U.S. patent application number 09/944907 was filed with the patent office on 2002-12-26 for secreted and transmembrane polypeptides and nucleic acids encoding the same.
This patent application is currently assigned to Genentech, Inc.. Invention is credited to Baker, Kevin P., Botstein, David, Eaton, Dan L., Ferrara, Napoleone, Filvaroff, Ellen, Gerritsen, Mary E., Goddard, Audrey, Godowski, Paul J., Grimaldi, J. Christopher, Gurney, Austin L., Hillan, Kenneth J., Kljavin, Ivar J., Napier, Mary A., Roy, Margaret Ann, Tumas, Daniel, Wood, William I..
Application Number | 20020198147 09/944907 |
Document ID | / |
Family ID | 43706161 |
Filed Date | 2002-12-26 |
United States Patent
Application |
20020198147 |
Kind Code |
A1 |
Baker, Kevin P. ; et
al. |
December 26, 2002 |
Secreted and transmembrane polypeptides and nucleic acids encoding
the same
Abstract
The present invention is directed to secreted and transmembrane
polypeptides and to nucleic acid molecules encoding those
polypeptides. Also provided herein are vectors and host cells
comprising those nucleic acid sequences, chimeric polypeptide
molecules comprising the polypeptides of the present invention
fused to heterologous polypeptide sequences, antibodies which bind
to the polypeptides of the present invention and to methods for
producing the polypeptides of the present invention.
Inventors: |
Baker, Kevin P.;
(Darnestown, MD) ; Botstein, David; (Belmont,
CA) ; Eaton, Dan L.; (San Rafael, CA) ;
Ferrara, Napoleone; (San Francisco, CA) ; Filvaroff,
Ellen; (San Francisco, CA) ; Gerritsen, Mary E.;
(San Mateo, CA) ; Goddard, Audrey; (San Francisco,
CA) ; Godowski, Paul J.; (Burlingame, CA) ;
Grimaldi, J. Christopher; (San Francisco, CA) ;
Gurney, Austin L.; (Belmont, CA) ; Hillan, Kenneth
J.; (San Francisco, CA) ; Kljavin, Ivar J.;
(Pacifica, CA) ; Napier, Mary A.; (Hillsborough,
CA) ; Roy, Margaret Ann; (San Francisco, CA) ;
Tumas, Daniel; (Orinda, CA) ; Wood, William I.;
(Hillsborough, CA) |
Correspondence
Address: |
Paul E. Rauch, Ph.D.
Brinks, Hofer, Gilson & Lione
NBC Tower - Suite 3600
455 N. Cityfront Plaza Drive
Chicago
IL
60611-5599
US
|
Assignee: |
Genentech, Inc.
|
Family ID: |
43706161 |
Appl. No.: |
09/944907 |
Filed: |
August 31, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09944907 |
Aug 31, 2001 |
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09866028 |
May 25, 2001 |
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60067411 |
Dec 3, 1997 |
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60069334 |
Dec 11, 1997 |
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60069335 |
Dec 11, 1997 |
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60069278 |
Dec 11, 1997 |
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60069425 |
Dec 12, 1997 |
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60069696 |
Dec 16, 1997 |
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60069694 |
Dec 16, 1997 |
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60069702 |
Dec 16, 1997 |
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60069870 |
Dec 17, 1997 |
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60069873 |
Dec 17, 1997 |
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60068017 |
Dec 18, 1997 |
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60070440 |
Jan 5, 1998 |
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60074086 |
Feb 9, 1998 |
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60074092 |
Feb 9, 1998 |
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60075945 |
Feb 25, 1998 |
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60112850 |
Dec 16, 1998 |
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60113296 |
Dec 22, 1998 |
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60146222 |
Jul 28, 1999 |
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Current U.S.
Class: |
435/69.1 ;
435/183; 435/320.1; 435/325; 514/1.9; 514/19.3; 514/3.8; 514/6.9;
530/350; 536/23.2 |
Current CPC
Class: |
C07K 14/70578 20130101;
G01N 33/5008 20130101; G01N 33/5085 20130101; C12N 2799/026
20130101; C07K 14/475 20130101; C07K 16/18 20130101; G01N 33/5005
20130101; A61K 38/00 20130101; C07K 14/4703 20130101; C07K 14/47
20130101; C07K 2317/24 20130101; C07K 2319/02 20130101; G01N
33/57484 20130101; C07K 2319/00 20130101; G01N 33/5011 20130101;
G01N 33/68 20130101 |
Class at
Publication: |
514/12 ; 530/350;
536/23.2; 435/69.1; 435/325; 435/183; 435/320.1 |
International
Class: |
A61K 038/17; C12P
021/02; C12N 005/06; C07K 014/435; C07H 021/04; C12N 009/00 |
Foreign Application Data
Date |
Code |
Application Number |
Sep 16, 1998 |
US |
PCT/US98/19330 |
Dec 1, 1998 |
US |
PCT/US98/25108 |
Jun 22, 1999 |
US |
PCT/US99/12252 |
Sep 15, 1999 |
US |
PCT/US99/21090 |
Nov 30, 1999 |
US |
PCT/US99/28409 |
Nov 30, 1999 |
US |
PCT/US99/28313 |
Dec 1, 1999 |
US |
PCT/US99/28301 |
Dec 16, 1999 |
US |
PCT/US99/30095 |
Feb 11, 2000 |
US |
PCT/US00/03565 |
Feb 22, 2000 |
US |
PCT/US00/04414 |
Mar 2, 2000 |
US |
PCT/US00/05841 |
Mar 30, 2000 |
US |
PCT/US00/08439 |
May 22, 2000 |
US |
PCT/US00/14042 |
Jul 28, 2000 |
US |
PCT/US00/20710 |
Dec 1, 2000 |
US |
PCT/US00/32678 |
Feb 28, 2001 |
US |
PCT/US01/06520 |
Claims
What is claimed is:
1. Isolated nucleic acid having at least 80% nucleic acid sequence
identity to a nucleotide sequence that encodes an amino acid
sequence selected from the group consisting of the amino acid
sequence shown in FIG. 2 (SEQ ID NO:2), FIG. 4 (SEQ ID NO:7), FIG.
6 (SEQ ID NO:15), FIG. 10 (SEQ ID NO:24), FIG. 14 (SEQ ID NO:32),
FIG. 16 (SEQ ID NO:37), FIG. 18 (SEQ ID NO:42), FIG. 20 (SEQ ID
NO:50), FIG. 22 (SEQ ID NO:55), FIG. 24 (SEQ ID NO:61), FIG. 26
(SEQ ID NO:69), FIG. 28 (SEQ ID NO:76), FIG. 30 (SEQ ID NO:78),
FIG. 32 (SEQ ID NO:83) and FIG. 34 (SEQ ID NO:91).
2. Isolated nucleic acid having at least 80% nucleic acid sequence
identity to a nucleotide sequence selected from the group
consisting of the nucleotide sequence shown in FIG. 1 (SEQ ID
NO:1), FIG. 3 (SEQ ID NO:6), FIG. 5 (SEQ ID NO:14), FIG. 9 (SEQ ID
NO:23), FIG. 13 (SEQ ID NO:31), FIG. 15 (SEQ ID NO:36), FIG. 17
(SEQ ID NO:41), FIG. 19 (SEQ ID NO:49), FIG. 21 (SEQ ID NO:54),
FIG. 23 (SEQ ID NO:60), FIG. 25 (SEQ ID NO:68), FIG. 27 (SEQ ID
NO:75), FIG. 29 (SEQ ID NO:77), FIG. 31 (SEQ ID NO:82) and FIG. 33
(SEQ ID NO:90).
3. Isolated nucleic acid having at least 80% nucleic acid sequence
identity to a nucleotide sequence selected from the group
consisting of the full-length coding sequence of the nucleotide
sequence shown in FIG. 1 (SEQ ID NO:1), FIG. 3 (SEQ ID NO:6), FIG.
2 (SEQ ID NO:14), FIG. 9 (SEQ ID NO:23), FIG. 13 (SEQ ID NO:31),
FIG. 15 (SEQ ID NO:36), FIG. 17 (SEQ ID NO :41), FIG. 19 (SEQ ID
NO:49), FIG. 21 (SEQ ID NO:54), FIG. 23 (SEQ ID NO:60), FIG. 25
(SEQ ID NO:68), FIG. 27 (SEQ ID NO:75), FIG. 29 (SEQ ID NO:77),
FIG. 31 (SEQ ID NO:82) and FIG. 33 (SEQ ID NO:90).
4. Isolated nucleic acid having at least 80% nucleic acid sequence
identity to the full-length coding sequence of the DNA deposited
under ATCC accession number 209526, 209508, 209524, 209528, 209530,
209523, 209492, 209532, 209531, 209529, 209527, 209570, 209618,
209621 or 209619.
5. A vector comprising the nucleic acid of any one of claims 1 to
4.
6. The vector of claim 5 operably linked to control sequences
recognized by a host cell transformed with the vector.
7. A host cell comprising the vector of claim 5.
8. The host cell of claim 7, wherein said cell is a CHO cell.
9. The host cell of claim 7, wherein said cell is an E. coli.
10. The host cell of claim 7, wherein said cell is a yeast
cell.
11. A process for producing a PRO polypeptides comprising culturing
the host cell of claim 7 under conditions suitable for expression
of said PRO polypeptide and recovering said PRO polypeptide from
the cell culture.
12. An isolated polypeptide having at least 80% amino acid sequence
identity to an amino acid sequence selected from the group
consisting of the amino acid sequence shown in FIG. 2 (SEQ ID
NO:2), FIG. 4 (SEQ ID NO:7), FIG. 6 (SEQ ID NO:15), FIG. 10 (SEQ ID
NO:24), FIG. 14 (SEQ ID NO:32), FIG. 16 (SEQ ID NO:37), FIG. 18
(SEQ ID NO:42), FIG. 20 (SEQ ID NO:50), FIG. 22 (SEQ ID NO:55),
FIG. 24 (SEQ ID NO:61), FIG. 26 (SEQ ID NO:69), FIG. 28 (SEQ ID
NO:76), FIG. 30 (SEQ ID NO:78), FIG. 32 (SEQ ID NO:83) and FIG. 34
(SEQ ID NO:91).
13. An isolated polypeptide scoring at least 80% positives when
compared to an amino acid sequence selected from the group
consisting of the amino acid sequence shown in FIG. 2 (SEQ ID
NO:2), FIG. 4 (SEQ ID NO:7), FIG. 6 (SEQ ID NO:15), FIG. 10 (SEQ ID
NO:24), FIG. 14 (SEQ ID NO:32), FIG. 16 (SEQ ID NO:37), FIG. 18
(SEQ ID NO:42), FIG. 20 (SEQ ID NO:50), FIG. 22 (SEQ ID NO:55),
FIG. 24 (SEQ ID NO:61), FIG. 26 (SEQ ID NO:69), FIG. 28 (SEQ ID
NO:76), FIG. 30 (SEQ ID NO:78), FIG. 32 (SEQ ID NO:83) and FIG. 34
(SEQ ID NO:91).
14. An isolated polypeptide having at least 80% amino acid sequence
identity to an amino acid sequence encoded by the full-length
coding sequence of the DNA deposited under ATCC accession number
209526, 209508, 209524, 209528, 209530, 209523, 209492, 209532,
209531, 209529, 209527, 209570, 209618, 209621 or 209619.
15. A chimeric molecule comprising a polypeptide according to any
one of claims 12 to 14 fused to a heterologous amino acid
sequence.
16. The chimeric molecule of claim 15, wherein said heterologous
amino acid sequence is an epitope tag sequence.
17. The chimeric molecule of claim 15, wherein said heterologous
amino acid sequence is a Fc region of an immunoglobulin.
18. An antibody which specifically binds to a polypeptide according
to any one of claims 12 to 14.
19. The antibody of claim 18, wherein said antibody is a monoclonal
antibody, a humanized antibody or a single-chain antibody.
20. Isolated nucleic acid having at least 80% nucleic acid sequence
identity to: (a) a nucleotide sequence encoding the polypeptide
shown in FIG. 2 (SEQ ID NO:2), FIG. 4 (SEQ ID NO:7), FIG. 6 (SEQ ID
NO:15), FIG. 10 (SEQ ID NO:24), FIG. 14 (SEQ ID NO:32), FIG. 16
(SEQ ID NO:37), FIG. 18 (SEQ ID NO:42), FIG. 20 (SEQ ID NO:50),
FIG. 22 (SEQ ID NO:55), FIG. 24 (SEQ ID NO:61), FIG. 26 (SEQ ID
NO:69), FIG. 28 (SEQ ID NO:76), FIG. 30 (SEQ ID NO:78), FIG. 32
(SEQ ID NO:83) or FIG. 34 (SEQ ID NO:91), lacking its associated
signal peptide; (b) a nucleotide sequence encoding an extracellular
domain of the polypeptide shown in FIG. 2 (SEQ ID NO:2), FIG. 4
(SEQ ID NO:7), FIG. 6 (SEQ ID NO:15), FIG. 10 (SEQ ID NO:24), FIG.
14 (SEQ ID NO:32), FIG. 16 (SEQ ID NO:37), FIG. 18 (SEQ ID NO:42),
FIG. 20 (SEQ ID NO:50), FIG. 22 (SEQ ID NO:55), FIG. 24 (SEQ ID
NO:61), FIG. 26 (SEQ ID NO:69), FIG. 28 (SEQ ID NO:76), FIG. 30
(SEQ ID NO:78), FIG. 32 (SEQ ID NO:83) or FIG. 34 (SEQ ID NO:91),
with its associated signal peptide; or (c) a nucleotide sequence
encoding an extracellular domain of the polypeptide shown in FIG. 2
(SEQ ID NO:2), FIG. 4 (SEQ ID NO:7), FIG. 6 (SEQ ID NO:15), FIG. 10
(SEQ ID NO:24), FIG. 14 (SEQ ID NO:32), FIG. 16 (SEQ ID NO:37),
FIG. 18 (SEQ ID NO:42), FIG. 20 (SEQ ID NO:50), FIG. 22 (SEQ ID
NO:55), FIG. 24 (SEQ ID NO:61), FIG. 26 (SEQ ID NO:69), FIG. 28
(SEQ ID NO:76), FIG. 30 (SEQ ID NO:78), FIG. 32 (SEQ ID NO:83) or
FIG. 34 (SEQ ID NO:91), lacking its associated signal peptide.
21. An isolated polypeptide having at least 80% amino acid sequence
identity to: (a) the polypeptide shown in FIG. 2 (SEQ ID NO:2),
FIG. 4 (SEQ ID NO:7), FIG. 6 (SEQ ID NO:15), FIG. 10 (SEQ ID
NO:24), FIG. 14 (SEQ ID NO:32), FIG. 16 (SEQ ID NO:37), FIG. 18
(SEQ ID NO:42), FIG. 20 (SEQ ID NO:50), FIG. 22 (SEQ ID NO:55),
FIG. 24 (SEQ ID NO:61), FIG. 26 (SEQ ID NO:69), FIG. 28 (SEQ ID
NO:76), FIG. 30 (SEQ ID NO:78), FIG. 32 (SEQ ID NO:83) or FIG. 34
(SEQ ID NO:91), lacking its associated signal peptide; (b) an
extracellular domain of the polypeptide shown in FIG. 2 (SEQ ID
NO:2), FIG. 4 (SEQ ID NO:7), FIG. 6 (SEQ ID NO:15), FIG. 10 (SEQ ID
NO:24), FIG. 14 (SEQ ID NO:32), FIG. 16 (SEQ ID NO:37), FIG. 18
(SEQ ID NO:42), FIG. 20 (SEQ ID NO:50), FIG. 22 (SEQ ID NO:55),
FIG. 24 (SEQ ID NO:61), FIG. 26 (SEQ ID NO:69), FIG. 28 (SEQ ID
NO:76), FIG. 30 (SEQ ID NO:78), FIG. 32 (SEQ ID NO:83) or FIG. 34
(SEQ ID NO:91), with its associated signal peptide; or (c) an
extracellular domain of the polypeptide shown in FIG. 2 (SEQ ID
NO:2), FIG. 4 (SEQ ID NO:7), FIG. 6 (SEQ ID NO:15), FIG. 10 (SEQ ID
NO:24), FIG. 14 (SEQ ID NO:32), FIG. 16 (SEQ ID NO:37), FIG. 18
(SEQ ID NO:42), FIG. 20 (SEQ ID NO:50), FIG. 22 (SEQ ID NO:55),
FIG. 24 (SEQ ID NO:61), FIG. 26 (SEQ ID NO:69), FIG. 28 (SEQ ID
NO:76), FIG. 30 (SEQ ID NO:78), FIG. 32 (SEQ ID NO:83) or FIG. 34
(SEQ ID NO:91), lacking its associated signal peptide.
Description
FIELD OF THE INVENTION
[0001] The present invention relates generally to the
identification and isolation of novel DNA and to the recombinant
production of novel polypeptides.
BACKGROUND OF THE INVENTION
[0002] Extracellular proteins play important roles in, among other
things, the formation, differentiation and maintenance of
multicellular organisms. The fate of many individual cells, e.g.,
proliferation, migration, differentiation, or interaction with
other cells, is typically governed by information received from
other cells and/or the immediate environment. This information is
often transmitted by secreted polypeptides (for instance, mitogenic
factors, survival factors, cytotoxic factors, differentiation
factors, neuropeptides, and hormones) which are, in turn, received
and interpreted by diverse cell receptors or membrane-bound
proteins. These secreted polypeptides or signaling molecules
normally pass through the cellular secretory pathway to reach their
site of action in the extracellular environment.
[0003] Secreted proteins have various industrial applications,
including as pharmaceuticals, diagnostics, biosensors and
bioreactors. Most protein drugs available at present, such as
thrombolytic agents, interferons, interleukins, erythropoietins,
colony stimulating factors, and various other cytokines, are
secretory proteins. Their receptors, which are membrane proteins,
also have potential as therapeutic or diagnostic agents. Efforts
are being undertaken by both industry and academia to identify new,
native secreted proteins. Many efforts are focused on the screening
of mammalian recombinant DNA libraries to identify the coding
sequences for novel secreted proteins. Examples of screening
methods and techniques are described in the literature [see, for
example, Klein et al., Proc. Natl. Acad. Sci. 93:7108-7113 (1996);
U.S. Patent No. 5,536,637)].
[0004] Membrane-bound proteins and receptors can play important
roles in, among other things, the formation, differentiation and
maintenance of multicellular organisms. The fate of many individual
cells, e.g., proliferation, migration, differentiation, or
interaction with other cells, is typically governed by information
received from other cells and/or the immediate environment. This
information is often transmitted by secreted polypeptides (for
instance, mitogenic factors, survival factors, cytotoxic factors,
differentiation factors, neuropeptides, and hormones) which are, in
turn, received and interpreted by diverse cell receptors or
membrane-bound proteins. Such membrane-bound proteins and cell
receptors include, but are not limited to, cytokine receptors,
receptor kinases, receptor phosphatases, receptors involved in
cell-cell interactions, and cellular adhesin molecules like
selectins and integrins. For instance, transduction of signals that
regulate cell growth and differentiation is regulated in part by
phosphorylation of various cellular proteins. Protein tyrosine
kinases, enzymes that catalyze that process, can also act as growth
factor receptors. Examples include fibroblast growth factor
receptor and nerve growth factor receptor.
[0005] Membrane-bound proteins and receptor molecules have various
industrial applications, including as pharmaceutical and diagnostic
agents. Receptor immunoadhesins, for instance, can be employed as
therapeutic agents to block receptor-ligand interactions. The
membrane-bound proteins can also be employed for screening of
potential peptide or small molecule inhibitors of the relevant
receptor/ligand interaction.
[0006] Efforts are being undertaken by both industry and academia
to identify new, native receptor or membrane-bound proteins. Many
efforts are focused on the screening of mammalian recombinant DNA
libraries to identify the coding sequences for novel receptor or
membrane-bound proteins.
[0007] 1. PRO241
[0008] Cartilage is a specialized connective tissue with a large
extracellular matrix containing a dense network of collagen fibers
and a high content of proteoglycan. While the majority of the
proteoglycan in cartilage is aggrecan, which contains many
chondroitin sulphate and keratin sulphate chains and forms
multimolecular aggregates by binding with link protein to
hyaluronan, cartilage also contains a number of smaller molecular
weight proteoglycans. One of these smaller molecular weight
proteoglycans is a protein called biglycan, a proteoglycan which is
widely distributed in the extracellular matrix of various other
connective tissues including tendon, sclera, skin, and the like.
Biglycan is known to possess leucine-rich repeat sequences and two
chondroitin sulphate/dermatan sulphate chains and functions to bind
to the cell-binding domain of fibronectin so as to inhibit cellular
attachment thereto. It is speculated that the small molecular
weight proteoglycans such as biglycan may play important roles in
the growth and/or repair of cartilage and in degenrative diseases
such as arthritis. As such, there is an interest in identifying and
characterizing novel polypeptides having homology to biglycan
protein.
[0009] We herein describe the identification and characterization
of novel polypeptides having homology to the biglycan protein,
wherein those polypeptides are herein designated PRO241
polypeptides.
[0010] 2. PRO243
[0011] Chordin (Xenopus, Xchd) is a soluble factor secreted by the
Spemann organizer which has potent dorsalizing activity (Sasai et
al., Cell 79: 779-90 (1994); Sasai et al, Nature 376: 333-36
(1995). Other dorsalizing factors secreted by the organizer are
noggin (Smith and Harlan, Cell 70: 829-840 (1992); Lamb et al,
Science 262: 713-718 (1993) and follistatin (Hemmanti-Brivanlou et
al., Cell 77: 283-295 (1994). Chordin subdivides primitive ectoderm
into neural versus non-neural domains, and induces notochord and
muscle formation by the dorsalization of the mesoderm. It does this
by functioning as an antagonist of the ventralizing BMP-4 signals.
This inhibition is mediated by direct binding of chordin to BMP4 in
the extracellular space, thereby preventing BMP-4 receptor
activation by BMP-4 (Piccolo et al., Develop. Biol. 182: 5-20
(1996).
[0012] BMP-4 is expressed in a gradient from the ventral side of
the embryo, while chordin is expressed in a gradient complementary
to that of BMP-4. Chordin antagonizes BMP4 to establish the low end
of the BMP4 gradient. Thus, the balance between the signal from
chordin and other organizer-derived factors versus the BMP signal
provides the ectodermal germ layer with its dorsal-ventral
positional information. Chordin may also be involved in the
dorsal-ventral patterning of the central nervous system (Sasai et
al, Cell 79: 779-90 (1994). It also induces exclusively anterior
neural tissues (forebrain-type), thereby anteriorizing the neural
type (Sasai et al, Cell 79: 779-90 (1997). Given its role in
neuronal induction and patterning, chordin may prove useful in the
treatment of neurodegenerative disorders and neural damage, e.g.,
due to trauma or after chemotherapy.
[0013] We herein describe the identification and characterization
of novel polypeptides having homology to the chordin protein,
wherein those polypeptides are herein designated PRO243
polypeptides.
[0014] 3. PRO299
[0015] The notch proteins are involved in signaling during
development. They may effect asymmetric development potential and
may signal expression of other proteins involved in development.
[See Robey, E., Curr. Opin. Genet. Dev., 7(4):551 (1997), Simpson,
P., Curr. Opin. Genet. Dev., 7(4):537 (1997), Blobel, C P., Cell,
90(4):589 (1997)], Nakayama, H. et al., Dev. Genet., 21(1):21
(1997), Nakayama, H. et al., Dev. Genet., 21(1):21 (1997),
Sullivan, S. A. et al., Dev. Genet., 20(3):208 (1997) and Hayashi,
H. et al., Int. J. Dev. Biol., 40(6):1089(1996).] Serrate-mediated
activation of notch has been observed in the dorsal compartment of
the Drosophila wing imaginal disc. Fleming et al., Development,
124(15):2973 (1997). Notch is of interest for both its role in
development as well as its signaling abilities. Also of interest
are novel polypeptides which may have a role in development and/or
signaling.
[0016] We herein describe the identification and characterization
of novel polypeptides having homology to the notch protein, wherein
those polypeptides are herein designated PRO299 polypeptides.
[0017] 4. PRO323
[0018] Dipeptidases are enzymatic proteins which function to cleave
a large variety of different dipeptides and which are involved in
an enormous number of very important biological processes in
mammalian and non-mammalian organisms. Numerous different
dipeptidase enzymes from a variety of different mammalian and
non-mammalian organisms have been both identified and
characterized. The mammalian dipeptidase enzymes play important
roles in many different biological processes including, for
example, protein digestion, activation, inactivation, or modulation
of dipeptide hormone activity, and alteration of the physical
properties of proteins and enzymes.
[0019] In light of the important physiological roles played by
dipeptidase enzymes, efforts are being undertaken by both industry
and academia to identify new, native dipeptidase homologs. Many
efforts are focused on the screening of mammalian recombinant DNA
libraries to identify the coding sequences for novel secreted and
membrane-bound receptor proteins. Examples of screening methods and
techniques are described in the literature [see, for example, Klein
et al., Proc. Natl. Acad. Sci., 93:7108-7113 (1996); U.S. Pat. No.
5,536,637)].
[0020] We herein describe the identification and characterization
of novel polypeptides having homology to various dipeptidase
enzymes, designated herein as PRO323 polypeptides.
[0021] 5. PRO327
[0022] The anterior pituitary hormone prolactin is encoded by a
member of the growth hormone/prolactin/placental lactogen gene
family. In mammals, prolactin is primarily responsible for the
development of the mammary gland and lactation. Prolactin functions
to stimulate the expression of milk protein genes by increasing
both gene transcription and mRNA half-life.
[0023] The physiological effects of the prolactin protein are
mediated through the ability of prolactin to bind to a cell surface
prolactin receptor. The prolactin receptor is found in a variety of
different cell types, has a molecular mass of approximately 40,000
and is apparently not linked by disulfide bonds to itself or to
other subunits. Prolactin receptor levels are differentially
regulated depending upon the tissue studied.
[0024] Given the important physiological roles played by cell
surface receptor molecules in vivo, efforts are currently being
undertaken by both industry and academia to identify new, native
membrane-bound receptor proteins, including those which share
sequence homology with the prolactin receptor. Many of these
efforts are focused on the screening of mammalian recombinant DNA
libraries to identify the coding sequences for novel membrane-bound
receptor proteins. Examples of screening methods and techniques are
described in the literature [see, for example, Klein et al., Proc.
Natl. Acad. Sci., 93:7108-7113 (1996); U.S. Pat. No.
5,536,637)].
[0025] We herein describe the identification and characterization
of novel polypeptides having significant homology to the prolactin
receptor protein, designated herein as PRO327 polypeptides.
[0026] 6. PRO233
[0027] Studies have reported that the redox state of the cell is an
important determinant of the fate of the cell. Furthermore,
reactive oxygen species have been reported to be cytotoxic, causing
inflammatory disease, including tissue necrosis, organ failure,
atherosclerosis, infertility, birth defects, premature aging,
mutations and malignancy. Thus, the control of oxidation and
reduction is important for a number of reasons, including the
control and prevention of strokes, heart attacks, oxidative stress
and hypertension.
[0028] Oxygen free radicals and antioxidants appear to play an
important role in the central nervous system after cerebral
ischemia and reperfusion. Moreover, cardiac injury, related to
ischaemia and reperfusion has been reported to be caused by the
action of free radicals. In this regard, reductases, and
particularly, oxidoreductases, are of interest. In addition, the
transcription factors, NF-kappa B and AP-1, are known to be
regulated by redox state and to affect the expression of a large
variety of genes thought to be involved in the pathogenesis of
AIDS, cancer, atherosclerosis and diabetic complications.
Publications further describing this subject matter include Kelsey
et al., Br. J. Cancer, 76(7):852-854 (1997); Friedrich and Weiss,
J. Theor. Biol., 187(4):529-540(1997) and Pieulle et al., J.
Bacteriol., 179(18):5684-5692 (1997). Given the physiological
importance of redox reactions in vivo, efforts are currently being
under taken to identify new, native proteins which are involved in
redox reactions. We describe herein the identification and
characterization of novel polypeptides which have homology to
reductase, designated herein as PRO233 polypeptides.
[0029] 7. PRO344
[0030] The complement proteins comprise a large group of serum
proteins some of which act in an enzymatic cascade, producing
effector molecules involved in inflammation. The complement
proteins are of particular physiological importance in regulating
movement and function of cells involved in inflammation. Given the
physiological importance of inflammation and related mechanisms in
vivo, efforts are currently being under taken to identify new,
native proteins which are involved in inflammation. We describe
herein the identification and characterization of novel
polypeptides which have homology to complement proteins, wherein
those polypeptides are herein designated as PRO344
polypeptides.
[0031] 8. PRO347
[0032] Cysteine-rich proteins are generally proteins which have
intricate three-dimensional structures and/or exist in multimeric
forms due to the presence of numerous cysteine residues which are
capable of forming disulfide bridges. One well known cysteine-rich
protein is the mannose receptor which is expressed in, among other
tissues, liver where it serves to bind to mannose and transport it
into liver cells. Other cysteine-rich proteins are known to play
important roles in many other physiological and biochemical
processes. As such, there is an interest in identifying novel
cysteine-rich proteins. In this regard, Applicants describe herein
the identification and characterization of novel cysteine-rich
polypeptides that has significant sequence homology to the
cysteine-rich secretory protein-3, designated herein as PRO347
polypeptides.
[0033] 9. PRO354
[0034] Inter-alpha-trypsin inhibitor (ITI) is a large (Mr
approximately 240,000) circulating protease inhibitor found in the
plasma of many mammalian species. The intact inhibitor is a
glycoprotein and consists of three glycosylated subunits that
interact through a strong glycosaminoglycan linkage. The
anti-trypsin activity of ITI is located on the smallest subunit
(i.e., the light chain) of the complex, wherein that light chain is
now known as the protein bikunin. The mature light chain consists
of a 21-amino acid N-terminal sequence, glycosylated at Ser-10,
followed by two tandem Kunitz-type domains, the first of which is
glycosylated at Asn-45 and the second of which is capable of
inhibiting trypsin, chymotrypsin and plasmin. The remaining two
chains of the ITI complex are heavy chains which function to
interact with the enzymatically active light chain of the
complex.
