthritis,
osteoarthritis), allergic inflammatory disorders (e.g., asthma,
psoriasis)).
[0472] As integrin family members play a role in cell growth,
survival, proliferation, and migration, A259 nucleic acids,
proteins, and modulators thereof can be used to treat apoptotic
disorders (e.g., rheumatoid arthritis, systemic lupus
erythematosus, insulin-dependent diabetes mellitus) proliferative
disorders (e.g., cancers, e.g., B cell cancers stimulated by TNF),
and disorders abnormal vascularization (e.g., cancer). In addition,
A259 nucleic acids, proteins, and modulators thereof can also be
used to promote vascularization (angiogenesis).
[0473] As integrins are cell adhesion molecules, A259 nucleic
acids, proteins, and modulators thereof can be used to modulate
disorders associated with adhesion and migration of cells, e.g.,
platelet aggregation disorders (e.g., Glanzmann's thromboasthemia,
which is a bleeding disorders characterized by failure of platelet
aggregation in response to cell stimuli), inflammatory disorders
(e.g., leukocyte adhesion deficiency, which is a disorder
associated with impaired migration of neutrophils to sites of
extravascular inflammation), disorders associated with abnormal
tissue migration during embryo development, and tumor
metastasis.
[0474] A259 polypeptides, nucleic acids, and modulators thereof,
can also be used to modulate the function, morphology,
proliferation and/or differentiation of cells in the tissues in
which it is expressed. Such molecules can be used to treat
disorders associated with abnormal or aberrant metabolism or
function of cells in the tissues in which it is expressed. Tissues
in which A259 is expressed, and disorders of which A259
polypeptides, nucleic acids, and modulators thereof can be used to
treat, include: bone (see disorders described herein); intestine
(e.g., ischemic bowel disease, infective enterocolitis, Crohn's
disease); brain (e.g., cerebral edema, hydrocephalus, brain
herniations, iatrogenic disease (due to, e.g., infection, toxins,
or drugs)); bladder (e.g., cystitis (bladder infection),
incontinence); liver (e.g., jaundice, hepatic failure, hepatic
circulatory disorders (e.g., hepatic vein thrombosis and portal
vein obstruction and thrombosis), hepatitis (e.g., chronic active
hepatitis, acute viral hepatitis, and toxic and drug-induced
hepatitis), cirrhosis (e.g., alcoholic cirrhosis, biliary
cirrhosis, and hemochromatosis)); spleen (e.g., amyloidosis,
Niemann-Pick disease, splenomegaly); placenta (e.g., toxemia of
pregnancy (e.g., preeclampsia and eclampsia, placentitis,
spontaneous abortion); and neuronal tissue (e.g., epilepsy,
muscular dystrophy, and neurodegenerative diseases such as
Alzheimer's disease, Parkinson's disease, and Huntington's
disease).
[0475] A259 is expressed at a higher level in the liver of patients
suffering from liver fibrosis than in patients not suffering from
liver fibrosis. Liver fibrosis, is caused by chronic injury to the
liver arising from, e.g, alcohol abuse, drugs, viral infections
(e.g., hepatitis B or hepatitis C), metabolic disorders (excessive
iron or copper), autoimmune attack on hepatocytes or the bile duct,
and congenital disorders. Liver fibrosis is a reversible condition
and injury can be present for months or years before significant
scar tissue accumulates. However, liver fibrosis leads to
cirrhosis, which is generally not reversible.
[0476] The liver has four major components: epithelial cells
(hepatocytes), endothelial cells; tissue macrophages (Kupffer
cells), and a stellate cells (a type of perivascular mesenchymal
cell). In normal liver the space between the epithelium and
sinusoidal endothelium is filled with a type of extracellular
matrix (ECM) that is somewhat similar to a basement membrane. In
fibrosis the ECM undergoes a number of changes. The total content
of collagens and other components increases several fold. In
addition, there is an increase in fibril-forming collagens.
Stellate cells are the primary fibrogenic cell of the liver. In
response to injury, quiescent stellate cells are activated and
become proliferative, fibrogenic, contractile myofibroblasts. Among
the key mediators of these changes are: TGF-.beta.1, MCP-1, PDGF,
ET-1, and MMP-2. Kupffer cells, endothelial cells and hepatocytes
produce factors which stimulate stellate cell activation. As noted
above, human A259 is expressed at a high level in activated
stellate cells. This result and the increased expression of A259 in
clinical liver fibrosis samples, suggest that A259 plays a role in
liver fibrosis. Thus, A259 nucleic acids, polypeptides, and
modulators thereof can be used to diagnose and treat liver fibrosis
as well as other types of fibrosis, e.g., kidney fibrosis or lung
fibrosis. Thus, liver fibrosis can be treated using antibodies
directed against A259, particularly the extracellular domain of
A259, the I domain of A259, or a repeat domain of A259. Also useful
are polypeptides which include one or more repeat domains of A259
and/or the I domain of A259.
[0477] Tables IV, V and VI below provide summaries of human A259
and murine A259 sequence information.
TABLE-US-00004 TABLE IV Summary of Sequence Information of Human
A259 and Murine A259. ATCC Open Reading Accession Gene cDNA Frame
Polypeptide No. Human A259 SEQ ID SEQ ID NO: 146 SEQ ID 207190 NO:
145 NO: 147 Murine A259 SEQ ID SEQ ID NO: 164 SEQ ID 207191 NO: 163
NO: 165
TABLE-US-00005 TABLE V Summary of Domains of Human A259 and Murine
A259. Signal Mature Extracellular Transmembrane Cytoplasmic Protein
Sequence Protein Domain Domain Domain Human aa 1-22 aa 23-1188 aa
1-1141 aa 1142-1164 aa 1165-1188 A259 SEQ ID SEQ ID SEQ ID SEQ ID
NO: 159 SEQ ID NO: 160 NO: 149 NO: 148 NO: 150 Murine aa 1-22 aa
23-1188 aa 1-1141 aa 1142-1164 aa 1165-1188 A259 SEQ ID SEQ ID SEQ
ID SEQ ID NO: 177 SEQ ID NO: 178 NO: 167 NO: 166 NO: 168
TABLE-US-00006 TABLE VI Summary of Domains of Human A259 and Murine
A259. Protein I Domain Repeat Domain Human aa 164-345 aa 39-74;
115-157; 367-392; 421-455; 478-516; A259 SEQ ID 540-575; 602-640,
SEQ ID NO: 152-158 NO: 151 Murine aa 164-345 aa 39-74; 115-157;
367-392; 421-455; 478-516; A259 SEQ ID 540-575; 602-640, SEQ ID NO:
170-176 NO: 169
Isolated Nucleic Acid Molecules of the Present Invention
[0478] One aspect of the invention pertains to isolated nucleic
acid molecules that encode a polypeptide of the invention or a
biologically active portion thereof, as well as nucleic acid
molecules sufficient for use as hybridization probes to identify
nucleic acid molecules encoding a polypeptide of the invention and
fragments of such nucleic acid molecules suitable for use as PCR
primers for the amplification or mutation of nucleic acid
molecules.
[0479] As described below, one aspect of the invention pertains to
isolated nucleic acids comprising nucleotide sequences encoding
Delta3 polypeptides, and/or equivalents of such polypeptides or
nucleic acids. The "term equivalent" is understood to include
nucleotide sequences encoding functionally equivalent Delta3
polypeptides or functionally equivalent peptides having an activity
of a Delta3 protein such as described herein. Equivalent nucleotide
sequences also include sequences that differ by one or more
nucleotide substitutions, additions or deletions, such as allelic
variants, and will, therefore, include, for example, sequences that
differ from the nucleotide sequence of the Delta3 nucleic acid
sequence shown in any of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33,
35, 37, 39, 41, 43 or 45 due to the degeneracy of the genetic
code.
[0480] Another aspect of the invention pertains to isolated nucleic
acid molecules that encode FTHMA-070 or T85 proteins or
biologically active portions thereof, as well as nucleic acid
molecules sufficient for use as hybridization probes to identify
FTHMA-070 or T85-encoding nucleic acids (e.g., FTHMA-070 or T85
mRNA) and fragments for use as PCR primers for the amplification or
mutation of FTHMA-070 or T85 nucleic acid molecules.
[0481] Another aspect of the invention pertains to isolated nucleic
acid molecules that encode Tango-77 proteins or biologically active
portions thereof, as well as nucleic acid molecules sufficient for
use as hybridization probes to identify Tango-77-encoding nucleic
acids (e.g., Tango-77 mRNA) and fragments for use as PCR primers
for the amplification or mutation of Tango-77 nucleic acid
molecules.
[0482] Yet another aspect of the invention pertains to isolated
nucleic acid molecules that encode SPOIL proteins or biologically
active portions thereof, as well as nucleic acid fragments
sufficient for use as hybridization probes to identify
SPOIL-encoding nucleic acids (e.g., SPOIL mRNA) and fragments for
use as PCR primers for the amplification or mutation of SPOIL
nucleic acid molecules.
[0483] Another aspect of the invention pertains to isolated nucleic
acid molecules that encode NEOKINE proteins or biologically active
portions thereof, as well as nucleic acid fragments sufficient for
use as hybridization probes to identify NEOKINE-encoding nucleic
acids (e.g., NEOKINE mRNA) and fragments for use as PCR primers for
the amplification or mutation of NEOKINE nucleic acid
molecules.
[0484] Another aspect of the invention pertains to isolated nucleic
acid molecules that encode T129 proteins or biologically active
portions thereof, as well as nucleic acid molecules sufficient for
use as hybridization probes to identify T129-encoding nucleic acids
(e.g., T129 mRNA) and fragments for use as PCR primers for the
amplification or mutation of T129 nucleic acid molecules.
[0485] As used herein, the term "nucleic acid molecule" is intended
to include DNA molecules (e.g., cDNA or genomic DNA) and RNA
molecules (e.g., mRNA) and analogs of the DNA or RNA generated
using nucleotide analogs. The nucleic acid molecule can be
single-stranded or double-stranded, but preferably is
double-stranded DNA.
[0486] An "isolated" nucleic acid molecule is one which is
separated from other nucleic acid molecules which are present in
the natural source of the nucleic acid. Preferably, an "isolated"
nucleic acid is free of sequences (preferably protein encoding
sequences) which naturally flank the nucleic acid (i.e., sequences
located at the 5' and 3' ends of the nucleic acid) in the genomic
DNA of the organism from which the nucleic acid is derived. For
example, in various embodiments, the isolated FTHMA-070, T85, Tango
77, SPOIL, NEOKINE, T129 or A259 nucleic acid molecule can contain
less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of
nucleotide sequences which naturally flank the nucleic acid
molecule in genomic DNA of the cell from which the nucleic acid is
derived. Moreover, an "isolated" nucleic acid molecule, such as a
cDNA molecule, can be substantially free of other cellular
material, or culture medium when produced by recombinant
techniques, or substantially free of chemical precursors or other
chemicals when chemically synthesized.
[0487] A nucleic acid molecule of the present invention, e.g., a
nucleic acid molecule having the nucleotide sequence of SEQ ID NOs:
1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 53, 55, 57,
58, 71, 73, 76, 80, 89, 101, 104, 112, 115, 118, 121, 124, 137,
139, 145, 146, 163 or 164 or the nucleotide sequence of the cDNA of
a clone deposited with the ATCC.RTM. as Accession Number 98348,
98807, 98883, 98984 or 98751 or a complement thereof, can be
isolated using standard molecular biology techniques and the
sequence information provided herein. Using all or a portion of the
nucleic acid sequences of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33,
35, 37, 39, 41, 43, 45, 53, 55, 57, 58, 71, 73, 76, 80, 89, 101,
104, 112, 115, 118, 121, 124, 137, 139, 145, 146, 163 or 164, or
the nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, 98807, 98883, 98984 or 98751,
as a hybridization probe, nucleic acid molecules of the invention
can be isolated using standard hybridization and cloning techniques
(e.g., as described in Sambrook et al., eds., Molecular Cloning: A
Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory, Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,
1989).
[0488] In another embodiment, a portion of the nucleic acid
sequence of SEQ ID NO:89, for example, from nucleotides 1 to 15 or
from nucleotides 447 or 495 to 746, can used as a hybridization
probe. In yet another embodiment, a portion of the nucleic acid
sequence of SEQ ID NO:101, for example, from nucleotides 1 to 280
or from nucleotides 390 to 1291, can be used as a hybridization
probe. In yet another embodiment, a portion of the nucleic acid
sequence of SEQ ID NO:106, for example, from nucleotides 1-371 or
from 481-1377, can be used as a hybridization probe. In yet another
embodiment, a portion of the nucleic acid sequence of SEQ ID
NO:112, for example, from nucleotides 225-364, from 96-575, or from
495-838, can be used as a hybridization probe.
[0489] Moreover, a nucleic acid molecule encompassing all or a
portion of SEQ ID NO:89, SEQ ID NO:101, SEQ ID NO:104, SEQ ID
NO:112, the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984, can be isolated by the
polymerase chain reaction (PCR) using synthetic oligonucleotide
primers designed based upon the sequence of SEQ ID NO:89, SEQ ID
NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the DNA insert of
the plasmid deposited with ATCC as Accession Number 98984.
[0490] Moreover, a nucleic acid molecule encompassing all or a
portion of SEQ ID NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID
NO:124, or the nucleotide sequence of the DNA insert of the plasmid
deposited with ATCC as Accession Number 98751, can be isolated by
the polymerase chain reaction (PCR) using synthetic oligonucleotide
primers designed based upon the sequence of SEQ ID NO:115, SEQ ID
NO:118, SEQ ID NO:121, SEQ ID NO:124, or the nucleotide sequence of
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98751.
[0491] A nucleic acid molecule of the invention can be amplified
using cDNA, mRNA or genomic DNA as a template and appropriate
oligonucleotide primers according to standard PCR amplification
techniques. The nucleic acid so amplified can be cloned into an
appropriate vector and characterized by DNA sequence analysis.
Furthermore, oligonucleotides corresponding to all or a portion of
a nucleic acid molecule of the invention can be prepared by
standard synthetic techniques, e.g., using an automated DNA
synthesizer.
[0492] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises a nucleic acid molecule which
is a complement of the nucleotide sequence of SEQ ID NOs: 1, 3, 24,
26, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 53, 55, 57, 58, 71, 73,
76, 80, 137, 139, 145, 146, 163 or 164, or the nucleotide sequence
of the cDNA of a clone deposited with the ATCC.RTM. as Accession
Number 98348, or 98807, or a portion thereof. A nucleic acid
molecule which is complementary to a given nucleotide sequence is
one which is sufficiently complementary to the given nucleotide
sequence that it can hybridize to the given nucleotide sequence
under the conditions set forth herein, thereby forming a stable
duplex.
[0493] In a preferred embodiment, an isolated nucleic acid molecule
of the invention comprises the nucleotide sequence shown in SEQ ID
NO:91. The sequence of SEQ ID NO:91 corresponds to murine SPOIL-I
cDNA. This cDNA comprises sequences encoding the murine SPOIL-I
protein (i.e., "the coding region", from nucleotides 135-428 of SEQ
ID NO:89).
[0494] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises the nucleotide sequence shown
in SEQ ID NO:92. The sequence of SEQ ID NO:92 corresponds to murine
SPOIL-I cDNA. This cDNA comprises sequences encoding the mature
SPOIL-I protein (i.e., from nucleotides 186-428 of SEQ ID NO:89
after the signal sequence has been cleaved).
[0495] In yet another embodiment, an isolated nucleic acid molecule
of the invention comprises the nucleotide sequence shown in SEQ ID
NO:89. The sequence of SEQ ID NO:89 corresponds coding and
noncoding regions of murine SPOIL-I cDNA. This cDNA comprises
sequences encoding the murine SPOIL-I protein (i.e., "the coding
region", from nucleotides 135-428) and noncoding regions (i.e.,
from nucleotides 1-134 and from nucleotides 429-746).
[0496] In yet another embodiment, an isolated nucleic acid molecule
of the invention comprises the nucleotide sequence shown in SEQ ID
NO:112. The sequence of SEQ ID NO:112 corresponds coding and
noncoding regions of murine SPOIL-II cDNA. This cDNA comprises
sequences encoding the murine SPOIL-II protein (i.e., "the coding
region", from nucleotides 96-575) and noncoding regions (i.e., from
nucleotides 1-95 and from nucleotides 576-838).
[0497] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises the nucleotide sequence shown
in SEQ ID NO:101. The sequence of SEQ ID NO:101 corresponds to the
human SPOIL-I cDNA. This cDNA comprises sequences encoding the
human SPOIL-I protein (i.e., "the coding region", from nucleotides
124 to 630), as well as 5' untranslated sequences (nucleotides 1 to
123) and 3' untranslated sequences (nucleotides 631 to 1291).
Alternatively, the nucleic acid molecule can comprise only the
coding region of SEQ ID NO:101 (e.g., nucleotides 124 to 630).
[0498] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises the nucleotide sequence shown
in SEQ ID NO:104. The sequence of SEQ ID NO:104 corresponds to the
human SPOIL-II cDNA. This cDNA comprises sequences encoding the
human SPOIL-II protein (i.e., "the coding region", from nucleotides
98-721, as well as 5' untranslated sequences (nucleotides 1-97 and
3' untranslated sequences (nucleotides 722-1377). Alternatively,
the nucleic acid molecule can comprise only the coding region of
SEQ ID NO:104 (e.g., nucleotides 98-721).
[0499] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises a nucleic acid molecule which
is a complement of the nucleotide sequence shown in SEQ ID NO:89,
SEQ ID NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA insert of the
plasmid deposited with ATCC as Accession Number 98883, or the DNA
insert of the plasmid deposited with ATCC as Accession Number
98984, or a portion of any of these nucleotide sequences. A nucleic
acid molecule which is complementary to the nucleotide sequence
shown in SEQ ID NO:89, SEQ ID NO:101, SEQ ID NO:104, SEQ ID NO:112,
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98883, or the DNA insert of the plasmid deposited with ATCC
as Accession Number 98984, is one which is sufficiently
complementary to the nucleotide sequence shown in SEQ ID NO:89, SEQ
ID NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA insert of the
plasmid deposited with ATCC as Accession Number 98883, or the DNA
insert of the plasmid deposited with ATCC as Accession Number
98984, such that it can hybridize to the nucleotide sequence shown
in SEQ ID NO:89, SEQ ID NO:101, SEQ ID NO:104, SEQ ID NO:112, the
DNA insert of the plasmid deposited with ATCC as Accession Number
98883, or the DNA insert of the plasmid deposited with ATCC as
Accession Number 98984, or a complement thereof, thereby forming a
stable duplex.
[0500] In still another preferred embodiment, an isolated nucleic
acid molecule of the present invention comprises a nucleotide
sequence which is at least about 50-55%, 60-65%, preferably at
least about 70-75%, more preferable at least about 80-85%, and even
more preferably at least about 90-95% or more identical to the
nucleotide sequences shown in SEQ ID NO:89, the nucleotide sequence
shown in SEQ ID NO:101, the nucleotide sequence shown in SEQ ID
NO:104, the nucleotide sequence shown in SEQ ID NO:112, the
nucleotide sequence of the DNA insert of the plasmid deposited with
ATCC as Accession Number 98883, the DNA insert of the plasmid
deposited with ATCC as Accession Number 98984, or a portion of any
of these nucleotide sequences.
[0501] In a preferred embodiment, an isolated nucleic acid molecule
of the invention comprises the nucleotide sequence shown in SEQ ID
NO:115. The sequence of SEQ ID NO:115 corresponds to the human
NEOKINE-1 cDNA. This cDNA comprises sequences encoding the human
NEOKINE-1 protein (i.e., "the coding region", from nucleotides
97-393), as well as 5' untranslated sequences (nucleotides 1-97)
and 3' untranslated sequences (nucleotides 394-1564).
Alternatively, the nucleic acid molecule can comprise only the
coding region of SEQ ID NO:115 (e.g., nucleotides 97-393,
corresponding to SEQ ID NO:117).
[0502] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises the nucleotide sequence shown
in SEQ ID NO:118. The sequence of SEQ ID NO:118 corresponds to a
murine NEOKINE-1 cDNA. This cDNA comprises sequences encoding the
murine NEOKINE-1 protein (i.e., "the coding region", from
nucleotides 212-508), as well as 5' untranslated sequences
(nucleotides 1-211) and 3' untranslated sequences (nucleotides
509-1656). Alternatively, the nucleic acid molecule can comprise
only the coding region of SEQ ID NO:118 (e.g., nucleotides 212-508,
corresponding to SEQ ID NO:120).
[0503] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises the nucleotide sequence shown
in SEQ ID NO:121. The sequence of SEQ ID NO:121 corresponds to a
rat NEOKINE-1 cDNA. This cDNA comprises sequences encoding at least
79 amino acid residues of the rat NEOKINE-1 protein (i.e., "the
coding region", from nucleotides 1-234), as well as 3' untranslated
sequences (nucleotides 235-1372). Alternatively, the nucleic acid
molecule can comprise only the coding region of SEQ ID NO:121
(e.g., nucleotides 235-1372, corresponding to SEQ ID NO:123).
[0504] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises the nucleotide sequence shown
in SEQ ID NO:124. The sequence of SEQ ID NO:124 corresponds to a
macaque NEOKINE-1 cDNA. This cDNA comprises sequences encoding at
least 94 amino acid residues of the macaque NEOKINE-1 protein
(i.e., "the coding region", from nucleotides 3-284), as well as 3'
untranslated sequences (nucleotides 285-1458). Alternatively, the
nucleic acid molecule can comprise only the coding region of SEQ ID
NO:124 (e.g., nucleotides 285-1458, corresponding to SEQ ID
NO:136).
[0505] In another preferred embodiment, an isolated nucleic acid
molecule of the invention comprises a nucleic acid molecule which
is a complement of the nucleotide sequence shown in SEQ ID NO:115,
SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or the nucleotide
sequence of the DNA insert of the plasmid deposited with ATCC as
Accession Number 98751, or a portion of any of these nucleotide
sequences. A nucleic acid molecule which is complementary to the
nucleotide sequence shown in SEQ ID NO:115, SEQ ID NO:118, SEQ ID
NO:121, SEQ ID NO:124, or the nucleotide sequence of the DNA insert
of the plasmid deposited with ATCC as Accession Number 98751, is
one which is sufficiently complementary to the nucleotide sequence
shown in SEQ ID NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID
NO:124, or the nucleotide sequence of the DNA insert of the plasmid
deposited with ATCC as Accession Number 98751, such that it can
hybridize to the nucleotide sequence shown in SEQ ID NO:115, SEQ ID
NO:118, SEQ ID NO:121, SEQ ID NO:124, or the nucleotide sequence of
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98751, thereby forming a stable duplex.
[0506] In still another preferred embodiment, an isolated nucleic
acid molecule of the present invention comprises a nucleotide
sequence which is at least about 60-65%, preferably at least about
70-75%, more preferable at least about 80-85%, and even more
preferably at least about 90-95%, 96-97%, 98-99% or more homologous
to the nucleotide sequences shown in SEQ ID NO:115, SEQ ID NO:118,
SEQ ID NO:121, SEQ ID NO:124, or the nucleotide sequence of the DNA
insert of the plasmid deposited with ATCC as Accession Number
98751, or a portion of any of these nucleotide sequences.
[0507] Moreover, a nucleic acid molecule of the invention can
comprise only a portion of a nucleic acid sequence encoding a
full-length polypeptide of the invention for example, a fragment
which can be used as a probe or primer or a fragment encoding a
biologically active portion of a polypeptide of the invention. The
nucleotide sequence determined from the cloning one gene allows for
the generation of probes and primers designed for use in
identifying and/or cloning homologs in other cell types, e.g., from
other tissues, as well as homologs from other mammals. The
probe/primer typically comprises substantially purified
oligonucleotide.
[0508] The oligonucleotide typically comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 50,
75, 100, 125, 150, 175, 200, 250, 300, 350 or 400 consecutive
nucleotides of the sense or anti-sense sequence of SEQ ID NOs: 1,
3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or the
nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, or of a naturally-occurring
mutant of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41,
43 or 45, or the nucleotide sequence of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348.
[0509] The oligonucleotide typically comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 50,
75, 100, 125, 150, 175, 200, 250, 300, 350 or 400 consecutive
nucleotides of the sense or anti-sense sequence of SEQ ID NO:53,
SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, or of a naturally
occurring mutant of SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ
ID NO:58.
[0510] The oligonucleotide typically comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 50,
75, 100, 125, 150, 175, 200, 250, 300, 350 or 400 consecutive
nucleotides of the sense or anti-sense sequence of SEQ ID NO:71,
SEQ ID NO:73, SEQ ID NO:76, SEQ ID NO:80, or the cDNA of ATCC
98807. Alternatively, the oligonucleotide can typically comprise a
region of nucleotide sequence that hybridizes under stringent
conditions to at least about 12, preferably about 25, more
preferably about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350 or
400 consecutive nucleotides of the sense or anti-sense sequence of
a naturally occurring mutant of SEQ ID NO:71, SEQ ID NO:73, SEQ ID
NO:76, SEQ ID NO:80, or the cDNA of ATCC 98807.
[0511] The oligonucleotide typically comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 40,
50 or 75 consecutive nucleotides of a sense sequence of SEQ ID
NO:89, SEQ ID NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA insert
of the plasmid deposited with ATCC as Accession Number 98883, or
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98984, of an anti-sense sequence of SEQ ID NO:89, SEQ ID
NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the DNA insert of
the plasmid deposited with ATCC as Accession Number 98984, or of a
naturally occurring mutant of either SEQ ID NO:89, SEQ ID NO:101,
SEQ ID NO:104, SEQ ID NO:112, the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the DNA insert of
the plasmid deposited with ATCC as Accession Number 98984.
[0512] The oligonucleotide typically comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 40,
50 or 75 consecutive nucleotides of a sense sequence of SEQ ID
NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or the
nucleotide sequence of the DNA insert of the plasmid deposited with
ATCC as Accession Number 98751, of an anti-sense sequence of SEQ ID
NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or the
nucleotide sequence of the DNA insert of the plasmid deposited with
ATCC as Accession Number 98751, or of a naturally occurring mutant
of SEQ ID NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or
the nucleotide sequence of the DNA insert of the plasmid deposited
with ATCC as Accession Number 98751. In an exemplary embodiment, a
nucleic acid molecule of the present invention comprises a
nucleotide sequence which is greater that 500 nucleotides in length
and hybridizes under stringent hybridization conditions to a
nucleic acid molecule of SEQ ID NO:115, SEQ ID NO:118, SEQ ID
NO:121, SEQ ID NO:124, or the nucleotide sequence of the DNA insert
of the plasmid deposited with ATCC as Accession Number 98751.
[0513] The oligonucleotide typically comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 50,
75, 100, 125, 150, 175, 200, 250, 300, 350 or 400 consecutive
nucleotides of the sense or anti-sense sequence of SEQ ID NO:137 or
SEQ ID NO:139, or of a naturally occurring mutant of SEQ ID NO:137
or SEQ ID NO:139.
[0514] The oligonucleotide typically comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 50,
75, 100, 125, 150, 175, 200, 250, 300, 350 or 400 consecutive
nucleotides of the sense or anti-sense sequence of SEQ ID NO:145,
146, 163, or 164 or of a naturally occurring mutant of SEQ ID NO:
145, 146, 163, or 164.
[0515] Probes based on the sequence of a nucleic acid molecule of
the invention can be used to detect transcripts or genomic
sequences encoding the same protein molecule encoded by a selected
nucleic acid molecule. The probe comprises a label group attached
thereto, e.g., a radioisotope, a fluorescent compound, an enzyme,
or an enzyme co-factor. Such probes can be used as part of a
diagnostic test kit for identifying cells or tissues which
mis-express the protein, such as by measuring levels of a nucleic
acid molecule encoding the protein in a sample of cells from a
subject, e.g., detecting mRNA levels or determining whether a gene
encoding the protein has been mutated or deleted.
[0516] A nucleic acid fragment encoding a biologically active
portion of a polypeptide of the invention can be prepared by
isolating a portion of any of SEQ ID NOs: 2, 25, 28, 30, 32, 34,
36, 38, 40, 42, 44 or 46, or the amino acid sequence encoded by the
cDNA of a clone deposited with the ATCC.RTM. as Accession Number
98348 expressing the encoded portion of the polypeptide protein
(e.g., by recombinant expression in vitro) and assessing the
activity of the encoded portion of the polypeptide.
[0517] A nucleic acid fragment encoding a "biologically active
portion of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259" can be prepared by isolating a portion of SEQ ID NO:53, 55,
57, 58, 71, 73, 76, 80, 89, 101, 104, 112, 115, 118, 121, 124, 137,
139, 146 or 164, or the nucleotide sequence of the cDNA of ATCC
98807, 98883, 98984 or 98751, which encodes a polypeptide having a
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
biological activity, expressing the encoded portion of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein (e.g.,
by recombinant expression in vitro) and assessing the activity of
the encoded portion of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259.
[0518] The invention further encompasses nucleic acid molecules
that differ from the nucleotide sequence of SEQ ID NOs: 1, 3, 24,
26, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 53, 55, 57, 58, 71, 73,
76, 80, 89, 101, 104, 112, 115, 118, 121, 124, 137, 139, 145, 146,
163 or 164, or the nucleotide sequence of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348, 98807,
98883, 98984 or 98751, due to degeneracy of the genetic code and
thus encode the same protein as that encoded by the nucleotide
sequence of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39,
41, 43, 45, 53, 55, 57, 58, 71, 73, 76, 80, 89, 101, 104, 112, 115,
118, 121, 124, 137, 139, 145, 146, 163 or 164, or the nucleotide
sequence of the cDNA of a clone deposited with the ATCC.RTM. as
Accession Number 98348, 98807, 98883, 98984 or 98751.
[0519] In addition to the nucleotide sequences of SEQ ID NOs: 1, 3,
24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 53, 55, 57, 58, 71,
73, 76, 80, 89, 101, 104, 112, 115, 118, 121, 124, 137, 139, 145,
146, 163 or 164, or the nucleotide sequence of the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348, 98807,
98883, 98984 or 98751, it will be appreciated by those skilled in
the art that DNA sequence polymorphisms that lead to changes in the
amino acid sequence may exist within a population (e.g., the human
population). Such genetic polymorphisms may exist among individuals
within a population due to natural allelic variation.
[0520] Such allelic variants of a polymorphic region of a Delta3
gene are also included as part of the present invention. For
example, the human gene for Delta3 was mapped to chromosome 15,
between markers D15S1244 and D15S144, and therefore, human Delta3
family members can include nucleotide sequence polymorphisms (e.g.,
nucleotide sequences that vary from SEQ ID NO: 1,3, 24, 26, 27, 29,
31, 33, 35, or 37) that map to this chromosome 15 region (i.e.,
between framework regions D15S1244 and D15S144), as well as
polypeptides encoded therefrom.
[0521] An allele is one of a group of genes which occur
alternatively at a given genetic locus. As used herein, the terms
"gene" and "recombinant gene" refer to nucleic acid molecules
comprising an open reading frame encoding a Delta3, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein,
preferably a mammalian Delta3, FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein. Such natural allelic variations
can typically result in 1-5% variance in the nucleotide sequence of
a given gene. Alternative alleles can be identified by sequencing
the gene of interest in a number of different individuals. This can
be readily carried out by using hybridization probes to identify
the same genetic locus in a variety of individuals. Any and all
such nucleotide variations and resulting amino acid polymorphisms
or variations that are the result of natural allelic variation and
that do not alter the functional activity are intended to be within
the scope of the invention.
[0522] In addition to naturally-occurring allelic variants of a
nucleic acid molecule of the invention sequence that may exist in
the population, the skilled artisan will further appreciate that
changes can be introduced by mutation thereby leading to changes in
the amino acid sequence of the encoded protein, without altering
the biological activity of the protein. For example, one can make
nucleotide substitutions leading to amino acid substitutions at
"non-essential" amino acid residues. A "non-essential" amino acid
residue is a residue that can be altered from the wild-type
sequence without altering the biological activity, whereas an
"essential" amino acid residue is required for biological activity.
For example, amino acid residues that are not conserved or only
semi-conserved among homologs of various species may be
non-essential for activity and thus would be likely targets for
alteration. Alternatively, amino acid residues that are conserved
among the orthologs of various species (e.g., murine and human) may
be essential for activity and thus would not be likely targets for
alteration.
[0523] In one embodiment of a nucleotide sequence of human Delta3,
the nucleotide at position 786 is an cytosine (C) (SEQ ID NO: 1).
In this embodiment, the amino acid at position 150 is a alanine (A)
(SEQ ID NO: 2). In an alternative embodiment, a species variant of
human Delta3 has a nucleotide at position 786 which is a thymidine
(T) (SEQ ID NO: 33). In this embodiment, the amino acid at position
150 is valine (V) (SEQ ID NO: 34), i.e., a conservative
substitution.
[0524] In one embodiment of a nucleotide sequence of human Delta3,
the nucleotide at position 594 is a cytosine (C) (SEQ ID NO: 1). In
this embodiment, the amino acid at position 86 is threonine (T)
(SEQ ID NO: 2). In an alternative embodiment, a species variant of
human Delta3 has a nucleotide at position 594 which is a guanine
(G) (SEQ ID NO: 35). In this embodiment, the amino acid at position
86 is serine (S) (SEQ ID NO: 36), i.e., a conservative
substitution.
[0525] In one embodiment of a nucleotide sequence of human Delta3,
wherein the nucleotide at position 883 is a thymidine (T) (SEQ ID
NO: 1). In this embodiment, the amino acid at position 182 is
aspartate (D) (SEQ ID NO: 2). In an alternative embodiment, a
species variant of human Delta3 has a nucleotide at position 883
which is an adenine (A) (SEQ ID NO: 37). In this embodiment, the
amino acid at position 182 is glutamate (E) (SEQ ID NO: 38), i.e.,
a conservative substitution.
[0526] In one embodiment of a nucleotide sequence of mouse Delta3,
the nucleotide at position 49 is cytosine (C) (SEQ ID NO: 24). In
this embodiment, the amino acid at position 4 is alanine (A) (SEQ
ID NO: 25). In an alternative embodiment, a species variant of
mouse Delta3 has a nucleotide at position 49 which is thymidine (T)
(SEQ ID NO: 39). In this embodiment, the amino acid at position 4
is valine (V) (SEQ ID NO: 40), i.e., a conservative
substitution.
[0527] In one embodiment of a nucleotide sequence of mouse Delta3,
the nucleotide at position 51 is thymidine (T) (SEQ ID NO: 24). In
this embodiment, the amino acid at position 5 is serine (S) (SEQ ID
NO: 25). In an alternative embodiment, a species variant of mouse
Delta3 has a nucleotide at position 51 which is a adenine (A) (SEQ
ID NO: 41). In this embodiment, the amino acid at position 5 is
threonine (T) (SEQ ID NO: 42), i.e., a conservative
substitution.
[0528] In one embodiment of a nucleotide sequence of mouse Delta3,
the nucleotide at position 109 is guanine (G) (SEQ ID NO: 24). In
this embodiment, the amino acid at position 24 is arginine (R) (SEQ
ID NO: 25). In an alternative embodiment, a species variant of
mouse Delta3 has a nucleotide at position 109 which is adenine (A)
(SEQ ID NO: 43). In this embodiment, the amino acid at position 24
is histidine (H) (SEQ ID NO: 44), i.e., a conservative
substitution.
[0529] In one embodiment of a nucleotide sequence of mouse Delta3,
wherein the nucleotide at position 130 is a thymidine (T) (SEQ ID
NO: 24). In this embodiment, the amino acid at position 31 is
phenylalanine (F) (SEQ ID NO: 25). In an alternative embodiment, a
species variant of mouse Delta3 has a nucleotide at position 130
which is adenine (A) (SEQ ID NO: 45). In this embodiment, the amino
acid at position 31 is tyrosine (Y) (SEQ ID NO: 46), i.e., a
conservative substitution.
[0530] The invention also pertains to nucleic acid molecules
encoding a polypeptide of the invention that contain changes in
amino acid residues that are not essential for activity. Such
polypeptides differ in amino acid sequence from SEQ ID NOs: 2, 25,
28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348 yet retain biological activity.
In one embodiment, the isolated nucleic acid molecule includes a
nucleotide sequence encoding a protein that includes an amino acid
sequence that is at least 65%, 75%, 85%, 95%, or 98% identical to
the amino acid sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36,
38, 40, 42, 44 or 46, or the amino acid sequence encoded by the
cDNA of a clone deposited with the ATCC.RTM. as Accession Number
98348.
[0531] Moreover, nucleic acid molecules encoding proteins of the
invention from other species (homologs), which have a nucleotide
sequence which differs from that of the human protein described
herein are intended to be within the scope of the invention.
Nucleic acid molecules corresponding to natural allelic variants
and homologs of a cDNA of the invention can be isolated based on
their identity to the human nucleic acid molecule disclosed herein
using the human cDNAs, or a portion thereof, as a hybridization
probe according to standard hybridization techniques under
stringent hybridization conditions. For example, a cDNA encoding a
soluble form of a membrane-bound protein of the invention isolated
based on its hybridization to a nucleic acid molecule encoding all
or part of the membrane-bound form. Likewise, a cDNA encoding a
membrane-bound form can be isolated based on its hybridization to a
nucleic acid molecule encoding all or part of the soluble form.
[0532] As used herein, the term "hybridizes under stringent
conditions" is intended to describe conditions for hybridization
and washing under which nucleotide sequences at least 60% (65%,
70%, preferably 75%) identical to each other typically remain
hybridized to each other. Such stringent conditions are known to
those skilled in the art and can be found in Current Protocols in
Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
A preferred, non-limiting example of stringent hybridization
conditions are hybridization in 6.times. sodium chloride/sodium
citrate (SSC) at about 45.degree. C., followed by one or more
washes in 0.2.times.SSC, 0.1% SDS at 50-65.degree. C. Preferably,
an isolated nucleic acid molecule of the invention that hybridizes
under stringent conditions to the sequence of SEQ ID NOs: 1, 3, 24,
26, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 53, 55, 57, 58, 71, 73,
76, 80, 89, 101, 104, 112, 115, 118, 121, 124, 137, 139, 145, 146,
163 or 164, or the cDNA of ATCC.RTM. as Accession Number 98348,
98807, 98883, 98984 or 98751 corresponds to a naturally-occurring
nucleic acid molecule. As used herein, a "naturally-occurring"
nucleic acid molecule refers to an RNA or DNA molecule having a
nucleotide sequence that occurs in nature (e.g., encodes a natural
protein).
[0533] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 480 (500, 550, 600, 650, 700,
800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800,
1900, 2000 or 2050) nucleotides in length and hybridizes under
stringent conditions to the nucleic acid molecule comprising the
nucleotide sequence, preferably the coding sequence, of SEQ ID NOs:
1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or the
nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348, or complement thereof.
[0534] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 300 (325, 350, 375, 400, 425,
450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides
in length and hybridizes under stringent conditions to the nucleic
acid molecule comprising the nucleotide sequence, preferably the
coding sequence, of SEQ ID NO:53, 55, 57 or 58.
[0535] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 300 (325, 350, 375, 400, 425,
450, 500, 550, 600, 650, 700, 800, or 989) nucleotides in length
and hybridizes under stringent conditions to the nucleic acid
molecule comprising the nucleotide sequence, preferably the coding
sequence, of SEQ ID NO:71, 73, 76, 80, or the cDNA of ATCC
98807.
[0536] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 15 nucleotides in length and
hybridizes under stringent conditions to the nucleic acid molecule
comprising the nucleotide sequence of SEQ ID NO:89, 101, 104, 112
or the DNA insert of the plasmid deposited with ATCC as Accession
Number 98883 or 98984, or a complement thereof. In other
embodiments, the nucleic acid is at least 30, 50, 100, 250, 300,
400, 500, 600 or 700 nucleotides in length.
[0537] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 15 nucleotides in length and
hybridizes under stringent conditions to the nucleic acid molecule
comprising the nucleotide sequence of SEQ ID NO:115, 118, 121, 124,
or the nucleotide sequence of the DNA insert of the plasmid
deposited with ATCC as Accession Number 98751. In other embodiment,
the nucleic acid is at least 30, 50, 100, 250 or 500 nucleotides in
length.
[0538] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 300 (325, 350, 375, 400, 425,
450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides
in length and hybridizes under stringent conditions to the nucleic
acid molecule comprising the nucleotide sequence, preferably the
coding sequence, of SEQ ID NO:137 or 139
[0539] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 400 (450, 500, 550, 600, 650,
700, 800, 900, 1000, 2000, or 3000) nucleotides in length and
hybridizes under stringent conditions to the nucleic acid molecule
comprising the nucleotide sequence, preferably the coding sequence,
of SEQ ID NO:145 or 163, or a complement thereof.
[0540] Preferably, such nucleic acid molecules, "specifically
hybridize" or "specifically detect" a nucleic acid molecule of the
invention by exhibiting the ability to hybridize to at least
approximately 6, 12, 20, 30, 50, 100, 150, 200, 300, 350, 400 or
425 consecutive nucleotides of a Delta3 nucleotide sequence
designated in one of SEQ ID Nos:1, 3, 24, 26, 27, 29, 31, 33, 35,
37, 39, 41, 43 or 45, or the nucleotide sequence of the cDNA of a
clone deposited with the ATCC.RTM. as Accession Number 98348, or a
sequence complementary thereto, such that more than 5, 10 or 20
times more hybridization (utilizing hybridization conditions
described above), preferably more than 50 times more hybridization,
and even more preferably more than 100 times more hybridization
than occurs relative to hybridization to a cellular nucleic acid
(e.g., mRNA or genomic DNA) encoding a protein other than a Delta3
protein as defined herein.
[0541] Delta3 nucleic acids can encode polypeptides that are at
least 55% identical to an amino acid sequence of SEQ ID NOs: 2, 25,
28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348. Nucleic acids which encode
polypeptides which are at least about 72%, and even more preferably
at least about 80%, 85%, 90%, 95%, or 98% similar with an amino
acid sequence represented in SEQ ID NO: 2, 25, 28, 30, 32, 34, 36,
38, 40, 42, 44 or 46, or the amino acid sequence encoded by the
cDNA of a clone deposited with the ATCC.RTM. as Accession Number
98348 are also within the scope of the invention.
[0542] In one embodiment, the nucleic acid of the present invention
encodes a polypeptide having an overall amino acid sequence
similarity of at least about 72%, at least about 80%, at least
about 85%, at least about 90%, at least about 95%, at least about
98%, or at least about 99% with the amino acid sequence shown in
SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46. In a
preferred embodiment, the nucleic acid encodes a protein comprising
the amino acid set forth in SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36,
38, 40, 42, 44 or 46, or the amino acid sequence encoded by the
cDNA of a clone deposited with the ATCC.RTM. as Accession Number
98348. Preferably, the nucleic acid includes all or a portion of
the nucleotide sequence corresponding to the coding region of SEQ
ID Nos: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or
the nucleotide sequence of the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348.
[0543] The nucleic acids of the invention can encode a Delta3
protein from any species, including insects. Preferred nucleic
acids encode vertebrate Delta3 proteins. Even more preferred
nucleic acids encode mammalian Delta3 proteins including primate
Delta3 proteins, e.g., human Delta3 proteins, and murine Delta3
proteins. Other nucleic acids of the invention can encode avian,
equine, canine, feline, bovine or porcine Delta3 proteins.
[0544] In a preferred embodiment of the invention, the nucleic acid
encodes a polypeptide comprising an extracellular domain of Delta3,
e.g., human or mouse Delta3 including allelic variants having SEQ
ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the
amino acid sequence encoded by the cDNA of a clone deposited with
the ATCC.RTM. as Accession Number 98348. Accordingly, preferred
nucleic acids encode a polypeptide comprising about amino acid 1 to
about amino acid 529 of SEQ ID NO: 2, 28, 30, 32, 34, 36 or 38, or
alternatively about amino acid 1 to about amino acid 530 of SEQ ID
NO: 25, 40, 42, 44, or 46.
[0545] Other preferred nucleic acids encode a polypeptide
corresponding to an extracellular domain of Delta3 lacking the
signal peptide, e.g., a polypeptide comprising about amino acid 18
to about amino acid 529 of SEQ ID NO: 2 or about amino acid 18 to
about amino acid 530 of SEQ ID NO: 25. Yet other preferred nucleic
acids encode a polypeptide comprising at least one of the conserved
motifs in the extracellular domain of Delta3, e.g., a DSL motif
(for example, amino acids 173-217 of SEQ ID NO: 2 or amino acids
174-218 of SEQ ID NO: 25) or an EGF-like motif (for example,
EGF-like 1, amino acids 222-250 of SEQ ID NO: 2), or also for
example amino acids 223-251 of SEQ ID NO: 25. Additional EGF-like
domains are from amino acids 253-281, 288-321, 328-359, 366-399,
411-437, 444-475, and 484-517 of SEQ ID NO: 2 and 254-282, 289-322,
329-360, 367-400, 412-438, 445-476, and 485-518 of SEQ ID NO:
25.
[0546] In one embodiment, the nucleic acid encodes a protein having
at least one EGF-like motif. In other embodiments, the nucleic acid
encodes proteins having at least 2, at least 3, at least 4, at
least 5, at least 6, at least 7, or 8 EGF-like domains or amino
acids 223-251, 254-282, 289-322, 329-360, 367-400, 412-438,
445-476, and 485-518 of SEQ ID NO: 25.
[0547] The polypeptide encoded by a nucleic acid encoding any of
these numbers of EGF-like domains can further comprise an amino
acid sequence encoding a DSL motif.
[0548] The DSL region or motif is shared by all known members of
the family of presumed ligands of Notch-like proteins (Delta1 and
Serrate in Drosophila; Lag-2 and Apx-1 in Caenorhabditis elegans)
(Henderson et al. (1994) Development 120:2913; Tax et al. (1994)
Nature 368:150; Fleming et al. (1990) Genes Dev. 4:2188; Thomas et
al. (1991) Development 11:749; Mello et al. (1994) Cell 77:95). The
DSL motif is located in the amino terminal portion of the protein,
i.e., extracellular, which is closely related to a similar domain
in the Drosophila Delta1 protein and which has been described as
being necessary and sufficient for in vitro binding to Notch
(Henrique et al. (1995) Nature 375:787; Muskavitch (1994) Dev.
Biol. 166:415).
[0549] In one embodiment, a nucleic acid of the invention encodes a
polypeptide that comprises a human or mouse Delta3 DSL domain and
which is capable of binding a receptor. A Delta3 DSL domain
conforms to the following DSL consensus sequence:
X-X-C-X-X-X-Y-[FY]-G-X-X-C-X-X-X-C-[HR]-X-R-X-D-X-F-G-[RH]-X-X-C-X-X-X-G--
X-X-X-C-X-X-X-C-X-X-G-W-X-G-X-Y-C (SEQ ID NO:23), wherein all amino
acids are indicated according to their universal single letter
designation, brackets indicate that the amino acid at that position
is selected from one of the amino acids within the brackets, and
"X" designates any amino acid, and wherein the DSL domain is at
least 60%, or more preferably at least 65%, 70%, 75%, 80%, 85%, or
most preferably 90%, 95%, 98% or 100% identical, i.e., no gaps in
the sequence, to the human Delta3 polypeptide sequence from amino
acids 173-217 of SEQ ID NO:2. In another embodiment, a Delta3 DSL
domain conforms to the above-described DSL consensus sequence and
is at least 60%, or more preferably at least 65%, 70%, 75%, 80%,
85%, or most preferably 90%, 95%, 98% or 100% identical to the
mouse Delta3 DSL sequence from amino acids 174-218 of SEQ ID NO:
25.
[0550] In another embodiment, a nucleic acid of the invention
encodes Delta3 DSL domain has a cysteine at amino acid positions
176, 185, 189, 201, 209, and 217 of SEQ ID NO: 2, and is at least
60%, or more preferably at least 65%, 70%, 75%, 80%, 85%, or most
preferably 90%, 95%, 98% or 100% identical to the human Delta3
polypeptide sequence from amino acids 173-217 of SEQ ID NO:2. In
another embodiment, a Delta3 DSL domain has a cysteine at amino
acid positions 177, 186, 190, 202, 210, and 218 of SEQ ID NO: 25,
and is at least 60%, or more preferably at least 65%, 70%, 75%,
80%, 85%, or most preferably 90%, 95%, 98% or 100% identical to the
mouse Delta3 DSL sequence from amino acids 174-218 of SEQ ID NO:
25.
[0551] In one embodiment, a nucleic acid of the invention encodes a
polypeptide that comprises a human or mouse Delta3 EGF-like domain.
An EGF-like domain has the following consensus sequence:
C-X.sub.4-8-C-X.sub.1-2-G-X-C-X.sub.5-9-[WFY]-X-C-X-C-X.sub.2-4-G-[WFY]-G-
-X.sub.1-3-[FY]-C (SEQ ID NO:52), wherein all amino acids are
indicated according to their universal single letter designation,
brackets indicate that the amino acid at that position is selected
from one of the amino acids within the brackets, and "X" designates
any amino acid. The numbers in subscript next to an amino acid
position indicate a range of possible amino acids, for example,
C-X.sub.5-9-C indicates that there is a cysteine followed by any 5
to 9 amino acids followed by a cysteine. In one embodiment, an
EGF-like domain of the invention is at least 75%, or more
preferably at least 80%, 85%, or most preferably 90%, 95%, 98% or
100% identical, i.e., no gaps in the sequence, to the human Delta3
polypeptide sequence from amino acids 222-250, amino acids 253-281,
amino acids 288-321, amino acids 328-359, amino acids 366-399,
amino acids 411-437, amino acids 444-475, and amino acids 484-517
of SEQ ID NO: 2. In another preferred embodiment, a Delta3 EGF-like
domain conforms to the above-described EGF-like consensus sequence
and is at least 60%, or more preferably at least 75%, 80%, 85%, or
most preferably 90%, 95%, 98% or 100% identical to the mouse Delta3
DSL sequence from amino acids 223-251, amino acids 254-282, amino
acids 289-322, amino acids 329-360, amino acids 367-400, amino
acids 412-438, amino acids 445-476, and amino acids 485-518 of SEQ
ID NO: 25.
[0552] In another embodiment, a nucleic acid of the invention
encodes Delta3 EGF-like domain is at least 75%, or more preferably
at least 80%, 85%, or most preferably 90%, 95%, 98% or 100%
identical to the human Delta3 polypeptide sequence from amino acids
222-250, amino acids 253-281, amino acids 288-321, amino acids
328-359, amino acids 366-399, amino acids 411-437, amino acids
444-475, or amino acids 484-517 of SEQ ID NO: 2. In another
embodiment, a Delta3 EGF-like domain is at least 75%, or more
preferably at least 80%, 85%, or most preferably 90%, 95%, 98% or
100% identical to the mouse Delta3 EGF-like domain sequence from
amino acids 223-251, amino acids 254-282, amino acids 289-322,
amino acids 329-360, amino acids 367-400, amino acids 412-438,
amino acids 445-476, or amino acids 485-518 of SEQ ID NO: 25.
[0553] Polypeptides encoded by any of the above-described nucleic
acids can be soluble. Preferred soluble peptides comprise at least
a portion of the extracellular domain of a Delta3 protein. Even
more preferred soluble polypeptides comprise an amino acid sequence
corresponding to about amino acid 1 to about amino acid 529 of SEQ
ID NO: 2, corresponding to about amino acid 18 to about amino acid
529 of SEQ ID NO: 2 or a homolog thereof. Alternatively, an
extracellular domain is comprised of about amino acid 1 to about
amino acid 530 of SEQ ID NO: 25, about amino acid 18 to about amino
acid 530 of SEQ ID NO: 25 or a homolog thereof.
[0554] Yet other preferred soluble Delta3 polypeptides comprise at
least one EGF-like domain. Such polypeptides may in addition
comprise a DSL domain and optionally a signal peptide.
[0555] In another embodiment, nucleic acids encode a Delta3
polypeptide as part of a fusion protein. A preferred fusion protein
is a Delta3 Immunoglobulin (Ig) fusion protein, or alternatively, a
Delta3 portion as described above fused to Ig. Such fusion proteins
can comprise at least a portion of the extracellular domain of a
Delta3 domain. A portion can be any portion of at least about 10
amino acids, such as the portions described above. Nucleic acids
encoding such fusion proteins can be prepared, e.g., as described
in U.S. Pat. No. 5,434,131.
[0556] Alternatively, polypeptides encoded by the nucleic acid of
the invention can be membrane bound. Membrane bound polypeptides of
the invention preferably comprise a transmembrane domain. As used
herein, a "transmembrane domain" refers to an amino acid sequence
having at least about 20 to 25 amino acid residues in length and
which contains at least about 65-70% hydrophobic amino acid
residues such as alanine, leucine, isoleucine, phenylalanine,
proline, tyrosine, tryptophan, or valine. The transmembrane domain
can be from a Delta3 protein, such as a transmembrane domain
comprising amino acid 530 to amino acid 553 of SEQ ID NO: 2, or
amino acid 531 to amino acid 554 of SEQ ID NO: 25.
[0557] In a one embodiment, a nucleic acid of the invention encodes
transmembrane domain contains at least about 15 to 30 amino acid
residues, preferably about 20-25 amino acid residues, and has at
least about 60-80%, more preferably 65-75%, and more preferably at
least about 70% hydrophobic residues from about amino acid 530 to
about amino acid 553 of SEQ ID NO: 2, or from about amino acid 531
to about amino acid 554 of SEQ ID NO: 25.
[0558] Alternatively, the transmembrane domain can be from another
membrane protein, such as to produce a chimeric membranous Delta3
protein. Yet other polypeptides of the invention can be
intracellular proteins. Accordingly, also within the scope of the
invention are proteins which do not comprise a transmembrane
domain. Other proteins of the invention do not include an
extracellular domain. Additional proteins of the invention do not
include an extracellular domain nor a transmembrane domain.
[0559] Polypeptides encoded by the nucleic acid of the invention
can comprise a cytoplasmic domain. In a preferred embodiment, a
nucleic acid of the invention encodes a polypeptide comprising a
Delta3 cytoplasmic domain. In an even more preferred embodiment,
the cytoplasmic domain has an amino acid sequence corresponding to
a sequence from about amino acid 554 to about amino acid 685 of SEQ
ID NO: 2, or a portion thereof, or from about amino acid 555 to
about amino acid 686 of SEQ ID NO: 25.
[0560] In yet other preferred embodiments, the nucleic acid of the
invention encodes a polypeptide comprising at least one domain of a
Delta3 protein selected from the group consisting of: a signal
peptide, a DSL motif, an EGF-like domain, a transmembrane domain,
and a cytoplasmic domain. The polypeptide of the invention can
comprise several of these domains from a Delta3 protein.
[0561] Alternatively, a nucleic acid of the invention encodes a
polypeptide that can be a chimeric protein, i.e., comprised of at
least one conserved domain of SEQ ID NO: 2, 25, 2, 25, 28, 30, 32,
34, 36, 38, 40, 42, 44 or 46, or the amino acid sequence encoded by
the cDNA of a clone deposited with the ATCC.RTM. as Accession
Number 98348 and at least one conserved domain from a polypeptide
other than a Delta3 protein. Accordingly, in one embodiment, a
nucleic acid of the invention encodes a Delta3 polypeptide of 2,
25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348 wherein, for example, the DSL
motif from amino acids 173-217 of SEQ ID NO: 2, are replaced with
amino acids from a comparable DSL domain of a Delta-like protein
other than Delta3.
[0562] In yet another embodiment, the nucleic acid encodes a Delta3
protein having a signal peptide from a protein other than a Delta3
protein. Also within the scope of the invention are Delta3 nucleic
acids which encode a Delta3 polypeptide, wherein the cytoplasmic
domain is other than a Delta3 cytoplasmic domain. In addition, the
invention contemplates a Delta3 nucleic acid molecule, wherein the
nucleic acid encodes a Delta3 polypeptide with a cytoplasmic domain
and a extracellular domain from a protein other than Delta3.
[0563] Delta-like proteins other than Delta3 proteins can be, e.g.,
toporythmic proteins. "Toporythmic proteins" is intended to include
Notch, Delta, Serrate, Enhancer of Split, Deltex, and other members
of this family of proteins sharing structural similarities. (See
e.g., International Patent Publication Nos. WO 97/01571 (Jan. 16,
1997); WO 92/19734 (Nov. 12, 1992) and WO 94/07474 (Apr. 14,
1994)).
[0564] Nucleic acids encoding polypeptides having an amino acid
sequence that is homologous to any of the above described portions
of SEQ ID NO: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or
the amino acid sequence encoded by the cDNA of a clone deposited
with the ATCC.RTM. as Accession Number 98348 are also within the
scope of the invention. Preferred nucleic acids of the invention
encode polypeptides comprising an amino acid sequence which are at
least about 70%, at least about 75%, at least about 80%, or at
least about 85% identical to the amino acid sequence of any of the
Delta3 domains. Even more preferred nucleic acids of the invention
encode polypeptides comprising an amino acid sequence which are at
least about 90%, at least about 95%, at least about 98%, or at
least about 99% identical to the amino acid sequence of any of the
Delta3 domains.
[0565] In one embodiment, the nucleic acid, e.g., cDNA, encodes a
peptide having at least one activity of the subject Delta3
polypeptide, such as the ability to bind to a Delta3 interacting
molecule, such as a Delta3 receptor e.g., Notch. Non-limiting
examples of binding assays for Delta3 interaction with a Delta3
interacting molecule include: measuring interaction of Delta3
polypeptides of the invention with a Delta3 interacting molecule,
such as for example Notch, include binding assays involving soluble
forms of Delta3 and a Delta3 interacting molecule, measuring a
Delta3 domain, e.g., the DSL domain, binding to a Delta3
interacting molecule, measuring Delta3 binding to receptors
expressed on cells, and measuring soluble Delta3 binding to an
immobilized Delta3 interacting molecule, i.e., solid-phase binding
assays. Specific examples of these assays are set forth in Shimizu
et al. (1999) J. Biol. Chem. 274:32961-32969.
[0566] Additional molecules, e.g., polypeptides or peptides,
capable of interacting with a Delta3 protein or fragment thereof
can be identified by various methods, e.g., methods based on
binding assays. For example, various types of expression libraries
can be screened with a Delta3 protein or portion thereof. A
two-hybrid system can be used to isolate cytoplasmic proteins
interacting with the cytoplasmic domain of Delta3. Portions of
Delta3 proteins which are capable of interacting with a ligand can
be determined by preparing fragments of Delta3 proteins and
screening these fragments for those that are capable of interacting
with the ligand.
[0567] Based at least in part on the observation that the
N-terminal portion of Drosophila Delta protein, which contains a
DSL domain and EGF-like domain, is necessary and sufficient for in
vitro binding to Notch (Henrique et al. (1995) Nature 375:787;
Muskavitch (1994) Dev. Biol. 166:415), it is likely that the domain
of Delta3 proteins capable of interacting with a ligand includes
the DSL domain and/or at least a portion of the EGF-like domain.
However, other portions of the extracellular domain of Delta3 could
be necessary for binding to at least some Delta3 ligands.
[0568] In other preferred embodiments, the subject Delta3
polypeptide can modulate proliferation and/or differentiation or
cell death of specific target cells, e.g., neural cells or
endothelial cells. Assays for determining that a Delta3 polypeptide
has at least one activity of a Delta3 protein are described
infra.
[0569] Still other preferred nucleic acids of the present invention
encode a Delta3 polypeptide which includes a polypeptide sequence
corresponding to all or a portion of amino acid residues in SEQ ID
NO: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, e.g., at least
2, 5, 10, 25, 50, 100, 150 or 200 amino acid residues of that
region. Preferred nucleic acids encode a polypeptide comprising at
least two consecutive amino acid residues from about amino acid 1
to about amino acid 570 of the amino acid sequence set forth in SEQ
ID NO: 2 or from about amino acid 1 to about amino acid 571 of the
amino acid sequence set forth in SEQ ID NO: 25.
[0570] Yet other preferred nucleic acids encode a polypeptide
comprising at least about 3, at least about 5, at least about 10,
at least about 15, at least about 20, or at least about 25
consecutive amino acids from about amino acid 1 to about amino acid
575 set forth in SEQ ID NO: 2, from about amino acid 18 to about
amino acid 575 set forth in SEQ ID NO: 2, from about amino acid 1
to about amino acid 576 set forth in SEQ ID NO: 25, or from about
amino acid 18 to about amino acid 576 set forth in SEQ ID NO:
25.
[0571] The invention further provides for nucleic acids encoding a
polypeptide having an amino acid sequence which is at least about
70%, preferably at least about 80%, and most preferably at least
about 90% to at least about 10 consecutive amino acids set forth in
SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or at
least about 10 consecutive amino acids from a portion of SEQ ID
NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46. In one
embodiment, the portion corresponds to about amino acid 1 to about
amino acid 575 of SEQ ID NO: 2, about amino acid 18 to about amino
acid 575 of SEQ ID NO: 2, from about amino acid 1 to about amino
acid 576 set forth in SEQ ID NO: 25, or from about amino acid 1 to
about amino acid 576 set forth in SEQ ID NO: 25. Coding nucleic
acid molecules of the invention preferably comprise at least about
200, 250, 300, 350, 400, 410, 420, 430, 435 or 440 base pairs.
[0572] The invention further pertains to nucleic acid molecules for
use as probes/primer or antisense molecules (i.e. non-coding
nucleic acid molecules), which can comprise at least about 6, 12,
20, 30, 50, 100, 125, 150 or 200 nucleotides or base pairs. Yet
other preferred nucleic acids of the invention comprise at least
about 300, at least about 350, at least about 400, at least about
450, at least about 500, or at least about 600 nucleotides of SEQ
ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45. In
some embodiments, the nucleic acids of the invention correspond to
a 5' portion of nucleic acid sequence SEQ ID NO: 1, 3, 24, 26, 27,
29, 31, 33, 35, 37, 39, 41, 43 or 45. For example, a nucleic acid
of the invention can correspond to a portion of about nucleotide 1
to about nucleotide 2000 of nucleic acid sequence SEQ ID NO: 1, 3,
24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45.
[0573] Preferred nucleic acids for use as a probe according to the
methods of the invention include nucleic acids comprising a
nucleotide sequence having at least about 6, preferably at least
about 9, more preferably at least about 12 and even more preferably
at least about 15 consecutive nucleotides from SEQ ID NOs: Nos:1,
3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or from a
portion thereof. In a preferred embodiment, the portion corresponds
to about nucleotide 1 to about nucleotide 2060 of SEQ ID NOs:
Nos:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45.
Alternatively a portion can be a nucleotide sequence encoding a
conserved motif of hDelta3 or mDelta3 protein. Alternatively, the
portion can be a nucleotide sequence located between nucleic acid
sequences encoding conserved motifs of a human or mouse Delta3
protein.
[0574] The invention further provides for a combination of at least
two nucleic acids corresponding to at least a portion of SEQ ID
NOs: Nos:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45, or
a homolog thereof. Accordingly, in one embodiment, the invention
provides a combination of two nucleic acids of at least about 6,
preferably at least about 9, more preferably at least about 12 and
even more preferably at least about 15 consecutive nucleotides from
SEQ ID NOs: Nos:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or
45, or from a portion thereof. In a preferred embodiment, at least
one of the nucleic acids is labeled.
[0575] Another aspect of the invention provides a nucleic acid
which hybridizes under stringent conditions to a nucleic acid
represented by one of SEQ ID Nos:1, 3, 24, 26, 27, 29, 31, 33, 35,
37, 39, 41, 43 or 45. In yet another embodiment, a naturally
occurring Delta3 nucleic acid of the invention, e.g., SEQ ID NO: 1,
3, 24 or 26 hybridizes under high stringency conditions to a
species variant of Delta3, such as a species variant shown in any
one of SEQ ID NOs: 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45. In yet
another embodiment, a Delta3 nucleic acid, e.g., SEQ ID NO: 1, 3,
24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45 hybridizes under
high stringency conditions to a representative mammalian
Delta3.
[0576] Preferred nucleic acids have a sequence at least about 75%
identical and more preferably at least about 80% and even more
preferably at least about 85% identical with a nucleic acid
sequence of a Delta3 gene, such as a human Delta3 gene or a mouse
Delta3 gene, e.g., such as a sequence shown in one of SEQ ID NOs:
1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or 45. Nucleic
acids at least about 90%, more preferably at least about 95%, and
most preferably at least about 98-99% homologous with a nucleic
sequence represented in one of SEQ ID NOs: 1, 3, 24, 26, 27, 29,
31, 33, 35, 37, 39, 41, 43 or 45 are of course also within the
scope of the invention. In preferred embodiments, the nucleic acid
is a human Delta3 gene and in particularly preferred embodiments,
includes all or a portion of the nucleotide sequence corresponding
to the coding region of one of SEQ ID NOs: 1, 3, 24, 26, 27, 29,
31, 33, 35, 37, 39, 41, 43 or 45.
[0577] In addition to naturally-occurring allelic variants of the
FTHMA-070, T85, Tango77, T129 or A259 sequence that may exist in
the population, the skilled artisan will further appreciate that
changes can be introduced by mutation into the nucleotide sequence
of SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, SEQ ID
NO:71, SEQ ID NO:73, SEQ ID NO:76, SEQ ID NO:80, 137, 139, 145,
146, 163, 164 or the cDNA of ATCC 98807, thereby leading to changes
in the amino acid sequence of the encoded FTHMA-070, T85, Tango77,
T129 or A259 protein, without altering the functional ability of
the FTHMA-070, T85, Tango77, T129 or A259 protein. For example, one
can make nucleotide substitutions leading to amino acid
substitutions at "non-essential" amino acid residues. A
"non-essential" amino acid residue is a residue that can be altered
from the wild-type sequence of FTHMA-070, T85, Tango77, T129 or
A259 (e.g., the sequence of SEQ ID NO:54, SEQ ID NO:72, SEQ ID
NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ
ID NO:138, SEQ ID NO:147 or SEQ ID NO:165) without altering the
biological activity, whereas an "essential" amino acid residue is
required for biological activity. For example, amino acid residues
that are conserved among the FTHMA-070, T85, Tango77, T129 or A259
proteins of various species are predicted to be particularly
unamenable to alteration.
[0578] For example, preferred T85 proteins of the present
invention, contain at least one fibronectin I11 or Ig superfamily
domain. Such conserved domains are less likely to be amenable to
mutation. Other amino acid residues, however, (e.g., those that are
not conserved or only semi-conserved among T85 of various species)
may not be essential for activity and thus are likely to be
amenable to alteration.
[0579] Accordingly, another aspect of the invention pertains to
nucleic acid molecules encoding FTHMA-070, T85, Tango77, T129 or
A259 proteins that contain changes in amino acid residues that are
not essential for activity. Such FTHMA-070, T85, Tango77, T129 or
A259 proteins differ in amino acid sequence from SEQ ID NO:54, SEQ
ID NO:58, SEQ ID NO:72, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79,
SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:138, SEQ ID NO:147 or SEQ ID
NO:165, respectively, yet retain biological activity.
[0580] For example, preferred T129 proteins of the present
invention, contain at least one TNFR/NGFR cysteine rich domain.
Such conserved domains are less likely to be amenable to mutation.
Other amino acid residues, however, (e.g., those that are not
conserved or only semi-conserved among T129 of various species) may
not be essential for activity and thus are likely to be amenable to
alteration.
[0581] In one embodiment, the isolated nucleic acid molecule
includes a nucleotide sequence encoding a protein that includes an
amino acid sequence that is at least about 45% identical, 65%, 75%,
85%, 95%, or 98% identical to the amino acid sequence of SEQ ID
NO:72, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ
ID NO:83, SEQ ID NO:138, SEQ ID NO:147 or SEQ ID NO:165.
[0582] An isolated nucleic acid molecule encoding a FTHMA-070, T85,
Tango77, T129 or A259 protein having a sequence which differs from
that of SEQ ID NO:54, SEQ ID NO:58, SEQ ID NO:72, SEQ ID NO:75, SEQ
ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:83,
SEQ ID NO:138, SEQ ID NO:147 or SEQ ID NO:165, respectively, can be
created by introducing one or more nucleotide substitutions,
additions or deletions into the nucleotide sequence of SEQ ID
NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:71, SEQ
ID NO:73, SEQ ID NO:76, SEQ ID NO:80, SEQ ID NO:137, SEQ ID NO:139,
SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:163 or SEQ ID NO:164 or the
cDNA of ATCC 98807 such that one or more amino acid substitutions,
additions or deletions are introduced into the encoded protein.
Mutations can be introduced by standard techniques, such as
site-directed mutagenesis and PCR-mediated mutagenesis. Preferably,
conservative amino acid substitutions are made at one or more
predicted non-essential amino acid residues. A "conservative amino
acid substitution" is one in which the amino acid residue is
replaced with an amino acid residue having a similar side chain.
Families of amino acid residues having similar side chains have
been defined in the art. These families include amino acids with
basic side chains (e.g., lysine, arginine, histidine), acidic side
chains (e.g., aspartic acid, glutamic acid), uncharged polar side
chains (e.g., glycine, asparagine, glutamine, serine, threonine,
tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine,
leucine, isoleucine, proline, phenylalanine, methionine,
tryptophan), beta-branched side chains (e.g., threonine, valine,
isoleucine) and aromatic side chains (e.g., tyrosine,
phenylalanine, tryptophan, histidine). Thus, a predicted
nonessential amino acid residue in FTHMA-070, T85, Tango77, T129 or
A259 is preferably replaced with another amino acid residue from
the same side chain family. Alternatively, mutations can be
introduced randomly along all or part of a FTHMA-070, T85, Tango77,
T129 or A259 coding sequence, such as by saturation mutagenesis,
and the resultant mutants can be screened for FTHMA-070, T85,
Tango77, T129 or A259 biological activity to identify mutants that
retain activity. Following mutagenesis, the encoded protein can be
expressed recombinantly and the activity of the protein can be
determined.
[0583] In a preferred embodiment, a mutant FTHMA-070 or T85 protein
can be assayed for the ability to form protein:protein interactions
with other proteins.
[0584] In a preferred embodiment, a mutant Tango-77 protein can be
assayed for: (1) the ability to form protein:protein interactions
with proteins in the Tango-77 signalling pathway; (2) the ability
to bind a Tango-77 ligand or receptor; or (3) the ability to bind
to an intracellular target protein or (4) the ability to interact
with a protein involved in inflammation or (5) the ability to bind
the IL-1 receptor. In yet another preferred embodiment, a mutant
Tango-77 can be assayed for the ability to modulate inflammation,
asthma, autoimmune diseases, and sepsis.
[0585] In a preferred embodiment, a mutant A259 polypeptide that is
a variant of a A259 polypeptide of the invention can be assayed
for: (1) the ability to form protein:protein interactions with
proteins in a signaling pathway of the polypeptide of the
invention; (2) the ability to bind a ligand of the polypeptide of
the invention; or (3) the ability to bind to an intracellular
target protein of the polypeptide of the invention. In yet another
preferred embodiment, the mutant polypeptide can be assayed for the
ability to modulate cellular proliferation, cellular migration or
chemotaxis, or cellular differentiation.
[0586] In addition to naturally-occurring allelic variants of the
SPOIL sequences that may exist in the population, the skilled
artisan will further appreciate that changes can be introduced by
mutation into the nucleotide sequences of SEQ ID NO:89, SEQ ID
NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the DNA insert of
the plasmid deposited with ATCC as Accession Number 98984, thereby
leading to changes in the amino acid sequence of the encoded SPOIL
proteins, without altering the functional ability of the SPOIL
proteins. For example, nucleotide substitutions leading to amino
acid substitutions at "non-essential" amino acid residues can be
made in the sequence of SEQ ID NO:89, SEQ ID NO:101, SEQ ID NO:104,
SEQ ID NO:112, the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984. A "non-essential" amino acid
residue is a residue that can be altered from the wild-type
sequence of SPOIL (e.g., the sequence of SEQ ID NO:90, SEQ ID
NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984) without altering the biological activity, whereas an
"essential" amino acid residue is required for biological activity.
For example, amino acid residues of SPOIL that are conserved among
the human and murine family numbers of this invention, (as
indicated by the alignment and comparison of the amino acid
sequences of SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID
NO:113) are predicted to be essential in SPOIL and, thus are not
likely to be amenable to alteration. Table III further sets forth
conserved amino residues among SPOIL proteins which are predicted
to be unamenable to alteration. Furthermore, amino acid residues
that are conserved among the SPOIL proteins of the present
invention, and the IL-1ra protein (as indicated by the alignment
presented in FIG. 7) are predicted to be unamenable to
alteration.
[0587] Accordingly, another aspect of the invention pertains to
nucleic acid molecules encoding SPOIL proteins that contain changes
in amino acid residues that are not essential for activity. Such
SPOIL proteins differ in amino acid sequence from SEQ ID NO:90, SEQ
ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984, yet retain biological activity. In one embodiment, the
isolated nucleic acid molecule comprises a nucleotide sequence
encoding a protein, wherein the protein comprises an amino acid
sequence at least about 60% identical to the amino acid sequence of
SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the
amino acid sequence encoded by the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the amino acid
sequence encoded by the DNA insert of the plasmid deposited with
ATCC as Accession Number 98984. Preferably, the protein encoded by
the nucleic acid molecule is at least about 65-70% identical to SEQ
ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98883, or the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98984, more preferably at least about 75-80%
identical to SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID
NO:113, the amino acid sequence encoded by the DNA insert of the
plasmid deposited with ATCC as Accession Number 98883, or the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984, even more preferably at least
about 85-90% identical to SEQ ID NO:90, SEQ ID NO:102, SEQ ID
NO:105, SEQ ID NO:113, the amino acid sequence encoded by the DNA
insert of the plasmid deposited with ATCC as Accession Number
98883, or the amino acid sequence encoded by the DNA insert of the
plasmid deposited with ATCC as Accession Number 98984, and most
preferably at least about 95% identical to SEQ ID NO:90, SEQ ID
NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984.
[0588] An isolated nucleic acid molecule encoding a SPOIL protein
homologous to the protein of SEQ ID NO:90, SEQ ID NO:102, SEQ ID
NO:105, SEQ ID NO:113, the amino acid sequence encoded by the DNA
insert of the plasmid deposited with ATCC as Accession Number
98883, or the amino acid sequence encoded by the DNA insert of the
plasmid deposited with ATCC as Accession Number 98984, can be
created by introducing one or more nucleotide substitutions,
additions or deletions into the nucleotide sequence of SEQ ID
NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the DNA insert
of the plasmid deposited with ATCC as Accession Number 98883, or
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98984, such that one or more amino acid substitutions,
additions or deletions are introduced into the encoded protein.
Mutations can be introduced into SEQ ID NO:89, SEQ ID NO:101, SEQ
ID NO:104, SEQ ID NO:112, the DNA insert of the plasmid deposited
with ATCC as Accession Number 98883, or the DNA insert of the
plasmid deposited with ATCC as Accession Number 98984, by standard
techniques, such as site-directed mutagenesis and PCR-mediated
mutagenesis.
[0589] Alternatively, in another embodiment, mutations can be
introduced randomly along all or part of a SPOIL coding sequence,
such as by saturation mutagenesis, and the resultant mutants can be
screened for SPOIL biological activity to identify mutants that
retain activity. Following mutagenesis of SEQ ID NO:89, SEQ ID
NO:101, SEQ ID NO:104, SEQ ID NO:112, the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the DNA insert of
the plasmid deposited with ATCC as Accession Number 98984, the
encoded protein can be expressed recombinantly and the activity of
the protein can be determined.
[0590] In a preferred embodiment, a mutant SPOIL-I protein can be
assayed for (1) the ability to modulate IL-1 signal transduction,
either in vitro or in vivo; (2) modulate IL-1 stimulated cell
development or differentiation, either in vitro or in vivo; and (3)
modulate IL-1 stimulated cellular proliferation, either in vitro or
in vivo. In yet another preferred embodiment, a mutant SPOIL can be
assayed for ability to 1) modulate cellular signal transduction; 2)
regulate cellular proliferation; 3) regulate cellular
differentiation; 4) modulate a cell involved in immune response;
and 5) modulate a cell involved in bone metabolism (e.g. osteoblast
or osteoclasts).
[0591] Moreover, nucleic acid molecules encoding other NEOKINE
family members (e.g., NEOKINE-2), and thus which have a nucleotide
sequence which differs from the NEOKINE-1 sequences of SEQ ID
NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or the
nucleotide sequence of the DNA insert of the plasmid deposited with
ATCC as Accession Number 98751 are intended to be within the scope
of the invention. For example, a NEOKINE-2 cDNA can be identified
based on the nucleotide sequence of human NEOKINE-1. Moreover,
nucleic acid molecules encoding NEOKINE proteins from different
species, and thus which have a nucleotide sequence which differs
from the NEOKINE sequences of SEQ ID NO:115, SEQ ID NO:118, SEQ ID
NO:121, SEQ ID NO:124, or the nucleotide sequence of the DNA insert
of the plasmid deposited with ATCC as Accession Number 98751 are
intended to be within the scope of the invention. For example, a
Xenopus NEOKINE cDNA can be identified based on the nucleotide
sequence of a human NEOKINE.
[0592] Nucleic acid molecules corresponding to natural allelic
variants and homologues of the NEOKINE cDNAs of the invention can
be isolated based on their homology to the NEOKINE nucleic acids
disclosed herein using the cDNAs disclosed herein, or a portion
thereof, as a hybridization probe according to standard
hybridization techniques under stringent hybridization
conditions.
[0593] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 15 nucleotides in length and
hybridizes under stringent conditions to the nucleic acid molecule
comprising the nucleotide sequence of SEQ ID NO:115, SEQ ID NO:118,
SEQ ID NO:121, SEQ ID NO:124, or the nucleotide sequence of the DNA
insert of the plasmid deposited with ATCC as Accession Number
98751. In other embodiment, the nucleic acid is at least 30, 50,
100, 250 or 500 nucleotides in length. As used herein, the term
"hybridizes under stringent conditions" is intended to describe
conditions for hybridization and washing under which nucleotide
sequences at least 60% homologous to each other typically remain
hybridized to each other. Preferably, the conditions are such that
sequences at least about 70%, more preferably at least about 80%,
even more preferably at least about 85% or 90% homologous to each
other typically remain hybridized to each other. Such stringent
conditions are known to those skilled in the art and can be found
in Current Protocols in Molecular Biology, John Wiley & Sons,
N.Y. (1989), 6.3.1-6.3.6. A preferred, non-limiting example of
stringent hybridization conditions are hybridization in 6.times.
sodium chloride/sodium citrate (SSC) at about 45.degree. C.,
followed by one or more washes in 0.2.times.SSC, 0.1% SDS at
50.degree. C., preferably 55.degree. C., and more preferably
60.degree. C. or 65.degree. C. Preferably, an isolated nucleic acid
molecule of the invention that hybridizes under stringent
conditions to the sequence of SEQ ID NO:115, SEQ ID NO:118, SEQ ID
NO:121, SEQ ID NO:124, corresponds to a naturally-occurring nucleic
acid molecule. As used herein, a "naturally-occurring" nucleic acid
molecule refers to an RNA or DNA molecule having a nucleotide
sequence that occurs in nature (e.g., encodes a natural
protein).
[0594] In addition to naturally-occurring allelic variants of the
NEOKINE sequences that may exist in the population, the skilled
artisan will further appreciate that changes can be introduced by
mutation into the nucleotide sequences of SEQ ID NO:115, SEQ ID
NO:118, SEQ ID NO:121, SEQ ID NO:124, or the nucleotide sequence of
the DNA insert of the plasmid deposited with ATCC as Accession
Number 98751, thereby leading to changes in the amino acid sequence
of the encoded NEOKINE proteins, without altering the functional
ability of the NEOKINE proteins. For example, nucleotide
substitutions leading to amino acid substitutions at
"non-essential" amino acid residues can be made in the sequence of
SEQ ID NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or the
nucleotide sequence of the DNA insert of the plasmid deposited with
ATCC as Accession Number 98751. A "non-essential" amino acid
residue is a residue that can be altered from the wild-type
sequence of NEOKINE (e.g., the sequence of SEQ ID NO:116, SEQ ID
NO:119, SEQ ID NO:122, or SEQ ID NO:125) without altering the
biological activity, whereas an "essential" amino acid residue is
required for biological activity. For example, amino acid residues
that are conserved among the NEOKINE proteins of the present
invention, are predicted to be particularly unamenable to
alteration (e.g., the four conserved cycteines). Moreover, amino
acid residues that are defined by the NEOKINE CXC motif are
particularly unamenable to alteration. Furthermore, additional
amino acid residues that are conserved between the NEOKINE proteins
of the present invention as depicted in FIG. 8 are not likely to be
amenable to alteration.
[0595] Accordingly, another aspect of the invention pertains to
nucleic acid molecules encoding NEOKINE proteins that contain
changes in amino acid residues that are not essential for activity.
Such NEOKINE proteins differ in amino acid sequence from SEQ ID
NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125 yet retain
biological activity. In one embodiment, the isolated nucleic acid
molecule comprises a nucleotide sequence encoding a protein,
wherein the protein comprises an amino acid sequence at least about
60% homologous to the amino acid sequence of SEQ ID NO:116, SEQ ID
NO:119, SEQ ID NO:122, or SEQ ID NO:125. Preferably, the protein
encoded by the nucleic acid molecule is at least about 65-70%
homologous to SEQ ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ
ID NO:125, more preferably at least about 75-80% homologous to SEQ
ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125, even
more preferably at least about 85-90% homologous to SEQ ID NO:116,
SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125, and most preferably
at least about 95% homologous to SEQ ID NO:116, SEQ ID NO:119, SEQ
ID NO:122, or SEQ ID NO:125.
[0596] An isolated nucleic acid molecule encoding a NEOKINE protein
homologous to the protein of SEQ ID NO:116, SEQ ID NO:119, SEQ ID
NO:122, or SEQ ID NO:125 can be created by introducing one or more
nucleotide substitutions, additions or deletions into the
nucleotide sequence of SEQ ID NO:115, SEQ ID NO:118, SEQ ID NO:121,
SEQ ID NO:124, or the nucleotide sequence of the DNA insert of the
plasmid deposited with ATCC as Accession Number 98751, such that
one or more amino acid substitutions, additions or deletions are
introduced into the encoded protein. Mutations can be introduced
into SEQ ID NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or
the nucleotide sequence of the DNA insert of the plasmid deposited
with ATCC as Accession Number 98751 by standard techniques, such as
site-directed mutagenesis and PCR-mediated mutagenesis. Thus, a
predicted nonessential amino acid residue in a NEOKINE protein is
preferably replaced with another amino acid residue from the same
side chain family. Alternatively, in another embodiment, mutations
can be introduced randomly along all or part of a NEOKINE coding
sequence, such as by saturation mutagenesis, and the resultant
mutants can be screened for NEOKINE biological activity to identify
mutants that retain activity. Following mutagenesis of SEQ ID
NO:115, SEQ ID NO:118, SEQ ID NO:121, SEQ ID NO:124, or the
nucleotide sequence of the DNA insert of the plasmid deposited with
ATCC as Accession Number 98751, the encoded protein can be
expressed recombinantly and the activity of the protein can be
determined.
[0597] In a preferred embodiment, a mutant NEOKINE protein can be
assayed for (1) modulation of cellular signal transduction, either
in vitro or in vivo; (2) regulation of gene transcription in a cell
expressing a NEOKINE receptor (e.g., RDC1) or receptor which is
specific for another chemokine; (3) regulation of gene
transcription in a cell expressing a NEOKINE receptor or receptor
which is specific for another chemokine, wherein said cell is
involved in angiogenesis or inflammation; (4) regulation of
angiogenesis; (5) regulation of angiogenesis, wherein said
regulation comprises inhibibition of angiogenesis; (6) regulation
of angiogenesis, wherein said regulation comprises maintenance of
angiostasis; (7) regulation of inflammation; and (8) regulation of
inflammation, wherein said regulation comprises inhibition of
chemoattraction (e.g., neutrophil chemoattraction).
[0598] The present invention encompasses antisense nucleic acid
molecules, i.e., molecules which are complementary to a sense
nucleic acid encoding a polypeptide of the invention, e.g.,
complementary to the coding strand of a double-stranded cDNA
molecule or complementary to an mRNA sequence. Accordingly, an
antisense nucleic acid can hydrogen bond to a sense nucleic acid.
The antisense nucleic acid can be complementary to an entire
Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 coding strand, or to only a portion thereof, e.g., all or part
of the protein coding region (or open reading frame). An antisense
nucleic acid molecule can be antisense to all or part of a Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
non-coding region of the coding strand of a nucleotide sequence
encoding a Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 polypeptide of the invention. The non-coding
regions ("5' and 3' untranslated regions") are the 5' and 3'
sequences which flank the coding region and are not translated into
amino acids.
[0599] Given the coding strand sequences encoding FTHMA-070 or T85
disclosed herein, antisense nucleic acids of the invention can be
designed according to the rules of Watson and Crick base pairing.
The antisense nucleic acid molecule can be complementary to the
entire coding region of FTHMA-070 or T85 mRNA, but more preferably
is an oligonucleotide which is antisense to only a portion of the
coding or noncoding region of FTHMA-070 or T85 mRNA.
[0600] Given the coding strand sequences encoding Tango-77
disclosed herein (e.g., SEQ ID NO:73, SEQ ID NO:75, or SEQ ID
NO:78), antisense nucleic acids of the invention can be designed
according to the rules of Watson and Crick base pairing. The
antisense nucleic acid molecule can be complementary to the entire
coding region of Tango-77 mRNA, but more preferably is an
oligonucleotide which is antisense to only a portion of the coding
or noncoding region of Tango-77 mRNA. For example, the antisense
oligonucleotide can be complementary to the region surrounding the
translation start site of Tango-77 mRNA, e.g., an oligonucleotide
having the sequence
TABLE-US-00007 5'-TGCAACTTTTACAGGAAACAC-3' (SEQ ID NO: 193) or
5'-CCTCACTTTTACCCGAGACTC-3' (SEQ ID NO: 194) or
5'-GACGGGTGGTACTTAAAACAA-3'. (SEQ ID NO: 195)
[0601] Given the coding strand sequences encoding SPOIL disclosed
herein (e.g., SEQ ID NO:89, SEQ ID NO:101, SEQ ID NO:104, SEQ ID
NO:112, the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984), antisense nucleic acids of
the invention can be designed according to the rules of Watson and
Crick base pairing. The antisense nucleic acid molecule can be
complementary to the entire coding region of SPOIL mRNA, but more
preferably is an oligonucleotide which is antisense to only a
portion of the coding region of SPOIL mRNA. For example, the
antisense oligonucleotide can be complementary to the region
surrounding the translation start site of SPOIL mRNA.
[0602] Given the coding strand sequences encoding NEOKINE disclosed
herein (e.g., SEQ ID NO:117, SEQ ID NO:120, or SEQ ID NO:123),
antisense nucleic acids of the invention can be designed according
to the rules of Watson and Crick base pairing. The antisense
nucleic acid molecule can be complementary to the entire coding
region of NEOKINE mRNA, but more preferably is an oligonucleotide
which is antisense to only a portion of the coding or noncoding
region of NEOKINE mRNA. For example, the antisense oligonucleotide
can be complementary to the region surrounding the translation
start site of NEOKINE mRNA.
[0603] Given the coding strand sequences encoding T129 disclosed
herein (e.g., SEQ ID NO:137 or SEQ ID NO:139), antisense nucleic
acids of the invention can be designed according to the rules of
Watson and Crick base pairing. The antisense nucleic acid molecule
can be complementary to the entire coding region of T129 mRNA, but
more preferably is an oligonucleotide which is antisense to only a
portion of the coding or noncoding region of T129 mRNA. For
example, the antisense oligonucleotide can be complementary to the
region surrounding the translation start site of T129 mRNA, e.g.,
an oligonucleotide having the sequence
TABLE-US-00008 CTGGTGGTCCCCGGACTCCTACTTCGGTT (SEQ ID NO: 143) or
GACTCCTACTTCGGTTCAGA. (SEQ ID NO: 144)
[0604] An antisense oligonucleotide can be, for example, about 5,
10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An
antisense nucleic acid of the invention can be constructed using
chemical synthesis and enzymatic ligation reactions using
procedures known in the art. For example, an antisense nucleic acid
(e.g., an antisense oligonucleotide) can be chemically synthesized
using naturally-occurring nucleotides or variously modified
nucleotides designed to increase the biological stability of the
molecules or to increase the physical stability of the duplex
formed between the antisense and sense nucleic acids, e.g.,
phosphorothioate derivatives and acridine substituted nucleotides
can be used. Examples of modified nucleotides which can be used to
generate the antisense nucleic acid include 5-fluorouracil,
5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine,
xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N6-adenine, 7-methylguanine,
5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil,
5-methoxyuracil, 2-methylthio-N-6-isopentenyladenine,
uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine,
2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,
5-methyluracil, uracil-5-oxyacetic acid methylester,
uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil,
3-(3-amino-3-N2-carboxypropyl) uracil, (acp3)w, and
2,6-diaminopurine. Alternatively, the antisense nucleic acid can be
produced biologically using an expression vector into which a
nucleic acid has been subcloned in an antisense orientation (i.e.,
RNA transcribed from the inserted nucleic acid will be of an
antisense orientation to a target nucleic acid of interest,
described further in the following subsection).
[0605] The antisense nucleic acid molecules of the invention are
typically administered, individually or in combination (that is
two, three, four, or more different antisense molecules), to a
subject or generated in situ such that they hybridize with or bind
to cellular mRNA and/or genomic DNA encoding a selected polypeptide
of the invention to thereby inhibit expression, e.g., by inhibiting
transcription and/or translation. The hybridization can be by
conventional nucleotide complementarity to form a stable duplex,
or, for example, in the case of an antisense nucleic acid molecule
which binds to DNA duplexes, through specific interactions in the
major groove of the double helix. An example of a route of
administration of antisense nucleic acid molecules of the invention
includes direct injection at a tissue site. Alternatively,
antisense nucleic acid molecules can be modified to target selected
cells and then administered systemically. For example, for systemic
administration, antisense molecules can be modified such that they
specifically bind to receptors or antigens expressed on a selected
cell surface, e.g., by linking the antisense nucleic acid molecules
to peptides or antibodies which bind to cell surface receptors or
antigens. The antisense nucleic acid molecules can also be
delivered to cells using the vectors described herein. To achieve
sufficient intracellular concentrations of the antisense molecules,
vector constructs in which the antisense nucleic acid molecule is
placed under the control of a strong pol II or pol III promoter are
preferred.
[0606] An antisense nucleic acid molecule of the invention can be
an .alpha.-anomeric nucleic acid molecule. An .alpha.-anomeric
nucleic acid molecule forms specific double-stranded hybrids with
complementary RNA in which, contrary to the usual .beta.-units, the
strands run parallel to each other (Gaultier et al. (1987) Nucleic
Acids Res. 15:6625-6641). The antisense nucleic acid molecule can
also comprise a 2'-o-methylribonucleotide (Inoue et al. (1987)
Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue
(Inoue et al. (1987) FEBS Lett. 215:327-330).
[0607] The invention also encompasses ribozymes. Ribozymes are
catalytic RNA molecules with ribonuclease activity which are
capable of cleaving a single-stranded nucleic acid, such as an
mRNA, to which they have a complementary region. Thus, ribozymes
(e.g., hammerhead ribozymes (described in Haselhoff and Gerlach
(1988) Nature 334:585-591)) can be used to catalytically cleave
mRNA transcripts to thereby inhibit translation of the protein
encoded by the mRNA. A ribozyme having specificity for a nucleic
acid molecule encoding a polypeptide of the invention can be
designed based upon the nucleotide sequence of a cDNA disclosed
herein. For example, a derivative of a Tetrahymena L-19 IVS RNA can
be constructed in which the nucleotide sequence of the active site
is complementary to the nucleotide sequence to be cleaved in a Cech
et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No.
5,116,742. Alternatively, an mRNA encoding a polypeptide of the
invention can be used to select a catalytic RNA having a specific
ribonuclease activity from a pool of RNA molecules. See, e.g.,
Bartel and Szostak (1993) Science 261:1411-1418.
[0608] The invention also encompasses nucleic acid molecules which
form triple helical structures. For example, expression of a
polypeptide of the invention can be inhibited by targeting
nucleotide sequences complementary to the regulatory region of the
gene encoding the polypeptide (e.g., the promoter and/or enhancer)
to form triple helical structures that prevent transcription of the
gene in target cells. See generally Helene (1991) Anticancer Drug
Des. 6(6):569-84; Helene (1992) Ann. N.Y. Acad. Sci. 660:27-36; and
Maher (1992) Bioassays 14(12):807-15.
[0609] In various embodiments, the nucleic acid molecules of the
invention can be modified at the base moiety, sugar moiety or
phosphate backbone to improve, e.g., the stability, hybridization,
or solubility of the molecule. For example, the deoxyribose
phosphate backbone of the nucleic acids can be modified to generate
peptide nucleic acids (see Hyrup et al. (1996) Bioorganic &
Medicinal Chemistry 4(1): 5-23). As used herein, the terms "peptide
nucleic acids" or "PNAs" refer to nucleic acid mimics, e.g., DNA
mimics, in which the deoxyribose phosphate backbone is replaced by
a pseudopeptide backbone and only the four natural nucleobases are
retained. The neutral backbone of PNAs has been shown to allow for
specific hybridization to DNA and RNA under conditions of low ionic
strength. The synthesis of PNA oligomers can be performed using
standard solid phase peptide synthesis protocols as described in
Hyrup et al. (1996) Bioorganic & Medicinal Chemistry 4(1):
5-23; Perry-O'Keefe et al. (1996) Proc. Natl. Acad. Sci. USA 93:
14670-675.
[0610] PNAs of Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 and A259 can be used in therapeutic and diagnostic
applications. For example, PNAs can be used as antisense or
antigene agents for sequence-specific modulation of gene expression
by, e.g., inducing transcription or translation arrest or
inhibiting replication. PNAs can also be used, e.g., in the
analysis of single base pair mutations in a gene by, e.g., PNA
directed PCR clamping; as artificial restriction enzymes when used
in combination with other enzymes, e.g., S1 nucleases (Hyrup et al.
(1996) Bioorganic & Medicinal Chemistry 4(1): 5-23; or as
probes or primers for DNA sequence and hybridization (Hyrup et al.
(1996) Bioorganic & Medicinal Chemistry 4(1): 5-23;
Perry-O'Keefe et al. (1996) Proc. Natl. Acad. Sci. USA 93:
14670-675).
[0611] In another embodiment, PNAs of Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 and A259 can be modified, e.g.,
to enhance their stability or cellular uptake, by attaching
lipophilic or other helper groups to PNA, by the formation of
PNA-DNA chimeras, or by the use of liposomes or other techniques of
drug delivery known in the art. For example, PNA-DNA chimeras can
be generated which may combine the advantageous properties of PNA
and DNA. Such chimeras allow DNA recognition enzymes, e.g., RNAse H
and DNA polymerases, to interact with the DNA portion while the PNA
portion would provide high binding affinity and specificity.
PNA-DNA chimeras can be linked using linkers of appropriate lengths
selected in terms of base stacking, number of bonds between the
nucleobases, and orientation (Hyrup et al. (1996) Bioorganic &
Medicinal Chemistry 4(1): 5-23). The synthesis of PNA-DNA chimeras
can be performed as described in Hyrup et al. (1996) Bioorganic
& Medicinal Chemistry 4(1): 5-23, and Finn et al. (1996)
Nucleic Acids Res. 24(17):3357-63. For example, a DNA chain can be
synthesized on a solid support using standard phosphoramidite
coupling chemistry and modified nucleoside analogs. Compounds such
as 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite can
be used as a link between the PNA and the 5' end of DNA (Mag et al.
(1989) Nucleic Acids Res. 17:5973-88). PNA monomers are then
coupled in a stepwise manner to produce a chimeric molecule with a
5' PNA segment and a 3' DNA segment (Finn et al. (1996) Nucleic
Acids Res. 24(17):3357-63). Alternatively, chimeric molecules can
be synthesized with a 5' DNA segment and a 3' PNA segment (Peterser
et al. (1975) Bioorganic Med. Chem. Lett. 5:1119-11124).
[0612] In other embodiments, the oligonucleotide may include other
appended groups such as peptides (e.g., for targeting host cell
receptors in vivo), or agents facilitating transport across the
cell membrane (see, e.g., Letsinger et al. (1989) Proc. Natl. Acad.
Sci. USA 86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad.
Sci. USA 84:648-652; PCT Publication NO: WO 88/09810) or the
blood-brain barrier (see, e.g., PCT Publication NO: WO 89/10134).
In addition, oligonucleotides can be modified with
hybridization-triggered cleavage agents (see, e.g., Krol et al.
(1988) Bio/Techniques 6:958-976) or intercalating agents (see,
e.g., Zon (1988) Pharm. Res. 5:539-549). To this end, the
oligonucleotide may be conjugated to another molecule, e.g., a
peptide, hybridization triggered cross-linking agent, transport
agent, hybridization-triggered cleavage agent, etc.
[0613] Nucleic acids having a sequence that differs from the
nucleotide sequences shown in one of SEQ ID Nos: 1, 3, 24, 26, 27,
29, 31, 33, 35, 37, 39, 41, 43 or 45 due to degeneracy in the
genetic code are also within the scope of the invention. Such
nucleic acids encode functionally equivalent peptides (i.e., a
peptide having a biological activity of a Delta3 polypeptide) but
differ from the sequence shown in the sequence listing due to
degeneracy in the genetic code. For example, a number of amino
acids are designated by more than one triplet. Codons that specify
the same amino acid, or synonyms (for example, CAU and CAC each
encode histidine) may result in "silent" mutations which do not
affect the amino acid sequence of a Delta3 polypeptide. However, it
is expected that DNA sequence polymorphisms that do lead to changes
in the amino acid sequences of the subject Delta3 polypeptides will
exist. One skilled in the art will appreciate that these variations
in one or more nucleotides (e.g., up to about 3-5% of the
nucleotides) of the nucleic acids encoding polypeptides having an
activity of a Delta3 polypeptide may exist among individuals of a
given species due to natural allelic variation.
[0614] As indicated by the examples set out below, Delta3
protein-encoding nucleic acids can be obtained from mRNA present in
any of a number of eukaryotic cells. It should also be possible to
obtain nucleic acids encoding Delta3 polypeptides of the present
invention from genomic DNA from both adults and embryos. For
example, a gene encoding a Delta3 protein can be cloned from either
a cDNA or a genomic library in accordance with protocols described
herein, as well as those generally known to persons skilled in the
art. Examples of tissues and/or libraries suitable for isolation of
the subject nucleic acids include endothelial cell libraries, among
others. A cDNA encoding a Delta3 protein can be obtained by
isolating total mRNA from a cell, e.g., a vertebrate cell, a
mammalian cell, or a human cell, including embryonic cells. Double
stranded cDNAs can then be prepared from the total mRNA, and
subsequently inserted into a suitable plasmid or bacteriophage
vector using any one of a number of known techniques. The gene
encoding a Delta3 protein can also be cloned using established
polymerase chain reaction techniques in accordance with the
nucleotide sequence information provided by the invention. The
nucleic acid of the invention can be DNA or RNA. A preferred
nucleic acid is a cDNA represented by a sequence selected from the
group consisting of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35,
37, 39, 41, 43 or 45.
Delta3 Vectors
[0615] This invention also provides expression vectors containing a
nucleic acid encoding a Delta3 polypeptide, operably linked to at
least one transcriptional regulatory sequence. "Operably linked" is
intended to mean that the nucleotide sequence is linked to a
regulatory sequence in a manner which allows expression of the
nucleotide sequence. Regulatory sequences are art-recognized and
are selected to direct expression of the subject Delta3 proteins.
Accordingly, the term "transcriptional regulatory sequence"
includes promoters, enhancers and other expression control
elements. Such regulatory sequences are described in Goeddel; Gene
Expression Technology: Methods in Enzymology 185, Academic Press,
San Diego, Calif. (1990). In one embodiment, the expression vector
includes a recombinant gene encoding a peptide having an agonistic
activity of a subject Delta3 polypeptide, or alternatively,
encoding a peptide which is an antagonistic form of the Delta3
protein. Such expression vectors can be used to transfect cells and
thereby produce polypeptides, including fusion proteins, encoded by
nucleic acids as described herein. Moreover, the gene constructs of
the present invention can also be used as a part of a gene therapy
protocol to deliver nucleic acids encoding either an agonistic or
antagonistic form of one of the subject Delta3 proteins. Thus,
another aspect of the invention features expression vectors for in
vivo or in vitro transfection and expression of a Delta3
polypeptide in particular cell types so as to reconstitute the
function of, or alternatively, abrogate the function of
Delta-induced signaling in a tissue. This could be desirable, for
example, when the naturally-occurring form of the protein is
expressed inappropriately; or to deliver a form of the protein
which alters differentiation of tissue. Expression vectors may also
be employed to inhibit neoplastic transformation.
[0616] In addition to viral transfer methods, such as those
illustrated above, non-viral methods can also be employed to cause
expression of a subject Delta3 polypeptide in the tissue of an
animal. Most nonviral methods of gene transfer rely on normal
mechanisms used by mammalian cells for the uptake and intracellular
transport of macromolecules. In preferred embodiments, non-viral
targeting means of the present invention rely on endocytic pathways
for the uptake of the subject Delta3 polypeptide gene by the
targeted cell. Exemplary targeting means of this type include
liposomal derived systems, polylysine conjugates, and artificial
viral envelopes.
Delta3 Probes and Primers
[0617] Moreover, the nucleotide sequences determined from the
cloning of hDelta3 genes will further allow for the generation of
probes and primers designed for use in identifying and/or cloning
Delta3 homologs in other cell types, e.g., from other tissues, as
well as Delta3 homologs from other mammalian organisms. Probes and
primers of the invention can also be used to determine the identity
of a Delta3 allele and/or the presence or absence of one or more
mutations in a Delta3 gene of a subject. In a preferred embodiment,
a probe or primer of the invention can be used to determine whether
a subject has or is at risk of developing a disease or condition
associated with a specific Delta3 allele, such as an allele
carrying a mutation.
[0618] In a preferred embodiment, the present invention also
provides a probe/primer comprising a substantially purified
oligonucleotide, which oligonucleotide comprises a region of
nucleotide sequence that hybridizes under stringent conditions to
at least about 12, preferably about 25, more preferably about 40,
50 or 75 consecutive nucleotides of sense or anti-sense sequence
selected from the group consisting of SEQ ID NO:1, 3, 24, 26, 27,
29, 31, 33, 35, 37, 39, 41, 43 or 45, or naturally-occurring
mutants thereof. For instance, primers based on the nucleic acid
represented in SEQ ID NOs:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39,
41, 43 or 45 can be used in PCR reactions to clone Delta3 homologs,
e.g., specific Delta3 alleles. Such primers are preferably selected
in a region which does not share significant homology to other
genes, e.g., other Delta genes. Examples of primers of the
invention are set forth as SEQ ID NOs:12-15, set forth below:
TABLE-US-00009 5' end primers: (SEQ ID NO: 12; corresponding to
nucleotides 356 to 375 of SEQ ID NO: 1) 5' AGCGCCTCTGGCTGGGCGCT 3';
(SEQ ID NO: 13; corresponding to nucleotides 725 to 744 of SEQ ID
NO: 1) 5' CGGCCAGAGGCCTTGCCACC 3'; 3' end primers: (SEQ ID NO: 14;
corresponding to the complement of nucleotides 1460 to 1479 of SEQ
ID NO: 1) 5' TTGCGCTCCCGGCTGGAGCC 3'; and (SEQ ID NO: 15;
corresponding to the complement of nucleotides 1592 to 2611 of SEQ
ID NO: 1) 5' ATGCGGCTTGGACCTCGGTT 3'.
[0619] Likewise, probes based on the subject Delta3 sequences can
be used to detect transcripts or genomic sequences encoding the
same or homologous proteins. In preferred embodiments, the probe
further comprises a label group attached thereto and able to be
detected, e.g., the label group is selected from amongst
radioisotopes, fluorescent compounds, enzymes, and enzyme
co-factors.
[0620] As discussed in more detail below, such probes can also be
used as a part of a diagnostic test kit for identifying cells or
tissue which misexpress a Delta3 protein, such as by measuring a
level of a Delta-encoding nucleic acid in a sample of cells from a
patient; e.g., detecting Delta3 mRNA levels or determining whether
a genomic Delta3 gene has been mutated or deleted. Briefly,
nucleotide probes can be generated from the subject Delta3 genes
which facilitate histological screening of intact tissue and tissue
samples for the presence (or absence) of Delta-encoding
transcripts. Similar to the diagnostic uses of anti-Delta3
antibodies, the use of probes directed to Delta3 messages, or to
genomic Delta3 sequences, can be used for both predictive and
therapeutic evaluation of allelic mutations which might be manifest
in, for example, neoplastic or hyperplastic disorders (e.g.,
unwanted cell growth) or abnormal differentiation of tissue. Used
in conjunction with immunoassays as described herein, the
oligonucleotide probes can help facilitate the determination of the
molecular basis for a developmental disorder which may involve some
abnormality associated with expression (or lack thereof) of a
Delta3 protein. For instance, variation in polypeptide synthesis
can be differentiated from a mutation in a coding sequence.
[0621] Also within the scope of the invention are kits for
determining whether a subject is at risk of developing a disease or
condition caused by or contributed by an aberrant Delta3 activity
and/or which is associated with one or more specific Delta3
alleles. In a preferred embodiment, the kit can be used for
determining whether a subject is at risk of developing a
neurological disease or disorder, e.g., a peripheral neuropathy,
e.g., ACCPN.
Delta3 Antisense, Ribozyme and Triplex Techniques
[0622] One aspect of the invention relates to the use of the
isolated nucleic acid in "antisense" therapy. As used herein,
"antisense" therapy refers to administration or in situ generation
of oligonucleotide molecules or their derivatives which
specifically hybridize (e.g., bind) under cellular conditions, with
the cellular mRNA and/or genomic DNA encoding one or more of the
subject Delta3 proteins so as to inhibit expression of that
protein, e.g., by inhibiting transcription and/or translation. The
binding may be by conventional base pair complementarity, or, for
example, in the case of binding to DNA duplexes, through specific
interactions in the major groove of the double helix. In general,
"antisense" therapy refers to the range of techniques generally
employed in the art, and includes any therapy which relies on
specific binding to oligonucleotide sequences.
[0623] An antisense construct of the present invention can be
delivered, for example, as an expression plasmid which, when
transcribed in the cell, produces RNA which is complementary to at
least a unique portion of the cellular mRNA which encodes a Delta3
protein. Alternatively, the antisense construct is an
oligonucleotide probe which is generated ex vivo and which, when
introduced into the cell causes inhibition of expression by
hybridizing with the mRNA and/or genomic sequences of a Delta3
gene. Such oligonucleotide probes are preferably modified
oligonucleotides which are resistant to endogenous nucleases, e.g.,
exonucleases and/or endonucleases, and are therefore stable in
vivo. Exemplary nucleic acid molecules for use as antisense
oligonucleotides are phosphoramidate, phosphothioate and
methylphosphonate analogs of DNA (see also U.S. Pat. Nos.
5,176,996; 5,264,564; and 5,256,775). Additionally, general
approaches to constructing oligomers useful in antisense therapy
have been reviewed, for example, by Van der Krol et al. (1988)
Biotechniques 6:958-976; and Stein et al. (1988) Cancer Res
48:2659-2668.
[0624] With respect to antisense DNA, oligodeoxyribonucleotides
derived from the translation initiation site, i.e., the ATG codon
which encodes the first methionine of the cDNA, e.g., between the
-10 and +10 regions of the Delta3 nucleotide sequence of interest,
are preferred. Preferred antisense molecules of the invention are
from nucleotides 328 to 348 of SEQ ID NO:1 or nucleotides 38 to 58
of SEQ ID NO:24. Non-limiting examples of preferred human and mouse
antisense primers are shown below:
TABLE-US-00010 (SEQ ID NO: 16) 5' TGCCGCCATCCCTCGGGGCGT 3'
(complement to nucleotides 326-346 of SEQ ID NO: 1) (SEQ ID NO: 17)
5' GGACGCTGCCGCCATCCCCT 3' (complement to nucleotides 333-352 of
SEQ ID NO: 1) (SEQ ID NO: 18) 5' GGACGCTGCCGCCATCCCCTCGGGGCGT 3'
(complement to nucleotides 326-352 of SEQ ID NO: 1) (SEQ ID NO: 47)
5' CTCCGGGACGCAGGCGTCATCCCT 3' (complement to nucleotides 38-58 of
SEQ ID NO: 24) (SEQ ID NO: 48) 5' ACAGGCGCTCCGGGACGCAGGCGTCATCC 3'
(complement to nucleotides 40-65 of SEQ ID NO: 24)
[0625] Antisense approaches involve the design of oligonucleotides
(either DNA or RNA) that are complementary to Delta3 mRNA. The
antisense oligonucleotides will bind to the Delta3 mRNA transcripts
and prevent translation. Absolute complementarity, although
preferred, is not required. A sequence "complementary" to a portion
of an RNA, as referred to herein, means a sequence having
sufficient complementarity to be able to hybridize with the RNA,
forming a stable duplex; in the case of double-stranded antisense
nucleic acids, a single strand of the duplex DNA may thus be
tested, or triplex formation may be assayed. The ability to
hybridize will depend on both the degree of complementarity and the
length of the antisense nucleic acid. Generally, the longer the
hybridizing nucleic acid, the more base mismatches with an RNA it
may contain and still form a stable duplex (or triplex, as the case
may be). One skilled in the art can ascertain a tolerable degree of
mismatch by use of standard procedures to determine the melting
point of the hybridized complex.
[0626] Oligonucleotides that are complementary to the 5' end of the
message, e.g., the 5' untranslated sequence up to and including the
AUG initiation codon, should work most efficiently at inhibiting
translation. However, sequences complementary to the 3'
untranslated sequences of mRNAs have recently been shown to be
effective at inhibiting translation of mRNAs as well. (Wagner, R.
(1994) Nature 372:333). Therefore, oligonucleotides complementary
to either the 5' or 3' untranslated, non-coding regions of a Delta3
gene could be used in an antisense approach to inhibit translation
of endogenous Delta3 mRNA. Oligonucleotides complementary to the 5'
untranslated region of the mRNA should include the complement of
the AUG start codon. Antisense oligonucleotides complementary to
mRNA coding regions are less efficient inhibitors of translation
but could be used in accordance with the invention. Whether
designed to hybridize to the 5', 3' or coding region of Delta3
mRNA, antisense nucleic acids should be at least six nucleotides in
length, and are preferably oligonucleotides ranging from 6 to about
50 nucleotides in length. In certain embodiments, the
oligonucleotide is at least 10 nucleotides, at least 17
nucleotides, at least 25 nucleotides, or at least 50
nucleotides.
[0627] Regardless of the choice of target sequence, it is preferred
that in vitro studies are first performed to quantitate the ability
of the antisense oligonucleotide to quantitate the ability of the
antisense oligonucleotide to inhibit gene expression. It is
preferred that these studies utilize controls that distinguish
between antisense gene inhibition and nonspecific biological
effects of oligonucleotides. It is also preferred that these
studies compare levels of the target RNA or protein with that of an
internal control RNA or protein. Additionally, it is envisioned
that results obtained using the antisense oligonucleotide are
compared with those obtained using a control oligonucleotide. It is
preferred that the control oligonucleotide is of approximately the
same length as the test oligonucleotide and that the nucleotide
sequence of the oligonucleotide differs from the antisense sequence
no more than is necessary to prevent specific hybridization to the
target sequence.
[0628] The oligonucleotides can be DNA or RNA or chimeric mixtures
or derivatives or modified versions thereof, single-stranded or
double-stranded. The oligonucleotide can be modified at the base
moiety, sugar moiety, or phosphate backbone, for example, to
improve stability of the molecule, hybridization, etc. The
oligonucleotide may include other appended groups such as peptides
(e.g., for targeting host cell receptors in vivo), or agents
facilitating transport across the cell membrane (see, e.g.,
Letsinger et al. (1989) Proc. Natl. Acad. Sci. U.S.A. 86:6553-6556;
Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT
Publication NO: WO 88/09810, Dec. 15, 1988) or the blood-brain
barrier (see, e.g., PCT Publication NO: WO 89/10134, Apr. 25,
1988), hybridization-triggered cleavage agents. (See, e.g., Krol et
al. (1988) BioTechniques 6:958-976) or intercalating agents. (See,
e.g., Zon (1988) Pharm. Res. 5:539-549). To this end, the
oligonucleotide may be conjugated to another molecule, e.g., a
peptide, hybridization triggered cross-linking agent, transport
agent, hybridization-triggered cleavage agent, etc.
[0629] The anti sense oligonucleotide may comprise at least one
modified base moiety which is selected from the group including but
not limited to 5-fluorouracil, 5-bromouracil, 5-chlorouracil,
5-iodouracil, hypoxanthine, xantine, 4-acetylcytosine,
5-(carboxyhydroxylmethyl) uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N6-adenine, 7-methylguanine,
5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil,
5-methoxyuracil, 2-methylthio-N-6-isopentenyladenine,
uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine,
2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,
5-methyluracil, uracil-5-oxyacetic acid methylester,
uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil,
3-(3-amino-3-N2-carboxypropyl) uracil, (acp3)w, and
2,6-diaminopurine.
[0630] The antisense oligonucleotide may also comprise at least one
modified sugar moiety selected from the group including but not
limited to arabinose, 2-fluoroarabinose, xylulose, and hexose.
[0631] In yet another embodiment, the antisense oligonucleotide
comprises at least one modified phosphate backbone selected from
the group consisting of a phosphorothioate, a phosphorodithioate, a
phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a
methylphosphonate, an alkyl phosphotriester, and a formacetal or
analog thereof.
[0632] In yet another embodiment, the antisense oligonucleotide is
an .alpha.-anomeric oligonucleotide. An .alpha.-anomeric
oligonucleotide forms specific double-stranded hybrids with
complementary RNA in which, contrary to the usual .beta.-units, the
strands run parallel to each other (Gautier et al. (1987) Nucl.
Acids Res. 15:6625-6641). The oligonucleotide is a
2'-O-methylribonucleotide (Inoue et al. (1987) Nucl. Acids Res.
15:6131-6148), or a chimeric RNA-DNA analogue (Inoue et al. (1987)
FEBS Lett. 215:327-330).
[0633] Oligonucleotides of the invention may be synthesized by
standard methods known in the art, e.g. by use of an automated DNA
synthesizer (such as are commercially available from Biosearch,
Applied Biosystems, etc.). As examples, phosphorothioate
oligonucleotides may be synthesized by the method of Stein et al.
(1988, Nucl. Acids Res. 16:3209), methylphosphonate
oligonucleotides can be prepared by use of controlled pore glass
polymer supports (Sarin et al. (1988) Proc. Natl. Acad. Sci. U.S.A.
85:7448-7451), etc.
[0634] While antisense nucleic acids complementary to the coding
region sequence could be used, those complementary to the
transcribed untranslated region are preferred. Antisense nucleic
acids overlapping the site of initiation of translation are even
more preferred. For example, antisense oligonucleotides as set
forth below can be utilized in accordance with the invention.
TABLE-US-00011 5' TCAATCTGGCTCTGTTCGCG 3' (SEQ ID NO: 19)
(complement to nucleotides 284-303 of SEQ ID NO: 1) 5'
CGCTCTCTCCACCCGCGGGCCCTCAA 3' (SEQ ID NO: 20) (complement to
nucleotides 300-325 of SEQ ID NO: 1) 5' GGTGTCCTCTCCACCGGACGCGTGGG
3' (SEQ ID NO: 49) (complement to nucleotides 6-31 of SEQ ID NO:
24) 5' GTCCTCTCCACCGGACGCGTGG 3' (SEQ ID NO: 50) (complement to
nucleotides 6-28 of SEQ ID NO: 24)
[0635] The antisense molecules should be delivered to cells which
express the Delta3 in vivo. A number of methods have been developed
for delivering antisense DNA or RNA to cells; e.g., antisense
molecules can be injected directly into the tissue site, or
modified antisense molecules, designed to target the desired cells
(e.g., antisense linked to peptides or antibodies that specifically
bind receptors or antigens expressed on the target cell surface)
can be administered systematically.
[0636] However, it is often difficult to achieve intracellular
concentrations of the antisense sufficient to suppress translation
on endogenous mRNAs. Therefore a preferred approach utilizes a
recombinant DNA construct in which the antisense oligonucleotide is
placed under the control of a strong pol III or pol II promoter.
The use of such a construct to transfect target cells in the
patient will result in the transcription of sufficient amounts of
single stranded RNAs that will form complementary base pairs with
the endogenous Delta3 transcripts and thereby prevent translation
of the Delta3 mRNA. For example, a vector can be introduced in vivo
such that it is taken up by a cell and directs the transcription of
an antisense RNA. Such a vector can remain episomal or become
chromosomally integrated, as long as it can be transcribed to
produce the desired antisense RNA. Such vectors can be constructed
by recombinant DNA technology methods standard in the art. Vectors
can be plasmid, viral, or others known in the art, used for
replication and expression in mammalian cells. Expression of the
sequence encoding the antisense RNA can be by any promoter known in
the art to act in mammalian, preferably human cells. Such promoters
can be inducible or constitutive. Such promoters include but are
not limited to: the SV40 early promoter region (Bernoist and
Chambon (1981) Nature 290:304-310), the promoter contained in the
3' long terminal repeat of Rous sarcoma virus (Yamamoto et al.
(1980) Cell 22:787-797), the herpes thymidine kinase promoter
(Wagner et al. (1981) Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445),
the regulatory sequences of the metallothionein gene (Brinster et
al. (1982) Nature 296:39-42), etc. Any type of plasmid, cosmid, YAC
or viral vector can be used to prepare the recombinant DNA
construct which can be introduced directly into the tissue site;
e.g., the choroid plexus or hypothalamus. Alternatively, viral
vectors can be used which selectively infect the desired tissue;
(e.g., for brain, herpesvirus vectors may be used), in which case
administration may be accomplished by another route (e.g.,
systematically).
[0637] Likewise, the antisense constructs of the present invention,
by antagonizing the normal biological activity of one of the Delta3
proteins, can be used in the modulation of cellular activity both
in vivo and for ex vivo tissue cultures.
[0638] Furthermore, the anti-sense techniques (e.g., microinjection
of antisense molecules, or transfection with plasmids whose
transcripts are anti-sense with regard to a Delta3 mRNA or gene
sequence) can be used to investigate the role of Delta3 in
developmental events, as well as the normal cellular function of
Delta3 in adult tissue. Such techniques can be utilized in cell
culture, but can also be used in the creation of transgenic
animals, as detailed below.
[0639] Ribozyme molecules designed to catalytically cleave Delta3
mRNA transcripts can also be used to prevent translation of mRNA
and expression of Delta3. (See, e.g., PCT International Publication
WO 94/11364, published Oct. 4, 1990; Sarver et al., 1990, Science
247:1222-1225). Ribozymes are enzymatic RNA molecules capable of
catalyzing the specific cleavage of RNA. The mechanism of ribozyme
action involves sequence specific hybridization of the ribozyme
molecule to complementary target RNA, followed by an
endonucleolytic cleavage. The composition of ribozyme molecules
must include one or more sequences complementary to the target gene
mRNA, and must include the well known catalytic sequence
responsible for mRNA cleavage. For this sequence, see U.S. Pat. No.
5,093,246. As such within the scope of the invention are engineered
hammerhead motif ribozyme molecules that specifically and
efficiently catalyze endonucleolytic cleavage of RNA sequences
encoding Delta3 proteins.
[0640] Specific ribozyme cleavage sites within any potential RNA
target are initially identified by scanning the molecule of
interest for ribozyme cleavage sites which include the following
sequences, GUA, GUU and GUC. Once identified, short RNA sequences
of between 15 and 20 ribonucleotides corresponding to the region of
the target gene containing the cleavage site may be evaluated for
predicted structural features, such as secondary structure, that
may render the oligonucleotide sequence unsuitable. The suitability
of candidate sequences may also be evaluated by testing their
accessibility to hybridization with complementary oligonucleotides,
using ribonuclease protection assays.
[0641] While ribozymes that cleave mRNA at site specific
recognition sequences can be used to destroy Delta3 mRNAs, the use
of hammerhead ribozymes is preferred. Hammerhead ribozymes cleave
mRNAs at locations dictated by flanking regions that form
complementary base pairs with the target mRNA. The sole requirement
is that the target mRNA have the following sequence of two bases:
5'-UG-3'. The construction and production of hammerhead ribozymes
is well known in the art and is described more fully in Haseloff
and Gerlach (1988) Nature 334:585-591. There are hundreds of
potential hammerhead ribozyme cleavage sites within the nucleotide
sequence of human Delta3 cDNA. Preferably the ribozyme is
engineered so that the cleavage recognition site is located near
the 5' end of the Delta3 mRNA; i.e., to increase efficiency and
minimize the intracellular accumulation of non-functional mRNA
transcripts.
[0642] The ribozymes of the present invention also include RNA
endoribonucleases (hereinafter "Cech-type ribozymes") such as the
one which occurs naturally in Tetrahymena Thermophila (known as the
IVS, or L-19 IVS RNA) and which has been extensively described by
Thomas Cech and collaborators (Zaug, et al. (1984) Science,
224:574-578; Zaug and Cech (1986) Science, 231:470-475; Zaug, et
al. (1986) Nature 324:429-433; PCT Publication WO 88/04300; Been
& Cech (1986) Cell 47:207-216). The Cech-type ribozymes have an
eight base pair active site which hybridizes to a target RNA
sequence whereafter cleavage of the target RNA takes place. The
invention encompasses those Cech-type ribozymes which target eight
base-pair active site sequences that are present in Delta3.
[0643] As in the antisense approach, the ribozymes can be composed
of modified oligonucleotides (e.g., for improved stability,
targeting, etc.) and should be delivered to cells which express the
Delta3 in vivo e.g., hypothalamus and/or the choroid plexus. A
preferred method of delivery involves using a DNA construct
"encoding" the ribozyme under the control of a strong constitutive
pol III or pol II promoter, so that transfected cells will produce
sufficient quantities of the ribozyme to destroy endogenous Delta3
messages and inhibit translation. Because ribozymes unlike
antisense molecules, are catalytic, a lower intracellular
concentration is required for efficiency.
[0644] Endogenous Delta3 gene expression can also be reduced by
inactivating or "knocking out" the Delta3 gene or its promoter
using targeted homologous recombination. (e.g., see Smithies et al.
(1985) Nature 317:230-234; Thomas & Capecchi (1987) Cell
51:503-512; Thompson et al. (1989) Cell 5:313-321). For example, a
mutant, non-functional Delta3 (or a completely unrelated DNA
sequence) flanked by DNA homologous to the endogenous Delta3 gene
(either the coding regions or regulatory regions of the Delta3
gene) can be used, with or without a selectable marker and/or a
negative selectable marker, to transfect cells that express Delta3
in vivo. Insertion of the DNA construct, via targeted homologous
recombination, results in inactivation of the Delta3 gene. Such
approaches are particularly suited in the agricultural field where
modifications to ES (embryonic stem) cells can be used to generate
animal offspring with an inactive Delta3 (e.g., see Thomas &
Capecchi (1987) and Thompson (1989), supra). However this approach
can be adapted for use in humans provided the recombinant DNA
constructs are directly administered or targeted to the required
site in vivo using appropriate viral vectors, e.g., herpes virus
vectors.
[0645] Alternatively, endogenous Delta3 gene expression can be
reduced by targeting deoxyribonucleotide sequences complementary to
the regulatory region of the Delta3 gene (i.e., the Delta3 promoter
and/or enhancers) to form triple helical structures that prevent
transcription of the Delta3 gene in target cells in the body. (See
generally, Helene, C. (1991) Anticancer Drug Des. 6(6):569-84;
Helene, C., et al. (1992) Ann. N.Y. Acad. Sci. 660:27-36; and
Maher, L. J. (1992) Bioassays 14(12):807-15).
[0646] Nucleic acid molecules to be used in triple helix formation
for the inhibition of transcription are preferably single stranded
and composed of deoxyribonucleotides. The base composition of these
oligonucleotides should promote triple helix formation via
Hoogsteen base pairing rules, which generally require sizable
stretches of either purines or pyrimidines to be present on one
strand of a duplex. Nucleotide sequences may be pyrimidine-based,
which will result in TAT and CGC triplets across the three
associated strands of the resulting triple helix. The
pyrimidine-rich molecules provide base complementarity to a
purine-rich region of a single strand of the duplex in a parallel
orientation to that strand. In addition, nucleic acid molecules may
be chosen that are purine-rich, for example, containing a stretch
of G residues. These molecules will form a triple helix with a DNA
duplex that is rich in GC pairs, in which the majority of the
purine residues are located on a single strand of the targeted
duplex, resulting in CGC triplets across the three strands in the
triplex.
[0647] Alternatively, the potential sequences that can be targeted
for triple helix formation may be increased by creating a so called
"switchback" nucleic acid molecule. Switchback molecules are
synthesized in an alternating 5'-3',3'-5' manner, such that they
base pair with first one strand of a duplex and then the other,
eliminating the necessity for a sizable stretch of either purines
or pyrimidines to be present on one strand of a duplex.
[0648] Antisense RNA and DNA, ribozyme, and triple helix molecules
of the invention may be prepared by any method known in the art for
the synthesis of DNA and RNA molecules. These include techniques
for chemically synthesizing oligo-deoxyribonucleotides and
oligoribonucleotides well known in the art such as for example
solid phase phosphoramidite chemical synthesis. Alternatively, RNA
molecules may be generated by in vitro and in vivo transcription of
DNA sequences encoding the antisense RNA molecule. Such DNA
sequences may be incorporated into a wide variety of vectors which
incorporate suitable RNA polymerase promoters such as the T7 or SP6
polymerase promoters. Alternatively, antisense cDNA constructs that
synthesize antisense RNA constitutively or inducibly, depending on
the promoter used, can be introduced stably into cell lines.
[0649] Moreover, various well-known modifications to nucleic acid
molecules may be introduced as a means of increasing intracellular
stability and half-life. Possible modifications include but are not
limited to the addition of flanking sequences of ribonucleotides or
deoxyribonucleotides to the 5' and/or 3' ends of the molecule or
the use of phosphorothioate or 2' O-methyl rather than
phosphodiesterase linkages within the oligodeoxyribonucleotide
backbone.
Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 and
A259 Recombinant Expression Vectors and Host Cells
[0650] Another aspect of the invention pertains to vectors,
preferably expression vectors, containing a nucleic acid encoding
Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 (or a portion thereof). As used herein, the term "vector"
refers to a nucleic acid molecule capable of transporting another
nucleic acid to which it has been linked. One type of vector is a
"plasmid", which refers to a circular double stranded DNA loop into
which additional DNA segments can be ligated. Another type of
vector is a viral vector, wherein additional DNA segments can be
ligated into the viral genome. Certain vectors are capable of
autonomous replication in a host cell into which they are
introduced (e.g., bacterial vectors having a bacterial origin of
replication and episomal mammalian vectors). Other vectors (e.g.,
non-episomal mammalian vectors) are integrated into the genome of a
host cell upon introduction into the host cell, and thereby are
replicated along with the host genome. Moreover, certain vectors,
expression vectors, are capable of directing the expression of
genes to which they are operatively linked. In general, expression
vectors of utility in recombinant DNA techniques are often in the
form of plasmids (vectors). However, the invention is intended to
include such other forms of expression vectors, such as viral
vectors (e.g., replication defective retroviruses, adenoviruses and
adeno-associated viruses), which serve equivalent functions.
[0651] The recombinant expression vectors of the invention comprise
a nucleic acid of the invention in a form suitable for expression
of the nucleic acid in a host cell, which means that the
recombinant expression vectors include one or more regulatory
sequences, selected on the basis of the host cells to be used for
expression, which is operatively linked to the nucleic acid
sequence to be expressed. Within a recombinant expression vector,
"operably linked" is intended to mean that the nucleotide sequence
of interest is linked to the regulatory sequence(s) in a manner
which allows for expression of the nucleotide sequence (e.g., in an
in vitro transcription/translation system or in a host cell when
the vector is introduced into the host cell). The term "regulatory
sequence" is intended to include promoters, enhancers and other
expression control elements (e.g., polyadenylation signals). Such
regulatory sequences are described, for example, in Goeddel; Gene
Expression Technology: Methods in Enzymology 185, Academic Press,
San Diego, Calif. (1990). Regulatory sequences include those which
direct constitutive expression of a nucleotide sequence in many
types of host cell and those which direct expression of the
nucleotide sequence only in certain host cells (e.g.,
tissue-specific regulatory sequences). It will be appreciated by
those skilled in the art that the design of the expression vector
can depend on such factors as the choice of the host cell to be
transformed, the level of expression of protein desired, etc. The
expression vectors of the invention can be introduced into host
cells to thereby produce proteins or peptides, including fusion
proteins or peptides, encoded by nucleic acids as described herein
(e.g., Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 proteins, mutant forms of Delta3, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259, fusion
proteins, etc.).
[0652] The recombinant expression vectors of the invention can be
designed for expression of Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 in prokaryotic or eukaryotic
cells, e.g., bacterial cells such as E. coli, insect cells (using
baculovirus expression vectors) yeast cells or mammalian cells.
Suitable host cells are discussed further in Goeddel, Gene
Expression Technology: Methods in Enzymology 185, Academic Press,
San Diego, Calif. (1990). Alternatively, the recombinant expression
vector can be transcribed and translated in vitro, for example
using T7 promoter regulatory sequences and T7 polymerase.
[0653] Expression of proteins in prokaryotes is most often carried
out in E. coli with vectors containing constitutive or inducible
promoters directing the expression of either fusion or non-fusion
proteins. Fusion vectors add a number of amino acids to a protein
encoded therein, usually to the amino terminus of the recombinant
protein. Such fusion vectors typically serve three purposes: 1) to
increase expression of recombinant protein; 2) to increase the
solubility of the recombinant protein; and 3) to aid in the
purification of the recombinant protein by acting as a ligand in
affinity purification. Often, in fusion expression vectors, a
proteolytic cleavage site is introduced at the junction of the
fusion moiety and the recombinant protein to enable separation of
the recombinant protein from the fusion moiety subsequent to
purification of the fusion protein. Such enzymes, and their cognate
recognition sequences, include Factor Xa, thrombin and
enterokinase. Typical fusion expression vectors include pGEX
(Pharmacia Biotech Inc; Smith and Johnson (1988) Gene 67:31-40),
pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia,
Piscataway, N.J.) which fuse glutathione S-transferase (GST),
maltose E binding protein, or protein A, respectively, to the
target recombinant protein.
[0654] Examples of suitable inducible non-fusion E. coli expression
vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pET
11d (Studier et al., Gene Expression Technology: Methods in
Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89).
Target gene expression from the pTrc vector relies on host RNA
polymerase transcription from a hybrid trp-lac fusion promoter.
Target gene expression from the pET 11d vector relies on
transcription from a T7 gn10-lac fusion promoter mediated by a
coexpressed viral RNA polymerase (T7 gn1). This viral polymerase is
supplied by host strains BL21(DE3) or HMS174(DE3) from a resident
.lamda. prophage harboring a 17 gn1 gene under the transcriptional
control of the lacUV 5 promoter.
[0655] One strategy to maximize recombinant protein expression in
E. coli is to express the protein in a host bacteria with an
impaired capacity to proteolytically cleave the recombinant protein
(Gottesman, Gene Expression Technology: Methods in Enzymology 185,
Academic Press, San Diego, Calif. (1990) 119-128). Another strategy
is to alter the nucleic acid sequence of the nucleic acid to be
inserted into an expression vector so that the individual codons
for each amino acid are those preferentially utilized in E. coli
(Wada et al. (1992) Nucleic Acids Res. 20:2111-2118). Such
alteration of nucleic acid sequences of the invention can be
carried out by standard DNA synthesis techniques.
[0656] In another embodiment, the Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 expression vector is a
yeast expression vector. Examples of vectors for expression in
yeast S. cerivisae include pYepSec1 (Baldari et al. (1987) EMBO J.
6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943),
pJRY88 (Schultz et al. (1987) Gene 54:113-123), pYES2 (Invitrogen
Corporation, San Diego, Calif.), and picZ (InVitrogen Corp, San
Diego, Calif.).
[0657] Alternatively, Delta3, FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 can be expressed in insect cells using
baculovirus expression vectors. Baculovirus vectors available for
expression of proteins in cultured insect cells (e.g., Sf 9 cells)
include the pAc series (Smith et al. (1983) Mol. Cell. Biol.
3:2156-2165) and the pVL series (Lucklow and Summers (1989)
Virology 170:31-39).
[0658] In yet another embodiment, a nucleic acid of the invention
is expressed in mammalian cells using a mammalian expression
vector. Examples of mammalian expression vectors include pCDM8
(Seed (1987) Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBO
J. 6:187-195). When used in mammalian cells, the expression
vector's control functions are often provided by viral regulatory
elements. For example, commonly used promoters are derived from
polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40. For
other suitable expression systems for both prokaryotic and
eukaryotic cells see chapters 16 and 17 of Sambrook et al. (1989)
Cold Spring Harbor Laboratory (supra).
[0659] In another embodiment, the recombinant mammalian expression
vector is capable of directing expression of the nucleic acid
preferentially in a particular cell type (e.g., tissue-specific
regulatory elements are used to express the nucleic acid).
Tissue-specific regulatory elements are known in the art.
Non-limiting examples of suitable tissue-specific promoters include
the albumin promoter (liver-specific; Pinkert et al. (1987) Genes
Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton
(1988) Adv. Immunol. 43:235-275), in particular promoters of T cell
receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) and
immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and
Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g.,
the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl.
Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund
et al. (1985) Science 230:912-916), and mammary gland-specific
promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and
European Application Publication No. 264,166).
Developmentally-regulated promoters are also encompassed, for
example the murine hox promoters (Kessel and Gruss (1990) Science
249:374-379) and the .alpha.-fetoprotein promoter (Camper and
Tilghman (1989) Genes Dev. 3:537-546).
[0660] The invention further provides a recombinant expression
vector comprising a DNA molecule of the invention cloned into the
expression vector in an antisense orientation. That is, the DNA
molecule is operatively linked to a regulatory sequence in a manner
which allows for expression (by transcription of the DNA molecule)
of an RNA molecule which is antisense to Delta3, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 mRNA. Regulatory
sequences operatively linked to a nucleic acid cloned in the
antisense orientation can be chosen which direct the continuous
expression of the antisense RNA molecule in a variety of cell
types, for instance viral promoters and/or enhancers, or regulatory
sequences can be chosen which direct constitutive, tissue specific
or cell type specific expression of antisense RNA. The antisense
expression vector can be in the form of a recombinant plasmid,
phagemid or attenuated virus in which antisense nucleic acids are
produced under the control of a high efficiency regulatory region,
the activity of which can be determined by the cell type into which
the vector is introduced. For a discussion of the regulation of
gene expression using antisense genes See Weintraub et al.,
Reviews--Trends in Genetics, Vol. 1(1) 1986.
[0661] Another aspect of the invention pertains to host cells into
which a recombinant expression vector of the invention has been
introduced.
[0662] Another aspect of the invention pertains to host cells into
which a SPOIL nucleic acid molecule of the invention is introduced,
e.g., a SPOIL nucleic acid molecule within a recombinant expression
vector or a SPOIL nucleic acid molecule in a form suitable for
homologous recombination in the genome of a host cell (e.g., a
SPOIL nucleic acid molecule which includes SPOIL nucleotide
sequences and additional 5' and 3' flanking sequences necessary for
homologous recombination).
[0663] The terms "host cell" and "recombinant host cell" are used
interchangeably herein. It is understood that such terms refer not
only to the particular subject cell but to the progeny or potential
progeny of such a cell. Because certain modifications may occur in
succeeding generations due to either mutation or environmental
influences, such progeny may not, in fact, be identical to the
parent cell, but are still included within the scope of the term as
used herein.
[0664] A host cell can be any prokaryotic or eukaryotic cell. For
example, Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein can be expressed in bacterial cells such
as E. coli, insect cells, yeast or mammalian cells (such as Chinese
hamster ovary cells (CHO) or COS cells). Other suitable host cells
are known to those skilled in the art.
[0665] Vector DNA can be introduced into prokaryotic or eukaryotic
cells via conventional transformation or transfection techniques.
As used herein, the terms "transformation" and "transfection" are
intended to refer to a variety of art-recognized techniques for
introducing foreign nucleic acid (e.g., DNA) into a host cell,
including calcium phosphate or calcium chloride co-precipitation,
DEAE-dextran-mediated transfection, lipofection, or
electroporation. Suitable methods for transforming or transfecting
host cells can be found in Sambrook, et al. (supra), and other
laboratory manuals.
[0666] For stable transfection of mammalian cells, it is known
that, depending upon the expression vector and transfection
technique used, only a small fraction of cells may integrate the
foreign DNA into their genome. In order to identify and select
these integrants, a gene that encodes a selectable marker (e.g.,
resistance to antibiotics) is generally introduced into the host
cells along with the gene of interest. Preferred selectable markers
include those which confer resistance to drugs, such as G418,
hygromycin and methotrexate. Nucleic acid encoding a selectable
marker can be introduced into a host cell on the same vector as
that encoding Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 or can be introduced on a separate vector. Cells
stably transfected with the introduced nucleic acid can be
identified by drug selection (e.g., cells that have incorporated
the selectable marker gene will survive, while the other cells
die).
[0667] In another embodiment, the expression characteristics of an
endogenous (e.g., Delta3) nucleic acid within a cell, cell line or
microorganism may be modified by inserting a DNA regulatory element
heterologous to the endogenous gene of interest into the genome of
a cell, stable cell line or cloned microorganism such that the
inserted regulatory element is operatively linked with the
endogenous gene (e.g., Delta3) and controls, modulates or activates
the endogenous gene. For example, endogenous Delta3 which is
normally "transcriptionally silent", i.e., Delta3 which is normally
not expressed, or is expressed only at very low levels in a cell
line or microorganism, may be activated by inserting a regulatory
element which is capable of promoting the expression of a normally
expressed gene product in that cell line or microorganism.
Alternatively, transcriptionally silent, endogenous Delta3 may be
activated by insertion of a promiscuous regulatory element that
works across cell types.
[0668] A heterologous regulatory element may be inserted into a
stable cell line or cloned microorganism, such that it is
operatively linked with and activates expression of endogenous
Delta3, using techniques, such as targeted homologous
recombination, which are well known to those of skill in the art,
and described e.g., in Chappel, U.S. Pat. No. 5,272,071,
incorporated herein by reference in its entirety; PCT publication
NO: WO 91/06667, published May 16, 1991.
[0669] A host cell of the invention, such as a prokaryotic or
eukaryotic host cell in culture, can be used to produce (i.e.,
express) Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein. Accordingly, the invention further
provides methods for producing Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein using the host cells of
the invention. In one embodiment, the method comprises culturing
the host cell of invention (into which a recombinant expression
vector encoding Delta3, FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 has been introduced) in a suitable medium
such that Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein is produced. In another embodiment, the
method further comprises isolating Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 from the medium or the
host cell.
[0670] The host cells of the invention can also be used to produce
nonhuman transgenic animals. For example, in one embodiment, a host
cell of the invention is a fertilized oocyte or an embryonic stem
cell into which Delta3, FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259-coding sequences have been introduced.
Such host cells can then be used to create non-human transgenic
animals in which exogenous Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 sequences have been introduced
into their genome or homologous recombinant animals in which
endogenous Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 sequences have been altered. Such animals are
useful for studying the function and/or activity of Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 and
for identifying and/or evaluating modulators of FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 activity. As used herein,
a "transgenic animal" is a non-human animal, preferably a mammal,
more preferably a rodent such as a rat or mouse, in which one or
more of the cells of the animal includes a transgene. Other
examples of transgenic animals include non-human primates, sheep,
dogs, cows, goats, chickens, amphibians, etc. A transgene is
exogenous DNA which is integrated into the genome of a cell from
which a transgenic animal develops and which remains in the genome
of the mature animal, thereby directing the expression of an
encoded gene product in one or more cell types or tissues of the
transgenic animal. As used herein, an "homologous recombinant
animal" is a non-human animal, preferably a mammal, more preferably
a mouse, in which an endogenous Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 gene has been altered by
homologous recombination between the endogenous gene and an
exogenous DNA molecule introduced into a cell of the animal, e.g.,
an embryonic cell of the animal, prior to development of the
animal.
[0671] A transgenic animal of the invention can be created by
introducing Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259-encoding nucleic acid into the male pronuclei of a
fertilized oocyte, e.g., by microinjection, retroviral infection,
and allowing the oocyte to develop in a pseudopregnant female
foster animal. The Delta3, FTHMA-070, T85 or A259 cDNA sequence can
be introduced as a transgene into the genome of a non-human animal.
The Tango-77 cDNA sequence e.g., that of (SEQ ID NO:71, SEQ ID
NO:73, SEQ ID NO:76; SEQ ID NO:80 or the cDNA of ATCC 98807) can be
introduced as a transgene into the genome of a non-human animal.
The human SPOIL cDNA sequence of SEQ ID NO:101, SEQ ID NO:104, the
DNA insert of the plasmid deposited with ATCC as Accession Number
98883, or the DNA insert of the plasmid deposited with ATCC as
Accession Number 98984, can be introduced as a transgene into the
genome of a non-human animal. The NEOKINE-1 cDNA sequence of SEQ ID
NO:115 can be introduced as a transgene into the genome of a
non-human animal. Alternatively, a nonhuman homologue of a human
NEOKINE-1 gene, such as a mouse NEOKINE-1 gene (SEQ ID NO:118), a
rat NEOKINE-1 gene (SEQ ID NO:121), or a macaque NEOKINE cDNA (SEQ
ID NO:124), can be used as a transgene. The T129 cDNA sequence
e.g., that of (SEQ ID NO:137 or SEQ ID NO:139) can be introduced as
a transgene into the genome of a non-human animal.
[0672] Alternatively, a nonhuman homologue of the human Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene,
such as a mouse Delta3, FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 gene, can be isolated based on
hybridization to the human Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 cDNA and used as a transgene.
Intronic sequences and polyadenylation signals can also be included
in the transgene to increase the efficiency of expression of the
transgene. A tissue-specific regulatory sequence(s) can be operably
linked to the Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 transgene to direct expression of Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein to particular cells. Methods for generating transgenic
animals via embryo manipulation and microinjection, particularly
animals such as mice, have become conventional in the art and are
described, for example, in U.S. Pat. Nos. 4,736,866 and 4,870,009,
U.S. Pat. No. 4,873,191 and in Hogan, Manipulating the Mouse
Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y., 1986). Similar methods are used for production of other
transgenic animals. A transgenic founder animal can be identified
based upon the presence of the Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 transgene in its genome and/or
expression of Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 mRNA in tissues or cells of the animals. A
transgenic founder animal can then be used to breed additional
animals carrying the transgene. Moreover, transgenic animals
carrying a transgene encoding Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 can further be bred to other
transgenic animals carrying other transgenes.
[0673] To create an homologous recombinant animal, a vector is
prepared which contains at least a portion of a Delta3, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene (e.g., a
human or a non-human homolog of the Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 gene, e.g., a murine
Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 gene) into which a deletion, addition or substitution has been
introduced to thereby alter, e.g., functionally disrupt, the
Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 gene. In a preferred embodiment, the vector is designed such
that, upon homologous recombination, the endogenous Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene
is functionally disrupted (i.e., no longer encodes a functional
protein; also referred to as a "knock out" vector). Alternatively,
the vector can be designed such that, upon homologous
recombination, the endogenous Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 gene is mutated or otherwise
altered but still encodes functional protein (e.g., the upstream
regulatory region can be altered to thereby alter the expression of
the endogenous Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein). In the homologous recombination vector,
the altered portion of the Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 gene is flanked at its 5' and 3'
ends by additional nucleic acid of the Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 gene to allow for
homologous recombination to occur between the exogenous Delta3,
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene
carried by the vector and an endogenous Delta3, FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 gene in an embryonic stem
cell. The additional flanking Delta3, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 nucleic acid is of sufficient
length for successful homologous recombination with the endogenous
gene. Typically, several kilobases of flanking DNA (both at the 5'
and 3' ends) are included in the vector (see e.g., Thomas and
Capecchi (1987) Cell 51:503 for a description of homologous
recombination vectors). The vector is introduced into an embryonic
stem cell line (e.g., by electroporation) and cells in which the
introduced Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 gene has homologously recombined with the
endogenous Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 gene are selected (see e.g., Li et al. (1992) Cell
69:915). The selected cells are then injected into a blastocyst of
an animal (e.g., a mouse) to form aggregation chimeras (see, e.g.,
Bradley in Teratocarcinomas and Embryonic Stem Cells: A Practical
Approach, Robertson, ed. (IRL, Oxford, 1987) pp. 113-152). A
chimeric embryo can then be implanted into a suitable
pseudopregnant female foster animal and the embryo brought to term.
Progeny harboring the homologously recombined DNA in their germ
cells can be used to breed animals in which all cells of the animal
contain the homologously recombined DNA by germline transmission of
the transgene. Methods for constructing homologous recombination
vectors and homologous recombinant animals are described further in
Bradley (1991) Current Opinion in Bio/Technology 2:823-829 and in
PCT Publication Nos. WO 90/11354, WO 91/01140, WO 92/0968, and WO
93/04169.
[0674] In another embodiment, transgenic non-humans animals can be
produced which contain selected systems which allow for regulated
expression of the transgene. One example of such a system is the
cre/loxP recombinase system of bacteriophage P1. For a description
of the cre/loxP recombinase system, see, e.g., Lakso et al. (1992)
Proc. Natl. Acad. Sci. USA 89:6232-6236. Another example of a
recombinase system is the FLP recombinase system of Saccharomyces
cerevisiae (O'Gorman et al. (1991) Science 251:1351-1355. If a
cre/loxP recombinase system is used to regulate expression of the
transgene, animals containing transgenes encoding both the Cre
recombinase and a selected protein are required. Such animals can
be provided through the construction of "double" transgenic
animals, e.g., by mating two transgenic animals, one containing a
transgene encoding a selected protein and the other containing a
transgene encoding a recombinase.
[0675] Clones of the non-human transgenic animals described herein
can also be produced according to the methods described in Wilmut
et al. (1997) Nature 385:810-813 and PCT Publication Nos. WO
97/07668 and WO 97/07669. In brief, a cell, e.g., a somatic cell,
from the transgenic animal can be isolated and induced to exit the
growth cycle and enter G.sub.o phase. The quiescent cell can then
be fused, e.g., through the use of electrical pulses, to an
enucleated oocyte from an animal of the same species from which the
quiescent cell is isolated. The reconstructed oocyte is then
cultured such that it develops to morula or blastocyte and then
transferred to pseudopregnant female foster animal. The offspring
borne of this female foster animal will be a clone of the animal
from which the cell, e.g., the somatic cell, is isolated.
Delta3 Peptides of the Present Invention
[0676] The present invention also makes available Delta3
polypeptides which are isolated from, or otherwise substantially
free of other cellular proteins, especially other signal
transduction factors and/or transcription factors which may
normally be associated with the Delta3 polypeptide. In general,
polypeptides of the invention exhibit an activity of a Delta3
protein. The invention provides various forms of Delta3 proteins,
specifically including all of the Delta3 proteins encoded by a
nucleic acid of the invention, as described above.
[0677] In one embodiment, a polypeptide of the invention is a
polypeptide that is a variant of a polypeptide of the invention can
be assayed for: (1) the ability to form protein:protein
interactions with proteins in a signaling pathway of the
polypeptide of the invention; (2) the ability to bind a ligand of
the polypeptide of the invention; or (3) the ability to bind to an
intracellular target protein of the polypeptide of the invention.
In yet another preferred embodiment, the mutant polypeptide can be
assayed for the ability to modulate cellular proliferation,
cellular migration or chemotaxis, or cellular differentiation.
[0678] Full-length proteins or fragments corresponding to one or
more particular motifs and/or domains or to arbitrary sizes, for
example, at least about 5, 10, 25, 50, 75, 100, 125, 150 amino
acids in length are within the scope of the present invention. The
invention encompasses all proteins encoded by the nucleic acids
described in the above section describing the nucleic acids of the
invention.
[0679] For example, isolated Delta3 polypeptides can include all or
a portion of an amino acid sequences corresponding to a Delta3
polypeptide represented in SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36,
38, 40, 42, 44 or 46, or the amino acid sequence encoded by the
cDNA of a clone deposited with the ATCC.RTM. as Accession Number
98348. Isolated portions of Delta3 proteins can be obtained, for
example, by screening peptides recombinantly produced from the
corresponding fragment of the nucleic acid encoding such peptides.
In addition, fragments can be chemically synthesized using
techniques known in the art such as conventional Merrifield solid
phase f-Moc or t-Boc chemistry. For example, a Delta3 polypeptide
of the present invention may be divided into fragments of desired
length with no overlap of the fragments, or preferably divided into
overlapping fragments of a desired length. The fragments can be
produced (recombinantly or by chemical synthesis) and tested to
identify those peptidyl fragments which can function as either
agonists or antagonists of a wild-type (e.g., "authentic") Delta3
protein.
[0680] In one embodiment, the Delta3 polypeptide of the invention
has an overall amino acid sequence similarity or identity of at
least about 70%, at least about 75%, at least about 80%, at least
about 85%, at least about 90%, at least about 95%, at least about
98%, or at least about 99% with the amino acid sequence SEQ ID NOs:
2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348. In a particularly preferred
embodiment a Delta3 protein has the amino acid sequence SEQ ID NOs:
2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino acid
sequence of the cDNA of a clone deposited with the ATCC.RTM. as
Accession Number 98348. In other particularly preferred
embodiments, the Delta3 protein has a Delta3 activity.
[0681] The present invention further pertains to forms of one of
the subject Delta3 polypeptides which are encoded by nucleotide
sequences derived from a mammalian organism, and which have amino
acid sequences evolutionarily related to the Delta3 protein
represented in SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42,
44 or 46, or the amino acid sequence encoded by the cDNA of a clone
deposited with the ATCC.RTM. as Accession Number 98348. Such
recombinant Delta3 polypeptides can, in certain embodiments,
preferably are capable of functioning in one of either role of an
agonist or antagonist of at least one biological activity of a
wild-type ("authentic") Delta3 protein of the appended sequence
listing. The term "evolutionarily related to", with respect to
amino acid sequences of human Delta3 proteins, refers to both
polypeptides having amino acid sequences which have arisen
naturally, and also to mutational variants of the Delta3
polypeptides which are derived, for example, by combinatorial
mutagenesis. Such evolutionarily derived Delta3 polypeptides
preferred by the present invention have a Delta3 activity and are
at least 80% homologous and more preferably 85% identical and most
preferably 90% identical with the amino acid sequence of SEQ ID
NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, or the amino
acid sequence encoded by the cDNA of a clone deposited with the
ATCC.RTM. as Accession Number 98348. In a particularly preferred
embodiment, a Delta3 protein comprises the amino acid coding
sequence of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, or the amino acid sequence of the cDNA of a clone deposited
with the ATCC.RTM. as Accession Number 98348.