[0035] Efforts are being undertaken by both industry and academia
to identify new, native proteins. Many efforts are focused on the
screening of mammalian recombinant DNA libraries to identify the
coding sequences for novel secreted and membrane-bound receptor
proteins. Examples of screening methods and techniques are
described in the literature [see, for example, Klein et al., Proc.
Natl. Acad. Sci., 93:7108-7113 (1996); U.S. Pat. No. 5,536,637)].
We herein describe the identification and characterization of novel
polypeptides having significant homology to the ITI heavy chain,
designated in the present application as PRO354 polypeptides.
[0036] 10. PRO355
[0037] Cytotoxic or regulatory T cell associated molecule or
"CRTAM" protein is structurally related to the immunoglobulin
superfamily. The CRTAM protein should be capable of mediating
various immune responses. Antibodies typically bind to CRTAM
proteins with high affinity. Zlotnik, A., Faseb, 10(6): A1037, Abr.
216, June 1996. Given the physiological importance of T cell
antigens and immune processes in vivo, efforts are currently being
under taken to identify new, native proteins which are involved in
immune responses. See also Kennedy et al., U.S. Pat. No. 5,686,257
(1997). We describe herein the identification and characterization
of novel polypeptides which have homology to CRTAM, designated in
the present application as PRO355 polypeptides.
[0038] 11. PRO357
[0039] Protein-protein interactions include receptor and antigen
complexes and signaling mechanisms. As more is known about the
structural and functional mechanisms underlying protein-protein
interactions, protein-protein interactions can be more easily
manipulated to regulate the particular result of the
protein-protein interaction. Thus, the underlying mechanisms of
protein-protein interactions are of interest to the scientific and
medical community.
[0040] All proteins containing leucine-rich repeats are thought to
be involved in protein-protein interactions. Leucine-rich repeats
are short sequence motifs present in a number of proteins with
diverse functions and cellular locations. The crystal structure of
ribonuclease inhibitor protein has revealed that leucine-rich
repeats correspond to beta-alpha structural units. These units are
arranged so that they form a parallel beta-sheet with one surface
exposed to solvent, so that the protein acquires an unusual,
nonglobular shape. These two features have been indicated as
responsible for the protein-binding functions of proteins
containing leucine-rich repeats. See, Kobe and Deisenhofer, Trends
Biochem. Sci., 19(10):415-421 (October 1994).
[0041] A study has been reported on leucine-rich proteoglycans
which serve as tissue organizers, orienting and ordering collagen
fibrils during ontogeny and are involved in pathological processes
such as wound healing, tissue repair, and tumor stroma formation.
Iozzo, R. V., Crit. Rev. Biochem. Mol. Biol., 32(2):141-174 (1997).
Others studies implicating leucine rich proteins in wound healing
and tissue repair are De La Salle, C., et al., Vouy. Rev. Fr.
Hematol. (Germany), 37(4):215-222 (1995), reporting mutations in
the leucine rich motif in a complex associated with the bleeding
disorder Bernard-Soulier syndrome, Chlemetson, K. J., Thromb.
Haemost. (Germany), 74(1): 111-116 (July 1995), reporting that
platelets have leucine rich repeats and Ruoslahti, E. I., et al.,
WO9110727-A by La Jolla Cancer Research Foundation reporting that
decorin binding to transforming growth factor.beta. has involvement
in a treatment for cancer, wound healing and scarring. Related by
function to this group of proteins is the insulin like growth
factor (IGF), in that it is useful in wound-healing and associated
therapies concerned with re-growth of tissue, such as connective
tissue, skin and bone; in promoting body growth in humans and
animals; and in stimulating other growth-related processes. The
acid labile subunit (ALS) of IGF is also of interest in that it
increases the half-life of IGF and is part of the IGF complex in
vivo.
[0042] Another protein which has been reported to have leucine-rich
repeats is the SLIT protein which has been reported to be useful in
treating neuro-degenerative diseases such as Alzheimer's disease,
nerve damage such as in Parkinson's disease, and for diagnosis of
cancer, see, Artavanistsakonas, S. and Rothberg, J. M.,
WO9210518-A1 by Yale University. Also of interest is LIG-1, a
membrane glycoprotein that is expressed specifically in glial cells
in the mouse brain, and has leucine rich repeats and
immunoglobulin-like domains. Suzuki, et al., J. Biol. Chem. (U.S.),
271(37):22522 (1996). Other studies reporting on the biological
functions of proteins having leucine rich repeats include: Tayar,
N., et al., Mol. Cell Endocrinol., (Ireland), 125(1-2):65-70
(December 1996) (gonadotropin receptor involvement); Miura, Y., et
al., Nippon Rinsho (Japan), 54(7): 1784-1789 (July 1996) (apoptosis
involvement); Harris, P. C., et al., J. Am. Soc. Nephrol.,
6(4):1125-1133 (October 1995) (kidney disease involvement).
[0043] Efforts are therefore being undertaken by both industry and
academia to identify new proteins having leucine rich repeats to
better understand protein-protein interactions. Of particular
interest are those proteins having leucine rich repeats and
homology to known proteins having leucine rich repeats such as the
acid labile subunit of insulin-like growth factor. Many efforts are
focused on the screening of mammalian recombinant DNA libraries to
identify the coding sequences for novel secreted and membrane-bound
proteins having leucine rich repeats. Examples of screening methods
and techniques are described in the literature [see, for example,
Klein et al., Proc. Natl. Acad. Sci. 93:7108-7113 (1996); U.S. Pat.
No. 5,536,637)].
[0044] We describe herein the identification and characterization
of novel polypeptides having homology to the acid labile subunit of
insulin-like growth factor, designated in the present application
as PRO357 polypeptides.
[0045] 12. PRO715
[0046] Control of cell numbers in mammals is believed to be
determined, in part, by a balance between cell proliferation and
cell death. One form of cell death, sometimes referred to as
necrotic cell death, is typically characterized as a pathologic
form of cell death resulting from some trauma or cellular injury.
In contrast, there is another, "physiologic" form of cell death
which usually proceeds in an orderly or controlled manner. This
orderly or controlled form of cell death is often referred to as
"apoptosis" [see, e.g., Barr et al., Bio/Technology, 12:487-493
(1994); Steller et al., Science, 267:1445-1449 (1995)]. Apoptotic
cell death naturally occurs in many physiological processes,
including embryonic development and clonal selection in the immune
system [Itoh et al., Cell, 66:233-243 (1991)]. Decreased levels of
apoptotic cell death have been associated with a variety of
pathological conditions, including cancer, lupus, and herpes virus
infection [Thompson, Science, 267:1456-1462 (1995)]. Increased
levels of apoptotic cell death may be associated with a variety of
other pathological conditions, including AIDS, Alzheimer's disease,
Parkinson's disease, amyotrophic lateral sclerosis, multiple
sclerosis, retinitis pigmentosa, cerebellar degeneration, aplastic
anemia, myocardial infarction, stroke, reperfusion injury, and
toxin-induced liver disease [see, Thompson, supra].
[0047] Apoptotic cell death is typically accompanied by one or more
characteristic morphological and biochemical changes in cells, such
as condensation of cytoplasm, loss of plasma membrane microvilli,
segmentation of the nucleus, degradation of chromosomal DNA or loss
of mitochondrial function. A variety of extrinsic and intrinsic
signals are believed to trigger or induce such morphological and
biochemical cellular changes [Raff, Nature, 356:397400 (1992);
Steller, supra; Sachs et al., Blood, 82:15 (1993)]. For instance,
they can be triggered by hormonal stimuli, such as glucocorticoid
hormones for immature thymocytes, as well as withdrawal of certain
growth factors [Watanabe-Fukunaga et al., Nature, 356:314-317
(1992)]. Also, some identified oncogenes such as myc, rel, and EIA,
and tumor suppressors, like p53, have been reported to have a role
in inducing apoptosis. Certain chemotherapy drugs and some forms of
radiation have likewise been observed to have apoptosis-inducing
activity [Thompson, supra].
[0048] Various molecules, such as tumor necrosis
factor-.beta."("TNF-.alph- a."), tumor necrosis
factor.beta.("TNF-.beta." or "lymphotoxin-.alpha."),
lymphotoxin-.beta. ("LT-.beta."), CD30 ligand, CD27 ligand, CD40
ligand, OX-40 ligand, 4-1BB ligand, Apo-1 ligand (also referred to
as Fas ligand or CD95 ligand), and Apo-2 ligand (also referred to
as TRAIL) have been identified as members of the tumor necrosis
factor ("TNF") family of cytokines [See, e.g., Gruss and Dower,
Blood, 85:3378-3404 (1995); Pitti et al., J. Biol. Chem.,
271:12687-12690 (1996); Wiley et al., Immunity, 3:673-682 (1995);
Browning et al., Cell, 72:847-856 (1993); Armitage et al. Nature,
357:80-82 (1992)]. Among these molecules, TNF-.alpha., TNF-.beta.,
CD30 ligand, 4-1BB ligand, Apo-1 ligand, and Apo-2 ligand (TRAIL)
have been reported to be involved in apoptotic cell death. Both
TNF-.alpha. and TNF-.beta. have been reported to induce apoptotic
death in susceptible tumor cells [Schmid et al., Proc. Natl. Acad.
Sci., 83:1881 (1986); Dealtry et al., Eur. J. Immunol., 17:689
(1987)]. Zheng et al. have reported that TNF-.alpha. is involved in
post-stimulation apoptosis of CD8-positive T cells [Zheng et al.,
Nature, 377:348-351 (1995)]. Other investigators have reported that
CD30 ligand may be involved in deletion of self-reactive T cells in
the thymus [Amakawa et al., Cold Spring Harbor Laboratory Symposium
on Programmed Cell Death, Abstr. No. 10, (1995)].
[0049] Mutations in the mouse Fas/Apo-1 receptor or ligand genes
(called lpr and gld, respectively) have been associated with some
autoimmune disorders, indicating that Apo-1 ligand may play a role
in regulating the clonal deletion of self-reactive lymphocytes in
the periphery [Krammer et al., Curr. Op. Immunol. 6:279-289 (1994);
Nagata et al., Science, 267:1449-1456 (1995)]. Apo-1 ligand is also
reported to induce post-stimulation apoptosis in CD4-positive T
lymphocytes and in B lymphocytes, and may be involved in the
elimination of activated lymphocytes when their function is no
longer needed [Krammer et al., supra; Nagata et al., supra].
Agonist mouse monoclonal antibodies specifically binding to the
Apo-1 receptor have been reported to exhibit cell killing activity
that is comparable to or similar to that of TNF-.alpha. [Yonehara
et al., J. Exp. Med., 169:1747-1756 (1989)].
[0050] Induction of various cellular responses mediated by such TNF
family cytokines is believed to be initiated by their binding to
specific cell receptors. Two distinct TNF receptors of
approximately 55-kDa (TNFR1) and 75-kDa (TNFR2) have been
identified [Hohman et al., J. Biol. Chem., 264:14927-14934 (1989);
Brockhaus et al., Proc. Natl. Acad. Sci., 87:3127-3131 (1990); EP
417,563, published Mar. 20, 1991] and human and mouse cDNAs
corresponding to both receptor types have been isolated and
characterized [Loetscher et al., Cell, 61:351 (1990); Schall et
al., Cell, 61:361 (1990); Smith et al., Science, 248:1019-1023
(1990); Lewis et al., Proc. Natl. Acad. Sci., 88:2830-2834 (1991);
Goodwin et al., Mol. Cell. Biol, 11:3020-3026 (1991)]. The TNF
family ligands identified to date, with the exception of
lymphotoxin-.alpha., are type II transmembrane proteins, whose
C-terminus is extracellular. In contrast, most receptors in the TNF
receptor (TNFR) family identified to date are type I transmembrane
proteins. In both the TNF ligand and receptor families, however,
homology identified between family members has been found mainly in
the extracellular domain ("ECD"). Several of the TNF family
cytokines, including TNF-.alpha., Apo-1 ligand and CD40 ligand, are
cleaved proteolytically at the cell surface; the resulting protein
in each case typically forms a homotrimeric molecule that functions
as a soluble cytokine. TNF receptor family proteins are also
usually cleaved proteolytically to release soluble receptor ECDs
that can function as inhibitors of the cognate cytokines.
[0051] Recently, other members of the TNFR family have been
identified. Such newly identified members of the TNFR family
include CAR1, HVEM and osteoprotegerin (OPG) [Brojatsch et al.,
Cell, 87:845-855 (1996); Montgomery et al., Cell, 87:427436 (1996);
Marsters et al., J. Biol. Chem., 272:14029-14032 (1997); Simonet et
al., Cell, 89:309-319 (1997)]. Unlike other known TNFR-like
molecules, Simonet et al., supra, report that OPG contains no
hydrophobic transmembrane-spanning sequence.
[0052] For a review of the TNF family of cytokines and their
receptors, see Gruss and Dower, supra.
[0053] Applicants herein describe the identification and
characterization of novel polypeptides having homology to members
of the tumor necrosis factor family of polypeptides, designated
herein as PRO715 polypeptides.
[0054] 13. PRO353
[0055] The complement proteins comprise a large group of serum
proteins some of which act in an enzymatic cascade, producing
effector molecules involved in inflammation. The complement
proteins are of particular importance in regulating movement and
function of cells involved in inflammation. Given the physiological
importance of inflammation and related mechanisms in vivo, efforts
are currently being under taken to identify new, native proteins
which are involved in inflammation. We describe herein the
identification and characterization of novel polypeptides which
have homology to complement proteins, designated herein as PRO353
polypeptides.
[0056] 14. PRO361
[0057] The mucins comprise a family of glycoproteins which have
been implicated in carcinogenesis. Mucin and mucin-like proteins
are secreted by both normal and transformed cells. Both qualitative
and quantitative changes in mucins have been implicated in various
types of cancer. Given the medical importance of cancer, efforts
are currently being under taken to identify new, native proteins
which may be useful for the diagnosis or treatment of cancer.
[0058] The chitinase proteins comprise a family of which have been
implicated in pathogenesis responses in plants. Chitinase proteins
are produced by plants and microorganisms and may play a role in
the defense of plants to injury. Given the importance of plant
defense mechanisms, efforts are currently being under taken to
identify new, native proteins which may be useful for modulation of
pathogenesis-related responses in plants. We describe herein the
identification and characterization of novel polypeptides which
have homology to mucin and chitinase, designated in the present
application as PRO361 polypeptides.
[0059] 15. PRO365
[0060] Polypeptides such as human 2-19 protein may function as
cytokines. Cytokines are low molecular weight proteins which
function to stimulate or inhibit the differentiation, proliferation
or function of immune cells. Cytokines often act as intercellular
messengers and have multiple physiological effects. Given the
physiological importance of immune mechanisms in vivo, efforts are
currently being under taken to identify new, native proteins which
are involved in effecting the immune system. We describe herein the
identification and characterization of novel polypeptides which
have homology to the human 2-19 protein, designated herein as
PRO365 polypeptides.
SUMMARY OF THE INVENTION
[0061] 1. PRO241
[0062] Applicants have identified a cDNA clone that encodes a novel
polypeptide having homology to biglycan protein, wherein the
polypeptide is designated in the present application as
"PRO241".
[0063] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO241 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO241 polypeptide having amino acid residues 1 to 379 of FIG. 2
(SEQ ID NO:2), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0064] In another embodiment, the invention provides isolated
PRO241 polypeptide. In particular, the invention provides isolated
native sequence PRO241 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 379 of
FIG. 2 (SEQ ID NO:2). Another embodiment of the present invention
is directed to a PRO241 polypeptide lacking the N-terminal signal
peptide, wherein the PRO241 polypeptide comprises about amino acids
16 to 379 of the full-length PRO241 amino acid sequence (SEQ ID
NO:2).
[0065] 2. PRO243
[0066] Applicants have identified a cDNA clone (DNA35917-1207) that
encodes a novel polypeptide, designated in the present application
as "PRO243".
[0067] In one embodiment, the invention provides an isolated
nucleic acid molecule having at least about 80% sequence identity
to (a) a DNA molecule encoding a PRO243 polypeptide comprising the
sequence of amino acids 1 or about 24 to 954 of FIG. 4 (SEQ ID
NO:7), or (b) the complement of the DNA molecule of (a). The
sequence identity preferably is about 85%, more preferably about
90%, most preferably about 95%. In one aspect, the isolated nucleic
acid has at least about 80%, preferably at least about 85%, more
preferably at least about 90%, and most preferably at least about
95% sequence identity with a polypeptide having amino acid residues
1 or about 24 to 954 of FIG. 4 (SEQ ID NO:7). Preferably, the
highest degree of sequence identity occurs within the four (4)
conserved cysteine clusters (amino acids 51 to 125; amino acids 705
to 761; amino acids 784 to 849; and amino acids 897 to 931) of FIG.
4 (SEQ ID NO:7). In a further embodiment, the isolated nucleic acid
molecule comprises DNA encoding a PRO243 polypeptide having amino
acid residues 1 or about 24 to 954 of FIG. 4 (SEQ ID NO:7), or is
complementary to such encoding nucleic acid sequence, and remains
stably bound to it under at least moderate, and optionally, under
high stringency conditions. In another aspect, the invention
provides a nucleic acid of the full length protein of clone
DNA35917-1207, deposited with the ATCC under accession number ATCC
209508, alternatively the coding sequence of clone DNA35917-1207,
deposited under accession number ATCC 209508.
[0068] In yet another embodiment, the invention provides isolated
PRO243 polypeptide. In particular, the invention provides isolated
native sequence PRO243 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 or about 24
to 954 of FIG. 4 (SEQ ID NO:7). Native PRO243 polypeptides with or
without the native signal sequence (amino acids 1 to 23 in FIG. 4
(SEQ ID NO:7)), and with or without the initiating methionine are
specifically included. Alternatively, the invention provides a
PRO243 polypeptide encoded by the nucleic acid deposited under
accession number ATCC 209508.
[0069] 3. PRO299
[0070] Applicants have identified a cDNA clone that encodes a novel
polypeptide, wherein the polypeptide is designated in the present
application as "PRO299".
[0071] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO299 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO299 polypeptide having amino acid residues 1 to 737 of FIG. 6
(SEQ ID NO: 15), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0072] In another embodiment, the invention provides isolated
PRO299 polypeptide. In particular, the invention provides isolated
native sequence PRO299 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 737 of
FIG. 6 (SEQ ID NO: 15). An additional embodiment of the present
invention is directed to an isolated extracellular domain of a
PRO299 polypeptide.
[0073] 4. PRO323
[0074] Applicants have identified a cDNA clone that encodes a novel
polypeptide having homology to a microsomal dipeptidase protein,
wherein the polypeptide is designated in the present application as
"PRO323".
[0075] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO323 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO323 polypeptide having amino acid residues 1 to 433 of FIG. 10
(SEQ ID NO:24), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0076] In another embodiment, the invention provides isolated
PRO323 polypeptide. In particular, the invention provides isolated
native sequence PRO323 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 433 of
FIG. 10 (SEQ ID NO:24).
[0077] 5. PRO327
[0078] Applicants have identified a cDNA clone that encodes a novel
polypeptide having homology to prolactin receptor, wherein the
polypeptide is designated in the present application as
"PRO327".
[0079] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO327 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO327 polypeptide having amino acid residues 1 to 422 of FIG. 14
(SEQ ID NO:32), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0080] In another embodiment, the invention provides isolated
PRO327 polypeptide. In particular, the invention provides isolated
native sequence PRO327 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 422 of
FIG. 14 (SEQ ID NO:32).
[0081] 6. PRO233
[0082] Applicants have identified a cDNA clone that encodes a novel
polypeptide, wherein the polypeptide is designated in the present
application as "PRO233".
[0083] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO233 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO233 polypeptide having amino acid residues 1 to 300 of FIG. 16
(SEQ ID NO:37), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0084] In another embodiment, the invention provides isolated
PRO233 polypeptide. In particular, the invention provides isolated
native sequence PRO233 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 300 of
FIG. 16 (SEQ ID NO:37).
[0085] 7. PRO344
[0086] Applicants have identified a cDNA clone that encodes a novel
polypeptide, wherein the polypeptides are designated in the present
application as "PRO344".
[0087] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO344 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO344 polypeptide having amino acid residues 1 to 243 of FIG. 18
(SEQ ID NO:42), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0088] In another embodiment, the invention provides isolated
PRO344 polypeptide. In particular, the invention provides isolated
native sequence PRO344 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 243 of
FIG. 18 (SEQ ID NO:42).
[0089] 8. PRO347
[0090] Applicants have identified a cDNA clone that encodes a novel
polypeptide having homology to cysteine-rich secretory protein-3,
wherein the polypeptide is designated in the present application as
"PRO347".
[0091] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO347 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO347 polypeptide having amino acid residues 1 to 455 of FIG. 20
(SEQ ID NO:50), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0092] In another embodiment, the invention provides isolated
PRO347 polypeptide. In particular, the invention provides isolated
native sequence PRO347 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 455 of
FIG. 20 (SEQ ID NO:50).
[0093] 9. PRO354
[0094] Applicants have identified a cDNA clone that encodes a novel
polypeptide having homology to the heavy chain of the
inter-alpha-trypsin inhibitor (ITI), wherein the polypeptide is
designated in the present application as "PRO354".
[0095] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO354 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO354 polypeptide having amino acid residues 1 to 694 of FIG. 22
(SEQ ID NO:55), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0096] In another embodiment, the invention provides isolated
PRO354 polypeptide. In particular, the invention provides isolated
native sequence PRO354 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 694 of
FIG. 22 (SEQ ID NO:55).
[0097] 10. PRO355
[0098] Applicants have identified a cDNA clone that encodes a novel
polypeptide, wherein the polypeptide is designated in the present
application as "PRO355".
[0099] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO355 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO355 polypeptide having amino acid residues 1 to 440 of FIG. 24
(SEQ ID NO:61), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0100] In another embodiment, the invention provides isolated
PRO355 polypeptide. In particular, the invention provides isolated
native sequence PRO355 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 440 of
FIG. 24 (SEQ ID NO:61). An additional embodiment of the present
invention is directed to an isolated extracellular domain of a
PRO355 polypeptide.
[0101] 11. PRO357
[0102] Applicants have identified a cDNA clone that encodes a novel
polypeptide having homology to insulin-like growth factor (IGF)
acid labile subunit (ALS), wherein the polypeptide is designated in
the present application as "PRO357".
[0103] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO357 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO357 polypeptide having amino acid residues 1 through 598 of FIG.
26 (SEQ ID NO:69), or is complementary to such encoding nucleic
acid sequence, and remains stably bound to it under at least
moderate, and optionally, under high stringency conditions.
[0104] In another embodiment, the invention provides isolated
PRO357 polypeptide. In particular, the invention provides isolated
native sequence PRO357 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 through 598
of FIG. 26 (SEQ ID NO:69). An additional embodiment of the present
invention is directed to an isolated extracellular domain of a
PRO357 polypeptide.
[0105] 12. PRO715
[0106] Applicants have identified cDNA clones that encode novel
polypeptides having homology to tumor necrosis factor family
polypeptides, wherein the polypeptides are designated in the
present application as "PRO715".
[0107] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO715 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO715 polypeptide having amino acid residues 1 to 250 of FIG. 28
(SEQ ID NO:76), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0108] In another embodiment, the invention provides isolated
PRO715 polypeptide. In particular, the invention provides isolated
native sequence PRO715 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 250 of
FIG. 28 (SEQ ID NO:76). An additional embodiment of the present
invention is directed to an isolated extracellular domain of a
PRO715 polypeptide.
[0109] 13. PRO353
[0110] Applicants have identified a cDNA clone that encodes a novel
polypeptide, wherein the polypeptides are designated in the present
application as "PRO353".
[0111] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO353 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO353 polypeptide having amino acid residues 1 to 281 of FIG. 30
(SEQ ID NO:78), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions.
[0112] In another embodiment, the invention provides an isolated
PRO353 polypeptide. In particular, the invention provides isolated
native sequence PRO353 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 281 of
FIG. 30 (SEQ ID NO:78).
[0113] 14. PRO361
[0114] Applicants have identified a cDNA clone that encodes a novel
polypeptide, wherein the polypeptide is designated in the present
application as "PRO361".
[0115] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO361 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO361 polypeptide having amino acid residues 1 to 431 of FIG. 32
(SEQ ID NO:83), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions. The isolated
nucleic acid sequence may comprise the cDNA insert of the vector
deposited on Feb. 5, 1998 as ATCC 209621 which includes the
nucleotide sequence encoding PRO361.
[0116] In another embodiment, the invention provides isolated
PRO361 polypeptide. In particular, the invention provides isolated
native sequence PRO361 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 431 of
FIG. 32 (SEQ ID NO:83). An additional embodiment of the present
invention is directed to an isolated extracellular domain of a
PRO361 polypeptide having amino acids 1 to 379 of the amino acids
sequence shown in FIG. 32 (SEQ ID NO:83). Optionally, the PRO361
polypeptide is obtained or is obtainable by expressing the
polypeptide encoded by the cDNA insert of the vector deposited on
Feb. 5, 1998 as ATCC 209621.
[0117] 15. PRO365
[0118] Applicants have identified a cDNA clone that encodes a novel
polypeptide, wherein the polypeptide is designated in the present
application as "PRO365".
[0119] In one embodiment, the invention provides an isolated
nucleic acid molecule comprising DNA encoding a PRO365 polypeptide.
In one aspect, the isolated nucleic acid comprises DNA encoding the
PRO365 polypeptide having amino acid residues 1 to 235 of FIG. 34
(SEQ ID NO:91), or is complementary to such encoding nucleic acid
sequence, and remains stably bound to it under at least moderate,
and optionally, under high stringency conditions. In another
aspect, the isolated nucleic acid comprises DNA encoding the PRO365
polypeptide having amino acid residues 1 to 235 of FIG. 34 (SEQ ID
NO:91), or is complementary to such encoding nucleic acid sequence,
and remains stably bound to it under at least moderate, and
optionally, under high stringency conditions.
[0120] In another embodiment, the invention provides isolated
PRO365 polypeptide. In particular, the invention provides isolated
native sequence PRO365 polypeptide, which in one embodiment,
includes an amino acid sequence comprising residues 1 to 235 of
FIG. 34 (SEQ ID NO:91). An additional embodiment of the present
invention is directed to an amino acid sequence comprising residues
21 to 235 of FIG. 34 (SEQ ID NO:91).
[0121] 16. Additional Embodiments
[0122] In other embodiments of the present invention, the invention
provides vectors comprising DNA encoding any of the herein
described polypeptides. Host cell comprising any such vector are
also provided. By way of example, the host cells may be CHO cells,
E. coli, or yeast. A process for producing any of the herein
described polypeptides is further provided and comprises culturing
host cells under conditions suitable for expression of the desired
polypeptide and recovering the desired polypeptide from the cell
culture.
[0123] In other embodiments, the invention provides chimeric
molecules comprising any of the herein described polypeptides fused
to a heterologous polypeptide or amino acid sequence. Example of
such chimeric molecules comprise any of the herein described
polypeptides fused to an epitope tag sequence or a Fc region of an
immunoglobulin.
[0124] In another embodiment, the invention provides an antibody
which specifically binds to any of the above or below described
polypeptides. Optionally, the antibody is a monoclonal antibody,
humanized antibody, antibody fragment or single-chain antibody.
[0125] In yet other embodiments, the invention provides
oligonucleotide probes useful for isolating genomic and cDNA
nucleotide sequences or as antisense probes, wherein those probes
may be derived from any of the above or below described nucleotide
sequences.
[0126] In other embodiments, the invention provides an isolated
nucleic acid molecule comprising a nucleotide sequence that encodes
a PRO polypeptide.
[0127] In one aspect, the isolated nucleic acid molecule comprises
a nucleotide sequence having at least about 80% sequence identity,
preferably at least about 81% sequence identity, more preferably at
least about 82% sequence identity, yet more preferably at least
about 83% sequence identity, yet more preferably at least about 84%
sequence identity, yet more preferably at least about 85% sequence
identity, yet more preferably at least about 86% sequence identity,
yet more preferably at least about 87% sequence identity, yet more
preferably at least about 88% sequence identity, yet more
preferably at least about 89% sequence identity, yet more
preferably at least about 90% sequence identity, yet more
preferably at least about 91% sequence identity, yet more
preferably at least about 92% sequence identity, yet more
preferably at least about 93% sequence identity, yet more
preferably at least about 94% sequence identity, yet more
preferably at least about 95% sequence identity, yet more
preferably at least about 96% sequence identity, yet more
preferably at least about 97% sequence identity, yet more
preferably at least about 98% sequence identity and yet more
preferably at least about 99% sequence identity to (a) a DNA
molecule encoding a PRO polypeptide having a full-length amino acid
sequence as disclosed herein, an amino acid sequence lacking the
signal peptide as disclosed herein, an extracellular domain of a
transmembrane protein, with or without the signal peptide, as
disclosed herein or any other specifically defined fragment of the
full-length amino acid sequence as disclosed herein, or (b))the
complement of the DNA molecule of (a).