[0682] The present invention further pertains to methods of
producing the subject Delta3 polypeptides. For example, a host cell
transfected with a nucleic acid vector directing expression of a
nucleotide sequence encoding the subject polypeptides can be
cultured under appropriate conditions to allow expression of the
peptide to occur. The cells may be harvested, lysed and the protein
isolated. A cell culture includes host cells, media and other
byproducts. Suitable media for cell culture are well known in the
art. The recombinant Delta3 polypeptide can be isolated from cell
culture medium, host cells, or both using techniques known in the
art for purifying proteins including ion-exchange chromatography,
gel filtration chromatography, ultrafiltration, electrophoresis,
and immunoaffinity purification with antibodies specific for such
peptide. In a preferred embodiment, the recombinant Delta3
polypeptide is a fusion protein containing a domain which
facilitates its purification, such as GST fusion protein or
poly(His) fusion protein.
[0683] Moreover, it will be generally appreciated that, under
certain circumstances, it may be advantageous to provide variants
of one of the subject Delta3 polypeptides which function in a
limited capacity as one of either a Delta3 agonist (mimetic) or a
Delta3 antagonist, in order to promote or inhibit only a subset of
the biological activities of the naturally-occurring form of the
protein. Thus, specific biological effects can be elicited by
treatment with a variant having a limited function, and with fewer
side effects relative to treatment with agonists or antagonists
which are directed to all of the biological activities of
naturally-occurring forms of Delta3 proteins.
[0684] Variants and/or mutants of each of the subject Delta3
proteins can be generated by mutagenesis, such as by discrete point
mutation(s), or by truncation. For instance, mutation can give rise
to homologs which retain substantially the same, or merely a
subset, of the biological activity of the Delta3 polypeptide from
which it was derived. Alternatively, antagonistic forms of the
protein can be generated which are able to inhibit the function of
the naturally-occurring form of the protein, such as by
competitively binding to a downstream or upstream member of the
Delta3 cascade which includes the Delta3 protein. In addition,
agonistic forms of the protein may be generated which are
constitutively active.
[0685] The recombinant Delta3 polypeptides of the present invention
also include homologs of the authentic Delta3 proteins, such as
versions of those protein which are resistant to proteolytic
cleavage, as for example, due to mutations which alter
ubiquitination or other enzymatic targeting associated with the
protein.
[0686] Delta3 polypeptides may also be chemically modified to
create Delta3 derivatives by forming covalent or aggregate
conjugates with other chemical moieties, such as glycosyl groups,
lipids, phosphate, acetyl groups and the like. Covalent derivatives
of Delta3 proteins can be prepared by linking the chemical moieties
to functional groups on amino acid sidechains of the protein or at
the N-terminus or at the C-terminus of the polypeptide.
[0687] Modification of the structure of the subject Delta3
polypeptides can be for such purposes as enhancing therapeutic or
prophylactic efficacy, stability (e.g., ex vivo shelf life and
resistance to proteolytic degradation in vivo), or
post-translational modifications (e.g., to alter phosphorylation
pattern of protein). Such modified peptides, when designed to
retain at least one activity of the naturally-occurring form of the
protein, or to produce specific antagonists thereof, are considered
functional equivalents of the Delta3 polypeptides described in more
detail herein. Such modified peptides can be produced, for
instance, by amino acid substitution, deletion, or addition.
[0688] For example, it is reasonable to expect that an isolated
replacement of a leucine with an isoleucine or valine, an aspartate
with a glutamate, a threonine with a serine, or a similar
replacement of an amino acid with a structurally related amino acid
(i.e. isosteric and/or isoelectric mutations) will not have a major
effect on the biological activity of the resulting molecule.
Conservative replacements are those that take place within a family
of amino acids that are related in their side chains. Genetically
encoded amino acids are can be divided into four families: (1)
acidic=aspartate, glutamate; (2) basic=lysine, arginine, histidine;
(3) nonpolar=alanine, valine, leucine, isoleucine, proline,
phenylalanine, methionine, tryptophan; and (4) uncharged
polar=glycine, asparagine, glutamine, cysteine, serine, threonine,
tyrosine. In similar fashion, the amino acid repertoire can be
grouped as (1) acidic=aspartate, glutamate; (2) basic=lysine,
arginine histidine, (3) aliphatic=glycine, alanine, valine,
leucine, isoleucine, serine, threonine, with serine and threonine
optionally be grouped separately as aliphatic-hydroxyl; (4)
aromatic=phenylalanine, tyrosine, tryptophan; (5) amide=asparagine,
glutamine; and (6) sulfur-containing=cysteine and methionine. (See,
for example, Biochemistry, 4th ed., Ed. by L. Stryer, WH Freeman
and Co.: 1995). Whether a change in the amino acid sequence of a
peptide results in a functional Delta3 homolog (e.g., functional in
the sense that the resulting polypeptide mimics or antagonizes the
wild-type form) can be readily determined by assessing the ability
of the variant peptide to produce a response in cells in a fashion
similar to the wild-type protein, or competitively inhibit such a
response. Polypeptides in which more than one replacement has taken
place can readily be tested in the same manner.
[0689] This invention further contemplates a method for generating
sets of combinatorial mutants of the subject Delta3 proteins as
well as truncation mutants, and is especially useful for
identifying potential functional variant sequences (e.g.,
homologs). The purpose of screening such combinatorial libraries is
to generate, for example, novel Delta3 homologs which can act as
either agonists or antagonist, or alternatively, possess novel
activities all together.
[0690] In one embodiment, the variegated library of Delta3 variants
is generated by combinatorial mutagenesis at the nucleic acid
level, and is encoded by a variegated gene library. For instance, a
mixture of synthetic oligonucleotides can be enzymatically ligated
into gene sequences such that the degenerate set of potential
Delta3 sequences are expressible as individual polypeptides, or
alternatively, as a set of larger fusion proteins (e.g., for phage
display) containing the set of Delta3 sequences therein.
[0691] There are many ways by which such libraries of potential
Delta3 variants can be generated from a degenerate oligonucleotide
sequence. Chemical synthesis of a degenerate gene sequence can be
carried out in an automatic DNA synthesizer, and the synthetic
genes then ligated into an appropriate expression vector. The
purpose of a degenerate set of genes is to provide, in one mixture,
all of the sequences encoding the desired set of potential Delta3
sequences. The synthesis of degenerate oligonucleotides is well
known in the art (see for example, Narang, S A (1983) Tetrahedron
39:3; Itakura et al. (1981) Recombinant DNA, Proc. 3rd Cleveland
Sympos. Macromolecules, ed. AG Walton, Amsterdam: Elsevier ppg.
273-289; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura
et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res.
11:477. Such techniques have been employed in the directed
evolution of other proteins (see, for example, Scott et al. (1990)
Science 249:386-390; Roberts et al. (1992) PNAS 89:2429-2433;
Devlin et al. (1990) Science 249: 404-406; Cwirla et al. (1990)
PNAS 87: 6378-6382; as well as U.S. Pat. Nos. 5,223,409, 5,198,346,
and 5,096,815).
[0692] Likewise, a library of coding sequence fragments can be
provided for a Delta3 clone in order to generate a variegated
population of Delta3 fragments for screening and subsequent
selection of bioactive fragments. A variety of techniques are known
in the art for generating such libraries, including chemical
synthesis. In one embodiment, a library of coding sequence
fragments can be generated by (i) treating a double stranded PCR
fragment of a Delta3 coding sequence with a nuclease under
conditions wherein nicking occurs only about once per molecule;
(ii) denaturing the double stranded DNA; (iii) renaturing the DNA
to form double stranded DNA which can include sense/antisense pairs
from different nicked products; (iv) removing single stranded
portions from reformed duplexes by treatment with S1 nuclease; and
(v) ligating the resulting fragment library into an expression
vector. By this exemplary method, an expression library can be
derived which codes for N-terminal, C-terminal and internal
fragments of various sizes.
[0693] A wide range of techniques are known in the art for
screening gene products of combinatorial libraries made by point
mutations or truncation, and for screening cDNA libraries for gene
products having a certain property. Such techniques will be
generally adaptable for rapid screening of the gene libraries
generated by the combinatorial mutagenesis of Delta3 homologs. The
most widely used techniques for screening large gene libraries
typically comprises cloning the gene library into replicable
expression vectors, transforming appropriate cells with the
resulting library of vectors, and expressing the combinatorial
genes under conditions in which detection of a desired activity
facilitates relatively easy isolation of the vector encoding the
gene whose product was detected. Each of the illustrative assays
described below are amenable to high through-put analysis as
necessary to screen large numbers of degenerate Delta3 sequences
created by combinatorial mutagenesis techniques.
[0694] Combinatorial mutagenesis has a potential to generate very
large libraries of mutant proteins, e.g., in the order of 1026
molecules. Combinatorial libraries of this size may be technically
challenging to screen even with high throughput screening assays.
To overcome this problem, a new technique has been developed
recently, recrusive ensemble mutagenesis (REM), which allows one to
avoid the very high proportion of non-functional proteins in a
random library and simply enhances the frequency of functional
proteins, thus decreasing the complexity required to achieve a
useful sampling of sequence space. REM is an algorithm which
enhances the frequency of functional mutants in a library when an
appropriate selection or screening method is employed (Arkin and
Yourvan, 1992, PNAS USA 89:7811-7815; Yourvan et al., 1992,
Parallel Problem Solving from Nature, 2., In Maenner and Manderick,
eds., Elsevir Publishing Co., Amsterdam, pp. 401-410; Delgrave et
al., 1993, Protein Engineering 6(3):327-331).
[0695] The invention also provides for reduction of the Delta3
proteins to generate mimetics, e.g., peptide or non-peptide agents,
which are able to bind to a Delta3 protein and/or to disrupt
binding of a Delta3 polypeptide of the present invention with
either upstream or downstream components of a Delta/Notch signaling
cascade, such as binding proteins or interactors. Thus, such
mutagenic techniques as described above are also useful to map the
determinants of the Delta3 proteins which participate in
protein-protein interactions involved in, for example, binding of
the subject Delta3 polypeptide to proteins which may function
upstream (including both activators and repressors of its activity)
or to proteins or nucleic acids which may function downstream of
the Delta3 polypeptide, whether they are positively or negatively
regulated by it, for example, Notch. To illustrate, the critical
residues of a subject Delta3 polypeptide which are involved in
molecular recognition of, for example, the Notch gene product or
other component upstream or downstream of a Delta3 gene can be
determined and used to generate Delta-derived peptidomimetics which
competitively inhibit binding of the authentic Delta3 protein with
that moiety. By employing, for example, scanning mutagenesis to map
the amino acid residues of each of the subject Delta3 proteins
which are involved in binding other extracellular proteins,
peptidomimetic compounds can be generated which mimic those
residues of the Delta3 protein which facilitate the interaction.
Such mimetics may then be used to interfere with the normal
function of a Delta3 protein. For instance, non-hydrolyzable
peptide analogs of such residues can be generated using
benzodiazepine (e.g., see Freidinger et al. in Peptides: Chemistry
and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden,
Netherlands, 1988), azepine (e.g., see Huffman et al. in Peptides:
Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden,
Netherlands, 1988), substituted gamma lactam rings (Garvey et al.
in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM
Publisher: Leiden, Netherlands, 1988), keto-methylene
pseudopeptides (Ewenson et al. (1986) J Med Chem 29:295; and
Ewenson et al. in Peptides: Structure and Function (Proceedings of
the 9th American Peptide Symposium) Pierce Chemical Co. Rockland,
Ill., 1985), b-turn dipeptide cores (Nagai et al. (1985)
Tetrahedron Lett 26:647; and Sato et al. (1986) J Chem Soc Perkin
Trans 1:1231), and b-aminoalcohols (Gordon et al. (1985) Biochem
Biophys Res Commun 126:419; and Dann et al. (1986) Biochem Biophys
Res Commun 134:71).
Delta3 Fusion Proteins and Immunogens.
[0696] In another embodiment, the coding sequences for the
polypeptide can be incorporated as a part of a fusion gene
including a nucleotide sequence encoding a different
polypeptide.
[0697] In one embodiment, the Delta3 polypeptide is a Delta3-Ig
polypeptide. The Delta3-Ig polypeptide can comprise the entire
extracellular domain of Delta3, e.g., human Delta3, or a variant
thereof. For example, a Delta3-Ig polypeptide can comprise an amino
acid sequences from about amino acid 1 to about amino acid 529 of
SEQ ID NO: 2 or from about amino acid 1 to about amino acid 530 of
SEQ ID NO: 25. Other preferred Delta3-Ig proteins do not comprise a
signal peptide and thus, preferably do not comprise about amino
acid 1 to about amino acid 17 or amino acid 18 of SEQ ID NO: 2 or
25. Alternatively, a Delta3-Ig fusion protein can comprise a
portion of the extracellular domain of a Delta3 protein or a
variant of a portion of the extracellular domain of a Delta3
protein. Preferred portions of the extracellular domain include
portions having at least one motif amino terminal to the
transmembrane domain. For example a Delta3-Ig fusion protein can
comprise at least one EGF-like domain. A Delta3-Ig fusion protein
can further comprise a DSL domain. A Delta3-Ig fusion protein can
also further comprise a signal peptide. Delta3-Ig fusion proteins
can be prepared as described, e.g., in U.S. Pat. No. 5,434,131.
[0698] This type of expression system can be useful under
conditions where it is desirable to produce an immunogenic fragment
of a Delta3 protein. For example, the VP6 capsid protein of
rotavirus can be used as an immunologic carrier protein for
portions of the Delta3 polypeptide, either in the monomeric form or
in the form of a viral particle. The nucleic acid sequences
corresponding to the portion of a subject Delta3 protein to which
antibodies are to be raised can be incorporated into a fusion gene
construct which includes coding sequences for a late vaccinia virus
structural protein to produce a set of recombinant viruses
expressing fusion proteins comprising Delta3 epitopes as part of
the virion. It has been demonstrated with the use of immunogenic
fusion proteins utilizing the Hepatitis B surface antigen fusion
proteins that recombinant Hepatitis B virions can be utilized in
this role as well. Similarly, chimeric constructs coding for fusion
proteins containing a portion of a Delta3 protein and the
poliovirus capsid protein can be created to enhance immunogenicity
of the set of polypeptide antigens (see, for example, EP
Publication No: 0259149; and Evans et al. (1989) Nature 339:385;
Huang et al. (1988) J. Virol. 62:3855; and Schlienger et al. (1992)
J. Virol. 66:2).
[0699] The Multiple Antigen Peptide system for peptide-based
immunization can also be utilized to generate an immunogen, wherein
a desired portion of a Delta3 polypeptide is obtained directly from
organo-chemical synthesis of the peptide onto an oligomeric
branching lysine core (see, for example, Posnett et al. (1988) J.
Biol. Chem. 263:1719 and Nardelli et al. (1992) J. Immunol.
148:914). Antigenic determinants of Delta3 proteins can also be
expressed and presented by bacterial cells.
[0700] In addition to utilizing fusion proteins to enhance
immunogenicity, it is widely appreciated that fusion proteins can
also facilitate the expression of proteins, and accordingly, can be
used in the expression of the Delta3 polypeptides of the present
invention. For example, Delta3 polypeptides can be generated as
glutathione-S-transferase (GST-fusion) proteins. Such GST-fusion
proteins can enable easy purification of the Delta3 polypeptide, as
for example by the use of glutathione-derivatized matrices (see,
for example, Current Protocols in Molecular Biology, eds. Ausubel
et al. (N.Y.: John Wiley & Sons, 1991)).
[0701] In another embodiment, a fusion gene coding for a
purification leader sequence, such as a poly-(His)/enterokinase
cleavage site sequence at the N-terminus of the desired portion of
the recombinant protein, can allow purification of the expressed
fusion protein by affinity chromatography using a Ni.sup.2+ metal
resin. The purification leader sequence can then be subsequently
removed by treatment with enterokinase to provide the purified
protein (e.g., see Hochuli et al. (1987) J. Chromatography 411:177;
and Janknecht et al. Proc. Natl. Acad. Sci. USA 88:8972).
Techniques for making fusion genes are known to those skilled in
the art. Essentially, the joining of various DNA fragments coding
for different polypeptide sequences is performed in accordance with
conventional techniques, employing blunt-ended or stagger-ended
termini for ligation, restriction enzyme digestion to provide for
appropriate termini, filling-in of cohesive ends as appropriate,
alkaline phosphatase treatment to avoid undesirable joining, and
enzymatic ligation. In another embodiment, the fusion gene can be
synthesized by conventional techniques including automated DNA
synthesizers. Alternatively, PCR amplification of gene fragments
can be carried out using anchor primers which give rise to
complementary overhangs between two consecutive gene fragments
which can subsequently be annealed to generate a chimeric gene
sequence (see, for example, Current Protocols in Molecular Biology,
eds. Ausubel et al. John Wiley & Sons: 1992).
Delta3 Antibodies
[0702] Another aspect of the invention pertains to an antibody that
binds to a Delta3 protein; that is, to antibodies directed against
a polypeptide of the invention. For example, by using immunogens
derived from a Delta3 protein, e.g., based on the cDNA sequences,
anti-protein/anti-peptide antisera or monoclonal antibodies can be
made by standard protocols (See, for example, Antibodies: A
Laboratory Manual ed. by Harlow and Lane (Cold Spring Harbor Press:
1988)). A mammal, such as a mouse, a hamster or rabbit can be
immunized with an immunogenic form of the peptide (e.g., a Delta3
polypeptide or an antigenic fragment which is capable of eliciting
an antibody response, or a fusion protein as described above).
Techniques for conferring immunogenicity on a protein or peptide
include conjugation to carriers or other techniques well known in
the art. An immunogenic portion of a Delta3 protein can be
administered in the presence of adjuvant. The progress of
immunization can be monitored by detection of antibody titers in
plasma or serum. Standard ELISA or other immunoassays can be used
with the immunogen as antigen to assess the levels of
antibodies.
[0703] Following immunization of an animal with an antigenic
preparation of a Delta3 polypeptide, anti-Delta3 antisera can be
obtained and, if desired, polyclonal anti-Delta3 antibodies
isolated from the serum. To produce monoclonal antibodies,
antibody-producing cells (lymphocytes) can be harvested from an
immunized animal and fused by standard somatic cell fusion
procedures with immortalizing cells such as myeloma cells to yield
hybridoma cells. Such techniques are well known in the art, and
include, for example, the hybridoma technique (originally developed
by Kohler and Milstein, (1975) Nature, 256: 495-497), the human B
cell hybridoma technique (Kozbar et al., (1983) Immunology Today,
4: 72), and the EBV-hybridoma technique to produce human monoclonal
antibodies (Cole et al., (1985) Monoclonal Antibodies and Cancer
Therapy, Alan R. Liss, Inc. pp. 77-96). Hybridoma cells can be
screened immunochemically for production of antibodies specifically
reactive with a Delta3 polypeptide of the present invention and
monoclonal antibodies isolated from a culture comprising such
hybridoma cells. In one embodiment anti-human Delta3 antibodies
specifically react with the proteins encoded by the DNA of
ATCC.RTM. Deposit Accession Number 98348.
[0704] Antibodies can be fragmented using conventional techniques
and the fragments screened for utility in the same manner as
described above for whole antibodies. For example, F(ab)2 fragments
can be generated by treating antibody with pepsin. The resulting
F(ab)2 fragment can be treated to reduce disulfide bridges to
produce Fab fragments. The antibody of the present invention is
further intended to include bispecific and chimeric molecules
having affinity for a Delta3 protein conferred by at least one CDR
region of the antibody.
[0705] Antibodies which specifically bind Delta3 epitopes can also
be used in immunohistochemical staining of tissue samples in order
to evaluate the abundance and pattern of expression of each of the
subject Delta3 polypeptides. Anti-Delta3 antibodies can be used
diagnostically in immuno-precipitation and immuno-blotting to
detect and evaluate Delta3 protein levels in tissue as part of a
clinical testing procedure. For instance, such measurements can be
useful in predictive valuations of the onset or progression of
neurodegenerative, neoplastic or hyperplastic disorders. Likewise,
the ability to monitor Delta3 protein levels in an individual can
allow determination of the efficacy of a given treatment regimen
for an individual afflicted with such a disorder. The level of
Delta3 polypeptides may be measured from cells in bodily fluid,
such as in samples of cerebral spinal fluid or amniotic fluid, or
can be measured in tissue, such as produced by biopsy. Diagnostic
assays using anti-Delta3 antibodies can include, for example,
immunoassays designed to aid in early diagnosis of a
neurodegenerative disorder, particularly ones which are manifest at
birth. Diagnostic assays using anti-Delta3 polypeptide antibodies
can also include immunoassays designed to aid in early diagnosis
and phenotyping neurodegenerative, neoplastic or hyperplastic
disorders.
[0706] Another application of anti-Delta3 antibodies of the present
invention is in the immunological screening of cDNA libraries
constructed in expression vectors such as .lamda.gt11,
.lamda.gt18-23, .lamda.ZAP, and ORF8. Messenger libraries of this
type, having coding sequences inserted in the correct reading frame
and orientation, can produce fusion proteins. For instance,
.lamda.gt11 will produce fusion proteins whose amino termini
consist of .beta.-galactosidase amino acid sequences and whose
carboxy termini consist of a foreign polypeptide. Antigenic
epitopes of a Delta3 protein, e.g., other orthologs of a particular
Delta3 protein or other paralogs from the same species, can then be
detected with antibodies, as, for example, reacting nitrocellulose
filters lifted from infected plates with anti-Delta3 antibodies.
Positive phage detected by this assay can then be isolated from the
infected plate. Thus, the presence of Delta3 homologs can be
detected and cloned from other animals, as can alternate isoforms
(including splicing variants) from humans.
[0707] Polyclonal antibodies can be prepared as described above by
immunizing a suitable subject with a polypeptide of the invention
as an immunogen. Preferred polyclonal antibody compositions are
ones that have been selected for antibodies directed against a
polypeptide or polypeptides of the invention. Particularly
preferred polyclonal antibody preparations are ones that contain
only antibodies directed against a polypeptide or polypeptides of
the invention. Particularly preferred immunogen compositions are
those that contain no other human proteins such as, for example,
immunogen compositions made using a non-human host cell for
recombinant expression of a polypeptide of the invention. In such a
manner, the only human epitope or epitopes recognized by the
resulting antibody compositions raised against this immunogen will
be present as part of a polypeptide or polypeptides of the
invention.
[0708] The antibody titer in the immunized subject can be monitored
over time by standard techniques, such as with an enzyme linked
immunosorbent assay (ELISA) using immobilized polypeptide. If
desired, the antibody molecules can be isolated from the mammal
(e.g., from the blood) and further purified by well-known
techniques, such as protein A chromatography to obtain the IgG
fraction. Alternatively, antibodies specific for a protein or
polypeptide of the invention can be selected for (e.g., partially
purified) or purified by, e.g., affinity chromatography. For
example, a recombinantly expressed and purified (or partially
purified) protein of the invention is produced as described herein,
and covalently or non-covalently coupled to a solid support such
as, for example, a chromatography column. The column can then be
used to affinity purify antibodies specific for the proteins of the
invention from a sample containing antibodies directed against a
large number of different epitopes, thereby generating a
substantially purified antibody composition, i.e., one that is
substantially free of contaminating antibodies. By a substantially
purified antibody composition is meant, in this context, that the
antibody sample contains at most only 30% (by dry weight) of
contaminating antibodies directed against epitopes other than those
on the desired protein or polypeptide of the invention, and
preferably at most 20%, yet more preferably at most 10%, and most
preferably at most 5% (by dry weight) of the sample is
contaminating antibodies. A purified antibody composition means
that at least 99% of the antibodies in the composition are directed
against the desired protein or polypeptide of the invention.
[0709] At an appropriate time after immunization, e.g., when the
specific antibody titers are highest, antibody-producing cells can
be obtained from the subject and used to prepare monoclonal
antibodies by standard techniques, such as the hybridoma technique
originally described by Kohler and Milstein (1975) Nature
256:495-497, the human B cell hybridoma technique (Kozbor et al.
(1983) Immunol. Today 4:72), the EBV-hybridoma technique (Cole et
al. (1985), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss,
Inc., pp. 77-96) or trioma techniques. The technology for producing
hybridomas is well known (see generally Current Protocols in
Immunology (1994) Coligan et al. (eds.) John Wiley & Sons,
Inc., New York, N.Y.). Hybridoma cells producing a monoclonal
antibody of the invention are detected by screening the hybridoma
culture supernatants for antibodies that bind the polypeptide of
interest, e.g., using a standard ELISA assay.
[0710] Alternative to preparing monoclonal antibody-secreting
hybridomas, a monoclonal antibody directed against a polypeptide of
the invention can be identified and isolated by screening a
recombinant combinatorial immunoglobulin library (e.g., an antibody
phage display library) with the polypeptide of interest. Kits for
generating and screening phage display libraries are commercially
available (e.g., the Pharmacia Recombinant Phage Antibody System,
Catalog NO: 27-9400-01; and the Stratagene SurfZAP Phage Display
Kit, Catalog NO: 240612). Additionally, examples of methods and
reagents particularly amenable for use in generating and screening
antibody display library can be found in, for example, U.S. Pat.
No. 5,223,409; PCT Publication No: WO 92/18619; PCT Publication No:
WO 91/17271; PCT Publication No: WO 92/20791; PCT Publication No:
WO 92/15679; PCT Publication No: WO 93/01288; PCT Publication No:
WO 92/01047; PCT Publication No: WO 92/09690; PCT Publication No:
WO 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et
al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989)
Science 246:1275-1281; Griffiths et al. (1993) EMBO J.
12:725-734.
[0711] Additionally, recombinant antibodies, such as chimeric and
humanized monoclonal antibodies, comprising both human and
non-human portions, which can be made using standard recombinant
DNA techniques, are within the scope of the invention. A chimeric
antibody is a molecule in which different portions are derived from
different animal species, such as those having a variable region
derived from a murine mAb and a human immunoglobulin constant
region. (See, e.g., Cabilly et al., U.S. Pat. No. 4,816,567; and
Boss et al., U.S. Pat. No. 4,816,397, which are incorporated herein
by reference in their entirety.) Humanized antibodies are antibody
molecules from non-human species having one or more complementarily
determining regions (CDRs) from the non-human species and a
framework region from a human immunoglobulin molecule. (See, e.g.,
Queen, U.S. Pat. No. 5,585,089.) Such chimeric and humanized
monoclonal antibodies can be produced by recombinant DNA techniques
known in the art, for example using methods described in PCT
Publication NO: WO 87/02671; European Patent Application 184,187;
European Patent Application 171,496; European Patent Application
173,494; PCT Publication NO: WO 86/01533; U.S. Pat. No. 4,816,567;
European Patent Application 125,023; Better et al. (1988) Science
240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA
84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sun et
al. (1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al.
(1987) Canc. Res. 47:999-1005; Wood et al. (1985) Nature
314:446-449; and Shaw et al. (1988) J. Natl. Cancer Inst.
80:1553-1559); Morrison (1985) Science 229:1202-1207; Oi et al.
(1986) Bio/Techniques 4:214; U.S. Pat. No. 5,225,539; Jones et al.
(1986) Nature 321:552-525; Verhoeyan et al. (1988) Science
239:1534; and Beidler et al. (1988) J. Immunol. 141:4053-4060.
[0712] Completely human antibodies are particularly desirable for
therapeutic treatment of human patients. Such antibodies can be
produced, for example, using transgenic mice which are incapable of
expressing endogenous immunoglobulin heavy and light chains genes,
but which can express human heavy and light chain genes. The
transgenic mice are immunized in the normal fashion with a selected
antigen, e.g., all or a portion of a polypeptide of the invention.
Monoclonal antibodies directed against the antigen can be obtained
using conventional hybridoma technology. The human immunoglobulin
transgenes harbored by the transgenic mice rearrange during B cell
differentiation, and subsequently undergo class switching and
somatic mutation. Thus, using such a technique, it is possible to
produce therapeutically useful IgG, IgA and IgE antibodies. For an
overview of this technology for producing human antibodies, see
Lonberg and Huszar (1995, Int. Rev. Immunol. 13:65-93). For a
detailed discussion of this technology for producing human
antibodies and human monoclonal antibodies and protocols for
producing such antibodies, see, e.g., U.S. Pat. No. 5,625,126; U.S.
Pat. No. 5,633,425; U.S. Pat. No. 5,569,825; U.S. Pat. No.
5,661,016; and U.S. Pat. No. 5,545,806. In addition, companies such
as Abgenix, Inc. (Freemont, Calif.), can be engaged to provide
human antibodies directed against a selected antigen using
technology similar to that described above.
[0713] Completely human antibodies which recognize a selected
epitope can be generated using a technique referred to as "guided
selection." In this approach a selected non-human monoclonal
antibody, e.g., a murine antibody, is used to guide the selection
of a completely human antibody recognizing the same epitope.
(Jespers et al. (1994) Bio/technology 12:899-903).
[0714] An antibody directed against a polypeptide of the invention
(e.g., monoclonal antibody) can be used to isolate the polypeptide
by standard techniques, such as affinity chromatography or
immunoprecipitation. Moreover, such an antibody can be used to
detect the protein (e.g., in a cellular lysate or cell supernatant)
in order to evaluate the abundance and pattern of expression of the
polypeptide. The antibodies can also be used diagnostically to
monitor protein levels in tissue as part of a clinical testing
procedure, e.g., to, for example, determine the efficacy of a given
treatment regimen. Detection can be facilitated by coupling the
antibody to a detectable substance. Examples of detectable
substances include various enzymes, prosthetic groups, fluorescent
materials, luminescent materials, bioluminescent materials, and
radioactive materials. Examples of suitable enzymes include
horseradish peroxidase, alkaline phosphatase, .beta.-galactosidase,
or acetylcholinesterase; examples of suitable prosthetic group
complexes include streptavidin/biotin and avidin/biotin; examples
of suitable fluorescent materials include umbelliferone,
fluorescein, fluorescein isothiocyanate, rhodamine,
dichlorotriazinylamine fluorescein, dansyl chloride or
phycoerythrin; an example of a luminescent material includes
luminol; examples of bioluminescent materials include luciferase,
luciferin, and aequorin, and examples of suitable radioactive
material include .sup.125I, .sup.131I, .sup.35S or .sup.3H.
[0715] Further, an antibody (or fragment thereof) can be conjugated
to a therapeutic moiety such as a cytotoxin, a therapeutic agent or
a radioactive metal ion. A cytotoxin or cytotoxic agent includes
any agent that is detrimental to cells. Examples include taxol,
cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin,
etoposide, tenoposide, vincristine, vinblastine, colchicin,
doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone,
mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids,
procaine, tetracaine, lidocaine, propranolol, and puromycin and
analogs or homologs thereof. Therapeutic agents include, but are
not limited to, antimetabolites (e.g., methotrexate,
6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil
decarbazine), alkylating agents (e.g., mechlorethamine, thioepa
chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU),
cyclothosphamide, busulfan, dibromomannitol, streptozotocin,
mitomycin C, and cis-dichlorodiamine platinum (II) (DDP)
cisplatin), anthracyclines (e.g., daunorubicin (formerly
daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin
(formerly actinomycin), bleomycin, mithramycin, and anthramycin
(AMC)), and anti-mitotic agents (e.g., vincristine and
vinblastine).
[0716] The conjugates of the invention can be used for modifying a
given biological response, the drug moiety is not to be construed
as limited to classical chemical therapeutic agents. For example,
the drug moiety may be a protein or polypeptide possessing a
desired biological activity. Such proteins may include, for
example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or
diphtheria toxin; a protein such as tumor necrosis factor,
.alpha.-interferon, .beta.-interferon, nerve growth factor,
platelet derived growth factor, tissue plasminogen activator; or,
biological response modifiers such as, for example, lymphokines,
interleukin-1 ("IL-1"), interleukin-2 ("IL-2"), interleukin-6
("IL-6"), granulocyte macrophase colony stimulating factor
("GM-CSF"), granulocyte colony stimulating factor ("G-CSF"), or
other growth factors.
[0717] Techniques for conjugating such therapeutic moiety to
antibodies are well known, see, e.g., Amon et al., "Monoclonal
Antibodies For Immunotargeting Of Drugs In Cancer Therapy", in
Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds.),
pp. 243-56 (Alan R. Liss, Inc. 1985); Hellstrom et al., "Antibodies
For Drug Delivery", in Controlled Drug Delivery (2nd Ed.), Robinson
et al. (eds.), pp. 623-53 (Marcel Dekker, Inc. 1987); Thorpe,
"Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A
Review", in Monoclonal Antibodies '84: Biological And Clinical
Applications, Pinchera et al. (eds.), pp. 475-506 (1985);
"Analysis, Results, And Future Prospective Of The Therapeutic Use
Of Radiolabeled Antibody In Cancer Therapy", in Monoclonal
Antibodies For Cancer Detection And Therapy, Baldwin et al. (eds.),
pp. 303-16 (Academic Press 1985), and Thorpe et al., "The
Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates",
Immunol. Rev., 62:119-58 (1982).
[0718] Alternatively, an antibody can be conjugated to a second
antibody to form an antibody heteroconjugate as described by Segal
in U.S. Pat. No. 4,676,980, incorporated herein by reference in its
entirety.
[0719] Accordingly, in one aspect, the invention provides
substantially purified antibodies or fragment thereof, and human
and non-human antibodies or fragments thereof, which antibodies or
fragments specifically bind to a polypeptide comprising an amino
acid sequence selected from the group consisting of: the amino acid
sequence of any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38,
40, 42, 44 or 46, or an amino acid sequence encoded by the cDNA of
a clone deposited as ATCC.RTM. 98348; a fragment of at least 15
amino acid residues of the amino acid sequence of any one of SEQ ID
NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, an amino acid
sequence which is at least 95% identical to the amino acid sequence
of any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, wherein the percent identity is determined using the ALIGN
program of the GCG software package with a PAM120 weight residue
table, a gap length penalty of 12, and a gap penalty of 4; and an
amino acid sequence which is encoded by a nucleic acid molecule
which hybridizes to the nucleic acid molecule consisting of any one
of SEQ ID Nos:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or
45, or the cDNA of a clone deposited as ATCC.RTM. 98348, or a
complement thereof, under conditions of hybridization of
6.times.SSC at 45.quadrature.C. and washing in 0.2.times.SSC, 0.1%
SDS at 65.quadrature.C. In various embodiments, the substantially
purified antibodies of the invention, or fragments thereof, can be
human, non-human, chimeric and/or humanized antibodies.
[0720] In another aspect, the invention provides human and
non-human antibodies or fragments thereof, which antibodies or
fragments specifically bind to a polypeptide comprising an amino
acid sequence selected from the group consisting of: the amino acid
sequence of any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38,
40, 42, 44 or 46, or an amino acid sequence encoded by the cDNA of
a clone deposited as ATCC.RTM. 98348; a fragment of at least 15
amino acid residues of the amino acid sequence of any one of SEQ ID
NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, an amino acid
sequence which is at least 95% identical to the amino acid sequence
of any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, wherein the percent identity is determined using the ALIGN
program of the GCG software package with a PAM120 weight residue
table, a gap length penalty of 12, and a gap penalty of 4; and an
amino acid sequence which is encoded by a nucleic acid molecule
which hybridizes to the nucleic acid molecule consisting of any one
of SEQ ID Nos:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or
45, or the cDNA of a clone deposited as ATCC.RTM. 98348, or a
complement thereof, under conditions of hybridization of
6.times.SSC at 45.quadrature.C. and washing in 0.2.times.SSC, 0.1%
SDS at 65.quadrature.C. Such non-human antibodies can be goat,
mouse, sheep, horse, chicken, rabbit, or rat antibodies.
Alternatively, the non-human antibodies of the invention can be
chimeric and/or humanized antibodies. In addition, the non-human
antibodies of the invention can be polyclonal antibodies or
monoclonal antibodies.
[0721] In still a further aspect, the invention provides monoclonal
antibodies or fragments thereof, which antibodies or fragments
specifically bind to a polypeptide comprising an amino acid
sequence selected from the group consisting of: the amino acid
sequence of any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38,
40, 42, 44 or 46, or an amino acid sequence encoded by the cDNA of
a clone deposited as ATCC.RTM. 98348; a fragment of at least 15
amino acid residues of the amino acid sequence of any one of SEQ ID
NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, an amino acid
sequence which is at least 95% identical to the amino acid sequence
of any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, wherein the percent identity is determined using the ALIGN
program of the GCG software package with a PAM120 weight residue
table, a gap length penalty of 12, and a gap penalty of 4; and an
amino acid sequence which is encoded by a nucleic acid molecule
which hybridizes to the nucleic acid molecule consisting of any one
of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or
45, or the cDNA of a clone deposited as any of ATCC.RTM. 98348, or
a complement thereof, under conditions of hybridization of
6.times.SSC at 45.quadrature.C. and washing in 0.2.times.SSC, 0.1%
SDS at 65.quadrature.C. The monoclonal antibodies can be human,
humanized, chimeric and/or non-human antibodies.
[0722] The substantially purified antibodies or fragments thereof
specifically bind to a signal peptide, a secreted sequence, an
extracellular domain, a transmembrane or a cytoplasmic domain
cytoplasmic membrane of a polypeptide of the invention. In a
particularly preferred embodiment, the substantially purified
antibodies or fragments thereof, the human and non-human antibodies
or fragments thereof, and/or the monoclonal antibodies or fragments
thereof, of the invention specifically bind to a secreted sequence
or an extracellular domain of the amino acid sequence of SEQ ID
NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46. Preferably,
the secreted sequence or extracellular domain to which the
antibody, or fragment thereof, binds comprises from about amino
acids 1-529 or 18-529 of SEQ ID NO: 2, or from amino acids 1-530 or
18-530 of SEQ ID NO: 25.
[0723] Any of the antibodies of the invention can be conjugated to
a therapeutic moiety or to a detectable substance. Non-limiting
examples of detectable substances that can be conjugated to the
antibodies of the invention are an enzyme, a prosthetic group, a
fluorescent material, a luminescent material, a bioluminescent
material, and a radioactive material.
[0724] The invention also provides a kit containing an antibody of
the invention, and instructions for use. In another embodiment, a
kit comprising an antibody of the invention conjugated to a
detectable substance and instructions for use. Still another aspect
of the invention is a pharmaceutical composition comprising an
antibody of the invention and a pharmaceutically acceptable
carrier. In preferred embodiments, the pharmaceutical composition
contains an antibody of the invention, a therapeutic moiety, and a
pharmaceutically acceptable carrier.
[0725] Still another aspect of the invention is a method of making
an antibody that binds, that is, is directed against, Delta3, the
method comprising immunizing a mammal with a polypeptide. The
polypeptide used as an immungen comprises an amino acid sequence
selected from the group consisting of: the amino acid sequence of
any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or
46, or an amino acid sequence encoded by the cDNA of a clone
deposited as ATCC.RTM. 98348; a fragment of at least 15 amino acid
residues of the amino acid sequence of any one of SEQ ID NOs: 2,
25, 28, 30, 32, 34, 36, 38, 40, 42, 44 or 46, an amino acid
sequence which is at least 95% identical to the amino acid sequence
of any one of SEQ ID NOs: 2, 25, 28, 30, 32, 34, 36, 38, 40, 42, 44
or 46, wherein the percent identity is determined using the ALIGN
program of the GCG software package with a PAM120 weight residue
table, a gap length penalty of 12, and a gap penalty of 4; and an
amino acid sequence which is encoded by a nucleic acid molecule
which hybridizes to the nucleic acid molecule consisting of any one
of SEQ ID NOs:1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41, 43 or
45, or the cDNA of a clone deposited as ATCC.RTM. 98348, or a
complement thereof, under conditions of hybridization of
6.times.SSC at 45.quadrature.C. and washing in 0.2.times.SSC, 0.1%
SDS at 65.quadrature.C. After immunization, a sample is collected
from the mammal that contains an antibody that specifically
recognizes Delta3. Preferably, the polypeptide is recombinantly
produced using a non-human host cell. Optionally, the antibodies
can be further purified from the sample using techniques well known
to those of skill in the art. The method can further comprise
producing a monoclonal antibody-producing cell from the cells of
the mammal. Optionally, antibodies are collected from the
antibody-producing cell.
Isolated FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 Proteins and Anti-FTHMA-070 or Anti-T85 Antibodies
[0726] One aspect of the invention pertains to isolated FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 proteins, and
biologically active portions thereof, as well as polypeptide
fragments suitable for use as immunogens to raise anti-FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 antibodies. In
one embodiment, native FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 proteins can be isolated from cells or tissue
sources by an appropriate purification scheme using standard
protein purification techniques. In another embodiment, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 proteins are
produced by recombinant DNA techniques. Alternative to recombinant
expression, a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein or polypeptide can be synthesized chemically using
standard peptide synthesis techniques.
[0727] An "isolated" or "purified" protein or biologically active
portion thereof is substantially free of cellular material or other
contaminating proteins from the cell or tissue source from which
the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein is derived, or substantially free from chemical precursors
or other chemicals when chemically synthesized. The language
"substantially free of cellular material" includes preparations of
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein in which the protein is separated from cellular components
of the cells from which it is isolated or recombinantly produced.
Thus, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein that is substantially free of cellular material includes
preparations of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein having less than about 30%, 20%, 10%, or
5% (by dry weight) of non-FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein (also referred to herein as a
"contaminating protein"). When the FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein or biologically active
portion thereof is recombinantly produced, it is also preferably
substantially free of culture medium, i.e., culture medium
represents less than about 20%, 10%, or 5% of the volume of the
protein preparation. When FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein is produced by chemical
synthesis, it is preferably substantially free of chemical
precursors or other chemicals, i.e., it is separated from chemical
precursors or other chemicals which are involved in the synthesis
of the protein. Accordingly such preparations of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein have
less than about 30%, 20%, 10%, 5% (by dry weight) of chemical
precursors or non-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 chemicals.
[0728] Biologically active portions of a FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 protein include peptides
comprising amino acid sequences sufficiently identical to or
derived from the amino acid sequence of the FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 protein, which include
less amino acids than the full length FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 proteins, and exhibit at least one
activity of a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein. Typically, biologically active portions comprise a
domain or motif with at least one activity of the FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein. A
biologically active portion of a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein can be a polypeptide which
is, for example, 10, 25, 50, 100 or more amino acids in length.
Preferred biologically active polypeptides include one or more
identified structural domains. Preferred biologically active
polypeptides include one or more identified T129 structural
domains, e.g., TNFR/NGFR cysteine-rich domain (SEQ ID NO:142).
[0729] Moreover, other biologically active portions, in which other
regions of the protein are deleted, can be prepared by recombinant
techniques and evaluated for one or more of the functional
activities of a native FTHMA-070 or T85 protein. Preferred
FTHMA-070 or T85 protein has the amino acid sequence shown of SEQ
ID NO:54 or SEQ ID NO:58, respectively. Other useful FTHMA-070 or
T85 proteins are substantially identical to SEQ ID NO:54 or SEQ ID
NO:58, respectively and retain the functional activity of the
reference protein yet differ in amino acid sequence due to natural
allelic variation or mutagenesis.
[0730] Accordingly, a useful FTHMA-070 protein is a protein which
includes an amino acid sequence at least about 45%, preferably 55%,
65%, 75%, 85%, 95%, or 99% identical to the amino acid sequence of
SEQ ID NO:54 and retains the functional activity of the FTHMA-070
protein of SEQ ID NO:54. In a preferred embodiment, the FTHMA-070
protein retains the functional activity of the FTHMA-070 protein of
SEQ ID NO:54.
[0731] Accordingly, a useful T85 protein is a protein which
includes an amino acid sequence at least about 45%, preferably 55%,
65%, 75%, 85%, 95%, or 99% identical to the amino acid sequence of
SEQ ID NO:58 and retains the functional activity of the T85 protein
of SEQ ID NO:58. In other instances, the T85 protein is a protein
having an amino acid sequence 55%, 65%, 75%, 85%, 95%, or 98%
identical to one of the T85 fibronectin type III or Ig superfamily
domains (SEQ ID NOs:61-67). In a preferred embodiment, the T85
protein retains the functional activity of the T85 protein of SEQ
ID NO:58.
[0732] Preferred Tango-77 protein has the amino acid sequence shown
of SEQ ID NO:72, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID
NO:81, or SEQ ID NO:83. Other useful Tango-77 proteins are
substantially identical to SEQ ID NO:72, SEQ ID NO:75, SEQ ID
NO:77, SEQ ID NO:79, SEQ ID NO:81, or SEQ ID NO:83 and retain the
functional activity of the protein of SEQ ID NO:72, SEQ ID NO:75,
SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, or SEQ ID NO:83 yet
differ in amino acid sequence due to natural allelic variation or
mutagenesis. Accordingly, a useful Tango-77 protein is a protein
which includes an amino acid sequence at least about 45%,
preferably 55%, 65%, 75%, 85%, 95%, or 99% identical to the amino
acid sequence of SEQ ID NO:72, SEQ ID NO:75, SEQ ID NO:77, SEQ ID
NO:79, SEQ ID NO:81, or SEQ ID NO:83 and retains the functional
activity of the Tango-77 proteins of SEQ ID NO:72, SEQ ID NO:75,
SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, or SEQ ID NO:83. In a
preferred embodiment, the Tango-77 protein retains a functional
activity of the Tango-77 protein of SEQ ID NO:72, SEQ ID NO:75, SEQ
ID NO:77, SEQ ID NO:79, SEQ ID NO:81, or SEQ ID NO:83.
[0733] In one embodiment, a biologically active portion of a SPOIL
protein comprises at least an IL-1 signature domain. In another
embodiment, a biologically active portion of a SPOIL protein
comprises a SPOIL signature motif. In yet another embodiment, a
biologically active portion of a SPOIL protein comprises a SPOIL
unique domain. In yet another embodiment, a biologically active
portion of a SPOIL protein comprises a SPOIL C-terminal unique
domain. In another embodiment, a biologically active portion of a
SPOIL protein comprises a signal sequence and/or is secreted. In
another embodiment, a biologically active portion of a SPOIL
protein lacks a signal sequence and/or is intracellular.
[0734] It is to be understood that a preferred biologically active
portion of a SPOIL protein of the present invention may contain at
least one of the above-identified structural domains. Another
preferred biologically active portion of a SPOIL protein may
contain at least two of the above-identified structural domains.
Another preferred biologically active portion of a SPOIL protein
may contain at least three or more of the above-identified
structural domains.
[0735] Moreover, other biologically active portions, in which other
regions of the protein are deleted, can be prepared by recombinant
techniques and evaluated for one or more of the functional
activities of a native SPOIL protein.
[0736] In a preferred embodiment, the SPOIL protein has an amino
acid sequence shown in SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105,
SEQ ID NO:113, the amino acid sequence encoded by the DNA insert of
the plasmid deposited with ATCC as Accession Number 98883, or the
amino acid sequence encoded by the DNA insert of the plasmid
deposited with ATCC as Accession Number 98984. In other
embodiments, the SPOIL protein is substantially homologous to SEQ
ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98883, or the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98984, and retains the functional activity of the
protein of SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID
NO:113, the amino acid sequence encoded by the DNA insert of the
plasmid deposited with ATCC as Accession Number 98883, or the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984, yet differs in amino acid
sequence due to natural allelic variation or mutagenesis, as
described in detail in subsection I above. Accordingly, in another
embodiment, the SPOIL protein is a protein which comprises an amino
acid sequence at least about 60-65% identical to the amino acid
sequence of SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID
NO:113, the amino acid sequence encoded by the DNA insert of the
plasmid deposited with ATCC as Accession Number 98883, or the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984, and, preferably, retains a
functional activity of the SPOIL proteins of SEQ ID NO:90, SEQ ID
NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984. Preferably, the protein is at least about 70-75% identical
to SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the
amino acid sequence encoded by the DNA insert of the plasmid
deposited with ATCC as Accession Number 98883, or the amino acid
sequence encoded by the DNA insert of the plasmid deposited with
ATCC as Accession Number 98984, more preferably at least about
80-85% identical to SEQ ID NO:90, SEQ ID NO:102, SEQ ID NO:105, SEQ
ID NO:113, the amino acid sequence encoded by the DNA insert of the
plasmid deposited with ATCC as Accession Number 98883, or the amino
acid sequence encoded by the DNA insert of the plasmid deposited
with ATCC as Accession Number 98984, even more preferably at least
about 90-95% identical to SEQ ID NO:90, SEQ ID NO:102, SEQ ID
NO:105, SEQ ID NO:113, the amino acid sequence encoded by the DNA
insert of the plasmid deposited with ATCC as Accession Number
98883, or the amino acid sequence encoded by the DNA insert of the
plasmid deposited with ATCC as Accession Number 98984, and most
preferably at least about 95% or more identical to SEQ ID NO:90,
SEQ ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid
sequence encoded by the DNA insert of the plasmid deposited with
ATCC as Accession Number 98883, or the amino acid sequence encoded
by the DNA insert of the plasmid deposited with ATCC as Accession
Number 98984.
[0737] In one embodiment, a biologically active portion of a
NEOKINE protein comprises at least a NEOKINE CXC signature motif.
In another embodiment, a biologically active portion of a NEOKINE
protein comprises at least a signal sequence. In another
embodiment, a biologically active portion of a NEOKINE protein
comprises a NEOKINE amino acid sequence lacking a signal sequence
(e.g., a mature NEOKINE protein).
[0738] It is to be understood that a preferred biologically active
portion of a NEOKINE protein of the present invention may contain
at least one of the above-identified structural domains. A more
preferred biologically active portion of a NEOKINE protein may
contain at least two of the above-identified structural domains.
Moreover, other biologically active portions, in which other
regions of the protein are deleted, can be prepared by recombinant
techniques and evaluated for one or more of the functional
activities of a native NEOKINE protein.
[0739] In a preferred embodiment, the NEOKINE protein has an amino
acid sequence shown in SEQ ID NO:116, SEQ ID NO:119, SEQ ID NO:122,
or SEQ ID NO:125. In other embodiments, the NEOKINE protein is
substantially homologous to SEQ ID NO:116, SEQ ID NO:119, SEQ ID
NO:122, or SEQ ID NO:125, and retains the functional activity of
the protein of SEQ ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ
ID NO:125, yet differs in amino acid sequence due to natural
allelic variation or mutagenesis, as described in detail in
subsection I above. Accordingly, in another embodiment, the NEOKINE
protein is a protein which comprises an amino acid sequence at
least about 60% homologous to the amino acid sequence of SEQ ID
NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125 and retains
the functional activity of the NEOKINE proteins of SEQ ID NO:116,
SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125, respectively.
Preferably, the protein is at least about 70% homologous to SEQ ID
NO:116, SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125, more
preferably at least about 80% homologous to SEQ ID NO:116, SEQ ID
NO:119, SEQ ID NO:122, or SEQ ID NO:125, even more preferably at
least about 90% homologous to SEQ ID NO:116, SEQ ID NO:119, SEQ ID
NO:122, or SEQ ID NO:125, and most preferably at least about 95% or
more homologous to SEQ ID NO:116, SEQ ID NO:119, SEQ ID NO:122, or
SEQ ID NO:125.
[0740] Preferred T129 protein has the amino acid sequence shown of
SEQ ID NO:138. Other useful T129 proteins are substantially
identical to SEQ ID NO:138 and retain the functional activity of
the protein of SEQ ID NO:138 yet differ in amino acid sequence due
to natural allelic variation or mutagenesis. Accordingly, a useful
T129 protein is a protein which includes an amino acid sequence at
least about 45%, preferably 55%, 65%, 75%, 85%, 95%, or 99%
identical to the amino acid sequence of SEQ ID NO:138 and retains
the functional activity of the T129 proteins of SEQ ID NO:138. In
other instances, the T129 protein is a protein having an amino acid
sequence 55%, 65%, 75%, 85%, 95%, or 98% identical to the T129
TNFR/NGFR cysteine rich domain (SEQ ID NO:141). In a preferred
embodiment, the T129 protein retains the functional activity of the
T129 protein of SEQ ID NO:138.
[0741] Preferred polypeptides have the amino acid sequence of SEQ
ID NO:147, 148, 165, or 166. Other useful proteins are
substantially identical (e.g., at least about 45%, preferably 55%,
65%, 75%, 85%, 95%, or 99%) to any of SEQ ID NO:147, 148, 165, or
166, and retain the functional activity of the protein of the
corresponding naturally-occurring protein yet differ in amino acid
sequence due to natural allelic variation or mutagenesis.
[0742] To determine the percent identity of two amino acid
sequences or of two nucleic acids, the sequences are aligned for
optimal comparison purposes (e.g., gaps can be introduced in the
sequence of a first amino acid or nucleic acid sequence for optimal
alignment with a second amino or nucleic acid sequence). The amino
acid residues or nucleotides at corresponding amino acid positions
or nucleotide positions are then compared.
[0743] To determine the percent identity of two amino acid
sequences or of two nucleic acids, the sequences are aligned for
optimal comparison purposes (e.g., gaps can be introduced in the
sequence of a first amino acid or nucleic acid sequence for optimal
alignment with a second amino or nucleic acid sequence and
non-homologous sequences can be disregarded for comparison
purposes). In one embodiment, an alignment is a global alignment,
e.g., an overall sequence alignment. In another embodiment, an
alignment is a local alignment. In a preferred embodiment, the
length of a sequence aligned for comparison purposes is at least
30%, preferably at least 40%, more preferably at least 50%, even
more preferably at least 60%, and even more preferably at least
70%, 80%, or 90% of the length of the reference sequence to which
it is aligned (e.g., when aligning a second sequence to the SPOIL
amino acid sequence of SEQ ID NO:90, at least 29, preferably at
least 39, more preferably at least 49, even more preferably at
least 59, and even more preferably at least 69, 78 or 88 amino acid
residues are aligned). In a particularly preferred embodiment,
percent identity is calculated over the entire length of a
reference sequence. The amino acid residues or nucleotides at
corresponding amino acid positions or nucleotide positions are then
compared.
[0744] To determine the percent homology of two amino acid
sequences or of two nucleic acids, the sequences are aligned for
optimal comparison purposes (e.g., gaps can be introduced in the
sequence of a first amino acid or nucleic acid sequence for optimal
alignment with a second amino or nucleic acid sequence and
non-homologous sequences can be disregarded for comparison
purposes). In a preferred embodiment, the length of a reference
sequence aligned for comparison purposes is at least 30%,
preferably at least 40%, more preferably at least 50%, even more
preferably at least 60%, and even more preferably at least 70%,
80%, or 90% of the length of the reference sequence (e.g., when
aligning a second sequence to the NEOKINE amino acid sequence of
SEQ ID NO:2 having 99 amino acid residues, at least 30, preferably
at least 40, more preferably at least 50, even more preferably at
least 59, and even more preferably at least 69, 79, or 89 are
aligned). The amino acid residues or nucleotides at corresponding
amino acid positions or nucleotide positions are then compared.
[0745] When a position in the first sequence is occupied by the
same amino acid residue or nucleotide as the corresponding position
in the second sequence, then the molecules are homologous at that
position (i.e., as used herein amino acid or nucleic acid
"homology" is equivalent to amino acid or nucleic acid "identity").
The percent homology between the two sequences is a function of the
number of identical positions shared by the sequences (i.e., %
homology=# of identical positions/total # of
positions.times.100).
[0746] The determination of percent homology between two sequences
can be accomplished using a mathematical algorithm. A preferred,
non-limiting example of a mathematical algorithm utilized for the
comparison of two sequences is the algorithm of Karlin and Altschul
(1990) Proc. Nat'l Acad. Sci. USA 87:2264-2268, modified as in
Karlin and Altschul (1993) Proc. Nat'l Acad. Sci. USA 90:5873-5877.
Such an algorithm is incorporated into the NBLAST and XBLAST
programs of Altschul, et al. (1990) J. Mol. Biol. 215:403-410.
BLAST nucleotide searches can be performed with the NBLAST program,
score=100, wordlength=12 to obtain nucleotide sequences homologous
to FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
nucleic acid molecules of the invention. BLAST protein searches can
be performed with the XBLAST program, score=50, wordlength=3 to
obtain amino acid sequences homologous to FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 protein molecules of the
invention. To obtain gapped alignments for comparison purposes,
Gapped BLAST can be utilized as described in Altschul et al.,
(1997) Nucleic Acids Res. 25:3389-3402. When utilizing BLAST and
Gapped BLAST programs, the default parameters of the respective
programs (e.g., XBLAST and NBLAST) can be used. Another preferred,
non-limiting example of a mathematical algorithm utilized for the
comparison of sequences is the algorithm of Myers and Miller,
CABIOS (1989). Such an algorithm is incorporated into the ALIGN
program (version 2.0) which is part of the GCG sequence alignment
software package. When utilizing the ALIGN program for comparing
amino acid sequences, a PAM120 weight residue table, a gap length
penalty of 12, and a gap penalty of 4 can be used.
[0747] The nucleic acid and protein sequences of the present
invention can further be used as a "query sequence" to perform a
search against public databases to, for example, identify other
family members or related sequences. Such searches can be performed
using the NBLAST and XBLAST programs (version 2.0) of Altschul, et
al. (1990) J. Mol. Biol. 215:403-10. BLAST nucleotide searches can
be performed with the NBLAST program, score=100, wordlength=12 to
obtain nucleotide sequences homologous to nucleic acid molecules of
the invention. BLAST protein searches can be performed with the
XBLAST program, score=50, wordlength=3 to obtain amino acid
sequences homologous to protein molecules of the invention. To
obtain gapped alignments for comparison purposes, Gapped BLAST can
be utilized as described in Altschul et al., (1997) Nucleic Acids
Res. 25(17):3389-3402. When utilizing BLAST and Gapped BLAST
programs, the default parameters of the respective programs (e.g.,
XBLAST and NBLAST) can be used.
[0748] Another preferred, non-limiting example of a mathematical
algorithm utilized for the comparison of sequences is the algorithm
of Myers and Miller, CABIOS (1989). Such an algorithm is
incorporated into the ALIGN program (version 2.0) which is part of
the CGC sequence alignment software package. When utilizing the
ALIGN program for comparing amino acid sequences, a PAM120 weight
residue table, a gap length penalty of 12, and a gap penalty of 4
can be used. Additional algorithms for sequence analysis are known
in the art and include ADVANCE and ADAM as described in Torellis
and Robotti (1994) Comput. Appl. Biosci., 10:3-5; and FASTA
described in Pearson and Lipman (1988) Proc. Natl. Acad. Sci.
85:2444-8. Within FASTA, ktup is a control option that sets the
sensitivity and speed of the search. If ktup=2, similar regions in
the two sequences being compared are found by looking at pairs of
aligned residues; if ktup=1, single aligned amino acids are
examined. ktup can be set to 2 or 1 for protein sequences, or from
1 to 6 for DNA sequences. The default if ktup is not specified is 2
for proteins and 6 for DNA.
[0749] The percent identity between two sequences can be determined
using techniques similar to those described above, with or without
allowing gaps. In calculating percent identity, only exact matches
are counted.
[0750] The invention also provides FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 chimeric or fusion proteins. As
used herein, a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 "chimeric protein" or "fusion protein" comprises a
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
polypeptide operatively linked to a non-FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 polypeptide. A FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 polypeptide
refers to a polypeptide having an amino acid sequence corresponding
to FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259,
whereas a non-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 polypeptide refers to a polypeptide having an amino acid
sequence corresponding to a protein which is not substantially
identical to the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein, e.g., a protein which is different from
the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein and which is derived from the same or a different organism.
Within a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 fusion protein the FTHMA-070 or T85 polypeptide can correspond
to all or a portion of a FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein, preferably at least one
biologically active portion of a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein. Within the fusion
protein, the term "operatively linked" is intended to indicate that
the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
polypeptide and the non-FTHMA-070 or T85 polypeptide are fused
in-frame to each other. The non-FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 polypeptide can be fused to the
N-terminus or C-terminus of the FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 polypeptide.
[0751] One useful fusion protein is a GST-FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 fusion protein in which
the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
sequences are fused to the C-terminus of the GST sequences. Such
fusion proteins can facilitate the purification of recombinant
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259.
[0752] In another embodiment, the fusion protein is a FTHMA-070,
Tango85, SPOIL, or NEOKINE protein containing a heterologous signal
sequence at its N-terminus. For example, the native FTHMA-070,
Tango85, SPOIL, or NEOKINE signal sequence can be removed and
replaced with a signal sequence from another protein. In certain
host cells (e.g., mammalian host cells), expression and/or
secretion of FTHMA-070, Tango85, SPOIL, or NEOKINE can be increased
through use of a heterologous signal sequence.
[0753] In another embodiment, the fusion protein is a Tango-77,
Tango129 or A259 protein containing a heterologous signal sequence
at its N-terminus. For example, the native Tango-77, Tango129 or
A259 signal sequence (i.e., about amino acids 1 to 63 of SEQ ID
NO:72; SEQ ID NO:74; or about amino acids 1 to 52 of SEQ ID NO:77;
SEQ ID NO:78; or about amino acids 1 to 21 of SEQ ID NO:81; SEQ ID
NO:82) can be removed and replaced with a signal sequence from
another protein. For example, the native T129 signal sequence
(i.e., about amino acids 1 to 22 of SEQ ID NO:138) can be removed
and replaced with a signal sequence from another protein. In
certain host cells (e.g., mammalian host cells), expression and/or
secretion of Tango-77 can be increased through use of a
heterologous signal sequence. For example, the gp67 secretory
sequence of the baculovirus envelope protein can be used as a
heterologous signal sequence (Ausubel et al., supra). Other
examples of eukaryotic heterologous signal sequences include the
secretory sequences of melittin and human placental alkaline
phosphatase (Stratagene; La Jolla, Calif.). In yet another example,
useful prokaryotic heterologous signal sequences include the phoA
secretory signal (Sambrook et al., supra) and the protein A
secretory signal (Pharmacia Biotech; Piscataway, N.J.).
[0754] In yet another embodiment, the fusion protein is an
FTHMA-070, Tango85, Tango77, Tango129 or A259-immunoglobulin fusion
protein in which all or part of FTHMA-070 or T85 is fused to
sequences derived from a member of the immunoglobulin protein
family. The FTHMA-070, Tango85, Tango77, Tango129 or
A259-immunoglobulin fusion proteins of the invention can be
incorporated into pharmaceutical compositions and administered to a
subject to inhibit an interaction between a FTHMA-070, Tango85,
Tango77, Tango129 or A259 ligand and a FTHMA-070, Tango85, Tango77,
Tango129 or A259 protein. The FTHMA-070, Tango85, Tango77, Tango129
or A259-immunoglobulin fusion proteins can be used to affect the
bioavailability of a FTHMA-070, Tango85, Tango77, Tango129 or A259
cognate ligand. Inhibition of the FTHMA-070, Tango85, Tango77,
Tango129 or A259 ligand/FTHMA-070, Tango85, Tango77, Tango129 or
A259 interaction may be useful therapeutically. Moreover, the
FTHMA-070, Tango85, Tango77, Tango129 or A259-immunoglobulin fusion
proteins of the invention can be used as immunogens to produce
anti-FTHMA-070, Tango85, Tango77, Tango129 or A259 antibodies in a
subject, to purify FTHMA-070, Tango85, Tango77, Tango129 or A259
ligands and in screening assays to identify molecules which inhibit
the interaction of FTHMA-070, Tango85, Tango77, Tango129 or A259
with a FTHMA-070, Tango85, Tango77, Tango129 or A259 ligand.
[0755] In yet another embodiment, the fusion protein is a SPOIL or
NEOKINE-immunoglobulin fusion protein in which the SPOIL or NEOKINE
sequence are fused to sequences derived from a member of the
immunoglobulin protein family. Soluble derivatives have also been
made of cell surface glycoproteins in the immunoglobulin gene
superfamily consisting of an extracellular domain of the cell
surface glycoprotein fused to an immunoglobulin constant (Fc)
region (see e.g., Capon et al. (1989) Nature 337:525-531 and Capon
U.S. Pat. Nos. 5,116,964 and 5,428,130 [CD4-IgG1 constructs];
Linsley, et al. (1991) J. Exp. Med. 173:721-730 [a CD28-IgG1
construct and a B7-1-IgG1 construct]; and Linsley et al. (1991) J.
Exp. Med. 174:561-569 and U.S. Pat. No. 5,434,131[a CTLA4-IgG1]).
Such fusion proteins have proven useful for modulating
receptor-ligand interactions. Soluble derivatives of cell surface
proteins of the tumor necrosis factor receptor (TNFR) superfamily
proteins have been made consisting of an extracellular domain of
the cell surface receptor fused to an immunoglobulin constant (Fc)
region (See for example Moreland et al. (1997) N. Engl. J. Med.
337(3):141-147; van der Poll et al. (1997) Blood 89(10):3727-3734;
and Ammann et al. (1997) J. Clin. Invest. 99(7):1699-1703.).
[0756] In yet another embodiment, the fusion protein comprises
NEOKINE sequences (e.g., the NEOKINE CXC signature motif) fused to
sequences form other CXC cytokines. For example, NEOKINE sequences
C-terminal to and including the first conserved cysteine residues
can be fused to N-terminal sequences of other non-NEOKINE
chemokines (e.g., comprising from the N-terminal amino acid residue
to the amino acid residue N-terminal to the first conserved
cysteine).
[0757] The SPOIL or NEOKINE-immunoglobulin fusion proteins of the
invention can be incorporated into pharmaceutical compositions and
administered to a subject to inhibit an interaction between a SPOIL
or NEOKINE protein and a SPOIL or NEOKINE target molecule on the
surface of a cell, to thereby suppress SPOIL or NEOKINE-mediated
signal transduction in vivo. The SPOIL or NEOKINE-immunoglobulin
fusion proteins can be used to affect the bioavailability of a
SPOIL or NEOKINE cognate ligand. Inhibition of the SPOIL or NEOKINE
ligand/SPOIL or NEOKINE interaction may be useful therapeutically
for both the treatment and modulation of inflammation and immune
disorders, as well as modulating (e.g., promoting or inhibiting)
immune cell responses, cell adhesion, and/or cell homing. Moreover,
the SPOIL or NEOKINE-immunoglobulin fusion proteins of the
invention can be used as immunogens to produce anti-SPOIL or
NEOKINE antibodies in a subject, to purify SPOIL or NEOKINE ligands
and in screening assays to identify molecules which inhibit the
interaction of SPOIL or NEOKINE with a SPOIL or NEOKINE target
molecule.
[0758] Preferably, a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 chimeric or fusion protein of the invention is
produced by standard recombinant DNA techniques. For example, DNA
fragments coding for the different polypeptide sequences are
ligated together in-frame in accordance with conventional
techniques, for example by employing blunt-ended or stagger-ended
termini for ligation, restriction enzyme digestion to provide for
appropriate termini, filling-in of cohesive ends as appropriate,
alkaline phosphatase treatment to avoid undesirable joining, and
enzymatic ligation. In another embodiment, the fusion gene can be
synthesized by conventional techniques including automated DNA
synthesizers. Alternatively, PCR amplification of gene fragments
can be carried out using anchor primers which give rise to
complementary overhangs between two consecutive gene fragments
which can subsequently be annealed and reamplified to generate a
chimeric gene sequence (see, e.g., Current Protocols in Molecular
Biology, Ausubel et al. eds., John Wiley & Sons: 1992).
Moreover, many expression vectors are commercially available that
already encode a fusion moiety (e.g., a GST polypeptide). An
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259-encoding nucleic acid can be cloned into such an expression
vector such that the fusion moiety is linked in-frame to the
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein.
[0759] A signal sequence of a polypeptide of the invention (SEQ ID
NO:149 and 163) can be used to facilitate secretion and isolation
of the secreted protein or other proteins of interest. Signal
sequences are typically characterized by a core of hydrophobic
amino acids which are generally cleaved from the mature protein
during secretion in one or more cleavage events. Such signal
peptides contain processing sites that allow cleavage of the signal
sequence from the mature proteins as they pass through the
secretory pathway. Thus, the invention pertains to the described
polypeptides having a signal sequence, as well as to the signal
sequence itself and to the polypeptide in the absence of the signal
sequence (i.e., the cleavage products). In one embodiment, a
nucleic acid sequence encoding a signal sequence of the invention
can be operably linked in an expression vector to a protein of
interest, such as a protein which is ordinarily not secreted or is
otherwise difficult to isolate. The signal sequence directs
secretion of the protein, such as from a eukaryotic host into which
the expression vector is transformed, and the signal sequence is
subsequently or concurrently cleaved. The protein can then be
readily purified from the extracellular medium by art recognized
methods. Alternatively, the signal sequence can be linked to the
protein of interest using a sequence which facilitates
purification, such as with a GST domain.
[0760] In another embodiment, the signal sequences of the present
invention can be used to identify regulatory sequences, e.g.,
promoters, enhancers, repressors. Since signal sequences are the
most amino-terminal sequences of a peptide, it is expected that the
nucleic acids which flank the signal sequence on its amino-terminal
side will be regulatory sequences which affect transcription. Thus,
a nucleotide sequence which encodes all or a portion of a signal
sequence can be used as a probe to identify and isolate signal
sequences and their flanking regions, and these flanking regions
can be studied to identify regulatory elements therein.
[0761] The present invention also pertains to variants of the
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
proteins which function as either FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 agonists (mimetics) or as
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
antagonists. Variants of the FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein can be generated by mutagenesis,
e.g., discrete point mutation or truncation of the FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein. An
agonist of the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein can retain substantially the same, or a
subset, of the biological activities of the naturally occurring
form of the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein. An antagonist of the FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein can inhibit one or more of
the activities of the naturally occurring form of the FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein by, for
example, competitively binding to a downstream or upstream member
of a cellular signaling cascade which includes the FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein. Thus,
specific biological effects can be elicited by treatment with a
variant of limited function. Treatment of a subject with a variant
having a subset of the biological activities of the naturally
occurring form of the protein can have fewer side effects in a
subject relative to treatment with the naturally occurring form of
the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
proteins.
[0762] In one embodiment, a SPOIL protein which acts as an IL-1
receptor antagonist can be converted into an IL-1 agonist by site
specific mutagenesis. For example, the aspartic acid at amino acid
residue 91 of SEQ ID NO:90 or amino acid residue 74 of SEQ ID
NO:93, can be substituted with a lysine to create an IL-1 agonist.
In a similar manner, the alanine at amino acid residue 162 of SEQ
ID NO:102 or the alanine residue at amino acid residue 201 of SEQ
ID NO:105 can be substituted with a lysine to create an IL-1
agonist. Exemplary methods of converting IL-1ra into an IL-1
agonist are set forth in Ju et al. (1991) Proc. Natl. Acad. Sci.
USA 88:2658-2662.
[0763] Variants of the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein which function as either FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 agonists
(mimetics) or as FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 antagonists can be identified by screening
combinatorial libraries of mutants, e.g., truncation mutants, of
the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein for FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein agonist or antagonist activity. In one embodiment,
a variegated library of FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 variants is generated by combinatorial
mutagenesis at the nucleic acid level and is encoded by a
variegated gene library. A variegated library of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 variants can be
produced by, for example, enzymatically ligating a mixture of
synthetic oligonucleotides into gene sequences such that a
degenerate set of potential FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 sequences is expressible as individual
polypeptides, or alternatively, as a set of larger fusion proteins
(e.g., for phage display) containing the set of FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 sequences therein. There
are a variety of methods which can be used to produce libraries of
potential FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 variants from a degenerate oligonucleotide sequence. Chemical
synthesis of a degenerate gene sequence can be performed in an
automatic DNA synthesizer, and the synthetic gene then ligated into
an appropriate expression vector. Use of a degenerate set of genes
allows for the provision, in one mixture, of all of the sequences
encoding the desired set of potential FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 sequences. Methods for
synthesizing degenerate oligonucleotides are known in the art (see,
e.g., Narang (1983) Tetrahedron 39:3; Itakura et al. (1984) Annu.
Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike
et al. (1983) Nucleic Acid Res. 11:477).
[0764] In addition, libraries of fragments of the FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein coding
sequence can be used to generate a variegated population of
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
fragments for screening and subsequent selection of variants of a
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein. In one embodiment, a library of coding sequence fragments
can be generated by treating a double stranded PCR fragment of a
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
coding sequence with a nuclease under conditions wherein nicking
occurs only about once per molecule, denaturing the double stranded
DNA, renaturing the DNA to form double stranded DNA which can
include sense/antisense pairs from different nicked products,
removing single stranded portions from reformed duplexes by
treatment with S1 nuclease, and ligating the resulting fragment
library into an expression vector. By this method, an expression
library can be derived which encodes N-terminal and internal
fragments of various sizes of the FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein.
[0765] Several techniques are known in the art for screening gene
products of combinatorial libraries made by point mutations or
truncation, and for screening cDNA libraries for gene products
having a selected property. Such techniques are adaptable for rapid
screening of the gene libraries generated by the combinatorial
mutagenesis of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 proteins. The most widely used techniques, which
are amenable to high through-put analysis, for screening large gene
libraries typically include cloning the gene library into
replicable expression vectors, transforming appropriate cells with
the resulting library of vectors, and expressing the combinatorial
genes under conditions in which detection of a desired activity
facilitates isolation of the vector encoding the gene whose product
was detected. Recursive ensemble mutagenesis (REM), a technique
which enhances the frequency of functional mutants in the
libraries, can be used in combination with the screening assays to
identify FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 variants (Arkin and Yourvan (1992) Proc. Natl. Acad. Sci. USA
89:7811-7815; Delgrave et al. (1993) Protein Engineering
6(3):327-331).
[0766] In one embodiment, cell based assays can be exploited to
analyze a variegated SPOIL library. For example, a library of
expression vectors can be transfected into a cell line which
ordinarily responds to a particular ligand in a SPOIL-dependent
manner. The transfected cells are then contacted with the ligand
and the effect of expression of the mutant on signaling by the
ligand can be detected, e.g., by measuring any of a number of
immune cell responses. Plasmid DNA can then be recovered from the
cells which score for inhibition, or alternatively, potentiation of
ligand induction, and the individual clones further
characterized.
[0767] In one embodiment, cell based assays can be exploited to
analyze a variegated NEOKINE library. For example, a library of
expression vectors can be transfected into a cell line which
ordinarily responds to a particular ligand in a NEOKINE-dependent
manner. The transfected cells are then contacted with the ligand
and the effect of expression of the mutant on signaling by the
ligand can be detected, e.g., by measuring any of a number of
inflammatory or angiogenic responses. Plasmid DNA can then be
recovered from the cells which score for inhibition, or
alternatively, potentiation of ligand induction, and the individual
clones further characterized.
[0768] An isolated FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein, or a portion or fragment thereof, can be
used as an immunogen to generate antibodies that bind FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 using standard
techniques for polyclonal and monoclonal antibody preparation. The
full-length FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein can be used or, alternatively, the invention
provides antigenic peptide fragments of FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 for use as
immunogens.
[0769] The antigenic peptide of FTHMA-070 or T85 comprises at least
8 (preferably 10, 15, 20, or 30) amino acid residues of the amino
acid sequence shown in SEQ ID NO:54 and encompasses an epitope of
FTHMA-070 or T85 such that an antibody raised against the peptide
forms a specific immune complex with FTHMA-070 or T85. Preferred
epitopes encompassed by the antigenic peptide are regions of
FTHMA-070 or T85 that are located on the surface of the protein,
e.g., hydrophilic regions.
[0770] The antigenic peptide of Tango-77 comprises at least 8
(preferably 10, 15, 20, or 30) amino acid residues of the amino
acid sequence shown in SEQ ID NO:72, SEQ ID NO:75, SEQ ID NO:77,
SEQ ID NO:79, SEQ ID NO:81 or SEQ ID NO:83 and encompasses an
epitope of Tango-77 such that an antibody raised against the
peptide forms a specific immune complex with Tango-77.
[0771] The antigenic peptide of SPOIL comprises at least 8 amino
acid residues of the amino acid sequence shown in SEQ ID NO:90, SEQ
ID NO:102, SEQ ID NO:105, SEQ ID NO:113, the amino acid sequence
encoded by the DNA insert of the plasmid deposited with ATCC as
Accession Number 98883, or the amino acid sequence encoded by the
DNA insert of the plasmid deposited with ATCC as Accession Number
98984, and encompasses an epitope of SPOIL such that an antibody
raised against the peptide forms a specific immune complex with
SPOIL. Preferably, the antigenic peptide comprises at least 10
amino acid residues, more preferably at least 15 amino acid
residues, even more preferably at least 20 amino acid residues, and
most preferably at least 30 amino acid residues.
[0772] The antigenic peptide of NEOKINE comprises at least 8 amino
acid residues of the amino acid sequence shown in SEQ ID NO:116,
SEQ ID NO:119, SEQ ID NO:122, or SEQ ID NO:125 and encompasses an
epitope of NEOKINE such that an antibody raised against the peptide
forms a specific immune complex with NEOKINE. Preferably, the
antigenic peptide comprises at least 10 amino acid residues, more
preferably at least 15 amino acid residues, even more preferably at
least 20 amino acid residues, and most preferably at least 30 amino
acid residues. Preferred epitopes encompassed by the antigenic
peptide are regions of NEOKINE that are located on the surface of
the protein, e.g., hydrophilic regions.
[0773] The antigenic peptide of T129 comprises at least 8
(preferably 10, 15, 20, or 30) amino acid residues of the amino
acid sequence shown in SEQ ID NO:138 and encompasses an epitope of
T129 such that an antibody raised against the peptide forms a
specific immune complex with T129.
[0774] The antigenic peptide of a259 comprises at least 8
(preferably 10, 15, 20, or 30) amino acid residues of the amino
acid sequence of SEQ ID NO:147 or 165, and encompasses an epitope
of the protein such that an antibody raised against the peptide
forms a specific immune complex with the protein.
[0775] Preferred epitopes encompassed by the antigenic peptide are
regions of T129 that are located on the surface of the protein,
e.g., hydrophilic regions. A hydrophobicity analysis of the human
T129 protein sequence indicates that the regions between, e.g.,
amino acids 120 and 130, between amino acids 140 and 160, and
between amino acids 400 and 420 of SEQ ID NO:2 are particularly
hydrophilic and, therefore, are likely to encode surface residues
useful for targeting antibody production.
[0776] A T129 immunogen typically is used to prepare antibodies by
immunizing a suitable subject, (e.g., rabbit, goat, mouse or other
mammal) with the immunogen. An appropriate immunogenic preparation
can contain, for example, recombinantly expressed T129 protein or a
chemically synthesized T129 polypeptide. The preparation can
further include an adjuvant, such as Freund's complete or
incomplete adjuvant, or similar immunostimulatory agent.
Immunization of a suitable subject with an immunogenic T129
preparation induces a polyclonal anti-T129 antibody response.
[0777] Preferred epitopes encompassed by the antigenic peptide are
regions that are located on the surface of the A259 protein, e.g.,
hydrophilic regions. FIGS. 10 and 11 are hydropathy plots of the
proteins of the invention. These plots or similar analyses can be
used to identify hydrophilic regions.
[0778] A FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 immunogen typically is used to prepare antibodies by
immunizing a suitable subject, (e.g., rabbit, goat, mouse or other
mammal) with the immunogen. An appropriate immunogenic preparation
can contain, for example, recombinantly expressed FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein or a
chemically synthesized FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 polypeptide. The preparation can further include
an adjuvant, such as Freund's complete or incomplete adjuvant, or
similar immunostimulatory agent. Immunization of a suitable subject
with an immunogenic FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 preparation induces a polyclonal anti-FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 antibody
response.
[0779] Accordingly, another aspect of the invention pertains to
anti-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
antibodies. The term "antibody" as used herein refers to
immunoglobulin molecules and immunologically active portions of
immunoglobulin molecules, i.e., molecules that contain an antigen
binding site which specifically binds an antigen, such as
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259. A
molecule which specifically binds to FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 is a molecule which binds
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259, but
does not substantially bind other molecules in a sample, e.g., a
biological sample, which naturally contains FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259. Examples of
immunologically active portions of immunoglobulin molecules include
F(ab) and F(ab').sub.2 fragments which can be generated by treating
the antibody with an enzyme such as pepsin. The invention provides
polyclonal and monoclonal antibodies that bind FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259. The term "monoclonal
antibody" or "monoclonal antibody composition", as used herein,
refers to a population of antibody molecules that contain only one
species of an antigen binding site capable of immunoreacting with a
particular epitope of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259. A monoclonal antibody composition thus typically
displays a single binding affinity for a particular FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein with
which it immunoreacts.
[0780] Polyclonal anti-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or
[0781] A259 antibodies can be prepared as described above by
immunizing a suitable subject with a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 immunogen. The anti-FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 antibody titer
in the immunized subject can be monitored over time by standard
techniques, such as with an enzyme linked immunosorbent assay
(ELISA) using immobilized FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259. If desired, the antibody molecules
directed against FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 can be isolated from the mammal (e.g., from the
blood) and further purified by well-known techniques, such as
protein A chromatography to obtain the IgG fraction. At an
appropriate time after immunization, e.g., when the anti-FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 antibody titers
are highest, antibody-producing cells can be obtained from the
subject and used to prepare monoclonal antibodies by standard
techniques, such as the hybridoma technique originally described by
Kohler and Milstein (1975) Nature 256:495-497, the human B cell
hybridoma technique (Kozbor et al. (1983) Immunol Today 4:72), the
EBV-hybridoma technique (Cole et al. (1985), Monoclonal Antibodies
and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma
techniques. The technology for producing various antibodies
monoclonal antibody hybridomas is well known (see generally Current
Protocols in Immunology (1994) Coligan et al. (eds.) John Wiley
& Sons, Inc., New York, N.Y.). Briefly, an immortal cell line
(typically a myeloma) is fused to lymphocytes (typically
splenocytes) from a mammal immunized with a FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 immunogen as described
above, and the culture supernatants of the resulting hybridoma
cells are screened to identify a hybridoma producing a monoclonal
antibody that binds FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259.
[0782] Any of the many well known protocols used for fusing
lymphocytes and immortalized cell lines can be applied for the
purpose of generating an anti-FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 monoclonal antibody (see, e.g., Current
Protocols in Immunology, supra; Galfre et al. (1977) Nature
266:55052; R. H. Kenneth, in Monoclonal Antibodies: A New Dimension
In Biological Analyses, Plenum Publishing Corp., New York, N.Y.
(1980); and Lerner (1981) Yale J. Biol. Med., 54:387-402. Moreover,
the ordinarily skilled worker will appreciate that there are many
variations of such methods which also would be useful. Typically,
the immortal cell line (e.g., a myeloma cell line) is derived from
the same mammalian species as the lymphocytes. For example, murine
hybridomas can be made by fusing lymphocytes from a mouse immunized
with an immunogenic preparation of the present invention with an
immortalized mouse cell line, e.g., a myeloma cell line that is
sensitive to culture medium containing hypoxanthine, aminopterin
and thymidine ("HAT medium"). Any of a number of myeloma cell lines
can be used as a fusion partner according to standard techniques,
e.g., the P3-NS1/1-Ag4-1, P3-x63-Ag8.653 or Sp2/O-Ag14 myeloma
lines. These myeloma lines are available from ATCC. Typically,
HAT-sensitive mouse myeloma cells are fused to mouse splenocytes
using polyethylene glycol ("PEG"). Hybridoma cells resulting from
the fusion are then selected using HAT medium, which kills unfused
and unproductively fused myeloma cells (unfused splenocytes die
after several days because they are not transformed). Hybridoma
cells producing a monoclonal antibody of the invention are detected
by screening the hybridoma culture supernatants for antibodies that
bind FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259,
e.g., using a standard ELISA assay.
[0783] Alternative to preparing monoclonal antibody-secreting
hybridomas, a monoclonal anti-FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 antibody can be identified and isolated
by screening a recombinant combinatorial immunoglobulin library
(e.g., an antibody phage display library) with FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 to thereby isolate
immunoglobulin library members that bind FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259. Kits for generating and
screening phage display libraries are commercially available (e.g.,
the Pharmacia Recombinant Phage Antibody System, Catalog No.
27-9400-01; and the Stratagene SudZAP.TM. Phage Display Kit,
Catalog No. 240612). Additionally, examples of methods and reagents
particularly amenable for use in generating and screening antibody
display library can be found in, for example, U.S. Pat. No.
5,223,409; PCT Publication No. WO 92/18619; PCT Publication No. WO
91/17271; PCT Publication WO 92/20791; PCT Publication No. WO
92/15679; PCT Publication WO 93/01288; PCT Publication No. WO
92/01047; PCT Publication No. WO 92/09690; PCT Publication No. WO
90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et
al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989)
Science 246:1275-1281; Griffiths et al. (1993) EMBO J.
12:725-734.
[0784] Additionally, recombinant anti-FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 antibodies, such as chimeric and
humanized monoclonal antibodies, comprising both human and
non-human portions, which can be made using standard recombinant
DNA techniques, are within the scope of the invention. Such
chimeric and humanized monoclonal antibodies can be produced by
recombinant DNA techniques known in the art, for example using
methods described in PCT Application No. PCT/US86/02269; European
Patent Application 184,187; European Patent Application 171,496;
European Patent Application 173,494; PCT Publication No. WO
86/01533; U.S. Pat. No. 4,816,567; European Patent Application
125,023; Better et al. (1988) Science 240:1041-1043; Liu et al.
(1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987)
J. Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci.
USA 84:214-218; Nishimura et al. (1987) Canc. Res. 47:999-1005;
Wood et al. (1985) Nature 314:446-449; and Shaw et al. (1988) J.
Natl. Cancer Inst. 80:1553-1559); Morrison, (1985) Science
229:1202-1207; Oi et al. (1986) Bio/techniques 4:214; U.S. Pat. No.
5,225,539; Jones et al. (1986) Nature 321:552-525; Verhoeyan et al.
(1988) Science 239:1534; and Beidler et al. (1988) J. Immunol.
141:4053-4060.
[0785] Completely human antibodies are particularly desirable for
therapeutic treatment of human patients. Such antibodies can be
produced using transgenic mice which are incapable of expressing
endogenous immunoglobulin heavy and light chains genes, but which
can express human heave and light chain genes. The transgenic mice
are immunized in the normal fashion with a selected antigen, e.g.,
all or a portion of Tango-77 or A259. Monoclonal antibodies
directed against the antigen can be obtained using conventional
hybridoma technology. The human immunoglobulin transgenes harbored
by the transgenic mice rearrange during B cell differentiation, and
subsequently undergo class switching and somatic mutation. Thus,
using such a technique, it is possible to produce therapeutically
useful IgG, IgA and IgE antibodies. For an overview of this
technology for producing human antibodies, see Lonberg and Huszar
(1995, Int. Rev. Immunol. 13:65-93). For a detailed discussion of
this technology for producing human antibodies and human monoclonal
antibodies and protocols for producing such antibodies, see, e.g.,
U.S. Pat. No. 5,625,126; U.S. Pat. No. 5,633,425; U.S. Pat. No.
5,569,825; U.S. Pat. No. 5,661,016; and U.S. Pat. No. 5,545,806. In
addition, companies such as Abgenix, Inc. (Freemont, Calif.), can
be engaged to provide human antibodies directed against a selected
antigen using technology similar to the described above.
[0786] Completely human antibodies which recognize a selected
epitope can be generated using a technique referred to as "guided
selection." In this approach a selected non-human monoclonal
antibody, e.g., a murine antibody, is used to guide the selection
of a completely human antibody recognizing the same epitope.
[0787] First, a non-human monoclonal antibody which binds a
selected antigen (epitope), e.g., an antibody which inhibits
Tango-77 or A259 activity, is identified. The heave chain and the
light chain of the non-human antibody are cloned and used to create
phage display Fab fragments. For example, the heave chain gene can
be cloned into a plasmid vector so that the heavy chain can be
secreted from bacteria. The light chain gene can be cloned into a
phage coat protein gene so that the light chain can be expressed on
the surface of phage. A repertoire (random collection) of human
light chains fused to phage is used to infect the bacteria which
express the non-human heavy chain. The resulting progeny phage
display hybrid antibodies (human light chain/non-human heavy
chain). The selected antigen is used in a panning screen to select
phage which bind the selected antigen. Several rounds of selection
may be required to identify such phage. Next, human light chain
genes are isolated from the selected phage which bind the selected
antigen. These selected human light chain genes are then used to
guide the selection of human heavy chain genes as follows. The
selected human light chain genes are inserted into vectors for
expression by bacteria. Bacteria expressing the selected human
light chains are infected with a repertoire of human heavy chains
fused to phage. The resulting progeny phage display human
antibodies (human light chain/human heavy chain).
[0788] Next, the selected antigen is used in a panning screen to
select phage which bind the selected antigen. The phage selected in
this step display completely human antibody which recognize the
same epitope recognized by the original selected, non-human
monoclonal antibody. The genes encoding both the heavy and light
chains are readily isolated and be further manipulated for
production of human antibody. This technology is described by
Jespers et al. (1994, Bio/technology 12:899-903).
[0789] An anti-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 antibody (e.g.; monoclonal antibody) can be used
to isolate FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 by standard techniques, such as affinity chromatography or
immunoprecipitation. An anti-FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 antibody can facilitate the purification
of natural FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 from cells and of recombinantly produced FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 expressed in host cells.
Moreover, an anti-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 antibody can be used to detect FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 protein (e.g., in a
cellular lysate or cell supernatant) in order to evaluate the
abundance and pattern of expression of the FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 protein. Anti-FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 antibodies can
be used diagnostically to monitor protein levels in tissue as part
of a clinical testing procedure, e.g., to, for example, determine
the efficacy of a given treatment regimen. Detection can be
facilitated by coupling the antibody to a detectable substance.
Examples of detectable substances include various enzymes,
prosthetic groups, fluorescent materials, luminescent materials,
bioluminescent materials, and radioactive materials. Examples of
suitable enzymes include horseradish peroxidase, alkaline
phosphatase, .beta.-galactosidase, or acetylcholinesterase;
examples of suitable prosthetic group complexes include
streptavidin/biotin and avidin/biotin; examples of suitable
fluorescent materials include umbelliferone, fluorescein,
fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine
fluorescein, dansyl chloride or phycoerythrin; an example of a
luminescent material includes luminol; examples of bioluminescent
materials include luciferase, luciferin, and aequorin, and examples
of suitable radioactive material include .sup.125I, .sup.131I,
.sup.35S or .sup.3H.
Delta3 Methods of Treating Disease
[0790] Based at least in part on the fact that the Notch signaling
pathway has been implicated in development of the nervous system,
in particular in regulating neuronal differentiation and
vasculature, e.g., CNS vasculature, a wide variety of pathological
diseases or conditions can benefit from treatment with Delta3
nucleic acids, proteins, and modulators thereof. In particular,
based at least in part on the observation that PS1 and PS2, genes
encoding amyloid precursor proteins, which are mutated in about 10%
of cases of Alzheimer's disease, are functionally linked to the
Notch signaling pathway, mutations in genes of the Notch signaling
pathway, e.g., Delta genes, could also result in Alzheimer's
disease or other neurodegenerative or neuro-developmental diseases.
The Notch signaling pathway plays a role in the development of
vasculature. For example, loss of Dll1 function mutants become
severally hemorrhagic after embryonic day 10. Furthermore,
mutations in Notch3 result in CADASIL, a disease characterized by
stroke. In addition, mice with a functionally ablated PS1 gene
exhibit hemorrhages in the brain and/or spinal cord after embryonic
day 11.5 (Wong et al. (1997) Nature 387:288). In addition, the
Notch pathway has been implicated in hematologic development.
Specifically, molecules in the Notch signaling pathway have been
shown to be expressed in a wide variety of blood cells, including
but not limited to those of myeloid and lymphoid origins. Notch-1
was shown to play a role in T-cell development. Furthermore, since
the Notch signaling pathway is involved in cell fate determination
at least in the nervous system, immune system and endothelial
system, it is likely that the Notch signaling pathway, and in
particular Delta3 is involved in cell fate determination in
additional biological systems. Accordingly, the invention also
provides methods for treating diseases or disorders arising from an
abnormal cell proliferation and/or differentiation of cells other
than cells from the nervous system, immune system, and
vasculature.
[0791] Among the disorders that can be treated or prevented
according to the methods of the invention include pathological
neurogenic, neoplastic or hyperplastic conditions. Neurologic
diseases, e.g., neurodegenerative, neuro-differentiative and
neuro-developmental diseases, that might benefit from this
methodology include, but are not limited to neuropathies, e.g.,
peripheral neuropathy such as ACCPN, stroke, dementia, e.g.,
cerebral autosomal dominant arteriopathy with subcortical infarcts
and leukoencephalopathy (CADASIL), degenerative lesions
(Parkinson's disease, Alzheimer's disease, Huntington's chorea,
amyotrophic lateral sclerosis, spinocerebellar degenerations),
demyelating diseases (multiple sclerosis, human immunodeficiency
associated myelopathy, transverse myelopathy, progressive
multifocal leukoencephalopathy, pontine myelinolysis), motor neuron
injuries, progressive spinal muscular atrophy, progressive bulbar
palsy, primary lateral sclerosis, infantile and juvenile muscular
atrophy, progressive bulbar paralysis of childhood (Fazio-Londe
syndrome), poliomyelitis, and hereditary motorsensory neuropathy
(Charcot-Marie-Tooth disease), spinal cord injuries, brain
injuries, lesions associated with surgery, ischemic lesions,
malignant lesions, infectious lesions.
[0792] Additional neurological diseases that can be treated
according to the method of the invention include neuropathies,
e.g., peripheral neuropathies, e.g., Agenesis of the Corpus
Callosum with Peripheral Neuropathy (ACCPN). In fact, as set forth
in the examples presented below, hDelta3 has been mapped to human
chromosome 15 close to framework markers D15S1244 and D15S144, a
chromosomal region which has been shown to be genetically linked
(ACCPN) (Casaubon et al. (1996) Am J. Hum. Genet. 58:28). The
disease is characterized by a progressive peripheral neuropathy
caused by axonal degeneration and a central nervous system (CNS)
malformation characterized by the absence of hypoplasia of the
corpus callosum. The disorder appears early in life, is progressive
and results in death in the third decade of life of the
subject.
[0793] Neuropathies refer to disorders of peripheral nerves and
includes both motor and sensory functions, since most motor and
sensory axons run in the same nerves. Neurophathies may be either
chronic or acute. One example of a acute neuropathy is the
Guillain-Barre syndrome, which often follow respiratory infection.
Chronic neuropathies include, e.g., acute intermittent porphyria,
Charcot-Marie-Tooth disease, metabolic diseases such as diabetes,
obesity, and B12 deficiency, intoxication, nutritional
disorders.
[0794] Disorders of the vasculature, also termed "vascular
disorders", in addition to CADASIL and stroke, that can be treated
or prevented according to the methods of the invention include
atheroma, tumor angiogenesis, wound healing, diabetic retinopathy,
hemangioma, psoriasis, and restenosis, e.g., restenosis resulting
from balloon angioplasty.
[0795] In one embodiment, diseases or disorders caused or
contributed to by aberrant Delta3 activity, such as aberrant Delta3
protein levels or an aberrant biological activity or which are
associated with one or more specific Delta3 alleles, e.g., a mutant
Delta3 allele, can be treated with Delta3 therapeutics. Aberrant
protein levels can be caused, e.g., by aberrant gene expression.
Such aberrant activity can result, for example, in aberrant cell
proliferation and/or differentiation or cell death. For example,
aberrant Delta3 activity in a subject can result in increased
proliferation of certain cells in the subject. Subjects having a
disorder characterized by abnormal cell proliferation can be
treated by administration of a Delta3 therapeutic inhibiting or
decreasing such proliferation. The specific Delta3 therapeutic used
may vary depending on the type of the cell that is proliferating
aberrantly. The appropriate Delta3 therapeutic to use can be
determined, e.g., by in vitro culture of a sample of such cells
which can be obtained from the subject, in the presence and in the
absence of Delta3 therapeutics.
[0796] Diseases or conditions associated with aberrant cell
proliferation which can be treated or prevented with Delta3
therapeutics include cancers, malignant conditions, premalignant
conditions, benign conditions. The condition to be treated or
prevented can be a solid tumor, such as a tumor arising in an
epithelial tissue. For example, the cancer can be colon or cervix
cancer. Cancer of the colon and cervix have in fact been found to
have increased levels of expression of Notch as compared to normal
tissue (PCT Publication No. WO/07474, Apr. 14, 1994). Accordingly,
treatment of such a cancer could comprise administration to the
subject of a Delta3 therapeutic decreasing the interaction of Notch
with Delta3. Other cancers that can be treated or prevented with a
Delta3 protein include sarcomas and carcinomas, e.g., lung cancer,
cancer of the esophagus, lung cancer, melanoma, seminoma, and
squamous adenocarcinoma. Additional solid tumors within the scope
of the invention include those that can be found in a medical
textbook. The condition to be treated or prevented can also be a
soluble tumor, such as leukemia, either chronic or acute, including
chronic or acute myelogenous leukemia, chronic or acute lymphocytic
leukemia, promyelocytic leukemia, monocytic leukemia,
myelomonocytic leukemia, and erythroleukemia. Yet other
proliferative disorders that can be treated with a Delta3
therapeutic of the invention include heavy chain disease, multiple
myeloma, lymphoma, e.g., Hodgkin's lymphoma and non-Hodgkin's
lymphoma, Waldenstroem's macroglobulemia, and fibroproliferative
disorders, particularly of cerebravascular tissue.
[0797] Diseases or conditions characterized by a solid or soluble
tumor can be treated by administrating a Delta3 therapeutic either
locally or systemically, such that proliferation of the cells
having an aberrant proliferation is inhibited or decreased. Methods
for administering the compounds of the invention are further
described below.
[0798] The invention also provides methods for preventing the
formation and/or development of tumors. For example, the
development of a tumor can be preceded by the presence of a
specific lesion, such as a pre-neoplastic lesion, e.g.,
hyperplasia, metaplasia, and dysplasia. Such lesions can be found,
e.g., in epithelial tissue. Thus, the invention provides a method
for inhibiting progression of such a lesion into a neoplastic
lesion, comprising administering to the subject having a
preneoplastic lesion a amount of a Delta3 therapeutic sufficient to
inhibit progression of the preneoplastic lesion into a neoplastic
lesion.
[0799] In a preferred embodiment, the invention provides a method
for inhibiting endothelial cell proliferation and/or
differentiation, comprising contacting a Delta3 therapeutic with a
tissue in which endothelial cells are proliferating, such as a
developing tumor or a hyperproliferative disease, i.e., a disease
associated with abnormal cellular proliferation. Blocking the
proliferation of endothelial cells will result in inhibition of
development of endothelium and blood vessels, thus limiting access
to the tumor of compounds necessary for tumor development.
[0800] The invention also provides for methods for treating or
preventing diseases or conditions associated with insufficient cell
proliferation. For example, Delta3 therapeutics can be used to
stimulate tissue repair, regeneration, and/or wound healing, e.g.,
of neural tissue, such as after surgery or to stimulate tissue
healing from burns. Other disease in which proliferation of cells
is desired are hypoproliferative diseases, i.e., diseases
characterized by an abnormally low proliferation of certain
cells.
[0801] In yet another embodiment, the invention provides a method
for treating or preventing diseases or conditions characterized by
aberrant cell differentiation. Accordingly, the invention provides
methods for stimulating cellular differentiation in conditions
characterized by an inhibition of normal cell differentiation which
may or may not be accompanied by excessive proliferation.
Alternatively, Delta3 therapeutics can be used to inhibit
differentiation of specific cells.
[0802] In one method, the aberrantly proliferating and/or
differentiating cell is a cell present in the nervous system.
Accordingly, the invention provides methods for treating diseases
or conditions associated with a central or peripheral nervous
system. For example, the invention provides methods for treating
lesions of the nervous system involving an aberrant Delta3 activity
in neurons, in Schwann cells, glial cells, or other types of neural
cells. Disorders of the nervous system are set forth above.
[0803] In another embodiment, a Delta3 therapeutic can be utilized
to ameliorate a symptom of obesity and/or disorders that accompany
or are exacerbated by an obese state, such as cardiovascular and
circulatory disorders, metabolic abnormalities typical of obesity,
such as hyperinsulinemia, insulin resistance, diabetes, including
non-insulin dependent diabetes mellitus (NIDDM), insulin dependent
diabetes mellitus (IDDM), and maturity onset diabetes of the young
(MODY), disorders of energy homeostasis, disorders associated with
lipid metabolism, such as cachexia.
[0804] With respect to cardiovascular disorders, symptoms of
coronary diseases (e.g., cardiovascular diseases including unstable
angina pectoris, myocardial infarction, acute myocardial
infarction, coronary artery disease, coronary revascularization,
coronary restenosis, ventricular thromboembolism, atherosclerosis,
coronary artery disease (e.g., arterial occlusive disorders),
plaque formation, cardiac ischemia, including complications related
to coronary procedures, such as percutaneous coronary artery
angioplasty (balloon angioplasty) procedures) can be ameliorated.
With respect to coronary procedures, such modulation can be
achieved via administration of Delta3 therapeutics prior to,
during, or subsequent to the procedure.
[0805] Delta3 therapeutics (e.g., nucleic acids, proteins and
modulators thereof) can, therefore, be used to modulate disorders
resulting from any blood vessel insult that can result in platelet
aggregation. Such blood vessel insults include, but are not limited
to, vessel wall injury, such as vessel injuries that result in a
highly thrombogenic surface exposed within an otherwise intact
blood vessel e.g., vessel wall injuries that result in release of
ADP, thrombin and/or epinephrine, fluid shear stress that occurs at
the site of vessel narrowing, ruptures and/or tears at the sites of
atherosclerotic plaques, and injury resulting from balloon
angioplasty or atherectomy. Preferably, such therapeutics do not
effect initial platelet adhesion to vessel surfaces, or effect such
adhesion to a relatively lesser extent than the effect on
platelet-platelet aggregation, e.g., unregulated platelet-platelet
aggregation, following the initial platelet adhesion.
[0806] In addition, Delta3 therapeutics can be utilized to
amieliorate a symptom of disorders associated with abnormal
vasculogenesis (e.g., cancers, including, but not limited to,
cancers of the epithelia (e.g., carcinomas of the pancreas,
stomach, liver, secretory glands (e.g., adenocarcinoma), bladder,
lung, breast, skin (e.g., fibromatosis or malignant melanoma),
reproductive tract including prostate gland, ovary, cervix and
uterus); cancers of the hematopoietic and immune system (e.g.,
leukemias and lymphomas); cancers of the central nervous, brain
system and eye (e.g., gliomas, neuroblastoma and retinoblastoma);
and cancers of connective tissues, bone, muscles and vasculature
(e.g., hemangiomas and sarcomas)), disorders related to fetal
development, in particular, disorders involving development of lung
and kidney, lung-related disorders, and immune-related disorders,
such as inflammatory-related disorders, e.g., asthma, allergy, and
autoimmune disorders, as well as neurological disorders, including
developmental, cognitive and personality-related disorders, renal
disorders, adrenal gland-related disorders; and disorders relating
to skeletal muscle, such as dystrophic disorders.
[0807] With respect to immune disorders, Delta3 therapeutics (e.g.,
nucleic acids, proteins and modulators thereof) can be utilized to
modulate processes involved in lymphocyte development,
differentiation and activity, including, but not limited to
development, differentiation and activation of T cells, including T
helper, T cytotoxic and non-specific T killer cell types and
subtypes, and B cells, immune functions associated with such cells,
and amelioration of one or more symptoms associated with abnormal
function of such cell types. Such disorders can include, but are
not limited to, autoimmune disorders, such as organ specific
autoimmune disorders, e.g., autoimmune thyroiditis, Type I diabetes
mellitus, insulin-resistant diabetes, autoimmune anemia, multiple
sclerosis, and/or systemic autoimmune disorders, e.g., rheumatoid
arthritis, lupus or sclerodoma, allergy, including allergic
rhinitis and food allergies, asthma, psoriasis, graft rejection,
transplantation rejection, graft versus host disease, pathogenic
susceptibilities, e.g., susceptibility to certain bacterial or
viral pathogens, wound healing and inflammatory reactions.
[0808] With respect to skeletal muscle-related disorders, Delta3
therapeutics can be utilized to ameliorate symptoms of disorders
including, for example, muscular dystrophy disorders, e.g.,
Duchenne's muscular dystrophy and X-linked recessive Emery-Dreifuss
dystrophy (EDMD), as well as developmental and other disorders that
involve skeletal muscle such as, for example, oculofacial-skeletal
myorhythmias, sarcoidosis, and malignant hyperthermia
susceptibility (MHS).
[0809] With respect to lung disorders, Delta3 therapeutics can be
utilized, for exampe, to ameliorate a symptom of such pulmonary
disorders, such as atelectasis, pulmonary congestion or edema,
chronic obstructive airway disease (e.g., emphysema, chronic
bronchitis, bronchial asthma, and bronchiectasis), diffuse
interstitial diseases (e.g., sarcoidosis, pneumoconiosis,
hypersensitivity pneumonitis, Goodpasture's syndrome, idiopathic
pulmonary hemosiderosis, pulmonary alveolar proteinosis,
desquamative interstitial pneumonitis, chronic interstitial
pneumonia, fibrosing alveolitis, hamman-rich syndrome, pulmonary
eosinophilia, diffuse interstitial fibrosis, Wegener's
granulomatosis, lymphomatoid granulomatosis, and lipid pneumonia),
or tumors (e.g., bronchogenic carcinoma, bronchiolovlveolar
carcinoma, bronchial carcinoid, hamartoma, and mesenchymal
tumors).
[0810] In another embodiment, the invention provides a method for
enhancing the survival and/or stimulating proliferation and/or
differentiation of cells and tissues in vitro. For example, tissues
from a subject can be obtained and grown in vitro in the presence
of a Delta3 therapeutic, such that the tissue cells are stimulated
to proliferate and/or differentiate. The tissue can then be
readministered to the subject.
[0811] In another embodiment, as Notch can function to maintain
cells in an immature state in vitro, i.e., as stem cells, e.g., the
invention provides a method to expand the pool of hematopoietic
stem cells through the interaction of Delta3 with Notch, which can
be utilized in cases where it is desirable to do so including, but
not limited to preparing cells harvested for subsequent bone marrow
transplantation. Thus, Delta 3 can be utilized in stem cell
preservation, that is, can be utilized to preserve stem cells in an
immature, undifferentiated state, and/or preserving the stem cells'
pluripotency, differentiation potential and proliferation
potential. In one embodiment of such a stem cell preservation
method, stem cells are contacted with cells expressing Delta3 and
exhibiting Delta3 on their cell surfaces. Such Delta3-expressing
cells can be presented, e.g., as stromal cells in culture. In
another embodiment, stem cells are contacted with full-length or
soluble Delta3 attached to a solid surface, e.g., a culture plate,
or microbeads.
[0812] In another embodiment, techniques such as that described
above for stem cell preservation can be utilized to prevent death
of CD4.sup.+/CD8.sup.+ T cells. Thus, such techniques can be used
to repopulate peripheral T cell populations (e.g., as part of a
leukemia therapy), or, and alternatively, can be used to produce
and screen for an antigen-specific T cell clone.
[0813] In another embodiment, the invention can function as a
method to determine the fate of T cells in the developing thymus.
Antagonists or antagonists of hDelta3 activity can determine
whether a T cell will develop the CD4 or CD8 phenotype and thus be
useful as a therapeutic agent in immunodeficiency disorders, such
as, but not limited to AIDS.
[0814] In another embodiment, as the Notch signaling pathway has
been shown to be involved in eye development in Drosophila, and
given the fact that mDelta3 was highly expressed in the developing
mouse eye, Delta3 nucleic acids, proteins, and modulators thereof
and/or agonists and antagonists can be used as therapeutics in such
eye disorders as diabetic retinopathy, characterized by a
hyper-proliferation of capillaries in the retina.
[0815] Since, in some cases, genes may be upregulated in a disease
state and in other cases may be down-regulated, it will be
desirable to activate and/or potentiate or suppress and/or
down-modulate Delta3 activity depending on the condition to be
treated using the techniques compounds and methods described
herein. Some genes may be under-expressed in certain disease
states. The activity of Delta3 nucleic acids, proteins, and
modulators thereof may be in some way impaired, leading to the
development of neurodegenerative disease symptoms. Such
down-regulation of Delta3 gene expression or decrease in the
activity of a Delta3 protein may have a causative or exacerbating
effect on the disease state.
[0816] Among the approaches which may be used to ameliorate disease
symptoms involving the misexpression of a Delta3 gene are, for
example, antisense, ribozyme, and triple helix molecules described
above. Compounds that compete with Delta3 nucleic acids, proteins,
and modulators thereof for binding to upstream or downstream
elements in a Delta/Notch signaling cascade will antagonize Delta3
nucleic acids, proteins, and modulators thereof, thereby inducing a
therapeutic effect. Examples of suitable compounds include the
antagonists or homologs described in detail above. In other
instances, the increased expression or activity of Delta3 nucleic
acids, proteins, and modulators thereof may be desirable and may be
accomplished by, for example the use of Delta3 agonists or mimetics
or by gene replacement therapy, as described herein.
[0817] Yet other Delta3 therapeutics comprise of a first peptide
comprising a Delta3 peptide capable of binding to a receptor, e.g.,
a Notch receptor, and a second peptide which is cytotoxic. Such
therapeutics can be used to specifically target and lyse cells
expressing or over-expressing a receptor for Delta3. For example, a
fusion protein containing a Delta3 peptide fused to a cytotoxic
peptide can be used to eliminate or reduce a tumor over-expressing
Notch, e.g., colon and cervix neoplastic tumors. Alternatively,
cells expressing or over-expressing Delta3 can be targeted for
lysis, by, for example, targeting to the cell an antibody binding
specifically to a Delta3 protein linked to a cytotoxic peptide.
[0818] Based at least in part on the similarity of protein
structure, it is likely that Delta3 nucleic acids, proteins, and
modulators thereof can also be used to treat diseases or conditions
caused by or contributed by an aberrant activity of a Delta family
gene product, e.g., an aberrant Delta1 or Delta2 activity or
diseases or disorders which are associated with one or more
specific Delta alleles, e.g., Delta1 or Delta2 alleles. Such
diseases or conditions could include neurological diseases and
cancer. Similarly, Delta therapeutics, e.g., Delta1 or Delta2
therapeutics, could be used to prevent or treat diseases or
disorders caused by or contributed to by an aberrant Delta3
activity, or diseases or disorders which are associated with a
specific Delta3 allele. Delta therapeutics can be prepared using,
e.g., the nucleotide and protein sequence information disclosed in
the PCT Patent Publication WO 97/01571 and tested using the assays
described herein for testing Delta3 therapeutics.
[0819] Compounds identified as increasing or decreasing Delta3 gene
expression or protein activity can be administered to a subject at
therapeutically effective dose to treat or ameliorate
cardiovascular disease. A therapeutically effective dose refers to
that amount of the compound sufficient to result in amelioration of
symptoms associated with the particular disease.
Pharmaceutical Compositions
[0820] The Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 nucleic acid molecules, Delta3, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 proteins, and
anti-Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 antibodies (also referred to herein as "active compounds")
of the invention can be incorporated into pharmaceutical
compositions suitable for administration. Such compositions
typically comprise the nucleic acid molecule, protein, or antibody
and a pharmaceutically acceptable carrier. As used herein the
language "pharmaceutically acceptable carrier" is intended to
include any and all solvents, dispersion media, coatings,
antibacterial and antifungal agents, isotonic and absorption
delaying agents, and the like, compatible with pharmaceutical
administration. The use of such media and agents for
pharmaceutically active substances is well known in the art. Except
insofar as any conventional media or agent is incompatible with the
active compound, use thereof in the compositions is contemplated.
Supplementary active compounds can also be incorporated into the
compositions.
[0821] The invention includes methods for preparing pharmaceutical
compositions for modulating the expression or activity of a
polypeptide or nucleic acid of the invention. Such methods comprise
formulating a pharmaceutically acceptable carrier with an agent
which modulates expression or activity of a polypeptide or nucleic
acid of the invention. Such compositions can further include
additional active agents. Thus, the invention further includes
methods for preparing a pharmaceutical composition by formulating a
pharmaceutically acceptable carrier with an agent which modulates
expression or activity of a polypeptide or nucleic acid of the
invention and one or more additional active compounds.
[0822] A pharmaceutical composition of the invention is formulated
to be compatible with its intended route of administration.
Examples of routes of administration include parenteral, e.g.,
intravenous, intradermal, subcutaneous, oral (e.g., inhalation),
transdermal (topical), transmucosal, intramuscular and rectal
administration. Solutions or suspensions used for parenteral,
intradermal, or subcutaneous application can include the following
components: a sterile diluent such as water for injection, saline
solution, fixed oils, polyethylene glycols, glycerine, propylene
glycol or other synthetic solvents; antibacterial agents such as
benzyl alcohol or methyl parabens; antioxidants such as ascorbic
acid or sodium bisulfite; chelating agents such as
ethylenediaminetetraacetic acid; buffers such as acetates, citrates
or phosphates and agents for the adjustment of tonicity such as
sodium chloride or dextrose. pH can be adjusted with acids or
bases, such as hydrochloric acid or sodium hydroxide. The
parenteral preparation can be enclosed in ampoules, disposable
syringes or multiple dose vials made of glass or plastic.
[0823] Pharmaceutical compositions suitable for injectable use
include sterile aqueous solutions (where water soluble) or
dispersions and sterile powders for the extemporaneous preparation
of sterile injectable solutions or dispersions. For intravenous
administration, suitable carriers include physiological saline,
bacteriostatic water, Cremophor EL (BASF; Parsippany, N.J.) or
phosphate buffered saline (PBS). In all'cases, the composition must
be sterile and should be fluid to the extent that easy
syringability exists. It must be stable under the conditions of
manufacture and storage and must be preserved against the
contaminating action of microorganisms such as bacteria and fungi.
The carrier can be a solvent or dispersion medium containing, for
example, water, ethanol, polyol (for example, glycerol, propylene
glycol, and liquid polyetheylene glycol, and the like), and
suitable mixtures thereof. The proper fluidity can be maintained,
for example, by the use of a coating such as lecithin, by the
maintenance of the required particle size in the case of dispersion
and by the use of surfactants. Prevention of the action of
microorganisms can be achieved by various antibacterial and
antifungal agents, for example, parabens, chlorobutanol, phenol,
ascorbic acid, thimerosal, and the like. In many cases, it will be
preferable to include isotonic agents, for example, sugars,
polyalcohols such as mannitol, sorbitol, sodium chloride in the
composition. Prolonged absorption of the injectable compositions
can be brought about by including in the composition an agent which
delays absorption, for example, aluminum monostearate and
gelatin.
[0824] Sterile injectable solutions can be prepared by
incorporating the active compound (e.g., a Delta3, FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein or
anti-Delta3, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 antibody) in the required amount in an appropriate solvent
with one or a combination of ingredients enumerated above, as
required, followed by filtered sterilization. Generally,
dispersions are prepared by incorporating the active compound into
a sterile vehicle which contains a basic dispersion medium and the
required other ingredients from those enumerated above. In the case
of sterile powders for the preparation of sterile injectable
solutions, the preferred methods of preparation are vacuum drying
and freeze-drying which yields a powder of the active ingredient
plus any additional desired ingredient from a previously
sterile-filtered solution thereof.
[0825] Oral compositions generally include an inert diluent or an
edible carrier. They can be enclosed in gelatin capsules or
compressed into tablets. For the purpose of oral therapeutic
administration, the active compound can be incorporated with
excipients and used in the form of tablets, troches, or capsules.
Oral compositions can also be prepared using a fluid carrier for
use as a mouthwash, wherein the compound in the fluid carrier is
applied orally and swished and expectorated or swallowed.
[0826] Pharmaceutically compatible binding agents, and/or adjuvant
materials can be included as part of the composition. The tablets,
pills, capsules, troches and the like can contain any of the
following ingredients, or compounds of a similar nature: a binder
such as microcrystalline cellulose, gum tragacanth or gelatin; an
excipient such as starch or lactose, a disintegrating agent such as
alginic acid, Primogel, or corn starch; a lubricant such as
magnesium stearate or Sterotes; a glidant such as colloidal silicon
dioxide; a sweetening agent such as sucrose or saccharin; or a
flavoring agent such as peppermint, methyl salicylate, or orange
flavoring.
[0827] For administration by inhalation, the compounds are
delivered in the form of an aerosol spray from a pressurized
container or dispenser which contains a suitable propellant, e.g.,
a gas such as carbon dioxide, or a nebulizer.
[0828] Systemic administration can also be by transmucosal or
transdermal means. For transmucosal or transdermal administration,
penetrants appropriate to the barrier to be permeated are used in
the formulation. Such penetrants are generally known in the art,
and include, for example, for transmucosal administration,
detergents, bile salts, and fusidic acid derivatives. Transmucosal
administration can be accomplished through the use of nasal sprays
or suppositories. For transdermal administration, the active
compounds are formulated into ointments, salves, gels, or creams as
generally known in the art.
[0829] The compounds can also be prepared in the form of
suppositories (e.g., with conventional suppository bases such as
cocoa butter and other glycerides) or retention enemas for rectal
delivery.
[0830] In one embodiment, the active compounds are prepared with
carriers that will protect the compound against rapid elimination
from the body, such as a controlled release formulation, including
implants and microencapsulated delivery systems. Biodegradable,
biocompatible polymers can be used, such as ethylene vinyl acetate,
polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and
polylactic acid. Methods for preparation of such formulations will
be apparent to those skilled in the art. The materials can also be
obtained commercially from Alza Corporation and Nova
Pharmaceuticals, Inc. Liposomal suspensions (including liposomes
targeted to infected cells with monoclonal antibodies to viral
antigens) can also be used as pharmaceutically acceptable carriers.
These can be prepared according to methods known to those skilled
in the art, for example, as described in U.S. Pat. No.
4,522,811.
[0831] It is especially advantageous to formulate oral or
parenteral compositions in dosage unit form for ease of
administration and uniformity of dosage. Dosage unit form as used
herein refers to physically discrete units suited as unitary
dosages for the subject to be treated; each unit containing a
predetermined quantity of active compound calculated to produce the
desired therapeutic effect in association with the required
pharmaceutical carrier. The specification for the dosage unit forms
of the invention are dictated by and directly dependent on the
unique characteristics of the active compound and the particular
therapeutic effect to be achieved, and the limitations inherent in
the art of compounding such an active compound for the treatment of
individuals.
[0832] For antibodies, the preferred dosage is 0.1 mg/kg to 100
mg/kg of body weight (generally 10 mg/kg to 20 mg/kg). If the
antibody is to act in the brain, a dosage of 50 mg/kg to 100 mg/kg
is usually appropriate. Generally, partially human antibodies and
fully human antibodies have a longer half-life within the human
body than other antibodies. Accordingly, lower dosages and less
frequent administration is often possible. Modifications such as
lipidation can be used to stabilize antibodies and to enhance
uptake and tissue penetration (e.g., into the brain). A method for
lipidation of antibodies is described by Cruikshank et al. ((1997)
J. Acquired Immune Deficiency Syndromes and Human Retrovirology
14:193).
[0833] As defined herein, a therapeutically effective amount of
protein or polypeptide (i.e., an effective dosage) ranges from
about 0.001 to 30 mg/kg body weight, preferably about 0.01 to 25
mg/kg body weight, more preferably about 0.1 to 20 mg/kg body
weight, and even more preferably about 1 to 10 mg/kg, 2 to 9 mg/kg,
3 to 8 mg/kg, 4 to 7 mg/kg, or 5 to 6 mg/kg body weight.
[0834] With regard to antibodies which are to act in the brain, a
dosage of 50 mg/kg to 100 mg/kg is typically appropriate.
Generally, partially human antibodies and fully human antibodies
have a longer half-life within the human body than other
antibodies. Accordingly, lower dosages and less frequent
administration is often possible. Modifications such as lipidation
can be used to stabilize antibodies and to enhance uptake and
tissue penetration (e.g., into the brain). A method for lipidation
of antibodies is described by Cruikshank et al. ((1997) J. Acquired
Immune Deficiency Syndromes and Human Retrovirology 14:193).
[0835] Toxicity and therapeutic efficacy of such compounds can be
determined by standard pharmaceutical procedures in cell cultures
or experimental animals, e.g., for determining the LD50 (the dose
lethal to 50% of the population) and the ED50 (the dose
therapeutically effective in 50% of the population). The dose ratio
between toxic and therapeutic effects is the therapeutic index and
it can be expressed as the ratio LD50/ED50. Compounds which exhibit
large therapeutic indices are preferred. While compounds that
exhibit toxic side effects may be used, care should be taken to
design a delivery system that targets such compounds to the site of
affected tissue in order to minimize potential damage to uninfected
cells and, thereby, reduce side effects.
[0836] The data obtained from the cell culture assays and animal
studies can be used in formulating a range of dosage for use in
humans. The dosage of such compounds lies preferably within a range
of circulating concentrations that include the ED50 with little or
no toxicity. The dosage may vary within this range depending upon
the dosage form employed and the route of administration utilized.
For any compound used in the method of the invention, the
therapeutically effective dose can be estimated initially from cell
culture assays. A dose may be formulated in animal models to
achieve a circulating plasma concentration range that includes the
IC50 (i.e., the concentration of the test compound which achieves a
half-maximal inhibition of symptoms) as determined in cell culture.
Such information can be used to more accurately determine useful
doses in humans. Levels in plasma may be measured, for example, by
high performance liquid chromatography.
[0837] The skilled artisan will appreciate that certain factors may
influence the dosage required to effectively treat a subject,
including but not limited to the severity of the disease or
disorder, previous treatments, the general health and/or age of the
subject, and other diseases present. Moreover, treatment of a
subject with a therapeutically effective amount of a protein,
polypeptide, or antibody can include a single treatment or,
preferably, can include a series of treatments. In one embodiment,
a subject is treated with a protein, or polypeptide in the range of
between about 0.1 to 20 mg/kg body weight, one time per week for
between about 1 to 10 weeks, preferably between about 2 to 8 weeks,
more preferably between about 3 to 8 weeks, and even more
preferably for about 4, 5, or 6 weeks. It will also be appreciated
that the effective dosage of antibody, protein, or polypeptide used
for treatment may increase or decrease over the course of a
particular treatment. Changes in dosage may result and become
apparent from the results of diagnostic assays as described
herein.
[0838] The nucleic acid molecules of the invention can be inserted
into vectors and used as gene therapy vectors. Gene therapy vectors
can be delivered to a subject by, for example, intravenous
injection, local administration (U.S. Pat. No. 5,328,470) or by
stereotactic injection (see, e.g., Chen et al. (1994) Proc. Natl.
Acad. Sci. USA 91:3054-3057). The pharmaceutical preparation of the
gene therapy vector can include the gene therapy vector in an
acceptable diluent, or can comprise a slow release matrix in which
the gene delivery vehicle is imbedded. Alternatively, where the
complete gene delivery vector can be produced intact from
recombinant cells, e.g. retroviral vectors, the pharmaceutical
preparation can include one or more cells which produce the gene
delivery system.
[0839] The pharmaceutical compositions can be included in a
container, pack, or dispenser together with instructions for
administration.
[0840] In clinical settings, the gene delivery systems for the
therapeutic Delta3 gene can be introduced into a patient by any of
a number of methods, each of which is familiar in the art. For
instance, a pharmaceutical preparation of the gene delivery system
can be introduced systemically, e.g., by intravenous injection, and
specific transduction of the protein in the target cells occurs
predominantly from specificity of transfection provided by the gene
delivery vehicle, cell-type or tissue-type expression due to the
transcriptional regulatory sequences controlling expression of the
receptor gene, or a combination thereof. In other embodiments,
initial delivery of the recombinant gene is more limited with
introduction into the animal being quite localized. For example,
the gene delivery vehicle can be introduced by catheter (see U.S.
Pat. No. 5,328,470) or by stereotactic injection (e.g., Chen et al.
(1994) Proc. Natl. Acad. Sci. USA 91: 3054-3057). A Delta3 gene,
such as any one of the sequences represented in the group
consisting of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39,
41, 43 or 45, or a sequence homologous thereto can be delivered in
a gene therapy construct by electroporation using techniques
described, for example, by Dev et al. ((1994) Cancer Treat. Rev.
20:105-115).
[0841] The pharmaceutical preparation of the gene therapy construct
can consist essentially of the gene delivery system in an
acceptable diluent, or can comprise a slow release matrix in which
the gene delivery vehicle is imbedded. Alternatively, where the
complete gene delivery system can be produced intact from
recombinant cells, e.g., retroviral vectors, the pharmaceutical
preparation can comprise one or more cells which produce the gene
delivery system.
[0842] The compositions may, if desired, be presented in a pack or
dispenser device which may contain one or more unit dosage forms
containing the active ingredient. The pack may for example comprise
metal or plastic foil, such as a blister pack. The pack or
dispenser device may be accompanied by instructions for
administration.
Uses and Methods of the Invention
[0843] The nucleic acid molecules, proteins, protein homologues,
and antibodies described herein can be used in one or more of the
following methods: a) screening assays; b) detection assays (e.g.,
chromosomal mapping, tissue typing, forensic biology), c)
predictive medicine (e.g., diagnostic assays, prognostic assays,
monitoring clinical trials, and pharmacogenomics); and d) methods
of treatment (e.g., therapeutic and prophylactic). The isolated
nucleic acid molecules of the invention can be used to express
FTHMA-070, Tango85, Tango77 or A259 protein (e.g., via a
recombinant expression vector in a host cell in gene therapy
applications), to detect FTHMA-070, Tango85, Tango77 or A259 mRNA
(e.g., in a biological sample) or a genetic lesion in a FTHMA-070,
Tango85, Tango77 or A259 gene, and to modulate FTHMA-070, Tango85,
Tango77 or A259 activity. In addition, the FTHMA-070, Tango85,
Tango77 or A259 proteins can be used to screen drugs or compounds
which modulate the FTHMA-070, Tango85, Tango77 or A259 activity or
expression as well as to treat disorders characterized by
insufficient or excessive production of FTHMA-070, Tango85, Tango77
or A259 protein or production of FTHMA-070, Tango85, Tango77 or
A259 protein forms which have decreased or aberrant activity
compared to FTHMA-070, Tango85, Tango77 or A259 wild type protein.
In addition, the anti-FTHMA-070, Tango85, Tango77 or A259
antibodies of the invention can be used to detect and isolate
FTHMA-070, Tango85, Tango77 or A259 proteins and modulate
FTHMA-070, Tango85, Tango77 or A259 activity.
[0844] The nucleic acid molecules, proteins, protein homologues,
and antibodies described herein can be used in one or more of the
following methods: a) screening assays; b) detection assays (e.g.,
chromosomal mapping, tissue typing, forensic biology), c)
predictive medicine (e.g., diagnostic assays, prognostic assays,
monitoring clinical trials); and d) methods of treatment (e.g.,
therapeutic and prophylactic methods as well as such methods in the
context of pharmacogenomics). As described herein, a SPOIL protein
of the invention has one or more of the following activities: (i)
interaction of a SPOIL protein in the extracellular milieu with a
protein molecule on the surface of the same cell which secreted the
SPOIL protein molecule (e.g., a SPOIL receptor or IL-1 receptor);
(ii) interaction of a SPOIL protein in the extracellular milieu
with a protein molecule on the surface of a different cell from
that which secreted the SPOIL protein molecule (e.g., a SPOIL
receptor or IL-1 receptor); (iii) complex formation between a SPOIL
protein and a cell-surface receptor; (iv) interaction of a SPOIL
protein with a target molecule in the extracellular milieu, and (v)
interaction of the SPOIL protein with a target molecule in the
cytoplasm of a cell, and can thus be used in, for example (1)
regulating a signal transduction pathway (e.g., an IL-1-dependent
or SPOIL-dependent pathway; (2) modulating cytokine production
and/or secretion; (3) modulating lymphokine production and/or
secretion; (4) modulating production of adhesion molecules; (5)
modulation of nuclear transcription factors; (6) modulating
secretion of IL-1; (7) competing with IL-1 to bind an IL-1
receptor; (8) modulating a proinflammatory cytokine; (9) modulating
cell proliferation, development or differentiation (e.g.,
IL-1-stimulated or SPOIL stimulated); (10) modulating bone
metabolism (e.g., bone formation and reabsorption); and (11)
mediating cellular "acute phase" response. The isolated nucleic
acid molecules of the invention can be used, for example, to
express SPOIL protein (e.g., via a recombinant expression vector in
a host cell in gene therapy applications), to detect SPOIL mRNA
(e.g., in a biological sample) or a genetic alteration in an SPOIL
gene, and to modulate IL-1 activity, as described further below. In
addition, the SPOIL proteins can be screened which modulate the
SPOIL activity as well as to treat disorders characterized by
insufficient or excessive production of IL-1 which have decreased
or aberrant activity compared to normal IL-1 expression (e.g.,
inflammatory diseases, e.g., rheumatoid arthritis, sepsis, stroke
or diabetes, or stimulated differentiative or developmental
disorders such as bone metabolism disorders, e.g., osteoporosis,
Paget's disease of bone, hypercalcemia of malignancy or osteolytic
metastases, or diseases that involve the bowel and are
characterized by the production of inflammation and/or ulceration
in the small or large bowel including, e.g., inflammatory bowl
disease (IBD), Crohn's disease, irritable bowel syndrome (IBS) and
ulcerative colitis. Soluble forms of the SPOIL protein can be used
to bind IL-1 receptors and influence bioavailability of such a
receptors cognate ligand. In addition, the anti-SPOIL antibodies of
the invention can be used to detect and isolate SPOIL proteins.
[0845] The nucleic acid molecules, proteins, protein homologues,
and antibodies described herein can be used in one or more of the
following methods: a) screening assays; b) predictive medicine
(e.g., diagnostic assays, prognostic assays, monitoring clinical
trials, and pharmacogenetics); and c) methods of treatment (e.g.,
therapeutic and prophylactic). As described herein, a NEOKINE
protein of the invention has one or more of the following
activities: (i) interaction of a NEOKINE protein with a
membrane-bound NEOKINE receptor; (ii) interaction of a NEOKINE
protein with a membrane-bound chemokine receptor; (iii) indirect
interaction of a NEOKINE protein with an intracellular protein via
a membrane-bound NEOKINE receptor; (iv) indirect interaction of a
NEOKINE protein with an intracellular protein via a membrane-bound
chemokine receptor; (v) complex formation between a soluble NEOKINE
protein and a NEOKINE binding partner; (vi) inhibition of the
interaction of chemokines (e.g., pro-inflammatory chemokines) by
binding to their cognate receptors; (vii) inhibition of the binding
of HIV to HIV co-receptors; and (vii) inhibition of the binding of
HIV to HIV co-receptors wherein said binding induces subsequent
infection of susceptible cells and can thus be used in, for
example, (1) modulation of cellular signal transduction, either in
vitro or in vivo; (2) regulation of gene transcription in a cell
expressing a NEOKINE receptor or a chemokine receptor; (3)
regulation of gene transcription in a cell expressing a NEOKINE
receptor or a chemokine receptor, wherein said cell is involved in
angiogenesis or inflammation; (4) regulation of angiogenesis; (5)
regulation of angiogenesis, wherein said regulation comprises
inhibibition of angiogenesis; (6) regulation of angiogenesis,
wherein said regulation comprises maintenance of angiostasis; (7)
regulation of inflammation; and (8) regulation of inflammation,
wherein said regulation comprises inhibition of chemoattraction
(e.g., neutrophil chemoattraction), inhibition of inflammation,
inhibition of inflammation by blocking the action of
pro-inflammatory chemokines by binding to their cognate receptors,
inhibition of psoriasis, suppression of immune rejection following
skin graft, suppression of immune rejection following kidney
transplant, inhibition of kidney inflammation in acute renal
failure, inhibition of brain inflammation following stroke or
ischaemia, or inhibition of brain inflammation following viral
infection. The isolated nucleic acid molecules of the invention can
be used, for example, to express NEOKINE protein (e.g., via a
recombinant expression vector in a host cell in gene therapy
applications), to detect NEOKINE mRNA (e.g., in a biological
sample) or a genetic alteration in a NEOKINE gene, and to modulate
NEOKINE activity, as described further below. The NEOKINE proteins
can be used to treat disorders characterized by insufficient or
excessive production of a non-NEOKINE chemokine or production of
chemokine forms which have decreased or aberrant activity compared
to wild type chemokines. In addition, the NEOKINE proteins can be
used to screen drugs or compounds which modulate the NEOKINE
activity as well as to treat disorders characterized by
insufficient or excessive production of NEOKINE protein or
production of NEOKINE protein forms which have decreased or
aberrant activity compared to NEOKINE wild type protein. Moreover,
the anti-NEOKINE antibodies of the invention can be used to detect
and isolate NEOKINE proteins, regulate the bioavailability of
NEOKINE proteins, and modulate NEOKINE activity.
[0846] The nucleic acid molecules, proteins, protein homologues,
and antibodies described herein can be used in one or more of the
following methods: a) screening assays; b) detection assays (e.g.,
chromosomal mapping, tissue typing, forensic biology), c)
predictive medicine (e.g., diagnostic assays, prognostic assays,
monitoring clinical trials, and pharmacogenomics); and d) methods
of treatment (e.g., therapeutic and prophylactic). A T129 protein
interacts with other cellular proteins and can thus be used for (i)
regulation of cellular proliferation; (ii) regulation of cellular
differentiation; and (iii) regulation of cell survival. The
isolated nucleic acid molecules of the invention can be used to
express T129 protein (e.g., via a recombinant expression vector in
a host cell in gene therapy applications), to detect T129 mRNA
(e.g., in a biological sample) or a genetic lesion in a T129 gene,
and to modulate T129 activity. In addition, the T129 proteins can
be used to screen drugs or compounds which modulate the T129
activity or expression as well as to treat disorders characterized
by insufficient or excessive production of T129 protein or
production of T129 protein forms which have decreased or aberrant
activity compared to T129 wild type protein. In addition, the
anti-T129 antibodies of the invention can be used to detect and
isolate T129 proteins and modulate T129 activity.
[0847] This invention further pertains to novel agents identified
by the above-described screening assays and uses thereof for
treatments as described herein.
FTHMA-070. T85, T129 or A259 Screening Assays
[0848] The invention provides a method (also referred to herein as
a "screening assay") for identifying modulators, i.e., candidate or
test compounds or agents (e.g., peptides, peptidomimetics, small
molecules or other drugs) which bind to FTHMA-070, T85, T129 or
A259 proteins or have a stimulatory or inhibitory effect on, for
example, FTHMA-070, T85, T129 or A259 expression or FTHMA-070, T85,
T129 or A259 activity.
[0849] In one embodiment, the invention provides assays for
screening candidate or test compounds which bind to or modulate the
activity of the membrane-bound form of a FTHMA-070, T85, T129 or
A259 protein or polypeptide or biologically active portion thereof.
The test compounds of the present invention can be obtained using
any of the numerous approaches in combinatorial library methods
known in the art, including: biological libraries; spatially
addressable parallel solid phase or solution phase libraries;
synthetic library methods requiring deconvolution; the `one-bead
one-compound` library method; and synthetic library methods using
affinity chromatography selection. The biological library approach
is limited to peptide libraries, while the other four approaches
are applicable to peptide, non-peptide oligomer or small molecule
libraries of compounds (Lam, (1997) Anticancer Drug Des.
12:145).
[0850] Examples of methods for the synthesis of molecular libraries
can be found in the art, for example in: DeWitt et al. (1993) Proc.
Natl. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl.
Acad. Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem.
37:2678; Cho et al. (1993) Science 261:1303; Carrell et al. (1994)
Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew.
Chem. Int. Ed. Engl. 33:2061; and Gallop et al. (1994) J. Med.
Chem. 37:1233. Libraries of compounds may be presented in solution
(e.g., Houghten (1992) Bio/Techniques 13:412-421), or on beads (Lam
(1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556),
bacteria (U.S. Pat. No. 5,223,409), spores (U.S. Pat. Nos.
5,571,698; 5,403,484; and 5,223,409), plasmids (Cull et al. (1992)
Proc. Natl. Acad. Sci. USA 89:1865-1869) or on phage (Scott and
Smith (1990) Science 249:386-390; Devlin (1990) Science
249:404-406; Cwirla et al. (1990) Proc. Natl. Acad. Sci.
87:6378-6382; and Felici (1991) J. Mol. Biol. 222:301-310).
[0851] In one embodiment, an assay is a cell-based assay in which a
cell which expresses a membrane-bound form of FTHMA-070, T85, T129
or A259 protein, or a biologically active portion thereof, on the
cell surface is contacted with a test compound and the ability of
the test compound to bind to a FTHMA-070, T85, T129 or A259 protein
determined. The cell, for example, can be a yeast cell or a cell of
mammalian origin. Determining the ability of the test compound to
bind to the FTHMA-070, T85, T129 or A259 protein can be
accomplished, for example, by coupling the test compound with a
radioisotope or enzymatic label such that binding of the test
compound to the FTHMA-070, T85, T129 or A259 protein or
biologically active portion thereof can be determined by detecting
the labeled compound in a complex. For example, test compounds can
be labeled with .sup.125I, .sup.35S, .sup.14C, or .sup.3H, either
directly or indirectly, and the radioisotope detected by direct
counting of radioemmission or by scintillation counting.
Alternatively, test compounds can be enzymatically labeled with,
for example, horseradish peroxidase, alkaline phosphatase, or
luciferase, and the enzymatic label detected by determination of
conversion of an appropriate substrate to product. In a preferred
embodiment, the assay comprises contacting a cell which expresses a
membrane-bound form of FTHMA-070, T85, T129 or A259 protein, or a
biologically active portion thereof, on the cell surface with a
known compound which binds FTHMA-070, T85, T129 or A259 to form an
assay mixture, contacting the assay mixture with a test compound,
and determining the ability of the test compound to interact with a
FTHMA-070, T85, T129 or A259 protein, wherein determining the
ability of the test compound to interact with a FTHMA-070, T85,
T129 or A259 protein comprises determining the ability of the test
compound to preferentially bind to FTHMA-070, T85, T129 or A259 or
a biologically active portion thereof as compared to the known
compound.
[0852] In another embodiment, an assay is a cell-based assay
comprising contacting a cell expressing a membrane-bound form of
FTHMA-070, T85, T129 or A259 protein, or a biologically active
portion thereof, on the cell surface with a test compound and
determining the ability of the test compound to modulate (e.g.,
stimulate or inhibit) the activity of the FTHMA-070, T85, T129 or
A259 protein or biologically active portion thereof. Determining
the ability of the test compound to modulate the activity of
FTHMA-070, T85, T129 or A259 or a biologically active portion
thereof can be accomplished, for example, by determining the
ability of the FTHMA-070, T85, T129 or A259 protein to bind to or
interact with a FTHMA-070, T85, T129 or A259 target molecule. As
used herein, a "target molecule" is a molecule with which a
FTHMA-070, T85, T129 or A259 protein binds or interacts in nature,
for example, a molecule on the surface of a cell which expresses a
FTHMA-070, T85, T129 or A259 protein, a molecule on the surface of
a second cell, a molecule in the extracellular milieu, a molecule
associated with the internal surface of a cell membrane or a
cytoplasmic molecule. A FTHMA-070, T85, T129 or A259 target
molecule can be a non-FTHMA-070, T85, T129 or A259 molecule or a
FTHMA-070, T85, T129 or A259 protein or polypeptide of the present
invention. In one embodiment, a FTHMA-070, T85, T129 or A259 target
molecule is a component of a signal transduction pathway which
facilitates transduction of an extracellular signal (e.g., a signal
generated by binding of a compound to a membrane-bound FTHMA-070,
T85, T129 or A259 molecule) through the cell membrane and into the
cell. The target, for example, can be a second intercellular
protein which has catalytic activity or a protein which facilitates
the association of downstream signaling molecules with FTHMA-070,
T85, T129 or A259.
[0853] Determining the ability of the FTHMA-070, T85, T129 or A259
polypeptide of the invention to bind to or interact with a target
molecule can be accomplished by one of the methods described above
for determining direct binding. As used herein, a "target molecule"
is a molecule with which a selected polypeptide (e.g., a
polypeptide of the invention) binds or interacts with in nature,
for example, a molecule on the surface of a cell which expresses
the selected protein, a molecule on the surface of a second cell, a
molecule in the extracellular milieu, a molecule associated with
the internal surface of a cell membrane or a cytoplasmic molecule.
A target molecule can be a FTHMA-070, T85, T129 or A259 polypeptide
of the invention or some other polypeptide or protein. For example,
a target molecule can be a component of a signal transduction
pathway which facilitates transduction of an extracellular signal
(e.g., a signal generated by binding of a compound to a polypeptide
of the invention) through the cell membrane and into the cell or a
second intercellular protein which has catalytic activity or a
protein which facilitates the association of downstream signaling
molecules with a polypeptide of the invention. Determining the
ability of a FTHMA-070, T85, T129 or A259 polypeptide of the
invention to bind to or interact with a target molecule can be
accomplished by determining the activity of the target molecule.
For example, the activity of the target molecule can be determined
by detecting induction of a cellular second messenger of the target
(e.g., intracellular Ca.sup.2+, diacylglycerol, IP3, etc.),
detecting catalytic/enzymatic activity of the target on an
appropriate substrate, detecting the induction of a reporter gene
(e.g., a regulatory element that is responsive to a polypeptide of
the invention operably linked to a nucleic acid encoding a
detectable marker, e.g., luciferase), or detecting a cellular
response, for example, cellular differentiation, or cell
proliferation.
[0854] In yet another embodiment, an assay of the present invention
is a cell-free assay comprising contacting a FTHMA-070, T85, T129
or A259 protein or biologically active portion thereof with a test
compound and determining the ability of the test compound to bind
to the FTHMA-070, T85, T129 or A259 protein or biologically active
portion thereof. Binding of the test compound to the FTHMA-070,
T85, T129 or A259 protein can be determined either directly or
indirectly as described above. In a preferred embodiment, the assay
includes contacting the FTHMA-070, T85, T129 or A259 protein or
biologically active portion thereof with a known compound which
binds FTHMA-070, T85, T129 or A259 to form an assay mixture,
contacting the assay mixture with a test compound, and determining
the ability of the test compound to interact with a FTHMA-070, T85,
T129 or A259 protein, wherein determining the ability of the test
compound to interact with a FTHMA-070, T85, T129 or A259 protein
comprises determining the ability of the test compound to
preferentially bind to FTHMA-070, T85, T129 or A259 or biologically
active portion thereof as compared to the known compound.
[0855] In another embodiment, an assay is a cell-free assay
comprising contacting FTHMA-070, T85, T129 or A259 protein or
biologically active portion thereof with a test compound and
determining the ability of the test compound to modulate (e.g.,
stimulate or inhibit) the activity of the FTHMA-070, T85, T129 or
A259 protein or biologically active portion thereof. Determining
the ability of the test compound to modulate the activity of
FTHMA-070, T85, T129 or A259 can be accomplished, for example, by
determining the ability of the FTHMA-070, T85, T129 or A259 protein
to bind to a FTHMA-070, T85, T129 or A259 target molecule by one of
the methods described above for determining direct binding. In an
alternative embodiment, determining the ability of the test
compound to modulate the activity of FTHMA-070, T85, T129 or A259
can be accomplished by determining the ability of the FTHMA-070,
T85, T129 or A259 protein further modulate a FTHMA-070, T85, T129
or A259 target molecule. For example, the catalytic/enzymatic
activity of the target molecule on an appropriate substrate can be
determined as previously described.
[0856] In yet another embodiment, the cell-free assay comprises
contacting the FTHMA-070, T85, T129 or A259 protein or biologically
active portion thereof with a known compound which binds FTHMA-070,
T85, T129 or A259 to form an assay mixture, contacting the assay
mixture with a test compound, and determining the ability of the
test compound to interact with a FTHMA-070, T85, T129 or A259
protein, wherein determining the ability of the test compound to
interact with a FTHMA-070, T85, T129 or A259 protein comprises
determining the ability of the FTHMA-070, T85, T129 or A259 protein
to preferentially bind to or modulate the activity of a FTHMA-070,
T85, T129 or A259 target molecule.
[0857] In the case of cell-free assays, it may be desirable to
utilize a solubilizing agent such that the membrane-bound form of
FTHMA-070, T85, T129 or A259 is maintained in solution. Examples of
such solubilizing agents include non-ionic detergents such as
n-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside,
octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton.RTM.
X-100, Triton.RTM. X-114, Thesit.RTM., Isotridecypoly(ethylene
glycol ether)n, 3-[(3-cholamidopropyl)dimethylamminio]-1-propane
sulfonate (CHAPS),
3-[(3-cholamidopropyl)dimethylamminio]-2-hydroxy-1-propane
sulfonate (CHAPSO), or N-dodecyl=N,N-dimethyl-3-ammonio-1-propane
sulfonate.
[0858] In more than one embodiment of the above assay methods of
the present invention, it may be desirable to immobilize either
FTHMA-070, T85, T129 or A259 or its target molecule to facilitate
separation of complexed from uncomplexed forms of one or both of
the proteins, as well as to accommodate automation of the assay.
Binding of a test compound to FTHMA-070, T85, T129 or A259, or
interaction of FTHMA-070, T85, T129 or A259 with a target molecule
in the presence and absence of a candidate compound, can be
accomplished in any vessel suitable for containing the reactants.
Examples of such vessels include microtitre plates, test tubes, and
micro-centrifuge tubes. In one embodiment, a fusion protein can be
provided which adds a domain that allows one or both of the
proteins to be bound to a matrix. For example,
glutathione-S-transferase/FTHMA-070, T85, T129 or A259 fusion
proteins or glutathione-S-transferase/target fusion proteins can be
adsorbed onto glutathione sepharose beads (Sigma Chemical; St.
Louis, Mo.) or glutathione derivatized microtitre plates, which are
then combined with the test compound or the test compound and
either the non-adsorbed target protein or FTHMA-070, T85, T129 or
A259 protein, and the mixture incubated under conditions conducive
to complex formation (e.g., at physiological conditions for salt
and pH). Following incubation, the beads or microtitre plate wells
are washed to remove any unbound components, the matrix immobilized
in the case of beads, complex determined either directly or
indirectly, for example, as described above. Alternatively, the
complexes can be dissociated from the matrix, and the level of
FTHMA-070, T85, T129 or A259 binding or activity determined using
standard techniques.
[0859] Other techniques for immobilizing proteins on matrices can
also be used in the screening assays of the invention. For example,
either FTHMA-070, T85, T129 or A259 or its target molecule can be
immobilized utilizing conjugation of biotin and streptavidin.
Biotinylated FTHMA-070, T85, T129 or A259 or target molecules can
be prepared from biotin-NHS (N-hydroxy-succinimide) using
techniques well known in the art (e.g., biotinylation kit, Pierce
Chemicals; Rockford, Ill.), and immobilized in the wells of
streptavidin-coated 96 well plates (Pierce Chemical).
Alternatively, antibodies reactive with. FTHMA-070, T85, T129 or
A259 or target molecules but which do not interfere with binding of
the FTHMA-070, T85, T129 or A259 protein to its target molecule can
be derivatized to the wells of the plate, and unbound target or
FTHMA-070, T85, T129 or A259 trapped in the wells by antibody
conjugation. Methods for detecting such complexes, in addition to
those described above for the GST-immobilized complexes, include
immunodetection of complexes using antibodies reactive with the
FTHMA-070, T85, T129 or A259 or target molecule, as well as
enzyme-linked assays which rely on detecting an enzymatic activity
associated with the FTHMA-070, T85, T129 or A259 or target
molecule.
[0860] In another embodiment, modulators of FTHMA-070, T85, T129 or
A259 expression are identified in a method in which a cell is
contacted with a candidate compound and the expression of
FTHMA-070, T85, T129 or A259 mRNA or protein in the cell is
determined. The level of expression of FTHMA-070, T85, T129 or A259
mRNA or protein in the presence of the candidate compound is
compared to the level of expression of FTHMA-070, T85, T129 or A259
mRNA or protein in the absence of the candidate compound. The
candidate compound can then be identified as a modulator of
FTHMA-070, T85, T129 or A259 expression based on this comparison.
For example, when expression of FTHMA-070, T85, T129 or A259 mRNA
or protein is greater (statistically significantly greater) in the
presence of the candidate compound than in its absence, the
candidate compound is identified as a stimulator of FTHMA-070, T85,
T129 or A259 mRNA or protein expression. Alternatively, when
expression of FTHMA-070, T85, T129 or A259 mRNA or protein is less
(statistically significantly less) in the presence of the candidate
compound than in its absence, the candidate compound is identified
as an inhibitor of FTHMA-070, T85, T129 or A259 mRNA or protein
expression. The level of FTHMA-070, T85, T129 or A259 mRNA or
protein expression in the cells can be determined by methods
described herein for detecting FTHMA-070, T85, T129 or A259 mRNA or
protein.
[0861] In yet another aspect of the invention, the FTHMA-070, T85,
T129 or A259 proteins can be used as "bait proteins" in a
two-hybrid assay or three hybrid assay (see, e.g., U.S. Pat. No.
5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al.
(1993) J. Biol. Chem. 268:12046-12054; Bartel et al. (1993)
Bio/Techniques 14:920-924; Iwabuchi et al. (1993) Oncogene
8:1693-1696; and WO94/10300), to identify other proteins, which
bind to or interact with FTHMA-070, T85, T129 or A259 and modulate
FTHMA-070, T85, T129 or A259 activity. Such FTHMA-070, T85, T129 or
A259-binding proteins are also likely to be involved in the
propagation of signals by the FTHMA-070, T85, T129 or A259 proteins
as, for example, upstream or downstream elements of the FTHMA-070,
T85, T129 or A259 pathway.
[0862] The two-hybrid system is based on the modular nature of most
transcription factors, which consist of separable DNA-binding and
activation domains. Briefly, the assay utilizes two different DNA
constructs. In one construct, the gene that codes for FTHMA-070,
T85, T129 or A259 is fused to a gene encoding the DNA binding
domain of a known transcription factor (e.g., GAL-4). In the other
construct, a DNA sequence, from a library of DNA sequences, that
encodes an unidentified protein ("prey" or "sample") is fused to a
gene that codes for the activation domain of the known
transcription factor. If the "bait" and the "prey" proteins are
able to interact, in vivo, forming an FTHMA-070, T85, T129 or
A259-dependent complex, the DNA-binding and activation domains of
the transcription factor are brought into close proximity. This
proximity allows transcription of a reporter gene (e.g., LacZ)
which is operably linked to a transcriptional regulatory site
responsive to the transcription factor. Expression of the reporter
gene can be detected and cell colonies containing the functional
transcription factor can be isolated and used to obtain the cloned
gene which encodes the protein which interacts with FTHMA-070, T85,
T129 or A259.
[0863] This invention further pertains to novel agents identified
by the above-described screening assays and uses thereof for
treatments as described herein.