[0128] In other aspects, the isolated nucleic acid molecule
comprises a nucleotide sequence having at least about 80% sequence
identity, preferably at least about 81% sequence identity, more
preferably at least about 82% sequence identity, yet more
preferably at least about 83% sequence identity, yet more
preferably at least about 84% sequence identity, yet more
preferably at least about 85% sequence identity, yet more
preferably at least about 86% sequence identity, yet more
preferably at least about 87% sequence identity, yet more
preferably at least about 88%sequence identity, yet more preferably
at least about 89% sequence identity, yet more preferably at least
about 90% sequence identity, yet more preferably at least about 91%
sequence identity, yet more preferably at least about 92% sequence
identity, yet more preferably at least about 93% sequence identity,
yet more preferably at least about 94% sequence identity, yet more
preferably at least about 95% sequence identity, yet more
preferably at least about 96% sequence identity, yet more
preferably at least about 97% sequence identity, yet more
preferably at least about 98% sequence identity and yet more
preferably at least about 99% sequence identity to (a) a DNA
molecule comprising the coding sequence of a full-length PRO
polypeptide cDNA as disclosed herein, the coding sequence of a PRO
polypeptide lacking the signal peptide as disclosed herein, the
coding sequence of an extracellular domain of a transmembrane PRO
polypeptide, with or without the signal peptide, as disclosed
herein or the coding sequence of any other specifically defined
fragment of the full-length amino acid sequence as disclosed
herein, or (b) the complement of the DNA molecule of (a).
[0129] In a further aspect, the invention concerns an isolated
nucleic acid molecule comprising a nucleotide sequence having at
least about 80% sequence identity, preferably at least about 81%
sequence identity, more preferably at least about 82% sequence
identity, yet more preferably at least about 83% sequence identity,
yet more preferably at least about 84% sequence identity, yet more
preferably at least about 85% sequence identity, yet more
preferably at least about 86% sequence identity, yet more
preferably at least about 87% sequence identity, yet more
preferably at least about 88% sequence identity, yet more
preferably at least about 89% sequence identity, yet more
preferably at least about 90% sequence identity, yet more
preferably at least about 91% sequence identity, yet more
preferably at least about 92% sequence identity, yet more
preferably at least about 93% sequence identity, yet more
preferably at least about 94% sequence identity, yet more
preferably at least about 95% sequence identity, yet more
preferably at least about 96% sequence identity, yet more
preferably at least about 97% sequence identity, yet more
preferably at least about 9 8% sequence identity and yet more
preferably at least about 99% sequence identity to (a) a DNA
molecule that encodes the same mature polypeptide encoded by any of
the human protein cDNAs deposited with the ATCC as disclosed
herein, or (b) the complement of the DNA molecule of (a).
[0130] Another aspect the invention provides an isolated nucleic
acid molecule comprising a nucleotide sequence encoding a PRO
polypeptide which is either transmembrane domain-deleted or
transmembrane domain-inactivated, or is complementary to such
encoding nucleotide sequence, wherein the transmembrane domain(s)
of such polypeptide are disclosed herein. Therefore, soluble
extracellular domains of the herein described PRO polypeptides are
contemplated.
[0131] Another embodiment is directed to fragments of a PRO
polypeptide coding sequence, or the complement thereof, that may
find use as, for example, hybridization probes, for encoding
fragments of a PRO polypeptide that may optionally encode a
polypeptide comprising a binding site for an anti-PRO antibody or
as antisense oligonucleotide probes. Such nucleic acid fragments
are usually at least about 20 nucleotides in length, preferably at
least about 30 nucleotides in length, more preferably at least
about 40 nucleotides in length, yet more preferably at least about
50 nucleotides in length, yet more preferably at least about 60
nucleotides in length, yet more preferably at least about 70
nucleotides in length, yet more preferably at least about 80
nucleotides in length, yet more preferably at least about 90
nucleotides in length, yet more preferably at least about 100
nucleotides in length, yet more preferably at least about 110
nucleotides in length, yet more preferably at least about 120
nucleotides in length, yet more preferably at least about 130
nucleotides in length, yet more preferably at least about 140
nucleotides in length, yet more preferably at least about 150
nucleotides in length, yet more preferably at least about 160
nucleotides in length, yet more preferably at least about 170
nucleotides in length, yet more preferably at least about 180
nucleotides in length, yet more preferably at least about 190
nucleotides in length, yet more preferably at least about 200
nucleotides in length, yet more preferably at least about 250
nucleotides in length, yet more preferably at least about 300
nucleotides in length, yet more preferably at least about 350
nucleotides in length, yet more preferably at least about 400
nucleotides in length, yet more preferably at least about 450
nucleotides in length, yet more preferably at least about 500
nucleotides in length, yet more preferably at least about 600
nucleotides in length, yet more preferably at least about 700
nucleotides in length, yet more preferably at least about 800
nucleotides in length, yet more preferably at least about 900
nucleotides in length and yet more preferably at least about 1000
nucleotides in length, wherein in this context the term "about"
means the referenced nucleotide sequence length plus or minus 10%
of that referenced length. It is noted that novel fragments of a
PRO polypeptide-encoding nucleotide sequence may be determined in a
routine manner by aligning the PRO polypeptide-encoding nucleotide
sequence with other known nucleotide sequences using any of a
number of well known sequence alignment programs and determining
which PRO polypeptide-encoding nucleotide sequence fragment(s) are
novel. All of such PRO polypeptide-encoding nucleotide sequences
are contemplated herein. Also contemplated are the PRO polypeptide
fragments encoded by these nucleotide molecule fragments,
preferably those PRO polypeptide fragments that comprise a binding
site for an anti-PRO antibody.
[0132] In another embodiment, the invention provides isolated PRO
polypeptide encoded by any of the isolated nucleic acid sequences
hereinabove identified.
[0133] In a certain aspect, the invention concerns an isolated PRO
polypeptide, comprising an amino acid sequence having at least
about 80% sequence identity, preferably at least about 81% sequence
identity, more preferably at least about 82% sequence identity, yet
more preferably at least about 83% sequence identity, yet more
preferably at least about 84% sequence identity, yet more
preferably at least about 85% sequence identity, yet more
preferably at least about 86% sequence identity, yet more
preferably at least about 87% sequence identity, yet more
preferably at least about 88% sequence identity, yet more
preferably at least about 89% sequence identity, yet more
preferably at least about 90% sequence identity, yet more
preferably at least about 91% sequence identity, yet more
preferably at least about 92% sequence identity, yet more
preferably at least about 93% sequence identity, yet more
preferably at least about 94% sequence identity, yet more
preferably at least about 95% sequence identity, yet more
preferably at least about 96% sequence identity, yet more
preferably at least about 97% sequence identity, yet more
preferably at least about 98% sequence identity and yet more
preferably at least about 99% sequence identity to a PRO
polypeptide having a full-length amino acid sequence as disclosed
herein, an amino acid sequence lacking the signal peptide as
disclosed herein, an extracellular domain of a transmembrane
protein, with or without the signal peptide, as disclosed herein or
any other specifically defined fragment of the full-length amino
acid sequence as disclosed herein.
[0134] In a further aspect, the invention concerns an isolated PRO
polypeptide comprising an amino acid sequence having at least about
80% sequence identity, preferably at least about 81% sequence
identity, more preferably at least about 82% sequence identity, yet
more preferably at least about 83% sequence identity, yet more
preferably at least about 84% sequence identity, yet more
preferably at least about 85% sequence identity, yet more
preferably at least about 86% sequence identity, yet more
preferably at least about 87% sequence identity, yet more
preferably at least about 88% sequence identity, yet more
preferably at least about 89% sequence identity, yet more
preferably at least about 90% sequence identity, yet more
preferably at least about 91% sequence identity, yet more
preferably at least about 92% sequence identity, yet more
preferably at least about 93% sequence identity, yet more
preferably at least about 94% sequence identity, yet more
preferably at least about 95% sequence identity, yet more
preferably at least about 96% sequence identity, yet more
preferably at least about 97% sequence identity, yet more
preferably at least about 98% sequence identity and yet more
preferably at least about 99% sequence identity to an amino acid
sequence encoded by any of the human protein cDNAs deposited with
the ATCC as disclosed herein.
[0135] In a further aspect, the invention concerns an isolated PRO
polypeptide comprising an amino acid sequence scoring at least
about 80% positives, preferably at least about 81% positives, more
preferably at least about 82% positives, yet more preferably at
least about 83% positives, yet more preferably at least about 84%
positives, yet more preferably at least about 85% positives, yet
more preferably at least about 86% positives, yet more preferably
at least about 87% positives, yet more preferably at least about
88% positives, yet more preferably at least about 89% positives,
yet more preferably at least about 90% positives, yet more
preferably at least about 91% positives, yet more preferably at
least about 92% positives, yet more preferably at least about 93%
positives, yet more preferably at least about 94% positives, yet
more preferably at least about 95% positives, yet more preferably
at least about 96% positives, yet more preferably at least about
97% positives, yet more preferably at least about 98% positives and
yet more preferably at least about 99% positives when compared with
the amino acid sequence of a PRO polypeptide having a full-length
amino acid sequence as disclosed herein, an amino acid sequence
lacking the signal peptide as disclosed herein, an extracellular
domain of a transmembrane protein, with or without the signal
peptide, as disclosed herein or any other specifically defined
fragment of the full-length amino acid sequence as disclosed
herein.
[0136] In a specific aspect, the invention provides an isolated PRO
polypeptide without the N-terminal signal sequence and/or the
initiating methionine and is encoded by a nucleotide sequence that
encodes such an amino acid sequence as hereinbefore described.
Processes for producing the same are also herein described, wherein
those processes comprise culturing a host cell comprising a vector
which comprises the appropriate encoding nucleic acid molecule
under conditions suitable for expression of the PRO polypeptide and
recovering the PRO polypeptide from the cell culture.
[0137] Another aspect the invention provides an isolated PRO
polypeptide which is either transmembrane domain-deleted or
transmembrane domain-inactivated. Processes for producing the same
are also herein described, wherein those processes comprise
culturing a host cell comprising a vector which comprises the
appropriate encoding nucleic acid molecule under conditions
suitable for expression of the PRO polypeptide and recovering the
PRO polypeptide from the cell culture.
[0138] In yet another embodiment, the invention concerns agonists
and antagonists of a native PRO polypeptide as defined herein. In a
particular embodiment, the agonist or antagonist is an anti-PRO
antibody or a small molecule.
[0139] In a further embodiment, the invention concerns a method of
identifying agonists or antagonists to a PRO polypeptide which
comprise contacting the PRO polypeptide with a candidate molecule
and monitoring a biological activity mediated by said PRO
polypeptide. Preferably, the PRO polypeptide is a native PRO
polypeptide.
[0140] In a still further embodiment, the invention concerns a
composition of matter comprising a PRO polypeptide, or an agonist
or antagonist of a PRO polypeptide as herein described, or an
anti-PRO antibody, in combination with a carrier. Optionally, the
carrier is a pharmaceutically acceptable carrier.
[0141] Another embodiment of the present invention is directed to
the use of a PRO polypeptide, or an agonist or antagonist thereof
as hereinbefore described, or an anti-PRO antibody, for the
preparation of a medicament useful in the treatment of a condition
which is responsive to the PRO polypeptide, an agonist or
antagonist thereof or an anti-PRO antibody.
BRIEF DESCRIPTION OF THE DRAWINGS
[0142] FIG. 1 shows a nucleotide sequence (SEQ ID NO:1) of a native
sequence PRO241 cDNA, wherein SEQ ID NO:1 is a clone designated
herein as "DNA34392-1170".
[0143] FIG. 2 shows the amino acid sequence (SEQ ID NO:2) derived
from the coding sequence of SEQ ID NO:1 shown in FIG. 1.
[0144] FIG. 3 shows a nucleotide sequence (SEQ ID NO:6) of a native
sequence PRO243 cDNA, wherein SEQ ID NO:6 is a clone designated
herein as "DNA35917-1207".
[0145] FIG. 4 shows the amino acid sequence (SEQ ID NO:7) derived
from the coding sequence of SEQ ID NO:6 shown in FIG. 3.
[0146] FIG. 5 shows a nucleotide sequence (SEQ ID NO:14) of a
native sequence PRO299 cDNA, wherein SEQ ID NO:14 is a clone
designated herein as "DNA39976-1215".
[0147] FIG. 6 shows the amino acid sequence (SEQ ID NO:15) derived
from the coding sequence of SEQ ID NO:14 shown in FIG. 5.
[0148] FIG. 7 shows a nucleotide sequence designated herein as
DNA28847 (SEQ ID NO:18).
[0149] FIG. 8 shows a nucleotide sequence designated herein as
DNA35877 (SEQ ID NO:19).
[0150] FIG. 9 shows a nucleotide sequence (SEQ ID NO:23) of a
native sequence PRO323 cDNA, wherein SEQ ID NO:23 is a clone
designated herein as "DNA35595-1228".
[0151] FIG. 10 shows the amino acid sequence (SEQ ID NO:24) derived
from the coding sequence of SEQ ID NO:23 shown in FIG. 9.
[0152] FIG. 11 shows a single-stranded nucleotide sequence (SEQ ID
NO:29) containing the nucleotide sequence (nucleotides 79-1416) of
a chimeric fusion protein between a PRO323-derived polypeptide and
a portion of an IgG constant domain, wherein the chimeric fusion
protein is designated herein as "PRO454". The single-stranded
nucleotide sequence (SEQ ID NO:29) encoding the PRO323/IgG fusion
protein (PRO454) is designated herein as "DNA35872".
[0153] FIG. 12 shows the amino acid sequence (SEQ ID NO:30) derived
from nucleotides 79-1416 of the nucleotide sequence shown in FIG.
11. The junction in the PRO454 amino acid sequence between the
PRO323-derived sequences and the IgG-derived sequences appears
between amino acids 415-416 in the figure.
[0154] FIG. 13 shows a nucleotide sequence (SEQ ID NO:31) of a
native sequence PRO327 cDNA, wherein SEQ ID NO:31 is a clone
designated herein as "DNA38113-1230".
[0155] FIG. 14 shows the amino acid sequence (SEQ ID NO:32) derived
from the coding sequence of SEQ ID NO:31 shown in FIG. 13.
[0156] FIG. 15 shows a nucleotide sequence (SEQ ID NO:36) of a
native sequence PRO233 cDNA, wherein SEQ ID NO:36 is a clone
designated herein as "DNA34436-1238".
[0157] FIG. 16 shows the amino acid sequence (SEQ ID NO:37) derived
from the coding sequence of SEQ ID NO:36 shown in FIG. 15.
[0158] FIG. 17 shows a nucleotide sequence (SEQ ID NO:41) of a
native sequence PRO344 cDNA, wherein SEQ ID NO:41 is a clone
designated herein as "DNA40592-1242".
[0159] FIG. 18 shows the amino acid sequence (SEQ ID NO:42) derived
from the coding sequence of SEQ ID NO:41 shown in FIG. 17.
[0160] FIG. 19 shows a nucleotide sequence (SEQ ID NO:49) of a
native sequence PRO347 cDNA, wherein SEQ ID NO:49 is a clone
designated herein as "DNA44176-1244".
[0161] FIG. 20 shows the amino acid sequence (SEQ ID NO:50) derived
from the coding sequence of SEQ ID NO:49 shown in FIG. 19.
[0162] FIG. 21 shows a nucleotide sequence (SEQ ID NO:54) of a
native sequence PRO354 cDNA, wherein SEQ ID NO:54 is a clone
designated herein as "DNA44192-1246".
[0163] FIG. 22 shows the amino acid sequence (SEQ ID NO:55) derived
from the coding sequence of SEQ ID NO:54 shown in FIG. 21.
[0164] FIG. 23 shows a nucleotide sequence (SEQ ID NO:60) of a
native sequence PRO355 cDNA, wherein SEQ ID NO:60 is a clone
designated herein as "DNA39518-1247".
[0165] FIG. 24 shows the amino acid sequence (SEQ ID NO:61) derived
from the coding sequence of SEQ ID NO:60 shown in FIG. 23.
[0166] FIG. 25 shows a nucleotide sequence (SEQ ID NO:68) of a
native sequence PRO357 cDNA, wherein SEQ ID NO:68 is a clone
designated herein as "DNA44804-1248".
[0167] FIG. 26 shows the amino acid sequence (SEQ ID NO:69) derived
from the coding sequence of SEQ ID NO:68 shown in FIG. 25.
[0168] FIG. 27 shows a nucleotide sequence (SEQ ID NO:75) of a
native sequence PRO715 cDNA, wherein SEQ ID NO:75 is a clone
designated herein as "DNA52722-1229".
[0169] FIG. 28 shows the amino acid sequence (SEQ ID NO:76) derived
from the coding sequence of SEQ ID NO:75 shown in FIG. 27.
[0170] FIG. 29 shows a nucleotide sequence (SEQ ID NO:77) of a
native sequence PRO353 cDNA, wherein SEQ ID NO:77 is a clone
designated herein as "DNA41234-1242".
[0171] FIG. 30 shows the amino acid sequence (SEQ ID NO:78) derived
from the coding sequence of SEQ ID NO:77 shown in FIG. 29.
[0172] FIG. 31 shows a nucleotide sequence (SEQ ID NO:82) of a
native sequence PRO361 cDNA, wherein SEQ ID NO:82 is a clone
designated herein as "DNA45410-1250".
[0173] FIG. 32 shows the amino acid sequence (SEQ ID NO:83) derived
from the coding sequence of SEQ ID NO:82 shown in FIG. 31.
[0174] FIG. 33 shows a nucleotide sequence (SEQ ID NO:90) of a
native sequence PRO365 cDNA, wherein SEQ ID NO:90 is a clone
designated herein as "DNA46777-1253".
[0175] FIG. 34 shows the amino acid sequence (SEQ ID NO:91) derived
from the coding sequence of SEQ ID NO:90 shown in FIG. 33.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0176] The terms "PRO polypeptide" and "PRO" as used herein and
when immediately followed by a numerical designation refer to
various polypeptides, wherein the complete designation (i.e.,
PRO/number) refers to specific polypeptide sequences as described
herein. The terms "PRO/number polypeptide" and "PRO/number" wherein
the term "number" is provided as an actual numerical designation as
used herein encompass native sequence polypeptides and polypeptide
variants (which are further defined herein). The PRO polypeptides
described herein may be isolated from a variety of sources, such as
from human tissue types or from another source, or prepared by
recombinant or synthetic methods.
[0177] A "native sequence PRO polypeptide" comprises a polypeptide
having the same amino acid sequence as the corresponding PRO
polypeptide derived from nature. Such native sequence PRO
polypeptides can be isolated from nature or can be produced by
recombinant or synthetic means. The term "native sequence PRO
polypeptide" specifically encompasses naturally-occurring truncated
or secreted forms of the specific PRO polypeptide (e.g., an
extracellular domain sequence), naturally-occurring variant forms
(e.g., alternatively spliced forms) and naturally-occurring allelic
variants of the polypeptide. In various embodiments of the
invention, the native sequence PRO polypeptides disclosed herein
are mature or full-length native sequence polypeptides comprising
the full-length amino acids sequences shown in the accompanying
figures. Start and stop codons are shown in bold font and
underlined in the figures. However, while the PRO polypeptide
disclosed in the accompanying figures are shown to begin with
methionine residues designated herein as amino acid position 1 in
the figures, it is conceivable and possible that other methionine
residues located either upstream or downstream from the amino acid
position 1 in the figures may be employed as the starting amino
acid residue for the PRO polypeptides.
[0178] The PRO polypeptide "extracellular domain" or "ECD" refers
to a form of the PRO polypeptide which is essentially free of the
transmembrane and cytoplasmic domains. Ordinarily, a PRO
polypeptide ECD will have less than 1% of such transmembrane and/or
cytoplasmic domains and preferably, will have less than 0.5% of
such domains. It will be understood that any transmembrane domains
identified for the PRO polypeptides of the present invention are
identified pursuant to criteria routinely employed in the art for
identifying that type of hydrophobic domain. The exact boundaries
of a transmembrane domain may vary but most likely by no more than
about 5 amino acids at either end of the domain as initially
identified herein. Optionally, therefore, an extracellular domain
of a PRO polypeptide may contain from about 5 or fewer amino acids
on either side of the transmembrane domain/extracellular domain
boundary as identified in the Examples or specification and such
polypeptides, with or without the associated signal peptide, and
nucleic acid encoding them, are comtemplated by the present
invention.
[0179] The approximate location of the "signal peptides" of the
various PRO polypeptides disclosed herein are shown in the present
specification and/or the accompanying figures. It is noted,
however, that the C-terminal boundary of a signal peptide may vary,
but most likely by no more than about 5 amino acids on either side
of the signal peptide C-terminal boundary as initially identified
herein, wherein the C-terminal boundary of the signal peptide may
be identified pursuant to criteria routinely employed in the art
for identifying that type of amino acid sequence element (e.g.,
Nielsen et al., Prot. Eng. 10:1-6 (1997) and von Heinje et al.,
Nucl. Acids. Res. 14:46834690 (1986)). Moreover, it is also
recognized that, in some cases, cleavage of a signal sequence from
a secreted polypeptide is not entirely uniform, resulting in more
than one secreted species. These mature polypeptides, where the
signal peptide is cleaved within no more than about 5 amino acids
on either side of the C-terminal boundary of the signal peptide as
identified herein, and the polynucleotides encoding them, are
contemplated by the present invention.
[0180] "PRO polypeptide variant" means an active PRO polypeptide as
defined above or below having at least about 80% amino acid
sequence identity with a full-length native sequence PRO
polypeptide sequence as disclosed herein, a PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO polypeptide, with or without the
signal peptide, as disclosed herein or any other fragment of a
full-length PRO polypeptide sequence as disclosed herein. Such PRO
polypeptide variants include, for instance, PRO polypeptides
wherein one or more amino acid residues are added, or deleted, at
the N- or C-terminus of the full-length native amino acid sequence.
Ordinarily, a PRO polypeptide variant will have at least about 80%
amino acid sequence identity, preferably at least about 81% amino
acid sequence identity, more preferably at least about 82% amino
acid sequence identity, more preferably at least about 83% amino
acid sequence identity, more preferably at least about 84% amino
acid sequence identity, more preferably at least about 85% amino
acid sequence identity, more preferably at least about 86% amino
acid sequence identity, more preferably at least about 87% amino
acid sequence identity, more preferably at least about 88% amino
acid sequence identity, more preferably at least about 89% amino
acid sequence identity, more preferably at least about 90% amino
acid sequence identity, more preferably at least about 91% amino
acid sequence identity, more preferably at least about 92% amino
acid sequence identity, more preferably at least about 93% amino
acid sequence identity, more preferably at least about 94% amino
acid sequence identity, more preferably at least about 95% amino
acid sequence identity, more preferably at least about 96% amino
acid sequence identity, more preferably at least about 97% amino
acid sequence identity, more preferably at least about 98% amino
acid sequence identity and most preferably at least about 99% amino
acid sequence identity with a full-length native sequence PRO
polypeptide sequence as disclosed herein, a PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO polypeptide, with or without the
signal peptide, as disclosed herein or any other specifically
defined fragment of a full-length PRO polypeptide sequence as
disclosed herein. Ordinarily, PRO variant polypeptides are at least
about 10 amino acids in length, often at least about 20 amino acids
in length, more often at least about 30 amino acids in length, more
often at least about 40 amino acids in length, more often at least
about 50 amino acids in length, more often at least about 60 amino
acids in length, more often at least about 70 amino acids in
length, more often at least about 96 amino acids in length, more
often at least about 90 amino acids in length, more often at least
about 100 amino acids in length, more often at least about 150
amino acids in length, more often at least about 200 amino acids in
length, more often a t least about 300 amino acids in length, or
more.
[0181] "Percent (%) amino acid sequence identity" with respect to
the PRO polypeptide sequences identified herein is defined as the
percentage of amino acid residues in a candidate sequence that are
identical with the amino acid residues in the specific PRO
polypeptide sequence, after aligning the sequences and introducing
gaps, if necessary, to achieve the maximum percent sequence
identity, and not considering any conservative substitutions as
part of the sequence identity. Alignment for purposes of
determining percent amino acid sequence identity can be achieved in
various ways that are within the skill in the art, for instance,
using publicly available computer software such as BLAST, BLAST-2,
ALIGN or Megalign (DNASTAR) software. Those skilled in the art can
determine appropriate parameters for measuring alignment, including
any algorithms needed to achieve maximal alignment over the full
length of the sequences being compared. For purposes herein,
however, % amino acid sequence identity values are generated using
the sequence comparison computer program ALIGN-2, wherein the
complete source code for the ALIGN-2 program is provided in Table 1
below. The ALIGN-2 sequence comparison computer program was
authored by Genentech, Inc. and the source code shown in Table 1
below has been filed with user documentation in the U.S. Copyright
Office, Washington D.C., 20559, where it is registered under U.S.
Copyright Registration No. TXU510087. The ALIGN-2 program is
publicly available through Genentech, Inc., South San Francisco,
Calif. or may be compiled from the source code provided in Table 1
below. The ALIGN-2 program should be compiled for use on a UNIX
operating system, preferably digital UNIX V4.0D. All sequence
comparison parameters are set by the ALIGN-2 program and do not
vary.
[0182] In situations where ALIGN-2 is employed for amino acid
sequence comparisons, the % amino acid sequence identity of a given
amino acid sequence A to, with, or against a given amino acid
sequence B (which can alternatively be phrased as a given amino
acid sequence A that has or comprises a certain % amino acid
sequence identity to, with, or against a given amino acid sequence
B) is calculated as follows:
100 times the fraction X/Y
[0183] where X is the number of amino acid residues scored as
identical matches by the sequence alignment program ALIGN-2 in that
program's alignment of A and B, and where Y is the total number of
amino acid residues in B. It will be appreciated that where the
length of amino acid sequence A is not equal to the length of amino
acid sequence B, the % amino acid sequence identity of A to B will
not equal the % amino acid sequence identity of B to A. As examples
of % amino acid sequence identity calculations using this method,
Tables 2 and 3 demonstrate how to calculate the % amino acid
sequence identity of the amino acid sequence designated "Comparison
Protein" to the amino acid sequence designated "PRO", wherein "PRO"
represents the amino acid sequence of a hypothetical PRO
polypeptide of interest, "Comparison Protein" represents the amino
acid sequence of a polypeptide against which the "PRO" polypeptide
of interest is being compared, and "X, "Y" and "Z" each represent
different hypothetical amino acid residues.
[0184] Unless specifically stated otherwise, all % amino acid
sequence identity values used herein are obtained as described in
the immediately preceding paragraph using the ALIGN-2 computer
program. However, % amino acid sequence identity values may also be
obtained as described below by using the WU-BLAST-2 computer
program (Altschul et al., Methods in Enzymology 266:460-480
(1996)). Most of the WU-BLAST-2 search parameters are set to the
default values. Those not set to default values, i.e., the
adjustable parameters, are set with the following values: overlap
span=1, overlap fraction=0.125, word threshold (T)=11, and scoring
matrix=BLOSUM62. When WU-BLAST-2 is employed, a % amino acid
sequence identity value is determined by dividing (a) the number of
matching identical amino acid residues between the amino acid
sequence of the PRO polypeptide of interest having a sequence
derived from the native PRO polypeptide and the comparison amino
acid sequence of interest (i.e., the sequence against which the PRO
polypeptide of interest is being compared which may be a PRO
variant polypeptide) as determined by WU-BLAST-2 by (b) the total
number of amino acid residues of the PRO polypeptide of interest.
For example, in the statement "a polypeptide comprising an the
amino acid sequence A which has or having at least 80% amino acid
sequence identity to the amino acid sequence B", the amino acid
sequence A is the comparison amino acid sequence of interest and
the amino acid sequence B is the amino acid sequence of the PRO
polypeptide of interest.
[0185] Percent amino acid sequence identity may also be determined
using the sequence comparison program NCBI-BLAST2 (Altschul et al.,
Nucleic Acids Res. 25:3389-3402 (1997)). The NCBI-BLAST2 sequence
comparison program may be downloaded from
http://www.ncbi.nlm.nih.gov. NCBI-BLAST2 uses several search
parameters, wherein all of those search parameters are set to
default values including, for example, unmask=yes, strand=all,
expected occurrences=10, minimum low complexity length=15/5,
multi-pass e-value=0.01, constant for multi-pass=25, dropoff for
final gapped alignment=25 and scoring matrix=BLOSUM62.
[0186] In situations where NCBI-BLAST2 is employed for amino acid
sequence comparisons, the % amino acid sequence identity of a given
amino acid sequence A to, with, or against a given amino acid
sequence B (which can alternatively be phrased as a given amino
acid sequence A that has or comprises a certain % amino acid
sequence identity to, with, or against a given amino acid sequence
B) is calculated as follows:
100 times the fraction X/Y
[0187] where X is the number of amino acid residues scored as
identical matches by the sequence alignment program NCBI-BLAST2 in
that program's alignment of A and B, and where Y is the total
number of amino acid residues in B. It will be appreciated that
where the length of amino acid sequence A is not equal to the
length of amino acid sequence B, the % amino acid sequence identity
of A to B will not equal the % amino acid sequence identity of B to
A.
[0188] "PRO variant polynucleotide" or "PRO variant nucleic acid
sequence" means a nucleic acid molecule which encodes an active PRO
polypeptide as defined below and which has at least about 80%
nucleic acid sequence identity with a nucleotide acid sequence
encoding a full-length native sequence PRO polypeptide sequence as
disclosed herein, a full-length native sequence PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO polypeptide, with or without the
signal peptide, as disclosed herein or any other fragment of a
full-length PRO polypeptide sequence as disclosed herein.