Tango-77 Screening Assays
[0864] The invention provides a method (also referred to herein as
a "screening assay") for identifying modulators, i.e., candidate or
test compounds or agents (e.g., peptides, peptidomimetics, small
molecules or other drugs) which bind to Tango-77 proteins or have a
stimulatory or inhibitory effect on, for example, Tango-77
expression or Tango-77 activity.
[0865] Examples of methods for the synthesis of molecular libraries
can be found in the art, for example in: DeWitt et al. (1993) Proc.
Natl. Acad. Sci. USA 90:6909; Erb et al. (1994) Proc. Natl. Acad.
Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678;
Cho et al. (1993) Science 261:1303; Carrell et al. (1994) Angew.
Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew. Chem.
Int. Ed. Engl. 33:2061; and Gallop et al. (1994) J. Med. Chem.
37:1233.
[0866] Libraries of compounds may be presented in solution (e.g.,
Houghten (1992) Bio/Techniques 13:412-421), or on beads (Lam (1991)
Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556),
bacteria (U.S. Pat. No. 5,223,409), spores (U.S. Pat. Nos.
5,571,698; 5,403,484; and 5,223,409), plasmids (Cull et al. (1992)
Proc. Natl. Acad. Sci. USA 89:1865-1869) or phage (Scott and Smith
(1990) Science 249:386-390; Devlin (1990) Science 249:404-406;
Cwirla et al. (1990) Proc. Natl. Acad. Sci. USA 87:6378-6382; and
Felici (1991) J. Mol. Biol. 222:301-310).
[0867] In another embodiment, an assay is used to determine the
ability of the test compound to modulate the activity of Tango-77
or a biologically active portion thereof, for example, by
determining the ability of the Tango-77 protein to bind to or
interact with a Tango-77 target molecule. As used herein, a "target
molecule" is a molecule with which a Tango-77 protein binds or
interacts in nature, for example, a molecule on the surface of a
cell. A Tango-77 target molecule can be a non-Tango-77 molecule or
a Tango-77 protein or polypeptide of the present invention. In one
embodiment, a Tango-77 target molecule is a component of a signal
transduction pathway, for example, Tango-77 may bind to a IL-1
receptor or another receptor thereby blocking the receptor and
inhibiting future signal transduction. Determining the ability of
the Tango-77 protein to bind to or interact with a Tango-77 target
molecule can be accomplished by one of the methods described above.
In a preferred embodiment, determining the ability of the Tango-77
protein to bind to or interact with a Tango-77 target molecule can
be accomplished by determining the activity of the target molecule.
For example, the activity of the target molecule can be determined
by detecting induction of a cellular second messenger of the target
(e.g., intracellular Ca.sup.2+, diacylglycerol, IP3, etc.),
detecting catalytic/enzymatic activity of the target on an
appropriate substrate, detecting the induction of a reporter gene
(e.g., a Tango-77-responsive regulatory element operably linked to
a nucleic acid encoding a detectable marker, e.g. luciferase), or
detecting a cellular response, for example, inflammation.
[0868] In yet another embodiment, an assay of the present invention
is a cell-free assay comprising contacting a Tango-77 protein or
biologically active portion thereof with a test compound and
determining the ability of the test compound to bind to the
Tango-77 protein or biologically active portion thereof. Binding of
the test compound to the Tango-77 protein can be determined either
directly or indirectly as described above. In a preferred
embodiment, the assay includes contacting the Tango-77 protein or
biologically active portion thereof with a known compound which
binds Tango-77 to form an assay mixture, contacting the assay
mixture with a test compound, and determining the ability of the
test compound to interact with a Tango-77 protein, wherein
determining the ability of the test compound to interact with a
Tango-77 protein comprises determining the ability of the test
compound to preferentially bind to Tango-77 or biologically active
portion thereof as compared to the known compound.
[0869] In another embodiment, an assay is a cell-free assay
comprising contacting Tango-77 protein or biologically active
portion thereof with a test compound and determining the ability of
the test compound to modulate (e.g., stimulate or inhibit) the
activity of the Tango-77 protein or biologically active portion
thereof. Determining the ability of the test compound to modulate
the activity of Tango-77 can be accomplished, for example, by
determining the ability of the Tango-77 protein to bind to a
Tango-77 target molecule by one of the methods described above for
determining direct binding. In an alternative embodiment,
determining the ability of the test compound to modulate the
activity of Tango-77 can be accomplished by determining the ability
of the Tango-77 protein to further modulate a Tango-77 target
molecule. For example, the catalytic/enzymatic activity of the
target molecule on an appropriate substrate can be determined as
previously described.
[0870] In yet another embodiment, the cell-free assay comprises
contacting the Tango-77 protein or biologically active portion
thereof with a known compound which binds Tango-77 to form an assay
mixture, contacting the assay mixture with a test compound, and
determining the ability of the test compound to interact with a
Tango-77 protein, wherein determining the ability of the test
compound to interact with a Tango-77 protein comprises determining
the ability of the Tango-77 protein to preferentially bind to or
modulate the activity of a Tango-77 target molecule.
[0871] It is possible that membrane-bound forms of Tango-77 exist.
The cell-free assays of the present invention are amenable to use
of both the forms Tango-77. In the case of cell-free assays
comprising a membrane-bound form of Tango-77, it may be desirable
to utilize a solubilizing agent such that the membrane-bound form
of Tango-77 is maintained in solution. Examples of such
solubilizing agents include non-ionic detergents such as
n-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside,
octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton.RTM.
X-100, Triton.RTM. X-114, Thesit.RTM., Isotridecypoly(ethylene
glycol ether)n, 3-[(3-cholamidopropyl)dimethylamminio]-1-propane
sulfonate (CHAPS),
3-[(3-cholamidopropyl)dimethylamminio]-2-hydroxy-1-propane
sulfonate (CHAPSO), or N-dodecyl=N,N-dimethyl-3-ammonio-1-propane
sulfonate.
[0872] In more than one embodiment of the above assay methods of
the present invention, it may be desirable to immobilize either
Tango-77 or its target molecule to facilitate separation of
complexed from uncomplexed forms of one or both of the proteins, as
well as to accommodate automation of the assay. Binding of a test
compound to Tango-77, or interaction of Tango-77 with a target
molecule in the presence and absence of a candidate compound, can
be accomplished in any vessel suitable for containing the
reactants. Examples of such vessels include microtitre plates, test
tubes, and micro-centrifuge tubes. In one embodiment, a fusion
protein can be provided which adds a domain that allows one or both
of the proteins to be bound to a matrix. For example,
glutathione-S-transferase/Tango-77 fusion proteins or
glutathione-S-transferase/target fusion proteins can be adsorbed
onto glutathione sepharose beads (Sigma Chemical Co.; St. Louis,
Mo.) or glutathione derivatized microtitre plates, which are then
combined with the test compound or the test compound and either the
non-adsorbed target protein or Tango-77 protein, and the mixture
incubated under conditions conducive to complex formation (e.g., at
physiological conditions for salt and pH). Following incubation,
the beads or microtitre plate wells are washed to remove any
unbound components and complex formation is measured either
directly or indirectly, for example, as described above.
Alternatively, the complexes can be dissociated from the matrix,
and the level of Tango-77 binding or activity determined using
standard techniques.
[0873] Other techniques for immobilizing proteins on matrices can
also be used in the screening assays of the invention. For example,
either Tango-77 or its target molecule can be immobilized utilizing
conjugation of biotin and streptavidin. Biotinylated Tango-77 or
target molecules can be prepared from biotin-NHS
(N-hydroxy-succinimide) using techniques well known in the art
(e.g., biotinylation kit, Pierce Chemicals; Rockford, Ill.), and
immobilized in the wells of streptavidin-coated 96 well plates
(Pierce Chemical). Alternatively, antibodies reactive with Tango-77
or target molecules but which do not interfere with binding of the
Tango-77 protein to its target molecule can be derivatized to the
wells of the plate, and unbound target or Tango-77 trapped in the
wells by antibody conjugation. Methods for detecting such
complexes, in addition to those described above for the
GST-immobilized complexes, include immunodetection of complexes
using antibodies reactive with the Tango-77 or target molecule, as
well as enzyme-linked assays which rely on detecting an enzymatic
activity associated with the Tango-77 or target molecule.
[0874] In another embodiment, modulators of Tango-77 expression are
identified in a method in which a cell is contacted with a
candidate compound and the expression of Tango-77 mRNA or protein
in the cell is determined. The level of expression of Tango-77 mRNA
or protein in the presence of the candidate compound is compared to
the level of expression of Tango-77 mRNA or protein in the absence
of the candidate compound. The candidate compound can then be
identified as a modulator of Tango-77 expression based on this
comparison. For example, when expression of Tango-77 mRNA or
protein is greater (statistically significantly greater) in the
presence of the candidate compound than in its absence, the
candidate compound is identified as a stimulator of Tango-77 mRNA
or protein expression. Alternatively, when expression of Tango-77
mRNA or protein is less (statistically significantly less) in the
presence of the candidate compound than in its absence, the
candidate compound is identified as an inhibitor of Tango-77 mRNA
or protein expression. The level of Tango-77 mRNA or protein
expression in the cells can be determined by methods described
herein for detecting Tango-77 mRNA or protein.
[0875] In yet another aspect of the invention, the Tango-77
proteins can be used as "bait proteins" in a two-hybrid assay or
three hybrid assay (see, e.g., U.S. Pat. No. 5,283,317; Zervos et
al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem.
268:12046-12054; Bartel et al. (1993) Bio/Techniques 14:920-924;
Iwabuchi et al. (1993) Oncogene 8:1693-1696; and PCT Publication
No. WO 94/10300), to identify other proteins, which bind to or
interact with Tango-77 ("Tango-77-binding proteins" or
"Tango-77-bp") and modulate Tango-77 activity. Such
Tango-77-binding proteins are also likely to be involved in the
propagation of signals by the Tango-77 proteins as, for example,
upstream or downstream elements of the Tango-77 pathway.
[0876] The two-hybrid system is based on the modular nature of most
transcription factors, which consist of separable DNA-binding and
activation domains. Briefly, the assay utilizes two different DNA
constructs. In one construct, the gene that codes for Tango-77 is
fused to a gene encoding the DNA binding domain of a known
transcription factor (e.g., GAL-4). In the other construct, a DNA
sequence, from a library of DNA sequences, that encodes an
unidentified protein ("prey" or "sample") is fused to a gene that
codes for the activation domain of the known transcription factor.
If the "bait" and the "prey" proteins are able to interact, in
vivo, forming an Tango-77-dependent complex, the DNA-binding and
activation domains of the transcription factor are brought into
close proximity. This proximity allows transcription of a reporter
gene (e.g., LacZ) which is operably linked to a transcriptional
regulatory site responsive to the transcription factor. Expression
of the reporter gene can be detected and cell colonies containing
the functional transcription factor can be isolated and used to
obtain the cloned gene which encodes the protein which interacts
with Tango-77.
[0877] This invention further pertains to novel agents identified
by the above-described screening assays and uses thereof for
treatments as described herein.
SPOIL Screening Assays:
[0878] The invention provides a method (also referred to herein as
a "screening assay") for identifying modulators, i.e., candidate or
test compounds or agents (e.g., peptides, peptidomimetics, small
molecules or other drugs) which bind to SPOIL proteins or have a
stimulatory or inhibitory effect on, for example, SPOIL expression
or SPOIL activity and/or have a stimulatory or inhibitory effect on
IL-1 stimulated activities.
[0879] In one embodiment, the invention provides assays for
screening candidate or test compounds which bind to or modulate the
activity of a SPOIL target molecule. The test compounds of the
present invention can be obtained using any of the numerous
approaches in combinatorial library methods known in the art,
including: biological libraries; spatially addressable parallel
solid phase or solution phase libraries; synthetic library methods
requiring deconvolution; the `one-bead one-compound` library
method; and synthetic library methods using affinity chromatography
selection. The biological library approach is limited to peptide
libraries, while the other four approaches are applicable to
peptide, non-peptide oligomer or small molecule libraries of
compounds (Lam (1997) Anticancer Drug Des. 12:145).
[0880] Examples of methods for the synthesis of molecular libraries
can be found in the art, for example in: DeWitt et al. (1993) Proc.
Natl. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl.
Acad. Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem.
37:2678; Cho et al. (1993) Science 261:1303; Carrell et al. (1994)
Angew. Chem. Mt. Ed. Engl. 33:2059; Carell et al. (1994) Angew.
Chem. Mt. Ed. Engl. 33:2061; and in Gallop et al. (1994) J. Med.
Chem. 37:1233. Libraries of compounds may be presented in solution
(e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam
(1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556),
bacteria (Ladner U.S. Pat. No. 5,223,409), spores (Ladner U.S. Pat.
No. '409), plasmids (Cull et al. (1992) Proc Natl Acad Sci USA
89:1865-1869) or on phage (Scott and Smith (1990) Science
249:386-390); (Devlin (1990) Science 249:404-406); (Cwirla et al.
(1990) Proc. Natl. Acad. Sci. 87:6378-6382); (Felici (1991) J. Mol.
Biol. 222:301-310); (Ladner supra.).
[0881] In one embodiment, the screening assay comprises contacting
a cell which expresses a SPOIL receptor on the cell surface with a
SPOIL protein or biologically-active portion thereof, to form an
assay mixture, contacting the assay mixture with a test compound,
and determining the ability of the test compound to interact with a
SPOIL receptor, wherein determining the ability of the test
compound to interact with a SPOIL receptor comprises determining
the ability of the test compound to preferentially bind to the
SPOIL receptor as compared to the ability of SPOIL, or a
biologically active portion thereof, to bind to the receptor. In
addition, the screening assay can also comprise contacting a cell
which expresses a SPOIL receptor on the cell surface with a SPOIL
protein or biological portion thereof, and IL-1, to form a
competitive binding assay. The binding assay can then be contacted
with a test compound in order to determine the ability of the test
compound to preferentially bind to the receptor as compared with
the SPOIL protein or biological portion thereof and/or modulate
IL-1 stimulated activity by the cell.
[0882] In another embodiment, an assay is a cell-based assay
comprising contacting a cell expressing a SPOIL target molecule
with a test compound and determining the ability of the test
compound to modulate (e.g. stimulate or inhibit) the activity of
the SPOIL target molecule. Determining the ability of the test
compound to modulate the activity of a SPOIL target molecule can be
accomplished, for example, by determining the ability of the SPOIL
protein to bind to or interact with the SPOIL target molecule in
the presence of the test compound. This assay can be performed in
the presence of IL-1, and the ability of the SPOIL protein to
interact with the target molecule can be determined by assessing
the activity of a cell that is normally stimulated by IL-1 as
compared to a control assay comprising cell expressing a SPOIL
target molecule, SPOIL protein and IL-1 without the test
compound.
[0883] Determining the ability of the SPOIL protein to bind to or
interact with a SPOIL target molecule can be accomplished by
determining the activity of the target molecule. For example, the
activity of the target molecule can be determined by detecting
induction or lack of induction of a cellular second messenger of
the target (i.e. intracellular Ca.sup.2+, diacylglycerol, IP.sub.3,
PGE.sub.2, etc.), detecting catalytic/enzymatic activity of the
target an appropriate substrate, detecting the induction of a
reporter gene (comprising a SPOIL and/or IL-1-responsive regulatory
element operatively linked to a nucleic acid encoding a detectable
marker, e.g., luciferase), or detecting a cellular response or lack
of a cellular response, for example, SPOIL and/or IL-1 stimulated
development, differentiation or rate of proliferation.
[0884] In yet another embodiment, the assay is a cell-free assay in
which a SPOIL protein or biologically active portion thereof is
contacted with a test compound and the ability of the test compound
to modulate (e.g., stimulate or inhibit) the activity of the SPOIL
protein or biologically active portion thereof is determined.
Determining the ability of the test compound to modulate the
activity of a SPOIL protein can be accomplished, for example, by
determining the ability of the SPOIL protein to bind to a SPOIL
target molecule in the presence and/or absence of the test
compound. Determining the ability of the test compound to modulate
the activity of a SPOIL protein can be accomplished in the presence
or absence of IL-1. Determining the ability of the SPOIL protein to
bind to a SPOIL target molecule can also be accomplished using a
technology such as real-time Biomolecular Interaction Analysis
(BIA). Sjolander et al. (1991) Anal. Chem. 63:2338-2345 and Szabo
et al. (1995) Curr. Opin. Struct. Biol. 5:699-705. As used herein,
"BIA" is a technology for studying biospecific interactions in real
time, without labeling any of the interactants (e.g., BIAcore.TM.).
Changes in the optical phenomenon surface plasmon resonance (SPR)
can be used as an indication of real-time reactions between
biological molecules.
[0885] In more than one embodiment of the above assay methods of
the present invention, it may be desirable to immobilize either
SPOIL or its target molecule to facilitate separation of complexed
from uncomplexed forms of one or both of the proteins, as well as
to accommodate automation of the assay. Binding of a test compound
to a SPOIL protein, or interaction of a SPOIL protein with a target
molecule in the presence and absence of a candidate compound, can
be accomplished in any vessel suitable for containing the
reactants. Examples of such vessels include microtitre plates, test
tubes, and micro-centrifuge tubes. In one embodiment, a fusion
protein can be provided which adds a domain that allows one or both
of the proteins to be bound to a matrix. For example,
glutathione-S-transferase/SPOIL fusion proteins or
glutathione-S-transferase/target fusion proteins can be adsorbed
onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.)
or glutathione derivatized microtitre plates, which are then
combined with the test compound or the test compound and either the
non-adsorbed target protein or SPOIL protein, and the mixture
incubated under conditions conducive to complex formation (e.g., at
physiological conditions for salt and pH). Following incubation,
the beads or microtitre plate wells are washed to remove any
unbound components, the matrix immobilized in the case of beads,
complex determined either directly or indirectly, for example, as
described above. Alternatively, the complexes can be dissociated
from the matrix, and the level of SPOIL binding or activity
determined using standard techniques.
[0886] Other techniques for immobilizing proteins on matrices can
also be used in the screening assays of the invention. For example,
either a SPOIL protein or a SPOIL target molecule can be
immobilized utilizing conjugation of biotin and streptavidin.
Biotinylated SPOIL protein or target molecules can be prepared from
biotin-NHS (N-hydroxy-succinimide) using techniques well known in
the art (e.g., biotinylation kit, Pierce Chemicals, Rockford,
Ill.), and immobilized in the wells of streptavidin-coated 96 well
plates (Pierce Chemical). Alternatively, antibodies reactive with
SPOIL protein or target molecules but which do not interfere with
binding of the SPOIL protein to its target molecule can be
derivatized to the wells of the plate, and unbound target or SPOIL
protein trapped in the wells by antibody conjugation. Methods for
detecting such complexes, in addition to those described above for
the GST-immobilized complexes, include immunodetection of complexes
using antibodies reactive with the SPOIL protein or target
molecule, as well as enzyme-linked assays which rely on detecting
an enzymatic activity associated with the SPOIL protein or target
molecule.
[0887] In yet another aspect of the invention, the SPOIL proteins
can be used as "bait proteins" in a two-hybrid assay or
three-hybrid assay (see, e.g., U.S. Pat. No. 5,283,317; Zervos et
al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem.
268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924;
Iwabuchi et al. (1993) Oncogene 8:1693-1696; and Brent WO94/10300),
to identify other proteins, which bind to or interact with SPOIL
("SPOIL-binding proteins" or "SPOIL-bp") and modulate SPOIL
activity. Such SPOIL-binding proteins are also likely to be
involved in the propagation of signals by the SPOIL proteins as,
for example, downstream elements of a SPOIL-mediated signaling
pathway. Alternatively, such SPOIL-binding proteins are likely to
be cell-surface molecules associated with non-SPOIL expressing
cells, wherein such SPOIL-binding proteins are involved in signal
transduction.
[0888] The two-hybrid system is based on the modular nature of most
transcription factors, which consist of separable DNA-binding and
activation domains. Briefly, the assay utilizes two different DNA
constructs. In one construct, the gene that codes for a SPOIL
protein is fused to a gene encoding the DNA binding domain of a
known transcription factor (e.g., GAL-4). In the other construct, a
DNA sequence, from a library of DNA sequences, that encodes an
unidentified protein ("prey" or "sample") is fused to a gene that
codes for the activation domain of the known transcription factor.
If the "bait" and the "prey" proteins are able to interact, in
vivo, forming a SPOIL-dependent complex, the DNA-binding and
activation domains of the transcription factor are brought into
close proximity. This proximity allows transcription of a reporter
gene (e.g., LacZ) which is operably linked to a transcriptional
regulatory site responsive to the transcription factor. Expression
of the reporter gene can be detected and cell colonies containing
the functional transcription factor can be isolated and used to
obtain the cloned gene which encodes the protein which interacts
with the SPOIL protein.
[0889] This invention further pertains to novel SPOIL agents such
as SPOIL proteins or biologically active portions thereof, SPOIL
variants which function as IL-1 receptor agonists and nucleic acid
molecules encoding a SPOIL protein or variant, which can be
screened to determine the efficacy of such agents on various SPOIL
and/or IL-1 stimulated activities (e.g., stimulated immune
response, proliferation, signal transduction pathway, or
differentiation).
[0890] In one embodiment, determining the ability of a SPOIL agent
to modulate the activity of SPOIL and/or IL-1 can be accomplished
by testing the ability of the agent to interfere with the
proliferation of T cells in the presence of SPOIL and/or IL-1.
[0891] It is also within the scope of this invention to further use
a SPOIL agent as described herein in an appropriate animal model.
For example, an agent as described herein (e.g., a modulating
agent) can be used in an animal model to determine the efficacy,
toxicity, or side effects of treatment with such an agent.
Alternatively, a SPOIL agent identified as described herein can be
used in an animal model to determine the mechanism of action of
such an agent. Animal models for use in determining the efficacy or
mechanism of action of a SPOIL agent of the present invention
include animal models demonstrating parameters of sepsis (e.g.,
animals injected with E. coli to induce hypotension) and animal
models for determining bone metabolism (e.g., lethally irradiated
mice which have been transplanted with SPOIL infected marrow
cells). Other animal models which are recognized in the art as
predictive of results in humans with various IL-1 induced disorders
are known in the art and described, for example, in Dinarello
(1991) Blood 77(8):1627-1652. Furthermore, this invention pertains
to uses of SPOIL agents and agents identified by the
above-described screening assays for treatments as described
herein.
NEOKINE Screening Assays:
[0892] The invention provides a method (also referred to herein as
a "screening assay") for identifying modulators, i.e., candidate or
test compounds or agents (e.g., peptides, peptidomimetics, small
molecules or other drugs) which bind to NEOKINE proteins, bind to
NEOKINE receptors, have a stimulatory or inhibitory effect on, for
example, NEOKINE expression, NEOKINE activity, or NEOKINE receptor
activity (e.g., RDC1 activity), or have a stimulatory or inhibitory
effect on, for example, the expression or activity of a non-NEOKINE
chemokine or non-NEOKINE chemokine receptor. It will be appreciated
by one of skill in the art that modulators identified by the
screening assays defined herein (e.g., modulators of NEOKINE and/or
NEOKINE receptor or RDC1) can be used in the prophylactic and
therapeutic treatment of diseases and disorders associated with
aberrant NEOKINE and/or NEOKINE receptor activity (e.g.,
proliferative disorders and diseases).
[0893] In one embodiment, the invention provides assays for
screening candidate or test compounds which bind to or modulate the
activity of a NEOKINE protein or polypeptide or biologically active
portion thereof. In another embodiment, the invention provides
assays for screening candidate or test compounds which bind to or
modulate the activity of a NEOKINE receptor. The test compounds of
the present invention can be obtained using any of the numerous
approaches in combinatorial library methods known in the art,
including: biological libraries; spatially addressable parallel
solid phase or solution phase libraries; synthetic library methods
requiring deconvolution; the `one-bead one-compound` library
method; and synthetic library methods using affinity chromatography
selection. The biological library approach is limited to peptide
libraries, while the other four approaches are applicable to
peptide, non-peptide oligomer or small molecule libraries of
compounds (Lam, K. S. (1997) Anticancer Drug Des. 12:145).
[0894] Examples of methods for the synthesis of molecular libraries
can be found in the art, for example in: DeWitt et al. (1993) Proc.
Natl. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl.
Acad. Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem.
37:2678; Cho et al. (1993) Science 261:1303; Carrell et al. (1994)
Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew.
Chem. Int. Ed. Engl. 33:2061; and in Gallop et al. (1994). J. Med.
Chem. 37:1233.
[0895] Libraries of compounds may be presented in solution (e.g.,
Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991)
Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556),
bacteria (Ladner U.S. Pat. No. 5,223,409), spores (Ladner U.S. Pat.
No. '409), plasmids (Cull et al. (1992) Proc Natl Acad Sci USA
89:1865-1869) or on phage (Scott and Smith (1990) Science
249:386-390); (Devlin (1990) Science 249:404-406); (Cwirla et al.
(1990) Proc. Natl. Acad. Sci. 87:6378-6382); (Felici (1991) J. Mol.
Biol. 222:301-310); (Ladner supra.).
[0896] In one embodiment, an assay is a cell-based assay in which a
cell which expresses a NEOKINE receptor on the cell surface is
contacted with a test compound and the ability of the test compound
to bind to a NEOKINE receptor determined. The cell, for example,
can be of mammalian origin or a yeast cell. The NEOKINE receptor
can be heterologously expressed or over expressed in a host cell
(e.g., a COS cell or fibroblastic cell, for example a HEK293 cell).
Alternatively, an assay cell can be selected which endogenously
expresses a NEOKINE receptor (e.g., RDC1), for example, a rat
pancreatic acinar cell line, AR4-2J, a PC12 pheochromocytoma cell,
a SK-N-MC neroblastoma cell, a MES-13 mesangial tumor cell, an
astrocyte, or a neutrophil). (Hesen et al. (1998) Immunogenetics
47:364-370 and Law and Rosenzweig (1994) Biochem. Biophys. Res.
Commun. 201:458-465). Yeast cells are also particularly amenable
for use in screening assays for G-protein-coupled receptors as
described, for example, in Pausch (1997) TIBTECH 15:487-494.
Determining the ability of the test compound to bind to a NEOKINE
receptor can be accomplished, for example, by coupling the test
compound with a radioisotope or enzymatic label such that binding
of the test compound to the NEOKINE receptor can be determined by
detecting the labeled compound in a complex. For example, test
compounds can be labeled with .sup.125I, .sup.35S, .sup.14C, or
.sup.3H, either directly or indirectly, and the radioisotope
detected by direct counting of radioemmission or by scintillation
counting. Alternatively, test compounds can be enzymatically
labeled with, for example, horseradish peroxidase, alkaline
phosphatase, or luciferase, and the enzymatic label detected by
determination of conversion of an appropriate substrate to
product.
[0897] It is also within the scope of this invention to determine
the ability of a test compound to interact with an NEOKINE receptor
without the labeling of any of the interactants. For example, a
microphysiometer can be used to detect the interaction of a test
compound with an NEOKINE receptor without the labeling of either
the test compound or the receptor. McConnell, H. M. et al. (1992)
Science 257:1906-1912. As used herein, a "microphysiometer" (e.g.,
Cytosensor.TM.) is an analytical instrument that measures the rate
at which a cell acidifies its environment using a light-addressable
potentiometric sensor (LAPS). Changes in this acidification rate
can be used as an indicator of the interaction between ligand and
receptor.
[0898] In a preferred embodiment, the assay comprises contacting a
cell which expresses an NEOKINE receptor on the cell surface with a
NEOKINE protein or biologically-active portion thereof and a test
compound, and determining the ability of the test compound to
modulate binding of the NEOKINE protein or biologically-active
portion thereof to the NEOKINE receptor. Determining the ability of
the test compound to modulate binding of the NEOKINE protein or
biologically-active portion thereof to the NEOKINE receptor can
comprise determining the ability of the test compound to
preferentially bind to the NEOKINE receptor as compared to the
ability of NEOKINE, or a biologically active portion thereof, to
bind to the receptor. Alternatively, determining the ability of the
test compound to modulate binding of the NEOKINE protein or
biologically-active portion thereof to the NEOKINE receptor can
comprise determining a change in the binding of the NEOKINE protein
or biologically-active portion thereof to the NEOKINE receptor
(e.g., a change in the amount of binding in the presence of the
test compound as compared to the absence of the test compound).
[0899] In another preferred embodiment, the assay comprises
contacting a cell which expresses a receptor specific for another
chemokine on the cell surface with an NEOKINE protein or
biologically-active portion thereof and a test compound, and
determining the ability of the test compound to interact with the
receptor, wherein determining the ability of the test compound to
interact with the receptor comprises determining the ability of the
test compound to preferentially bind to the receptor as compared to
the ability of the NEOKINE, or a biologically active portion
thereof, to bind to the receptor. Alternatively, determining the
ability of the test compound to interact with the NEOKINE receptor
can comprise determining a change in the binding of the NEOKINE
protein or biologically-active portion thereof to the NEOKINE
receptor (e.g., a change in the amount of binding).
[0900] In another embodiment, an assay is a cell-based assay
comprising contacting a cell expressing a NEOKINE target molecule
(e.g. a NEOKINE receptor) with a test compound and determining the
ability of the test compound to modulate (e.g. stimulate or
inhibit) the activity of the NEOKINE target molecule. In yet
another embodiment, an assay is a cell-based assay comprising
contacting a cell expressing a NEOKINE receptor with a NEOKINE
protein or biologically-active portion thereof and a test compound
and determining the ability of the test compound to modulate the
activity of the NEOKINE target molecule.
[0901] Determining the ability of the NEOKINE protein to bind to or
interact with an NEOKINE target molecule can be accomplished by one
of the methods described above for determining direct binding. The
activity of the target molecule can be determined by detecting
induction of a cellular second messenger of the target (i.e.
intracellular Ca.sup.2+, diacylglycerol, IP.sub.3, etc.), detecting
catalytic/enzymatic activity of the target an appropriate
substrate, detecting the induction of a reporter gene (comprising
an NEOKINE-responsive regulatory element operatively linked to a
nucleic acid encoding a detectable marker, e.g., luciferase), or
detecting a cellular response, for example, an angiogenic response
or an inflammatory response.
[0902] In yet another embodiment, an assay of the present invention
is a cell-free assay in which an NEOKINE protein or biologically
active portion thereof is contacted with a test compound and the
ability of the test compound to bind to the NEOKINE protein or
biologically active portion thereof is determined. Binding of the
test compound to the NEOKINE protein can be determined either
directly or indirectly as described above. In a preferred
embodiment, the assay includes contacting the NEOKINE protein or
biologically active portion thereof with a known compound which
binds NEOKINE to form an assay mixture, contacting the assay
mixture with a test compound, and determining the ability of the
test compound to interact with an NEOKINE protein, wherein
determining the ability of the test compound to interact with an
NEOKINE protein comprises determining the ability of the test
compound to preferentially bind to NEOKINE or biologically active
portion thereof as compared to the known compound.
[0903] In another embodiment, the assay is a cell-free assay in
which an NEOKINE protein or biologically active portion thereof is
contacted with a test compound and the ability of the test compound
to modulate (e.g., stimulate or inhibit) the activity of the
NEOKINE protein or biologically active portion thereof is
determined. Determining the ability of the test compound to
modulate the activity of an NEOKINE protein can be accomplished,
for example, by determining the ability of the NEOKINE protein to
bind to an NEOKINE target molecule by one of the methods described
above for determining direct binding. Determining the ability of
the NEOKINE protein to bind to an NEOKINE target molecule can also
be accomplished using a technology such as real-time Biomolecular
Interaction Analysis (BIA). Sjolander and Urbaniczky (1991) Anal.
Chem. 63:2338-2345 and Szabo et al. (1995) Curr. Opin. Struct.
Biol. 5:699-705. As used herein, "BIA" is a to technology for
studying biospecific interactions in real time, without labeling
any of the interactants (e.g., BIAcore.TM.). Changes in the optical
phenomenon of surface plasmon resonance (SPR) can be used as an
indication of real-time reactions between biological molecules.
[0904] In an alternative embodiment, determining the ability of the
test compound to modulate the activity of an NEOKINE protein can be
accomplished by determining the ability of the NEOKINE protein to
further modulate the activity of a downstream effector (e.g., an
intracellular signaling molecule) of an NEOKINE target molecule
(e.g., an NEOKINE receptor). For example, the catalytic/enzymatic
activity of the effector molecule on an appropriate substrate can
be determined as previously described.
[0905] In yet another embodiment, the cell-free assay involves
contacting an NEOKINE protein or biologically active portion
thereof with a known compound which binds the NEOKINE protein to
form an assay mixture, contacting the assay mixture with a test
compound, and determining the ability of the test compound to
interact with the NEOKINE protein, wherein determining the ability
of the test compound to interact with the NEOKINE protein comprises
determining the ability of the NEOKINE protein to preferentially
bind to or modulate the activity of an NEOKINE target molecule.
[0906] The assays of the present invention are based at least in
part on the discovery that NEOKINE receptor is the previously
identified orphan chemokine receptor, RDC1. The nucleic acid
sequence of human, murine and canine RDC1 are set forth in SEQ ID
NO:129, SEQ ID NO:131 and SEQ ID NO:133, respectively. The amino
acid sequences of human, murine and canine RDC1 are set forth in
SEQ ID NO:130, SEQ ID NO:132 or SEQ ID NO:134, respectively. Human,
murine and canine RDC1 sequences can be further found at Accession
Nos. U73141 & U67784, AF000236, and X14048, respectively.
Accordingly, in one embodiment, the NEOKINE receptor has the amino
acid set forth in any of SEQ ID NO:130, SEQ ID NO:132 or SEQ ID
NO:134. In another embodiment, the NEOKINE receptor is selected
encoded by a nucleic acid molecule selected from the group
consisting of SEQ ID NO:129, SEQ ID NO:131 or SEQ ID NO:133. In
another embodiment the NEOKINE receptor is selected from the group
consisting of a receptor having an amino acid sequence which is
substantially homologous to the amino acid sequence of any of SEQ
ID NO:130, SEQ ID NO:132 or SEQ ID NO:134; a receptor which is
encoded by an isolated nucleic acid molecule which is substantially
homologous to any of SEQ ID NO:129, SEQ ID NO:131 or SEQ ID NO:133;
or a receptor which is encoded by an isolated nucleic acid molecule
which hybridizes under stringent conditions to a nucleic acid
molecule having any of SEQ ID NO:129, SEQ ID NO:131 or SEQ ID
NO:133.
[0907] The cell-free assays of the present invention are amenable
to use of both soluble and/or membrane-bound forms of isolated
proteins (e.g. NEOKINE proteins or biologically active portions
thereof or NEOKINE receptors). In the case of cell-free assays in
which a membrane-bound form an isolated protein is used (e.g., a
NEOKINE receptor) it may be desirable to utilize a solubilizing
agent such that the membrane-bound form of the isolated protein is
maintained in solution. Examples of such solubilizing agents
include non-ionic detergents such as n-octylglucoside,
n-dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide,
decanoyl-N-methylglucamide, Triton.RTM. X-100, Triton.RTM. X-114,
Thesit.RTM., Isotridecypoly(ethylene glycol ether)n,
3-[(3-cholamidopropyl)dimethylamminio]-1-propane sulfonate (CHAPS),
3-[(3-cholamidopropyl)dimethylamminio]-2-hydroxy-1-propane
sulfonate (CHAPSO), or N-dodecyl=N,N-dimethyl-3-ammonio-1-propane
sulfonate.
[0908] In more than one embodiment of the above assay methods of
the present invention, it may be desirable to immobilize either
NEOKINE or its target molecule to facilitate separation of
complexed from uncomplexed forms of one or both of the proteins, as
well as to accommodate automation of the assay. Binding of a test
compound to a NEOKINE protein, or interaction of a NEOKINE protein
with a target molecule in the presence and absence of a candidate
compound, can be accomplished in any vessel suitable for containing
the reactants. Examples of such vessels include microtitre plates,
test tubes, and micro-centrifuge tubes. In one embodiment, a fusion
protein can be provided which adds a domain that allows one or both
of the proteins to be bound to a matrix. For example,
glutathione-S-transferase/NEOKINE fusion proteins or
glutathione-S-transferase/target fusion proteins can be adsorbed
onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.)
or glutathione derivatized microtitre plates, which are then
combined with the test compound or the test compound and either the
non-adsorbed target protein or NEOKINE protein, and the mixture
incubated under conditions conducive to complex formation (e.g., at
physiological conditions for salt and pH). Following incubation,
the beads or microtitre plate wells are washed to remove any
unbound components, the matrix immobilized in the case of beads,
complex determined either directly or indirectly, for example, as
described above. Alternatively, the complexes can be dissociated
from the matrix, and the level of NEOKINE binding or activity
determined using standard techniques.
[0909] Other techniques for immobilizing proteins on matrices can
also be used in the screening assays of the invention. For example,
either a NEOKINE protein or a NEOKINE target molecule can be
immobilized utilizing conjugation of biotin and streptavidin.
Biotinylated NEOKINE protein or target molecules can be prepared
from biotin-NHS (N-hydroxy-succinimide) using techniques well known
in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford,
Ill.), and immobilized in the wells of streptavidin-coated 96 well
plates (Pierce Chemical). Alternatively, antibodies reactive with
NEOKINE protein or target molecules but which do not interfere with
binding of the NEOKINE protein to its target molecule can be
derivatized to the wells of the plate, and unbound target or
NEOKINE protein trapped in the wells by antibody conjugation.
Methods for detecting such complexes, in addition to those
described above for the GST-immobilized complexes, include
immunodetection of complexes using antibodies reactive with the
NEOKINE protein or target molecule, as well as enzyme-linked assays
which rely on detecting an enzymatic activity associated with the
NEOKINE protein or target molecule.
[0910] In another embodiment, modulators of NEOKINE expression are
identified in a method wherein a cell is contacted with a candidate
compound and the expression of NEOKINE mRNA or protein in the cell
is determined. The level of expression of NEOKINE mRNA or protein
in the presence of the candidate compound is compared to the level
of expression of NEOKINE mRNA or protein in the absence of the
candidate compound. The candidate compound can then be identified
as a modulator of NEOKINE expression based on this comparison. For
example, when expression of NEOKINE mRNA or protein is greater
(statistically significantly greater) in the presence of the
candidate compound than in its absence, the candidate compound is
identified as a stimulator of NEOKINE mRNA or protein expression.
Alternatively, when expression of NEOKINE mRNA or protein is less
(statistically significantly less) in the presence of the candidate
compound than in its absence, the candidate compound is identified
as an inhibitor of NEOKINE mRNA or protein expression. The level of
NEOKINE mRNA or protein expression in the cells can be determined
by methods described herein for detecting NEOKINE mRNA or
protein.
[0911] In yet another aspect of the invention, the NEOKINE proteins
can be used as "bait proteins" in a two-hybrid assay or
three-hybrid assay (see, e.g., U.S. Pat. No. 5,283,317; Zervos et
al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem.
268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924;
Iwabuchi et al. (1993) Oncogene 8:1693-1696; and Brent WO94/10300),
to identify other proteins, which bind to or interact with NEOKINE
("NEOKINE-binding proteins" or "NEOKINE-bp") and are involved in
NEOKINE activity. Such NEOKINE-binding proteins are also likely to
be involved in the propagation of signals by the NEOKINE proteins
as, for example, downstream elements of a NEOKINE-mediated
signaling pathway. Alternatively, such NEOKINE-binding proteins are
likely to be cell-surface molecules associated with non-NEOKINE
expressing cells, wherein such NEOKINE-binding proteins are
involved in chemoattraction.
[0912] The two-hybrid system is based on the modular nature of most
transcription factors, which consist of separable DNA-binding and
activation domains. Briefly, the assay utilizes two different DNA
constructs. In one construct, the gene that codes for a NEOKINE
protein is fused to a gene encoding the DNA binding domain of a
known transcription factor (e.g., GAL-4). In the other construct, a
DNA sequence, from a library of DNA sequences, that encodes an
unidentified protein ("prey" or "sample") is fused to a gene that
codes for the activation domain of the known transcription factor.
If the "bait" and the "prey" proteins are able to interact, in
vivo, forming a NEOKINE-dependent complex, the DNA-binding and
activation domains of the transcription factor are brought into
close proximity. This proximity allows transcription of a reporter
gene (e.g., LacZ) which is operably linked to a transcriptional
regulatory site responsive to the transcription factor. Expression
of the reporter gene can be detected and cell colonies containing
the functional transcription factor can be isolated and used to
obtain the cloned gene which encodes the protein which interacts
with the NEOKINE protein.
[0913] This invention further pertains to novel agents identified
by the above-described screening assays. Accordingly, it is within
the scope of this invention to further use an agent identified as
described herein in an appropriate animal model. For example, an
agent identified as described herein (e.g., a NEOKINE modulating
agent, an antisense NEOKINE nucleic acid molecule, a
NEOKINE-specific antibody, or a NEOKINE-binding partner) can be
used in an animal model to determine the efficacy, toxicity, or
side effects of treatment with such an agent. Alternatively, an
agent identified as described herein can be used in an animal model
to determine the mechanism of action of such an agent. Furthermore,
this invention pertains to uses of novel agents identified by the
above-described screening assays for treatments as described
herein.
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Detection Assays
[0914] Portions or fragments of the cDNA sequences identified
herein (and the corresponding complete gene sequences) can be used
in numerous ways as polynucleotide reagents. For example, these
sequences can be used to: (i) map their respective genes on a
chromosome; and, thus, locate gene regions associated with genetic
disease; (ii) identify an individual from a minute biological
sample (tissue typing); and (iii) aid in forensic identification of
a biological sample. These applications are described in the
subsections below.
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Chromosome Mapping
[0915] Once the sequence (or a portion of the sequence) of a gene
has been isolated, this sequence can be used to map the location of
the gene on a chromosome. Accordingly, FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 nucleic acid molecules described
herein or fragments thereof, can be used to map the location of
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 genes
on a chromosome. The mapping of the FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 sequences to chromosomes is an
important first step in correlating these sequences with genes
associated with disease.
[0916] Briefly, FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 genes can be mapped to chromosomes by preparing
PCR primers (preferably 15-25 bp in length) from the FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 sequences.
Computer analysis of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 sequences can be used to rapidly select primers
that do not span more than one exon in the genomic DNA, thus
complicating the amplification process. These primers can then be
used for PCR screening of somatic cell hybrids containing
individual human chromosomes. Only those hybrids containing the
human gene corresponding to the FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 sequences will yield an amplified
fragment.
[0917] Somatic cell hybrids are prepared by fusing somatic cells
from different mammals (e.g., human and mouse cells). As hybrids of
human and mouse cells grow and divide, they gradually lose human
chromosomes in random order, but retain the mouse chromosomes. By
using media in which mouse cells cannot grow, because they lack a
particular enzyme, but human cells can, the one human chromosome
that contains the gene encoding the needed enzyme, will be
retained. By using various media, panels of hybrid cell lines can
be established. Each cell line in a panel contains either a single
human chromosome or a small number of human chromosomes, and a full
set of mouse chromosomes, allowing easy mapping of individual genes
to specific human chromosomes. (D'Eustachio et al. (1983) Science
220:919-924). Somatic cell hybrids containing only fragments of
human chromosomes can also be produced by using human chromosomes
with translocations and deletions.
[0918] PCR mapping of somatic cell hybrids is a rapid procedure for
assigning a particular sequence to a particular chromosome. Three
or more sequences can be assigned per day using a single thermal
cycler. Using the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 sequences to design oligonucleotide primers,
sublocalization can be achieved with panels of fragments from
specific chromosomes. Other mapping strategies which can similarly
be used to map a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 sequence to its chromosome include in situ
hybridization (described in Fan et al. (1990) Proc. Natl. Acad.
Sci. USA 87:6223-27), pre-screening with labeled flow-sorted
chromosomes, and pre-selection by hybridization to chromosome
specific cDNA libraries.
[0919] Fluorescence in situ hybridization (FISH) of a DNA sequence
to a metaphase chromosomal spread can further be used to provide, a
precise chromosomal location in one step. Chromosome spreads can be
made using cells whose division has been blocked in metaphase by a
chemical like colcemid that disrupts the mitotic spindle. The
chromosomes can be treated briefly with trypsin, and then stained
with Giemsa. A pattern of light and dark bands develops on each
chromosome, so that the chromosomes can be identified individually.
The FISH technique can be used with a DNA sequence as short as 500
or 600 bases. However, clones larger than 1,000 bases have a higher
likelihood of binding to a unique chromosomal location with
sufficient signal intensity for simple detection. Preferably 1,000
bases, and more preferably 2,000 bases will suffice to get good
results at a reasonable amount of time. For a review of this
technique, see Verma et al., Human Chromosomes: A Manual of Basic
Techniques (Pergamon Press, New York, 1988).
[0920] Reagents for chromosome mapping can be used individually to
mark a single chromosome or a single site on that chromosome, or
panels of reagents can be used for marking multiple sites and/or
multiple chromosomes. Reagents corresponding to noncoding regions
of the genes actually are preferred for mapping purposes. Coding
sequences are more likely to be conserved within gene families,
thus increasing the chance of cross hybridizations during
chromosomal mapping.
[0921] Once a sequence has been mapped to a precise chromosomal
location, the physical position of the sequence on the chromosome
can be correlated with genetic map data. (Such data are found, for
example, in V. McKusick, Mendelian Inheritance in Man, available
on-line through Johns Hopkins University Welch Medical Library).
The relationship between genes and disease, mapped to the same
chromosomal region, can then be identified through linkage analysis
(co-inheritance of physically adjacent genes), described in, e.g.,
Egeland et al. (1987) Nature, 325:783-787.
[0922] Moreover, differences in the DNA sequences between
individuals affected and unaffected with a disease associated with
the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
gene can be determined. If a mutation is observed in some or all of
the affected individuals but not in any unaffected individuals,
then the mutation is likely to be the causative agent of the
particular disease. Comparison of affected and unaffected
individuals generally involves first looking for structural
alterations in the chromosomes such as deletions or translocations
that are visible from chromosome spreads or detectable using PCR
based on that DNA sequence. Ultimately, complete sequencing of
genes from several individuals can be performed to confirm the
presence of a mutation and to distinguish mutations from
polymorphisms.
2. FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Tissue Typing
[0923] The FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 sequences of the present invention can also be used to
identify individuals from minute biological samples. The United
States military, for example, is considering the use of restriction
fragment length polymorphism (RFLP) for identification of its
personnel. In this technique, an individual's genomic DNA is
digested with one or more restriction enzymes, and probed on a
Southern blot to yield unique bands for identification. This method
does not suffer from the current limitations of "Dog Tags" which
can be lost, switched, or stolen, making positive identification
difficult. The sequences of the present invention are useful as
additional DNA markers for RFLP (described in U.S. Pat. No.
5,272,057).
[0924] Furthermore, the sequences of the present invention can be
used to provide an alternative technique which determines the
actual base-by-base DNA sequence of selected portions of an
individual's genome. Thus, the FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 sequences described herein can be used to
prepare two PCR primers from the 5' and 3' ends of the sequences.
These primers can then be used to amplify an individual's DNA and
subsequently sequence it.
[0925] Panels of corresponding DNA sequences from individuals,
prepared in this manner, can provide unique individual
identifications, as each individual will have a unique set of such
DNA sequences due to allelic differences. The sequences of the
present invention can be used to obtain such identification
sequences from individuals and from tissue. The FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 sequences of the
invention uniquely represent portions of the human genome. Allelic
variation occurs to some degree in the coding regions of these
sequences, and to a greater degree in the noncoding regions. It is
estimated that allelic variation between individual humans occurs
with a frequency of about once per each 500 bases. Each of the
sequences described herein can, to some degree, be used as a
standard against which DNA from an individual can be compared for
identification purposes. Because greater numbers of polymorphisms
occur in the noncoding regions, fewer sequences are necessary to
differentiate individuals. The noncoding sequences of SEQ ID NO:53,
57, 71, 89, 101, 16, 112, 115, 137, 145 or 163 can comfortably
provide positive individual identification with a panel of perhaps
10 to 1,000 primers which each yield a noncoding amplified sequence
of 100 bases. If predicted coding sequences, such as those in SEQ
ID NO:55, 59, 73, 76, 80, 91, 103, 106, 117, 139, 146 or 164 are
used, a more appropriate number of primers for positive individual
identification would be 500-2,000.
[0926] If a panel of reagents from FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 sequences described herein is used
to generate a unique identification database for an individual,
those same reagents can later be used to identify tissue from that
individual. Using the unique identification database, positive
identification of the individual, living or dead, can be made from
extremely small tissue samples.
3. Use of Partial FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259
Sequences in Forensic Biology
[0927] DNA-based identification techniques can also be used in
forensic biology. Forensic biology is a scientific field employing
genetic typing of biological evidence found at a crime scene as a
means for positively identifying, for example, a perpetrator of a
crime. To make such an identification, PCR technology can be used
to amplify DNA sequences taken from very small biological samples
such as tissues, e.g., hair or skin, or body fluids, e.g., blood,
saliva, or semen found at a crime scene. The amplified sequence can
then be compared to a standard, thereby allowing identification of
the origin of the biological sample.
[0928] The sequences of the present invention can be used to
provide polynucleotide reagents, e.g., PCR primers, targeted to
specific loci in the human genome, which can enhance the
reliability of DNA-based forensic identifications by, for example,
providing another "identification marker" (i.e. another DNA
sequence that is unique to a particular individual). As mentioned
above, actual base sequence information can be used for
identification as an accurate alternative to patterns formed by
restriction enzyme generated fragments. Sequences targeted to
noncoding regions are particularly appropriate for this use as
greater numbers of polymorphisms occur in the noncoding regions,
making it easier to differentiate individuals using this technique.
Examples of polynucleotide reagents include the FTHMA-070, T85 or
A259 sequences or portions thereof, e.g., fragments derived from
the noncoding regions having a length of at least 20 or 30
bases.
[0929] The sequences of the present invention can be used to
provide polynucleotide reagents, e.g., PCR primers, targeted to
specific loci in the human genome, which can enhance the
reliability of DNA-based forensic identifications by, for example,
providing another "identification marker" (i.e. another DNA
sequence that is unique to a particular individual). As mentioned
above, actual base sequence information can be used for
identification as an accurate alternative to patterns formed by
restriction enzyme generated fragments. Sequences targeted to
noncoding regions of SEQ ID NO:71, SEQ ID NO:89, SEQ ID NO:101, or
SEQ ID NO:104, SEQ ID NO:112, SEQ ID NO:115 are particularly
appropriate for this use as greater numbers of polymorphisms occur
in the noncoding regions, making it easier to differentiate
individuals using this technique. Examples of polynucleotide
reagents include the Tango77, SPOIL, NEOKINE or Tango129 nucleotide
sequences or portions thereof, e.g., fragments derived from the
noncoding regions of SEQ ID NO:71, SEQ ID NO:89, SEQ ID NO:101, or
SEQ ID NO:104, SEQ ID NO:112, SEQ ID NO:115 having a length of at
least 20 bases, preferably at least 30 bases.
[0930] The FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 sequences described herein can further be used to provide
polynucleotide reagents, e.g., labeled or labelable probes which
can be used in, for example, an in situ hybridization technique, to
identify a specific tissue, e.g., brain tissue. This can be very
useful in cases where a forensic pathologist is presented with a
tissue of unknown origin. Panels of such FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 probes can be used to
identify tissue by species and/or by organ type.
[0931] In a similar fashion, these reagents, e.g., FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 primers or
probes can be used to screen tissue culture for contamination
(i.e., screen for the presence of a mixture of different types of
cells in a culture).
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Predictive Medicine
[0932] The present invention also pertains to the field of
predictive medicine in which diagnostic assays, prognostic assays,
pharmacogenomics, and monitoring clinical trails are used for
prognostic (predictive) purposes to thereby treat an individual
prophylactically. Accordingly, one aspect of the present invention
relates to diagnostic assays for determining FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 protein and/or nucleic
acid expression as well as FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 activity, in the context of a biological
sample (e.g., blood, serum, cells, tissue) to thereby determine
whether an individual is afflicted with a disease or disorder, or
is at risk of developing a disorder, associated with aberrant
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
expression or activity. The invention also provides for prognostic
(or predictive) assays for determining whether an individual is at
risk of developing a disorder associated with FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 protein, nucleic acid
expression or activity. For example, mutations in a FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene can be
assayed in a biological sample. Such assays can be used for
prognostic or predictive purpose to thereby prophylactically treat
an individual prior to the onset of a disorder characterized by or
associated with FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein, nucleic acid expression or activity.
[0933] Another aspect of the invention provides methods for
determining FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein, nucleic acid expression or FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 activity in an individual
to thereby select appropriate therapeutic or prophylactic agents
for that individual (referred to herein as "pharmacogenomics").
Pharmacogenomics allows for the selection of agents (e.g., drugs)
for therapeutic or prophylactic treatment of an individual based on
the genotype of the individual (e.g., the genotype of the
individual examined to determine the ability of the individual to
respond to a particular agent.)
[0934] Yet another aspect of the invention pertains to monitoring
the influence of agents (e.g., drugs or other compounds) on the
expression or activity of FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 in clinical trials.
[0935] These and other agents are described in further detail in
the following sections.
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Diagnostic Assays
[0936] An exemplary method for detecting the presence or absence of
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 in a
biological sample involves obtaining a biological sample from a
test subject and contacting the biological sample with a compound
or an agent capable of detecting FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein or nucleic acid (e.g.,
mRNA, genomic DNA) that encodes FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein such that the presence of
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 is
detected in the biological sample. A preferred agent for detecting
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 mRNA
or genomic DNA is a labeled nucleic acid probe capable of
hybridizing to FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 mRNA or genomic DNA. The nucleic acid probe can
be, for example, a full-length FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango 129 or A259 nucleic acid, such as the nucleic acid
of SEQ ID NO:53, 55, 57, 58, 71, 73, 76, 80, 89, 101, 104, 112,
115, 118, 121, 124, 137, 139, 145, 146, 163 or 164, or the DNA
insert of the plasmid deposited with ATCC as Accession Number
98751, or a portion thereof, such as an oligonucleotide of at least
15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to
specifically hybridize under stringent conditions to FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 mRNA or genomic
DNA. Other suitable probes for use in the diagnostic assays of the
invention are described herein.
[0937] A preferred agent for detecting FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein is an antibody capable of
binding to FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 protein, preferably an antibody with a detectable label.
Antibodies can be polyclonal, or more preferably, monoclonal. An
intact antibody, or a fragment thereof (e.g., Fab or F(ab').sub.2)
can be used. The term "labeled", with regard to the probe or
antibody, is intended to encompass direct labeling of the probe or
antibody by coupling (i.e., physically linking) a detectable
substance to the probe or antibody, as well as indirect labeling of
the probe or antibody by reactivity with another reagent that is
directly labeled. Examples of indirect labeling include detection
of a primary antibody using a fluorescently labeled secondary
antibody and end-labeling of a DNA probe with biotin such that it
can be detected with fluorescently labeled streptavidin. The term
"biological sample" is intended to include tissues, cells and
biological fluids isolated from a subject, as well as tissues,
cells and fluids present within a subject. That is, the detection
method of the invention can be used to detect FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 mRNA, protein, or genomic
DNA in a biological sample in vitro as well as in vivo. For
example, in vitro techniques for detection of FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 mRNA include Northern
hybridizations and in situ hybridizations. In vitro techniques for
detection of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein include enzyme linked immunosorbent assays
(ELISAs), Western blots, immunoprecipitations and
immunofluorescence. In vitro techniques for detection of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 genomic DNA
include Southern hybridizations. Furthermore, in vivo techniques
for detection of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein include introducing into a subject a
labeled anti-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 antibody. For example, the antibody can be labeled with a
radioactive marker whose presence and location in a subject can be
detected by standard imaging techniques.
[0938] In one embodiment, the biological sample contains protein
molecules from the test subject. Alternatively, the biological
sample can contain mRNA molecules from the test subject or genomic
DNA molecules from the test subject. A preferred biological sample
is a peripheral blood leukocyte sample isolated by conventional
means from a subject.
[0939] In another embodiment, the methods further involve obtaining
a control biological sample from a control subject, contacting the
control sample with a compound or agent capable of detecting
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
protein, mRNA, or genomic DNA, such that the presence of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein, mRNA or
genomic DNA is detected in the biological sample, and comparing the
presence of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein, mRNA or genomic DNA in the control sample with the
presence of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 protein, mRNA or genomic DNA in the test sample.
[0940] The invention also encompasses kits for detecting the
presence of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 in a biological sample (a test sample). Such kits can be
used to determine if a subject is suffering from or is at increased
risk of developing a disorder associated with aberrant expression
of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
(e.g., an immunological disorder or proliferative disorder, e.g.,
psoriasis or cancer). For example, the kit can comprise a labeled
compound or agent capable of detecting FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein or mRNA in a biological
sample and means for determining the amount of FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 in the sample (e.g., an
anti-FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
antibody or an oligonucleotide probe which binds to DNA encoding
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259).
Kits may also include instruction for observing that the tested
subject is suffering from or is at risk of developing a disorder
associated with aberrant expression of FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 if the amount of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 protein or mRNA
is above or below a normal level.
[0941] For antibody-based kits, the kit may comprise, for example:
(1) a first antibody (e.g., attached to a solid support) which
binds to FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 protein; and, optionally, (2) a second, different antibody
which binds to FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein or the first antibody and is conjugated to
a detectable agent.
[0942] For oligonucleotide-based kits, the kit may comprise, for
example: (1) a oligonucleotide, e.g., a detectably labelled
oligonucleotide, which hybridizes to a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 nucleic acid sequence or (2) a
pair of primers useful for amplifying a FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 nucleic acid
molecule;
[0943] The kit may also comprise, e.g., a buffering agent, a
preservative, or a protein stabilizing agent. The kit may also
comprise components necessary for detecting the detectable agent
(e.g., an enzyme or a substrate). The kit may also contain a
control sample or a series of control samples which can be assayed
and compared to the test sample contained. Each component of the
kit is usually enclosed within an individual container and all of
the various containers are within a single package along with
instructions for observing whether the tested subject is suffering
from or is at risk of developing a disorder associated with
aberrant expression of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango 129 or A259.
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Prognostic Assays
[0944] The methods described herein can furthermore be utilized as
diagnostic or prognostic assays to identify subjects having or at
risk of developing a disease or disorder associated with aberrant
FTHMA-070, Tango85, Tango77 or Tango129 expression or activity. For
example, the assays described herein, such as the preceding
diagnostic assays or the following assays, can be utilized to
identify a subject having or at risk of developing a disorder
associated with FTHMA-070, Tango85, Tango77 or Tango129 protein,
nucleic acid expression or activity such as an immune system
disorder. Alternatively, the prognostic assays can be utilized to
identify a subject having or at risk for developing such a disease
or disorder. Thus, the present invention provides a method in which
a test sample is obtained from a subject and FTHMA-070, Tango85,
Tango77 or Tango129 protein or nucleic acid (e.g., mRNA, genomic
DNA) is detected, wherein the presence of FTHMA-070, Tango85,
Tango77 or Tango129 protein or nucleic acid is diagnostic for a
subject having or at risk of developing a disease or disorder
associated with aberrant FTHMA-070, Tango85, Tango77 or Tango129
expression or activity. As used herein, a "test sample" refers to a
biological sample obtained from a subject of interest. For example,
a test sample can be a biological fluid (e.g., serum), cell sample,
or tissue.
[0945] The diagnostic methods described herein can furthermore be
utilized to identify subjects having or at risk of developing a
disease or disorder associated with aberrant SPOIL and/or IL-1
expression or activity. For example, the assays described herein,
such as the preceding diagnostic assays or the following assays,
can be utilized to identify a subject having or at risk of
developing a disorder associated with aberrant SPOIL protein,
nucleic acid expression or activity and/or characterized by
aberrant IL-1 expression or activity such as an inflammatory
disorder, an immune disorder, or a differentiative disorder (e.g.,
a bone metabolism disorder). Alternatively, the prognostic assays
can be utilized to identify a subject having or at risk for
developing a differentiative or proliferative disease (e.g.,
leukemia), an inflammatory disease, or an immune disease. Thus, the
present invention provides a method for identifying a disease or
disorder associated with aberrant SPOIL and/or IL-1 expression or
activity in which a test sample is obtained from a subject and
SPOIL protein or nucleic acid (e.g, mRNA, genomic DNA) is detected,
wherein the presence of SPOIL protein or nucleic acid is diagnostic
for a subject having or at risk of developing a disease or disorder
characterized aberrant SPOIL and/or IL-1 expression or activity. As
used herein, a "test sample" refers to a biological sample obtained
from a subject of interest. For example, a test sample can be a
biological fluid (e.g., serum), cell sample, or tissue.
[0946] The diagnostic methods described herein can furthermore be
utilized to identify subjects having or at risk of developing a
disease or disorder associated with aberrant NEOKINE expression or
activity. For example, the assays described herein, such as the
preceding diagnostic assays or the following assays, can be
utilized to identify a subject having or at risk of developing a
disorder associated with NEOKINE protein, nucleic acid expression
or activity such as an inflammatory disorder. Alternatively, the
prognostic assays can be utilized to identify a subject having or
at risk for developing an inflammatory disorder. Thus, the present
invention provides a method for identifying a disease or disorder
associated with aberrant NEOKINE expression or activity in which a
test sample is obtained from a subject and NEOKINE protein or
nucleic acid (e.g, mRNA, genomic DNA) is detected, wherein the
presence of NEOKINE protein or nucleic acid is diagnostic for a
subject having or at risk of developing a disease or disorder
associated with aberrant NEOKINE expression or activity. As used
herein, a "test sample" refers to a biological sample obtained from
a subject of interest. For example, a test sample can be a
biological fluid (e.g., serum), cell sample, or tissue.
[0947] The methods described herein can furthermore be utilized as
diagnostic or prognostic assays to identify subjects having or at
risk of developing a disease or disorder associated with aberrant
expression or activity of a A259 polypeptide of the invention. For
example, the assays described herein, such as the preceding
diagnostic assays or the following assays, can be utilized to
identify a subject having or at risk of developing a disorder
associated with aberrant expression or activity of a A259
polypeptide of the invention, e.g., an immunologic disorder, e.g.,
asthma, anaphylaxis, or atopic dermatitis. Alternatively, the
prognostic assays can be utilized to identify a subject having or
at risk for developing such a disease or disorder. Thus, the
present invention provides a method in which a test sample is
obtained from a subject and a A259 polypeptide or nucleic acid
(e.g., mRNA, genomic DNA) of the invention is detected, wherein the
presence of the A259 polypeptide or nucleic acid is diagnostic for
a subject having or at risk of developing a disease or disorder
associated with aberrant expression or activity of the A259
polypeptide. As used herein, a "test sample" refers to a biological
sample obtained from a subject of interest. For example, a test
sample can be a biological fluid (e.g., serum), cell sample, or
tissue.
[0948] Furthermore, the prognostic assays described herein can be
used to determine whether a subject can be administered an agent
(e.g., an agonist, antagonist, peptidomimetic, protein, peptide,
nucleic acid, small molecule, or other drug candidate) to treat a
disease or disorder associated with aberrant FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 expression or activity.
For example, such methods can be used to determine whether a
subject can be effectively treated with a specific agent or class
of agents (e.g., agents of a type which decrease FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 activity). Thus,
the present invention provides methods for determining whether a
subject can be effectively treated with an agent for a disorder
associated with aberrant FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 expression or activity in which a test
sample is obtained and FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein or nucleic acid is detected (e.g., wherein
the presence of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 protein or nucleic acid is diagnostic for a
subject that can be administered the agent to treat a disorder
associated with aberrant FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 expression or activity).
[0949] The methods of the invention can also be used to detect
genetic lesions or mutations in a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 gene, thereby determining if a
subject with the lesioned gene is at risk for a disorder
characterized by aberrant cell proliferation and/or
differentiation. In preferred embodiments, the methods include
detecting, in a sample of cells from the subject, the presence or
absence of a genetic lesion characterized by at least one of an
alteration affecting the integrity of a gene encoding a FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259-protein, or the
mis-expression of the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 gene. For example, such genetic lesions can be
detected by ascertaining the existence of at least one of 1) a
deletion of one or more nucleotides from a FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 gene; 2) an addition of
one or more nucleotides to a FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 gene; 3) a substitution of one or more
nucleotides of a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 gene, 4) a chromosomal rearrangement of a
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene;
5) an alteration in the level of a messenger RNA transcript of a
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene,
6) aberrant modification of a FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 gene, such as of the methylation pattern
of the genomic DNA, 7) the presence of a non-wild type splicing
pattern of a messenger RNA transcript of a FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango 129 or A259 gene, 8) a non-wild type
level of a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259-protein, 9) allelic loss of a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 gene, and 10) inappropriate
post-translational modification of a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259-protein. As described herein,
there are a large number of assay techniques known in the art which
can be used for detecting lesions in a FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 gene. A preferred biological
sample is a peripheral blood leukocyte sample isolated by
conventional means from a subject.
[0950] In certain embodiments, detection of the lesion involves the
use of a probe/primer in a polymerase chain reaction (PCR) (see,
e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor PCR
or RACE PCR, or, alternatively, in a ligation chain reaction (LCR)
(see, e.g., Landegran et al. (1988) Science 241:1077-1080; and
Nakazawa et al. (1994) Proc. Nail. Acad. Sci. USA 91:360-364), the
latter of which can be particularly useful for detecting point
mutations in the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259-gene (see Abravaya et al. (1995) Nucleic Acids
Res. 23:675-682). This method can include the steps of collecting a
sample of cells from a patient, isolating nucleic acid (e.g.,
genomic, mRNA or both) from the cells of the sample, contacting the
nucleic acid sample with one or more primers which specifically
hybridize to a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 gene under conditions such that hybridization and
amplification of the FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259-gene (if present) occurs, and detecting the
presence or absence of an amplification product, or detecting the
size of the amplification product and comparing the length to a
control sample. It is anticipated that PCR and/or LCR may be
desirable to use as a preliminary amplification step in conjunction
with any of the techniques used for detecting mutations described
herein.
[0951] Alternative amplification methods include: self sustained
sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci.
USA 87:1874-1878), transcriptional amplification system (Kwoh, et
al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta
Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), or any
other nucleic acid amplification method, followed by the detection
of the amplified molecules using techniques well known to those of
skill in the art. These detection schemes are especially useful for
the detection of nucleic acid molecules if such molecules are
present in very low numbers.
[0952] In an alternative embodiment, mutations in a FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene from a
sample cell can be identified by alterations in restriction enzyme
cleavage patterns. For example, sample and control DNA is isolated,
amplified (optionally), digested with one or more restriction
endonucleases, and fragment length sizes are determined by gel
electrophoresis and compared. Differences in fragment length sizes
between sample and control DNA indicates mutations in the sample
DNA. Moreover, the use of sequence specific ribozymes (see, e.g.,
U.S. Pat. No. 5,498,531) can be used to score for the presence of
specific mutations by development or loss of a ribozyme cleavage
site.
[0953] In other embodiments, genetic mutations in FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 can be
identified by hybridizing a sample and control nucleic acids, e.g.,
DNA or RNA, to high density arrays containing hundreds or thousands
of oligonucleotides probes (Cronin et al. (1996) Human Mutation
7:244-255; Kozal et al. (1996) Nature Medicine 2:753-759). For
example, genetic mutations in FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 can be identified in two-dimensional
arrays containing light-generated DNA probes as described in Cronin
et al. supra. Briefly, a first hybridization array of probes can be
used to scan through long stretches of DNA in a sample and control
to identify base changes between the sequences by making linear
arrays of sequential overlapping probes. This step allows the
identification of point mutations. This step is followed by a
second hybridization array that allows the characterization of
specific mutations by using smaller, specialized probe arrays
complementary to all variants or mutations detected. Each mutation
array is composed of parallel probe sets, one complementary to the
wild-type gene and the other complementary to the mutant gene.
[0954] In yet another embodiment, any of a variety of sequencing
reactions known in the art can be used to directly sequence the
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango 129 or A259 gene
and detect mutations by comparing the sequence of the sample
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 with
the corresponding wild-type (control) sequence. Examples of
sequencing reactions include those based on techniques developed by
Maxim and Gilbert ((1977) Proc. Natl. Acad. Sci. USA 74:560) or
Sanger ((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also
contemplated that any of a variety of automated sequencing
procedures can be utilized when performing the diagnostic assays
((1995) Bio/Techniques 19:448), including sequencing by mass
spectrometry (see, e.g., PCT Publication No. WO 94/16101; Cohen et
al. (1996) Adv. Chromatogr. 36:127-162; and Griffin et al. (1993)
Appl. Biochem. Biotechnol. 38:147-159).
[0955] Other methods for detecting mutations in the FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 gene include
methods in which protection from cleavage agents is used to detect
mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al.
(1985) Science 230:1242). In general, the art technique of
"mismatch cleavage" starts by providing heteroduplexes of formed by
hybridizing (labeled) RNA or DNA containing the wild-type
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
sequence with potentially mutant RNA or DNA obtained from a tissue
sample. The double-stranded duplexes are treated with an agent
which cleaves single-stranded regions of the duplex such as which
will exist due to basepair mismatches between the control and
sample strands. For instance, RNA/DNA duplexes can be treated with
RNase and DNA/DNA hybrids treated with S1 nuclease to enzymatically
digesting the mismatched regions. In other embodiments, either
DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or
osmium tetroxide and with piperidine in order to digest mismatched
regions. After digestion of the mismatched regions, the resulting
material is then separated by size on denaturing polyacrylamide
gels to determine the site of mutation. See, e.g., Cotton et al
(1988) Proc. Natl Acad Sci USA 85:4397; Saleeba et al (1992)
Methods Enzymol. 217:286-295. In a preferred embodiment, the
control DNA or RNA can be labeled for detection.
[0956] In still another embodiment, the mismatch cleavage reaction
employs one or more proteins that recognize mismatched base pairs
in double-stranded DNA (so called "DNA mismatch repair" enzymes) in
defined systems for detecting and mapping point mutations in
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 cDNAs
obtained from samples of cells. For example, the mutY enzyme of E.
coli cleaves A at G/A mismatches and the thymidine DNA glycosylase
from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994)
Carcinogenesis 15:1657-1662). According to an exemplary embodiment,
a probe based on a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 sequence, e.g., a wild-type FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 sequence, is hybridized
to a cDNA or other DNA product from a test cell(s). The duplex is
treated with a DNA mismatch repair enzyme, and the cleavage
products, if any, can be detected from electrophoresis protocols or
the like. See, e.g., U.S. Pat. No. 5,459,039.
[0957] In other embodiments, alterations in electrophoretic
mobility will be used to identify mutations in FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 genes. For example,
single strand conformation polymorphism (SSCP) may be used to
detect differences in electrophoretic mobility between mutant and
wild type nucleic acids (Orita et al. (1989) Proc Natl. Acad. Sci.
USA: 86:2766, see also Cotton (1993) Mutat. Res. 285:125-144; and
Hayashi (1992) Genet Anal Tech Appl 9:73-79). Single-stranded DNA
fragments of sample and control FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 nucleic acids will be denatured and
allowed to renature. The secondary structure of single-stranded
nucleic acids varies according to sequence, the resulting
alteration in electrophoretic mobility enables the detection of
even a single base change. The DNA fragments may be labeled or
detected with labeled probes. The sensitivity of the assay may be
enhanced by using RNA (rather than DNA), in which the secondary
structure is more sensitive to a change in sequence. In a preferred
embodiment, the subject method utilizes heteroduplex analysis to
separate double stranded heteroduplex molecules on the basis of
changes in electrophoretic mobility (Keen et al. (1991) Trends
Genet 7:5).
[0958] In yet another embodiment, the movement of mutant or
wild-type fragments in polyacrylamide gels containing a gradient of
denaturant is assayed using denaturing gradient gel electrophoresis
(DGGE) (Myers et al. (1985) Nature 313:495). When DGGE is used as
the method of analysis, DNA will be modified to insure that it does
not completely denature, for example by adding a GC clamp of
approximately 40 bp of high-melting GC-rich DNA by PCR. In a
further embodiment, a temperature gradient is used in place of a
denaturing gradient to identify differences in the mobility of
control and sample DNA (Rosenbaum and Reissner (1987) Biophys Chem
265:12753).
[0959] Examples of other techniques for detecting point mutations
include, but are not limited to, selective oligonucleotide
hybridization, selective amplification, or selective primer
extension. For example, oligonucleotide primers may be prepared in
which the known mutation is placed centrally and then hybridized to
target DNA under conditions which permit hybridization only if a
perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki
et al. (1989) Proc. Natl. Acad. Sci. USA 86:6230). Such allele
specific oligonucleotides are hybridized to PCR amplified target
DNA or a number of different mutations when the oligonucleotides
are attached to the hybridizing membrane and hybridized with
labeled target DNA.
[0960] Alternatively, allele specific amplification technology
which depends on selective PCR amplification may be used in
conjunction with the instant invention. Oligonucleotides used as
primers for specific amplification may carry the mutation of
interest in the center of the molecule (so that amplification
depends on differential hybridization) (Gibbs et al. (1989) Nucleic
Acids Res. 17:2437-2448) or at the extreme 3' end of one primer
where, under appropriate conditions, mismatch can prevent, or
reduce polymerase extension (Prossner (1993) Tibtech 11:238). In
addition, it may be desirable to introduce a novel restriction site
in the region of the mutation to create cleavage-based detection
(Gasparini et al. (1992) Mol. Cell. Probes 6:1). It is anticipated
that in certain embodiments amplification may also be performed
using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad.
Sci. USA 88:189). In such cases, ligation will occur only if there
is a perfect match at the 3' end of the 5' sequence making it
possible to detect the presence of a known mutation at a specific
site by looking for the presence or absence of amplification.
[0961] The methods described herein may be performed, for example,
by utilizing pre-packaged diagnostic kits comprising at least one
probe nucleic acid or antibody reagent described herein, which may
be conveniently used, e.g., in clinical settings to diagnose
patients exhibiting symptoms or family history of a disease or
illness involving a FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 gene.
[0962] Furthermore, any cell type or tissue, e.g., chondrocytes, or
peripheral blood leukocytes, in which FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 is expressed may be utilized in
the prognostic assays described herein.
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Pharmacogenomics
[0963] Agents, or modulators which have a stimulatory or inhibitory
effect on FTHMA-070, T85 or A259 activity (e.g., FTHMA-070, T85 or
A259 gene expression) as identified by a screening assay described
herein can be administered to individuals to treat
(prophylactically or therapeutically) disorders (e.g., an
immunological disorder) associated with aberrant FTHMA-070, T85 or
A259 activity. Agents, or modulators which have a stimulatory or
inhibitory effect on Tango-77 activity (e.g., Tango-77 gene
expression) as identified by a screening assay described herein can
be administered to individuals to treat (prophylactically or
therapeutically) disorders (e.g., acute or chronic inflammation and
asthma) associated with aberrant Tango-77 activity. The SPOIL
molecules of the present invention or SPOIL modulators as
identified by a screening assay described herein can be
administered to individuals to treat (prophylactically or
therapeutically) disorders (e.g, inflammatory or developmental
disorders) associated with aberrant SPOIL and/or IL-1 activity. The
NEOKINE molecules of the present invention, as well as agents, or
modulators which have a stimulatory or inhibitory effect on NEOKINE
activity (e.g., NEOKINE gene expression) as identified by a
screening assay described herein can be administered to individuals
to treat (prophylactically or therapeutically) disorders (e.g,
inflammatory disorders) associated with aberrant NEOKINE activity.