Ordinarily, a PRO variant polynucleotide will have at least about
80% nucleic acid sequence identity, more preferably at least about
81% nucleic acid sequence identity, more preferably at least about
82% nucleic acid sequence identity, more preferably at least about
83% nucleic acid sequence identity, more preferably at least about
84% nucleic acid sequence identity, more preferably at least about
85% nucleic acid sequence identity, more preferably at least about
86% nucleic acid sequence identity, more preferably at least about
87% nucleic acid sequence identity, more preferably at least about
88% nucleic acid sequence identity, more preferably at least about
89% nucleic acid sequence identity, more preferably at least about
90% nucleic acid sequence identity, more preferably at least about
91% nucleic acid sequence identity, more preferably at least about
92% nucleic acid sequence identity, more preferably at least about
93% nucleic acid sequence identity, more preferably at least about
94% nucleic acid sequence identity, more preferably at least about
95% nucleic acid sequence identity, more preferably at least about
96% nucleic acid sequence identity, more preferably at least about
97% nucleic acid sequence identity, more preferably at least about
98% nucleic acid sequence identity and yet more preferably at least
about 99% nucleic acid sequence identity with a nucleic acid
sequence encoding a full-length native sequence PRO polypeptide
sequence as disclosed herein, a full-length native sequence PRO
polypeptide sequence lacking the signal peptide as disclosed
herein, an extracellular domain of a PRO polypeptide, with or
without the signal sequence, as disclosed herein or any other
fragment of a full-length PRO polypeptide sequence as disclosed
herein. Variants do not encompass the native nucleotide
sequence.
[0189] Ordinarily, PRO variant polynucleotides are at least about
30 nucleotides in length, often at least about 60 nucleotides in
length, more often at least about 90 nucleotides in length, more
often at least about 120 nucleotides in length, more often at least
about 150 nucleotides in length, more often at least about 180
nucleotides in length, more often at least about 210 nucleotides in
length, more often at least about 240 nucleotides in length, more
often at least about 270 nucleotides in length, more often at least
about 300 nucleotides in length, more often at least about 450
nucleotides in length, more often at least about 600 nucleotides in
length, more often at least about 900 nucleotides in length, or
more.
[0190] "Percent (%) nucleic acid sequence identity" with respect to
PRO-encoding nucleic acid sequences identified herein is defined as
the percentage of nucleotides in a candidate sequence that are
identical with the nucleotides in the PRO nucleic acid sequence of
interest, after aligning the sequences and introducing gaps, if
necessary, to achieve the maximum percent sequence identity.
Alignment for purposes of determining percent nucleic acid sequence
identity can be achieved in various ways that are within the skill
in the art, for instance, using publicly available computer
software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR)
software. For purposes herein, however, % nucleic acid sequence
identity values are generated using the sequence comparison
computer program ALIGN-2, wherein the complete source code for the
ALIGN-2 program is provided in Table 1 below. The ALIGN-2 sequence
comparison computer program was authored by Genentech, Inc. and the
source code shown in Table 1 below has been filed with user
documentation in the U.S. Copyright Office, Washington D.C., 20559,
where it is registered under U.S. Copyright Registration No.
TXU510087. The ALIGN-2 program is publicly available through
Genentech, Inc., South San Francisco, Calif. or may be compiled
from the source code provided in Table 1 below. The ALIGN-2 program
should be compiled for use on a UNIX operating system, preferably
digital UNIX V4.0D. All sequence comparison parameters are set by
the ALIGN-2 program and do not vary.
[0191] In situations where ALIGN-2 is employed for nucleic acid
sequence comparisons, the % nucleic acid sequence identity of a
given nucleic acid sequence C to, with, or against a given nucleic
acid sequence D (which can alternatively be phrased as a given
nucleic acid sequence C that has or comprises a certain % nucleic
acid sequence identity to, with, or against a given nucleic acid
sequence D) is calculated as follows:
100 times the fraction W/Z
[0192] where W is the number of nucleotides scored as identical
matches by the sequence alignment program ALIGN-2 in that program's
alignment of C and D, and where Z is the total number of
nucleotides in D. It will be appreciated that where the length of
nucleic acid sequence C is not equal to the length of nucleic acid
sequence D, the % nucleic acid sequence identity of C to D will not
equal the % nucleic acid sequence identity of D to C. As examples
of % nucleic acid sequence identity calculations, Tables 4 and 5,
demonstrate how to calculate the % nucleic acid sequence identity
of the nucleic acid sequence designated "Comparison DNA" to the
nucleic acid sequence designated "PRO-DNA", wherein "PRO-DNA"
represents a hypothetical PRO-encoding nucleic acid sequence of
interest, "Comparison DNA" represents the nucleotide sequence of a
nucleic acid molecule against which the "PRO-DNA" nucleic acid
molecule of interest is being compared, and "N", "L" and "V" each
represent different hypothetical nucleotides.
[0193] Unless specifically stated otherwise, all % nucleic acid
sequence identity values used herein are obtained as described in
the immediately preceding paragraph using the ALIGN-2 computer
program. However, % nucleic acid sequence identity values may also
be obtained as described below by using the WU-BLAST-2 computer
program (Altschul et al., Methods in Enzymology 266:460-480
(1996)). Most of the WU-BLAST-2 search parameters are set to the
default values. Those not set to default values, i.e., the
adjustable parameters, are set with the following values: overlap
span=1, overlap fraction=0.125, word threshold (T)=11, and scoring
matrix=BLOSUM62. When WU-BLAST-2 is employed, a % nucleic acid
sequence identity value is determined by dividing (a) the number of
matching identical nucleotides between the nucleic acid sequence of
the PRO polypeptide-encoding nucleic acid molecule of interest
having a sequence derived from the native sequence PRO
polypeptide-encoding nucleic acid and the comparison nucleic acid
molecule of interest (i.e., the sequence against which the PRO
polypeptide-encoding nucleic acid molecule of interest is being
compared which may be a variant PRO polynucleotide) as determined
by WU-BLAST-2 by (b) the total number of nucleotides of the PRO
polypeptide-encoding nucleic acid molecule of interest. For
example, in the statement "an isolated nucleic acid molecule
comprising a nucleic acid sequence A which has or having at least
80% nucleic acid sequence identity to the nucleic acid sequence B",
the nucleic acid sequence A is the comparison nucleic acid molecule
of interest and the nucleic acid sequence B is the nucleic acid
sequence of the PRO polypeptide-encoding nucleic acid molecule of
interest.
[0194] Percent nucleic acid sequence identity may also be
determined using the sequence comparison program NCBI-BLAST2
(Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). The
NCBI-BLAST2 sequence comparison program may be downloaded from
http:I/www.ncbi.nlm.nih.gov. NCBI-BLAST2 uses several search
parameters, wherein all of those search parameters are set to
default values including, for example, unmask=yes, strand=all,
expected occurrences=10, minimum low complexity length=15/5,
multi-pass e-value=0.01, constant for multi-pass=25, dropoff for
final gapped alignment=25 and scoring matrix=BLOSUM62.
[0195] In situations where NCBI-BLAST2 is employed for sequence
comparisons, the % nucleic acid sequence identity of a given
nucleic acid sequence C to, with, or against a given nucleic acid
sequence D (which can alternatively be phrased as a given nucleic
acid sequence C that has or comprises a certain % nucleic acid
sequence identity to, with, or against a given nucleic acid
sequence D) is calculated as follows:
100 times the fraction W/Z
[0196] where W is the number of nucleotides scored as identical
matches by the sequence alignment program NCBI-BLAST2 in that
program's alignment of C and D, and where Z is the total number of
nucleotides in D. It will be appreciated that where the length of
nucleic acid sequence C is not equal to the length of nucleic acid
sequence D, the % nucleic acid sequence identity of C to D will not
equal the % nucleic acid sequence identity of D to C.
[0197] In other embodiments, PRO variant polynucleotides are
nucleic acid molecules that encode an active PRO polypeptide and
which are capable of hybridizing, preferably under stringent
hybridization and wash conditions, to nucleotide sequences encoding
a full-length PRO polypeptide as disclosed herein. PRO variant
polypeptides may be those that are encoded by a PRO variant
polynucleotide.
[0198] The term "positives", in the context of sequence comparison
performed as described above, includes residues in the sequences
compared that are not identical but have similar properties (e.g.
as a result of conservative substitutions, see Table 6 below). For
purposes herein, the % value of positives is determined by dividing
(a) the number of amino acid residues scoring a positive value
between the PRO polypeptide amino acid sequence of interest having
a sequence derived from the native PRO polypeptide sequence and the
comparison amino acid sequence of interest (i.e., the amino acid
sequence against which the PRO polypeptide sequence is being
compared) as determined in the BLOSUM62 matrix of WU-BLAST-2 by (b)
the total number of amino acid residues of the PRO polypeptide of
interest.
[0199] Unless specifically stated otherwise, the % value of
positives is calculated as described in the immediately preceding
paragraph. However, in the context of the amino acid sequence
identity comparisons performed as described for ALIGN-2 and
NCBI-BLAST-2 above, includes amino acid residues in the sequences
compared that are not only identical, but also those that have
similar properties. Amino acid residues that score a positive value
to an amino acid residue of interest are those that are either
identical to the amino acid residue of interest or are a preferred
substitution (as defined in Table 6 below) of the amino acid
residue of interest.
[0200] For amino acid sequence comparisons using ALIGN-2 or
NCBI-BLAST2, the % value of positives of a given amino acid
sequence A to, with, or against a given amino acid sequence B
(which can alternatively be phrased as a given amino acid sequence
A that has or comprises a certain % positives to, with, or against
a given amino acid sequence B) is calculated as follows:
100 times the fraction X/Y
[0201] where X is the number of amino acid residues scoring a
positive value as defined above by the sequence alignment program
ALIGN-2 or NCBI-BLAST2 in that program's alignment of A and B, and
where Y is the total number of amino acid residues in B. It will be
appreciated that where the length of amino acid sequence A is not
equal to the length of amino acid sequence B, the % positives of A
to B will not equal the % positives of B to A.
[0202] "Isolated, " when used to describe the various polypeptides
disclosed herein, means polypeptide that has been identified and
separated and/or recovered from a component of its natural
environment. Contaminant components of its natural environment are
materials that would typically interfere with diagnostic or
therapeutic uses for the polypeptide, and may include enzymes,
hormones, and other proteinaceous or non-proteinaceous solutes. In
preferred embodiments, the polypeptide will be purified (1) to a
degree sufficient to obtain at least residues of N-terminal or
internal amino acid sequence by use of a spinning cup sequenator,
or (2) to homogeneity by SDS-PAGE under non-reducing or reducing
conditions using Coomassie blue or, preferably, silver stain.
Isolated polypeptide includes polypeptide in situ within
recombinant cells, since at least one component of the PRO
polypeptide natural environment will not be present. Ordinarily,
however, isolated polypeptide will be prepared by at least one
purification step.
[0203] An "isolated" PRO polypeptide-encoding nucleic acid or other
polypeptide-encoding nucleic acid is a nucleic acid molecule that
is identified and separated from at least one contaminant nucleic
acid molecule with which it is ordinarily associated in the natural
source of the polypeptide-encoding nucleic acid. An isolated
polypeptide-encoding nucleic acid molecule is other than in the
form or setting in which it is found in nature. Isolated
polypeptide-encoding nucleic acid molecules therefore are
distinguished from the specific polypeptide-encoding nucleic acid
molecule as it exists in natural cells. However, an isolated
polypeptide-encoding nucleic acid molecule includes
polypeptide-encoding nucleic acid molecules contained in cells that
ordinarily express the polypeptide where, for example, the nucleic
acid molecule is in a chromosomal location different from that of
natural cells.
[0204] The term "control sequences" refers to DNA sequences
necessary for the expression of an operably linked coding sequence
in a particular host organism. The control sequences that are
suitable for prokaryotes, for example, include a promoter,
optionally an operator sequence, and a ribosome binding site.
Eukaryotic cells are known to utilize promoters, polyadenylation
signals, and enhancers.
[0205] Nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
example, DNA for a presequence or secretory leader is operably
linked to DNA for a polypeptide if it is expressed as a preprotein
that participates in the secretion of the polypeptide; a promoter
or enhancer is operably linked to a coding sequence if it affects
the transcription of the sequence; or a ribosome binding site is
operably linked to a coding sequence if it is positioned so as to
facilitate translation. Generally, "operably linked" means that the
DNA sequences being linked are contiguous, and, in the case of a
secretory leader, contiguous and in reading phase. However,
enhancers do not have to be contiguous. Linking is accomplished by
ligation at convenient restriction sites. If such sites do not
exist, the synthetic oligonucleotide adaptors or linkers are used
in accordance with conventional practice.
[0206] The term "antibody" is used in the broadest sense and
specifically covers, for example, single anti-PRO monoclonal
antibodies (including agonist, antagonist, and neutralizing
antibodies), anti-PRO antibody compositions with polyepitopic
specificity, single chain anti-PRO antibodies, and fragments of
anti-PRO antibodies (see below). The term "monoclonal antibody" as
used herein refers to an antibody obtained from a population of
substantially homogeneous antibodies, i.e., the individual
antibodies comprising the population are identical except for
possible naturally-occurring mutations that may be present in minor
amounts.
[0207] "Stringency" of hybridization reactions is readily
determinable by one of ordinary skill in the art, and generally is
an empirical calculation dependent upon probe length, washing
temperature, and salt concentration. In general, longer probes
require higher temperatures for proper annealing, while shorter
probes need lower temperatures. Hybridization generally depends on
the ability of denatured DNA to reanneal when complementary strands
are present in an environment below their melting temperature. The
higher the degree of desired homology between the probe and
hybridizable sequence, the higher the relative temperature which
can be used. As a result, it follows that higher relative
temperatures would tend to make the reaction conditions more
stringent, while lower temperatures less so. For additional details
and explanation of stringency of hybridization reactions, see
Ausubel et al., Current Protocols in Molecular Biology, Wiley
Interscience Publishers, (1995).
[0208] "Stringent conditions" or "high stringency conditions", as
defined herein, may be identified by those that: (1) employ low
ionic strength and high temperature for washing, for example 0.015
M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl
sulfate at 50.degree. C.; (2) employ during hybridization a
denaturing agent, such as formamide, for example, 50% (v/v)
formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1%
polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with
750 mM sodium chloride, 75 mM sodium citrate at 42.degree. C.; or
(3) employ 50% formamide, 5.times.SSC (0.75 M NaCl, 0.075 M sodium
citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium
pyrophosphate, 5.times.Denhardt's solution, sonicated salmon sperm
DNA (50 .mu.g/ml), 0.1% SDS, and 10% dextran sulfate at 42.degree.
C., with washes at 42.degree. C. in 0.2.times.SSC (sodium
chloride/sodium citrate) and 50% formamide at 55.degree. C.,
followed by a high-stringency wash consisting of 0.1.times.SSC
containing EDTA at 55.degree. C.
[0209] "Moderately stringent conditions" may be identified as
described by Sambrook et al., Molecular Cloning: A Laboratory
Manual, New York: Cold Spring Harbor Press, 1989, and include the
use of washing solution and hybridization conditions (e.g.,
temperature, ionic strength and %SDS) less stringent that those
described above. An example of moderately stringent conditions is
overnight incubation at 37.degree. C. in a solution comprising: 20%
formamide, 5.times.SSC (150 mM NaCl, 15 mM trisodium citrate), 50
mM sodium phosphate (pH 7.6), 5.times.Denhardt's solution, 10%
dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA,
followed by washing the filters in 1.times.SSC at about
37-50.degree. C. The skilled artisan will recognize how to adjust
the temperature, ionic strength, etc. as necessary to accommodate
factors such as probe length and the like.
[0210] The term "epitope tagged" when used herein refers to a
chimeric polypeptide comprising a PRO polypeptide fused to a "tag
polypeptide". The tag polypeptide has enough residues to provide an
epitope against which an antibody can be made, yet is short enough
such that it does not interfere with activity of the polypeptide to
which it is fused. The tag polypeptide preferably also is fairly
unique so that the antibody does not substantially cross-react with
other epitopes. Suitable tag polypeptides generally have at least
six amino acid residues and usually between about 8 and 50 amino
acid residues (preferably, between about 10 and 20 amino acid
residues).
[0211] As used herein, the term "immunoadhesin" designates
antibody-like molecules which combine the binding specificity of a
heterologous protein (an "adhesin") with the effector functions of
immunoglobulin constant domains. Structurally, the immunoadhesins
comprise a fusion of an amino acid sequence with the desired
binding specificity which is other than the antigen recognition and
binding site of an antibody (i.e., is "heterologous"), and an
immunoglobulin constant domain sequence. The adhesin part of an
immunoadhesin molecule typically is a contiguous amino acid
sequence comprising at least the binding site of a receptor or a
ligand. The immunoglobulin constant domain sequence in the
immunoadhesin may be obtained from any immunoglobulin, such as
IgG-1, IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA- I and
IgA-2), IgE, IgD or IgM.
[0212] "Active" or "activity" for the purposes herein refers to
form(s) of a PRO polypeptide which retain a biological and/or an
immunological activity of native or naturally-occurring PRO,
wherein "biological" activity refers to a biological function
(either inhibitory or stimulatory) caused by a native or
naturally-occurring PRO other than the ability to induce the
production of an antibody against an antigenic epitope possessed by
a native or naturally-occurring PRO and an "immunological" activity
refers to the ability to induce the production of an antibody
against an antigenic epitope possessed by a native or
naturally-occurring PRO.
[0213] The term "antagonist" is used in the broadest sense, and
includes any molecule that partially or fully blocks, inhibits, or
neutralizes a biological activity of a native PRO polypeptide
disclosed herein. In a similar manner, the term "agonist" is used
in the broadest sense and includes any molecule that mimics a
biological activity of a native PRO polypeptide disclosed herein.
Suitable agonist or antagonist molecules specifically include
agonist or antagonist antibodies or antibody fragments, fragments
or amino acid sequence variants of native PRO polypeptides,
peptides, antisense oligonucleotides, small organic molecules, etc.
Methods for identifying agonists or antagonists of a PRO
polypeptide may comprise contacting a PRO polypeptide with a
candidate agonist or antagonist molecule and measuring a detectable
change in one or more biological activities normally associated
with the PRO polypeptide.
[0214] "Treatment" refers to both therapeutic treatment and
prophylactic or preventative measures, wherein the object is to
prevent or slow down (lessen) the targeted pathologic condition or
disorder. Those in need of treatment include those already with the
disorder as well as those prone to have the disorder or those in
whom the disorder is to be prevented.
[0215] "Chronic" administration refers to administration of the
agent(s) in a continuous mode as opposed to an acute mode, so as to
maintain the initial therapeutic effect (activity) for an extended
period of time. "Intermittent" administration is treatment that is
not consecutively done without interruption, but rather is cyclic
in nature.
[0216] "Mammal" for purposes of treatment refers to any animal
classified as a mammal, including humans, domestic and farm
animals, and zoo, sports, or pet animals, such as dogs, cats,
cattle, horses, sheep, pigs, goats, rabbits, etc. Preferably, the
mammal is human.
[0217] Administration "in combination with" one or more further
therapeutic agents includes simultaneous (concurrent) and
consecutive administration in any order.
[0218] "Carriers" as used herein include pharmaceutically
acceptable carriers, excipients, or stabilizers which are nontoxic
to the cell or mammal being exposed thereto at the dosages and
concentrations employed. Often the physiologically acceptable
carrier is an aqueous pH buffered solution. Examples of
physiologically acceptable carriers include buffers such as
phosphate, citrate, and other organic acids; antioxidants including
ascorbic acid; low molecular weight (less than about 10 residues)
polypeptide; proteins, such as serum albumin, gelatin, or
immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone;
amino acids such as glycine, glutamine, asparagine, arginine or
lysine; monosaccharides, disaccharides, and other carbohydrates
including glucose, mannose, or dextrins; chelating agents such as
EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming
counterions such as sodium; and/or nonionic surfactants such as
TWEEN.TM., polyethylene glycol (PEG), and PLURONICS.TM..
[0219] "Antibody fragments" comprise a portion of an intact
antibody, preferably the antigen binding or variable region of the
intact antibody. Examples of antibody fragments include Fab, Fab',
F(ab').sub.2, and Fv fragments; diabodies; linear antibodies
(Zapata et al., Protein Eng. 8(10): 1057-1062 [1995]); single-chain
antibody molecules; and multispecific antibodies formed from
antibody fragments.
[0220] Papain digestion of antibodies produces two identical
antigen-binding fragments, called "Fab" fragments, each with a
single antigen-binding site, and a residual "Fc" fragment, a
designation reflecting the ability to crystallize readily. Pepsin
treatment yields an F(ab').sub.2 fragment that has two
antigen-combining sites and is still capable of cross-linking
antigen.
[0221] "Fv" is the minimum antibody fragment which contains a
complete antigen-recognition and -binding site. This region
consists of a dimer of one heavy- and one light-chain variable
domain in tight, non-covalent association. It is in this
configuration that the three CDRs of each variable domain interact
to define an antigen-binding site on the surface of the
V.sub.H-V.sub.L dimer. Collectively, the six CDRs confer
antigen-binding specificity to the antibody. However, even a single
variable domain (or half of an Fv comprising only three CDRs
specific for an antigen) has the ability to recognize and bind
antigen, although at a lower affinity than the entire binding
site.
[0222] The Fab fragment also contains the constant domain of the
light chain and the first constant domain (CH1) of the heavy chain.
Fab fragments differ from Fab' fragments by the addition of a few
residues at the carboxy terminus of the heavy chain CH1 domain
including one or more cysteines from the antibody hinge region.
Fab'-SH is the designation herein for Fab' in which the cysteine
residue(s) of the constant domains bear a free thiol group.
F(ab').sub.2 antibody fragments originally were produced as pairs
of Fab' fragments which have hinge cysteines between them. Other
chemical couplings of antibody fragments are also known.
[0223] The "light chains" of antibodies (immunoglobulins) from any
vertebrate species can be assigned to one of two clearly distinct
types, called kappa and lambda, based on the amino acid sequences
of their constant domains.
[0224] Depending on the amino acid sequence of the constant domain
of their heavy chains, immunoglobulins can be assigned to different
classes. There are five major classes of immunoglobulins: IgA, IgD,
IgE, IgG, and IgM, and several of these may be further divided into
subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA, and
IgA2.
[0225] "Single-chain Fv" or "sFv" antibody fragments comprise the
V.sub.H and V.sub.L domains of antibody, wherein these domains are
present in a single polypeptide chain. Preferably, the Fv
polypeptide further comprises a polypeptide linker between the
V.sub.H and V.sub.L domains which enables the sFv to form the
desired structure for antigen binding. For a review of sFv, see
Pluckthun in The Pharmacology of Monoclonal Antibodies. vol. 113,
Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315
(1994).
[0226] The term "diabodies" refers to small antibody fragments with
two antigen-binding sites, which fragments comprise a heavy-chain
variable domain (V.sub.H) connected to a light-chain variable
domain (V.sub.L) in the same polypeptide chain (V.sub.H-V.sub.L).
By using a linker that is too short to allow pairing between the
two domains on the same chain, the domains are forced to pair with
the complementary domains of another chain and create two
antigen-binding sites. Diabodies are described more fully in, for
example, EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl.
Acad. Sci. USA, 90:6444-6448 (1993).
[0227] An "isolated" antibody is one which has been identified and
separated and/or recovered from a component of its natural
environment. Contaminant components of its natural environment are
materials which would interfere with diagnostic or therapeutic uses
for the antibody, and may include enzymes, hormones, and other
proteinaceous or nonproteinaceous solutes. In preferred
embodiments, the antibody will be purified (1) to greater than 95%
by weight of antibody as determined by the Lowry method, and most
preferably more than 99% by weight, (2) to a degree sufficient to
obtain at least 15 residues of N-terminal or internal amino acid
sequence by use of a spinning cup sequenator, or (3) to homogeneity
by SDS-PAGE under reducing or nonreducing conditions using
Coomassie blue or, preferably, silver stain. Isolated antibody
includes the antibody in situ within recombinant cells since at
least one component of the antibody's natural environment will not
be present. Ordinarily, however, isolated antibody will be prepared
by at least one purification step.
[0228] The word "label" when used herein refers to a detectable
compound or composition which is conjugated directly or indirectly
to the antibody so as to generate a "labeled" antibody. The label
may be detectable by itself (e.g. radioisotope labels or
fluorescent labels) or, in the case of an enzymatic label, may
catalyze chemical alteration of a substrate compound or composition
which is detectable.
[0229] By "solid phase" is meant a non-aqueous matrix to which the
antibody of the present invention can adhere. Examples of solid
phases encompassed herein include those formed partially or
entirely of glass (e.g., controlled pore glass), polysaccharides
(e.g., agarose), polyacrylamides, polystyrene, polyvinyl alcohol
and silicones. In certain embodiments, depending on the context,
the solid phase can comprise the well of an assay plate; in others
it is a purification column (e.g., an affinity chromatography
column). This term also includes a discontinuous solid phase of
discrete particles, such as those described in U.S. Pat. No.
4,275,149.
[0230] A "liposome" is a small vesicle composed of various types of
lipids, phospholipids and/or surfactant which is useful for
delivery of a drug (such as a PRO polypeptide or antibody thereto)
to a mammal. The components of the liposome are commonly arranged
in a bilayer formation, similar to the lipid arrangement of
biological membranes.
[0231] A "small molecule" is defined herein to have a molecular
weight below about 500 Daltons.
1TABLE 2 PRO XXXXXXXXXXXXXXX (Length = 15 amino acids) Comparison
XXXXXYYYYYYY (Length = 12 amino acids) Protein % amino acid
sequence identity = (the number of identically matching amino acid
residues between the two polypeptide sequences as determined by
ALIGN-2) divided by (the total number of amino acid residues of the
PRO polypeptide) = 5 divided by 15 = 33.3%
[0232]
2TABLE 3 PRO XXXXXXXXXX (Length = 10 amino acids) Comparison
XXXXXYYYYYYZZYZ (Length = 15 amino acids) Protein % amino acid
sequence identity = (the number of identically matching amino acid
residues between the two polypeptide sequences as determined by
ALIGN-2) divided by (the total number of amino acid residues of the
PRO polypeptide) = 5 divided by 10 = 50%
[0233]
3TABLE 4 PRO-DNA NNNNNNNNNNNNNN (Length = 14 nucleotides)
Comparison NNNNNNLLLLLLLLLL (Length = 16 nucleotides) DNA % nucleic
acid sequence identity = (the number of identically matching
nucleotides between the two nucleic acid sequences as determined by
ALIGN-2) divided by (the total number of nucleotides of the PRO-DNA
nucleic acid sequence) = 6 divided by 14 = 42.9%
[0234]
4TABLE 5 PRO-DNA NNNNNNNNNNNN (Length = 12 nucleotides) Comparison
NNNNLLLVV (Length = 9 nucleotides) DNA % nucleic acid sequence
identity = (the number of identically matching nucleotides between
the two nucleic acid sequences as determined by ALIGN-2) divided by
(the total number of nucleotides of the PRO-DNA nucleic acid
sequence) = 4 divided by 12 = 33.3%
[0235] II. Compositions and Methods of the Invention
[0236] A. Full-Length PRO Polypeptides
[0237] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO polypeptides. In particular, cDNAs
encoding various PRO polypeptides have been identified and
isolated, as disclosed in further detail in the Examples below. It
is noted that proteins produced in separate expression rounds may
be given different PRO numbers but the UNQ number is unique for any
given DNA and the encoded protein, and will not be changed.
However, for sake of simplicity, in the present specification the
protein encoded by the full length native nucleic acid molecules
disclosed herein as well as all further native homologues and
variants included in the foregoing definition of PRO, will be
referred to as "PRO/number", regardless of their origin or mode of
preparation.
[0238] As disclosed in the Examples below, various cDNA clones have
been deposited with the ATCC. The actual nucleotide sequences of
those clones can readily be determined by the skilled artisan by
sequencing of the deposited clone using routine methods in the art.
The predicted amino acid sequence can be determined from the
nucleotide sequence using routine skill. For the PRO polypeptides
and encoding nucleic acids described herein, Applicants have
identified what is believed to be the reading frame best
identifiable with the sequence information available at the
time.
[0239] 1. Full-length PRO241 Polypeptides
[0240] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PR0241. In particular, Applicants have
identified and isolated cDNA encoding a PRO241 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
portions of the PR0241 polypeptide have certain homology with the
various biglycan proteins. Accordingly, it is presently believed
that PRO241 polypeptide disclosed in the present application is a
newly identified biglycan homolog polypeptide and may possess
activity typical of biglycan proteins.
[0241] 2. Full-length PRO243 Polypeptides
[0242] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO243. In particular, Applicants have
identified and isolated cDNA encoding a PRO243 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST,
BLAST-2 and FastA sequence alignment computer programs, Applicants
found that a full-length native sequence PRO243 (shown in FIG. 4
and SEQ ID NO:7) has certain amino acid sequence identity with
African clawed frog and Xenopus chordin and certain homology with
rat chordin. Accordingly, it is presently believed that PRO243
disclosed in the present application is a newly identified member
of the chordin protein family and may possess ability to influence
notochord and muscle formation by the dorsalization of the
mesoderm.
[0243] 3. Full-length PRO299
[0244] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO299. In particular, Applicants have
identified and isolated cDNA encoding a PRO299 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO299 polypeptide have certain homology
with the notch protein. Accordingly, it is presently believed that
PRO299 polypeptide disclosed in the present application is a newly
identified member of the notch protein family and possesses
signaling properties typical of the notch protein family.
[0245] 4. Full-length PRO323 Polypeptides
[0246] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO323. In particular, Applicants have
identified and isolated cDNA encoding a PRO323 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO323 polypeptide have certain homology
with various dipeptidase proteins. Accordingly, it is presently
believed that PRO323 polypeptide disclosed in the present
application is a newly identified dipeptidase homolog that has
dipeptidase activity
[0247] 5. Full-length PRO327 Polypeptides
[0248] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO327. In particular, Applicants have
identified and isolated cDNA encoding a PRO327 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
portions of the PRO327 polypeptide have certain homology with
various prolactin receptor proteins. Accordingly, it is presently
believed that PRO327 polypeptide disclosed in the present
application is a newly identified prolactin receptor homolog and
has activity typical of a prolactin receptor protein.