Agents, or modulators which have a stimulatory or inhibitory effect
on T129 activity (e.g., T129 gene expression) as identified by a
screening assay described herein can be administered to individuals
to treat (prophylactically or therapeutically) disorders (e.g., an
immunological disorder) associated with aberrant T129 activity. In
conjunction with such treatment, the pharmacogenomics (i.e., the
study of the relationship between an individual's genotype and that
individual's response to a foreign compound or drug) of the
individual may be considered. Differences in metabolism of
therapeutics can lead to severe toxicity or therapeutic failure by
altering the relation between dose and blood concentration of the
pharmacologically active drug. Thus, the pharmacogenomics of the
individual permits the selection of effective agents (e.g., drugs)
for prophylactic or therapeutic treatments based on a consideration
of the individual's genotype. Such pharmacogenomics can further be
used to determine appropriate dosages and therapeutic regimens.
Accordingly, the activity of FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein, expression of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 nucleic acid, or
mutation content of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 genes in an individual can be determined to
thereby select appropriate agent(s) for therapeutic or prophylactic
treatment of the individual.
[0964] Pharmacogenomics deals with clinically significant
hereditary variations in the response to drugs due to altered drug
disposition and abnormal action in affected persons. See, e.g.,
Linder (1997) Clin. Chem. 43(2):254-266. In general, two types of
pharmacogenetic conditions can be differentiated. Genetic
conditions transmitted as a single factor altering the way drugs
act on the body (altered drug action) or genetic conditions
transmitted as single factors altering the way the body acts on
drugs (altered drug metabolism). These pharmacogenetic conditions
can occur either as rare defects or as polymorphisms. For example,
glucose-6-phosphate dehydrogenase deficiency (G6PD) is a common
inherited enzymopathy in which the main clinical complication is
haemolysis after ingestion of oxidant drugs (anti-malarials,
sulfonamides, analgesics, nitrofurans) and consumption of fava
beans.
[0965] One pharmacogenomics approach to identifying genes that
predict drug response, known as "a genome-wide association", relies
primarily on a high-resolution map of the human genome consisting
of already known gene-related markers (e.g., a "bi-allelic" gene
marker map which consists of 60,000-100,000 polymorphic or variable
sites on the human genome, each of which has two variants). Such a
high-resolution genetic map can be compared to a map of the genome
of each of a statistically significant number of patients taking
part in a Phase II/III drug trial to identify markers associated
with a particular observed drug response or side effect.
Alternatively, such a high resolution map can be generated from a
combination of some ten-million known single nucleotide
polymorphisms (SNPs) in the human genome. As used herein, a "SNP"
is a common alteration that occurs in a single nucleotide base in a
stretch of DNA. For example, a SNP may occur once per every 1000
bases of DNA. A SNP may be involved in a disease process, however,
the vast majority may not be disease-associated. Given a genetic
map based on the occurrence of such SNPs, individuals can be
grouped into genetic categories depending on a particular pattern
of SNPs in their individual genome. In such a manner, treatment
regimens can be tailored to groups of genetically similar
individuals, taking into account traits that may be common among
such genetically similar individuals.
[0966] Alternatively, a method termed the "candidate gene
approach", can be utilized to identify genes that predict drug
response. According to this method, if a gene that encodes a drug
target is known (e.g., a SPOIL or NEOKINE protein or SPOIL or
NEOKINE receptor of the present invention), all common variants of
that gene can be identified in the population and a particular drug
response can be associated with one or more genes.
[0967] As an illustrative embodiment, the activity of drug
metabolizing enzymes is a major determinant of both the intensity
and duration of drug action. The discovery of genetic polymorphisms
of drug metabolizing enzymes (e.g., N-acetyltransferase 2 (NAT 2)
and cytochrome P450 enzymes CYP2D6 and CYP2C19) has provided an
explanation as to why some patients do not obtain the expected drug
effects or show exaggerated drug response and serious toxicity
after taking the standard and safe dose of a drug. These
polymorphisms are expressed in two phenotypes in the population,
the extensive metabolizer (EM) and poor metabolizer (PM). The
prevalence of PM is different among different populations. For
example, the gene coding for CYP2D6 is highly polymorphic and
several mutations have been identified in PM, which all lead to the
absence of functional CYP2D6. Poor metabolizers of CYP2D6 and
CYP2C19 quite frequently experience exaggerated drug response and
side effects when they receive standard doses. If a metabolite is
the active therapeutic moiety, PM show no therapeutic response, as
demonstrated for the analgesic effect of codeine mediated by its
CYP2D6-formed metabolite morphine. The other extreme are the so
called ultra-rapid metabolizers who do not respond to standard
doses. Recently, the molecular basis of ultra-rapid metabolism has
been identified to be due to CYP2D6 gene amplification.
[0968] Alternatively, a method termed the "gene expression
profiling", can be utilized to identify genes that predict drug
response. For example, the gene expression of an animal dosed with
a drug (e.g., a SPOIL or NEOKINE molecule or SPOIL or NEOKINE
modulator of the present invention) indicate whether gene pathways
related to toxicity have been turned on.
[0969] Information generated from more than one of the above
pharmacogenomics approaches can be used to determine appropriate
dosage and treatment regimens for prophylactic or therapeutic
treatment an individual. This knowledge, when applied to dosing or
drug selection, can avoid adverse reactions or therapeutic failure
and thus enhance therapeutic or prophylactic efficiency when
treating a subject with a SPOIL or NEOKINE molecule or SPOIL or
NEOKINE modulator, such as a modulator identified by one of the
exemplary screening assays described herein.
[0970] Thus, the activity of FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein, expression of FTHMA-070,
Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 nucleic acid, or
mutation content of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 genes in an individual can be determined to
thereby select appropriate agent(s) for therapeutic or prophylactic
treatment of the individual. In addition, pharmacogenetic studies
can be used to apply genotyping of polymorphic alleles encoding
drug-metabolizing enzymes to the identification of an individual's
drug responsiveness phenotype. This knowledge, when applied to
dosing or drug selection, can avoid adverse reactions or
therapeutic failure and thus enhance therapeutic or prophylactic
efficiency when treating a subject with a FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 modulator, such as a
modulator identified by one of the exemplary screening assays
described herein.
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Monitoring of Effects During Clinical Trials
[0971] Monitoring the influence of agents (e.g., drugs, compounds)
on the expression or activity of FTHMA-070 or T85 (e.g., the
ability to modulate aberrant cell proliferation and/or
differentiation) can be applied not only in basic drug screening,
but also in clinical trials. For example, the effectiveness of an
agent determined by a screening assay as described herein to
increase FTHMA-070 or T85 gene expression, protein levels, or
upregulate FTHMA-070 or T85 activity, can be monitored in clinical
trails of subjects exhibiting decreased FTHMA-070 or T85 gene
expression, protein levels, or downregulated FTHMA-070 or T85
activity. Alternatively, the effectiveness of an agent determined
by a screening assay to decrease FTHMA-070 or T85 gene expression,
protein levels, or downregulated FTHMA-070 or T85 activity, can be
monitored in clinical trails of subjects exhibiting increased
FTHMA-070 or T85 gene expression, protein levels, or upregulated
FTHMA-070 or T85 activity. In such clinical trials, the expression
or activity of FTHMA-070 or T85 and, preferably, other genes that
have been implicated in, for example, a cellular proliferation
disorder can be used as a "read out" or markers of the immune
responsiveness of a particular cell.
[0972] Monitoring the influence of agents (e.g., drugs, compounds)
on the expression or activity of Tango-77 (e.g., the ability to
modulate aberrant inflammation) can be applied not only in basic
drug screening, but also in clinical trials. For example, the
effectiveness of an agent, as determined by a screening assay as
described herein, to increase Tango-77 gene expression, increase
protein levels, or upregulate Tango-77 activity, can be monitored
in clinical trials of subjects exhibiting decreased Tango-77 gene
expression, decreased protein levels, or downregulated Tango-77
activity. Alternatively, the effectiveness of an agent, as
determined by a screening assay, to decrease Tango-77 gene
expression, decrease protein levels, or downregulate Tango-77
activity, can be monitored in clinical trials of subjects
exhibiting increased Tango-77 gene expression, increased protein
levels, or upregulated Tango-77 activity.
[0973] Monitoring the influence of SPOIL agents (e.g., modulatory
agents and/or SPOIL proteins) on the expression or activity of
SPOIL and/or IL-1 (e.g., modulation of signal transduction,
modulation of cell development or differentiation, regulation of
cellular proliferation) can be applied not only in basic drug
screening, but also in clinical trials. For example, the
effectiveness of an agent determined by a screening assay (as
described herein) to modulate SPOIL and/or IL-1 expression or
activity can be monitored in clinical trails of subjects exhibiting
increased SPOIL and/or IL-1 expression or activity and/or decreased
SPOIL and/or IL-1 gene expression, protein levels or activity.
Alternatively, the effectiveness of an agent determined by a
screening assay to increase SPOIL and/or IL-1 expression or
activity and/or downregulate SPOIL and/or IL-1 gene expression,
protein levels or activity, can be monitored in clinical trails of
subjects exhibiting increased SPOIL and/or IL-1 expression or
activity and/or decreased SPOIL and/or IL-1 gene expression,
protein levels or activity. In such clinical trials, the expression
or activity of SPOIL and/or IL-1 and, preferably, other genes that
have been implicated in, for example, a proinflammatory disorder,
an immune disorder, or a bone metabolism disorder can be used as a
"read out" or markers of the phenotype of a particular cell.
[0974] Monitoring the influence of agents (e.g., drugs, compounds)
on the expression or activity of a NEOKINE protein (e.g.,
modulation of angiogenesis or of an inflammatory response) an be
applied not only in basic drug screening, but also in clinical
trials. For example, the effectiveness of an agent determined by a
screening assay as described herein to increase NEOKINE gene
expression, protein levels, or upregulate NEOKINE activity, can be
monitored in clinical trials of subjects exhibiting decreased
NEOKINE gene expression, protein levels, or downregulated NEOKINE
activity. Alternatively, the effectiveness of an agent determined
by a screening assay to decrease NEOKINE gene expression, protein
levels, or downregulate NEOKINE activity, can be monitored in
clinical trials of subjects exhibiting increased NEOKINE gene
expression, protein levels, or upregulated NEOKINE activity. In
such clinical trials, the expression or activity of a NEOKINE gene,
and preferably, other genes that have been implicated in, for
example, an inflammatory disorder can be used as a "read out" or
markers of the phenotype of a particular cell.
[0975] Monitoring the influence of agents (e.g., drugs, compounds)
on the expression or activity of T129 or A259 (e.g., the ability to
modulate aberrant cell proliferation and/or differentiation) can be
applied not only in basic drug screening, but also in clinical
trials. For example, the effectiveness of an agent determined by a
screening assay as described herein to increase T129 or A259 gene
expression, protein levels, or upregulate T129 or A259 activity,
can be monitored in clinical trails of subjects exhibiting
decreased T129 or A259 gene expression, protein levels, or
downregulated T129 or A259 activity. Alternatively, the
effectiveness of an agent determined by a screening assay to
decrease T129 or A259 gene expression, protein levels, or
downregulated T129 or A259 activity, can be monitored in clinical
trails of subjects exhibiting increased T129 or A259 gene
expression, protein levels, or upregulated T129 or A259 activity.
In such clinical trials, the expression or activity of T129 or A259
and, preferably, other genes that have been implicated in, for
example, a cellular proliferation disorder can be used as a "read
out" or markers of the immune responsiveness of a particular
cell.
[0976] For example, and not by way of limitation, genes, including
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259, that
are modulated in cells by treatment with an agent (e.g., compound,
drug or small molecule) which modulates FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 activity (e.g.,
identified in a screening assay as described herein) can be
identified. Thus, to study the effect of agents on cellular
proliferation disorders, proinflammatory disorders, or
developmental or differentiative disorders (e.g., a bone metabolism
disorder) for example, in a clinical trial, cells can be isolated
and RNA prepared and analyzed for the levels of expression of
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259 and
other genes implicated in the disorder. The levels of gene
expression (i.e., a gene expression pattern) can be quantified by
Northern blot analysis or RT-PCR, as described herein, or
alternatively by measuring the amount of protein produced, by one
of the methods as described herein, or by measuring the levels of
activity of FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129
or A259 or other genes. In this way, the gene expression pattern
can serve as a marker, indicative of the physiological response of
the cells to the agent. Accordingly, this response state may be
determined before, and at various points during, treatment of the
individual with the agent.
[0977] In a preferred embodiment, the present invention provides a
method for monitoring the effectiveness of treatment of a subject
with an agent (e.g., an agonist, antagonist, peptidomimetic,
protein, peptide, nucleic acid, small molecule, or other drug
candidate identified by the screening assays described herein)
comprising the steps of (i) obtaining a pre-administration sample
from a subject prior to administration of the agent; (ii) detecting
the level of expression of a FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein, mRNA, or genomic DNA in the
preadministration sample; (iii) obtaining one or more
post-administration samples from the subject; (iv) detecting the
level of expression or activity of the FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein, mRNA, or genomic DNA in
the post-administration samples; (v) comparing the level of
expression or activity of the FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 protein, mRNA, or genomic DNA in the
pre-administration sample with the FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 protein, mRNA, or genomic DNA in
the post administration sample or samples; and (vi) altering the
administration of the agent to the subject accordingly. For
example, increased administration of the agent may be desirable to
increase the expression or activity of FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 to higher levels than detected,
i.e., to increase the effectiveness of the agent. Alternatively,
decreased administration of the agent may be desirable to decrease
expression or activity of FTHMA-070, Tango85, Tango77, SPOIL,
NEOKINE, Tango129 or A259 to lower levels than detected, i.e., to
decrease the effectiveness of the agent.
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
Methods of Treatment
[0978] The present invention provides for both prophylactic and
therapeutic methods of treating a subject at risk of (or
susceptible to) a disorder or having a disorder associated with
aberrant FTHMA-070, Tango85, SPOIL or NEOKINE expression or
activity.
[0979] The present invention provides for both prophylactic and
therapeutic methods of treating a subject at risk of (or
susceptible to) developing or having a disorder associated with
aberrant Tango-77 expression or activity. Alternatively, disorders
associated with aberrant IL-1 production can be treated with
Tango-77. Such disorders include acute and chronic inflammation,
asthma, some classes of arthritis, autoimmune diabetes, systemic
lupus erythematosus and inflammatory bowel disease.
[0980] The present invention provides for both prophylactic and
therapeutic methods of treating a subject at risk of (or
susceptible to) a disorder or having a disorder associated with
aberrant T129 expression or activity. Such disorders include
immunological disorders, e.g., disorders associated with abnormal
lymphoid and/or thymic development, T-cell mediated immune
response, T-cell dependent help for B cells, and abnormal humoral B
cell activity, and, possibly, disorders of the skeletal muscle.
[0981] The present invention provides for both prophylactic and
therapeutic methods of treating a subject at risk of (or
susceptible to) a disorder or having a disorder associated with
aberrant A259 expression or activity of a polypeptide of the
invention. For example, disorders characterized by aberrant A259
expression or activity of the polypeptides of the invention include
immunologic disorders. In addition, the A259 nucleic acids,
polypeptides, and modulators thereof of the invention can be used
to treat immunologic diseases and disorders, including but not
limited to inflammatory disorders (e.g., atopic dermatitis). A259
polypeptides of the invention can also treat diseases associated
and bone and cartilage degenerative diseases and disorders (e.g.,
arthritis, e.g., rheumatoid arthritis), as well as other disorders
described herein.
Prophylactic Methods
[0982] In one aspect, the invention provides a method for
preventing in a subject, a disease or condition associated with an
aberrant FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 expression or activity, by administering to the subject an
agent which modulates FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE,
Tango129 or A259 expression or at least one FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 activity. Subjects at
risk for a disease which is caused or contributed to by aberrant
FTHMA-070, Tango85, Tango77, NEOKINE, Tango129 or A259 expression
or activity can be identified by, for example, any or a combination
of diagnostic or prognostic assays as described herein.
Administration of a prophylactic agent can occur prior to the
manifestation of symptoms characteristic of the FTHMA-070, Tango85,
Tango77, SPOIL, NEOKINE, Tango129 or A259 aberrancy, such that a
disease or disorder is prevented or, alternatively, delayed in its
progression. Depending on the type of FTHMA-070, Tango85, Tango77,
SPOIL, NEOKINE, Tango129 or A259 aberrancy, for example, a
FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or A259
agonist or FTHMA-070, Tango85, Tango77, SPOIL, NEOKINE, Tango129 or
A259 antagonist agent can be used for treating the subject. The
appropriate agent can be determined based on screening assays
described herein. For example, an antagonist of an A259 protein may
be used to treat an arthropathic disorder, e.g., rheumatoid
arthritis. The appropriate agent can be determined based on
screening assays described herein.
Therapeutic Methods
[0983] Another aspect of the invention pertains to methods of
modulating FTHMA-070, Tango85, Tango77, Tango129 or A259 expression
or activity for therapeutic purposes. The modulatory method of the
invention involves contacting a cell with an agent that modulates
one or more of the activities of FTHMA-070, Tango85, Tango77,
Tango129 or A259 protein activity associated with the cell. An
agent that modulates FTHMA-070, Tango85, Tango77, Tango129 or A259
protein activity can be an agent as described herein, such as a
nucleic acid or a protein, a naturally-occurring cognate ligand of
a FTHMA-070, Tango85, Tango77, Tango129 or A259 protein, a peptide,
a FTHMA-070, Tango85, Tango77, Tango129 or A259 peptidomimetic, or
other small molecule. In one embodiment, the agent stimulates one
or more of the biological activities of FTHMA-070, Tango85,
Tango77, Tango129 or A259 protein. Examples of such stimulatory
agents include active FTHMA-070, Tango85, Tango77, Tango129 or A259
protein and a nucleic acid molecule encoding FTHMA-070, Tango85,
Tango77, Tango129 or A259 that has been introduced into the cell.
In another embodiment, the agent inhibits one or more of the
biological activities of FTHMA-070, Tango85, Tango77, Tango129 or
A259 protein. Examples of such inhibitory agents include antisense
FTHMA-070, Tango85, Tango77, Tango129 or A259 nucleic acid
molecules and anti-FTHMA-070, Tango85, Tango77, Tango129 or A259
antibodies. These modulatory methods can be performed in vitro
(e.g., by culturing the cell with the agent) or, alternatively, in
vivo (e.g, by administering the agent to a subject). As such, the
present invention provides methods of treating an individual
afflicted with a disease or disorder characterized by aberrant
expression or activity of a FTHMA-070, Tango85, Tango77, Tango129
or A259 protein or nucleic acid molecule. In one embodiment, the
method involves administering an agent (e.g., an agent identified
by a screening assay described herein), or combination of agents
that modulates (e.g., upregulates or down-regulates) FTHMA-070,
Tango85, Tango77, Tango129 or A259 expression or activity. In
another embodiment, the method involves administering a FTHMA-070,
Tango85, Tango77, Tango129 or A259 protein or nucleic acid molecule
as therapy to compensate for reduced or aberrant FTHMA-070,
Tango85, Tango77, Tango129 or A259 expression or activity.
[0984] Another aspect of the invention pertains to methods of
modulating SPOIL and/or IL-1 expression or activity for therapeutic
purposes. The modulatory method of the invention involves
contacting a cell with an agent that modulates one or more of the
activities of SPOIL and/or IL-1 associated with the cell or one or
more of the activities involved in inflammation, immune response,
or bone turnover. An agent that modulates SPOIL and/or IL-1
activity can be an agent as described herein, such as a SPOIL
modulator, a nucleic acid encoding a SPOIL protein or a SPOIL
protein, a SPOIL peptide, or SPOIL peptidomimetic. In one
embodiment, the agent stimulates one or more SPOIL and/or IL-1
protein activity. Examples of such stimulatory agents include SPOIL
variants which have SPOIL receptor and/or IL-1 receptor agonist
function or a nucleic acid molecule encoding such a SPOIL variant
that has been introduced into a cell. In another embodiment, the
agent inhibits one or more SPOIL and/or IL-1 activity. Examples of
such inhibitory agents include SPOIL proteins and nucleic acid
molecules, mutant SPOIL proteins and nucleic acid molecules,
antisense SPOIL nucleic acid molecules and SPOIL antibodies. These
modulatory methods can be performed in vitro (e.g., by culturing
the cell with the agent) or, alternatively, in vivo (e.g, by
administering the agent to a subject). As such, the present
invention provides methods of treating an individual afflicted with
a disease or disorder characterized by aberrant SPOIL and/or IL-1
expression or activity. In one embodiment, the method involves
administering a SPOIL agent (e.g., an agent described herein), or
combination of agents that modulates (e.g., upregulates or
downregulates) SPOIL and/or IL-1 expression or activity. In another
embodiment, the method involves administering a SPOIL protein or
nucleic acid molecule as therapy to compensate for reduced SPOIL
expression or activity.
[0985] Another aspect of the invention pertains to methods of
modulating NEOKINE or chemokine expression or activity for
therapeutic purposes. It has been determined that NEOKINE-1 is
strongly expressed in the kidney. This expression of NEOKINE-1
indicates that the NEOKINES have utility in treating kidney
inflammation, a major cause of renal failure in chronic and acute
renal failure and transplantation. It is known in the art that
expression of chemokines in the kidney is not only correlated with
inflammation pathology, but also that blocking chemokine action by
anti-chemokine antibodies limits or halts progression of the
inflammation and resulting tissue damage. The fact that normal
human kidney expresses abundant NEOKINE transcript suggests that
the kidney makes significant quantities of the protein and that
therefore the pro-inflammatory activity low or non-existent. This
is consistent with the proposed natural antagonist function of the
NEOKINE proteins. Furthermore, signal peptide cleavage prediction
on NEOKINE implies that the mature protein will have only two
residues before the first cysteine. In an analogous situation, an
artificially truncated form of IL-8 with only one residue before
the first cysteine instead of the naturally-occurring 6 residues
converts the protein from an agonist to an antagonist.
[0986] Accordingly, in an exemplary embodiment, the modulatory
method of the invention involves contacting a cell with a NEOKINE
such that the activity of a chemokine is modulated. Alternatively,
the modulatory method of the invention involves contacting a cell
with a NEOKINE or agent that modulates one or more of the
activities of NEOKINE protein activity associated with the cell. An
agent that modulates NEOKINE protein activity can be an agent as
described herein, such as a nucleic acid or a protein, a
naturally-occurring target molecule of a NEOKINE protein (e.g., a
carbohydrate), a NEOKINE antibody, a NEOKINE agonist or antagonist,
a peptidomimetic of a NEOKINE agonist or antagonist, or other small
molecule. In one embodiment, the agent stimulates one or more
NEOKINE activities. Examples of such stimulatory agents include
active NEOKINE protein and a nucleic acid molecule encoding NEOKINE
that has been introduced into the cell. In another embodiment, the
agent inhibits one or more NEOKINE activities. Examples of such
inhibitory agents include antisense NEOKINE nucleic acid molecules
and anti-NEOKINE antibodies. These modulatory methods can be
performed in vitro (e.g., by culturing the cell with the agent) or,
alternatively, in vivo (e.g, by administering the agent to a
subject). As such, the present invention provides methods of
treating an individual afflicted with a disease or disorder
characterized by aberrant expression or activity of a NEOKINE
protein or nucleic acid molecule. Alternatively, the present
invention provides methods of treating an individual afflicted with
a disease or disorder characterized by aberrant expression or
activity of a chemokine. In one embodiment, the method involves
administering an agent (e.g., an agent identified by a screening
assay described herein), or combination of agents that modulates
(e.g., upregulates or downregulates) NEOKINE expression or activity
or the expression or activity of a chemokine. In another
embodiment, the method involves administering a NEOKINE protein or
nucleic acid molecule as therapy to compensate for reduced or
aberrant NEOKINE expression or activity. In another embodiment, the
method involves administering a NEOKINE protein or nucleic acid
molecule as therapy to compensate for reduced or aberrant chemokine
expression or activity.
[0987] A preferred embodiment of the present invention involves a
method for treatment of a SPOIL or NEOKINE associated disease or
disorder which includes the step of administering a therapeutically
effective amount of a SPOIL or NEOKINE antibody to a subject. As
defined herein, a therapeutically effective amount of antibody
(i.e., an effective dosage) ranges from about 0.001 to 30 mg/kg
body weight, preferably about 0.01 to 25 mg/kg body weight, more
preferably about 0.1 to 20 mg/kg body weight, and even more
preferably about 1 to 10 mg/kg, 2 to 9 mg/kg, 3 to 8 mg/kg, 4 to 7
mg/kg, or 5 to 6 mg/kg body weight. The skilled artisan will
appreciate that certain factors may influence the dosage required
to effectively treat a subject, including but not limited to the
severity of the disease or disorder, previous treatments, the
general health and/or age of the subject, and other diseases
present. Moreover, treatment of a subject with a therapeutically
effective amount of an antibody can include a single treatment or,
preferably, can include a series of treatments. In a preferred
example, a subject is treated with antibody in the range of between
about 0.1 to 20 mg/kg body weight, one time per week for between
about 1 to 10 weeks, preferably between 2 to 8 weeks, more
preferably between about 3 to 7 weeks, and even more preferably for
about 4, 5, or 6 weeks. It will also be appreciated that the
effective dosage of antibody used for treatment may increase or
decrease over the course of a particular treatment. Changes in
dosage may result from the results of diagnostic assays as
described herein.
[0988] Stimulation of FTHMA-070, Tango85, Tango77, Tango129 or A259
activity is desirable in situations in which FTHMA-070, Tango85,
Tango77, Tango129 or A259 is abnormally downregulated and/or in
which increased FTHMA-070, Tango85, Tango77, Tango129 or A259
activity is likely to have a beneficial effect. Conversely,
inhibition of FTHMA-070, Tango85, Tango77, Tango129 or A259
activity is desirable in situations in which FTHMA-070, Tango85,
Tango77, Tango129 or A259 is abnormally upregulated and/or in which
decreased FTHMA-070, Tango85, Tango77, Tango129 or A259 activity is
likely to have a beneficial effect.
[0989] Stimulation of expression or activity is desirable in
situations in which SPOIL and/or IL-1 is abnormally downregulated
and/or in which increased expression or activity is likely to have
a beneficial effect. Likewise, inhibition of expression or activity
is desirable in situations in which SPOIL and/or IL-1 is abnormally
upregulated and/or in which decreased expression or activity is
likely to have a beneficial effect. One example of such a situation
is where a subject has a disorder characterized by aberrant
cellular differentiation (e.g., a bone resorption disorder).
Another example of such a situation is where the subject has a
proinflammatory disorder (e.g., sepsis) characterized by an
aberrant SPOIL and/or IL-1 response.
[0990] Stimulation of NEOKINE activity is desirable in situations
in which NEOKINE is abnormally downregulated and/or in which
increased NEOKINE activity is likely to have a beneficial effect.
For example, stimulation of NEOKINE activity is desirable in
situations in which a chemokine is upregulated and/or in which
increased NEOKINE activity is likely to have a beneficial effect
(e.g., a situation is where a subject has a disorder characterized
by aberrant angiogenesis or inflammation, such as kidney
inflammation. Likewise, inhibition of NEOKINE activity is desirable
in situations in which NEOKINE is abnormally upregulated and/or in
which decreased NEOKINE activity is likely to have a beneficial
effect.
Delta3 Diagnostic and Prognostic Assays
[0991] The present methods provides means for determining if a
subject is at risk of developing a disorder characterized by an
aberrant Delta3 activity, such as aberrant cell proliferation,
degeneration, and/or differentiation resulting for example in a
neurodegenerative disease or cancer. The invention also provides
methods for determining whether a subject is at risk of developing
a disease or disorder associated with one or more specific alleles
of a Delta3 gene. In fact, specific Delta3 alleles may be
associated with specific diseases or disorders. For example, at
least one allele of hDelta3 is likely to be associated with the
neurological disease ACCPN. Accordingly, the invention provides
methods for determining whether a subject has or is at risk of
developing a neurological disease, e.g., ACCPN. In another
embodiment, the invention provides methods for determining whether
a subject has or is at risk of developing a vascular disorder or a
disorder associated with cell fate determination. In one
embodiment, the invention comprises determining the identity of the
Delta3 allele in a subject and comparing the molecular structure of
the Delta3 gene of the subject with the molecular structure of a
Delta3 gene from a subject which does not have the neurological
disease. Determining the molecular structure can be, e.g.,
determining the identity of at least one nucleotide, determining
the nucleotide composition or determining the methylation pattern
of the gene.
[0992] In one embodiment, the invention provides a method for
determining whether a subject has genetic lesion in a Delta3 gene
or a specific allelic variant of a polymorphic region in a Delta3
gene. The specific allele can be a mutant allele. In another
embodiment, the invention provides methods for determining whether
a subject has an aberrant Delta3 protein, resulting from aberrant
post-translational modifications of the protein, such as aberrant
phosphorogulation or glycosylation. Also, within the scope of the
invention are methods for determining whether a subject has an
aberrant expression level of a Delta3 protein, which could be due
to a genetic lesion in the Delta3 gene or due to an aberrant level
or activity of a protein regulating the expression of a Delta3
gene.
[0993] In preferred embodiments, the methods can be characterized
as comprising detecting, in a sample of cells from the subject, the
presence or absence of a genetic lesion characterized by at least
one of (i) an alteration affecting the integrity of a gene encoding
a Delta-protein, or (ii) the mis-expression of a Delta3 gene. To
illustrate, such genetic lesions can be detected by ascertaining
the existence of at least one of (i) a deletion of one or more
nucleotides from a Delta3 gene, (ii) an addition of one or more
nucleotides to a Delta3 gene, (iii) a substitution of one or more
nucleotides of a Delta3 gene, (iv) a gross chromosomal
rearrangement of a Delta3 gene, (v) a gross alteration in the level
of a messenger RNA transcript of a Delta3 gene, (vii) aberrant
modification of a Delta3 gene, such as of the methylation pattern
of the genomic DNA, (vii) the presence of a non-wild type splicing
pattern of a messenger RNA transcript of a Delta3 gene, (viii) a
non-wild type level of a Delta-protein, (ix) allelic loss of a
Delta3 gene, and (x) inappropriate post-translational modification
of a Delta-protein. As set out below, the present invention
provides a large number of assay techniques for detecting lesions
in a Delta3 gene, and importantly, provides the ability to discern
between different molecular causes underlying Delta-dependent
aberrant cell proliferation and/or differentiation.
[0994] For determining whether a subject has or is at risk of
developing a disease or condition associated with a specific allele
of a Delta3 gene, preliminary experiments can be performed to
determine the identity of the allele associated with a disease. For
example, for determining the identity of the hDelta3 allele
associated with ACCPN, one can perform mutation detection studies
of the Delta3 gene in populations having a high risk of developing
ACCPN. For example, one can perform mutation detection analysis of
the genomic DNA from subjects in the French Canadian population in
the Charlevoix and Saguenay-Lac St Jean regions of the province of
Quebec (Casaubon et al. (1996) Am. J. Hum. Genet. 58:28). Such an
analysis will reveal the identity of the Delta3 allele or alleles
associated with ACCPN. Comparison of the Delta3 allele of a subject
with this allele or alleles associated with ACCPN will indicate
whether a subject has a Delta3 allele associated with ACCPN and
thus whether the subject has or is likely to develop ACCPN.
Similarly, mutation detection analysis can also be carried out to
determine the identity of Delta3 alleles associated with other
diseases or conditions.
[0995] In an exemplary embodiment, there is provided a nucleic acid
composition comprising a (purified) oligonucleotide probe including
a region of nucleotide sequence which is capable of hybridizing to
a sense or antisense sequence of a Delta3 gene, such as represented
by any of SEQ ID NOs: 1, 3, 24, 26, 27, 29, 31, 33, 35, 37, 39, 41,
43 or 45, alleles thereof, naturally-occurring mutants thereof, or
5' or 3' flanking sequences or intronic sequences naturally
associated with the subject Delta3 genes or naturally-occurring
mutants thereof. The nucleic acid of a cell is rendered accessible
for hybridization, the probe is exposed to nucleic acid of the
sample, and the hybridization of the probe to the sample nucleic
acid is detected. Such techniques can be used to detect lesions at
either the genomic or mRNA level, including deletions,
substitutions, etc., as well as to determine mRNA transcript
levels.
[0996] As set out above, one aspect of the present invention
relates to diagnostic assays for determining, in the context of
cells isolated from a patient, if mutations have arisen in one or
more Delta3 genes of the sample cells. The present method provides
a method for determining if a subject is at risk for a disorder
characterized by aberrant Delta3 activity, e.g., cell proliferation
and/or differentiation. In preferred embodiments, the method can be
generally characterized as comprising detecting, in a sample of
cells from the subject, the presence or absence of a genetic lesion
characterized by an alteration affecting the integrity of a gene
encoding a Delta protein. To illustrate, such genetic lesions can
be detected by ascertaining the existence of at least one of (i) a
deletion of one or more nucleotides from a Delta-gene, (ii) an
addition of one or more nucleotides to a Delta-gene, (iii) a
substitution of one or more nucleotides of a Delta-gene, and (iv)
the presence of a non-wild type splicing pattern of a messenger RNA
transcript of a Delta-gene. As set out below, the present invention
provides a large number of assay techniques for detecting lesions
in Delta3 genes, and importantly, provides the ability to discern
between different molecular causes underlying Delta-dependent
aberrant cell proliferation and/or differentiation.
[0997] In certain embodiments, detection of the lesion in a Delta
gene or the identity of an allelic variant of a polymorphic region
of a Delta gene comprises utilizing the probe/primer in a
polymerase chain reaction (PCR) (see, e.g., U.S. Pat. Nos.
4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or,
alternatively, in a ligation chain reaction (LCR) (see, e.g.,
Landegran et al. (1988) Science 241:1077-1080; and Nakazawa et al.
(1994) PNAS 91:360-364), the latter of which can be particularly
useful for detecting point mutations in the Delta-gene (see
Abravaya et al. (1995) Nuc Acid Res 23:675-682). In a merely
illustrative embodiment, the method includes the steps of (i)
collecting a sample of cells from a patient, (ii) isolating nucleic
acid (e.g., genomic, mRNA or both) from the cells of the sample,
(iii) contacting the nucleic acid sample with one or more primers
which specifically hybridize to a Delta gene under conditions such
that hybridization and amplification of the Delta-gene (if present)
occurs, and (iv) detecting the presence or absence of an
amplification product, or detecting the size of the amplification
product and comparing the length to a control sample. It is
anticipated that PCR and/or LCR may be desirable to use as a
preliminary amplification step in conjunction with any of the
techniques used for detecting mutations described herein.
[0998] Alternative amplification methods include: self sustained
sequence replication (Guatelli, J. C. et al., 1990, Proc. Natl.
Acad. Sci. USA 87:1874-1878), transcriptional amplification system
(Kwoh, D. Y. et al., 1989, Proc. Natl. Acad. Sci. USA
86:1173-1177), Q-Beta Replicase (Lizardi, P. M. et al., 1988,
Bio/Technology 6:1197), or any other nucleic acid amplification
method, followed by the detection of the amplified molecules using
techniques well known to those of skill in the art. These detection
schemes are especially useful for the detection of nucleic acid
molecules if such molecules are present in very low numbers.
[0999] In a preferred embodiment of the subject assay, mutations in
a Delta3 gene or specific alleles of a Delta3 gene from a sample
cell are identified by alterations in restriction enzyme cleavage
patterns. For example, sample and control DNA is isolated,
amplified (optionally), digested with one or more restriction
endonucleases, and fragment length sizes are determined by gel
electrophoresis. Moreover, the use of sequence specific ribozymes
(see, for example, U.S. Pat. No. 5,498,531, incorporated herein by
reference in its entirety) can be used to score for the presence of
specific mutations by development or loss of a ribozyme cleavage
site.
[1000] In yet another embodiment, any of a variety of sequencing
reactions known in the art can be used to directly sequence the
Delta3 gene and detect mutations or allelic variants of polymorphic
regions by comparing the sequence of the sample Delta3 with the
corresponding wild-type (control) sequence. Exemplary sequencing
reactions include those based on techniques developed by Maxim and
Gilbert (Proc. Natl. Acad Sci USA (1977) 74:560) or Sanger (Sanger
et al (1977) Proc. Nat. Acad. Sci. 74:5463). It is also
contemplated that any of a variety of automated sequencing
procedures may be utilized when performing the subject assays
(Biotechniques (1995) 19:448), including by sequencing by mass
spectrometry (see, for example PCT publication WO 94/16101; Cohen
et al. (1996) Adv Chromatogr 36:127-162; and Griffin et al. (1993)
Appl Biochem Biotechnol 38:147-159). It will be evident to one
skilled in the art that, for certain embodiments, the occurrence of
only one, two or three of the nucleic acid bases need be determined
in the sequencing reaction. For instance, A-tract or the like,
e.g., where only one nucleic acid is detected, can be carried
out.
[1001] In a further embodiment, protection from cleavage agents
(such as a nuclease, hydroxylamine or osmium tetroxide and with
piperidine) can be used to detect mismatched bases in RNA/RNA or
RNA/DNA heteroduplexes (Myers, et al. (1985) Science 230:1242). In
general, the art technique of "mismatch cleavage" starts by
providing heteroduplexes of formed by hybridizing (labeled) RNA or
DNA containing the wild-type Delta3 sequence with potentially
mutant RNA or DNA obtained from a tissue sample. The
double-stranded duplexes are treated with an agent which cleaves
single-stranded regions of the duplex such as which will exist due
to basepair mismatches between the control and sample strands. For
instance, RNA/DNA duplexes can be treated with RNase and DNA/DNA
hybrids treated with S1 nuclease to enzymatically digesting the
mismatched regions. In other embodiments, either DNA/DNA or RNA/DNA
duplexes can be treated with hydroxylamine or osmium tetroxide and
with piperidine in order to digest mismatched regions. After
digestion of the mismatched regions, the resulting material is then
separated by size on denaturing polyacrylamide gels to determine
the site of mutation. See, for example, Cotton et al (1988) Proc.
Natl. Acad Sci USA 85:4397; Saleeba et al (1992) Methods Enzymod.
217:286-295. In a preferred embodiment, the control DNA or RNA can
be labeled for detection.
[1002] In still another embodiment, the mismatch cleavage reaction
employs one or more proteins that recognize mismatched base pairs
in double-stranded DNA (so called "DNA mismatch repair" enzymes) in
defined systems for detecting and mapping point mutations in Delta3
cDNAs obtained from samples of cells. For example, the mutY enzyme
of E. coli cleaves A at G/A mismatches and the thymidine DNA
glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al.
(1994) Carcinogenesis 15:1657-1662). According to an exemplary
embodiment, a probe based on a Delta3 sequence, e.g., a wild-type
Delta3 sequence, is hybridized to a cDNA or other DNA product from
a test cell(s). The duplex is treated with a DNA mismatch repair
enzyme, and the cleavage products, if any, can be detected from
electrophoresis protocols or the like. See, for example, U.S. Pat.
No. 5,459,039, incorporated herein by reference in its
entirety.
[1003] In other embodiments, alterations in electrophoretic
mobility will be used to identify mutations in Delta3 genes or for
determining the identity of the Delta3 allele. For example, single
strand conformation polymorphism (SSCP) may be used to detect
differences in electrophoretic mobility between mutant and wild
type nucleic acids (Orita et al. (1989) Proc Natl. Acad. Sci. USA
86:2766, see also Cotton (1993) Mutat Res 285:125-144; and Hayashi
(1992) Genet Anal Tech Appl 9:73-79). Single-stranded DNA fragments
of sample and control Delta3 nucleic acids will be denatured and
allowed to renature. The secondary structure of single-stranded
nucleic acids varies according to sequence, the resulting
alteration in electrophoretic mobility enables the detection of
even a single base change. The DNA fragments may be labelled or
detected with labelled probes. The sensitivity of the assay may be
enhanced by using RNA (rather than DNA), in which the secondary
structure is more sensitive to a change in sequence. In a preferred
embodiment, the subject method utilizes heteroduplex analysis to
separate double stranded heteroduplex molecules on the basis of
changes in electrophoretic mobility (Keen et al. (1991) Trends
Genet 7:5).
[1004] In yet another embodiment the movement of mutant or
wild-type fragments in polyacrylamide gels containing a gradient of
denaturant is assayed using denaturing gradient gel electrophoresis
(DGGE) (Myers et al (1985) Nature 313:495). When DGGE is used as
the method of analysis, DNA will be modified to insure that it does
not completely denature, for example by adding a GC clamp of
approximately 40 bp of high-melting GC-rich DNA by PCR. In a
further embodiment, a temperature gradient is used in place of a
denaturing agent gradient to identify differences in the mobility
of control and sample DNA (Rosenbaum and Reissner (1987) Biophys
Chem 265:12753).
[1005] Examples of other techniques for detecting point mutations
include, but are not limited to, selective oligonucleotide
hybridization, selective amplification, or selective primer
extension. For example, oligonucleotide primers may be prepared in
which the known mutation is placed centrally and then hybridized to
target DNA under conditions which permit hybridization only if a
perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki
et al (1989) Proc. Natl. Acad. Sci. USA 86:6230). Such allele
specific oligonucleotide hybridization techniques may be used to
test one mutation per reaction when oligonucleotides are hybridized
to PCR amplified target DNA or a number of different mutations when
the oligonucleotides are attached to the hybridizing membrane and
hybridized with labeled target DNA.
[1006] Alternatively, allele specific amplification technology
which depends on selective PCR amplification may be used in
conjunction with the instant invention. Oligonucleotides used as
primers for specific amplification may carry the mutation of
interest in the center of the molecule (so that amplification
depends on differential hybridization) (Gibbs et al (1989) Nucleic
Acids Res. 17:2437-2448) or at the extreme 3' end of one primer
where, under appropriate conditions, mismatch can prevent, or
reduce polymerase extension (Prossner (1993) Tibtech 11:238. In
addition it may be desirable to introduce a novel restriction site
in the region of the mutation to create cleavage-based detection
(Gasparini et al. (1992) Mol. Cell. Probes 6:1). It is anticipated
that in certain embodiments amplification may also be performed
using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad.
Sci. USA 88:189). In such cases, ligation will occur only if there
is a perfect match at the 3' end of the 5' sequence making it
possible to detect the presence of a known mutation at a specific
site by looking for the presence or absence of amplification.
[1007] Another embodiment of the invention provides for a nucleic
acid composition comprising a (purified) oligonucleotide probe
including a region of nucleotide sequence which is capable of
hybridizing to a sense or antisense sequence of a Delta-gene, or
naturally-occurring mutants thereof, or 5' or 3' flanking sequences
or intronic sequences naturally associated with the subject
Delta-genes or naturally-occurring mutants thereof. The nucleic
acid of a cell is rendered accessible for hybridization, the probe
is exposed to nucleic acid of the sample, and the hybridization of
the probe to the sample nucleic acid is detected. Such techniques
can be used to detect lesions at either the genomic or mRNA level,
including deletions, substitutions, etc., as well as to determine
mRNA transcript levels. Such oligonucleotide probes can be used for
both predictive and therapeutic evaluation of allelic mutations
which might be manifest in, for example, a neurodegenerative,
neoplastic or hyperplastic disorders (e.g., aberrant cell
growth).
[1008] The methods described herein may be performed, for example,
by utilizing pre-packaged diagnostic kits comprising at least one
probe nucleic acid or antibody reagent described herein, which may
be conveniently used, e.g., in clinical settings to diagnose
patients exhibiting symptoms or family history of a disease or
illness involving a Delta3 gene.
[1009] Any cell type or tissue, preferably neural or endothelial
cells, in which the Delta3 is expressed may be utilized in the
diagnostics described below. For example, a subject's bodily fluid
(e.g., blood) can be obtained by known techniques (e.g.,
venipuncture). Alternatively, nucleic acid tests can be performed
on dry samples (e.g., hair or skin). Fetal nucleic acid samples can
be obtained from maternal blood as described in International
Patent Application NO: WO91/07660 to Bianchi. Alternatively,
amniocytes or chorionic villi may be obtained for performing
prenatal testing, e.g., of ACCPN, which is a disease which is
usually fatal in the third decade of life.
[1010] Diagnostic procedures may also be performed in situ directly
upon tissue sections (fixed and/or frozen) of patient tissue
obtained from biopsies or resections, such that no nucleic acid
purification is necessary. Nucleic acid reagents may be used as
probes and/or primers for such in situ procedures (see, for
example, Nuovo, G. J., 1992, PCR in situ hybridization: protocols
and applications, Raven Press, NY).
[1011] In addition to methods which focus primarily on the
detection of one nucleic acid sequence, profiles may also be
assessed in such detection schemes. Fingerprint profiles may be
generated, for example, by utilizing a differential display
procedure, Northern analysis and/or RT-PCR.
[1012] Antibodies directed against wild type or mutant Delta3
proteins, which are discussed, above, may also be used in disease
diagnostics and prognostics. Such diagnostic methods, may be used
to detect abnormalities in the level of Delta3 protein expression,
or abnormalities in the structure and/or tissue, cellular, or
subcellular location of Delta3 proteins. Structural differences may
include, for example, differences in the size, electronegativity,
or antigenicity of the mutant Delta3 protein relative to the normal
Delta3 protein. Protein from the tissue or cell type to be analyzed
may easily be detected or isolated using techniques which are well
known to one of skill in the art, including but not limited to
western blot analysis. For a detailed explanation of methods for
carrying out western blot analysis, see Sambrook et al, 1989,
supra, at Chapter 18. The protein detection and isolation methods
employed herein may also be such as those described in Harlow and
Lane, for example, (Harlow, E. and Lane, D., 1988, "Antibodies: A
Laboratory Manual", Cold Spring Harbor Laboratory Press, Cold
Spring Harbor, N.Y.).
[1013] This can be accomplished, for example, by immunofluorescence
techniques employing a fluorescently labeled antibody (see below)
coupled with light microscopic, flow cytometric, or fluorimetric
detection. The antibodies (or fragments thereof) useful in the
present invention may, additionally, be employed histologically, as
in immunofluorescence or immunoelectron microscopy, for in situ
detection of Delta3 proteins. In situ detection may be accomplished
by removing a histological specimen from a patient, and applying
thereto a labeled antibody of the present invention. The antibody
(or fragment) is preferably applied by overlaying the labeled
antibody (or fragment) onto a biological sample. Through the use of
such a procedure, it is possible to determine not only the presence
of the Delta3 protein, but also its distribution in the examined
tissue. Using the present invention, one of ordinary skill will
readily perceive that any of a wide variety of histological methods
(such as staining procedures) can be modified in order to achieve
such in situ detection.
[1014] Often a solid phase support or carrier is used as a support
capable of binding an antigen or an antibody. Well-known supports
or carriers include glass, polystyrene, polypropylene,
polyethylene, dextran, nylon, amylases, natural and modified
celluloses, polyacrylamides, gabbros, and magnetite. The nature of
the carrier can be either soluble to some extent or insoluble for
the purposes of the present invention. The support material may
have virtually any possible structural configuration so long as the
coupled molecule is capable of binding to an antigen or antibody.
Thus, the support configuration may be spherical, as in a bead, or
cylindrical, as in the inside surface of a test tube, or the
external surface of a rod. Alternatively, the surface may be flat
such as a sheet, test strip, etc. Preferred supports include
polystyrene beads. Those skilled in the art will know many other
suitable carriers for binding antibody or antigen, or will be able
to ascertain the same by use of routine experimentation.
[1015] One means for labeling an anti-Delta3 protein specific
antibody is via linkage to an enzyme and use in an enzyme
immunoassay (EIA) (Voller, "The Enzyme Linked Immunosorbent Assay
(ELISA)", Diagnostic Horizons 2:1-7, 1978, Microbiological
Associates Quarterly Publication, Walkersville, Md.; Voller, et
al., J. Clin. Pathol. 31:507-520 (1978); Butler, Meth. Enzymol.
73:482-523 (1981); Maggio, (ed.) Enzyme Immunoassay, CRC Press,
Boca Raton, Fla., 1980; Ishikawa, et al., (eds.) Enzyme
Immunoassay, Kgaku Shoin, Tokyo, 1981). The enzyme which is bound
to the antibody will react with an appropriate substrate,
preferably a chromogenic substrate, in such a manner as to produce
a chemical moiety which can be detected, for example, by
spectrophotometric, fluorimetric or by visual means. Enzymes which
can be used to detectably label the antibody include, but are not
limited to, malate dehydrogenase, staphylococcal nuclease,
delta-5-steroid isomerase, yeast alcohol dehydrogenase,
alpha-glycerophosphate, dehydrogenase, triose phosphate isomerase,
horseradish peroxidase, alkaline phosphatase, asparaginase, glucose
oxidase, beta-galactosidase, ribonuclease, urease, catalase,
glucose-6-phosphate dehydrogenase, glucoamylase and
acetylcholinesterase. The detection can be accomplished by
colorimetric methods which employ a chromogenic substrate for the
enzyme. Detection may also be accomplished by visual comparison of
the extent of enzymatic reaction of a substrate in comparison with
similarly prepared standards.
[1016] Detection may also be accomplished using any of a variety of
other immunoassays. For example, by radioactively labeling the
antibodies or antibody fragments, it is possible to detect
fingerprint gene wild type or mutant peptides through the use of a
radioimmunoassay (RIA) (see, for example, Weintraub, B., Principles
of Radioimmunoassays, Seventh Training Course on Radioligand Assay
Techniques, The Endocrine Society, March, 1986). The radioactive
isotope can be detected by such means as the use of a gamma counter
or a scintillation counter or by autoradiography.
[1017] It is also possible to label the antibody with a fluorescent
compound. When the fluorescently labeled antibody is exposed to
light of the proper wave length, its presence can then be detected
due to fluorescence. Among the most commonly used fluorescent
labeling compounds are fluorescein isothiocyanate, rhodamine,
phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and
fluorescamine.
[1018] The antibody can also be detectably labeled using
fluorescence emitting metals such as 152Eu, or others of the
lanthanide series. These metals can be attached to the antibody
using such metal chelating groups as diethylenetriaminepentacetic
acid (DTPA) or ethylenediaminetetraacetic acid (EDTA).
[1019] The antibody also can be detectably labeled by coupling it
to a chemiluminescent compound. The presence of the
chemiluminescent-tagged antibody is then determined by detecting
the presence of luminescence that arises during the course of a
chemical reaction. Examples of particularly useful chemiluminescent
labeling compounds are luminol, isoluminol, theromatic acridinium
ester, imidazole, acridinium salt and oxalate ester.
[1020] Likewise, a bioluminescent compound may be used to label the
antibody of the present invention. Bioluminescence is a type of
chemiluminescence found in biological systems in, which a catalytic
protein increases the efficiency of the chemiluminescent reaction.
The presence of a bioluminescent protein is determined by detecting
the presence of luminescence. Important bioluminescent compounds
for purposes of labeling are luciferin, luciferase and
aequorin.
[1021] Moreover, it will be understood that any of the above
methods for detecting alterations in a Delta3 gene or gene product
can be used to monitor the course of treatment or therapy.
Delta3 Drug Screening Assays
[1022] The invention provides for compounds, e.g., therapeutic
compounds, for treating diseases or conditions caused by, or
contributed to by an abnormal Delta3 activity. The compounds that
can be used for this purpose can be any type of compound, including
a protein, a peptide, peptidomimetic, small molecule, and nucleic
acid. A nucleic acid can be, e.g., a gene, an antisense nucleic
acid, a ribozyme, or a triplex molecule. A compound of the
invention can be an agonist or an antagonist. A compound can act on
a Delta3 gene, e.g., to modulate its expression. A compound can
also act on a Delta3 protein, e.g., to modulate signal transduction
from the receptor. Accordingly, a compound of the invention can be
a compound which binds to Delta3 and induces signal transduction
from the receptor, such that, e.g., a Delta3 activity is induced.
Alternatively, a compound of the invention can be a compound which
inhibits interaction of a Delta3 protein with a toporythmic
protein, e.g., Notch. In one embodiment, a compound of the
invention which interacts with a Delta protein, which is either an
agonist or an antagonist, is a toporythmic protein or other protein
interacting with Delta3. In an even more preferred embodiment, the
compound is a soluble toporythmic protein or other protein
interacting with Delta3. For example, a soluble antagonistic
toporythmic protein can be a protein which competes with the wild
type toporythmic proteins for binding to Delta3. A soluble
agonistic toporythmic protein can be a protein which binds to a
Delta3 protein in essentially the same manner as a wild-type
toporythmic protein, such as to induce at least one Delta3
activity, e.g., signal transduction from the Delta3 protein.
Accordingly, a soluble toporythmic protein can be stimulatory form
of a toporythmic protein or an inhibitory form of a toporythmic,
depending on whether the particular toporythmic protein stimulates
or inhibits a Delta3 activity.
[1023] Similarly, a soluble Delta3 protein, e.g., Delta3-Ig, can be
used to modulate an activity of a toporythmic protein, e.g., Notch.
For example, a soluble Delta3 protein can be a stimulatory form of
a Delta3 protein, i.e., a Delta3 protein which is capable of
stimulating an activity of a toporythmic protein. In one
embodiment, such a protein acts in essentially the same manner as
wild-type Delta3. In another embodiment, a soluble Delta3 protein
is an inhibitory form of a Delta3 protein, i.e., a Delta3 protein
which is capable of inhibiting an activity of a toporythmic
protein. For example, such a Delta3 protein could inhibit the
interaction of wild-type Delta3 with the toporythmic protein. In a
preferred embodiment, an inhibitory form of a Delta3 protein
inhibits the interaction of several proteins which normally
interact with a toporythmic protein, by, e.g., binding to a site of
the toporythmic protein that is also a binding site to various
other proteins, e.g., other Delta proteins. Accordingly, a Delta3
therapeutic can generally affect the interaction of various
toporythmic proteins with each other. Similarly, based at least in
part on the sequence and structural similarities between Delta
proteins, a Delta therapeutic, other than a Delta3 therapeutic, can
also be used for modulating the interaction between a Delta3
protein and a Delta3 interacting binding molecule.
[1024] The compounds of the invention can be identified using
various assays depending on the type of compound and activity of
the compound that is desired. Set forth below are at least some
assays that can be used for identifying Delta3 therapeutics. It is
within the skill of the art to design additional assays for
identifying Delta therapeutics, e.g., Delta3 therapeutics.
[1025] By making available purified and recombinant Delta3
polypeptides, the present invention facilitates the development of
assays which can be used to screen for drugs, including Delta3
variants, which are either agonists or antagonists of the normal
cellular function of the subject Delta3 polypeptides, or of their
role in the pathogenesis of cellular differentiation and/or
proliferation and disorders related thereto. In one embodiment, the
assay evaluates the ability of a compound to modulate binding
between a Delta3 polypeptide and a molecule, be it protein or DNA,
that interacts either upstream or downstream of the Delta/Notch
signaling pathway. A variety of assay formats will suffice and, in
light of the present inventions, will be comprehended by a skilled
artisan.
Delta3 Cell-Free Assays
[1026] Cell free assays can be used to identify compounds which
interact with a Delta3 protein. Such assays are available for
testing compounds which are proteins, e.g., toporythmic proteins or
variants thereof, as well as for testing compounds which are
peptidomimetics, small molecules or nucleic acids. The specific
assay used for testing these compounds may vary with the type of
compound.
[1027] In one embodiment, a compound that interacts with a Delta3
protein is identified by screening, e.g., a library of compounds,
for binding to a recombinant or purified Delta3 protein or at least
a portion thereof. Such assays can involve labeling one or the two
components and measuring the extent of their interaction, by, e.g.,
determining the level of the one or two labels. In these assays, it
may be preferable to attach the Delta3 protein to a solid phase
surface. Methods for achieving this are further described infra. In
one embodiment, the library of compounds is a library of small
molecules. In another embodiment, the library of compounds is a
library of Delta3 variants, which can be produced according to
methods described infra.
[1028] Identification of a compound which inhibits an interaction
between a Delta3 protein and a toporythmic protein can also be
performed by screening compounds using aggregation assays, as
described, e.g., in Fehon et al. (1990) Cell 61:523-534.
[1029] In another embodiment, the invention provides methods for
identifying compounds which inhibit the interaction of a Delta3
protein with a molecule, e.g., a toporythmic protein or a protein
interacting with the cytoplasmic domain of a Delta3 protein. Such
methods, which are preferably used in high throughput assays can be
performed as follows.
[1030] In many drug screening programs which test libraries of
compounds and natural extracts, high throughput assays are
desirable in order to maximize the number of compounds surveyed in
a given period of time. Assays which are performed in cell-free
systems, such as may be derived with purified or semi-purified
proteins, are often preferred as "primary" screens in that they can
be generated to permit rapid development and relatively easy
detection of an alteration in a molecular target which is mediated
by a test compound. Moreover, the effects of cellular toxicity
and/or bioavailability of the test compound can be generally
ignored in the in vitro system, the assay instead being focused
primarily on the effect of the drug on the molecular target as may
be manifest in an alteration of binding affinity with upstream or
downstream elements. Accordingly, in an exemplary screening assay
of the present invention, the compound of interest is contacted
with proteins which may function upstream (including both
activators and repressors of its activity) or to proteins or
nucleic acids which may function downstream of the Delta3
polypeptide, whether they are positively or negatively regulated by
it. For example, a protein functioning upstream of a Delta3
polypeptide can be a compound interacting with the extracellular
portion of the Delta3 molecule. A protein functioning downstream of
a Delta3 polypeptide can be a protein interacting with the
cytoplasmic domain of Delta3 and, e.g., transducing a signal to the
nucleus. To the mixture of the compound and the upstream or
downstream element is then added a composition containing a Delta3
polypeptide. Detection and quantification of complexes of Delta3
with it's upstream or downstream elements provide a means for
determining a compound's efficacy at inhibiting (or potentiating)
complex formation between Delta3 and the Delta-binding elements.
The efficacy of the compound can be assessed by generating dose
response curves from data obtained using various concentrations of
the test compound. Moreover, a control assay can also be performed
to provide a baseline for comparison. In the control assay,
isolated and purified Delta3 polypeptide is added to a composition
containing the Delta-binding element, and the formation of a
complex is quantitated in the absence of the test compound.
[1031] Complex formation between the Delta3 polypeptide and a
Delta3 binding element may be detected by a variety of techniques.
Modulation of the formation of complexes can be quantitated using,
for example, detectably labeled proteins such as radiolabeled,
fluorescently labeled, or enzymatically labeled Delta3
polypeptides, by immunoassay, or by chromatographic detection.
[1032] Typically, it will be desirable to immobilize either Delta3
or its binding protein to facilitate separation of complexes from
uncomplexed forms of one or both of the proteins, as well as to
accommodate automation of the assay. Binding of Delta3 to an
upstream or downstream element, in the presence and absence of a
candidate agent, can be accomplished in any vessel suitable for
containing the reactants. Examples include microtitre plates, test
tubes, and micro-centrifuge tubes. In one embodiment, a fusion
protein can be provided which adds a domain that allows the protein
to be bound to a matrix. For example,
glutathione-S-transferase/Delta3 (GST/Delta) fusion proteins can be
adsorbed onto glutathione sepharose beads (Sigma Chemical, St.
Louis, Mo.) or glutathione derivatized microtitre plates, which are
then combined with the cell lysates, e.g., an .sup.35S-labeled, and
the test compound, and the mixture incubated under conditions
conducive to complex formation, e.g., at physiological conditions
for salt and pH, though slightly more stringent conditions may be
desired. Following incubation, the beads are washed to remove any
unbound label, and the matrix immobilized and radiolabel determined
directly (e.g., beads placed in scintilant), or in the supernatant
after the complexes are subsequently dissociated. Alternatively,
the complexes can be dissociated from the matrix, separated by
SDS-PAGE, and the level of Delta-binding protein found in the bead
fraction quantitated from the gel using standard electrophoretic
techniques such as described in the appended examples.
[1033] Other techniques for immobilizing proteins on matrices are
also available for use in the subject assay. For instance, either
Delta3 or its cognate binding protein can be immobilized utilizing
conjugation of biotin and streptavidin. For instance, biotinylated
Delta3 molecules can be prepared from biotin-NHS
(N-hydroxy-succinimide) using techniques well known in the art
(e.g., biotinylation kit, Pierce Chemicals, Rockford, Ill.), and
immobilized in the wells of streptavidin-coated 96 well plates
(Pierce Chemical). Alternatively, antibodies reactive with Delta3
but which do not interfere with binding of upstream or downstream
elements can be derivatized to the wells of the plate, and Delta3
trapped in the wells by antibody conjugation. As above,
preparations of a Delta-binding protein and a test compound are
incubated in the Delta-presenting wells of the plate, and the
amount of complex trapped in the well can be quantitated. Exemplary
methods for detecting such complexes, in addition to those
described above for the GST-immobilized complexes, include
immunodetection of complexes using antibodies reactive with the
Delta3 binding element, or which are reactive with Delta3 protein
and compete with the binding element; as well as enzyme-linked
assays which rely on detecting an enzymatic activity associated
with the binding element, either intrinsic or extrinsic activity.
In the instance of the latter, the enzyme can be chemically
conjugated or provided as a fusion protein with the Delta-BP. To
illustrate, the Delta-BP can be chemically cross-linked or
genetically fused with horseradish peroxidase, and the amount of
polypeptide trapped in the complex can be assessed with a
chromogenic substrate of the enzyme, e.g., 3,3'-diamino-benzadine
terahydrochloride or 4-chloro-1-naphthol. Likewise, a fusion
protein comprising the polypeptide and glutathione-S-transferase
can be provided, and complex formation quantitated by detecting the
GST activity using 1-chloro-2,4-dinitrobenzene (Habig et al (1974)
J Biol Chem 249:7130).
[1034] For processes which rely on immunodetection for quantitating
one of the proteins trapped in the complex, antibodies against the
protein, such as anti-Delta3 antibodies, can be used.
Alternatively, the protein to be detected in the complex can be
"epitope tagged" in the form of a fusion protein which includes, in
addition to the Delta3 sequence, a second polypeptide for which
antibodies are readily available (e.g., from commercial sources).
For instance, the GST fusion proteins described above can also be
used for quantification of binding using antibodies against the GST
moiety. Other useful epitope tags include myc-epitopes (e.g., see
Ellison et al. (1991) J Biol Chem 266:21150-21157) which includes a
10-residue sequence from c-myc, as well as the pFLAG system
(International Biotechnologies, Inc.) or the pEZZ-protein A system
(Pharmacia, NJ).
Delta3 Cell Based Assays
[1035] In addition to cell-free assays, such as described above,
the readily available source of Delta3 proteins provided by the
present invention also facilitates the generation of cell-based
assays for identifying small molecule agonists/antagonists and the
like. For example, cells which are sensitive to bFGF/VEGF or
matrigel can be caused to overexpress a recombinant Delta3 protein
in the presence and absence of a test agent of interest, with the
assay scoring for modulation in Delta3 responses by the target cell
mediated by the test agent. As with the cell-free assays, agents
which produce a statistically significant change in Delta-dependent
responses (either inhibition or potentiation) can be identified. In
an illustrative embodiment, the expression or activity of a Delta3
is modulated in embryos or cells and the effects of compounds of
interest on the readout of interest (such as tissue
differentiation, proliferation, tumorigenesis) are measured. For
example, the expression of genes which are up- or down-regulated in
response to a Delta-dependent signal cascade can be assayed. In
preferred embodiments, the regulatory regions of such genes, e.g.,
the 5' flanking promoter and enhancer regions, are operably linked
to a detectable marker (such as luciferase) which encodes a gene
product that can be readily detected.
[1036] Exemplary cell lines may include endothelial cells such as
MVEC's and bovine aortic endothelial cells (BAEC's); as well as
generic mammalian cell lines such as HeLa cells and COS cells,
e.g., COS-7 (ATCC.RTM.# CRL-1651). Further, the transgenic animals
discussed herein may be used to generate cell lines, containing one
or more cell types involved in cardiovascular disease, that can be
used as cell culture models for this disorder. While primary
cultures derived from the transgenic animals of the invention may
be utilized, the generation of continuous cell lines is preferred.
For examples of techniques which may be used to derive a continuous
cell line from the transgenic animals, see Small et al., 1985, Mol.
Cell. Biol. 5:642-648.
[1037] In one embodiment, a test compound that modifies a Delta3
activity can be identified by incubating a cell having a Delta3
protein with the test compound and measuring signal transduction
from the Delta3 protein. Comparison of the signal transduction in
the cells incubated with or without the test compound will reveal
whether the test compound is a Delta3 therapeutic. Similarly, a
test compound that modifies a Delta3 activity can be identified by
incubating a cell having a Delta3 ligand with the test compound,
e.g., a Delta3 derived compound, and measuring signal transduction
from the Delta3 ligand. Comparison of the signal transduction in
the cells incubated with or without the test compound will reveal
whether the test compound is a Delta3 therapeutic.
[1038] In the event that the Delta3 proteins themselves, or in
complexes with other proteins, are capable of binding DNA and/or
modifying transcription of a gene, a transcriptional based assay
could be used, for example, in which a Delta3 responsive regulatory
sequence is operably linked to a detectable marker gene, e.g., a
luciferase gene. Similarly, Delta3 therapeutics could also be
identified by using an assay in which expression of genes that are
modulated upon binding of a Delta3 protein to a Delta3 ligand on a
cell is monitored. Genes that are responsive to interaction with a
Delta3 protein or Delta3 ligand can be identified according to
methods known in the art, e.g., differential hybridization or
differential display.
[1039] In another embodiment, a silicon-based device, called a
microphysiometer, can be used to detect and measure the response of
cells having a Delta3 protein to test compounds to identify Delta3
therapeutics. This instrument measures the rate at which cells
acidify their environment, which is indicative of cellular growth
and/or differentiation (McConnel et al. (1992) Science
257:1906).
[1040] Monitoring the influence of compounds on cells may be
applied not only in basic drug screening, but also in clinical
trials. In such clinical trials, the expression of a panel of genes
may be used as a "read out" of a particular drug's therapeutic
effect.
[1041] In yet another aspect of the invention, the subject Delta3
polypeptides can be used to generate a "two hybrid" assay (see, for
example, U.S. Pat. No. 5,283,317; Zervos et al. (1993) Cell
72:223-232; Madura et al. (1993) J Biol Chem 268:12046-12054;
Bartel et al. (1993) Biotechniques 14:920-924; Iwabuchi et al.
(1993) Oncogene 8:1693-1696; and Brent WO94/10300), for isolating
coding sequences for other cellular proteins which bind to or
interact with Delta3 ("Delta-binding proteins" or "Delta-bp"), such
as Notch, and the like.
[1042] Briefly, the two hybrid assay relies on reconstituting in
vivo a functional transcriptional activator protein from two
separate fusion proteins. In particular, the method makes use of
chimeric genes which express hybrid proteins. To illustrate, a
first hybrid gene comprises the coding sequence for a DNA-binding
domain of a transcriptional activator fused in frame to the coding
sequence for a Delta3 polypeptide. The second hybrid protein
encodes a transcriptional activation domain fused in frame to a
sample gene from a cDNA library. If the bait and sample hybrid
proteins are able to interact, e.g., form a Delta-dependent
complex, they bring into close proximity the two domains of the
transcriptional activator. This proximity is sufficient to cause
transcription of a reporter gene which is operably linked to a
transcriptional regulatory site responsive to the transcriptional
activator, and expression of the reporter gene can be detected and
used to score for the interaction of the Delta3 and sample
proteins. This system can be used to identify compounds which
modify, e.g., inhibit the interaction between a Delta3 protein and
another protein, by adding 1 test compound to a cell containing the
above-described plasmids. The effect of the test compound on the
reporter gene expression and then measured to determine the effect
of the test compound on the interaction.
[1043] In another embodiment, the invention provides arrays for
identifying compounds that can induce apoptosis of cells through a
Delta3 protein. Apoptotic arrays are known in the act and are
described, e.g., in Grimm et al. (1996) Proc. Natl. Acad. Sci. USA
93:10923.
Delta3 Detection Assays
[1044] Portions or fragments of the cDNA sequences identified
herein (and the corresponding complete gene sequences) can be used
in numerous ways as polynucleotide reagents. For example, these
sequences can be used to: (i) map their respective genes on a
chromosome and, thus, locate gene regions associated with genetic
disease; (ii) identify an individual from a minute biological
sample (tissue typing); and (iii) aid in forensic identification of
a biological sample. These applications are described in the
subsections below.
Delta3 Chromosome Mapping
[1045] Once the sequence (or a portion of the sequence) of a gene
has been isolated, this sequence can be used to map the location of
the gene on a chromosome. Accordingly, nucleic acid molecules
described herein or fragments thereof, can be used to map the
location of the corresponding genes on a chromosome. The mapping of
the sequences to chromosomes is an important first step in
correlating these sequences with genes associated with disease.
[1046] Briefly, genes can be mapped to chromosomes by preparing PCR
primers (preferably 15-25 bp in length) from the sequence of a gene
of the invention. Computer analysis of the sequence of a gene of
the invention can be used to rapidly select primers that do not
span more than one exon in the genomic DNA, thus complicating the
amplification process. These primers can then be used for PCR
screening of somatic cell hybrids containing individual human
chromosomes. Only those hybrids containing the human gene
corresponding to the gene sequences will yield an amplified
fragment. For a review of this technique, see D'Eustachio et al.
((1983) Science 220:919-924).
[1047] PCR mapping of somatic cell hybrids is a rapid procedure for
assigning a particular sequence to a particular chromosome. Three
or more sequences can be assigned per day using a single thermal
cycler. Using the nucleic acid sequences of the invention to design
oligonucleotide primers, sublocalization can be achieved with
panels of fragments from specific chromosomes. Other mapping
strategies which can similarly be used to map a gene to its
chromosome include in situ hybridization (described in Fan et al.
(1990) Proc. Natl. Acad. Sci. USA 87:6223-27), pre-screening with
labeled flow-sorted chromosomes (CITE), and pre-selection by
hybridization to chromosome specific cDNA libraries. Fluorescence
in situ hybridization (FISH) of a DNA sequence to a metaphase
chromosomal spread can further be used to provide a precise
chromosomal location in one step. For a review of this technique,
see Verma et al., (Human Chromosomes: A Manual of Basic Techniques
(Pergamon Press, New York, 1988)).
[1048] Reagents for chromosome mapping can be used individually to
mark a single chromosome or a single site on that chromosome, or
panels of reagents can be used for marking multiple sites and/or
multiple chromosomes. Reagents corresponding to noncoding regions
of the genes actually are preferred for mapping purposes. Coding
sequences are more likely to be conserved within gene families,
thus increasing the chance of cross hybridizations during
chromosomal mapping.
[1049] Once a sequence has been mapped to a precise chromosomal
location, the physical position of the sequence on the chromosome
can be correlated with genetic map data. (Such data are found, for
example, in V. McKusick, Mendelian Inheritance in Man, available
on-line through Johns Hopkins University Welch Medical Library).
The relationship between genes and disease, mapped to the same
chromosomal region, can then be identified through linkage analysis
(co-inheritance of physically adjacent genes), described in, e.g.,
Egeland et al. (1987) Nature 325:783-787.
[1050] Moreover, differences in the DNA sequences between
individuals affected and unaffected with a disease associated with
a gene of the invention can be determined. If a mutation is
observed in some or all of the affected individuals but not in any
unaffected individuals, then the mutation is likely to be the
causative agent of the particular disease. Comparison of affected
and unaffected individuals generally involves first looking for
structural alterations in the chromosomes such as deletions or
translocations that are visible from chromosome spreads or
detectable using PCR based on that DNA sequence. Ultimately,
complete sequencing of genes from several individuals can be
performed to confirm the presence of a mutation and to distinguish
mutations from polymorphisms.
[1051] Furthermore, the nucleic acid sequences disclosed herein can
be used to perform searches against "mapping databases", e.g.,
BLAST-type search, such that the chromosome position of the gene is
identified by sequence homology or identity with known sequence
fragments which have been mapped to chromosomes.
[1052] A polypeptide and fragments and sequences thereof and
antibodies specific thereto can be used to map the location of the
gene encoding the polypeptide on a chromosome. This mapping can be
carried out by specifically detecting the presence of the
polypeptide in members of a panel of somatic cell hybrids between
cells of a first species of animal from which the protein
originates and cells from a second species of animal and then
determining which somatic cell hybrid(s) expresses the polypeptide
and noting the chromosome(s) from the first species of animal that
it contains. For examples of this technique, see Pajunen et al.
(1988) Cytogenet. Cell Genet. 47:37-41 and Van Keuren et al. (1986)
Hum. Genet. 74:34-40. Alternatively, the presence of the
polypeptide in the somatic cell hybrids can be determined by
assaying an activity or property of the polypeptide, for example,
enzymatic activity, as described in Bordelon-Riser et al. (1979)
Somatic Cell Genetics 5:597-613 and Owerbach et al. (1978) Proc.
Natl. Acad. Sci. USA 75:5640-5644.
Delta3 Tissue Typing
[1053] The nucleic acid sequences of the present invention can also
be used to identify individuals from minute biological samples. The
United States military, for example, is considering the use of
restriction fragment length polymorphism (RFLP) for identification
of its personnel. In this technique, an individual's genomic DNA is
digested with one or more restriction enzymes, and probed on a
Southern blot to yield unique bands for identification. This method
does not suffer from the current limitations of "Dog Tags" which
can be lost, switched, or stolen, making positive identification
difficult. The sequences of the present invention are useful as
additional DNA markers for RFLP (described in U.S. Pat. No.
5,272,057).
[1054] Furthermore, the sequences of the present invention can be
used to provide an alternative technique which determines the
actual base-by-base DNA sequence of selected portions of an
individual's genome. Thus, the nucleic acid sequences described
herein can be used to prepare two PCR primers from the 5' and 3'
ends of the sequences. These primers can then be used to amplify an
individual's DNA and subsequently sequence it.
[1055] Panels of corresponding DNA sequences from individuals,
prepared in this manner, can provide unique individual
identifications, as each individual will have a unique set of such
DNA sequences due to allelic differences. The sequences of the
present invention can be used to obtain such identification
sequences from individuals and from tissue. The nucleic acid
sequences of the invention uniquely represent portions of the human
genome. Allelic variation occurs to some degree in the coding
regions of these sequences, and to a greater degree in the
noncoding regions. It is estimated that allelic variation between
individual humans occurs with a frequency of about once per each
500 bases. Each of the sequences described herein can, to some
degree, be used as a standard against which DNA from an individual
can be compared for identification purposes. Because greater
numbers of polymorphisms occur in the noncoding regions, fewer
sequences are necessary to differentiate individuals. The noncoding
sequences of SEQ ID NO: 1 and 24, can comfortably provide positive
individual identification with a panel of perhaps 10 to 1,000
primers which each yield a noncoding amplified sequence of 100
bases. If predicted coding sequences, such as those in SEQ ID NO: 3
and 25 are used, a more appropriate number of primers for positive
individual identification would be 500-2,000.
[1056] If a panel of reagents from the nucleic acid sequences
described herein is used to generate a unique identification
database for an individual, those same reagents can later be used
to identify tissue from that individual. Using the unique
identification database, positive identification of the individual,
living or dead, can be made from extremely small tissue
samples.
Delta3 Use of Partial Gene Sequences in Forensic Biology
[1057] DNA-based identification techniques can also be used in
forensic biology. Forensic biology is a scientific field employing
genetic typing of biological evidence found at a crime scene as a
means for positively identifying, for example, a perpetrator of a
crime. To make such an identification, PCR technology can be used
to amplify DNA sequences taken from very small biological samples
such as tissues, e.g., hair or skin, or body fluids, e.g., blood,
saliva, or semen found at a crime scene. The amplified sequence can
then be compared to a standard, thereby allowing identification of
the origin of the biological sample.
[1058] The sequences of the present invention can be used to
provide polynucleotide reagents, e.g., PCR primers, targeted to
specific loci in the human genome, which can enhance the
reliability of DNA-based forensic identifications by, for example,
providing another "identification marker" (i.e., another DNA
sequence that is unique to a particular individual). As mentioned
above, actual base sequence information can be used for
identification as an accurate alternative to patterns formed by
restriction enzyme generated fragments. Sequences targeted to
noncoding regions are particularly appropriate for this use as
greater numbers of polymorphisms occur in the noncoding regions,
making it easier to differentiate individuals using this technique.
Examples of polynucleotide reagents include the nucleic acid
sequences of the invention or portions thereof, e.g., fragments
derived from noncoding regions having a length of at least 20 or 30
bases.
[1059] The nucleic acid sequences described herein can further be
used to provide polynucleotide reagents, e.g., labeled or labelable
probes which can be used in, for example, an in situ hybridization
technique, to identify a specific tissue, e.g., brain tissue. This
can be very useful in cases where a forensic pathologist is
presented with a tissue of unknown origin. Panels of such probes
can be used to identify tissue by species and/or by organ type.
Delta3 Predictive Medicine
[1060] The present invention also pertains to the field of
predictive medicine in which diagnostic assays, prognostic assays,
pharmacogenomics, and monitoring clinical trails are used for
prognostic (predictive) purposes to thereby treat an individual
prophylactically. Accordingly, one aspect of the present invention
relates to diagnostic assays for determining expression of a
polypeptide or nucleic acid of the invention and/or activity of a
polypeptide of the invention, in the context of a biological sample
(e.g., blood, serum, cells, tissue) to thereby determine whether an
individual is afflicted with a disease or disorder, or is at risk
of developing a disorder, associated with aberrant expression or
activity of a polypeptide of the invention. The invention also
provides for prognostic (or predictive) assays for determining
whether an individual is at risk of developing a disorder
associated with aberrant expression or activity of a polypeptide of
the invention. For example, mutations in a gene of the invention
can be assayed in a biological sample. Such assays can be used for
prognostic or predictive purpose to thereby prophylactically treat
an individual prior to the onset of a disorder characterized by or
associated with aberrant expression or activity of a polypeptide of
the invention.
[1061] Another aspect of the invention provides methods for
expression of a nucleic acid or polypeptide of the invention or
activity of a polypeptide of the invention in an individual to
thereby select appropriate therapeutic or prophylactic agents for
that individual (referred to herein as "pharmacogenomics").
Pharmacogenomics allows for the selection of agents (e.g., drugs)
for therapeutic or prophylactic treatment of an individual based on
the genotype of the individual (e.g., the genotype of the
individual examined to determine the ability of the individual to
respond to a particular agent).
[1062] Yet another aspect of the invention pertains to monitoring
the influence of agents (e.g., drugs or other compounds) on the
expression or activity of a polypeptide of the invention in
clinical trials. These and other agents are described in further
detail in the following sections.
Delta3 Prognostic Assays
[1063] The methods described herein can furthermore be utilized as
diagnostic or prognostic assays to identify subjects having or at
risk of developing a disease or disorder associated with aberrant
expression or activity of a polypeptide of the invention. For
example, the assays described herein, such as the preceding
diagnostic assays or the following assays, can be utilized to
identify a subject having or at risk of developing a disorder
associated with aberrant expression or activity of a polypeptide of
the invention. Alternatively, the prognostic assays can be utilized
to identify a subject having or at risk for developing such a
disease or disorder. Thus, the present invention provides a method
in which a test sample is obtained from a subject and a polypeptide
or nucleic acid (e.g., mRNA, genomic DNA) of the invention is
detected, wherein the presence of the polypeptide or nucleic acid
is diagnostic for a subject having or at risk of developing a
disease or disorder associated with aberrant expression or activity
of the polypeptide. As used herein, a "test sample" refers to a
biological sample obtained from a subject of interest. For example,
a test sample can be a biological fluid (e.g., serum), cell sample,
or tissue.
[1064] Furthermore, the prognostic assays described herein can be
used to determine whether a subject can be administered an agent
(e.g., an agonist, antagonist, peptidomimetic, protein, peptide,
nucleic acid, small molecule, or other drug candidate) to treat a
disease or disorder associated with aberrant expression or activity
of a polypeptide of the invention. For example, such methods can be
used to determine whether a subject can be effectively treated with
a specific agent or class of agents (e.g., agents of a type which
decrease activity of the polypeptide). Thus, the present invention
provides methods for determining whether a subject can be
effectively treated with an agent for a disorder associated with
aberrant expression or activity of a polypeptide of the invention
in which a test sample is obtained and the polypeptide or nucleic
acid encoding the polypeptide is detected (e.g., wherein the
presence of the polypeptide or nucleic acid is diagnostic for a
subject that can be administered the agent to treat a disorder
associated with aberrant expression or activity of the
polypeptide).
[1065] The methods of the invention can also be used to detect
genetic lesions or mutations in a gene of the invention, thereby
determining if a subject with the lesioned gene is at risk for a
disorder characterized aberrant expression or activity of a
polypeptide of the invention. In preferred embodiments, the methods
include detecting, in a sample of cells from the subject, the
presence or absence of a genetic lesion or mutation characterized
by at least one of an alteration affecting the integrity of a gene
encoding the polypeptide of the invention, or the mis-expression of
the gene encoding the polypeptide of the invention. For example,
such genetic lesions or mutations can be detected by ascertaining
the existence of at least one of: 1) a deletion of one or more
nucleotides from the gene; 2) an addition of one or more
nucleotides to the gene; 3) a substitution of one or more
nucleotides of the gene; 4) a chromosomal rearrangement of the
gene; 5) an alteration in the level of a messenger RNA transcript
of the gene; 6) an aberrant modification of the gene, such as of
the methylation pattern of the genomic DNA; 7) the presence of a
non-wild type splicing pattern of a messenger RNA transcript of the
gene; 8) a non-wild type level of a the protein encoded by the
gene; 9) an allelic loss of the gene; and 10) an inappropriate
post-translational modification of the protein encoded by the gene.
As described herein, there are a large number of assay techniques
known in the art which can be used for detecting lesions in a
gene.
[1066] In certain embodiments, detection of the lesion involves the
use of a probe/primer in a polymerase chain reaction (PCR) (see,
e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor PCR
or RACE PCR, or, alternatively, in a ligation chain reaction (LCR)
(see, e.g., Landegran et al. (1988) Science 241:1077-1080; and
Nakazawa et al. (1994) Proc. Natl. Acad. Sci. USA 91:360-364), the
latter of which can be particularly useful for detecting point
mutations in a gene (see, e.g., Abravaya et al. (1995) Nucleic
Acids Res. 23:675-682). This method can include the steps of
collecting a sample of cells from a patient, isolating nucleic acid
(e.g., genomic, mRNA or both) from the cells of the sample,
contacting the nucleic acid sample with one or more primers which
specifically hybridize to the selected gene under conditions such
that hybridization and amplification of the gene (if present)
occurs, and detecting the presence or absence of an amplification
product, or detecting the size of the amplification product and
comparing the length to a control sample. It is anticipated that
PCR and/or LCR may be desirable to use as a preliminary
amplification step in conjunction with any of the techniques used
for detecting mutations described herein.
[1067] Alternative amplification methods include: self sustained
sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci.
USA 87:1874-1878), transcriptional amplification system (Kwoh, et
al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta
Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), or any
other nucleic acid amplification method, followed by the detection
of the amplified molecules using techniques well known to those of
skill in the art. These detection schemes are especially useful for
the detection of nucleic acid molecules if such molecules are
present in very low numbers.
[1068] In an alternative embodiment, mutations in a selected gene
from a sample cell can be identified by alterations in restriction
enzyme cleavage patterns. For example, sample and control DNA is
isolated, amplified (optionally), digested with one or more
restriction endonucleases, and fragment length sizes are determined
by gel electrophoresis and compared. Differences in fragment length
sizes between sample and control DNA indicates mutations in the
sample DNA. Moreover, the use of sequence specific ribozymes (see,
e.g., U.S. Pat. No. 5,498,531) can be used to score for the
presence of specific mutations by development or loss of a ribozyme
cleavage site.
[1069] In other embodiments, genetic mutations can be identified by
hybridizing a sample and control nucleic acids, e.g., DNA or RNA,
to high density arrays containing hundreds or thousands of
oligonucleotides probes (Cronin et al. (1996) Human Mutation
7:244-255; Kozal et al. (1996) Nature Medicine 2:753-759). For
example, genetic mutations can be identified in two-dimensional
arrays containing light-generated DNA probes as described in Cronin
et al. (1996) Human Mutation 7:244-255. Briefly, a first
hybridization array of probes can be used to scan through long
stretches of DNA in a sample and control to identify base changes
between the sequences by making linear arrays of sequential
overlapping probes. This step allows the identification of point
mutations. This step is followed by a second hybridization array
that allows the characterization of specific mutations by using
smaller, specialized probe arrays complementary to all variants or
mutations detected. Each mutation array is composed of parallel
probe sets, one complementary to the wild-type gene and the other
complementary to the mutant gene.
[1070] In yet another embodiment, any of a variety of sequencing
reactions known in the art can be used to directly sequence the
selected gene and detect mutations by comparing the sequence of the
sample nucleic acids with the corresponding wild-type (control)
sequence. Examples of sequencing reactions include those based on
techniques developed by Maxim and Gilbert ((1977) Proc. Natl. Acad.
Sci. USA 74:560) or Sanger ((1977) Proc. Natl. Acad. Sci. USA
74:5463). It is also contemplated that any of a variety of
automated sequencing procedures can be utilized when performing the
diagnostic assays ((1995) Bio/Techniques 19:448), including
sequencing by mass spectrometry (see, e.g., PCT Publication NO: WO
94/16101; Cohen et al. (1996) Adv. Chromatogr. 36:127-162; and
Griffin et al. (1993) Appl. Biochem. Biotechnol. 38:147-159).
[1071] Other methods for detecting mutations in a selected gene
include methods in which protection from cleavage agents is used to
detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers
et al. (1985) Science 230:1242). In general, the technique of
mismatch cleavage entails providing heteroduplexes formed by
hybridizing (labeled) RNA or DNA containing the wild-type sequence
with potentially mutant RNA or DNA obtained from a tissue sample.
The double-stranded duplexes are treated with an agent which
cleaves single-stranded regions of the duplex such as which will
exist due to basepair mismatches between the control and sample
strands. RNA/DNA duplexes can be treated with RNase to digest
mismatched regions, and DNA/DNA hybrids can be treated with S1
nuclease to digest mismatched regions.
[1072] In other embodiments, either DNA/DNA or RNA/DNA duplexes can
be treated with hydroxylamine or osmium tetroxide and with
piperidine in order to digest mismatched regions. After digestion
of the mismatched regions, the resulting material is then separated
by size on denaturing polyacrylamide gels to determine the site of
mutation. See, e.g., Cotton et al. (1988) Proc. Natl. Acad. Sci.
USA 85:4397; Saleeba et al. (1992) Methods Enzymol. 217:286-295. In
a preferred embodiment, the control DNA or RNA can be labeled for
detection.
[1073] In still another embodiment, the mismatch cleavage reaction
employs one or more proteins that recognize mismatched base pairs
in double-stranded DNA (so called "DNA mismatch repair enzymes") in
defined systems for detecting and mapping point mutations in cDNAs
obtained from samples of cells. For example, the mutY enzyme of E.
coli cleaves A at G/A mismatches and the thymidine DNA glycosylase
from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994)
Carcinogenesis 15:1657-1662). According to an exemplary embodiment,
a probe based on a selected sequence, e.g., a wild-type sequence,
is hybridized to a cDNA or other DNA product from a test cell(s).
The duplex is treated with a DNA mismatch repair enzyme, and the
cleavage products, if any, can be detected from electrophoresis
protocols or the like. See, e.g., U.S. Pat. No. 5,459,039.
[1074] In other embodiments, alterations in electrophoretic
mobility will be used to identify mutations in genes. For example,
single strand conformation polymorphism (SSCP) may be used to
detect differences in electrophoretic mobility between mutant and
wild type nucleic acids (Orita et al. (1989) Proc. Natl. Acad. Sci.
USA 86:2766; see also Cotton (1993) Mutat. Res. 285:125-144;
Hayashi (1992) Genet. Anal. Tech. Appl. 9:73-79). Single-stranded
DNA fragments of sample and control nucleic acids will be denatured
and allowed to renature. The secondary structure of single-stranded
nucleic acids varies according to sequence, and the resulting
alteration in electrophoretic mobility enables the detection of
even a single base change. The DNA fragments may be labeled or
detected with labeled probes. The sensitivity of the assay may be
enhanced by using RNA (rather than DNA), in which the secondary
structure is more sensitive to a change in sequence. In a preferred
embodiment, the subject method utilizes heteroduplex analysis to
separate double stranded heteroduplex molecules on the basis of
changes in electrophoretic mobility (Keen et al. (1991) Trends
Genet. 7:5).
[1075] In yet another embodiment, the movement of mutant or
wild-type fragments in polyacrylamide gels containing a gradient of
denaturant is assayed using denaturing gradient get electrophoresis
(DGGE) (Myers et al. (1985) Nature 313:495). When DGGE is used as
the method of analysis, DNA will be modified to insure that it does
not completely denature, for example by adding a GC clamp of
approximately 40 bp of high-melting GC-rich DNA by PCR. In a
further embodiment, a temperature gradient is used in place of a
denaturing gradient to identify differences in the mobility of
control and sample DNA (Rosenbaum and Reissner (1987) Biophys.
Chem. 265:12753).
[1076] Examples of other techniques for detecting point mutations
include, but are not limited to, selective oligonucleotide
hybridization, selective amplification, or selective primer
extension. For example, oligonucleotide primers may be prepared in
which the known mutation is placed centrally and then hybridized to
target DNA under conditions which permit hybridization only if a
perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki
et al. (1989) Proc. Natl. Acad. Sci. USA 86:6230). Such allele
specific oligonucleotides are hybridized to PCR amplified target
DNA or a number of different mutations when the oligonucleotides
are attached to the hybridizing membrane and hybridized with
labeled target DNA.
[1077] Alternatively, allele specific amplification technology
which depends on selective PCR amplification may be used in
conjunction with the instant invention. Oligonucleotides used as
primers for specific amplification may carry the mutation of
interest in the center of the molecule (so that amplification
depends on differential hybridization) (Gibbs et al. (1989) Nucleic
Acids Res. 17:2437-2448) or at the extreme 3' end of one primer
where, under appropriate conditions, mismatch can prevent or reduce
polymerase extension (Prossner (1993) Tibtech 11:238). In addition,
it may be desirable to introduce a novel restriction site in the
region of the mutation to create cleavage-based detection
(Gasparini et al. (1992) Mol. Cell. Probes 6:1). It is anticipated
that in certain embodiments amplification may also be performed
using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad.
Sci. USA 88:189). In such cases, ligation will occur only if there
is a perfect match at the 3' end of the 5' sequence making it
possible to detect the presence of a known mutation at a specific
site by looking for the presence or absence of amplification.
[1078] The methods described herein may be performed, for example,
by utilizing pre-packaged diagnostic kits comprising at least one
probe nucleic acid or antibody reagent described herein, which may
be conveniently used, e.g., in clinical settings to diagnose
patients exhibiting symptoms or family history of a disease or
illness involving a gene encoding a polypeptide of the invention.
Furthermore, any cell type or tissue, preferably peripheral blood
leukocytes, in which the polypeptide of the invention is expressed
may be utilized in the prognostic assays described herein.
Delta3 Pharmacogenomics
[1079] Agents, or modulators which have a stimulatory or inhibitory
effect on activity or expression of a polypeptide of the invention
as identified by a screening assay described herein can be
administered to individuals to treat (prophylactically or
therapeutically) disorders associated with aberrant activity of the
polypeptide. In conjunction with such treatment, the
pharmacogenomics (i.e., the study of the relationship between an
individual's genotype and that individual's response to a foreign
compound or drug) of the individual may be considered. Differences
in metabolism of therapeutics can lead to severe toxicity or
therapeutic failure by altering the relation between dose and blood
concentration of the pharmacologically active drug. Thus, the
pharmacogenomics of the individual permits the selection of
effective agents (e.g., drugs) for prophylactic or therapeutic
treatments based on a consideration of the individual's genotype.
Such pharmacogenomics can further be used to determine appropriate
dosages and therapeutic regimens. Accordingly, the activity of a
polypeptide of the invention, expression of a nucleic acid of the
invention, or mutation content of a gene of the invention in an
individual can be determined to thereby select appropriate agent(s)
for therapeutic or prophylactic treatment of the individual.
[1080] Pharmacogenomics deals with clinically significant
hereditary variations in the response to drugs due to altered drug
disposition and abnormal action in affected persons. See, e.g.,
Linder (1997) Clin. Chem. 43(2):254-266. In general, two types of
pharmacogenetic conditions can be differentiated. Genetic
conditions transmitted as a single factor altering the way drugs
act on the body are referred to as "altered drug action." Genetic
conditions transmitted as single factors altering the way the body
acts on drugs are referred to as "altered drug metabolism". These
pharmacogenetic conditions can occur either as rare defects or as
polymorphisms. For example, glucose-6-phosphate dehydrogenase
deficiency (G6PD) is a common inherited enzymopathy in which the
main clinical complication is haemolysis after ingestion of oxidant
drugs (anti-malarials, sulfonamides, analgesics, nitrofurans) and
consumption of fava beans.
[1081] As an illustrative embodiment, the activity of drug
metabolizing enzymes is a major determinant of both the intensity
and duration of drug action. The discovery of genetic polymorphisms
of drug metabolizing enzymes (e.g., N-acetyltransferase 2 (NAT 2)
and cytochrome P450 enzymes CYP2D6 and CYP2C19) has provided an
explanation as to why some patients do not obtain the expected drug
effects or show exaggerated drug response and serious toxicity
after taking the standard and safe dose of a drug. These
polymorphisms are expressed in two phenotypes in the population,
the extensive metabolizer (EM) and poor metabolizer (PM). The
prevalence of PM is different among different populations. For
example, the gene coding for CYP2D6 is highly polymorphic and
several mutations have been identified in PM, which all lead to the
absence of functional CYP2D6. Poor metabolizers of CYP2D6 and
CYP2C19 quite frequently experience exaggerated drug response and
side effects when they receive standard doses. If a metabolite is
the active therapeutic moiety, a PM will show no therapeutic
response, as demonstrated for the analgesic effect of codeine
mediated by its CYP2D6-formed metabolite morphine. The other
extreme are the so called ultra-rapid metabolizers who do not
respond to standard doses. Recently, the molecular basis of
ultra-rapid metabolism has been identified to be due to CYP2D6 gene
amplification.
[1082] Thus, the activity of a polypeptide of the invention,
expression of a nucleic acid encoding the polypeptide, or mutation
content of a gene encoding the polypeptide in an individual can be
determined to thereby select appropriate agent(s) for therapeutic
or prophylactic treatment of the individual. In addition,
pharmacogenetic studies can be used to apply genotyping of
polymorphic alleles encoding drug-metabolizing enzymes to the
identification of an individual's drug responsiveness phenotype.
This knowledge, when applied to dosing or drug selection, can avoid
adverse reactions or therapeutic failure and thus enhance
therapeutic or prophylactic efficiency when treating a subject with
a modulator of activity or expression of the polypeptide, such as a
modulator identified by one of the exemplary screening assays
described herein.
Delta3 Monitoring of Effects During Clinical Trials
[1083] Monitoring the influence of agents (e.g., drugs, compounds)
on the expression or activity of a polypeptide of the invention
(e.g., the ability to modulate aberrant cell proliferation
chemotaxis, and/or differentiation) can be applied not only in
basic drug screening, but also in clinical trials. For example, the
effectiveness of an agent, as determined by a screening assay as
described herein, to increase gene expression, protein levels or
protein activity, can be monitored in clinical trials of subjects
exhibiting decreased gene expression, protein levels, or protein
activity. Alternatively, the effectiveness of an agent, as
determined by a screening assay, to decrease gene expression,
protein levels or protein activity, can be monitored in clinical
trials of subjects exhibiting increased gene expression, protein
levels, or protein activity. In such clinical trials, expression or
activity of a polypeptide of the invention and preferably, that of
other polypeptide that have been implicated in for example, a
cellular proliferation disorder, can be used as a marker of the
immune responsiveness of a particular cell.
[1084] For example, and not by way of limitation, genes, including
those of the invention, that are modulated in cells by treatment
with an agent (e.g., compound, drug or small molecule) which
modulates activity or expression of a polypeptide of the invention
(e.g., as identified in a screening assay described herein) can be
identified. Thus, to study the effect of agents on cellular
proliferation disorders, for example, in a clinical trial, cells
can be isolated and RNA prepared and analyzed for the levels of
expression of a gene of the invention and other genes implicated in
the disorder. The levels of gene expression (i.e., a gene
expression pattern) can be quantified by Northern blot analysis or
RT-PCR, as described herein, or alternatively by measuring the
amount of protein produced, by one of the methods as described
herein, or by measuring the levels of activity of a gene of the
invention or other genes. In this way, the gene expression pattern
can serve as a marker, indicative of the physiological response of
the cells to the agent. Accordingly, this response state may be
determined before, and at various points during, treatment of the
individual with the agent.
[1085] In a preferred embodiment, the present invention provides a
method for monitoring the effectiveness of treatment of a subject
with an agent (e.g., an agonist, antagonist, peptidomimetic,
protein, peptide, nucleic acid, small molecule, or other drug
candidate identified by the screening assays described herein)
comprising the steps of (i) obtaining a pre-administration sample
from a subject prior to administration of the agent; (ii) detecting
the level of the polypeptide or nucleic acid of the invention in
the preadministration sample; (iii) obtaining one or more
post-administration samples from the subject; (iv) detecting the
level the of the polypeptide or nucleic acid of the invention in
the post-administration samples; (v) comparing the level of the
polypeptide or nucleic acid of the invention in the
pre-administration sample with the level of the polypeptide or
nucleic acid of the invention in the post-administration sample or
samples; and (vi) altering the administration of the agent to the
subject accordingly. For example, increased administration of the
agent may be desirable to increase the expression or activity of
the polypeptide to higher levels than detected, i.e., to increase
the effectiveness of the agent. Alternatively, decreased
administration of the agent may be desirable to decrease expression
or activity of the polypeptide to lower levels than detected, i.e.,
to decrease the effectiveness of the agent.
Delta3 Transgenic Animals
[1086] These systems may be used in a variety of applications. For
example, the cell- and animal-based model systems may be used to
further characterize Delta3 genes and proteins. In addition, such
assays may be utilized as part of screening strategies designed to
identify compounds which are capable of ameliorating disease
symptoms. Thus, the animal- and cell-based models may be used to
identify drugs, pharmaceuticals, therapies and interventions which
may be effective in treating disease.
Delta3 Animal-Based Systems
[1087] One aspect of the present invention concerns transgenic
animals which are comprised of cells (of that animal) which contain
a transgene of the present invention and which preferably (though
optionally) express an exogenous Delta3 protein in one or more
cells in the animal. A Delta3 transgene can encode the wild-type
form of the protein, or can encode homologs thereof, including both
alleles of Delta3 genes, agonists and antagonists, as well as
antisense constructs. In preferred embodiments, the expression of
the transgene is restricted to specific subsets of cells, tissues
or developmental stages utilizing, for example, cis-acting
sequences that control expression in the desired pattern. In the
present invention, such mosaic expression of a Delta3 protein can
be essential for many forms of lineage analysis and can
additionally provide a means to assess the effects of, for example,
lack of Delta3 expression which might grossly alter development in
small patches of tissue within an otherwise normal embryo. In a
preferred embodiment, the invention provides transgenic mice having
an allele of hDelta3 gene which is associated with ACCPN and the
mouse can be used, e.g., to determine the effect of this specific
hDelta3 allele. Toward this and, tissue-specific regulatory
sequences and conditional regulatory sequences can be used to
control expression of the transgene in certain spatial patterns.
Moreover, temporal patterns of expression can be provided by, for
example, conditional recombination systems or prokaryotic
transcriptional regulatory sequences.
[1088] Genetic techniques which allow for the expression of
transgenes can be regulated via site-specific genetic manipulation
in vivo are known to those skilled in the art. For instance,
genetic systems are available which allow for the regulated
expression of a recombinase that catalyzes the genetic
recombination a target sequence. As used herein, the phrase "target
sequence" refers to a nucleotide sequence that is genetically
recombined by a recombinase. The target sequence is flanked by
recombinase recognition sequences and is generally either excised
or inverted in cells expressing recombinase activity. Recombinase
catalyzed recombination events can be designed such that
recombination of the target sequence results in either the
activation or repression of expression of one of the subject Delta3
proteins. For example, excision of a target sequence which
interferes with the expression of a recombinant Delta3 gene, such
as one which encodes an antagonistic homolog or an antisense
transcript, can be designed to activate expression of that gene.
This interference with expression of the protein can result from a
variety of mechanisms, such as spatial separation of the Delta3
gene from the promoter element or an internal stop codon. Moreover,
the transgene can be made wherein the coding sequence of the gene
is flanked by recombinase recognition sequences and is initially
transfected into cells in a 3' to 5' orientation with respect to
the promoter element. In such an instance, inversion of the target
sequence will reorient the subject gene by placing the 5' end of
the coding sequence in an orientation with respect to the promoter
element which allow for promoter driven transcriptional
activation.
[1089] The transgenic animals of the present invention all include
within a plurality of their cells a transgene of the present
invention, which transgene alters the phenotype of the "host cell"
with respect to regulation of cell growth, death and/or
differentiation. Since it is possible to produce transgenic
organisms of the invention utilizing one or more of the transgene
constructs described herein, a general description will be given of
the production of transgenic organisms by referring generally to
exogenous genetic material. This general description can be adapted
by those skilled in the art in order to incorporate specific
transgene sequences into organisms utilizing the methods and
materials described below.
[1090] In an illustrative embodiment, either the cre/loxP
recombinase system of bacteriophage P1 (Lakso et al. (1992) PNAS
89:6232-6236; Orban et al. (1992) PNAS 89:6861-6865) or the FLP
recombinase system of Saccharomyces cerevisiae (O'Gorman et al.
(1991) Science 251:1351-1355; PCT publication WO 92/15694) can be
used to generate in vivo site-specific genetic recombination
systems. Cre recombinase catalyzes the site-specific recombination
of an intervening target sequence located between loxP sequences.
loxP sequences are 34 base pair nucleotide repeat sequences to
which the Cre recombinase binds and are required for Cre
recombinase mediated genetic recombination. The orientation of loxP
sequences determines whether the intervening target sequence is
excised or inverted when Cre recombinase is present (Abremski et
al. (1984) J. Biol. Chem. 259:1509-1514); catalyzing the excision
of the target sequence when the loxP sequences are oriented as
direct repeats and catalyzes inversion of the target sequence when
loxP sequences are oriented as inverted repeats.
[1091] Accordingly, genetic recombination of the target sequence is
dependent on expression of the Cre recombinase. Expression of the
recombinase can be regulated by promoter elements which are subject
to regulatory control, e.g., tissue-specific, developmental
stage-specific, inducible or repressible by externally added
agents. This regulated control will result in genetic recombination
of the target sequence only in cells where recombinase expression
is mediated by the promoter element. Thus, the activation
expression of a recombinant Delta3 protein can be regulated via
control of recombinase expression.
[1092] Use of the cre/loxP recombinase system to regulate
expression of a recombinant Delta3 protein requires the
construction of a transgenic animal containing transgenes encoding
both the Cre recombinase and the subject protein. Animals
containing both the Cre recombinase and a recombinant Delta3 gene
can be provided through the construction of "double" transgenic
animals. A convenient method for providing such animals is to mate
two transgenic animals each containing a transgene, e.g., a Delta3
gene and recombinase gene.
[1093] One advantage derived from initially constructing transgenic
animals containing a Delta3 transgene in a recombinase-mediated
expressible format derives from the likelihood that the subject
protein, whether agonistic or antagonistic, can be deleterious upon
expression in the transgenic animal. In such an instance, a founder
population, in which the subject transgene is silent in all
tissues, can be propagated and maintained. Individuals of this
founder population can be crossed with animals expressing the
recombinase in, for example, one or more tissues and/or a desired
temporal pattern. Thus, the creation of a founder population in
which, for example, an antagonistic Delta3 transgene is silent will
allow the study of progeny from that founder in which disruption of
Delta3 mediated induction in a particular tissue or at certain
developmental stages would result in, for example, a lethal
phenotype.
[1094] Similar conditional transgenes can be provided using
prokaryotic promoter sequences which require prokaryotic proteins
to be simultaneous expressed in order to facilitate expression of
the Delta3 transgene. Exemplary promoters and the corresponding
trans-activating prokaryotic proteins are given in U.S. Pat. No.
4,833,080.
[1095] Moreover, expression of the conditional transgenes can be
induced by gene therapy-like methods wherein a gene encoding the
trans-activating protein, e.g., a recombinase or a prokaryotic
protein, is delivered to the tissue and caused to be expressed,
such as in a cell-type specific manner. By this method, a Delta3
transgene could remain silent into adulthood until "turned on" by
the introduction of the trans-activator.
[1096] In an exemplary embodiment, the "transgenic non-human
animals" of the invention are produced by introducing transgenes
into the germline of the non-human animal. Embryonal target cells
at various developmental stages can be used to introduce
transgenes. Different methods are used depending on the stage of
development of the embryonal target cell. The specific line(s) of
any animal used to practice this invention are selected for general
good health, good embryo yields, good pronuclear visibility in the
embryo, and good reproductive fitness. In addition, the haplotype
is a significant factor. For example, when transgenic mice are to
be produced, strains such as C57BL/6 or FVB lines are often used
(Jackson Laboratory, Bar Harbor, Me.). Preferred strains are those
with H-2b, H-2d or H-2q haplotypes such as C57BL/6 or DBA/1. The
line(s) used to practice this invention may themselves be
transgenics, and/or may be knockouts (i.e., obtained from animals
which have one or more genes partially or completely
suppressed).
[1097] In one embodiment, the transgene construct is introduced
into a single stage embryo. The zygote is the best target for
micro-injection. In the mouse, the male pronucleus reaches the size
of approximately 20 micrometers in diameter which allows
reproducible injection of 1-2 .mu.l of DNA solution. The use of
zygotes as a target for gene transfer has a major advantage in that
in most cases the injected DNA will be incorporated into the host
gene before the first cleavage (Brinster et al. (1985) PNAS
82:4438-4442). As a consequence, all cells of the transgenic animal
will carry the incorporated transgene. This will in general also be
reflected in the efficient transmission of the transgene to
offspring of the founder since 50% of the germ cells will harbor
the transgene.
[1098] Normally, fertilized embryos are incubated in suitable media
until the pronuclei appear. At about this time, the nucleotide
sequence comprising the transgene is introduced into the female or
male pronucleus as described below. In some species such as mice,
the male pronucleus is preferred. It is most preferred that the
exogenous genetic material be added to the male DNA complement of
the zygote prior to its being processed by the ovum nucleus or the
zygote female pronucleus. It is thought that the ovum nucleus or
female pronucleus release molecules which affect the male DNA
complement, perhaps by replacing the protamines of the male DNA
with histones, thereby facilitating the combination of the female
and male DNA complements to form the diploid zygote.
[1099] Thus, it is preferred that the exogenous genetic material be
added to the male complement of DNA or any other complement of DNA
prior to its being affected by the female pronucleus. For example,
the exogenous genetic material is added to the early male
pronucleus, as soon as possible after the formation of the male
pronucleus, which is when the male and female pronuclei are well
separated and both are located close to the cell membrane.
Alternatively, the exogenous genetic material could be added to the
nucleus of the sperm after it has been induced to undergo
decondensation. Sperm containing the exogenous genetic material can
then be added to the ovum or the decondensed sperm could be added
to the ovum with the transgene constructs being added as soon as
possible thereafter.
[1100] Introduction of the transgene nucleotide sequence into the
embryo may be accomplished by any means known in the art such as,
for example, microinjection, electroporation, or lipofection.
Following introduction of the transgene nucleotide sequence into
the embryo, the embryo may be incubated in vitro for varying
amounts of time, or reimplanted into the surrogate host, or both.
In vitro incubation to maturity is within the scope of this
invention. One common method in to incubate the embryos in vitro
for about 1-7 days, depending on the species, and then reimplant
them into the surrogate host.
[1101] For the purposes of this invention a zygote is essentially
the formation of a diploid cell which is capable of developing into
a complete organism. Generally, the zygote will be comprised of an
egg containing a nucleus formed, either naturally or artificially,
by the fusion of two haploid nuclei from a gamete or gametes. Thus,
the gamete nuclei must be ones which are naturally compatible,
i.e., ones which result in a viable zygote capable of undergoing
differentiation and developing into a functioning organism.
Generally, a euploid zygote is preferred. If an aneuploid zygote is
obtained, then the number of chromosomes should not vary by more
than one with respect to the euploid number of the organism from
which either gamete originated.
[1102] In addition to similar biological considerations, physical
ones also govern the amount (e.g., volume) of exogenous genetic
material which can be added to the nucleus of the zygote or to the
genetic material which forms a part of the zygote nucleus. If no
genetic material is removed, then the amount of exogenous genetic
material which can be added is limited by the amount which will be
absorbed without being physically disruptive. Generally, the volume
of exogenous genetic material inserted will not exceed about 10
picoliters. The physical effects of addition must not be so great
as to physically destroy the viability of the zygote. The
biological limit of the number and variety of DNA sequences will
vary depending upon the particular zygote and functions of the
exogenous genetic material and will be readily apparent to one
skilled in the art, because the genetic material, including the
exogenous genetic material, of the resulting zygote must be
biologically capable of initiating and maintaining the
differentiation and development of the zygote into a functional
organism.
[1103] The number of copies of the transgene constructs which are
added to the zygote is dependent upon the total amount of exogenous
genetic material added and will be the amount which enables the
genetic transformation to occur. Theoretically only one copy is
required; however, generally, numerous copies are utilized, for
example, 1,000-20,000 copies of the transgene construct, in order
to insure that one copy is functional. As regards the present
invention, there will often be an advantage to having more than one
functioning copy of each of the inserted exogenous DNA sequences to
enhance the phenotypic expression of the exogenous DNA
sequences.
[1104] Any technique which allows for the addition of the exogenous
genetic material into nucleic genetic material can be utilized so
long as it is not destructive to the cell, nuclear membrane or
other existing cellular or genetic structures. The exogenous
genetic material is preferentially inserted into the nucleic
genetic material by microinjection. Microinjection of cells and
cellular structures is known and is used in the art.
[1105] Reimplantation is accomplished using standard methods.
Usually, the surrogate host is anesthetized, and the embryos are
inserted into the oviduct. The number of embryos implanted into a
particular host will vary by species, but will usually be
comparable to the number of off spring the species naturally
produces.
[1106] Transgenic offspring of the surrogate host may be screened
for the presence and/or expression of the transgene by any suitable
method. Screening is often accomplished by Southern blot or
Northern blot analysis, using a probe that is complementary to at
least a portion of the transgene. Western blot analysis using an
antibody against the protein encoded by the transgene may be
employed as an alternative or additional method for screening for
the presence of the transgene product. Typically, DNA is prepared
from tail tissue and analyzed by Southern analysis or PCR for the
transgene. Alternatively, the tissues or cells believed to express
the transgene at the highest levels are tested for the presence and
expression of the transgene using Southern analysis or PCR,
although any tissues or cell types may be used for this
analysis.
[1107] Alternative or additional methods for evaluating the
presence of the transgene include, without limitation, suitable
biochemical assays such as enzyme and/or immunological assays,
histological stains for particular marker or enzyme activities,
flow cytometric analysis, and the like. Analysis of the blood may
also be useful to detect the presence of the transgene product in
the blood, as well as to evaluate the effect of the transgene on
the levels of various types of blood cells and other blood
constituents.
[1108] Progeny of the transgenic animals may be obtained by mating
the transgenic animal with a suitable partner, or by in vitro
fertilization of eggs and/or sperm obtained from the transgenic
animal. Where mating with a partner is to be performed, the partner
may or may not be transgenic and/or a knockout; where it is
transgenic, it may contain the same or a different transgene, or
both. Alternatively, the partner may be a parental line. Where in
vitro fertilization is used, the fertilized embryo may be implanted
into a surrogate host or incubated in vitro, or both. Using either
method, the progeny may be evaluated for the presence of the
transgene using methods described above, or other appropriate
methods.
[1109] The transgenic animals produced in accordance with the
present invention will include exogenous genetic material. As set
out above, the exogenous genetic material will, in certain
embodiments, be a DNA sequence which results in the production of a
Delta3 protein (either agonistic or antagonistic), and antisense
transcript, or a Delta3 mutant. Further, in such embodiments the
sequence will be attached to a transcriptional control element,
e.g., a promoter, which preferably allows the expression of the
transgene product in a specific type of cell.
[1110] Retroviral infection can also be used to introduce transgene
into a non-human animal. The developing non-human embryo can be
cultured in vitro to the blastocyst stage. During this time, the
blastomeres can be targets for retroviral infection (Jaenich, R.
(1976) PNAS 73:1260-1264). Efficient infection of the blastomeres
is obtained by enzymatic treatment to remove the zona pellucida
(Manipulating the Mouse Embryo, Hogan eds. (Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, 1986). The viral vector
system used to introduce the transgene is typically a
replication-defective retrovirus carrying the transgene (Jahner et
al. (1985) PNAS 82:6927-6931; Van der Putten et al. (1985) PNAS
82:6148-6152). Transfection is easily and efficiently obtained by
culturing the blastomeres on a monolayer of virus-producing cells
(Van der Putten et al. (1985) PNAS 82:6148-6152; Stewart et al.
(1987) EMBO J. 6:383-388). Alternatively, infection can be
performed at a later stage. Virus or virus-producing cells can be
injected into the blastocoele (Jahner et al. (1982) Nature
298:623-628). Most of the founders will be mosaic for the transgene
since incorporation occurs only in a subset of the cells which
formed the transgenic non-human animal. Further, the founder may
contain various retroviral insertions of the transgene at different
positions in the genome which generally will segregate in the
offspring. In addition, it is also possible to introduce transgenes
into the germ line by intrauterine retroviral infection of the
midgestation embryo (Jahner et al. (1982) Nature 298:623-628).
[1111] A third type of target cell for transgene introduction is
the embryonal stem cell (ES). ES cells are obtained from
pre-implantation embryos cultured in vitro and fused with embryos
(Evans et al. (1981) Nature 292:154-156; Bradley et al. (1984)
Nature 309:255-258; Gossler et al. (1986) PNAS 83: 9065-9069; and
Robertson et al. (1986) Nature 322:445-448). Transgenes can be
efficiently introduced into the ES cells by DNA transfection or by
retrovirus-mediated transduction. Such transformed ES cells can
thereafter be combined with blastocysts from a non-human animal.
The ES cells thereafter colonize the embryo and contribute to the
germ line of the resulting chimeric animal. For review see
Jaenisch, R. (1988) Science 240:1468-1474.
[1112] In one embodiment, gene targeting, which is a method of
using homologous recombination to modify an animal's genome, can be
used to introduce changes into cultured embryonic stem cells. By
targeting a Delta3 gene of interest in ES cells, these changes can
be introduced into the germlines of animals to generate chimeras.
The gene targeting procedure is accomplished by introducing into
tissue culture cells a DNA targeting construct that includes a
segment homologous to a target Delta3 locus, and which also
includes an intended sequence modification to the Delta3 genomic
sequence (e.g., insertion, deletion, point mutation). The treated
cells are then screened for accurate targeting to identify and
isolate those which have been properly targeted.
[1113] Gene targeting in embryonic stem cells is in fact a scheme
contemplated by the present invention as a means for disrupting a
Delta3 gene function through the use of a targeting transgene
construct designed to undergo homologous recombination with one or
more Delta3 genomic sequences. The targeting construct can be
arranged so that, upon recombination with an element of a Delta3
gene, a positive selection marker is inserted into (or replaces)
coding sequences of the targeted Delta3 gene. The inserted sequence
functionally disrupts the Delta3 gene, while also providing a
positive selection trait. Exemplary Delta3 targeting constructs are
described in more detail below.
[1114] Generally, the embryonic stem cells (ES cells) used to
produce the knockout animals will be of the same species as the
knockout animal to be generated. Thus for example, mouse embryonic
stem cells will usually be used for generation of knockout
mice.
[1115] Embryonic stem cells are generated and maintained using
methods well known to the skilled artisan such as those described
by Doetschman et al. (1985) J. Embryol. Exp. Morphol. 87:27-45).
Any line of ES cells can be used, however, the line chosen is
typically selected for the ability of the cells to integrate into
and become part of the germ line of a developing embryo so as to
create germ line transmission of the knockout construct. Thus, any
ES cell line that is believed to have this capability is suitable
for use herein. One mouse strain that is typically used for
production of ES cells, is the 129J strain. Another ES cell line is
murine cell line D3 (American Type Culture Collection, catalog NO:
CKL 1934) Still another preferred ES cell line is the WW6 cell line
(Ioffe et al. (1995) PNAS 92:7357-7361). The cells are cultured and
prepared for knockout construct insertion using methods well known
to the skilled artisan, such as those set forth by Robertson in:
Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E.
J. Robertson, ed. IRL Press, Washington, D.C. [1987]); by Bradley
et al. (1986) Current Topics in Devel. Biol. 20:357-371); and by
Hogan et al. (Manipulating the Mouse Embryo: A Laboratory Manual,
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
[1986]).
[1116] Insertion of the knockout construct into the ES cells can be
accomplished using a variety of methods well known in the art
including for example, electroporation, microinjection, and calcium
phosphate treatment. A preferred method of insertion is
electroporation.
[1117] Each knockout construct to be inserted into the cell must
first be in the linear form. Therefore, if the knockout construct
has been inserted into a vector (described infra), linearization is
accomplished by digesting the DNA with a suitable restriction
endonuclease selected to cut only within the vector sequence and
not within the knockout construct sequence.
[1118] For insertion, the knockout construct is added to the ES
cells under appropriate conditions for the insertion method chosen,
as is known to the skilled artisan. Where more than one construct
is to be introduced into the ES cell, each knockout construct can
be introduced simultaneously or one at a time.
[1119] If the ES cells are to be electroporated, the ES cells and
knockout construct DNA are exposed to an electric pulse using an
electroporation machine and following the manufacturer's guidelines
for use. After electroporation, the ES cells are typically allowed
to recover under suitable incubation conditions. The cells are then
screened for the presence of the knockout construct.
[1120] Screening can be accomplished using a variety of methods.
Where the marker gene is an antibiotic resistance gene, for
example, the ES cells may be cultured in the presence of an
otherwise lethal concentration of antibiotic. Those ES cells that
survive have presumably integrated the knockout construct. If the
marker gene is other than an antibiotic resistance gene, a Southern
blot of the ES cell genomic DNA can be probed with a sequence of
DNA designed to hybridize only to the marker sequence
Alternatively, PCR can be used. Finally, if the marker gene is a
gene that encodes an enzyme whose activity can be detected (e.g.,
b-galactosidase), the enzyme substrate can be added to the cells
under suitable conditions, and the enzymatic activity can be
analyzed. One skilled in the art will be familiar with other useful
markers and the means for detecting their presence in a given cell.
All such markers are contemplated as being included within the
scope of the teaching of this invention.
[1121] The knockout construct may integrate into several locations
in the ES cell genome, and may integrate into a different location
in each ES cell's genome due to the occurrence of random insertion
events. The desired location of insertion is in a complementary
position to the DNA sequence to be knocked out, e.g., the Delta3
coding sequence, transcriptional regulatory sequence, etc.
Typically, less than about 1-5% of the ES cells that take up the
knockout construct will actually integrate the knockout construct
in the desired location. To identify those ES cells with proper
integration of the knockout construct, total DNA can be extracted
from the ES cells using standard methods. The DNA can then be
probed on a Southern blot with a probe or probes designed to
hybridize in a specific pattern to genomic DNA digested with
particular restriction enzyme(s). Alternatively, or additionally,
the genomic DNA can be amplified by PCR with probes specifically
designed to amplify DNA fragments of a particular size and sequence
(i.e., only those cells containing the knockout construct in the
proper position will generate DNA fragments of the proper
size).
[1122] After suitable ES cells containing the knockout construct in
the proper location have been identified, the cells can be inserted
into an embryo. Insertion may be accomplished in a variety of ways
known to the skilled artisan, however a preferred method is by
microinjection. For microinjection, about 10-30 cells are collected
into a micropipet and injected into embryos that are at the proper
stage of development to permit integration of the foreign ES cell
containing the knockout construct into the developing embryo. For
instance, as the appended Examples describe, the transformed ES
cells can be microinjected into blastocytes.
[1123] The suitable stage of development for the embryo used for
insertion of ES cells is very species dependent, however for mice
it is about 3.5 days. The embryos are obtained by perfusing the
uterus of pregnant females. Suitable methods for accomplishing this
are known to the skilled artisan, and are set forth by, e.g., et
al. (1986) Current Topics in Devel. Biol. 20:357-371.
[1124] While any embryo of the right stage of development is
suitable for use, preferred embryos are male. In mice, the
preferred embryos also have genes coding for a coat color that is
different from the coat color encoded by the ES cell genes. In this
way, the offspring can be screened easily for the presence of the
knockout construct by looking for mosaic coat color (indicating
that the ES cell was incorporated into the developing embryo).
Thus, for example, if the ES cell line carries the genes for white
fur, the embryo selected will carry genes for black or brown
fur.
[1125] After the ES cell has been introduced into the embryo, the
embryo may be implanted into the uterus of a pseudopregnant foster
mother for gestation. While any foster mother may be used, the
foster mother is typically selected for her ability to breed and
reproduce well, and for her ability to care for the young. Such
foster mothers are typically prepared by mating with vasectomized
males of the same species. The stage of the pseudopregnant foster
mother is important for successful implantation, and it is species
dependent. For mice, this stage is about 2-3 days
pseudopregnant.
[1126] Offspring that are born to the foster mother may be screened
initially for mosaic coat color where the coat color selection
strategy (as described above, and in the appended examples) has
been employed. In addition, or as an alternative, DNA from tail
tissue of the offspring may be screened for the presence of the
knockout construct using Southern blots and/or PCR as described
above. Offspring that appear to be mosaics may then be crossed to
each other, if they are believed to carry the knockout construct in
their germ line, in order to generate homozygous knockout animals.
Homozygotes may be identified by Southern blotting of equivalent
amounts of genomic DNA from mice that are the product of this
cross, as well as mice that are known heterozygotes and wild type
mice.
[1127] Other means of identifying and characterizing the knockout
offspring are available. For example, Northern blots can be used to
probe the mRNA for the presence or absence of transcripts encoding
either the gene knocked out, the marker gene, or both. In addition,
Western blots can be used to assess the level of expression of the
Delta3 gene knocked out in various tissues of the offspring by
probing the Western blot with an antibody against the particular
Delta3 protein, or an antibody against the marker gene product,
where this gene is expressed. Finally, in situ analysis (such as
fixing the cells and labeling with antibody) and/or FACS
(fluorescence activated cell sorting) analysis of various cells
from the offspring can be conducted using suitable antibodies to
look for the presence or absence of the knockout construct gene
product.
[1128] Yet other methods of making knock-out or disruption
transgenic animals are also generally known. See, for example,
Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory
Press, Cold Spring Harbor, N.Y., 1986). Recombinase dependent
knockouts can also be generated, e.g., by homologous recombination
to insert target sequences, such that tissue specific and/or
temporal control of inactivation of a Delta-gene can be controlled
by recombinase sequences (described infra).
[1129] Animals containing more than one knockout construct and/or
more than one transgene expression construct are prepared in any of
several ways. The preferred manner of preparation is to generate a
series of mammals, each containing one of the desired transgenic
phenotypes. Such animals are bred together through a series of
crosses, backcrosses and selections, to ultimately generate a
single animal containing all desired knockout constructs and/or
expression constructs, where the animal is otherwise congenic
(genetically identical) to the wild type except for the presence of
the knockout construct(s) and/or transgene(s).
[1130] The present invention is further illustrated by the
following examples which should not be construed as limiting in any
way. The contents of all cited references (including literature
references, issued patents, published patent applications as cited
throughout this application are hereby expressly incorporated by
reference. The practice of the present invention will employ,
unless otherwise indicated, conventional techniques of cell
biology, cell culture, molecular biology, transgenic biology,
microbiology, recombinant DNA, and immunology, which are within the
skill of the art. Such techniques are explained fully in the
literature. See, for example, Molecular Cloning A Laboratory
Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring
Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D.
N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed.,
1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid
Hybridization (B. D. Hames & S. J. Higgins eds. 1984);
Transcription And Translation (B. D. Hames & S. J. Higgins eds.
1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc.,
1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal,
A Practical Guide To Molecular Cloning (1984); the treatise,
Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer
Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds.,
1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols.
154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And
Molecular Biology (Mayer and Walker, eds., Academic Press, London,
1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M.
Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse
Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y., 1986).
Electronic Apparatus Readable Media and Arrays
[1131] Electronic apparatus readable media comprising the SPOIL
molecules of the present invention is also provided. As used
herein, "electronic apparatus readable media" refers to any
suitable medium for storing, holding or containing data or
information that can be read and accessed directly by an electronic
apparatus. Such media can include, but are not limited to: magnetic
storage media, such as floppy discs, hard disc storage medium, and
magnetic tape; optical storage media such as compact disc;
electronic storage media such as RAM, ROM, EPROM, EEPROM and the
like; general hard disks and hybrids of these categories such as
magnetic/optical storage media. The medium is adapted or configured
for having recorded thereon a marker of the present invention.
[1132] As used herein, the term "electronic apparatus" is intended
to include any suitable computing or processing apparatus or other
device configured or adapted for storing data or information.
Examples of electronic apparatus suitable for use with the present
invention include stand-alone computing apparatus; networks,
including a local area network (LAN), a wide area network (WAN)
Internet, Intranet, and Extranet; electronic appliances such as a
personal digital assistants (PDAs), cellular phone, pager and the
like; and local and distributed processing systems.
[1133] As used herein, "recorded" refers to a process for storing
or encoding information on the electronic apparatus readable
medium. Those skilled in the art can readily adopt any of the
presently known methods for recording information on known media to
generate manufactures comprising the SPOIL molecules of the present
invention.
[1134] A variety of software programs and formats can be used to
store the marker information of the present invention on the
electronic apparatus readable medium. For example, the nucleic acid
sequence corresponding to the SPOIL molecules can be represented in
a word processing text file, formatted in commercially-available
software such as WordPerfect and MicroSoft Word, or represented in
the form of an ASCII file, stored in a database application, such
as DB2, Sybase, Oracle, or the like, as well as in other forms. Any
number of dataprocessor structuring formats (e.g., text file or
database) may be employed in order to obtain or create a medium
having recorded thereon the SPOIL molecules of the present
invention.
[1135] By providing the SPOIL molecules of the invention in
readable form, one can routinely access the marker sequence
information for a variety of purposes. For example, one skilled in
the art can use the nucleotide or amino acid sequences of the
present invention in readable form to compare a target sequence or
target structural motif with the sequence information stored within
the data storage means. Search means are used to identify fragments
or regions of the sequences of the invention which match a
particular target sequence or target motif.
[1136] The present invention therefore provides a medium for
holding instructions for performing a method for determining
whether a subject has a bone metabolism disorder, an inflammatory
disorder, or an immune disorder or a pre-disposition to a bone
metabolism disorder, an inflammatory disorder, or an immune
disorder, wherein the method comprises the steps of determining the
presence, absence, or aberrant production of a SPOIL molecule or a
SPOIL variant and based on the presence, absence or aberrant
production of a SPOIL molecule or a SPOIL variant, determining
whether the subject has a bone metabolism disorder, an inflammatory
disorder, or an immune disorder or a pre-disposition to a bone
metabolism disorder, an inflammatory disorder, or an immune
disorder and/or recommending a particular treatment for the bone
metabolism disorder, an inflammatory disorder, or an immune
disorder.
[1137] The present invention therefore provides a medium for
holding instructions for performing a method for determining
whether a subject has a bone metabolism disorder, an inflammatory
disorder, or an immune disorder or a pre-disposition to a bone
metabolism disorder, an inflammatory disorder, or an immune
disorder, wherein the method comprises the steps of determining the
presence, absence, or aberrant production of a SPOIL molecule or a
SPOIL variant and based on the presence, absence or aberrant
production of a SPOIL molecule or a SPOIL variant, determining
whether the subject has a bone metabolism disorder, an inflammatory
disorder, or an immune disorder or a pre-disposition to a bone
metabolism disorder, an inflammatory disorder, or an immune
disorder and/or recommending a particular treatment for the bone
metabolism disorder, an inflammatory disorder, or an immune
disorder. The method may further comprise the step of receiving
phenotypic information associated with the subject and/or acquiring
from a network phenotypic information associated with the
subject.
[1138] The present invention also provides in a network, a method
for determining whether a subject has a hematological disorder or a
pre-disposition to a bone metabolism disorder, an inflammatory
disorder, or an immune disorder or a pre-disposition to a bone
metabolism disorder, an inflammatory disorder, or an immune
disorder associated with the SPOIL molecules, said method
comprising the steps of receiving information associated with the
SPOIL molecule, receiving phenotypic information associated with
the subject, acquiring information from the network corresponding
to the SPOIL molecule and its associated disorders, and based on
one or more of the phenotypic information, the SPOIL molecule, and
the acquired information, determining whether the subject has a
bone metabolism disorder, an inflammatory disorder, or an immune
disorder or a pre-disposition to a bone metabolism disorder, an
inflammatory disorder, or an immune disorder. The method may
further comprise the step of recommending a particular treatment
for the bone metabolism disorder, the inflammatory disorder, or the
immune disorder or a pre-disposition to the bone metabolism
disorder, the inflammatory disorder, or the immune disorder.
[1139] The present invention also provides a business method for
determining whether a subject has a bone metabolism disorder, an
inflammatory disorder, or an immune disorder or a pre-disposition
to a bone metabolism disorder, an inflammatory disorder, or an
immune disorder, said method comprising the steps of receiving
information associated with the SPOIL molecules, receiving
phenotypic information associated with the subject, acquiring
information from the network corresponding to the SPOIL molecules
and its associated disorders, and based on one or more of the
phenotypic information, the SPOIL molecule, and the acquired
information, determining whether the subject has a bone metabolism
disorder, an inflammatory disorder, or an immune disorder or a
pre-disposition to a bone metabolism disorder, an inflammatory
disorder, or an immune disorder. The method may further comprise
the step of recommending a particular treatment for the bone
metabolism disorder, the inflammatory disorder, or the immune
disorder or a pre-disposition to the bone metabolism disorder, the
inflammatory disorder, or the immune disorder.
[1140] The invention also includes an array comprising a SPOIL
molecule of the present invention. The array can be used to assay
expression of one or more genes in the array. In one embodiment,
the array can be used to assay gene expression in a tissue to
ascertain tissue specificity of genes in the array. In this manner,
up to about 7600 genes can be simultaneously assayed for
expression. This allows a profile to be developed showing a battery
of genes specifically expressed in one or more tissues.
[1141] In addition to such qualitative determination, the invention
allows the quantitation of gene expression. Thus, not only tissue
specificity, but also the level of expression of a battery of genes
in the tissue is ascertainable. Thus, genes can be grouped on the
basis of their tissue expression per se and level of expression in
that tissue. This is useful, for example, in ascertaining the
relationship of gene expression between or among tissues. Thus, one
tissue can be perturbed and the effect on gene expression in a
second tissue can be determined. In this context, the effect of one
cell type on another cell type in response to a biological stimulus
can be determined. Such a determination is useful, for example, to
know the effect of cell-cell interaction at the level of gene
expression. If an agent is administered therapeutically to treat
one cell type but has an undesirable effect on another cell type,
the invention provides an assay to determine the molecular basis of
the undesirable effect and thus provides the opportunity to
co-administer a counteracting agent or otherwise treat the
undesired effect. Similarly, even within a single cell type,
undesirable biological effects can be determined at the molecular
level. Thus, the effects of an agent on expression of other than
the target gene can be ascertained and counteracted.
[1142] In another embodiment, the array can be used to monitor the
time course of expression of one or more genes in the array. This
can occur in various biological contexts, as disclosed herein, for
example development of hematological disorder, progression of
hematological disorder, and processes, such a cellular
transformation associated with hematological disorder.
[1143] The array is also useful for ascertaining the effect of the
expression of a gene on the expression of other genes in the same
cell or in different cells. This provides, for example, for a
selection of alternate molecular targets for therapeutic
intervention if the ultimate or downstream target cannot be
regulated.
[1144] The array is also useful for ascertaining differential
expression patterns of one or more genes in normal and abnormal
cells. This provides a battery of genes that could serve as a
molecular target for diagnosis or therapeutic intervention.
[1145] This invention is further illustrated by the following
examples which should not be construed as limiting. The contents of
all references, patents and published patent applications cited
throughout this application, as well as the Figures and the
Sequence Listing are incorporated herein by reference.
EXAMPLES
Example 1
Isolation of a Full-Length cDNA Encoding Human Delta3
[1146] Human microvascular endothelial cells (HMVEC catalog
#CC2543; Clonetics, San Diego, Calif.) were separated into four
samples of cells which were treated as follows. The first sample
was untreated. The second sample was treated with human TGF-.beta.1
(hTGF-.beta.1) (10 ng/ml) (Upstate Biotechnology, Lake Placid,
N.Y., Catalog NO: 01-134). The third sample was treated with bFGF
(10 ng/ml)/VEGF (25 ng/ml) (Upstate Biotechnology, Lake Placid,
N.Y., Catalog NO: 01-134, Catalog Nos. 01-106 and 01-185,
respectively). The fourth sample was differentiated on Matrigel
(Collaborative Biomedical Products, Becton Dickinson Labware,
Bedford, Mass.). Cells were treated as indicated for 24 hours, the
4 samples were pooled, and RNA was extracted from the pooled cells
using a QIAGEN RNeasy kit. The resulting cDNA library was subjected
to high throughput random sequencing. This allowed identification
of a cDNA fragment comprising the following 171 nucleotide long
sequence:
TABLE-US-00012 (SEQ ID NO: 21)
GCCCAGGCNGACCCTGGTGTGGACTGTGAGCTGGAGCTCAGCGAGTGT
GACAGCAACCCCTGTCGCANTGGAGGCAGCTGTAAGGACCANGAGGAT
GGCTACCACTGCCTGTGTCCTCCGGGCTACTACGGCNTGCATCGTGAA
CACNGCACCTCTTAGCTGNGCCGACTC.
[1147] Comparison of the nucleotide sequence of this partial cDNA
with the sequences in GenBank using the BLAST program (Altschul et
al. (1990) J. Mol. Biol. 215:403) revealed that the nucleotide
sequence encoded a protein fragment having a significant homology
to Delta proteins. In fact, the amino acid sequence had significant
homology with a chicken Delta1 protein (GenBank Accession NO:
U26590), a Xenopus Delta1 protein (GenBank Accession NO: L42229), a
rat Delta1 protein (GenBank Accession NO: U78889), a Xenopus Delta2
protein (GenBank Accession NO: U70843) as well as Notch
proteins.
[1148] A full-length cDNA of about 3.2 kb was then isolated by
screening a human microvascular endothelial cell (HMVEC) cDNA
library using the partial cDNA (SEQ ID NO:21). This nucleic acid
was deposited at the American Type Culture Collection (ATCC.RTM.)
on Mar. 5, 1997, and has been assigned ATCC.RTM. Accession NO:
98348. The nucleotide sequence of the cDNA isolated is shown in SEQ
ID NO:1.
[1149] A nucleic acid sequence comparison of SEQ ID NO:1 against
EST sequence databases using the BLAST program (Altschul et al.
(1990) J. Mol. Biol. 215:403) indicated that 5 ESTs have a homology
to portions of SEQ ID NO:1. These are all located 3' of the
nucleotide sequence encoding the transmembrane domain, i.e.,
downstream of nucleotide 1996 of SEQ ID NO:1. Three of these ESTs
(having accession Nos. T33770, T33811, and T07963) have a
nucleotide sequence starting at about nucleotide 2044 of SEQ ID
NO:1. However, the nucleotide sequence of the three EST is
significantly different from the nucleotide sequence of hDelta3 in
about the first 50 nucleotides 3' of nucleotide 2044 of SEQ ID
NO:1. Two ESTs (having Accession Nos. R32717 and T07962) are
located further downstream of the three ESTs.
[1150] The nucleic acid having SEQ ID NO:1 encodes a protein of 685
amino acids having SEQ ID NO:2. A comparison of the amino acid
sequence of SEQ ID NO:2 with sequences in GenBank using BLASTP
(Altschul et al. (1990) J. Mol. Biol. 215:403) reveals that this
protein has a certain homology to previously described Delta
proteins. An alignment of the human Delta3 protein having SEQ ID
NO:2 with the amino acid sequence of mouse Delta1 protein
(Accession NO: X80903), rat Delta1 protein (Accession NO: U78889),
chicken Delta1 protein (Accession NO: U26590), two Xenopus Delta1
proteins (Accession Nos. L42229 and U70843) and Drosophila Delta1
protein (Accession NO: AA142228) indicates that human Delta3
protein has the general structure of a Delta3 protein. In
particular, human Delta3 protein has a signal peptide corresponding
to about amino acid 1 to about amino acid 17 of SEQ ID NO:2, a DSL
motif corresponding to the sequence from about amino acid 173 to
about amino acid 217, a first EGF-like domain corresponding to the
sequence from about amino acid 222 to about amino acid 250, a
second EGF-like domain corresponding to the sequence from about
amino acid 253 to about amino acid 281, a third EGF-like domain
corresponding to the sequence from about amino acid 288 to about
amino acid 321, a fourth EGF-like domain corresponding to the
sequence from about amino acid 328 to about amino acid 359, a fifth
EGF-like domain corresponding to the sequence from about amino acid
366 to about amino acid 399, a sixth EGF-like domain corresponding
to the sequence from about amino acid 411 to about amino acid 437,
a seventh EGF-like domain corresponding to the sequence from about
amino acid 444 to about amino acid 475, an eight EGF-like domain
corresponding to the sequence from about amino acid 484 to about
amino acid 517, a transmembrane domain corresponding to the
sequence from about amino acid 530 to about amino acid 553, and a
cytoplasmic domain corresponding to the sequence from about amino
acid 554 to about amino acid 685 of SEQ ID NO:2.
[1151] An amino acid and nucleotide sequence comparison between the
members of the Delta1 and Delta3 protein family and human Delta3 on
one hand and between the members of the Delta1 family reveals that
the homology between the Delta3 family members is stronger than the
homology between human Delta3 and any of the Delta1 family members.
For example, although hDelta3 is only approximately 58% similar to
the Drosophila Delta1 protein; approximately 70% similar to the
mouse Delta1 protein; approximately 70% similar to the rat Delta1
protein; approximately 68% similar to the chick Delta1 protein; and
approximately 68% similar to the Xenopus Delta1 proteins; the
drosophila, mouse, rat, chick and Xenopus Delta1 proteins are very
similar to each other (e.g., the mouse and rat Delta1 are about 96%
similar to each other). Published PCT application WO97/01571
discloses a partial nucleotide and amino acid sequence of a protein
having significant homology to Delta1 family members, indicating
that it is likely to be a human Delta1 protein. The homology
between the partial amino acid sequence of human Delta1 and the
amino acid sequence of human Delta3 is indicated in Table I and
shows that the proteins are encoded by different genes. All these
amino acid and nucleotide sequence comparisons indicate that human
Delta3 is an additional species of Delta proteins, sharing some
sequence and structure homology with the Delta1 proteins.
[1152] In one embodiment of a nucleotide sequence of human Delta3,
the nucleotide at position 455 is a guanine (G) (SEQ ID NO:1). In
this embodiment, the amino acid at position 40 is glutamate (E)
(SEQ ID NO:2). In another embodiment of a nucleotide sequence of
human Delta3, the nucleotide at position 455 is a cytosine (C) (SEQ
ID NO:27). In this embodiment, the amino acid at position 40 is
glutamine (Q) (SEQ ID NO:28). In another embodiment of a nucleotide
sequence of human Delta3, the nucleotide at position 455 is a
thymidine (T) (SEQ ID NO:29). In this embodiment, the amino acid at
position 40 is a stop codon (SEQ ID NO:30). In another embodiment
of a nucleotide sequence of human Delta3, the nucleotide at
position 455 is a adenine (A) (SEQ ID NO:31). In this embodiment,
the amino acid at position 40 is lysine (K) (SEQ ID NO:32).
[1153] In one embodiment of a nucleotide sequence of human Delta3,
the nucleotide at position 786 is an cytosine (C) (SEQ ID NO:1). In
this embodiment, the amino acid at position 150 is a alanine (A)
(SEQ ID NO:2). In an alternative embodiment, a species variant of
human Delta3 has a nucleotide at position 786 which is a thymidine
(T) (SEQ ID NO:33). In this embodiment, the amino acid at position
150 is valine (V) (SEQ ID NO:34), i.e., a conservative
substitution.
[1154] In one embodiment of a nucleotide sequence of human Delta3,
the nucleotide at position 594 is a cytosine (C) (SEQ ID NO:1). In
this embodiment, the amino acid at position 86 is threonine (T)
(SEQ ID NO:2). In an alternative embodiment, a species variant of
human Delta3 has a nucleotide at position 594 which is a guanine
(G) (SEQ ID NO:35). In this embodiment, the amino acid at position
86 is serine (S) (SEQ ID NO:36), i.e., a conservative
substitution.
[1155] In one embodiment of a nucleotide sequence of human Delta3,
wherein the nucleotide at position 883 is a thymidine (T) (SEQ ID
NO:1). In this embodiment, the amino acid at position 182 is
aspartate (D) (SEQ ID NO:2). In an alternative embodiment, a
species variant of human Delta3 has a nucleotide at position 883
which is an adenine (A) (SEQ ID NO:37). In this embodiment, the
amino acid at position 182 is glutamate (E) (SEQ ID NO:38), i.e., a
conservative substitution.
Example 2
Isolation of a Full-Length cDNA Encoding Mouse Delta3
[1156] A mouse Delta3 cDNA was identified from mouse lung database
library of expressed sequences using the human Delta3 cDNA (SEQ ID
NO:1) as a query sequence. The most homologous sequence, SEQ ID
NO:24 was identified as a 3.2 kb cDNA.
[1157] The nucleic acid having SEQ ID NO:24 encodes a protein of
686 amino acids having the amino acid sequence shown in SEQ ID
NO:25. An alignment of the human and mouse Delta3 proteins having
SEQ ID NO:2 and 25, respectively, indicates that human and mouse
Delta3 proteins have significant similarity and identity (i.e.,
88.2% similar and 86.6% identical) suggesting evolutionary
conservation due to an essential biological function.
[1158] Mouse Delta3 protein has a signal peptide corresponding to
about amino acid 1 to about amino acid 17 of SEQ ID NO:25, a DSL
motif corresponding to the sequence from about amino acid 174 to
about amino acid 218, a first EGF-like domain corresponding to the
sequence from about amino acid 223 to about amino acid 251, a
second EGF-like domain corresponding to the sequence from about
amino acid 254 to about amino acid 282, a third EGF-like domain
corresponding to the sequence from about amino acid 289 to about
amino acid 322, a fourth EGF-like domain corresponding to the
sequence from about amino acid 329 to about amino acid 360, a fifth
EGF-like domain corresponding to the sequence from about amino acid
367 to about amino acid 400, a sixth EGF-like domain corresponding
to the sequence from about amino acid 412 to about amino acid 438,
a seventh EGF-like domain corresponding to the sequence from about
amino acid 445 to about amino acid 476, an eight EGF-like domain
corresponding to the sequence from about amino acid 485 to about
amino acid 518, a transmembrane domain corresponding to the
sequence from about amino acid 531 to about amino acid 554, and a
cytoplasmic domain corresponding to the sequence from about amino
acid 555 to about amino acid 686 of SEQ ID NO:25.
[1159] In one embodiment of a nucleotide sequence of mouse Delta3,
the nucleotide at position 49 is cytosine (C) (SEQ ID NO:24). In
this embodiment, the amino acid at position 4 is alanine (A) (SEQ
ID NO:25). In an alternative embodiment, a species variant of mouse
Delta3 has a nucleotide at position 49 which is thymidine (T) (SEQ
ID NO:39). In this embodiment, the amino acid at position 4 is
valine (V) (SEQ ID NO:40), i.e., a conservative substitution.
[1160] In one embodiment of a nucleotide sequence of mouse Delta3,
the nucleotide at position 51 is thymidine (T) (SEQ ID NO:24). In
this embodiment, the amino acid at position 5 is serine (S) (SEQ ID
NO:25). In an alternative embodiment, a species variant of mouse
Delta3 has a nucleotide at position 51 which is a adenine (A) (SEQ
ID NO:41). In this embodiment, the amino acid at position 5 is
threonine (T) (SEQ ID NO:42), i.e., a conservative
substitution.
[1161] In one embodiment of a nucleotide sequence of mouse Delta3,
the nucleotide at position 109 is guanine (G) (SEQ ID NO:24). In
this embodiment, the amino acid at position 24 is arginine (R) (SEQ
ID NO:25). In an alternative embodiment, a species variant of mouse
Delta3 has a nucleotide at position 109 which is adenine (A) (SEQ
ID NO:43). In this embodiment, the amino acid at position 24 is
histidine (H) (SEQ ID NO:44), i.e., a conservative
substitution.
[1162] In one embodiment of a nucleotide sequence of mouse Delta3,
wherein the nucleotide at position 130 is a thymidine (T) (SEQ ID
NO:24). In this embodiment, the amino acid at position 31 is
phenylalanine (F) (SEQ ID NO:25). In an alternative embodiment, a
species variant of mouse Delta3 has a nucleotide at position 130
which is adenine (A) (SEQ ID NO:45). In this embodiment, the amino
acid at position 31 is tyrosine (Y) (SEQ ID NO:46), i.e., a
conservative substitution.
Example 3
Tissue Expression of the hDelta3 Gene
[1163] This Example describes the tissue distribution of Delta3
protein, as determined by Northern blot hybridization with a 1.6 kb
fragment of human Delta3 cDNA corresponding to the extreme 3' end
of SEQ ID NO:1 and by in situ hybridization using a probe
complementary to nucleotides 1290-1998 of SEQ ID NO:1.
[1164] Northern blot hybridizations with the various RNA samples
were performed under standard conditions and washed under stringent
conditions, i.e., in 0.2.times.SSC at 65.degree. C. In each sample,
the probe hybridized to a single RNA of about 3.5 kb. The results
of hybridization of the probe to various mRNA samples are described
below.
[1165] Hybridization of a Clontech Fetal Multiple Tissue Northern
(MTN) blot (Clontech, LaJolla, Calif.) containing RNA from fetal
brain, lung, liver, and kidney indicated the presence of Delta3 RNA
in each of these fetal tissues. Expression was significantly higher
in fetal lung and kidney than in fetal brain and liver.
Hybridization of a Clontech human Multiple Tissue Northern I (MTNI)
and Multiple Tissue Northern H (MTNII) blots (Clontech, LaJolla,
Calif.) containing RNA from adult heart, brain, placenta, lung,
liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate,
testis, ovary, small intestine, mucosal lining of the colon, and
peripheral blood leukocytes with the human 1.6 kb Delta3 probe
indicated expression in heart, placenta, lung, skeletal muscle,
kidney, pancreas, spleen, thymus, prostate, testis, ovary, small
intestine and colon. Expression was particularly strong in adult
heart, placenta, lung, and skeletal muscle. Expression was also
found in adult brain, liver and testis. However, no significant
amount of hDelta3 mRNA was detected in adult peripheral blood
leukocytes.
[1166] Further, Northern blot hybridization of total mRNA from
HMVEC cells treated with TGF-.beta.1 at 10 ng/ml for 24 hours, bFGF
at 10 ng/ml/VEGF at 25 ng/ml for 24 hours, or untreated for 24
hours indicated that Delta3 expression was induced upon induction
with bFGF/VEGF. Accordingly, expression of Delta3 is up-regulated
in HMV endothelial cells in response to certain growth factors.
[1167] Hybridization of a "cancer" Northern blot containing RNA
from HL-60, HeLa, K562, MoLT4, Raji, SW480, A549, and G361 cells,
revealed that Delta3 is expressed at high levels in the colorectal
carcinoma cell line SW480. Thus, Delta3 expression is high in at
least certain tumor cells.
[1168] Delta-3 in situs on paraffin embedded mouse embryos were
performed. Expression was seen in endothelial cells of the
secondary vasculature and in preendothelial cells in the bone
marrow. There is no expression in endothelial cells after day P
1.5.
[1169] For in situ hybridization analysis of mDelta3, 10 m sagittal
sections of fresh frozen day E13.5, E14.5, E15.5, E16.5, E18.5 and
P1.5 embryos of B6 mice, as well as 8 m cross sections of brain,
spinal cord, eye and harderian gland, submandibular gland, white
fat, stomach, heart, lung, liver, spleen, thymus, small intestine,
lymph node, pancreas, skeletal muscle, testes, ovary, placenta,
kidney and adrenal gland from adult B6 mice were used for
hybridization. Sections were postfixed with 4% formaldehyde in
DEPC-treated 1.times. phosphate-buffered saline at room temperature
for 10 minutes before being rinsed twice in DEPC-treated 1.times.
phosphate-buffered saline and once in 0.1 M triethanolamine-HCl
(pH8.0). Following incubation in 0.25% acetic anhydride-0.1 M
triethanolamine-HCl for 10 minutes, sections were rinsed in
DEPC-treated 2.times.SSC (1.times.SSC is 0.15M NaCl plus 0.015M
sodium citrate). Tissue was dehydrated through a series of ethanol
washes, incubated in 100% chloroform for 5 minutes, and then rinsed
in 100% ethanol for 1 minute and 95% ethanol for 1 minute and
allowed to air dry.
[1170] The hybridization was performed using a
.sup.35S-radiolabeled cRNA probe from the DNA sequence of
nucleotides 1290-1998 of SEQ ID NO:1.
[1171] Tissues were incubated with probe (approximately
5.times.10.sup.7 cpm/ml) in the presence of a solution containing
600 mM NaCl, 10 mM Tris (pH 7.5), 1 mM EDTA, 0.01% sheared salmon
sperm DNA, 0.01% yeast tRNA, 0.05% yeast total RNA type X1,
1.times.Denhardt's solution, 50% formamide, 10% dextran sulfate,
100 mM dithiothreitol, 0.1% sodium dodecylsulfate (SDS), and 0.1%
sodium thiosulfate for 18 h at 55 C.
[1172] After hybridization, slides were washed with 2.times.SSC.
Sections were then sequentially incubated at 37 C in TNE (a
solution containing 10 mM Tris-HCl (pH 7.6), 500 mM NaCl, and 1 mM
EDTA), for 10 minutes, in TNE with 10 ug of RNase A per ml for 30
minutes, and finally in TNE for minutes. Slides were then rinsed
with 2.times.SSC at room temp, washed with 2.times.SSC at
50.degree. C. for 1 hour, washed with 0.2.times.SSC at 55.degree.
C. for 1 hour, and 0.2.times.SSC at 60.degree. C. for 1 hour.
Sections were then dehydrated rapidly through serial ethanol-0.3 M
sodium acetate concentrations before being air dried and exposed to
Kodak Biomax MR scientific imaging film for 6 days at room
temperature.
[1173] Expression was most abundant and wide spread during
embryogenesis. Strongest expression was observed in the eye in all
of the embryonic ages tested. Signal in a pattern suggestive of
neuronal expression was not observed in any other tissues making
the expression in the eye unique. Moderate ubiquitous expression
was also detected in lung, thymus and brown fat during
embryogenesis. A multifocal, scattered signal was also observed
throughout the embryo. This signal pattern was more focused in the
cortical region of the kidney and outlining the intestinal tract.