[0249] 6. Full-length PRO233 Polypeptides
[0250] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO233. In particular, Applicants have
identified and isolated cDNA encoding a PRO233 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO233 polypeptide have certain homology
with various reductase proteins. Applicants have also found that
the DNA encoding the PRO233 polypeptide has significant homology
with proteins from Caenorhabditis elegans. Accordingly, it is
presently believed that PRO233 polypeptide disclosed in the present
application is a newly identified member of the reductase family
and possesses the ability to effect the redox state of a cell
typical of the reductase family.
[0251] 7. Full-length PRO344 Polypeptides
[0252] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO344. In particular, Applicants have
identified and isolated cDNA encoding PRO344 polypeptides, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO344 polypeptide have certain homology
with the human and mouse complement proteins. Accordingly, it is
presently believed that the PRO344 polypeptide disclosed in the
present application is a newly identified member of the complement
family and possesses the ability to affect the inflammation process
as is typical of the complement family of proteins.
[0253] 8. Full-length PRO347 Polypeptides
[0254] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO347. In particular, Applicants have
identified and isolated cDNA encoding a PRO347 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
portions of the PRO347 polypeptide have certain homology with
various cysteine-rich secretory proteins. Accordingly, it is
presently believed that PRO347 polypeptide disclosed in the present
application is a newly identified cysteine-rich secretory protein
and may possess activity typical of the cysteine-rich secretory
protein family.
[0255] 9. Full-length PRO354 Polypeptides
[0256] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO354. In particular, Applicants have
identified and isolated cDNA encoding a PRO354 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
portions of the PRO354 polypeptide have certain homology with the
inter-alpha-trypsin inhibitor heavy chain protein. Accordingly, it
is presently believed that PRO354 polypeptide disclosed in the
present application is a newly identified inter-alpha-trypsin
inhibitor heavy chain homolog.
[0257] 10. Full-length PRO355 Polypeptides
[0258] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO355. In particular, Applicants have
identified and isolated cDNA encoding a PRO355 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO355 polypeptide have certain homology
with the CRTAM protein. Applicants have also found that the DNA
encoding the PRO355 polypeptide also has homology to the thymocyte
activation and developmental protein, the H20A receptor, the H20B
receptor, the poliovirus receptor and the Cercopithecus aethiops
AGM delta 1 protein. Accordingly, it is presently believed that
PRO355 polypeptide disclosed in the present application is a newly
identified member of the CRTAM protein family.
[0259] 11. Full-length PRO357 Polypeptides
[0260] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO357. In particular, Applicants have
identified and isolated cDNA encoding a PRO357 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO357 polypeptide have certain homology
with the acid labile subunit of insulin-like growth factor.
Applicants have also found that non-coding regions of the
DNA44804-1248 align with a human gene signature as described in WO
95/14772. Applicants have further found that non-coding regions of
the DNA44804-1248 align with the adenovirus type 12/human
recombinant viral DNA as described in Deuring and Doerfler, Gene,
26:283-289 (1983). Based on the coding region homology, it is
presently believed that PRO357 polypeptide disclosed in the present
application is a newly identified member of the leucine rich repeat
family of proteins, and particularly, is related to the acid labile
subunit of insulin-like growth factor. As such, PRO357 is likely to
be involved in binding mechanisms, and may be part of a
complex.
[0261] 12. Full-length PRO715 Polypeptides
[0262] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO715. In particular, Applicants have
identified and isolated cDNA molecules encoding PRO715
polypeptides, as disclosed in further detail in the Examples below.
Using BLAST and FastA sequence alignment computer programs,
Applicants found that various portions of the PRO715 polypeptides
have certain homology with the various members of the tumor
necrosis family of proteins. Accordingly, it is presently believed
that the PRO715 polypeptides disclosed in the present application
are newly identified members of the tumor necrosis factor family of
proteins.
[0263] 13. Full-length PRO353 Polypeptides
[0264] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO353. In particular, Applicants have
identified and isolated cDNA encoding PRO353 polypeptides, as
disclosed in further detail in the Examples below. Using BLAST and,
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO353 polypeptides have certain homology
with the human and mouse complement proteins. Accordingly, it is
presently believed that the PRO353 polypeptides disclosed in the
present application are newly identified members of the complement
protein family and possesses the ability to effect the inflammation
process as is typical of the complement family of proteins.
[0265] 14. Full-length PRO361 Polypeptides
[0266] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO361. In particular, Applicants have
identified and isolated cDNA encoding a PRO361 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO361 polypeptide have certain homology
with the mucin and chitinase proteins. Accordingly, it is presently
believed that PRO361 polypeptide disclosed in the present
application is a newly identified member of the mucin and/or
chitinase protein families and may be associated with cancer, plant
pathogenesis or receptor functions typical of the mucin and
chitinase protein families, respectively.
[0267] 15. Full-length PRO365 Polypeptides
[0268] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO365. In particular, Applicants have
identified and isolated cDNA encoding a PRO365 polypeptide, as
disclosed in further detail in the Examples below. Using BLAST and
FastA sequence alignment computer programs, Applicants found that
various portions of the PRO365 polypeptide have certain homology
with the human 2-19 protein. Accordingly, it is presently believed
that PRO365 polypeptide disclosed in the present application is a
newly identified member of the human 2-19 protein family.
[0269] 2. PRO Polypeptide Variants
[0270] In addition to the full-length native sequence PRO
polypeptides described herein, it is contemplated that PRO variants
can be prepared. PRO variants can be prepared by introducing
appropriate nucleotide changes into the PRO DNA, and/or by
synthesis of the desired PRO polypeptide. Those skilled in the art
will appreciate that amino acid changes may alter
post-translational processes of the PRO, such as changing the
number or position of glycosylation sites or altering the membrane
anchoring characteristics.
[0271] Variations in the native full-length sequence PRO or in
various domains of the PRO described herein, can be made, for
example, using any of the techniques and guidelines for
conservative and non-conservative mutations set forth, for
instance, in U.S. Pat. No. 5,364,934. Variations may be a
substitution, deletion or insertion of one or more codons encoding
the PRO that results in a change in the amino acid sequence of the
PRO as compared with the native sequence PRO. Optionally the
variation is by substitution of at least one amino acid with any
other amino acid in one or more of the domains of the PRO. Guidance
in determining which amino acid residue may be inserted,
substituted or deleted without adversely affecting the desired
activity may be found by comparing the sequence of the PRO with
that of homologous known protein molecules and minimizing the
number of amino acid sequence changes made in regions of high
homology. Amino acid substitutions can be the result of replacing
one amino acid with another amino acid having similar structural
and/or chemical properties, such as the replacement of a leucine
with a serine, i.e., conservative amino acid replacements.
Insertions or deletions may optionally be in the range of about 1
to 5 amino acids. The variation allowed may be determined by
systematically making insertions, deletions or substitutions of
amino acids in the sequence and testing the resulting variants for
activity exhibited by the full-length or mature native
sequence.
[0272] PRO polypeptide fragments are provided herein. Such
fragments may be truncated at the N-terminus or C-terminus, or may
lack internal residues, for example, when compared with a full
length native protein. Certain fragments lack amino acid residues
that are not essential for a desired biological activity of the PRO
polypeptide.
[0273] PRO fragments may be prepared by any of a number of
conventional techniques. Desired peptide fragments may be
chemically synthesized. An alternative approach involves generating
PRO fragments by enzymatic digestion, e.g., by treating the protein
with an enzyme known to cleave proteins at sites defined by
particular amino acid residues, or by digesting the DNA with
suitable restriction enzymes and isolating the desired fragment.
Yet another suitable technique involves isolating and amplifying a
DNA fragment encoding a desired polypeptide fragment, by polymerase
chain reaction (PCR). Oligonucleotides that define the desired
termini of the DNA fragment are employed at the 5' and 3' primers
in the PCR. Preferably, PRO polypeptide fragments share at least
one biological and/or immunological activity with the native PRO
polypeptide disclosed herein.
[0274] In particular embodiments, conservative substitutions of
interest are shown in Table 1 under the heading of preferred
substitutions. If such substitutions result in a change in
biological activity, then more substantial changes, denominated
exemplary substitutions in Table 6, or as further described below
in reference to amino acid classes, are introduced and the products
screened.
5 TABLE 6 Original Exemplary Preferred Residue Substitutions
Substitutions Ala (A) val; leu; ile val Arg (R) lys; gln; asn lys
Asn (N) gln; his; lys; arg gln Asp (D) glu glu Cys (C) ser ser Gln
(Q) asn asn Glu (E) asp asp Gly (G) pro; ala ala His (H) asn; gln;
lys; arg arg Ile (I) leu; val; met; ala; phe; leu norleucine Leu
(L) norleucine; ile; val; ile met; ala; phe Lys (K) arg; gln; asn
arg Met (M) leu; phe; ile leu Phe (F) leu; val; ile; ala; tyr leu
Pro (P) ala ala Ser (S) thr thr Thr (T) ser ser Trp (W) tyr; phe
tyr Tyr (Y) trp; phe; thr; ser phe Val (V) ile; leu; met; phe; leu
ala; norleucine
[0275] Substantial modifications in function or
immunologicalidentity of the PRO polypeptide are accomplished by
selecting substitutions that differ significantly in their effect
on maintaining (a) the structure of the polypeptide backbone in the
area of the substitution, for example, as a sheet or helical
conformation, (b) the charge or hydrophobicity of the molecule at
the target site, or (c) the bulk of the side chain. Naturally
occurring residues are divided into groups based on common
side-chain properties:
[0276] (1) hydrophobic: norleucine, met, ala, val, leu, ile;
[0277] (2) neutral hydrophilic: cys, ser, thr;
[0278] (3) acidic: asp, glu;
[0279] (4) basic: asn, gln, his, lys, arg;
[0280] (5) residues that influence chain orientation: gly, pro;
and
[0281] (6) aromatic: trp, tyr, phe.
[0282] Non-conservative substitutions will entail exchanging a
member of one of these classes for another class. Such substituted
residues also may be introduced into the conservative substitution
sites or, more preferably, into the remaining (non-conserved)
sites.
[0283] The variations can be made using methods known in the art
such as oligonucleotide-mediated (site-directed) mutagenesis,
alanine scanning, and PCR mutagenesis. Site-directed mutagenesis
[Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al.,
Nucl. Acids Res., 10:6487 (1987)], cassette mutagenesis [Wells et
al., Gene, 34:315 (1985)], restriction selection mutagenesis [Wells
et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)] or
other known techniques can be performed on the cloned DNA to
produce the PRO variant DNA.
[0284] Scanning amino acid analysis can also be employed to
identify one or more amino acids along a contiguous sequence. Among
the preferred scanning amino acids are relatively small, neutral
amino acids. Such amino acids include alanine, glycine, serine, and
cysteine. Alanine is typically a preferred scanning amino acid
among this group because it eliminates the side-chain beyond the
beta-carbon and is less likely to alter the main-chain conformation
of the variant [Cunningham and Wells, Science, 244: 1081-1085
(1989)]. Alanine is also typically preferred because it is the most
common amino acid. Further, it is frequently found in both buried
and exposed positions [Creighton, The Proteins, (W. H. Freeman
& Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)]. If alanine
substitution does not yield adequate amounts of variant, an
isoteric amino acid can be used.
[0285] C. Modifications of PRO
[0286] Covalent modifications of PRO are included within the scope
of this invention. One type of covalent modification includes
reacting targeted amino acid residues of a PRO polypeptide with an
organic derivatizing agent that is capable of reacting with
selected side chains or the N- or C-terminal residues of the PRO.
Derivatization with bifunctional agents is useful, for instance,
for crosslinking PRO to a water-insoluble support matrix or surface
for use in the method for purifying anti-PRO antibodies, and
vice-versa. Commonly used crosslinking agents include, e.g.,
1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde,
N-hydroxysuccinimide esters, for example, esters with
4-azidosalicylic acid, homobifunctional imidoesters, including
disuccinimidyl esters such as
3,3'-dithiobis(succinimidylpropionate), bifunctional maleimides
such as bis-N-maleimido-1,8-octane and agents such as
methyl-3-[(p-azidophenyl- )dithio]propioimidate.
[0287] Other modifications include deamidation of glutaminyl and
asparaginyl residues to the corresponding glutamyl and aspartyl
residues, respectively, hydroxylation of proline and lysine,
phosphorylation of hydroxyl groups of seryl or threonyl residues,
methylation of the .alpha.-amino groups of lysine, arginine, and
histidine side chains [T. E. Creighton, Proteins: Structure and
Molecular Properties. W.H. Freeman & Co., San Francisco, pp.
79-86 (1983)], acetylation of the N-terminal amine, and amidation
of any C-terminal carboxyl group.
[0288] Another type of covalent modification of the PRO polypeptide
included within the scope of this invention comprises altering the
native glycosylation pattern of the polypeptide. "Altering the
native glycosylation pattern" is intended for purposes herein to
mean deleting one or more carbohydrate moieties found in native
sequence PRO (either by removing the underlying glycosylation site
or by deleting the glycosylation by chemical and/or enzymatic
means), and/or adding one or more glycosylation sites that are not
present in the native sequence PRO. In addition, the phrase
includes qualitative changes in the glycosylation of the native
proteins, involving a change in the nature and proportions of the
various carbohydrate moieties present.
[0289] Addition of glycosylation sites to the PRO polypeptide may
be accomplished by altering the amino acid sequence. The alteration
may be made, for example, by the addition of, or substitution by,
one or more serine or threonine residues to the native sequence PRO
(for O-linked glycosylation sites). The PRO amino acid sequence may
optionally be altered through changes at the DNA level,
particularly by mutating the DNA encoding the PRO polypeptide at
preselected bases such that codons are generated that will
translate into the desired amino acids.
[0290] Another means of increasing the number of carbohydrate
moieties on the PRO polypeptide is by chemical or enzymatic
coupling of glycosides to the polypeptide. Such methods are
described in the art, e.g., in WO 87/05330 published Sep. 11, 1987,
and in Aplin and Wriston, CRC Crit. Rev. Biochem., pp. 259-306
(1981).
[0291] Removal of carbohydrate moieties present on the PRO
polypeptide may be accomplished chemically or enzymatically or by
mutational substitution of codons encoding for amino acid residues
that serve as targets for glycosylation. Chemical deglycosylation
techniques are known in the art and described, for instance, by
Hakimuddin, et al., Arch. Biochem. Biophys., 259:52 (1987) and by
Edge et al., Anal. Biochem., 118:131 (1981). Enzymatic cleavage of
carbohydrate moieties on polypeptides can be achieved by the use of
a variety of endo- and exo-glycosidases as described by Thotakura
et al., Meth. Enzymol., 138:350 (1987).
[0292] Another type of covalent modification of PRO comprises
linking the PRO polypeptide to one of a variety of nonproteinaceous
polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or
polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos.
4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or
4,179,337.
[0293] The PRO of the present invention may also be modified in a
way to form a chimeric molecule comprising PRO fused to another,
heterologous polypeptide or amino acid sequence.
[0294] In one embodiment, such a chimeric molecule comprises a
fusion of the PRO with a tag polypeptide which provides an epitope
to which an anti-tag antibody can selectively bind. The epitope tag
is generally placed at the amino- or carboxyl-terminus of the PRO.
The presence of such epitope-tagged forms of the PRO can be
detected using an antibody against the tag polypeptide. Also,
provision of the epitope tag enables the PRO to be readily purified
by affinity purification using an anti-tag antibody or another type
of affinity matrix that binds to the epitope tag. Various tag
polypeptides and their respective antibodies are well known in the
art. Examples include poly-histidine (poly-his) or
poly-histidine-glycine (poly-his-gly) tags; the flu HA tag
polypeptide and its antibody 12CA5 [Field et al., Mol. Cell. Biol.,
8-2159-2165 (1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7
and 9E10 antibodies thereto [Evan et al., Molecular and Cellular
Biology, 5:3610-3616 (1985Herpes Simplex virus glycoprotein D (gD)
tag and its antibody [Paborsky et al., Protein Engineering,
1(6):547-553 (1990)]. Other tag polypeptides include the
Flag-peptide [Hopp et al., Biotechnology 6:1204-1210 (1988)]; the
KT3 epitope peptide [Martin et al., Science 255:192-194 (1992)]; an
.alpha.-tubulin epitope peptide [Skinner et al., J. Biol. Chem.,
266:15163-15166 (1991)]; and the T7 gene 10 protein peptide tag
[Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA, 87:6393-6397
(1990)].
[0295] In an alternative embodiment, the chimeric molecule may
comprise a fusion of the PRO with an immunoglobulin or a particular
region of an immunoglobulin. For a bivalent form of the chimeric
molecule (also referred to as an "immunoadhesin"), such a fusion
could be to the Fc region of an IgG molecule. The Ig fusions
preferably include the substitution of a soluble (transmembrane
domain deleted or inactivated) form of a PRO polypeptide in place
of at least one variable region within an Ig molecule. In a
particularly preferred embodiment, the immunoglobulin fusion
includes the hinge, CH2 and CH3, or the hinge, CH1, CH2 and CH3
regions of an IgG1 molecule. For the production of immunoglobulin
fusions see also U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.
[0296] D. Preparation of PRO
[0297] The description below relates primarily to production of PRO
by culturing cells transformed or transfected with a vector
containing PRO nucleic acid. It is, of course, contemplated that
alternative methods, which are well known in the art, may be
employed to prepare PRO. For instance, the PRO sequence, or
portions thereof, may be produced by direct peptide synthesis using
solid-phase techniques [see, e.g., Stewart et al., Solid-Phase
Peptide Synthesis, W.H. Freeman Co., San Francisco, Calif. (1969);
Merrifield, J. Am. Chem, Soc., 85:2149-2154 (1963)]. In vitro
protein synthesis may be performed using manual techniques or by
automation. Automated synthesis may be accomplished, for instance,
using an Applied Biosystems Peptide Synthesizer (Foster City,
Calif.) using manufacturer's instructions. Various portions of the
PRO may be chemically synthesized separately and combined using
chemical or enzymatic methods to produce the full-length PRO.
[0298] 1. Isolation of DNA Encoding PRO
[0299] DNA encoding PRO may be obtained from a cDNA library
prepared from tissue believed to possess the PRO mRNA and to
express it at a detectable level. Accordingly, human PRO DNA can be
conveniently obtained from a cDNA library prepared from human
tissue, such as described in the Examples. The PRO-encoding gene
may also be obtained from a genomic library or by known synthetic
procedures (e.g., automated nucleic acid synthesis).
[0300] Libraries can be screened with probes (such as antibodies to
the PRO or oligonucleotides of at least about 20-80 bases) designed
to identify the gene of interest or the protein encoded by it.
Screening the cDNA or genomic library with the selected probe may
be conducted using standard procedures, such as described in
Sambrook et al., Molecular Cloning: A Laboratory Manual (New York:
Cold Spring Harbor Laboratory Press, 1989). An alternative means to
isolate the gene encoding PRO is to use PCR methodology [Sambrook
et al., supra; Dieffenbach et al., PCR Primer: A Laboratory Manual
(Cold Spring Harbor Laboratory Press, 1995)].
[0301] The Examples below describe techniques for screening a cDNA
library. The oligonucleotide sequences selected as probes should be
of sufficient length and sufficiently unambiguous that false
positives are minimized. The oligonucleotide is preferably labeled
such that it can be detected upon hybridization to DNA in the
library being screened. Methods of labeling are well known in the
art, and include the use of radiolabels like .sup.32P-labeled ATP,
biotinylation or enzyme labeling. Hybridization conditions,
including moderate stringency and high stringency, are provided in
Sambrook et al., supra.
[0302] Sequences identified in such library screening methods can
be compared and aligned to other known sequences deposited and
available in public databases such as GenBank or other private
sequence databases. Sequence identity (at either the amino acid or
nucleotide level) within defined regions of the molecule or across
the full-length sequence can be determined using methods known in
the art and as described herein.
[0303] Nucleic acid having protein coding sequence may be obtained
by screening selected cDNA or genomic libraries using the deduced
amino acid sequence disclosed herein for the first time, and, if
necessary, using conventional primer extension procedures as
described in Sambrook et al., supra, to detect precursors and
processing intermediates of mRNA that may not have been
reverse-transcribed into cDNA.
[0304] 2. Selection and Transformation of Host Cells
[0305] Host cells are transfected or transformed with expression or
cloning vectors described herein for PRO production and cultured in
conventional nutrient media modified as appropriate for inducing
promoters, selecting transformants, or amplifying the genes
encoding the desired sequences. The culture conditions, such as
media, temperature, pH and the like, can be selected by the skilled
artisan without undue experimentation. In general, principles,
protocols, and practical techniques for maximizing the productivity
of cell cultures can be found in Mammalian Cell Biotechnology: a
Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook
et al., supra.
[0306] Methods of eukaryotic cell transfection and prokaryotic cell
transformation are known to the ordinarily skilled artisan, for
example, CaCl.sub.2, CaPO.sub.4, liposome-mediated and
electroporation. Depending on the host cell used, transformation is
performed using standard techniques appropriate to such cells. The
calcium treatment employing calcium chloride, as described in
Sambrook et al., supra, or electroporation is generally used for
prokaryotes. Infection with Agrobacterium tumefaciens is used for
transformation of certain plant cells, as described by Shaw et al.,
Gene, 23:315 (1983) and WO 89/05859 published June 29, 1989. For
mammalian cells without such cell walls, the calcium phosphate
precipitation method of Graham and van der Eb, Virology, 52:456-457
(1978) can be employed. General aspects of mammalian cell host
system transfections have been described in U.S. Pat. No.
4,399,216. Transformations into yeast are typically carried out
according to the method of Van Solingen et al., J. Bact., 130:946
(1977) and Hsiao et al., Proc. Natl. Acad. Sci. (USA), 76:3829
(1979). However, other methods for introducing DNA into cells, such
as by nuclear microinjection, electroporation, bacterial protoplast
fusion with intact cells, or polycations, e.g., polybrene,
polyornithine, may also be used. For various techniques for
transforming mammalian cells, see Keown et al., Methods in
Enzymology 185:527-537 (1990) and Mansour et al., Nature.
336:348-352 (1988).
[0307] Suitable host cells for cloning or expressing the DNA in the
vectors herein include prokaryote, yeast, or higher eukaryote
cells. Suitable prokaryotes include but are not limited to
eubacteria, such as Gram-negative or Gram-positive organisms, for
example, Enterobacteriaceae such as E. coli. Various E. coli
strains are publicly available, such as E. coli K12 strain MM294
(ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W3110
(ATCC 27,325) and K5 772 (ATCC 53,635). Other suitable prokaryotic
host cells include Enterobacteriaceae such as Escherichia, e.g., E.
coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g.,
Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and
Shigella, as well as Bacilli such as B. subtilis and B.
licheniformis (e.g., B. licheniformis 41P disclosed in DD 266,710
published Apr. 12, 1989), Pseudomonas such as P. aeruginosa, and
Streptomyces. These examples are illustrative rather than limiting.
Strain W3110 is one particularly preferred host or parent host
because it is a common host strain for recombinant DNA product
fermentations. Preferably, the host cell secretes minimal amounts
of proteolytic enzymes. For example, strain W3110 may be modified
to effect a genetic mutation in the genes encoding proteins
endogenous to the host, with examples of such hosts including E.
coli W3110 strain 1A2, which has the complete genotype tonA; E.
coli W3110 strain 9E4, which has the complete genotype tonA ptr3;
E. coli W3110 strain 27C7 (ATCC 55,244), which has the complete
genotype tonA ptr3phoA E15 (argF-lac)169 degP ompT kan.sup.r; E.
coli W3110 strain 37D6, which has the complete genotype tonA ptr3
phoA E15 (argF-lac)169 degP ompT rbs7 ilvG kan.sup.r; E. coli W3110
strain 40B4, which is strain 37D6 with a non-kanamycin resistant
degP deletion mutation; and an E. coli strain having mutant
periplasmic protease disclosed in U.S. Pat. No. 4,946,783 issued
Aug. 7, 1990. Alternatively, in vitro methods of cloning, e.g., PCR
or other nucleic acid polymerase reactions, are suitable.
[0308] In addition to prokaryotes, eukaryotic microbes such as
filamentous fungi or yeast are suitable cloning or expression hosts
for PRO-encoding vectors. Saccharomyces cerevisiae is a commonly
used lower eukaryotic host microorganism. Others include
Schizosaccharomyces pombe (Beach and Nurse, Nature, 290:140[1981];
EP 139,383 published May 2, 1985); Kluyveromyces hosts (U.S. Pat.
No. 4,943,529; Fleer et al., Bio/Technology 9:968-975 (1991)) such
as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et a J.
Bacteriol., 154(2):737-742 [1983]), K. fragilis (ATCC 12,424), K.
bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii
(ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al.,
Biol/Technology 8:135 (1990)), K. thermotolerans, and K. marxianus;
yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et
al., J. Basic Microbiol. 28:265-278 [1988]); Candida; Trichoderma
reesia (EP 244,234); Neurospora crassa (Case et al., Proc. Natl.
Acad. Sci. USA, 76:5259-5263 [1979]); Schwanniomyces such as
Schwannionmyces occidentalis (EP 394,538 published Oct. 31, 1990);
and filamentous fungi such as, e.g., Neurospora, Penicillium,
Tolypocladium (WO 91/00357 published Jan. 10, 1991), and
Aspergillus hosts such as A. nidulans (Ballance et al., Biochem.
Biophys. Res. Commun., 112:284-289 [1981]; Tilburn et al., Gene,
26:205-221 [1983]; Yelton et al., Proc. Natl. Acad. Sci. USA, 81:
1470-1474 [1984]) and A. niger(Kelly and Hynes, EMBO J., 4:475-479
[1985]). Methylotropic yeasts are suitable herein and include, but
are not limited to, yeast capable of growth on methanol selected
from the genera consisting of Hansenula, Candida, Kloeckera,
Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A list of
specific species that are exemplary of this class of yeasts may be
found in C. Anthony, The Biochemistry of Methylotrophs. 269
(1982).
[0309] Suitable host cells for the expression of glycosylated PRO
are derived from multicellular organisms. Examples of invertebrate
cells include insect cells such as Drosophila S2 and Spodoptera
Sf9, as well as plant cells. Examples of useful mammalian host cell
lines include Chinese hamster ovary (CHO) and COS cells. More
specific examples include monkey kidney CV1 line transformed by
SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or
293 cells subcloned for growth in suspension culture, Graham et
al., J. Gen Virol., 36:59 (1977)); Chinese hamster ovary
cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA,
77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod.,
23:243-251 (1980)); human lung cells (W138, ATCC CCL 75); human
liver cells (Hep G2, HB 8065); and mouse mammary tumor (MMT 060562,
ATCC CCL51). The selection of the appropriate host cell is deemed
to be within the skill in the art.
[0310] 3. Selection and Use of a Replicable Vector
[0311] The nucleic acid (e.g., cDNA or genomic DNA) encoding PRO
may be inserted into a replicable vector for cloning (amplification
of the DNA) or for expression. Various vectors are publicly
available. The vector may, for example, be in the form of a
plasmid, cosmid, viral particle, or phage. The appropriate nucleic
acid sequence may be inserted into the vector by a variety of
procedures. In general, DNA is inserted into an appropriate
restriction endonuclease site(s) using techniques known in the art.
Vector components generally include, but are not limited to, one or
more of a signal sequence, an origin of replication, one or more
marker genes, an enhancer element, a promoter, and a transcription
termination sequence. Construction of suitable vectors containing
one or more of these components employs standard ligation
techniques which are known to the skilled artisan.
[0312] The PRO may be produced recombinantly not only directly, but
also as a fusion polypeptide with a heterologous polypeptide, which
may be a signal sequence or other polypeptide having a specific
cleavage site at the N-terminus of the mature protein or
polypeptide. In general, the signal sequence may be a component of
the vector, or it may be a part of the PRO-encoding DNA that is
inserted into the vector. The signal sequence may be a prokaryotic
signal sequence selected, for example, from the group of the
alkaline phosphatase, penicillinase, lpp, or heat-stable
enterotoxin II leaders. For yeast secretion the signal sequence may
be, e.g., the yeast invertase leader, alpha factor leader
(including Saccharomyces and Kluyveromyces .alpha.-factor leaders,
the latter described in U.S. Pat. No. 5,010,182), or acid
phosphatase leader, the C. albicans glucoamylase leader (EP 362,179
published April 4, 1990), or the signal described in WO 90/13646
published Nov. 15, 1990. In mammalian cell expression, mammalian
signal sequences may be used to direct secretion of the protein,
such as signal sequences from secreted polypeptides of the same or
related species, as well as viral secretory leaders.
[0313] Both expression and cloning vectors contain a nucleic acid
sequence that enables the vector to replicate in one or more
selected host cells. Such sequences are well known for a variety of
bacteria, yeast, and viruses. The origin of replication from the
plasmid pBR322 is suitable for most Gram-negative bacteria, the
2.mu. plasmid origin is suitable for yeast, and various viral
origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for
cloning vectors in mammalian cells.
[0314] Expression and cloning vectors will typically contain a
selection gene, also termed a selectable marker. Typical selection
genes encode proteins that (a) confer resistance to antibiotics or
other toxins, e.g., ampicillin, neomycin, methotrexate, or
tetracycline, (b) complement auxotrophic deficiencies, or (c)
supply critical nutrients not available from complex media, e.g.,
the gene encoding D-alanine racemase for Bacilli.
[0315] An example of suitable selectable markers for mammalian
cells are those that enable the identification of cells competent
to take up the PRO-encoding nucleic acid, such as DHFR or thymidine
kinase. An appropriate host cell when wild-type DHFR is employed is
the CHO cell line deficient in DHFR activity, prepared and
propagated as described by Urlaub et al., Proc. Natl. Acad. Sci.
USA, 77:4216 (1980). A suitable selection gene for use in yeast is
the trp1 gene present in the yeast plasmid YRp7[Stinchcomb et al.,
Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979);
Tschemper et al., Gene, 10:157 (1980)]. The trp1 gene provides a
selection marker for a mutant strain of yeast lacking the ability
to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1
[Jones, Genetics, 85:12 (1977)].
[0316] Expression and cloning vectors usually contain a promoter
operably linked to the PRO-encoding nucleic acid sequence to direct
mRNA synthesis. Promoters recognized by a variety of potential host
cells are well known. Promoters suitable for use with prokaryotic
hosts include the B-lactamase and lactose promoter systems [Chang
et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281:544
(1979)], alkaline phosphatase, a tryptophan (trp) promoter system
[Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], and hybrid
promoters such as the tac promoter [deBoer et al., Proc. Natl.
Acad. Sci. USA, 80:21-25 (1983)]. Promoters for use in bacterial
systems also will contain a Shine-Dalgarno (S.D.) sequence operably
linked to the DNA encoding PRO.
[0317] Examples of suitable promoting sequences for use with yeast
hosts include the promoters for 3-phosphoglycerate kinase [Hitzeman
et al., J. Biol. Chem., 255:2073 (1980)] or other glycolytic
enzymes [Hess et al., J. Adv. Enzyme Reg., 7:149 (1968); Holland,
Biochemistry, 17:4900 (1978)], such as enolase,
glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate
decarboxylase ,phosphofructokinase, glucose-6-phosphate isomerase,
3-phosphoglycerate mutase, pyruvate kinase,
triosephosphateisomerase,phosphoglucose isomerase, and
glucokinase.
[0318] Other yeast promoters, which are inducible promoters having
the additional advantage of transcription controlled by growth
conditions, are the promoter regions for alcohol dehydrogenase 2,
isocytochrome C, acid phosphatase, degradative enzymes associated
with nitrogen metabolism, metallothionein,
glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible
for maltose and galactose utilization. Suitable vectors and
promoters for use in yeast expression are further described in EP
73,657.
[0319] PRO transcription from vectors in mammalian host cells is
controlled, for example, by promoters obtained from the genomes of
viruses such as polyoma virus, fowlpox virus (UK 2,211,504
published Jul. 5, 1989), adenovirus (such as Adenovirus 2), bovine
papilloma virus, avian sarcoma virus, cytomegalovirus, a
retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from
heterologous mammalian promoters, e.g., the actin promoter or an
immunoglobulin promoter, and from heat-shock promoters, provided
such promoters are compatible with the host cell systems.
[0320] Transcription of a DNA encoding the PRO by higher eukaryotes
may be increased by inserting an enhancer sequence into the vector.
Enhancers are cis-acting elements of DNA, usually about from 10 to
300 bp, that act on a promoter to increase its transcription. Many
enhancer sequences are now known from mammalian genes (globin,
elastase, albumin, .alpha.-fetoprotein, and insulin). Typically,
however, one will use an enhancer from a eukaryotic cell virus.
Examples include the SV40 enhancer on the late side of the
replication origin (bp 100-270), the cytomegalovirus early promoter
enhancer, the polyoma enhancer on the late side of the replication
origin, and adenovirus enhancers. The enhancer may be spliced into
the vector at a position 5' or 3' to the PRO coding sequence, but
is preferably located at a site 5' from the promoter.
[0321] Expression vectors used in eukaryotic host cells (yeast,
fungi, insect, plant, animal, human, or nucleated cells from other
multicellular organisms) will also contain sequences necessary for
the termination of transcription and for stabilizing the mRNA. Such
sequences are commonly available from the 5' and, occasionally 3',
untranslated regions of eukaryotic or viral DNAs or cDNAs. These
regions contain nucleotide segments transcribed as polyadenylated
fragments in the untranslated portion of the mRNA encoding PRO.
[0322] Still other methods, vectors, and host cells suitable for
adaptation to the synthesis of PRO in recombinant vertebrate cell
culture are described in Gething et al., Nature, 293:620-625
(1981); Mantei et al., Nature, 281:4046 (1979); EP 117,060; and EP
117,058.
[0323] 4. Detecting, Gene Amplification/Expression
[0324] Gene amplification and/or expression may be measured in a
sample directly, for example, by conventional Southern blotting,
Northern blotting to quantitate the transcription of mRNA [Thomas,
Proc. Nat. Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA
analysis), or in situ hybridization, using an appropriately labeled
probe, based on the sequences provided herein. Alternatively,
antibodies may be employed that can recognize specific duplexes,
including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes
or DNA-protein duplexes. The antibodies in turn may be labeled and
the assay may be carried out where the duplex is bound to a
surface, so that upon the formation of duplex on the surface, the
presence of antibody bound to the duplex can be detected.
[0325] Gene expression, alternatively, may be measured by
immunological methods, such as immunohistochemical staining of
cells or tissue sections and assay of cell culture or body fluids,
to quantitate directly the expression of gene product. Antibodies
useful for immunohistochemical staining and/or assay of sample
fluids may be either monoclonal or polyclonal, and may be prepared
in any mammal. Conveniently, the antibodies may be prepared against
a native sequence PRO polypeptide or against a synthetic peptide
based on the DNA sequences provided herein or against exogenous
sequence fused to PRO DNA and encoding a specific antibody
epitope.
[0326] 5. Purification of Polypeptide
[0327] Forms of PRO may be recovered from culture medium or from
host cell lysates. If membrane-bound, it can be released from the
membrane using a suitable detergent solution (e.g. Triton-X 100) or
by enzymatic cleavage. Cells employed in expression of PRO can be
disrupted by various physical or chemical means, such as
freeze-thaw cycling, sonication, mechanical disruption, or cell
lysing agents.
[0328] It may be desired to purify PRO from recombinant cell
proteins or polypeptides. The following procedures are exemplary of
suitable purification procedures: by fractionation on an
ion-exchange column; ethanol precipitation; reverse phase HPLC;
chromatography on silica or on a cation-exchange resin such as
DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation;
gel filtration using, for example, Sephadex G-75; protein A
Sepharose columns to remove contaminants such as IgG; and metal
chelating columns to bind epitope-tagged forms of the PRO. Various
methods of protein purification may be employed and such methods
are known in the art and described for example in Deutscher,
Methods in Enzymology, 182 (1990); Scopes, Protein Purification:
Principles and Practice, Springer-Verlag, New York (1982). The
purification step(s) selected will depend, for example, on the
nature of the production process used and the particular PRO
produced.
[0329] E. Uses for PRO
[0330] Nucleotide sequences (or their complement) encoding PRO have
various applications in the art of molecular biology, including
uses as hybridization probes, in chromosome and gene mapping and in
the generation of anti-sense RNA and DNA. PRO nucleic acid will
also be useful for the preparation of PRO polypeptides by the
recombinant techniques described herein.
[0331] The full-length native sequence PRO gene, or portions
thereof, may be used as hybridization probes for a cDNA library to
isolate the full-length PRO cDNA or to isolate still other cDNAs
(for instance, those encoding naturally-occurring variants of PRO
or PRO from other species) which have a desired sequence identity
to the native PRO sequence disclosed herein. Optionally, the length
of the probes will be about 20 to about 50 bases. The hybridization
probes may be derived from at least partially novel regions of the
full length native nucleotide sequence wherein those regions may be
determined without undue experimentation or from genomic sequences
including promoters, enhancer elements and introns of native
sequence PRO. By way of example, a screening method will comprise
isolating the coding region of the PRO gene using the known DNA
sequence to synthesize a selected probe of about 40 bases.
Hybridization probes may be labeled by a variety of labels,
including radionucleotides such as .sup.32P or .sup.35S, or
enzymatic labels such as alkaline phosphatase coupled to the probe
via avidin/biotin coupling systems. Labeled probes having a
sequence complementary to that of the PRO gene of the present
invention can be used to screen libraries of human cDNA, genomic
DNA or mRNA to determine which members of such libraries the probe
hybridizes to. Hybridization techniques are described in further
detail in the Examples below.
[0332] Any EST sequences disclosed in the present application may
similarly be employed as probes, using the methods disclosed
herein.
[0333] Other useful fragments of the PRO nucleic acids include
antisense or sense oligonucleotides comprising a singe-stranded
nucleic acid sequence (either RNA or DNA) capable of binding to
target PRO mRNA (sense) or PRO DNA (antisense) sequences. Antisense
or sense oligonucleotides, according to the present invention,
comprise a fragment of the coding region of PRO DNA. Such a
fragment generally comprises at least about 14 nucleotides,
preferably from about 14 to 30 nucleotides. The ability to derive
an antisense or a sense oligonucleotide, based upon a cDNA sequence
encoding a given protein is described in, for example, Stein and
Cohen (Cancer Res. 48:2659, 1988) and van der Krol et
al.(BioTechniques 6:958, 1988).
[0334] Binding of antisense or sense oligonucleotides to target
nucleic acid sequences results in the formation of duplexes that
block transcription or translation of the target sequence by one of
several means, including enhanced degradation of the duplexes,
premature termination of transcription or translation, or by other
means. The antisense oligonucleotides thus may be used to block
expression of PRO proteins. Antisense or sense oligonucleotides
further comprise oligonucleotides having modified
sugar-phosphodiester backbones (or other sugar linkages, such as
those described in WO 91/06629) and wherein such sugar linkages are
resistant to endogenous nucleases. Such oligonucleotides with
resistant sugar linkages are stable in vivo (i.e., capable of
resisting enzymatic degradation) but retain sequence specificity to
be able to bind to target nucleotide sequences.
[0335] Other examples of sense or antisense oligonucleotides
include those oligonucleotides which are covalently linked to
organic moieties, such as those described in WO 90/10048, and other
moieties that increases affinity of the oligonucleotide for a
target nucleic acid sequence, such as poly-(L-lysine). Further
still, intercalating agents, such as ellipticine, and alkylating
agents or metal complexes may be attached to sense or antisense
oligonucleotides to modify binding specificities of the antisense
or sense oligonucleotide for the target nucleotide sequence.
[0336] Antisense or sense oligonucleotides may be introduced into a
cell containing the target nucleic acid sequence by any gene
transfer method, including, for example, CaPO.sub.4-mediated DNA
transfection, electroporation, or by using gene transfer vectors
such as Epstein-Barr virus. In a preferred procedure, an antisense
or sense oligonucleotide is inserted into a suitable retroviral
vector. A cell containing the target nucleic acid sequence is
contacted with the recombinant retroviral vector, either in vivo or
ex vivo. Suitable retroviral vectors include, but are not limited
to, those derived from the murine retrovirus M-MuLV, N2 (a
retrovirus derived from M-MuLV), or the double copy vectors
designated DCT5A, DCT5B and DCT5C (see WO 90/13641).
[0337] Sense or antisense oligonucleotides also may be introduced
into a cell containing the target nucleotide sequence by formation
of a conjugate with a ligand binding molecule, as described in WO
91/04753. Suitable ligand binding molecules include, but are not
limited to, cell surface receptors, growth factors, other
cytokines, or other ligands that bind to cell surface receptors.
Preferably, conjugation of the ligand binding molecule does not
substantially interfere with the ability of the ligand binding
molecule to bind to its corresponding molecule or receptor, or
block entry of the sense or antisense oligonucleotide or its
conjugated version into the cell.
[0338] Alternatively, a sense or an antisense oligonucleotide may
be introduced into a cell containing the target nucleic acid
sequence by formation of an oligonucleotide-lipid complex, as
described in WO 90/10448. The sense or antisense
oligonucleotide-lipid complex is preferably dissociated within the
cell by an endogenous lipase.
[0339] Antisense or sense RNA or DNA molecules are generally at
least about 5 bases in length, about 10 bases in length, about 15
bases in length, about 20 bases in length, about 25 bases in
length, about 30 bases in length, about 35 bases in length, about
40 bases in length, about 45 bases in length, about 50 bases in
length, about 55 bases in length, about 60 bases in length, about
65 bases in length, about 70 bases in length, about 75 bases in
length, about 80 bases in length, about 85 bases in length, about
90 bases in length, about 95 bases in length, about 100 bases in
length, or more.
[0340] The probes may also be employed in PCR techniques to
generate a pool of sequences for identification of closely related
PRO coding sequences.
[0341] Nucleotide sequences encoding a PRO can also be used to
construct hybridization probes for mapping the gene which encodes
that PRO and for the genetic analysis of individuals with genetic
disorders. The nucleotide sequences provided herein may be mapped
to a chromosome and specific regions of a chromosome using known
techniques, such as in situ hybridization, linkage analysis against
known chromosomal markers, and hybridization screening with
libraries.
[0342] When the coding sequences for PRO encode a protein which
binds to another protein (example, where the PRO is a receptor),
the PRO can be used in assays to identify the other proteins or
molecules involved in the binding interaction. By such methods,
inhibitors of the receptor/ligand binding interaction can be
identified. Proteins involved in such binding interactions can also
be used to screen for peptide or small molecule inhibitors or
agonists of the binding interaction. Also, the receptor PRO can be
used to isolate correlative ligand(s). Screening assays can be
designed to find lead compounds that mimic the biological activity
of a native PRO or a receptor for PRO. Such screening assays will
include assays amenable to high-throughput screening of chemical
libraries, making them particularly suitable for identifying small
molecule drug candidates. Small molecules contemplated include
synthetic organic or inorganic compounds. The assays can be
performed in a variety of formats, including protein-protein
binding assays, biochemical screening assays, immunoassays and cell
based assays, which are well characterized in the art.
[0343] Nucleic acids which encode PRO or its modified forms can
also be used to generate either transgenic animals or "knock out"
animals which, in turn, are useful in the development and screening
of therapeutically useful reagents. A transgenic animal (e.g., a
mouse or rat) is an animal having cells that contain a transgene,
which transgene was introduced into the animal or an ancestor of
the animal at a prenatal, e.g., an embryonic stage. A transgene is
a DNA which is integrated into the genome of a cell from which a
transgenic animal develops. In one embodiment, cDNA encoding PRO
can be used to clone genomic DNA encoding PRO in accordance with
established techniques and the genomic sequences used to generate
transgenic animals that contain cells which express DNA encoding
PRO. Methods for generating transgenic animals, particularly
animals such as mice or rats, have become conventional in the art
and are described, for example, in U.S. Pat. Nos. 4,736,866 and
4,870,009. Typically, particular cells would be targeted for PRO
transgene incorporation with tissue-specific enhancers. Transgenic
animals that include a copy of a transgene encoding PRO introduced
into the germ line of the animal at an embryonic stage can be used
to examine the effect of increased expression of DNA encoding PRO.
Such animals can be used as tester animals for reagents thought to
confer protection from, for example, pathological conditions
associated with its overexpression. In accordance with this facet
of the invention, an animal is treated with the reagent and a
reduced incidence of the pathological condition, compared to
untreated animals bearing the transgene, would indicate a potential
therapeutic intervention for the pathological condition.
[0344] Alternatively, non-human homologues of PRO can be used to
construct a PRO "knock out" animal which has a defective or altered
gene encoding PRO as a result of homologous recombination between
the endogenous gene encoding PRO and altered genomic DNA encoding
PRO introduced into an embryonic stem cell of the animal. For
example, cDNA encoding PRO can be used to clone genomic DNA
encoding PRO in accordance with established techniques. A portion
of the genomic DNA encoding PRO can be deleted or replaced with
another gene, such as a gene encoding a selectable marker which can
be used to monitor integration. Typically, several kilobases of
unaltered flanking DNA (both at the 5' and 3' ends) are included in
the vector [see e.g., Thomas and Capecchi, Cell, 51:503 (1987) 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 DNA has
homologously recombined with the endogenous DNA are selected [see
e.g., Li et al., Cell, 69:915 (1992)]. The selected cells are then
injected into a blastocyst of an animal (e.g., a mouse or rat) to
form aggregation chimeras [see e.g., Bradley, in Teratocarcinomas
and Embryonic Stem Cells: A Practical Approach, E. J. 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 to create a "knock out" animal.
Progeny harboring the homologously recombined DNA in their germ
cells can be identified by standard techniques and used to breed
animals in which all cells of the animal contain the homologously
recombined DNA. Knockout animals can be characterized for instance,
for their ability to defend against certain pathological conditions
and for their development of pathological conditions due to absence
of the PRO polypeptide.
[0345] Nucleic acid encoding the PRO polypeptides may also be used
in gene therapy. In gene therapy applications, genes are introduced
into cells in order to achieve in vivo synthesis of a
therapeutically effective genetic product, for example for
replacement of a defective gene. "Gene therapy" includes both
conventional gene therapy where a lasting effect is achieved by a
single treatment, and the administration of gene therapeutic
agents, which involves the one time or repeated administration of a
therapeutically effective DNA or mRNA. Antisense RNAs and DNAs can
be used as therapeutic agents for blocking the expression of
certain genes in vivo. It has already been shown that short
antisense oligonucleotides can be imported into cells where they
act as inhibitors, despite their low intracellular concentrations
caused by their restricted uptake by the cell membrane. (Zamecnik
et al., Proc. Natl. Acad. Sci. USA 83:4143-4146 [1986]). The
oligonucleotides can be modified to enhance their uptake, e.g. by
substituting their negatively charged phosphodiester groups by
uncharged groups.
[0346] There are a variety of techniques available for introducing
nucleic acids into viable cells. The techniques vary depending upon
whether the nucleic acid is transferred into cultured cells in
vitro, or in vivo in the cells of the intended host. Techniques
suitable for the transfer of nucleic acid into mammalian cells in
vitro include the use of liposomes, electroporation,
microinjection, cell fusion, DEAE-dextran, the calcium phosphate
precipitation method, etc. The currently preferred in vivo gene
transfer techniques include transfection with viral (typically
retroviral) vectors and viral coat protein-liposome mediated
transfection (Dzau et al., Trends in Biotechnology 11, 205-210
[1993]). In some situations it is desirable to provide the nucleic
acid source with an agent that targets the target cells, such as an
antibody specific for a cell surface membrane protein or the target
cell, a ligand for a receptor on the target cell, etc. Where
liposomes are employed, proteins which bind to a cell surface
membrane protein associated with endocytosis may be used for
targeting and/or to facilitate uptake, e.g. capsid proteins or
fragments thereof tropic for a particular cell type, antibodies for
proteins which undergo internalization in cycling, proteins that
target intracellular localization and enhance intracellular
half-life. The technique of receptor-mediated endocytosis is
described, for example, by Wu et al., J. Biol. Chem. 262, 4429-4432
(1987); and Wagner et al., Proc. Natl. Acad. Sci. USA 87, 3410-3414
(1990). For review of gene marking and gene therapy protocols see
Anderson et al., Science 256, 808-813 (1992).
[0347] The PRO polypeptides described herein may also be employed
as molecular weight markers for protein electrophoresis purposes
and the isolated nucleic acid sequences may be used for
recombinantly expressing those markers.
[0348] The nucleic acid molecules encoding the PRO polypeptides or
fragments thereof described herein are useful for chromosome
identification. In this regard, there exists an ongoing need to
identify new chromosome markers, since relatively few chromosome
marking reagents, based upon actual sequence data are presently
available. Each PRO nucleic acid molecule of the present invention
can be used as a chromosome marker.
[0349] The PRO polypeptides and nucleic acid molecules of the
present invention may also be used for tissue typing, wherein the
PRO polypeptides of the present invention may be differentially
expressed in one tissue as compared to another. PRO nucleic acid
molecules will find use for generating probes for PCR, Northern
analysis, Southern analysis and Western analysis.
[0350] The PRO polypeptides described herein may also be employed
as therapeutic agents. The PRO polypeptides of the present
invention can be formulated according to known methods to prepare
pharmaceutically useful compositions, whereby the PRO product
hereof is combined in admixture with a pharmaceutically acceptable
carrier vehicle. Therapeutic formulations are prepared for storage
by mixing the active ingredient having the desired degree of purity
with optional physiologically acceptable carriers, excipients or
stabilizers (Remington's Pharmaceutical Sciences 16th edition,
Osol, A. Ed. (1980)), in the form of lyophilized formulations or
aqueous solutions. Acceptable carriers, excipients or stabilizers
are nontoxic to recipients at the dosages and concentrations
employed, and include buffers such as phosphate, citrate and other
organic acids; antioxidants including ascorbic acid; low molecular
weight (less than about 10 residues) polypeptides; proteins, such
as serum albumin, gelatin or immunoglobulins; hydrophilic polymers
such as polyvinylpyrrolidone, amino acids such as glycine,
glutamine, asparagine, arginine or lysine; monosaccharides,
disaccharides and other carbohydrates including glucose, mannose,
or dextrins; chelating agents such as EDTA; sugar alcohols such as
mannitol or sorbitol; salt-forming counterions such as sodium;
and/or nonionic surfactants such as TWEEN.TM., PLURONICS.TM. or
PEG.
[0351] The formulations to be used for in vivo administration must
be sterile. This is readily accomplished by filtration through
sterile filtration membranes, prior to or following lyophilization
and reconstitution.
[0352] Therapeutic compositions herein generally are placed into a
container having a sterile access port, for example, an intravenous
solution bag or vial having a stopper pierceable by a hypodermic
injection needle.
[0353] The route of administration is in accord with known methods,
e.g. injection or infusion by intravenous, intraperitoneal,
intracerebral, intramuscular, intraocular, intraarterial or
intralesional routes, topical administration, or by sustained
release systems.
[0354] Dosages and desired drug concentrations of pharmaceutical
compositions of the present invention may vary depending on the
particular use envisioned. The determination of the appropriate
dosage or route of administration is well within the skill of an
ordinary physician. Animal experiments provide reliable guidance
for the determination of effective doses for human therapy.
Interspecies scaling of effective doses can be performed following
the principles laid down by Mordenti, J. and Chappell, W. "The use
of interspecies scaling in toxicokinetics" In Toxicokinetics and
New Drug Development, Yacobi et al., Eds., Pergamon Press, New York
1989, pp. 42-96.
[0355] When in vivo administration of a PRO polypeptide or agonist
or antagonist thereof is employed, normal dosage amounts may vary
from about 10 ng/kg to up to 100 mg/kg of mammal body weight or
more per day, preferably about 1 .mu.g/kg/day to 10 mg/kg/day,
depending upon the route of administration. Guidance as to
particular dosages and methods of delivery is provided in the
literature; see, for example, U.S. Pat. Nos. 4,657,760; 5,206,344;
or 5,225,212. It is anticipated that different formulations will be
effective for different treatment compounds and different
disorders, that administration targeting one organ or tissue, for
example, may necessitate delivery in a manner different from that
to another organ or tissue.
[0356] Where sustained-release administration of a PRO polypeptide
is desired in a formulation with release characteristics suitable
for the treatment of any disease or disorder requiring
administration of the PRO polypeptide, microencapsulation of the
PRO polypeptide is contemplated. Microencapsulation of recombinant
proteins for sustained release has been successfully performed with
human growth hormone (rhGH), interferon-(rhIFN-), interleukin-2,
and MN rgpl120. Johnson et al., Nat. Med., 2:795-799 (1996);
Yasuda, Biomed. Ther., 27:1221-1223 (1993); Hora et al.,
Bio/Technology, 8:755-758 (1990); Cleland, "Design and Production
of Single Immunization Vaccines Using Polylactide Polyglycolide
Microsphere Systems," in Vaccine Design: The Subunit and Adjuvant
Approach, Powell and Newman, eds, (Plenum Press: New York, 1995),
pp. 439-462; WO 97/03692, WO 96/40072, WO 96/07399; and U.S. Pat.
No. 5,654,010.
[0357] The sustained-release formulations of these proteins were
developed using poly-lactic-coglycolic acid (PLGA) polymer due to
its biocompatibility and wide range of biodegradable properties.
The degradation products of PLGA, lactic and glycolic acids, can be
cleared quickly within the human body. Moreover, the degradability
of this polymer can be adjusted from months to years depending on
its molecular weight and composition. Lewis, "Controlled release of
bioactive agents from lactide/glycolide polymer," in: M. Chasin and
R. Langer (Eds.), Biodegradable Polymers as Drug Delivery Systems
(Marcel Dekker:New York, 1990), pp. 1-41.
[0358] This invention encompasses methods of screening compounds to
identify those that mimic the PRO polypeptide (agonists) or prevent
the effect of the PRO polypeptide (antagonists). Screening assays
for antagonist drug candidates are designed to identify compounds
that bind or complex with the PRO polypeptides encoded by the genes
identified herein, or otherwise interfere with the interaction of
the encoded polypeptides with other cellular proteins. Such
screening assays will include assays amenable to high-throughput
screening of chemical libraries, making them particularly suitable
for identifying small molecule drug candidates.
[0359] The assays can be performed in a variety of formats,
including protein-protein binding assays, biochemical screening
assays, immunoassays, and cell-based assays, which are well
characterized in the art.
[0360] All assays for antagonists are common in that they call for
contacting the drug candidate with a PRO polypeptide encoded by a
nucleic acid identified herein under conditions and for a time
sufficient to allow these two components to interact.
[0361] In binding assays, the interaction is binding and the
complex formed can be isolated or detected in the reaction mixture.
In a particular embodiment, the PRO polypeptide encoded by the gene
identified herein or the drug candidate is immobilized on a solid
phase, e.g., on a microtiter plate, by covalent or non-covalent
attachments. Non-covalent attachment generally is accomplished by
coating the solid surface with a solution of the PRO polypeptide
and drying. Alternatively, an immobilized antibody, e.g., a
monoclonal antibody, specific for the PRO polypeptide to be
immobilized can be used to anchor it to a solid surface. The assay
is performed by adding the non-immobilized component, which may be
labeled by a detectable label, to the immobilized component, e.g.,
the coated surface containing the anchored component. When the
reaction is complete, the non-reacted components are removed, e.g.,
by washing, and complexes anchored on the solid surface are
detected. When the originally non-immobilized component carries a
detectable label, the detection of label immobilized on the surface
indicates that complexing occurred. Where the originally
non-immobilized component does not carry a label, complexing can be
detected, for example, by using a labeled antibody specifically
binding the immobilized complex.
[0362] If the candidate compound interacts with but does not bind
to a particular PRO polypeptide encoded by a gene identified
herein, its interaction with that polypeptide can be assayed by
methods well known for detecting protein-protein interactions. Such
assays include traditional approaches, such as, e.g.,
cross-linking, co-immunoprecipitation, and co-purification through
gradients or chromatographic columns. In addition, protein-protein
interactions can be monitored by using a yeast-based genetic system
described by Fields and co-workers (Fields and Song, Nature
(London), 340:245-246 (1989); Chien et al., Proc. Natl. Acad. Sci.
USA, 88:9578-9582 (1991)) as disclosed by Chevray and Nathans,
Proc. Natl. Acad. Sci. USA, 89: 5789-5793 (1991). Many
transcriptional activators, such as yeast GALA, consist of two
physically discrete modular domains, one acting as the DNA-binding
domain, the other one functioning as the transcription-activation
domain. The yeast expression system described in the foregoing
publications (generally referred to as the "two-hybrid system")
takes advantage of this property, and employs two hybrid proteins,
one in which the target protein is fused to the DNA-binding domain
of GALA, and another, in which candidate activating proteins are
fused to the activation domain. The expression of a GAL1-lacZ
reporter gene under control of a GAL4-activated promoter depends on
reconstitution of GALA activity via protein-protein interaction.
Colonies containing interacting polypeptides are detected with a
chromogenic substrate for P-galactosidase. A complete kit
(MATCHMAKER.TM.) for identifying protein-protein interactions
between two specific proteins using the two-hybrid technique is
commercially available from Clontech. This system can also be
extended to map protein domains involved in specific protein
interactions as well as to pinpoint amino acid residues that are
crucial for these interactions.
[0363] Compounds that interfere with the interaction of a gene
encoding a PRO polypeptide identified herein and other intra- or
extracellular components can be tested as follows: usually a
reaction mixture is prepared containing the product of the gene and
the intra- or extracellular component under conditions and for a
time allowing for the interaction and binding of the two products.
To test the ability of a candidate compound to inhibit binding, the
reaction is run in the absence and in the presence of the test
compound. In addition, a placebo may be added to a third reaction
mixture, to serve as positive control. The binding (complex
formation) between the test compound and the intra- or
extracellular component present in the mixture is monitored as
described hereinabove. The formation of a complex in the control
reaction(s) but not in the reaction mixture containing the test
compound indicates that the test compound interferes with the
interaction of the test compound and its reaction partner.
[0364] To assay for antagonists, the PRO polypeptide may be added
to a cell along with the compound to be screened for a particular
activity and the ability of the compound to inhibit the activity of
interest in the presence of the PRO polypeptide indicates that the
compound is an antagonist to the PRO polypeptide. Alternatively,
antagonists may be detected by combining the PRO polypeptide and a
potential antagonist with membrane-bound PRO polypeptide receptors
or recombinant receptors under appropriate conditions for a
competitive inhibition assay. The PRO polypeptide can be labeled,
such as by radioactivity, such that the number of PRO polypeptide
molecules bound to the receptor can be used to determine the
effectiveness of the potential antagonist. The gene encoding the
receptor can be identified by numerous methods known to those of
skill in the art, for example, ligand panning and FACS sorting.
Coligan et al., Current Protocols in Immun., 1(2): Chapter 5
(1991). Preferably, expression cloning is employed wherein
polyadenylated RNA is prepared from a cell responsive to the PRO
polypeptide and a cDNA library created from this RNA is divided
into pools and used to transfect COS cells or other cells that are
not responsive to the PRO polypeptide. Transfected cells that are
grown on glass slides are exposed to labeled PRO polypeptide. The
PRO polypeptide can be labeled by a variety of means including
iodination or inclusion of a recognition site for a site-specific
protein kinase. Following fixation and incubation, the slides are
subjected to autoradiographic analysis. Positive pools are
identified and sub-pools are prepared and re-transfected using an
interactive sub-pooling and re-screening process, eventually
yielding a single clone that encodes the putative receptor.
[0365] As an alternative approach for receptor identification,
labeled PRO polypeptide can be photoaffinity-linked with cell
membrane or extract preparations that express the receptor
molecule. Cross-linked material is resolved by PAGE and exposed to
X-ray film. The labeled complex containing the receptor can be
excised, resolved into peptide fragments, and subjected to protein
micro-sequencing. The amino acid sequence obtained from
micro-sequencing would be used to design a set of degenerate
oligonucleotide probes to screen a cDNA library to identify the
gene encoding the putative receptor.