Adult expression was highest in the ovary and the cortical regions
of the kidney and adrenal gland.
[1174] Thus, Delta3 is expressed in numerous tissues, but is not
detected in certain tissues, e.g., peripheral blood leukocytes and
adult heart tissue (at least when using Northern blot
hybridization), is expressed at relatively high levels in at least
some tumor cells, e.g., colon carcinoma cells, and its expression
can be up-regulated in response to some growth factors, e.g., bFGF
and VEGF. Furthermore, in situ hybridization shows that mDelta3 is
expressed most strongly in developing tissues of eye, thymus, lung
and brown fat.
[1175] A Southern blot containing DNA from a panel of a
human/hamster mono-chromosomal somatic cell hybrids was probed with
an hDelta1 cDNA probe. The results obtained clearly indicates that
the human Delta3 gene resides on chromosome 15.
Example 4
Increased Expression of hDelta3 in Differentiating Endothelial
Cells
[1176] This Example shows that the expression of the hDelta3 gene
increases in differentiating endothelial cells relative to
non-differentiating endothelial cells.
[1177] HMVEC cells were separated into 5 cultures and treated as
follows: (1) cells were induced to quiescence by growth in basal
endothelial growth medium (EGM) (Clontech) which contains 10% fetal
calf serum (FCS); (2) cells were grown in complete endothelial
growth medium (EGM-MV) (Clontech, Catalog NO: CC-3125) which
contains 10% FCS and growth factors; (3) cells were stimulated to
proliferate by culture in EGM-MV in the presence of bFGF at 10
ng/ml and VEGF at 25 ng/ml; (4) cells were stimulated to
proliferate by culture in EGM-MV in the presence of TGF-131 at 10
ng/ml; and (5) cells were stimulated to differentiate by culture in
EGM-MV on Matrigel. After 24 hours of culture, the cells were
harvested, the RNA was extracted and submitted to Northern blot
analysis. Hybridization was performed with the 1.6 kb hDelta3 probe
described above. The results indicate that among the culture
conditions tested, quiescent cells express the lowest amount of
hDelta3 (at a barely detectable level). Cells which are
proliferating express a higher level of hDelta3. Interestingly, the
mRNA level of hDelta3 was strongly increased in cells induced to
differentiate by plating on Matrigel.
[1178] Thus, this Example clearly demonstrates that hDelta3
expression is strongly increased in cells induced to differentiate
and also in cells induced to proliferate.
Example 5
hDelta3 is Located in a Chromosomal Region Associated with
ACCPN
[1179] The location of hDelta3 on human chromosome 15 was
determined using radiation hybrid (RH) mapping.
[1180] A sequence tagged site (STS) was generated from the 3'
untranslated region of the gene using a forward primer having the
nucleotide sequence GTTTACATTGCATCCTGGAT (SEQ ID NO:51) and a
reverse primer having the nucleotide sequence CTCTTCTGTTCCTCTGGTTG
(SEQ ID NO:22). The STS was used to screen the Genebridge 4 (Gyapay
et al. (1996) Human Molecular Genetics 5:339) and the Standford G3
(Stewart et al. (1997) Genome Res. 7:422) radiation hybrid panels.
These panels were derived by fusion of irradiated human donor cells
with rodent recipient cells and can be used for positioning STS
markers within existing framework maps, ordering markers in the
region of interest as well as establishing the distance between
markers.
[1181] RH mapping was performed by PCR under the following
conditions: 25 ng DNA/20 .mu.l reaction, 0.5 of each primer, 0.2 mM
of each nucleotide, 1.5 mM MgCl.sub.2, 1.times. buffer as provided
by the manufacturer of the enzyme, 35 cycles at 94.degree. C.,
55.degree. C., 72.degree. C. for 30 seconds each.
[1182] The results of the RH mapping indicated that hDelta3 maps to
15q12-15 close to framework marker D15S1244 on the Stanford G3
panel and close to framework marker D15S144 on the Genebridge 4
panel with a LOD score >3. Searching of the OMIM database
(Online Mendelian Inheritance in Man) indicated that this region
has previously been genetically linked to a neurological disorder
called Agenesis of the Corpus Callosum with Peripheral Neuropathy
(ACCPN) (Casaubon et al. (1996) Am. J. Hum. Genet. 58:28).
Example 6
Delta3 Encodes a Notch Ligand
[1183] The example presented herein demonstrates that Delta3
encodes a Notch Ligand. In particular, the data presented herein
shows, first, that hDelta3 encodes a functional Notch ligand as
determined by its ability to block differentiation of C2C12 cells.
When C2C12 cells are co-cultured, under low mitogenic conditions,
with NIH3T3 cells expressing a Notch ligand, the differentiation to
myotubes by the C2C12 cells is blocked. (Lindsell et al. (1995)
Cell 80:909). If the cells differentiate troponin T is expressed,
if differentiation is blocked no troponin T expression is seen. In
addition, the data presented herein directly demonstrates that
Delta3 binds Notch one and Notch 2. Third, the data presented in
this section identifies several cell types that endogenously
exhibit Delta3 receptors.
[1184] To determine whether hDelta3 in fact encodes a functional
Notch ligand, NIH3T3 cells were engineered to express hDelta3,
co-cultured with C2C12 cells and analyzed for troponin T
expression. Briefly, NIH3T3 cells were infected with a retrovirus
containing the hDelta3 coding region cloned into the MIGR
retroviral vector (Pear et al. (1998) Blood 92:3780). This vector
contains an Internal Ribosome Entry Site (IRES) downstream of the
cloning site, followed by the cDNA for the green fluorescent
protein (GFP). GFP expression from the vector is monitored to
assess the efficiency of transduction of the vector into the target
cells. C2C12 cells were plated in 10 cm dishes and cultured in DMEM
media with 10%
[1185] Inactivated Fetal Calf Serum (10% IFS) until 70% confluent.
C2C12 cells were then washed 1.times. with PBS. 5.times.10.sup.6
NIH3T3 cells harboring either an empty vector, a vector expressing
hDelta3 or a vector expressing Jagged-1 were resuspended in 10 mls
DMEM media containing 10% Horse serum (10% HS), and laid on top of
the C2C12 cells.
[1186] Control experiments involved the solitary culture of C2C12
cells in differentiation media (10% HS) as well as in growth media
(10% IFS). The whole population of cells was lysed three to four
days later and equal amounts of protein was resolved on an
SDS-polyacrylamide gel. The proteins were then transferred onto a
nitrocellulose membrane and probed with an anti-Troponin T antibody
(Sigma, 1:200). A secondary incubation with an anti-mouse antibody
conjugated to horseradish peroxidase allowed for detection using
chemiluminescence reagents (Amersham). When cells NIH3T3 cells
containing the empty vector were co-cultured with C2C12 cells,
troponin T was expressed, indicating that the C2C12 cells had
indeed differentiated into myotubes. When NIH3T3 cells expressing
hDelta3 were co-cultured with C2C12 cells, no expression of
troponin T was seen, indicating that C2C12 differentiation was
blocked by hDelta3. This result is similar to that seen when NIH3T3
cells expressing Jagged 1 (a functional Notch ligand).
[1187] Next, Delta3 was tested for its ability to bind human notch1
and notch2. 293T cells were transiently transfected with expression
plasmids (PCMV poly-neo) encoding full-length Notch1 or Notch2. Two
days after transfection cells were incubated with purified protein
consisting of the extracellular domain of hDelta3 fused in frame to
the Fc portion of immunoglobulin G (hDelta3-Fc) at 10 .mu.g/ml or
with control protein consisting of human immunoglobulin G1 (hIgG1)
at 10 ug/ml in staining buffer (PBS containing 3% fetal calf serum,
1 mM CaCl.sub.2 and 0.02% sodium azide). After one hour of
incubation, cells were washed three times in staining buffer and
bound protein was detected by incubating the cells with
FITC-conjugated anti-human IgG for 30 minutes. Cells were analyzed
under fluorescence microscopy.
[1188] Binding of hDelta3-Fc fusions to cells expressing Notch1 and
Notch2 but not to cells transfected with empty expression vector,
was detected. Binding was calcium-dependent and was abolished in
the presence of 5 mM EDTA. Control-Fc fusions and hIgG1 did not
show any binding to transfected cells. These results establish
hDelta3 as a ligand for Notch1 and Notch2 and show that the
extracellular domain of hDelta3 is sufficient to mediate binding to
Notch.
[1189] Therefore, Delta3, including hDelta3, represents a
polypeptide which can function as a bona fide Notch ligand.
[1190] Next, Cell lines were tested for the presence of an
endogenous receptor for hDelta3. Briefly, cells were washed two
times in staining buffer and incubated with hDelta3-Fc or hIgG1 (10
.mu.g/ml in staining buffer) at a cell concentration of
5.times.10.sup.6 per ml. After an incubation of one hour on ice,
cells were washed three times in staining buffer and bound protein
was detected by incubating the cells with FITC-conjugated secondary
antibody (anti-human hIgG1) for 30 min on ice. Cells were analyzed
by flow cytometry on a FACSCalibur. Binding of hDelta3-Fc was seen
to Jurkat, 32D, C2C12 and Cos cells. A control Fc fusion protein
and hIgG1 did not show binding to these cell lines. The binding of
hDelta3-Fc was dependent on calcium since the binding was abolished
by the addition of 5 mM EDTA to the binding buffer.
Example 7
Delta3 Affects Early Development and Muscle Cell
Differentiation
[1191] The data presented herein demonstrate that among the roles
of Delta3 is a function that involves early development and muscle
cell differentiation.
Materials and Methods
[1192] Preparation of hDelta3 RNA: The template for the hDelta3 in
vitro transcription reaction was prepared from the DNA construct
containing the hDelta3 sequence inserted in a pCS2++ vector, which
was then linearized using AscI. Capped RNA was synthesized using
SP6 RNA polymerase from the linearized plasmid using mMESSAGE
mMACHINE kit (Ambion, Austin, Tex.) according to the manufacturer's
instructions. In vitro transcribed capped RNA was purified using
RNAesy kit (Qiagen) and analyzed by gel electrophoresis.
[1193] HDelta3 RNA injection into Xenopus embryos: Xenopus embryos
were obtained by in vitro fertilization, dejellied in 2% cysteine
HCl (pH 7.6), washed thoroughly in Modified Ringer's solution, and
incubated at 15-25.degree. C. Embryos were transferred to injection
solution (Modified Ringer's solution containing 3% Ficoll) prior to
injections. One ng and 2.5 ng of hDelta3 RNA were injected into one
blastomere at the 2-cell stage. Embryos were transferred to
0.1.times.MMR from the injection solution after approximately 6
hours and grown until the appropriate stage.
[1194] Embryos for histological examination were fixed in 4%
formaldehyde in PBS overnight, embedded in paraffin and stained
with Heidenhain's Azan stain by standard procedures. Transverse
sections of injected embryos show disruption of somitic
organization and somite boundaries on the injected side.
[1195] Xenopus animal cap assay: 2 ng of hDelta3 RNA was injected
into the animal pole of each of the 2 Xenopus blastomeres at the
2-cell stage. Animal caps from uninjected or injected embryos were
explanted at stage 9 and cultured in 1XModified Ringers containing
0.01% BSA and 50 ug/ml gentamycin. Animal caps were cultured until
control embryos have reached stage 23-24. Animal cap tissue was
lysed and total RNA was extracted using RNeasy kit (Qiagen).
RT-PCRs were performed on these samples using gene-specific primers
and appropriate annealing temperatures and the products analyzed by
gel electrophoresis. The primers used in this experiment were
specific to genes EF1-alpha, XCG-1, NCAM, Xbra, M-actin, Sox-17
(Amaravadi et al. (1997). Dev. Biol. 192:392-404). RT-PCR analysis
did not indicate expression of any of the specific marker genes
tested.
Results:
[1196] Examination of embryos injected with hDelta3 RNA two days
post-injection showed an overexpression phenotype involving axial
disruption indicative of an effect on somites and anterior dorsal
structures such as eyes and cement glands were not well
differentiated in half of the injected embryos. These results
suggest that hDelta3 has an effect on early tissue
development/differentiation.
[1197] The differential stain used in this study also indicated an
enlargement of somite size on the injected side demonstrating that
hDelta3 has an effect on muscle cells and overexpression can lead
to enlarged muscle mass. Notch/Delta signaling has been shown to
play a key role in somitogenesis/myogenesis in various species
(Wittenberger et al., (1999) EMBO J. 18:915-922); Dornseifer et al.
(1997) Mech. Dev. 63:159-171); Kusumi et al. (1998) Nat. Genet.
19:274-278).
[1198] Therefore, the results presented herein indicate that Delta3
can be involved in early development (e.g., can have a role
downstream of germ layer specification function), and can be
involved in modulating myogenesis and muscle cell
differentiation.
Example 8
Identification of Delta Therapeutics
[1199] This Example describes a simple assay for isolating Delta
therapeutics, (e.g., agonist or antagonist of a Delta activity),
e.g., Delta3 therapeutics. Based at least in part on the results
described in the previous Examples, Delta therapeutics can be used
for treating various diseases, including neurological diseases,
and/or hyper- or hypoproliferative diseases, hematologic disorders,
immunodeficiency states and diseases or conditions associated with
defects in vasculature and/or conditions requiring
neovascularization and/or conditions hallmarked by aberrant
neovascularization, e.g., diabetic retinopathy. In addition, based
at least in part on the similarity of amino acid sequence and
structure between the various Delta proteins, Delta3 therapeutics
can be used to treat diseases or conditions associated with an
aberrant Delta3 activity or an aberrant Delta activity other than a
Delta3 activity. Similarly, Delta3 therapeutics as well as Delta
therapeutics other than Delta3 therapeutics can be used to treat
diseases or conditions associated with an aberrant Delta3 activity.
The assay set forth below is applicable to Delta proteins other
than Delta3 proteins.
[1200] A Delta3 therapeutic can be identified by using an in vitro
assay, in which the interaction between a Delta3 protein and a
Delta3 binding protein, e.g., a Notch protein, is determined in the
presence and in the absence of a test compound. A soluble binding
fragment of a Delta3 protein can be prepared by expression of the
extracellular portion of human Delta3, e.g., about amino acids
1-529 of SEQ ID NO:2 or about amino acids 1-530 of SEQ ID NO:25, in
E. coli according to methods known in the art. Alternatively, the
Delta3 protein fragment can be about amino acid 173 to about amino
acid 517 of SEQ ID NO:2 or from about amino acid 174 to about amino
acid 508 of SEQ ID NO:25. Similarly, a Delta3 binding fragment of a
Delta3 binding protein (i.e., Delta3 binding partner) can be
produced recombinantly.
[1201] A Delta3 binding protein can be a Notch protein and can be
identified, e.g., by determining whether the protein is capable of
binding to a Delta3 protein. A nucleic acid encoding a Notch
protein can be obtained, e.g., by PCR amplifying a portion of a
Notch gene encoding at least an EGF-like domain, using primers
having a nucleotide sequence derived from the nucleotide sequence
of a Notch gene present in GenBank or disclosed in PCT Application
NO: PCT/US92/03651 or PCT/US93/09338.
[1202] Test compounds can then be tested to determine whether they
inhibit the interaction between the Delta3 and the Delta3 binding
protein by using an ELISA type assay. Accordingly, one of the
recombinantly produced Delta3 protein and the Delta3 binding
protein, e.g., Notch protein, is attached to a solid phase surface
and the other protein is labeled, e.g., such as by tagging the
protein with an epitope, for which an antibody is available (e.g.,
FLAG epitope, available from International Biotechnologies, Inc.).
As a non-limiting example of an assay, the Delta3 protein can be
linked to the wells of a microtiter (96 well) plate by overnight
incubation of the protein at a concentration of 10 .mu.g/ml in PBS.
After blocking unoccupied sites on the plate with a BSA solution,
various amounts of test compounds and the recombinantly produced
Delta3 binding protein are added to the wells in a buffer suitable
for a specific interaction between the proteins.
[1203] After an incubation time of several hours, the wells are
rinsed with buffer, and the amount of Delta3 binding protein
attached to the wells is determined. The amount of bound protein
can be determined by incubating the wells with an anti-tag, e.g.,
anti-myc, antibody, which can then be detected by enzyme
immunoassay. The amount of bound protein is then determined by
determining the optical density using an ELISA reader. A lower
amount of Delta3 binding protein in a well that contained a test
compound relative to a well that did not contain a test compound is
indicative that the test compound inhibits the interaction between
Delta3 and a Delta3 binding protein.
[1204] In a further non-limiting example of a binding assay, a
recombinantly produced and labeled Delta3 polypeptide, or fragment
thereof capable of binding a Delta3 binding protein, is incubated,
with or without a test compound, with cells expressing the Delta3
binding protein (Shimizu et al. (1999) J. Biol. Chem.
274:32961-32969). Alternatively, the recombinant Delta3 polypeptide
is not labeled and is detected upon binding the cell by a second
Delta3 binding protein, such as an antibody. A lower amount of
Delta3 binding protein in a well that contained a test compound
relative to a well that did not contain a test compound is
indicative that the test compound inhibits the interaction between
Delta3 and a Delta3 binding protein.
[1205] A Delta3 therapeutic can also be identified by using a
reporter assay in which the level of expression of a reporter
construct under the control of a Delta3 promoter is measured in the
presence or absence of a test compound. A Delta3 promoter can be
isolated by screening a genomic library with a Delta3 cDNA which
preferably contains the 5' end of the cDNA. A portion of the Delta3
promoter, typically from about 50 to about 500 base pairs long is
then cloned upstream of a reporter gene, e.g., a luciferase gene,
in a plasmid. This reporter construct is then transfected into
cells, e.g., neural cells or endothelial cells. Transfected cells
are then be distributed into wells of a multiwell plate and various
concentrations of test compounds are added to the wells. After
several hours incubation, the level of expression of the reporter
construct is determined according to methods known in the art. A
difference in the level of expression of the reporter construct in
transfected cells incubated with the test compound relative to
transfected cells incubated without the test compound will indicate
that the test compound is capable of modulating the expression of
the Delta3 gene and is thus a Delta3 therapeutic.
Example 9
Isolation and Characterization of Human FTHMA-070 cDNAs
[1206] The nucleic acid molecule encoding FTHMA-070 was identified
during the sequencing of clones present in a cardiac coronary
artery smooth muscle cell library. A clone was identified which
appeared to have some homology to TNF receptor. This clone proved
to encode FTHMA-070. The nucleic acid sequence and deduced amino
acid sequence of FTHMA-070, which has homology to tumor necrosis
factor receptor (including the death domain) are shown in SEQ ID
NO:53 and SEQ ID NO:54, respectively.
Example 10
Characterization of FTHMA-070 Proteins
[1207] The human FTHMA-070 cDNA isolated as described above (SEQ ID
NO:53) encodes a 401 amino acid protein (SEQ ID NO:54). FTHMA-070
is predicted to include a 21 amino acid signal peptide (amino acid
1 to about amino acid 21 of SEQ ID NO:54) preceding the 380 mature
protein (about amino acid 22 to amino acid 401; SEQ ID NO:56).
Example 11
Preparation of FTHMA-070 Proteins
[1208] Recombinant FTHMA-070 can be produced in a variety of
expression systems. For example, the mature FTHMA-070 peptide can
be expressed as a recombinant glutathione-S-transferase (GST)
fusion protein in E. coli and the fusion protein can be isolated
and characterized. Specifically, as described above, FTHMA-070 can
be fused to GST and this fusion protein can be expressed in E. coli
strain PEB199. Expression of the GST-FTHMA-070 fusion protein in
PEB 199 can be induced with IPTG. The recombinant fusion protein
can be purified from crude bacterial lysates of the induced PEB 199
strain by affinity chromatography on glutathione beads.
Example 12
Isolation and Characterization of Human FTHMA-070 cDNAs
[1209] The nucleic acid molecule encoding T85 (originally called
FMHB-6D4 and FMHB-SD4) was identified using a screen designed to
identify genes encoding proteins having a functional signal
sequence. Briefly, a library was prepared in which each of the
clones contained a human fetal brain cDNA ligated to a sequence
encoding a detectable protein which lacked a signal sequence. If
the human fetal cDNA encodes a functional signal sequence, it will
permit the secretion and detection of the detecable protein. This
clone library was used to transfect mammalian cells. Clones which
secreted the detectable protein were then identified and the
corresponding human fetal brain cDNA was isolated and sequenced
using standard techniques. In this way it was possible to identify
a clone encoding T85. The nucleic acid sequence and deduced amino
acid sequence of T85 are shown in SEQ ID NO:57 and SEQ ID NO:58,
respectively.
Example 13
Characterization of T85 Proteins
[1210] The human T85 cDNA isolated as described above (SEQ ID
NO:57) encodes a 753 amino acid protein (SEQ ID NO:58). The signal
peptide prediction program SIGNALP (Nielsen et al. (1997) Protein
Engineering 10:1-6) predicted that T85 includes a 20 amino acid
signal peptide (amino acid 1 to about amino acid 20 of SEQ ID
NO:58) preceding the 733 amino acid mature protein (about amino
acid 21 to amino acid 753 of SEQ ID NO:58; SEQ ID NO:60). For
general information regarding PFAM identifiers and Hidden Markov
Model (HMM) consensus sequences refer to Sonnhammer et al. (1997)
Protein 28:405-420.
[1211] T85 has a two regions (amino acids 525-610 and 638-727 of
SEQ ID NO:58; SEQ ID NO:61 and SEQ ID NO:62, respectively) of
homology to a fibronectin type III domain (based on HMM PF00041;
SEQ ID NO:70). Also, T85 has a five regions (amino acids 43-101;
145-203; 237-298; 329-394; and 433-491 of SEQ ID NO:58; SEQ ID
NOs:63-67) of homology to a Ig superfamily domain. T85 also
includes an RGD motif starting at amino acid 247 of SEQ ID NO:58; a
cytokine receptor homolgy N-terminal (BC) domain (CC-CC) at amino
acids 516-600 of SEQ ID NO:58.
Example 14
Preparation of T85 Proteins
[1212] Recombinant T85 can be produced in a variety of expression
systems. For example, the mature T85 peptide can be expressed as a
recombinant glutathione-S-transferase (GST) fusion protein in E.
coli and the fusion protein can be isolated and characterized.
Specifically, as described above, FTHMA-070 can be fused to GST and
this fusion protein can be expressed in E. coli strain PEB 199.
Expression of the GST-T85 fusion protein in PEB 199 can be induced
with IPTG. The recombinant fusion protein can be purified from
crude bacterial lysates of the induced PEB 199 strain by affinity
chromatography on glutathione beads.
Example 15
[1213] As shown in FIGS. 2A-D, T85 exhibits considerable homology
to human Robo protein (Kidd et al. (1997) Cell 92:205-215), an axon
guidance receptor that is thought to play and important role in
neuronal development, specifically, control of midline crossing.
Accordingly, T85 may also play a role in neuronal development.
Thus, T85 nucleic acids, polypeptides, T85 agonists, and T85
antagonists may be useful in the treatment of neurological
disorders.
Example 16
Isolation and Characterization of Human Tango-77 cDNAs
[1214] Cytokine genes IL-1.alpha., IL-1.beta. and IL-1ra have been
found to be closely clustered on chromosome 2, i.e., IL-1.alpha.,
IL-1.beta. and IL-1ra are located within 450 kb of each other. BAC
clones containing IL-1.alpha. and IL-1.beta. were used to identify
other proximal unknown cytokine genes. To do this, a BAC clone
containing IL-1.alpha. and IL-1.beta. was selected from a BAC
library (Research Genetics, Huntsville, Ala.) using specific
primers designed against IL-1.alpha. and IL-1.beta.. The DNA from
the BAC was extracted and used to make a random-sheared genomic
library. From this BAC library, 4000 clones were selected for
sequencing. The resulting genomic sequences were then assembled
into contigs and used to screen proprietary and public data bases.
One genomic contig was found to contain two segments of sequences
which resemble IL-1ra. These two segments are potential exons of
Tango-77 gene.
[1215] Two PCR primers were then designed from the two potential
exons and used to screen a panel of cDNA libraries for the
expression of a Tango-77 message. A cDNA library from TNF-.alpha.
treated human lung epithelia showed a positive band of the
predicted size (i.e., if the two exons are spliced together). Using
the PCR fragment as a probe, a single cDNA clone was isolated from
the same library. This cDNA contains an insert of 989 bp. The cDNA
clone contains three possible open reading frames. The first open
reading frame encompasses 534 nucleotides (nucleotides 356-889 of
SEQ ID NO:71; SEQ ID NO:73) and encodes a 178 amino acid protein
(SEQ ID NO:72). This protein may include a predicted signal
sequence of about 63 amino acids (from amino acid 1 to about amino
acid 63 of SEQ ID NO:72 (SEQ ID NO:74)) and a predicted mature
protein of about 115 amino acids (from about amino acid 64 to amino
acid 178 of SEQ ID NO:72 (SEQ ID NO:75)).
[1216] The second putative nucleotide open reading frame
encompasses 498 nucleotides (nucleotides 389-889 of SEQ ID NO:71;
SEQ ID NO:76) and encodes a 167 amino acid protein (SEQ ID NO:77).
This protein includes a predicted signal sequence of about 52 amino
acids (from amino acid 1 to about amino acid 52 of SEQ ID NO:77
(SEQ ID NO:78)) and a predicted mature protein of about 115 amino
acids (from about amino acid 53 to amino acid 167 of SEQ ID NO:77
(SEQ ID NO:79)).
[1217] The third open reading frame (nucleotides 372-889 of SEQ ID
NO:71; SEQ ID NO:80) encompasses 408 nucleotides and encodes a 136
amino acid protein (SEQ ID NO:81). This protein includes a
predicted signal sequence of about 21 amino acids (from amino acid
1 to about amino acid 21 of SEQ ID NO:81 (SEQ ID NO:82)) and a
predicted mature protein of about 115 amino acids (from about amino
acid 22 to amino acid 136 of SEQ ID NO:81 (SEQ ID NO:83)).
[1218] Tango-77 is predicted to be 35% identical to human IL-1ra at
the amino acid level.
Example 17
Expression of Tango-77 mRNA in Human Tissues
[1219] The expression of Tango-77 was analyzed using Northern blot
hybridization. A PCR generated 989 bp Tango-77 product was
radioactively labeled with .sup.32P-dCTP using the Prime-It kit
(Stratagene; La Jolla, Calif.) according to the instructions of the
supplier. Filters containing human mRNA (MTNI and MTNII: Clontech;
Palo Alto, Calif.) were probed in ExpressHyb hybridization solution
(Clontech) and washed at high stringency according to
manufacturer's recommendations.
[1220] Tango-77 mRNA was not detected in any unstimulated tissues
(brain, liver, spleen, skeletal muscle, testis, pancreas, heart,
kidney and peripheral blood leukocytes) mRNA on Clontech Northern
blots.
[1221] Over 96 cDNA libraries were then tested for the presence of
Tango-77 using PCR amplification. Only three libraries displayed a
positive signal. These libraries were the TNF.alpha.-treated
bronchoepithelium, TNF.alpha.-treated SSC cell line and
anti-CD3-treated T cells.
Example 18
Characterization of Tango-77 Proteins
[1222] In this example, the predicted amino acid sequence of human
Tango-77 protein was compared to the amino acid sequence of known
protein IL-1ra. In addition, the molecular weight of the human
Tango-77 proteins was predicted.
[1223] The human Tango-77 cDNA (SEQ ID NO:71) isolated as described
above encodes a 178 amino acid protein (SEQ ID NO:72) or a 167
amino acid protein (SEQ ID NO:77) or a 136 amino acid protein (SEQ
ID NO:81). The signal peptide prediction program SIGNALP Optimized
Tool (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted
that Tango-77 includes a 63 amino acid signal peptide (amino acid 1
to about amino acid 63 of SEQ ID NO:72 (SEQ ID NO:74)) preceding
the 115 mature protein; or preceding the 115 mature protein (about
amino acid 52 to amino acid 167 of SEQ ID NO:77 (SEQ ID NO:78)); or
preceding the 115 mature protein (about amino acid 21 to amino acid
136 of SEQ ID NO:81; SEQ ID NO:82).
[1224] As shown in FIG. 3, Tango-77 has a region of homology to
IL-1ra (SEQ ID NO:84).
[1225] Mature Tango-77 has a predicted MW of about 13 kDa and the
predicted MW for the immature Tango-77 is 19.6 kDa, 18.5 kDa or
15.2 kDa, not including post-translational modifications.
Example 19
Preparation of Tango-77 Proteins
[1226] Recombinant Tango-77 can be produced in a variety of
expression systems. For example, the mature Tango-77 peptide can be
expressed as a recombinant glutathione-S-transferase (GST) fusion
protein in E. coli and the fusion protein can be isolated and
characterized. Specifically, as described above, Tango-77 can be
fused to GST and this fusion protein can be expressed in E. coli
strain PEB 199. Expression of the GST-Tango-77 fusion protein in
PEB 199 can be induced with IPTG. The recombinant fusion protein
can be purified from crude bacterial lysates of the induced PEB199
strain by affinity chromatography on glutathione beads.
Example 20
Alternatively Spliced Forms of IL-1ra and Tango-77
[1227] Computer program Procrustes (Gelfand et al., 1996, Proc.
Natl. Acad. Sci. USA, 93:9061-9066) is an alignment algorithm that
predicts the presence of alternatively spliced exons for a protein
of interest in a stretch of genomic DNA. Using the IL-1ra sequence,
Proscustes was used to search for the presence of additional
sequences that might encode for alternatively spliced forms of
IL-1ra in the two overlapping BAC genomic sequences. Potential
sequences that encode variant exons for IL-1ra were identified.
These predicted exons aligned well with the N-terminal region of
IL-1ra, but were not present in Tango-77. The results from
Procrustes predicts the existence of more spliced forms of
IL-1ra.
[1228] Furthermore, Procrustes also predicted an additional
sequence in BAC1 (SEQ ID NO:86) and BAC2 (SEQ ID NO:87) that
encodes an alternatively spliced exon for Tango-77
(T77-procrustes). This predicted splice variant form of Tango-77,
T77-procrustes, was aligned with Tango-77 and with IL-1ra and
IL-1.beta..
[1229] PCR primers within this sequence can be used to generate a
product that can be used to screen a panel of cDNA libraries using
standard techniques. Suitable cDNA libraries include libraries made
from TNF.alpha.-treated bronchoepithelium, TNF.alpha.-treated SSC
cell line and anti-CD3-treated T cells. The resulting cDNA clone(s)
can be isolated from the library and sequenced to identify
additional Tango-77 cDNAs.
Example 21
Isolation and Characterization of Human and Murine SPOIL cDNAs
[1230] In this example, the isolation of the genes encoding human
and murine SPOIL proteins (also referred to as "TANGO 080"
proteins) are described.
Isolation of Murine SPOIL-I and SPOIL-II cDNAs
[1231] A murine SPOIL-I cDNA was identified by searching with a
murine cDNA encoding an IL-1 signature region (Prosite.TM.
Accession Number PDOC00226) against a copy of the GenBank
nucleotide database using the BLASTN.TM. program (BLASTN 1.3 MP:
Altschul et al., J. Mol. Bio. 215:403, 1990). A clone with 48%
homology with the murine cDNA IL-1 signature region was found by
this search. The sequence was analyzed against a non-redundant
protein database with the BLASTX.TM. program, which translates a
nucleic acid sequence in all six frames and compares it against
available protein databases (BLASTX 1.3 MP:Altschul et al., supra).
This protein database is a combination of the SwissProt, PIR, and
NCBI GenPept protein databases. One clone was obtained from the
IMAGE consortium, and fully sequenced. The additional sequencing of
this clone extended the original EST by 267 nucleotides at both the
5' and 3' ends. The cDNA for this clone is approximately 746
nucleotides in length and has an open reading frame of 297
nucleotides that is predicted to encode a protein of 98 amino
acids.
[1232] The original first pass sequence of the clone showed
homology to horse IL-1ra and murine IL-1ra using the BLASTX.TM.
program. The nucleotide sequence and predicted amino acid sequences
are shown in SEQ ID NO:89 and SEQ ID NO:90, respectively. The
murine SPOIL-I protein (corresponding to amino acids 1-98 of the
predicted amino acid sequence, SEQ ID NO:90) shows 37.0% identity
to the horse IL-1ra protein and 39.0% identity to the murine IL-1ra
protein.
[1233] Alignment of murine SPOIL-I protein with murine IL-1.alpha.
(SwissProt.TM. Accession Number P01582) and murine IL-1.beta.
(SwissProt.TM. Accession Number P10749) indicates the presence of
an aspartic acid at amino acid residue 91 of SEQ ID NO:90 and amino
acid residue 74 of SEQ ID NO:93 which corresponds to an aspartic
acid found at amino acid residue 266 of murine IL-1.alpha. and
amino acid residue 261 of murine IL-1.beta.. In addition, alignment
of murine SPOIL-I with murine IL-1ra indicates that this aspartic
acid residue of SPOIL-I corresponds with a lysine at amino acid
residue 171 of murine IL-1ra (or amino acid residue 145 of mature
murine IL-1ra) which has been shown to convert IL-1ra into an
agonist by mutating this lysine residue to an aspartic acid
residue. (Ju et al. (1991) Proc. Natl. Acad. Sci. USA
88:2658-2662).
[1234] This murine SPOIL-I protein contains an IL-1 signature
domain (corresponding to amino acids 58-80 of the predicted amino
acid sequence, SEQ ID NO:90 and amino acids 41-63 of SEQ ID NO:93)
and a signal sequence (corresponding to amino acids 1-17 of the
predicted amino acid sequence, SEQ ID NO:90) which is cleaved to
form a mature SPOIL-I protein (corresponding to amino acids 1-81 of
SEQ ID NO:93). The predicted molecular weight for the 98 amino acid
SPOIL-I is approximately 10.96 kDa and the predicted molecular
weight for mature SPOIL-I (SEQ ID NO:93) is approximately 9.1
kDa.
[1235] A GenBank.TM. search using the murine SPOIL nucleotide
sequence of SEQ ID NO:89 revealed a human EST (W78043) which was
similar to a region of the nucleotide sequence of SEQ ID NO:89. As
no reading frame can be determined from an EST (such as the EST
identified in the above database search) an amino acid sequence
encoded by an EST can not be determined.
[1236] The entire cDNA of mouse SPOIL-I was used as a probe to
screen a mouse esophagus library to search for alternate SPOIL
transcripts. A second form of mouse SPOIL was isolated and
sequenced. This second form encodes a protein of 160 amino acid
residues that lacks a signal peptide. Accordingly, this isoform,
designated murine SPOIL-II is predicted to be an intracellular
protein. Alignment of the 2 mouse SPOIL proteins (FIG. 5B) shows
that they are identical at the C-terminus but have differing
N-termini. For example, murine SPOIL-I and SPOIL-II exhibit 100%
identity when amino acid residues 29-98 of murine SPOIL-I are
aligned to amino acid residues 91-160 of murine SPOIL-II . It is
predicted that the two isoforms of murine SPOIL are splice variants
of the murine SPOIL gene.
[1237] A global alignment of murine SPOIL-I (SEQ ID NO:90) with
murine SPOIL-II (SEQ ID NO:113) using the ALIGN program version 2.0
(global alignment program, Myers and Miller, CABIOS, 1989) using a
PAM120 weight residue table, a gap length penalty of 12 and a gap
penalty of 4 indicated that the proteins are 46.3% identical over
the entire length of the sequences (FIG. 5B).
Isolation of Human SPOIL-I and SPOIL-II cDNAs
[1238] A cDNA library was constructed using mRNA isolated from near
confluent monolayers of human keratinocytes (Clonetics.TM.) which
had been stimulated with 50 ng/ml PMA, 1 .mu.g/ml ionomycin, 10
ng/ml TNF, and 40 .mu.g/ml cycloheximide for 4 hours. EST
sequencing information was gathered to create a proprietary
database of information describing the keratinocyte cDNA clones.
Three clones were identified by performing a TBLASTN search of the
proprietary EST database using the sequence of murine SPOIL-I as a
query sequence (the three clones having a probability score of at
least 1.4e-48).
[1239] The nucleotide sequence and predicted amino acid sequences
of human SPOIL-I are shown in SEQ ID NO:101 and SEQ ID NO:102,
respectively. The nucleotide sequence and predicted amino acid
sequences of human SPOIL-II are shown in SEQ ID NO:104 and SEQ ID
NO:105, respectively. A global alignment of human SPOIL-I (SEQ ID
NO:102) with human SPOIL-II (SEQ ID NO:105) using the ALIGN program
version 2.0 (global alignment program, Myers and Miller, CABIOS,
1989) using a PAM120 weight residue table, a gap length penalty of
12 and a gap penalty of 4 indicated that the proteins are 80.8%
identical over the entire length of the sequences (FIG. 5A).
[1240] As was the case with the two murine isoforms of SPOIL, the
two human SPOIL isoforms exhibit exact identity at the C-terminus
and are variant at their N-termini. Human SPOIL-II has an insertion
of 40 amino acid residues close to the N-terminus of the protein
which are not present in human SPOIL-I. Like murine SPOIL-II, both
human SPOIL isoforms lack a signal sequence, and accordingly, are
predicted to be intracellular proteins. Human SPOIL-I and SPOIL-II
may be splice variants of a common gene. An alignment of human
SPOIL-I (SEQ ID NO:102) with murine SPOIL-I (SEQ ID NO:90) using
the ALIGN program (parameters set as described for the alignment of
human SPOILS I and II) indicated that the proteins are 26.3%
identical over the entire length of the sequences, e.g., global
alignment. Moreover, using the same program and parameters, it was
determined that the nucleic acids which encode murine SPOIL-I (SEQ
ID NO:89) and human SPOIL-II (SEQ ID NO:101) are 39.8% identical at
the nucleotide level. An alignment of human SPOIL-II (SEQ ID
NO:105) with murine SPOIL-II (SEQ ID NO:113) using the ALIGN
program (parameters set as described above) indicated that the
proteins are 37.3% identical over the entire length of the
sequences, e.g., global alignment.
[1241] When locally aligned, the identity between the four SPOIL
proteins described above is significant. TABLE VII sets forth the %
identity among SPOIL family members (when the C-terminal unique
domains of each family member are compared). Moreover, TABLE VII
sets forth the % identity between each SPOIL C-terminal unique
domain and murine IL-1ra. The alignment was performed using the
Lipman-Pearson Algorithm (Lipman et al. (1985) Science
227:1435-1441), with a K-tuple of 2, a Gap Penalty of 4, and a Gap
Weight Penalty of 12.
TABLE-US-00013 TABLE VII muSPOIL- muSPOIL- huSPOIL- huSPOIL- muIL-
I II I II 1ra muSPOIL-I 100 muSPOIL-II 97.1 100 huSPOIL-I 52.2 53.6
100 huSPOIL-II 52.2 53.6 100 100 muIL-ra 36.2 37.7 39.7 39.7
100
[1242] Alignment of the four SPOIL family members resulted in the
generation of at least two SPOIL consensus motifs, due to the
highly conserved nature of specific amino acid residues among the
family members. The SPOIL consensus motifs ("SPOIL signature
motifs") are set forth as SEQ ID NOs:110-111 (SEQ ID NO:110
corresponds to the short SPOIL signature motif and SEQ ID NO:111
corresponds to the long SPOIL consensus motif). Short and long
SPOIL consensus motifs are found, for example, from amino acid
residues 26-69 and 26-93 of muSPOIL-I, from residues 88-131 and
88-155 of muSPOIL-II, from residues 98-141 and 98-164 of huSPOIL-I,
and from residues 137-180 and 137-203 of huSPOIL-II.
[1243] Further alignment of the intracellular SPOIL isoforms
indicates that the proteins have at least 50% identity among the
SPOIL unique domains of the proteins. TABLE VIII sets forth the %
identity among SPOIL family members (when the SPOIL unique domains
of each family member are compared). The alignment was performed
using the Lipman-Pearson Algorithm (Lipmanet al. (1985) Science
227:1435-1441), with a K-tuple of 2, a Gap Penalty of 4, and a Gap
Weight Penalty of 12.
TABLE-US-00014 TABLE VIII muSPOIL-II huSPOIL-I huSPOIL-II
muSPOIL-II 100 huSPOIL-I 50.3 100 huSPOIL-II 50.3 100 100
Example 22
Distribution and Expression of SPOIL-I mRNA in Mouse and Human
Tissues In Situ Hybridization Analysis of Mouse Tissues
[1244] In situ analysis revealed the following expression patterns
when tissue sections were hybridized with SPOIL-I probes. SPOIL-I
mRNA was expressed almost exclusively in the squamous epithelium of
the esophagus in both adult and embryonic mouse tissues. SPOIL-I
mRNA was also expressed in the epithelial lining of the mouth in
adult mouse tissues and embryonic mouse tissues.
[1245] Moreover, in situ analysis of tissue samples for mice which
had been intravenously injected with 20 mg/kg of
lippopolysaccharide (LPS) revealed that SPOIL-I expression was
induced in the kidney.
Northern Blot Analysis of Human Tissues
[1246] Northern blot analysis of human tissues confirmed the
pattern of SPOIL expression with SPOIL-I transcripts being detected
in esophagus and, likely, trachea, among the tissues tested. In
addition, SPOIL-I was also present on human esophageal tumor
samples and overexpressed in moderately differentiated squamous
cell carcinoma of the esophagus.
Expression of SPOIL in Human and Mouse Cell Lines
[1247] Human SPOIL-I expression was induced in keratinocytes
(Clonetics) 2 hours following induction with 50 ng/ml PMA, 1 ug/mL
ionomycin, 10 ng/ml TNF and 40 ug/mL cyclohexamide. No expression
was observed in unstimulated cultures.
[1248] Moreover, inducible expression of mouse SPOIL-I was observed
in the monocytic cell line J774, 24 h after treatment with 0.1
.mu.g/ml LPS.
Example 23
Expression of Recombinant SPOIL-I Protein in Bacterial Cells
[1249] SPOIL can be expressed as a recombinant
glutathione-S-transferase (GST) fusion polypeptide in E. coli and
the fusion polypeptide can be isolated and characterized.
Specifically, SPOIL is fused to GST and this fusion polypeptide is
expressed in E. coli, e.g., strain PEB199. As, for example, the
murine SPOIL-I protein is predicted to be approximately 9.1 kDa and
the GST is predicted to be approximately 26 kDa, the fusion
polypeptide is predicted to be approximately 35.1kDa in molecular
weight. Expression of the GST-SPOIL-I fusion protein in PEB199 is
induced with IPTG. The recombinant fusion polypeptide is purified
from crude bacterial lysates of the induced PEB 199 strain by
affinity chromatography on glutathione beads. Using polyacrylamide
gel electrophoretic analysis of the polypeptide purified from the
bacterial lysates, the molecular weight of the resultant fusion
polypeptide is determined.
Example 24
Expression of Recombinant SPOIL Proteins in COS Cells
[1250] To express the murine SPOIL-I gene, for example, in COS
cells, the pcDNA/Amp vector by Invitrogen Corporation (San Diego,
Calif.) is used. This vector contains an SV40 origin of
replication, an ampicillin resistance gene, an E. coli replication
origin, a CMV promoter followed by a polylinker region, and an SV40
intron and polyadenylation site. A DNA fragment encoding the entire
SPOIL-I protein and a HA tag (Wilson et al. (1984) Cell 37:767)
fused in-frame to its 3' end of the fragment is cloned into the
polylinker region of the vector, thereby placing the expression of
the recombinant protein under the control of the CMV promoter.
[1251] To construct the plasmid, the SPOIL-I DNA sequence is
amplified by PCR using two primers. The 5' primer contains the
restriction site of interest followed by approximately twenty
nucleotides of the SPOIL-I coding sequence starting from the
initiation codon; the 3' end sequence contains complementary
sequences to the other restriction site of interest, a translation
stop codon, the HA tag and the last 20 nucleotides of the SPOIL-I
coding sequence. The PCR amplified fragment and the pcDNA/Amp
vector are digested with the appropriate restriction enzymes and
the vector is dephosphorylated using the CIAP enzyme (New England
Biolabs, Beverly, Mass.). Preferably the two restriction sites
chosen are different so that the SPOIL-I gene is inserted in the
correct orientation. The ligation mixture is transformed into E.
coli cells (strains HB101, DH5a, SURE, available from Stratagene
Cloning Systems, La Jolla, Calif., can be used), the transformed
culture is plated on ampicillin media plates, and resistant
colonies are selected. Plasmid DNA is isolated from transformants
and examined by restriction analysis for the presence of the
correct fragment.
[1252] COS cells are subsequently transfected with the
SPOIL-I-pcDNA/Amp plasmid DNA using the calcium phosphate or
calcium chloride co-precipitation methods, DEAE-dextran-mediated
transfection, lipofection, or electroporation. Other suitable
methods for transfecting host cells can be found in Sambrook, J.,
Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory
Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, NY, 1989. The expression of
the SPOIL-I protein is detected by radiolabelling
(.sup.35S-methionine or .sup.35S-cysteine available from NEN,
Boston, Mass., can be used) and immunoprecipitation (Harlow, E. and
Lane, D. Antibodies: A Laboratory Manual, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y., 1988) using an HA
specific monoclonal antibody. Briefly, the cells are labeled for 8
hours with .sup.35S-methionine (or .sup.35S-cysteine). The culture
media are then collected and the cells are lysed using detergents
(RIPA buffer, 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM
Tris, pH 7.5). Both the cell lysate and the culture media are
precipitated with an HA specific monoclonal antibody. Precipitated
proteins are then analyzed by SDS-PAGE.
[1253] Alternatively, DNA containing the SPOIL-I coding sequence is
cloned directly into the polylinker of the pcDNA/Amp vector using
the appropriate restriction sites. The resulting plasmid is
transfected into COS cells in the manner described above, and the
expression of the SPOIL-I protein is detected by radiolabelling and
immunoprecipitation using a SPOIL-I specific monoclonal
antibody
Example 25
Retroviral Delivery of SPOIL Proteins
[1254] Full length SPOIL-I genes were expressed in vivo by
retroviral-mediated infection. In this example, the sequence for
murine SPOIL-I (amino acids 1-98) was amplified using the following
primers;
TABLE-US-00015 Forward Primer (SEQ ID NO: 96): 5' AAAAAAGAAT
TCGCCACCAT GTTCAGGATC TTA 3' Reverse Primer (SEQ ID NO: 97): 5'
TCCTCTGTCG ACTCACTTGT CGTCGTCGTC CTTGTAGTCA TGTACCACAA TCAT 3'
[1255] The reverse primer placed an epitope tag (Flag sequence) on
the 3' end of the protein. Amplified products were then subcloned
into the retroviral vector MSCVneo (Hawley et al. (1994) Gene
Therapy 1:136-138), and sequence verified. Bone marrow from
5-fluorouracil treated mice infected with the retrovirus was then
transplanted into irradiated mouse recipients and the pathology was
reviewed after 5 weeks.
[1256] The spleen and bones of the mouse recipients were taken 5
weeks after transplantation. Disassociated spleen cells, which are
a source of osteoclast progenitors, from the SPOIL-I infected mice
were plated on top of ST2 bone marrow stromal line in the presence
of 1, 25 dihdroxyvitamin D3 as described by Lacey et al. (1995)
Endocrinology 136:2367-2376 and Udagawa et al. (1989) Endocrinology
125:1805-1813. In addition, spleen cells from control mice
transplanted with marrow infected with retrovirus without the
inserted SPOIL-I gene, were plated. After nine days of culture, the
number of osteoclasts was determined by staining for tartrate
resistant acid phosphatase (TRAP).
[1257] The results of these experiments demonstrated that the
number of TRAP positive osteoclasts was dramatically decreased in
cultures with the SPOIL-I infected spleen cells as compared to the
control cells. Histologically, the bones of mice recipients
transplanted with SPOIL-I infected marrow, also appeared to be
thicker than the bones of the corresponding control mice.
Generally, there was less trabecular bone at the growth plate. The
trabecular bone was compressed and thickened with more osteoloid
formation and more osteoblasts present.
Example 26
Identification And Characterization of NEOKINE-1 cDNAs
[1258] In this example, the identification and characterization of
the genes encoding human, murine, rat and macaque NEOKINE-1 (also
referred to as "ANTIKINE-1", "TANGO 112", or T112) is
described.
Isolation of the Murine and Human NEOKINE-1 cDNAs
[1259] The invention is based, at least in part, on the discovery
of the murine and human genes encoding a novel protein, referred to
herein as NEOKINE-1. In order to identify potentially novel
chemokines, using an automated procedure, the human amino acid
sequences of the chemokines, interleukin-8, gamma-IP10, Sis-Delta,
fractalkine, and SDF-1 were used to search proprietary databases
and the dbEST databases using TBLASTN (Wash U. version, 2.0,
BLOSUM62 search matrix). Sequences exhibiting 90% or greater
identity to any protein present in Genpept, SwissProt, or PIR were
marked as examples of these proteins and removed. This analysis
identified a mouse EST (accession number AA013634) potentially
encoding a chemokine. As the encoded protein was quite divergent
from all other chemokine family members, and the open reading frame
constituted a small percentage of the total cDNA length (see
below), to establish whether this transcript encoded a novel
chemokine family member, the nucleotide sequence of the entire cDNA
was determined. To do this, first, additional ESTs from the mouse
gene were retrieved from public databases by similarity searches. A
total of 33 murine sequences were thus retrieved. Second, these
sequences were used to create an extensive length of continuous
sequence (contig). The 33 murine ESTs were aligned and edited at
discrepant bases into a single contig of 1420 bp. The 5' end of the
contig appeared to be missing part of the open reading frame. To
extend this sequence, the sizes of the inserts of several of the
murine cDNA clones from which the ESTs were derived was determined
and one with the largest insert (about 1.45 kb) was subsequently
re-sequenced in its entirety. This extended the sequence by 5 by to
1425 bp and corrected some remaining discrepancies.
[1260] 72 human ESTs from a presumptive human orthologue of the
above-described mouse gene were identified. However, these ESTs,
after a similar assembly and editing, aligned into two
non-overlapping contigs of 364 and 1101 bp. Comparison with the
murine sequence suggested that the 364-bp contig derived from the
5' part of the human gene, while the 1101-bp contig derived from
the 3' part of the human gene and included the poly(A) tail. The
distribution of 5' EST reads implied that there was no cDNA clone
which contained both halves of the gene. At the 3' end of the 5'
contig, there was a naturally occurring run of adenosine
nucleotides (see below), to which the oligo-d(T) primer used in
reverse transcription would have annealed (i.e., this primer would
have annealed at two sites: the actual poly (A) tail and this
internal oligo (A) stretch). This ectopic primer would have blocked
reverse transcription in the human sequence at about 1.1 kb from
the 3' end, but also would have allowed a second set of cDNA
molecules to be synthesized which covered the 5' end of the gene.
The two human EST contigs that can be derived from these 72 ESTs
therefore would appear on inspection and in the absence of further
information, to derive from two genes instead of one. That this is
the case is shown by the fact that automated assembly of ESTs
produced distinct "UniGene" numbers for the two contigs (Hs.21210
for the 5' contig and Hs.24395 for the 3' contig).
[1261] To establish that the two human contigs derived from the
same transcript, two primers lacking oligo d(T) were designed from
the two assembled human contigs such that they would amplify an
.about.300 bp fragment spanning the contigs. Using first-strand
cDNA prepared from human placental poly (A)+ RNA, a unique
.about.300 bp fragment aws amplified by standard techniques. This
cDNA was subsequently cloned and sequenced. The sequence did span
the two contigs and provided the missing sequence between them. The
primers were h112/227f (CCAAGCGCTTCATCAAGTGG) (SEQ ID NO:125) and
h112/526r (GCAGCCTGTGATGAAGTCTGG) (SEQ ID NO:126).
[1262] The 5' end of the contig, which included part of the open
reading frame, was missing from the assembled single contig. To
obtain the complete transcript sequence at the 5' end for the human
gene, a cDNA clone (rthp112) extending from the 5' end of the human
transcript to beyond the end of the open reading frame was
generated by the RACE procedure. The gene-specific primer used was
t112racel (CAGCCTATTCTTCGTAGACCCTGC) (SEQ ID NO:127). The 5'-most
35 bp of this clone formed a palindrome and thus appeared to be a
cloning artifact, as is well known in the art, and was removed from
the final sequence. The remaining sequence extended the human cDNA
sequence by 108 bp to 1564 bp and corrected some remaining
discrepancies. Clone rthp112, comprising the entire coding region
of human NEOKINE-1 has been deposited with the ATTC and has
Accession No. 98751.
[1263] The nucleotide sequence encoding the human NEOKINE-1 protein
is set forth as SEQ ID NO:115. The full length protein encoded by
this nucleic acid is comprised of about 99 amino acids and has the
amino acid sequence set forth as SEQ ID NO:116. The coding portion
(open reading frame) of SEQ ID NO:115 is set forth as SEQ ID
NO:117.
[1264] To identify a murine cDNA clone containing a near
full-length insert, the sizes of the inserts of several of the
murine cDNA clones from which the ESTs were derived was determined
and one with the largest insert (about 1.45 kb) was subsequently
re-sequenced in its entirety. This extended the sequence by 5 bp to
1425 bp and corrected some remaining discrepancies.
[1265] The nucleotide sequence encoding the murine NEOKINE-1
protein is set forth as SEQ ID NO:118. The full length protein
encoded by this nucleic acid is comprised of about 92 amino acids
and has the amino acid sequence set forth as SEQ ID NO:119. The
coding portion (open reading frame) of SEQ ID NO:118 is set forth
as SEQ ID NO:120.
Analysis of Murine and Human NEOKINE-1
[1266] Examination of the assembled and corrected cDNA sequences
depicted in SEQ ID NO:115 and SEQ ID NO:118 showed that they likely
encoded highly-conserved proteins, human and mouse NEOKINE-1. Based
on the presence of 4 cysteine residues, which presumably form 2
disulfide bonds, a predicted signal sequence, a predicted mature
peptide mass of about 10,000 daltons, and a characteristic spacing
of one residue between the first two cysteines, it was judged that
the encoded protein was a novel member of the alpha chemokine
family, and a member of the subfamily that lacked the
glutamine-leucine-arginine sequence before the first cysteine.
However, three atypical features were also present but conserved
between species. These were, first, the presence of an extra 5
residues between the second pair of cysteines; second, the fewest
residues before the predicted amino terminus of the mature protein
and the first cysteine of any naturally-occurring chemokine; and
third, a general dissimilarity to all other chemokines in the
region between the second and third cysteines.
[1267] A BLAST search (Altschul et al. (1990) J. Mol. Biol.
215:403) of the nucleotide sequence of human NEOKINE-1 has revealed
that NEOKINE-1 is significantly similar to a human STS
(TIGR-A002114, Accession No. G26440) which was sequenced as part of
the WI/MIT human gene mapping project and derived from a
TIGR-assembled contig that lacks any of the open reading frame of
human NEOKINE-1. (The TIGR-assembled contig failed to reveal the
true ORF of human NEOKINE-1, most likely to the existence of a
significant number of potential ORFs which fortuitously exist in
the long 3' UTR of the human NEOKINE cDNA, but do not, in fact
encode the human NEOKINE-1 protein.) The gene is located to human
5q31.1 near the marker D5S396, distinct from the chemokine cluster
on chromosome 4q. Plausible human disease genes that map to this
region include a hereditary eosinophilia (EOS) and a hereditary
high serum IgE associated with hypersuppression of inflammation in
the skin (IGES).
[1268] The clones of both the human and murine EST sequences used
in the assembly of the human and murine contigs derive
predominantly from prenatal tissues. In particular, 6 human ESTs
derive from clones isolated from neonatal female placenta, 4 human
ESTs derive from clones isolated from 8-9-week placenta, 4 human
ESTs derive from clones isolated from fetal heart, 4 human ESTs
derive from clones isolated from 20-week male liver and spleen, 4
human ESTs derive from clones isolated from breast tumor, 4 human
ESTs derive from clones isolated from colon tumor, 3 human ESTs
derive from clones isolated from adult breast, 2 human ESTs derive
from clones isolated from pregnant uterus, 2 human ESTs derive from
clones isolated from endometrial tumor, 1 human EST derives from a
clone isolated from fetal brain, 1 human EST derives from a clone
isolated from alveolar rhabdomyosarcoma, 1 human EST derives from a
clone isolated from ovary tumor, 1 human EST derives from a clone
isolated from 8-9-week total fetus, 1 human EST derives from a
clone isolated from TIGR placenta II, 1 human EST derives from a
clone isolated from corneal stroma, 1 human EST derives from a
clone isolated from 3 m muscular atrophy, 1 human EST derives from
a clone isolated from thyroid tumor, 1 human EST derives from a
clone isolated from a 6-week embryo, and 1 human EST derives from a
clone isolated from a 12-week embryo. murine ESTs derive from
clones isolated from 13.5+14.5d whole embryo, 5 murine ESTs derive
from clones isolated from 19.5d embryo, 4 murine ESTs derive from
clones isolated from 8.5d embryo, 3 murine ESTs derive from clones
isolated from 12.5d embryo, 3 murine ESTs derive from clones
isolated from 7d kidney. 2 murine ESTs derive from clones isolated
from 13.5+14.5d placenta, 1 murine EST derives from a clone
isolated from 6.5/8.5d embryo, 1 murine EST derives from a clone
isolated from liver, 1 murine EST derives from a clone isolated
from 4-week male thymus, 1 murine EST derives from a clone isolated
from diaphragm, and 1 murine, EST derives from a clone isolated
from 11-week skin.
Tissue Distribution of NEOKINE-1 mRNA
[1269] This Example describes the tissue distribution of NEOKINE
mRNA, as determined by Northern blot and in situ hybridization.
[1270] Northern blot hybridizations with the various RNA samples
were performed under standard conditions and washed under stringent
conditions, i.e., 0.2.times.SSC at 65.degree. C. In each sample,
the probe hybridized to a single RNA of about 1.9 kb. The results
of hybridization of the probe to various mRNA samples are described
below.
[1271] Expression in mouse embryos was examined using a
developmental mouse Northern (Clontech) and in situ hybridization.
This blot had poly(A)+ RNA isolated from whole embryos of age 7,
11, 15 and 17 days. The analysis using the mouse gene as a probe
revealed intense expression of a unique 1.9 kb transcript in the 7
d sample, but this may be due to contaminating RNA from the
placenta. In the remaining samples, expression was low at 11d,
highest on day 15, and then dropped again on day 17.
[1272] Expression in diverse human tissue was examined using
tissue-specific Northern blots (Clontech). These blots had poly(A)+
RNA isolated from various disease-free human organs. The analysis
using a PCR fragment of the human gene as a probe revealed
strongest expression of a unique 1.9 kb transcript in the kidney
and small intestine, followed by strong expression in the spleen,
uterus and colon, and lower expression in thymus, prostate,
stomach, thyroid, spinal cord, lymph node, trachea, adrenal gland,
bone marrow, heart, brain placenta, liver, smooth muscle and
pancreas. There was little/no expression in lung, peripheral blood
leukocytes and testis. The size of the poly(A)+transcript in both
human and mouse (1.9 kb) is consistent with the length of the
full-length cDNAs (1.56 kb) which lack the poly(A) tails.
[1273] In situ hybridization of a murine antisense probe to various
embryonic, post-natal and adult tissues was performed as follows. 8
.mu.m sagittal sections of fresh frozen embryonic day 14.5, 16.5
and postnatal day 1.5 B6 mice, as well as 8 .mu.m sections of
various adult B6 mouse tissues (listed below) were used for
hybridization. Sections were postfixed with 4% formaldehyde in DEPC
treated 1.times. phosphate-buffered saline at room temperature for
10 min before being rinsed twice in DEPC 1.times.
phosphate-buffered saline and once in 0.1 M triethanolamine-HCl (pH
8.0). Following incubation in 0.25% acetic anhydride-0.1 M
triethanolamine-HCl for 10 min, sections were rinsed in DEPC
2.times.SSC (1.times.SSC is 0.15M NaCl plus 0.015M sodium citrate).
Tissue was dehydrated through a series of ethanol washes, incubated
in 100% chloroform for 5 min, and then rinsed in 100% ethanol for 1
min and 95% ethanol for 1 min and allowed to air dry.
[1274] The hybridization was performed using a
.sup.35S-radiolabeled cRNA (antisense) probe from the following DNA
sequence,
TABLE-US-00016 (SEQ ID NO: 128)
GTCCAAGTGTAAGTGTTCCCGGAAGGGGCCCAAGATCCGCTACAGCGA
CGTGAAGAAGCTGGAAATGAAGCCAAAGTACCCACACTGCGAGGAGAA
GATGGTTATCGTCACCACCAAGAGCATGTCCAGGTACCGGGGCCAGGA
GCACTGCCTGCACCCTAAGCTGCAGAGCACCAAACGCTTCATCAAGTG
GTACAATGCCTGGAACGAGAAGCGCAGGGTCTACGAAGAATAGGGTGG
ACGATCATGGAAAGAAAAACTCCAGGCCAGTTGAGAGACTTCAGCAGA
GGACTTTGCAGATTAAAATAAAAGCCCTTTCTTTCTCACAAGCATAAG
ACAAATTATATATTGCTATGAAGCTCTTCTTACCAGGGTCAGTTTTTA
CATTTTATAGCTGTGTGTGAAAGGCTTCCAGATGTGAGATCCAGCTCG
CCTGCGCACCAGACTTCATTACAAGTGGCTTTTTGCTGGGCGGTTG.
[1275] A sense RNA probe made from the same DNA sequence was used
to determine specificity of the antisense probe. Tissues were
incubated with probes (approximately 5.times.10.sup.7 cpm/ml) in
the presence of a solution containing 600 mM NaCl, 10 mM Tris (pH
7.5), 1 mM EDTA, 0.01% sheared salmon sperm DNA, 0.01% yeast tRNA,
0.05% yeast total RNA type X1, 1.times.Denhardt's solution, 50%
formamide, 10% dextran sulfate, 100 mM dithiothreitol, 0.1% sodium
dodecyl sulfate (SDS), and 0.1% sodium thiosulfate for 18 h at
55.degree. C. After hybridization, slides were washed with
2.times.SSC. Sections were then sequentially incubated at
37.degree. C. in TNE (a solution containing 10 mM Tris-HCl (pH
7.6), 500 mM NaCl, and 1 mM EDTA), for 10 min, in TNE with 10 .mu.g
of RNase A per ml for 30 min, and finally in TNE for 10 min. Slides
were then rinsed with 2.times.SSC at room temp, washed with
2.times.SSC at 50.degree. C. for 1 h, washed with 0.2.times.SSC at
55.degree. C. for 1 h, and 0.2.times.SSC at 60.degree. C. for 1 h.
Sections were then dehydrated rapidly through serial ethanol-0.3 M
sodium acetate concentrations before being air dried and exposed to
Kodak Biomax MR scientific imaging film for 4 days at room
temperature.
[1276] Following a 4 day film exposure, NEOKINE mRNA was detectable
in the following tissues (Note: Tissues incubated with sense probe
showed no signal in any tissues):
Adult Mouse:
[1277] Brain--multifocal signal in the cortex Purkinje cell layer
of the cerebellum areas of the hippocampus and forebrain a small
discrete region in the ventral portion of the hindbrain low level
ubiquitous signal in most other regions eye--multifocal signal seen
in harderian gland anterior surface of lens/cornea retina
descending colon--focal signal transverse/ascending
colon--multifocal signal small Intestine--villi kidney--cortical
region adrenal gland--medulla region and capsule heart--multifocal
signal skeletal muscle--multifocal signal lung--signal outlining
the large airways thymus--low signal bladder--high signal from the
transitional epithelium placenta--signal seen in the outer
membrane/cell layer The following tissues were tested but no signal
was detected in: spleen liver Postnatal Day 1.5 mouse:
brain--specific regions, most notably the cortex no ubiquitous
expression as seen in adult nasal turbinates developing upper and
lower teeth trachea uterus sternebral cartilage kidney--medulla and
outermost cortex in a multifocal pattern skin and hair
follicles--very strong signal intestine note: no signal observed in
lung Embryonic Day 16.5 mouse: brain--specific regions, most
notably the cortex no ubiquitous expression as seen in adult spinal
cord--low signal esophagus lung--signal from large airways adrenal
gland--cortical region (note: opposite of adult) kidney--medulla
and outermost cortex in a multifocal pattern skin--very strong
signal intestine Embryonic Day 14.5 mouse: brain--discrete regions,
most notable a region in the hindbrain lung--signal from large
airways skin--very strong signal especially from whisker pads and
tip of nose and tail umbilical cord intestine
[1278] These results reveal a striking distribution of NEOKINE mRNA
in various non-lymphoid organs. The fact that many normal tissues
express abundant NEOKINE transcript suggests that these tissues
make significant quantities of NEOKINE protein and that therefore
the pro-inflammatory or chemoattractive activities of NEOKINE are
very low or non-existent. Indeed, NEOKINE is expressed most
significantly in highly immunoreactive tissues that are involved in
barrier functions. This observation is consistent with a proposed
role of NEOKINE as a suppressor of inflammation. Furthermore, the
predicted amino terminus of mature NEOKINE lies just two residues
from the first cysteine. In an analogous situation, an artificially
truncated form of human IL-8 with only one residue before the first
cysteine instead of the normal 6 residues converts the protein from
an agonist to an antagonist of its cognate receptor. These
observations are further consistent with the proposed
anti-inflammatory activity being mediated by antagonizing the
action of other pro-inflammatory chemokines. The general divergence
of NEOKINE from other alpha chemokines while being highly conserved
itself, and the presence of the extra 5 residues between the second
pair of cysteines could also be consistent with a broad antagonist
function on a diverse set of chemokine receptors. The strong
expression in the skin, the kidney, the bronchii and the brain
indicates that NEOKINES have utility in treating inflammation of
these organs, such as occurs in acute renal failure,
transplantation, allergy and infection. Furthermore, since the
human AIDS virus HIV uses some chemokine receptors as co-receptors
for infection, NEOKINES may also have utility in slowing or
blocking infection by HIV.
Example 27
Isolation And Characterization of Rat and Macaque NEOKINE-1
cDNAs
[1279] During routine tests for sequences similar to mouse or human
NEOKINE cDNA, one EST deriving from a rat brain cDNA and three ESTs
deriving from macaque brain cDNAs were identified in a database of
proprietary sequences. The database derives, at least in part, from
sequencing of various mammalian clones generated from cDNA
libraries created according to routine procedures. The cDNAs
originated from rat brain and macaque brain libraries,
respectively.
[1280] The nucleotide sequence encoding the at least 78 amino acid
residues of the rat NEOKINE-1 protein (corresponding to the
predicted mature protein) is set forth as SEQ ID NO:121. The amino
acid sequence for mature rat NEOKINE-1 is set forth as SEQ ID
NO:122. The coding portion (open reading frame) of SEQ ID NO:121 is
set forth as SEQ ID NO:123. The nucleotide sequence and predicted
amino acid sequence of macaque NEOKINE-1 are set forth as SEQ ID
NO:124 and SEQ ID NO:135, respectively.
[1281] Examination of the cDNA sequence depicted in SEQ ID NO:121
shows that rat NEOKINE-1 comprises four cysteine residues which are
conserved among all NEOKINE-1 family members identified thus far.
Structural analysis of these proteins indicates that these
cysteines are capable of forming 2 disulfide bridges. FIG. 8
depicts the alignment between the four NEOKINE-1 amino acid
sequences identified according to these Examples.
Example 28
Secretion of NEOKINE Chemokines
[1282] Expression constructs for RGSHis6 epitope-tagged
(C-terminus) human NEOKINE were transfected into 293T cells using
lipofectamine (GIBCO/BRL) according to the manufacturers
instructions. After culturing in appropriate medium for 48-72
hours, conditioned medium was harvested, spun, filtered, and passed
over nickel metal chelating column (Qiagen). After washing, bound
material was eluted 200 mM imidazole buffer and fractions
collected. Peak fractions were analyzed by SDS-PAGE and western
blot using anti His6 antibodies (Quiagen). Purified NEOKINE protein
bound to PVDF membrane after SDS-PAGE and electroblotting was
sequenced for N-terminal amino acid analysis using Edman-based
chemistry protein sequencing. The amino acid residues were analyzed
by HPLC and determined by separation and peak height as compared to
standards.
[1283] The N-terminal sequence of band NEOKINE was found to be
SKCKCSRKGP which corresponds exactly to the predicted signal
peptide cleavage site (between Gly22 and Ser23). Because the same
band is identified by anti-His6 antibodies, which recognize the
C-terminal epitope tag, the band was identified as the full length,
mature NEOKINE protein.
Example 29
Binding of NEOKINE to the NEOKINE Receptor (e.g., RDC1)
[1284] T112 (NEOKINE) was radioiodinated with lactoperoxidase
according to standard protocols. RDC-1 in vector Pcdna3.1 was
transiently transfected into 293 cells using calcium phosphate
precipitation methodology. 72 hours after transfection, cells were
harvested and binding assays performed under standard binding
conditions for chemokines (e.g., low salt binding, high salt wash,
binding at 24.degree. C., 1 hour). Cells were then pelleted,
washed, and radioactivity was counted. Binding was demonstrated and
was determined to be high affinity by competition with unlabelled
T112. The cpm bound in cell pellets in indicated below.
TABLE-US-00017 .sup.125I-T112 0.1 nm 37613.0 cpm 27014.0 cpm T112
3.0 nm 8343.0 cpm 9229.0 cpm
Example 30
Isolation and Characterization of Human T129 cDNAs
[1285] Human mesangial cells (Clonetics Corporation; San Diego,
Calif.) were expanded in culture with Mesangial Cell Growth Media
(Clonetics) according to the recommendations of the supplier. When
the cells reached 80-90% confluence, they were stimulated with
tumor necrosis factor (TNF; 10 ng/ml) and cycloheximide (CHI; 40
micrograms/ml) for 4 hours. Total RNA was isolated using the RNeasy
Midi Kit (Qiagen; Chatsworth, Calif.), and the poly A+ fraction was
further purified using Oligotex beads (Qiagen).
[1286] Three micrograms of poly A+ RNA were used to synthesize a
cDNA library using the Superscript cDNA Synthesis kit (Gibco BRL;
Gaithersburg, Md.). Complementary DNA was directionally cloned into
the expression plasmid pMET7 using the SalI and NotI sites in the
polylinker to construct a plasmid library. Transformants were
picked and grown up for single-pass sequencing.
[1287] One clone, jthKb042d12, showed limited homology to OX40
(Latza et al. (1994) Eur. J. Immunol. 24:677), a member of the TNF
receptor superfamily, and was sequenced further. Complete
sequencing of the clone revealed an approximately 2.5 kb cDNA
insert with a 1290 base pair open reading frame predicted to encode
a novel 430 amino transmembrane protein.
Example 31
Distribution of T129 mRNA in Human Tissues
[1288] The expression of T129 was analyzed using Northern blot
hybridization. A 567 bp portion of T129 cDNA encoding the amino
terminus of T129 protein was generated by PCR. The DNA was
radioactively labeled with .sup.32P-dCTP using the Prime-It kit
(Stratagene; La Jolla, Calif.) according to the instructions of the
supplier. Filters containing human mRNA (MTNI and MTNII: Clontech;
Palo Alto, Calif.) were probed in ExpressHyb hybridization solution
(Clontech) and washed at high stringency according to
manufacturer's recommendations.
[1289] These studies revealed that T129 is expressed as an
approximately 3.0 kilobase transcript at moderate levels in
peripheral blood leukocytes, spleen, and skeletal muscle. Lower
levels of transcript were seen in heart, brain and placenta. In
addition, a hybridization signal was seen in peripheral blood
leukocytes at >15 kb.
Example 32
Characterization of T129 Proteins
[1290] In this example, the predicted amino acid sequence of human
T129 protein was compared to amino acid sequences of known proteins
and various motifs were identified. In addition, the molecular
weight of the human T129 proteins was predicted.
[1291] The human T129 cDNA isolated as described above (SEQ ID
NO:137) encodes a 430 amino acid protein (SEQ ID NO:138). The
signal peptide prediction program SIGNALP Optimized Tool (Nielsen
et al. (1997) Protein Engineering 10:1-6) predicted that T129
includes a 22 amino acid signal peptide (amino acid 1 to about
amino acid 22 of SEQ ID NO:137) preceding the 408 mature protein
(about amino acid 23 to amino acid 430; SEQ ID NO:140). T129 also
include one predicted transmembrane domain (amino acids 163-186 of
SEQ ID NO:138). A hydropathy plot of T129 is presented in FIG. 9.
This plot shows the two predicted TM domains as well as a
extracellular region (labelled "OUT"; amino acids 31 to 162 of SEQ
ID NO:138) and a cytoplasmic region (labelled "IN"; amino acids 187
to 430 of SEQ ID NO:138) as well as the location of cysteines
("cys"; short vertical lines just below plot) and the TNFR/NGFR
cysteine-rich domain indicated by its PFAM identifier (PF0020; bar
just above plot). For general information regarding PFAM
identifiers refer to Sonnhammer et al. (1997) Protein
28:405-420.
[1292] T129 has a region (amino acids 51-90; SEQ ID NO:142) of
homology to a TNFR/NGFR cysteine-rich domain consensus derived from
a hidden Markov model (SEQ ID NO:141). The TNFR/NGFR cysteine-rich
domain of T129 does not include all the conserved cysteines usually
present in such domains (4 of 6). Moreover, unlike other members of
the TNF superfamily, T129 includes only one such domain; most TNF
family members include two to four such cysteine rich domains.
[1293] Mature T129 has a predicted MW of 43.5 kDa (46 kDa for
immature T129), not including post-translational modifications.
Example 33
Preparation of T129 Proteins
[1294] Recombinant T129 can be produced in a variety of expression
systems. For example, the mature T129 peptide can be expressed as a
recombinant glutathione-S-transferase (GST) fusion protein in E.
coli and the fusion protein can be isolated and characterized.
Specifically, as described above, T129 can be fused to GST and this
fusion protein can be expressed in E. coli strain PEB199.
Expression of the GST-T129 fusion protein in PEB 199 can be induced
with IPTG. The recombinant fusion protein can be purified from
crude bacterial lysates of the induced PEB 199 strain by affinity
chromatography on glutathione beads.
Deposit of Microorganisms
[1295] A nucleic acid encoding a full-length human Delta protein is
contained in a plasmid which was deposited with the American Type
Culture Collection, 10801 University Boulevard, Manassas, Va.
20110-2209 (ATCC.RTM.) on Mar. 5, 1997 and has been assigned
ATCC.RTM. accession number 98348.
[1296] A clone containing the cDNA molecule encoding human A259,
(clone Human 12) was deposited with the American Type Culture
Collection, 10801 University Boulevard, Manassas, Va., 20110-2209,
on Apr. 2, 1999 as Accession Number 207190, as a single
deposit.
[1297] A clone containing the cDNA molecule encoding mouse A259,
(clone Mouse 12) was deposited with the American Type Culture
Collection, 10801 University Boulevard, Manassas, Va., 20110-2209,
on Apr. 2, 1999 as Accession Number 207191, as a single
deposit.
EQUIVALENTS
[1298] Those skilled in the art will recognize, or be able to
ascertain using no more than routine experimentation, many
equivalents of the specific embodiments of the invention described
herein.
[1299] Such equivalents are intended to be encompassed by the
following claims.
[1300] All publications, patents and patent applications mentioned
in this specification are herein incorporated by reference into the
specification to the same extent as if each individual publication,
patent or patent application was specifically and individually
indicated to be incorporated herein by reference.
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20110306044A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20110306044A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References