[0366] In another assay for antagonists, mammalian cells or a
membrane preparation expressing the receptor would be incubated
with labeled PRO polypeptide in the presence of the candidate
compound. The ability of the compound to enhance or block this
interaction could then be measured.
[0367] More specific examples of potential antagonists include an
oligonucleotide that binds to the fusions of immunoglobulin with
PRO polypeptide, and, in particular, antibodies including, without
limitation, poly- and monoclonal antibodies and antibody fragments,
single-chain antibodies, anti-idiotypic antibodies, and chimeric or
humanized versions of such antibodies or fragments, as well as
human antibodies and antibody fragments. Alternatively, a potential
antagonist may be a closely related protein, for example, a mutated
form of the PRO polypeptide that recognizes the receptor but
imparts no effect, thereby competitively inhibiting the action of
the PRO polypeptide.
[0368] Another potential PRO polypeptide antagonist is an antisense
RNA or DNA construct prepared using antisense technology, where,
e.g., an antisense RNA or DNA molecule acts to block directly the
translation of mRNA by hybridizing to targeted mRNA and preventing
protein translation. Antisense technology can be used to control
gene expression through triple-helix formation or antisense DNA or
RNA, both of which methods are based on binding of a polynucleotide
to DNA or RNA. For example, the 5' coding portion of the
polynucleotide sequence, which encodes the mature PRO polypeptides
herein, is used to design an antisense RNA oligonucleotide of from
about 10 to 40 base pairs in length. A DNA oligonucleotide is
designed to be complementary to a region of the gene involved in
transcription (triple helix--see Lee et al., Nucl. Acids Res.
6:3073 (1979); Cooney et al., Science, 241: 456 (1988); Dervan et
al., Science, 251:1360 (1991)), thereby preventing transcription
and the production of the PRO polypeptide. The antisense RNA
oligonucleotide hybridizes to the mRNA in vivo and blocks
translation of the mRNA molecule into the PRO polypeptide
(antisense--Okano, Neurochem., 56:560 (1991); Oligodeoxynucleotides
as Antisense Inhibitors of Gene Expression (CRC Press: Boca Raton,
Fla., 1988). The oligonucleotides described above can also be
delivered to cells such that the antisense RNA or DNA may be
expressed in vivo to inhibit production of the PRO polypeptide.
When antisense DNA is used, oligodeoxyribonucleotides derived from
the translation-initiation site, e.g., between about -10 and +10
positions of the target gene nucleotide sequence, are
preferred.
[0369] Potential antagonists include small molecules that bind to
the active site, the receptor binding site, or growth factor or
other relevant binding site of the PRO polypeptide, thereby
blocking the normal biological activity of the PRO polypeptide.
Examples of small molecules include, but are not limited to, small
peptides or peptide-like molecules, preferably soluble peptides,
and synthetic non-peptidyl organic or inorganic compounds.
[0370] Ribozymes are enzymatic RNA molecules capable of catalyzing
the specific cleavage of RNA. Ribozymes act by sequence-specific
hybridization to the complementary target RNA, followed by
endonucleolytic cleavage. Specific ribozyme cleavage sites within a
potential RNA target can be identified by known techniques. For
further details see, e.g., Rossi, Current Biology 4:469-471 (1994),
and PCT publication No. WO 97/33551 (published Sept. 18, 1997).
[0371] Nucleic acid molecules in triple-helix formation used to
inhibit transcription should be single-stranded and composed of
deoxynucleotides. The base composition of these oligonucleotides is
designed such that it promotes triple-helix formation via Hoogsteen
base-pairing rules, which generally require sizeable stretches of
purines or pyrimidines on one strand of a duplex. For further
details see, e.g., PCT publication No. WO 97/33551, supra.
[0372] These small molecules can be identified by any one or more
of the screening assays discussed hereinabove and/or by any other
screening techniques well known for those skilled in the art.
[0373] PRO241 polypeptides of the present invention which possess
biological activity related to that of the endogenous biglycan
protein may be employed both in vivo for therapeutic purposes and
in vitro. Those of ordinary skill in the art will well know how to
employ the PRO241 polypeptides of the present invention for such
purposes.
[0374] Chordin is a candidate gene for a dysmorphia syndrome known
as Cornelia de Lange Syndrome (CDL) which is characterized by
distinctive facial features (low anterior hairline, synophrys,
antenerted nares, maxillary prognathism, long philtrum, `carp`
mouth), prenatal and postnatal growth retardation, mental
retardation and, often but not always, upper limb abnormalities.
There are also rare cases where CDL is present in association with
thrombocytopenia. The gene for CDL has been mapped by linkage to
3q26.3 (OMIM #122470). Xchd involvement in early Xenopus patterning
and nervous system development makes CHD in intriguing candidate
gene. CHD maps to the appropriate region on chromosome 3. It is
very close to THPO, and deletions encompassing both THPO and CHD
could result in rare cases of thrombocytopenia and developmental
abnormalities. In situ analysis of CD revealed that almost all
adult tissues are negative for CHD expression, the only positive
signal was observed in the cleavage line of the developing synovial
joint forming between the femoral head and acetabulum (hip joint)
implicating CHD in the development and presumably growth of long
bones. Such a function, if disrupted, could result in growth
retardation.
[0375] The human CHD amino acid sequence predicted from the cDNA is
50% identical (and 66% conserved) to Xchd. All 40 cysteines in the
4 cysteine-rich domains are conserved. These cysteine rich domains
are similar to those observed in thrombospondin, procollagen and
von Willebrand factor. Bornstein, P. FASEB J 6: 3290-3299(1992);
Hunt, L. & Barker, W. Biochem. Biophys. Res. Commun. 144:
876-882 (1987).
[0376] The human CHD locus (genomic PRO243) comprises 23 exons in
9.6 kb of genomic DNA. The initiating methionine is in exon 1 and
the stop codon in exon 23. A CpG island is located at the 5' and of
the gene, beginning approximately 100 bp 5' of exon 1 and extends
through the first exon and ends within the first intron. The THPO
and CHD loci are organized in a head-to-head fashion with
approximately 2.2 kb separating their transcription start sites. At
the protein level, PRO243 is 51% identical to Xenopus chordin
(Xchd). All forty cysteines in the one amino terminal and three
carboxy terminal cysteine-rich clusters are conserved.
[0377] PRO243 is a 954 amino acid polypeptide having a signal
sequence at residues 1 to about 23. There are 4 cysteine clusters:
(1) residues about 51 to about 125; (2) residues about 705 to about
761; (3) residues about 784 to about 849; and (4) residues about
897 to about 931. There are potential leucine zippers at residues
about 315 to about 396, and N-glycosylation sites at residues 217,
351, 365 and 434.
[0378] PRO299 polypeptides and portions thereof which have homology
to the notch protein may be useful for in vivo therapeutic
purposes, as well as for various other applications. The
identification of novel notch proteins and related molecules may be
relevant to a number of human disorders such as those effecting
development. Thus, the identification of new notch proteins and
notch-like molecules is of special importance in that such proteins
may serve as potential therapeutics for a variety of different
human disorders. Such polypeptides may also play important roles in
biotechnological and medical research as well as various industrial
applications. As a result, there is particular scientific and
medical interest in new molecules, such as PRO299.
[0379] PRO323 polypeptides of the present invention which possess
biological activity related to that of one or more endogenous
dipeptidase proteins may be employed both in vivo for therapeutic
purposes and in vitro. Those of ordinary skill in the art will well
know how to employ the PRO323 polypeptides of the present invention
for such purposes.
[0380] PRO327 polypeptides of the present invention which possess
biological activity related to that of the endogenous prolactin
receptor protein may be employed both in vivo for therapeutic
purposes and in vitro. Those of ordinary skill in the art will well
know how to employ the PRO327 polypeptides of the present invention
for such purposes. PRO327 polypeptides which possess the ability to
bind to prolactin may function both in vitro and in vivo as
prolactin antagonists.
[0381] PRO233 polypeptides and portions thereof which have homology
to reductase may also be useful for in vivo therapeutic purposes,
as well as for various other applications. The identification of
novel reductase proteins and related molecules may be relevant to a
number of human disorders such as inflammatory disease, organ
failure, atherosclerosis, cardiac injury, infertility, birth
defects, premature aging, AIDS, cancer, diabetic complications and
mutations in general. Given that oxygen free radicals and
antioxidants appear to play important roles in a number of disease
processes, the identification of new reductase proteins and
reductase-like molecules is of special importance in that such
proteins may serve as potential therapeutics for a variety of
different human disorders. Such polypeptides may also play
important roles in biotechnological and medical research, as well
as various industrial applications. As a result, there is
particular scientific and medical interest in new molecules, such
as PRO233.
[0382] PRO344 polypeptides and portions thereof which have homology
to complement proteins may also be useful for in vivo therapeutic
purposes, as well as for various other applications. The
identification of novel complement proteins and related molecules
may be relevant to a number of human disorders such as effecting
the inflammatory response of cells of the immune system. Thus, the
identification of new complement proteins and complement-like
molecules is of special importance in that such proteins may serve
as potential therapeutics for a variety of different human
disorders. Such polypeptides may also play important roles in
biotechnological and medical research as well as various industrial
applications. As a result, there is particular scientific and
medical interest in new molecules, such as PRO344.
[0383] PRO347 polypeptides of the present invention which possess
biological activity related to that of cysteine-rich secretory
proteins may be employed both in vivo for therapeutic purposes and
in vitro. Those of ordinary skill in the art will well know how to
employ the PRO347 polypeptides of the present invention for such
purposes.
[0384] PRO354 polypeptides of the present invention which possess
biological activity related to that of the heavy chain of the
inter-alpha-trypsin inhibitor protein may be employed both in vivo
for therapeutic purposes and in vitro. Those of ordinary skill in
the art will well know how to employ the PRO354 polypeptides of the
present invention for such purposes.
[0385] PRO355 polypeptides and portions thereof which have homology
to CRTAM may also be useful for in vivo therapeutic purposes, as
well as for various other applications. The identification of novel
molecules associated with T cells may be relevant to a number of
human disorders such as conditions involving the immune system in
general. Given that the CRTAM protein binds antibodies which play
important roles in a number of disease processes, the
identification of new CRTAM proteins and CRTAM-like molecules is of
special importance in that such proteins may serve as potential
therapeutics for a variety of different human disorders. Such
polypeptides may also play important roles in biotechnological and
medical research, as well as various industrial applications. As a
result, there is particular scientific and medical interest in new
molecules, such as PRO355.
[0386] PRO357 can be used in competitive binding assays with ALS to
determine its activity with respect to ALS. Moreover, PRO357 can be
used in assays to determine if it prolongs polypeptides which it
may complex with to have longer half-lives in vivo. PRO357 can be
used similarly in assays with carboxypeptidase, to which it also
has homology. The results can be applied accordingly.
[0387] PRO715 polypeptides of the present invention which possess
biological activity related to that of the tumor necrosis factor
family of proteins may be employed both in vivo for therapeutic
purposes and in vitro. Those of ordinary skill in the art will well
know how to employ the PRO715 polypeptides of the present invention
for such purposes. PRO715 polypeptides will be expected to bind to
their specific receptors, thereby activating such receptors.
Variants of the PRO715 polypeptides of the present invention may
function as agonists or antagonists of their specific receptor
activity.
[0388] PRO353 polypeptides and portions thereof which have homology
to the complement protein may also be useful for in vivo
therapeutic purposes, as well as for various other applications.
The identification of novel complement proteins and related
molecules may be relevant to a number of human disorders such as
effecting the inflammatory response of cells of the immune system.
Thus, the identification of new complement proteins complement-like
molecules is of special importance in that such proteins may serve
as potential therapeutics for a variety of different human
disorders. Such polypeptides may also play important roles in
biotechnological and medical research as well as various industrial
applications. As a result, there is particular scientific and
medical interest in new molecules, such as PRO353.
[0389] PRO361 polypeptides and portions thereof which have homology
to mucin and/or chitinase proteins may also be useful for in vivo
therapeutic purposes, as well as for various other applications.
The identification of novel mucin and/or chitinase proteins and
related molecules may be relevant to a number of human disorders
such as cancer or those involving cell surface molecules or
receptors. Thus, the identification of new mucin and/or chitinase
proteins is of special importance in that such proteins may serve
as potential therapeutics for a variety of different human
disorders. Such polypeptides may also play important roles in
biotechnological and medical research as well as various industrial
applications. As a result, there is particular scientific and
medical interest in new molecules, such as PRO361.
[0390] PRO365 polypeptides and portions thereof which have homology
to the human 2-19 protein may also be useful for in vivo
therapeutic purposes, as well as for various other applications.
The identification of novel human 2-19 proteins and related
molecules may be relevant to a number of human disorders such as
modulating the binding or activity of cells of the immune system.
Thus, the identification of new human 2-19 proteins and human 2-19
protein-like molecules is of special importance in that such
proteins may serve as potential therapeutics for a variety of
different human disorders. Such polypeptides may also play
important roles in biotechnological and medical research as well as
various industrial applications. As a result, there is particular
scientific and medical interest in new molecules, such as
PRO365.
[0391] F. Anti-PRO Antibodies
[0392] The present invention further provides anti-PRO antibodies.
Exemplary antibodies include polyclonal, monoclonal, humanized,
bispecific, and heteroconjugate antibodies.
[0393] 1. Polyclonal Antibodies
[0394] The anti-PRO antibodies may comprise polyclonal antibodies.
Methods of preparing polyclonal antibodies are known to the skilled
artisan. Polyclonal antibodies can be raised in a mammal, for
example, by one or more injections of an immunizing agent and, if
desired, an adjuvant. Typically, the immunizing agent and/or
adjuvant will be injected in the mammal by multiple subcutaneous or
intraperitoneal injections. The immunizing agent may include the
PRO polypeptide or a fusion protein thereof. It may be useful to
conjugate the immunizing agent to a protein known to be immunogenic
in the mammal being immunized. Examples of such immunogenic
proteins include but are not limited to keyhole limpet hemocyanin,
serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.
Examples of adjuvants which may be employed include Freund's
complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A,
synthetic trehalose dicorynomycolate). The immunization protocol
may be selected by one skilled in the art without undue
experimentation.
[0395] 2. Monoclonal Antibodies
[0396] The anti-PRO antibodies may, alternatively, be monoclonal
antibodies. Monoclonal antibodies may be prepared using hybridoma
methods, such as those described by Kohler and Milstein, Nature,
256:495 (1975). In a hybridoma method, a mouse, hamster, or other
appropriate host animal, is typically immunized with an immunizing
agent to elicit lymphocytes that produce or are capable of
producing antibodies that will specifically bind to the immunizing
agent. Alternatively, the lymphocytes may be immunized in
vitro.
[0397] The immunizing agent will typically include the PRO
polypeptide or a fusion protein thereof. Generally, either
peripheral blood lymphocytes ("PBLs") are used if cells of human
origin are desired, or spleen cells or lymph node cells are used if
non-human mammalian sources are desired. The lymphocytes are then
fused with an immortalized cell line using a suitable fusing agent,
such as polyethylene glycol, to form a hybridoma cell [Goding,
Monoclonal Antibodies: Principles and Practice, Academic Press,
(1986) pp. 59-103]. Immortalized cell lines are usually transformed
mammalian cells, particularly myeloma cells of rodent, bovine and
human origin. Usually, rat or mouse myeloma cell lines are
employed. The hybridoma cells may be cultured in a suitable culture
medium that preferably contains one or more substances that inhibit
the growth or survival of the unfused, immortalized cells. For
example, if the parental cells lack the enzyme hypoxanthine guanine
phosphoribosyl transferase (HGPRT or HPRT), the culture medium for
the hybridomas typically will include hypoxanthine, aminopterin,
and thymidine ("HAT medium"), which substances prevent the growth
of HGPRT-deficient cells.
[0398] Preferred immortalized cell lines are those that fuse
efficiently, support stable high level expression of antibody by
the selected antibody-producing cells, and are sensitive to a
medium such as HAT medium. More preferred immortalized cell lines
are murine myeloma lines, which can be obtained, for instance, from
the Salk Institute Cell Distribution Center, San Diego, Calif. and
the American Type Culture Collection, Manassas, Va. Human myeloma
and mouse-human heteromyeloma cell lines also have been described
for the production of human monoclonal antibodies [Kozbor, J.
Immunol. 1133:3001 (1984); Brodeur et al., Monoclonal Antibody
Production Techniques and Applications, Marcel Dekker, Inc., New
York, (1987) pp. 51-63].
[0399] The culture medium in which the hybridoma cells are cultured
can then be assayed for the presence of monoclonal antibodies
directed against PRO. Preferably, the binding specificity of
monoclonal antibodies produced by the hybridoma cells is determined
by immunoprecipitation or by an in vitro binding assay, such as
radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay
(ELISA). Such techniques and assays are known in the art. The
binding affinity of the monoclonal antibody can, for example, be
determined by the Scatchard analysis of Munson and Pollard, Anal.
Biochem., 107:220 (1980).
[0400] After the desired hybridoma cells are identified, the clones
may be subcloned by limiting dilution procedures and grown by
standard methods [Goding, supra]. Suitable culture media for this
purpose include, for example, Dulbecco's Modified Eagle's Medium
and RPMI-1640 medium. Alternatively, the hybridoma cells may be
grown in vivo as ascites in a mammal.
[0401] The monoclonal antibodies secreted by the subclones may be
isolated or purified from the culture medium or ascites fluid by
conventional immunoglobulin purification procedures such as, for
example, protein A-Sepharose, hydroxylapatite chromatography, gel
electrophoresis, dialysis, or affinity chromatography.
[0402] The monoclonal antibodies may also be made by recombinant
DNA methods, such as those described in U.S. Pat. No. 4,816,567.
DNA encoding the monoclonal antibodies of the invention can be
readily isolated and sequenced using conventional procedures (e.g.,
by using oligonucleotide probes that are capable of binding
specifically to genes encoding the heavy and light chains of murine
antibodies). The hybridoma cells of the invention serve as a
preferred source of such DNA. Once isolated, the DNA may be placed
into expression vectors, which are then transfected into host cells
such as simian COS cells, Chinese hamster ovary (CHO) cells, or
myeloma cells that do not otherwise produce immunoglobulin protein,
to obtain the synthesis of monoclonal antibodies in the recombinant
host cells. The DNA also may be modified, for example, by
substituting the coding sequence for human heavy and light chain
constant domains in place of the homologous murine sequences [U.S.
Pat. No. 4,816,567; Morrison et al., supra] or by covalently
joining to the immunoglobulin coding sequence all or part of the
coding sequence for a non-immunoglobulin polypeptide. Such a
non-immunoglobulin polypeptide can be substituted for the constant
domains of an antibody of the invention, or can be substituted for
the variable domains of one antigen-combining site of an antibody
of the invention to create a chimeric bivalent antibody.
[0403] The antibodies may be monovalent antibodies. Methods for
preparing monovalent antibodies are well known in the art. For
example, one method involves recombinant expression of
immunoglobulin light chain and modified heavy chain. The heavy
chain is truncated generally at any point in the Fc region so as to
prevent heavy chain crosslinking. Alternatively, the relevant
cysteine residues are substituted with another amino acid residue
or are deleted so as to prevent crosslinking.
[0404] In vitro methods are also suitable for preparing monovalent
antibodies. Digestion of antibodies to produce fragments thereof,
particularly, Fab fragments, can be accomplished using routine
techniques known in the art.
[0405] 3. Human and Humanized Antibodies
[0406] The anti-PRO antibodies of the invention may further
comprise humanized antibodies or human antibodies. Humanized forms
of non-human (e.g., murine) antibodies are chimeric
immunoglobulins, immunoglobulin chains or fragments thereof (such
as Fv, Fab, Fab', F(ab').sub.2 or other antigen-binding
subsequences of antibodies) which contain minimal sequence derived
from non-human immunoglobulin. Humanized antibodies include human
immunoglobulins (recipient antibody) in which residues from a
complementary determining region (CDR) of the recipient are
replaced by residues from a CDR of a non-human species (donor
antibody) such as mouse, rat or rabbit having the desired
specificity, affinity and capacity. In some instances, Fv framework
residues of the human immunoglobulin are replaced by corresponding
non-human residues. Humanized antibodies may also comprise residues
which are found neither in the recipient antibody nor in the
imported CDR or framework sequences. In general, the humanized
antibody will comprise substantially all of at least one, and
typically two, variable domains, in which all or substantially all
of the CDR regions correspond to those of a non-human
immunoglobulin and all or substantially all of the FR regions are
those of a human immunoglobulin consensus sequence. The humanized
antibody optimally also will comprise at least a portion of an
immunoglobulin constant region (Fc), typically that of a human
immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann
et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct.
Biol., 2:593-596 (1992)].
[0407] Methods for humanizing non-human antibodies are well known
in the art. Generally, a humanized antibody has one or more amino
acid residues introduced into it from a source which is non-human.
These non-human amino acid residues are often referred to as
"import" residues, which are typically taken from an "import"
variable domain. Humanization can be essentially performed
following the method of Winter and co-workers [Jones et al.,
Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327
(1988); Verhoeyen et al., Science, 239:1534-1536 (1988)], by
substituting rodent CDRs or CDR sequences for the corresponding
sequences of a human antibody. Accordingly, such "humanized"
antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567),
wherein substantially less than an intact human variable domain has
been substituted by the corresponding sequence from a non-human
species. In practice, humanized antibodies are typically human
antibodies in which some CDR residues and possibly some FR residues
are substituted by residues from analogous sites in rodent
antibodies.
[0408] Human antibodies can also be produced using various
techniques known in the art, including phage display libraries
[Hoogenboom and Winter, J. Mol. Biol. 227:381 (1991); Marks et al.,
J. Mol. Biol., 222:581 (1991)]. The techniques of Cole et al. and
Boerner et al. are also available for the preparation of human
monoclonal antibodies (Cole et al., Monoclonal Antibodies and
Cancer Therapy. Alan R. Liss, p. 77 (1985) and Boerner et al., J.
Immunol., 147(1):86-95 (1991)]. Similarly, human antibodies can be
made by introducing of human immunoglobulin loci into transgenic
animals, e.g., mice in which the endogenous immunoglobulin genes
have been partially or completely inactivated. Upon challenge,
human antibody production is observed, which closely resembles that
seen in humans in all respects, including gene rearrangement,
assembly, and antibody repertoire. This approach is described, for
example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825;
5,625,126; 5,633,425; 5,661,016, and in the following scientific
publications: Marks et al., Bio/Technology 10, 779-783(1992);
Lonberg et al., Nature 368856-859(1994); Morrison, Nature 368,
812-13 (1994); Fishwild et al., Nature Biotechnology 14, 845-51
(1996); Neuberger, Nature Biotechnology 14, 826 (1996); Lonberg and
Huszar, Intern. Rev. Immunol. 13 65-93 (1995).
[0409] 4. Bispecific Antibodies
[0410] Bispecific antibodies are monoclonal, preferably human or
humanized, antibodies that have binding specificities for at least
two different antigens. In the present case, one of the binding
specificities is for the PRO, the other one is for any other
antigen, and preferably for a cell-surface protein or receptor or
receptor subunit.
[0411] Methods for making bispecific antibodies are known in the
art. Traditionally, the recombinant production of bispecific
antibodies is based on the co-expression of two imununoglobulin
heavy-chain/light-chain pairs, where the two heavy chains have
different specificities [Milstein and Cuello, Nature 305:537-539
(1983)]. Because of the random assortment of immunoglobulin heavy
and light chains, these hybridomas (quadromas) produce a potential
mixture of ten different antibody molecules, of which only one has
the correct bispecific structure. The purification of the correct
molecule is usually accomplished by affinity chromatography steps.
Similar procedures are disclosed in WO 93/08829, published May 13,
1993, and in Traunecker et al., EMBO J., 10:3655-3659 (1991).
[0412] Antibody variable domains with the desired binding
specificities (antibody-antigen combining sites) can be fused to
immunoglobulin constant domain sequences. The fusion preferably is
with an immunoglobulin heavy-chain constant domain, comprising at
least part of the hinge, CH2, and CH3 regions. It is preferred to
have the first heavy-chain constant region (CH 1) containing the
site necessary for light-chain binding present in at least one of
the fusions. DNAs encoding the immunoglobulin heavy-chain fusions
and, if desired, the immunoglobulin light chain, are inserted into
separate expression vectors, and are co-transfected into a suitable
host organism. For further details of generating bispecific
antibodies see, for example, Suresh et al., Methods in Enzymology
121:210 (1986).
[0413] According to another approach described in WO 96/27011, the
interface between a pair of antibody molecules can be engineered to
maximize the percentage of heterodimers which are recovered from
recombinant cell culture. The preferred interface comprises at
least a part of the CH3 region of an antibody constant domain. In
this method, one or more small amino acid side chains from the
interface of the first antibody molecule are replaced with larger
side chains (e.g. tyrosine or tryptophan). Compensatory "cavities"
of identical or similar size to the large side chain(s) are created
on the interface of the second antibody molecule by replacing large
amino acid side chains with smaller ones (e.g. alanine or
threonine). This provides a mechanism for increasing the yield of
the heterodimer over other unwanted end-products such as
homodimers.
[0414] Bispecific antibodies can be prepared as full length
antibodies or antibody fragments (e.g. F(ab').sub.2 bispecific
antibodies). Techniques for generating bispecific antibodies from
antibody fragments have been described in the literature. For
example, bispecific antibodies can be prepared can be prepared
using chemical linkage. Brennan et al., Science 229:81 (1985)
describe a procedure wherein intact antibodies are proteolytically
cleaved to generate F(ab').sub.2 fragments. These fragments are
reduced in the presence of the dithiol complexing agent sodium
arsenite to stabilize vicinal dithiols and prevent intermolecular
disulfide formation. The Fab' fragments generated are then
converted to thionitrobenzoate (TNB) derivatives. One of the
Fab'-TNB derivatives is then reconverted to the Fab'-thiol by
reduction with mercaptoethylamine and is mixed with an equimolar
amount of the other Fab'-TNB derivative to form the bispecific
antibody. The bispecific antibodies produced can be used as agents
for the selective immobilization of enzymes.
[0415] Fab' fragments may be directly recovered from E. coli and
chemically coupled to form bispecific antibodies. Shalaby et al.,
J. Exp. Med. 175:217-225 (1992) describe the production of a fully
humanized bispecific antibody F(ab').sub.2 molecule. Each Fab
fragment was separately secreted from E. coli and subjected to
directed chemical coupling in vitro to form the bispecific
antibody. The bispecific antibody thus formed was able to bind to
cells overexpressing the ErbB2 receptor and normal human T cells,
as well as trigger the lytic activity of human cytotoxic
lymphocytes against human breast tumor targets.
[0416] Various technique for making and isolating bispecific
antibody fragments directly from recombinant cell culture have also
been described. For example, bispecific antibodies have been
produced using leucine zippers. Kostelny et al., J. Immunol.
148(5):1547-1553 (1992). The leucine zipper peptides from the Fos
and Jun proteins were linked to the Fab' portions of two different
antibodies by gene fusion. The antibody homodimers were reduced at
the hinge region to form monomers and then re-oxidized to form the
antibody heterodimers. This method can also be utilized for the
production of antibody homodimers. The "diabody" technology
described by Hollinger et al., Proc. Natl. Acad. Sci. USA
90:6444-6448 (1993) has provided an alternative mechanism for
making bispecific antibody fragments. The fragments comprise a
heavy-chain variable domain (V.sub.H) connected to a light-chain
variable domain (V.sub.L) by a linker which is too short to allow
pairing between the two domains on the same chain. Accordingly, the
V.sub.H and V.sub.L domains of one fragment are forced to pair with
the complementary V.sub.L and V.sub.H domains of another fragment,
thereby forming two antigen-binding sites. Another strategy for
making bispecific antibody fragments by the use of single-chain Fv
(sFv) dimers has also been reported. See, Gruber et al., J.
Immunol. 152:5368 (1994). Antibodies with more than two valencies
are contemplated. For example, trispecific antibodies can be
prepared. Tutt et al., J. Immunol. 147:60 (1991).
[0417] Exemplary bispecific antibodies may bind to two different
epitopes on a given PRO polypeptide herein. Alternatively, an
anti-PRO polypeptide arm may be combined with an arm which binds to
a triggering molecule on a leukocyte such as a T-cell receptor
molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG
(Fc.gamma.R), such as Fc.gamma.RI (CD64), Fc.gamma.RII (CD32) and
Fc.gamma.RIII (CD16) so as to focus cellular defense mechanisms to
the cell expressing the particular PRO polypeptide. Bispecific
antibodies may also be used to localize cytotoxic agents to cells
which express a particular PRO polypeptide. These antibodies
possess a PRO-binding arm and an arm which binds a cytotoxic agent
or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA.
Another bispecific antibody of interest binds the PRO polypeptide
and further binds tissue factor (TF).
[0418] 5. Heteroconjugate Antibodies
[0419] Heteroconjugate antibodies are also within the scope of the
present invention. Heteroconjugate antibodies are composed of two
covalently joined antibodies. Such antibodies have, for example,
been proposed to target immune system cells to unwanted cells [U.S.
Pat. No. 4,676,980], and for treatment of HIV infection [WO
91/00360; WO 92/200373; EP 03089]. It is contemplated that the
antibodies may be prepared in vitro using known methods in
synthetic protein chemistry, including those involving crosslinking
agents. For example, immunotoxins may be constructed using a
disulfide exchange reaction or by forming a thioether bond.
Examples of suitable reagents for this purpose include
iminothiolate and methyl4-mercaptobutyrimidate and those disclosed,
for example, in U.S. Pat. No. 4,676,980.
[0420] 6. Effector Function Engineering
[0421] It may be desirable to modify the antibody of the invention
with respect to effector function, so as to enhance, e.g., the
effectiveness of the antibody in treating cancer. For example,
cysteine residue(s) may be introduced into the Fc region, thereby
allowing interchain disulfide bond formation in this region. The
homodimeric antibody thus generated may have improved
internalization capability and/or increased complement-mediated
cell killing and antibody-dependent cellular cytotoxicity (ADCC).
See Caron et al., J. Exp. Med., 176: 1191-1195 (1992) and Shopes,
J. Immunol. 148: 2918-2922 (1992). Homodimeric antibodies with
enhanced anti-tumor activity may also be prepared using
heterobifunctional cross-linkers as described in Wolff et al.
Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody
can be engineered that has dual Fc regions and may thereby have
enhanced complement lysis and ADCC capabilities. See Stevenson et
al., Anti-Cancer Drug Design, 3: 219-230 (1989).
[0422] 7. Immunoconjugates
[0423] The invention also pertains to immunoconjugates comprising
an antibody conjugated to a cytotoxic agent such as a
chemotherapeutic agent, toxin (e.g., an enzymatically active toxin
of bacterial, fungal, plant, or animal origin, or fragments
thereof), or a radioactive isotope (i.e., a radioconjugate).
[0424] Chemotherapeutic agents useful in the generation of such
immunoconjugates have been described above. Enzymatically active
toxins and fragments thereof that can be used include diphtheria A
chain, nonbinding active fragments of diphtheria toxin, exotoxin A
chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain,
modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin
proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S),
momordica charantia inhibitor, curcin, crotin, sapaonaria
officinalis inhibitor, gelonin, mitogellin, restrictocin,
phenomycin, enomycin, and the tricothecenes. A variety of
radionuclides are available for the production of radioconjugated
antibodies. Examples include .sup.212Bi, .sup.131I, .sup.131In,
.sup.90Y, and .sup.186Re.
[0425] Conjugates of the antibody and cytotoxic agent are made
using a variety of bifunctional protein-coupling agents such as
N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP),
iminothiolane (IT), bifunctional derivatives of imidoesters (such
as dimethyl adipimidate HCL), active esters (such as disuccinimidyl
suberate), aldehydes (such as glutareldehyde), bis-azido compounds
(such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium
derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active
fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For
example, a ricin immunotoxin can be prepared as described in
Vitetta et al., Science, 238: 1098 (1987). Carbon-14-labeled
1-isothiocyanatobenzyl-3 methyldiethylene triaminepentaacetic acid
(MX-DTPA) is an exemplary chelating agent for conjugation of
radionucleotide to the antibody. See WO94/11026.
[0426] In another embodiment, the antibody may be conjugated to a
"receptor" (such streptavidin) for utilization in tumor
pretargeting wherein the antibody-receptor conjugate is
administered to the patient, followed by removal of unbound
conjugate from the circulation using a clearing agent and then
administration of a "ligand" (e.g., avidin) that is conjugated to a
cytotoxic agent (e.g., a radionucleotide).
[0427] 8. Immunoliposomes
[0428] The antibodies disclosed herein may also be formulated as
immunoliposomes. Liposomes containing the antibody are prepared by
methods known in the art, such as described in Epstein et al.,
Proc. Natl. Acad. Sci. USA, 82: 3688 (1985); Hwang et al., Proc.
Natl. Acad. Sci. USA, 77: 4030 (1980); and U.S. Pat. Nos. 4,485,045
and 4,544,545. Liposomes with enhanced circulation time are
disclosed in U.S. Pat. No. 5,013,556.
[0429] Particularly useful liposomes can be generated by the
reverse-phase evaporation method with a lipid composition
comprising phosphatidylcholine, cholesterol, and
PEG-derivatizedphosphatidylethanola- mine (PEG-PE). Liposomes are
extruded through filters of defined pore size to yield liposomes
with the desired diameter. Fab' fragments of the antibody of the
present invention can be conjugated to the liposomes as described
in Martin et al ., J. Biol. Chem., 257: 286-288 (1982) via a
disulfide-interchange reaction. A chemotherapeutic agent (such as
Doxorubicin) is optionally contained within the liposome. See
Gabizon et al., J. National Cancer Inst., 81(19): 1484 (1989).
[0430] 9. Pharmaceutical Compositions of Antibodies
[0431] Antibodies specifically binding a PRO polypeptide identified
herein, as well as other molecules identified by the screening
assays disclosed hereinbefore, can be administered for the
treatment of various disorders in the form of pharmaceutical
compositions.
[0432] If the PRO polypeptide is intracellular and whole antibodies
are used as inhibitors, internalizing antibodies are preferred.
However, lipofections or liposomes can also be used to deliver the
antibody, or an antibody fragment, into cells. Where antibody
fragments are used, the smallest inhibitory fragment that
specifically binds to the binding domain of the target protein is
preferred. For example, based upon the variable-region sequences of
an antibody, peptide molecules can be designed that retain the
ability to bind the target protein sequence. Such peptides can be
synthesized chemically and/or produced by recombinant DNA
technology. See, e.g., Marasco et al., Proc. Natl. Acad. Sci. USA.
90: 7889-7893 (1993). The formulation herein may also contain more
than one active compound as necessary for the particular indication
being treated, preferably those with complementary activities that
do not adversely affect each other. Alternatively, or in addition,
the composition may comprise an agent that enhances its function,
such as, for example, a cytotoxic agent, cytokine, chemotherapeutic
agent, or growth-inhibitory agent. Such molecules are suitably
present in combination in amounts that are effective for the
purpose intended.
[0433] The active ingredients may also be entrapped in
microcapsules prepared, for example, by coacervation techniques or
by interfacial polymerization, for example, hydroxymethylcellulose
or gelatin-microcapsules and poly-(methylmethacylate)
microcapsules, respectively, in colloidal drug delivery systems
(for example, liposomes, albumin microspheres, microemulsions,
nano-particles, and nanocapsules) or in macroemulsions. Such
techniques are disclosed in Remington's Pharmaceutical Sciences,
supra.
[0434] The formulations to be used for in vivo administration must
be sterile. This is readily accomplished by filtration through
sterile filtration membranes.
[0435] Sustained-release preparations may be prepared. Suitable
examples of sustained-release preparations include semipermeable
matrices of solid hydrophobic polymers containing the antibody,
which matrices are in the form of shaped articles, e.g., films, or
microcapsules. Examples of sustained-release matrices include
polyesters, hydrogels (for example,
poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)),
polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic
acid and .gamma. ethyl-L-glutamate, non-degradable ethylene-vinyl
acetate, degradable lactic acid-glycolic acid copolymers such as
the LUPRON DEPOT .TM. (injectable microspheres composed of lactic
acid-glycolic acid copolymer and leuprolide acetate), and
poly-D-(-)-3-hydroxybutyric acid. While polymers such as
ethylene-vinyl acetate and lactic acid-glycolic acid enable release
of molecules for over 100 days, certain hydrogels release proteins
for shorter time periods. When encapsulated antibodies remain in
the body for a long time, they may denature or aggregate as a
result of exposure to moisture at 37.degree. C., resulting in a
loss of biological activity and possible changes in immunogenicity.
Rational strategies can be devised for stabilization depending on
the mechanism involved. For example, if the aggregation mechanism
is discovered to be intermolecularS-S bond formation through
thio-disulfide interchange, stabilization may be achieved by
modifying sulfhydryl residues, lyophilizing from acidic solutions,
controlling moisture content, using appropriate additives, and
developing specific polymer matrix compositions.
[0436] G. Uses for Anti-PRO Antibodies
[0437] The anti-PRO antibodies of the invention have various
utilities. For example, anti-PRO antibodies may be used in
diagnostic assays for PRO, e.g., detecting its expression in
specific cells, tissues, or serum. Various diagnostic assay
techniques known in the art may be used, such as competitive
binding assays, direct or indirect sandwich assays and
immunoprecipitation assays conducted in either heterogeneous or
homogeneous phases [Zola, Monoclonal Antibodies: A Manual of
Techniques. CRC Press, Inc. (1987) pp. 147-158]. The antibodies
used in the diagnostic assays can be labeled with a detectable
moiety. The detectable moiety should be capable of producing,
either directly or indirectly, a detectable signal. For example,
the detectable moiety may be a radioisotope, such as .sup.3H,
.sup.14C, .sup.32P, .sup.35S, or .sup.125I, a fluorescent or
chemiluminescent compound, such as fluorescein isothiocyanate,
rhodamine, or luciferin, or an enzyme, such as alkaline
phosphatase, beta-galactosidase or horseradish peroxidase. Any
method known in the art for conjugating the antibody to the
detectable moiety may be employed, including those methods
described by Hunter et al., Nature 144:945 (1962); David et al.,
Biochemistry, 13:1014 (1974); Pain et al., J. Immunol. Meth.,
40:219 (1981); and Nygren, J. Histochem. and Cytochem., 30:407
(1982).
[0438] Anti-PRO antibodies also are useful for the affinity
purification of PRO from recombinant cell culture or natural
sources. In this process, the antibodies against PRO are
immobilized on a suitable support, such a Sephadex resin or filter
paper, using methods well known in the art. The immobilized
antibody then is contacted with a sample containing the PRO to be
purified, and thereafter the support is washed with a suitable
solvent that will remove substantially all the material in the
sample except the PRO, which is bound to the immobilized antibody.
Finally, the support is washed with another suitable solvent that
will release the PRO from the antibody.
[0439] The following examples are offered for illustrative purposes
only, and are not intended to limit the scope of the present
invention in any way.
[0440] All patent and literature references cited in the present
specification are hereby incorporated by reference in their
entirety.
EXAMPLES
[0441] Commercially available reagents referred to in the examples
were used according to manufacturer's instructions unless otherwise
indicated. The source of those cells identified in the following
examples, and throughout the specification, by ATCC accession
numbers is the American Type Culture Collection, Manassas, Va.
EXAMPLE 1
Extracellular Domain Homology Screening to Identify Novel
Polypeptides and cDNA Encoding Therefor
[0442] The extracellular domain (ECD) sequences (including the
secretion signal sequence, if any) from about 950 known secreted
proteins from the Swiss-Prot public database were used to search
EST databases. The EST databases included public databases (e.g.,
Dayhoff, GenBank), and proprietary databases (e.g. LIFESEQ.TM.,
Incyte Pharmaceuticals, Palo Alto, Calif.). The search was
performed using the computer program BLAST or BLAST-2 (Altschul et
al., Methods in Enzymology 266:460-480 (1996)) as a comparison of
the ECD protein sequences to a 6 frame translation of the EST
sequences. Those comparisons with a BLAST score of 70 (or in some
cases 90) or greater that did not encode known proteins were
clustered and assembled into consensus DNA sequences with the
program "phrap" (Phil Green, University of Washington, Seattle,
Wash.).
[0443] Using this extracellular domain homology screen, consensus
DNA sequences were assembled relative to the other identified EST
sequences using phrap. In addition, the consensus DNA sequences
obtained were often (but not always) extended using repeated cycles
of BLAST or BLAST-2 and phrap to extend the consensus sequence as
far as possible using the sources of EST sequences discussed
above.
[0444] Based upon the consensus sequences obtained as described
above, oligonucleotides were then synthesized and used to identify
by PCR a cDNA library that contained the sequence of interest and
for use as probes to isolate a clone of the full-length coding
sequence for a PRO polypeptide. Forward and reverse PCR primers
generally range from 20 to 30 nucleotides and are often designed to
give a PCR product of about 100-1000 bp in length. The probe
sequences are typically 40-55 bp in length. In some cases,
additional oligonucleotides are synthesized when the consensus
sequence is greater than about 1-1.5 kbp. In order to screen
several libraries for a full-length clone, DNA from the libraries
was screened by PCR amplification, as per Ausubel et al., Current
Protocols in Molecular Biology, with the PCR primer pair. A
positive library was then used to isolate clones encoding the gene
of interest using the probe oligonucleotide and one of the primer
pairs.
[0445] The cDNA libraries used to isolate the cDNA clones were
constructed by standard methods using commercially available
reagents such as those from Invitrogen, San Diego, Calif. The cDNA
was primed with oligo dT containing a NotI site, linked with blunt
to SalI hemikinased adaptors, cleaved with NotI, sized
appropriately by gel electrophoresis, and cloned in a defined
orientation into a suitable cloning vector (such as pRKB or pRKD;
pRK5B is a precursor of pRK5D that does not contain the SfiI site;
see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique
XhoI and NotI sites.
EXAMPLE 2
Isolation of cDNA Clones by Amylase Screening
[0446] 1. Preparation of Oligo dT Primed cDNA Library
[0447] mRNA was isolated from a human tissue of interest using
reagents and protocols from Invitrogen, San Diego, Calif. (Fast
Track 2). This RNA was used to generate an oligo dT primed cDNA
library in the vector pRK5D using reagents and protocols from Life
Technologies, Gaithersburg, Md. (Super Script Plasmid System). In
this procedure, the double stranded cDNA was sized to greater than
1000 bp and the SalI/NotI linkered cDNA was cloned into XhoI/NotI
cleaved vector. pRK5D is a cloning vector that has an sp6
transcription initiation site followed by an SfiI restriction
enzyme site preceding the XhoI/NotI cDNA cloning sites.
[0448] 2. Preparation of Random Primed cDNA Library
[0449] A secondary cDNA library was generated in order to
preferentially represent the 5' ends of the primary cDNA clones.
Sp6 RNA was generated from the primary library (described above),
and this RNA was used to generate a random primed cDNA library in
the vector pSST-AMY.0 using reagents and protocols from Life
Technologies (Super Script Plasmid System, referenced above). In
this procedure the double stranded cDNA was sized to 500-1000 bp,
linkered with blunt to NotI adaptors, cleaved with SfiI, and cloned
into SfiI/NotI cleaved vector. pSST-AMY.0 is a cloning vector that
has a yeast alcohol dehydrogenase promoter preceding the cDNA
cloning sites and the mouse amylase sequence (the mature sequence
without the secretion signal) followed by the yeast alcohol
dehydrogenase terminator, after the cloning sites. Thus, cDNAs
cloned into this vector that are fused in frame with amylase
sequence will lead to the secretion of amylase from appropriately
transfected yeast colonies.
[0450] 3. Transformation and Detection
[0451] DNA from the library described in paragraph 2 above was
chilled on ice to which was added electrocompetent DH10B bacteria
(Life Technologies, 20 ml). The bacteria and vector mixture was
then electroporated as recommended by the manufacturer.
Subsequently, SOC media (Life Technologies, 1 ml) was added and the
mixture was incubated at 37.degree. C. for 30 minutes. The
transformants were then plated onto 20 standard 150 mm LB plates
containing ampicillin and incubated for 16 hours (37.degree. C.).
Positive colonies were scraped off the plates and the DNA was
isolated from the bacterial pellet using standard protocols, e.g.
CsCl-gradient. The purified DNA was then carried on to the yeast
protocols below.
[0452] The yeast methods were divided into three categories: (1)
Transformation of yeast with the plasmid/cDNA combined vector; (2)
Detection and isolation of yeast clones secreting amylase; and (3)
PCR amplification of the insert directly from the yeast colony and
purification of the DNA for sequencing and further analysis.
[0453] The yeast strain used was HD56-5A (ATCC-90785). This strain
has the following genotype: MAT alpha, ura3-52, leu2-3, leu2-112,
his3-11, his3-15, MAL.sup.+, SUC.sup.+, GAL.sup.+. Preferably,
yeast mutants can be employed that have deficient
post-translational pathways. Such mutants may have translocation
deficient alleles in sec71, sec72, sec62, with truncated sec71
being most preferred. Alternatively, antagonists (including
antisense nucleotides and/or ligands) which interfere with the
normal operation of these genes, other proteins implicated in this
post translation pathway (e.g., SEC61p, SEC72p, SEC62p, SEC63p,
TDJ1p or SSA1p-4p) or the complex formation of these proteins may
also be preferably employed in combination with the
amylase-expressing yeast.
[0454] Transformation was performed based on the protocol outlined
by Gietz et al., Nucl. Acid. Res., 20:1425 (1992). Transformed
cells were then inoculated from agar into YEPD complex media broth
(100 ml) and grown overnight at 30.degree. C. The YEPD broth was
prepared as described in Kaiser et al., Methods in Yeast Genetics,
Cold Spring Harbor Press, Cold Spring Harbor, N.Y., p. 207 (1994).
The overnight culture was then diluted to about 2.times.10.sup.6
cells/ml (approx. OD.sub.600=0.1) into fresh YEPD broth (500 ml)
and regrown to 1.times.10.sup.7 cell/ml (approx.
OD.sub.600=0.40-0.5).
[0455] The cells were then harvested and prepared for
transformation by transfer into GS3 rotor bottles in a Sorval GS3
rotor at 5,000 rpm for 5 minutes, the supernatant discarded, and
then resuspended into sterile water, and centrifuged again in 50 ml
falcon tubes at 3,500 rpm in a Beckman GS-6KR centrifuge. The
supernatant was discarded and the cells were subsequently washed
with LiAc/TE (10 ml, 10 mM Tris-HCl, 1 mM EDTA pH 7.5, 100 mM
Li.sub.2OOCCH.sub.3), and resuspended into LiAc/TE (2.5 ml).
[0456] Transformation took place by mixing the prepared cells (100
.mu.l) with freshly denatured single stranded salmon testes DNA
(Lofstrand Labs, Gaithersburg, Md.) and transforming DNA (1 .mu.g,
vol.<10 .mu.l) in microfuge tubes. The mixture was mixed briefly
by vortexing, then 40% PEG/TE (600 .mu.l, 40% polyethylene
glycol-4000, 10 mM Tris-HCl, 1 mM EDTA, 100 mM Li.sub.2OOCCH.sub.3,
pH 7.5) was added. This mixture was gently mixed and incubated at
30.degree. C. while agitating for 30 minutes. The cells were then
heat shocked at 42.degree. C. for 15 minutes, and the reaction
vessel centrifuged in a microfuge at 12,000 rpm for 5-10 seconds,
decanted and resuspended into TE (500 .mu.l, 10 mM Tris-HCl, 1 mM
EDTA pH 7.5) followed by recentrifugation. The cells were then
diluted into TE (1 ml) and aliquots (200 .mu.l) were spread onto
the selective media previously prepared in 150 mm growth plates
(VWR).
[0457] Alternatively, instead of multiple small reactions, the
transformation was performed using a single, large scale reaction,
wherein reagent amounts were scaled up accordingly.
[0458] The selective media used was a synthetic complete dextrose
agar lacking uracil (SCD-Ura) prepared as described in Kaiser et
al., Methods in Yeast Genetics, Cold Spring Harbor Press, Cold
Spring Harbor, N.Y., p. 208-210 (1994). Transformants were grown at
30.degree. C. for 2-3 days.
[0459] The detection of colonies secreting amylase was performed by
including red starch in the selective growth media. Starch was
coupled to the red dye (Reactive Red-120, Sigma) as per the
procedure described by Biely et al., Anal. Biochem., 172:176-179
(1988). The coupled starch was incorporated into the SCD-Ura agar
plates at a final concentration of 0.15% (w/v), and was buffered
with potassium phosphate to a pH of 7.0 (50-100 mM final
concentration).
[0460] The positive colonies were picked and streaked across fresh
selective media (onto 150 mm plates) in order to obtain well
isolated and identifiable single colonies. Well isolated single
colonies positive for amylase secretion were detected by direct
incorporation of red starch into buffered SCD-Ura agar. Positive
colonies were determined by their ability to break down starch
resulting in a clear halo around the positive colony visualized
directly.
[0461] 4. Isolation of DNA by PCR Amplification
[0462] When a positive colony was isolated, a portion of it was
picked by a toothpick and diluted into sterile water (30 .mu.l) in
a 96 well plate. At this time, the positive colonies were either
frozen and stored for subsequent analysis or immediately amplified.
An aliquot of cells (5 .mu.l) was used as a template for the PCR
reaction in a 25 .mu.l volume containing: 0.5 .mu.l Klentaq
(Clontech, Palo Alto, Calif.); 4.0 .mu.l 10 mM dNTP's (Perkin
Elmer-Cetus); 2.5 .mu.l Kentaq buffer (Clontech); 0.25 .mu.l
forward oligo 1; 0.25 .mu.l reverse oligo 2; 12.5 .mu.l distilled
water.
6 The sequence of the forward oligonucleotide 1 was:
5'-TGTAAAACGACGGCCAGTTAAATAGACCTGCAATTATTAATCT-3' (SEQ ID NO:16)
The sequence of reverse oligonucleotide 2 was:
5'-CAGGAAACAGCTATGACCACCTGCACACCTGCAAATCCATT-3' (SEQ ID NO:17)
[0463] PCR was then performed as follows:
7 a. Denature 92.degree. C., 5 minutes b. 3 cycles of: Denature
92.degree. C., 30 seconds Anneal 59.degree. C., 30 seconds Extend
72.degree. C., 60 seconds c. 3 cycles of: Denature 92.degree. C.,
30 seconds Anneal 57.degree. C., 30 seconds Extend 72.degree. C.,
60 seconds d. 25 cycles of: Denature 92.degree. C., 30 seconds
Anneal 55.degree. C., 30 seconds Extend 72.degree. C., 60 seconds
e. Hold 4.degree. C.
[0464] The underlined regions of the oligonucleotides annealed to
the ADH promoter region and the amylase region, respectively, and
amplified a 307 bp region from vector pSST-AMY.0 when no insert was
present. Typically, the first 18 nucleotides of the 5' end of these
oligonucleotides contained annealing sites for the sequencing
primers. Thus, the total product of the PCR reaction from an empty
vector was 343 bp. However, signal sequence-fused cDNA resulted in
considerably longer nucleotide sequences.
[0465] Following the PCR, an aliquot of the reaction (5 .mu.l) was
examined by agarose gel electrophoresis in a 1% agarose gel using a
Tris-Borate-EDTA (TBE) buffering system as described by Sambrook et
al., supra. Clones resulting in a single strong PCR product larger
than 400 bp were further analyzed by DNA sequencing after
purification with a 96 Qiaquick PCR clean-up column (Qiagen Inc.,
Chatsworth, Calif.).
EXAMPLE 3
Isolation of cDNA Clones Encoding Human PRO241
[0466] A consensus DNA sequence was assembled relative to other EST
sequences as described in Example 1 above. This consensus sequence
is herein designated DNA30876. Based on the DNA30876 consensus
sequence, oligonucleotides were synthesized: 1) to identify by PCR
a cDNA library that contained the sequence of interest, and 2) for
use as probes to isolate a clone of the full-length coding sequence
for PRO241.
[0467] PCR primers (forward and reverse) were synthesized:
8 forward PCR primer 5'-GGAAATGAGTGCAAACCCTC-3' (SEQ ID NO:3)
reverse PCR primer 5'-TCCCAAGCTGAACACTCATTCTGC-3' (SEQ ID NO:4)
[0468] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA30876 sequence which
had the following nucleotide sequence hybridization probe
5'-GGGTGACGGTGTTCCATATCAGAATTGCAG- AAGCAAAACTGACCTCAGTT-3' (SEQ ID
NO:5)
[0469] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with the PCR primer pair identified above. A positive
library was then used to isolate clones encoding the PRO241 gene
using the probe oligonucleotide and one of the PCR primers. RNA for
construction of the cDNA libraries was isolated from human fetal
kidney tissue (LIB29).
[0470] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO241 [herein designated as
DNA34392-1170] (SEQ ID NO:1) and the derived protein sequence for
PRO241.
[0471] The entire nucleotide sequence of DNA34392-1170 is shown in
FIG. 1 (SEQ ID NO:1). Clone DNA34392-1170 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 234-236 and ending at the stop codon at
nucleotide positions 1371-1373 (FIG. 1). The predicted polypeptide
precursor is 379 amino acids long (FIG. 2). The full-length PRO241
protein shown in FIG. 2 has an estimated molecular weight of about
43,302 daltons and a pI of about 7.30. Clone DNA34392-1170 has been
deposited with ATCC and is assigned ATCC deposit no. ATCC
209526.
[0472] Analysis of the amino acid sequence of the full-length
PRO241 polypeptide suggests that it possess significant homology to
the various biglycan proteoglycan proteins, thereby indicating that
PRO241 is a novel biglycan homolog polypeptide.
EXAMPLE 4
Isolation of cDNA Clones Encoding Human PRO243 by Genomic
Walking
[0473] Introduction
[0474] Human thrombopoietin (THPO) is a glycosylated hormone of 352
amino acids consisting of two domains. The N-terminal domain,
sharing 50% similarity to erythropoietin, is responsible for the
biological activity. The C-terminal region is required for
secretion. The gene for thrombopoietin (THPO) maps to human
chromosome 3q27-q28 where the six exons of this gene span 7
kilobase base pairs of genomic DNA (Gurney et al., Blood 85:
981-988 (1995). In order to determine whether there were any genes
encoding THPO homologues located in close proximity to THPO,
genomic DNA fragments from this region were identified and
sequenced. Three P1 clones and one PAC clones (Genome Systems Inc.,
St. Louis, Mo.; cat. Nos. P1-2535 and PAC-6539) encompassing the
THPO locus were isolated and a 140 kb region was sequenced using
the ordered shotgun strategy (Chen et al., Genomics 17: 651-656
(1993)), coupled with a PCR-based gap filling approach. Analysis
reveals that the region is gene-rich with four additional genes
located very close to THPO: tumor necrosis factor-receptor type 1
associated protein 2 (TRAP2) and elongation initiation factor gamma
(elF4 g), chloride channel 2 (CLCN2) and RNA polymerase II subunit
hRPB17. While no THPO homolog was found in the region, four novel
genes have been predicted by computer-assisted gene detection
(GRAIL)(Xu et al., Gen. Engin. 16: 241-253 (1994), the presence of
CpG islands (Cross, S. and Bird, A., Curr. Opin. Genet. &
Devel. 5: 109-314 (1995), and homology to known genes (as detected
by WU-BLAST2.0)(Altschul and Gish, Methods Enzymol. 266: 460-480
(1996) (http:/blast.wustl.edu/blast/README.html).
[0475] P1 and PAC Clones
[0476] The initial human P1 clone was isolated from a genomic P1
library (Genome Systems Inc., St. Louis, Mo.; cat. no.: P1-2535)
screened with PCR primers designed from the THPO genomic sequence
(A. L. Gurney, et al., Blood 85: 981-88 (1995). PCR primers were
designed from the end sequences derived from this P1 clone were
then used to screen P1 and PAC libraries (Genome Systems, Cat.
Nos.: P1-2535 & PAC-6539) to identify overlapping clones.
[0477] Ordered Shotgun Strategy
[0478] The Ordered Shotgun Strategy (OSS) (Chen et al., Genomics
17: 651-656 (1993)) involves the mapping and sequencing of large
genomic DNA clones with a hierarchical approach. The P1 or PAC
clone was sonicated and the fragments subcloned into lambda vector
(.lambda.Bluestar) (Novagen, Inc., Madison, Wis.; cat. no.
69242-3). The lambda subclone inserts were isolated by long-range
PCR (Barnes, W. Proc. Natl. Acad. Sci. USA 91: 2216-2220 (1994) and
the ends sequenced. The lambda-end sequences were overlapped to
create a partial map of the original clone. Those lambda clones
with overlapping end-sequences were identified, the insets
subcloned into a plasmid vector (pUC9 or pUC 18) and the ends of
the plasmid subclones were sequenced and assembled to generate a
contiguous sequence. This directed sequencing strategy minimizes
the redundancy required while allowing one to scan for and
concentrate on interesting regions.
[0479] In order to define better the THPO locus and to search for
other genes related to the hematopoietin family, four genomic
clones were isolated from this region by PCR screening of human P1
and PAC libraries (Genome System, Inc., Cat. Nos.: P1-2535 and
PAC-6539). The sizes of the genomic fragments are as follows: P1.t
is 40 kb; P1.g is 70 kb; P1.u is 70 kb; and PAC.z is 200 kb.
Approximately 80% of the 200 kb genomic DNA region was sequenced by
the Ordered Shotgun Strategy (OSS) (Chen et al., Genomics 17:
651-56 (1993), and assembled into contigs using AutoAssembler.TM.
(Applied Biosystems, Perkin Elmer, Foster City, Calif., cat. no.
903227). The preliminary order of these contigs was determined by
manual analysis. There were 46 contigs and filling in the gaps was
employed. Table 7 summarized the number and sizes of the gaps.
9TABLE 7 Summary of the gaps in the 140 kb region Size of gap
number <50 bp 13 50-150 bp 7 150-300 bp 7 300-1000 bp 10
1000-5000 bp 7 >5000 bp 2 ( 15,000 bp)
[0480] DNA Sequencing
[0481] ABI DYE-primer.TM. chemistry (PE Applied Biosystems, Foster
City, Calif.; Cat. No.: 402112) was used to end-sequence the lambda
and plasmid subclones. ABI DYE-terminater.TM. chemistry (PE Applied
Biosystems, Foster City, Calif., Cat. No: 403044) was used to
sequence the PCR products with their respective PCR primers. The
sequences were collected with an ABI377 instrument. For PCR
products larger than 1 kb, walking primers were used. The sequences
of contigs generated by the OSS strategy in AutoAssembler.TM. a (PE
Applied Biosystems, Foster City, Calif.; Cat. No: 903227) and the
gap-filling sequencing trace files were imported into
Sequencher.TM. (Gene Codes Corp., Ann Arbor, Mich.) for overlapping
and editing.
[0482] PCR-Based Gap Filling Strategy
[0483] Primers were designed based on the 5'- and 3'-end sequenced
of each contig, avoiding repetitive and low quality sequence
regions. All primers were designed to be 19-24-mers with 50-70% G/C
content. Oligos were synthesized and gel-purified by standard
methods.
[0484] Since the orientation and order of the contigs were unknown,
permutations of the primers were used in the amplification
reactions. Two PCR kits were used: first, XL PCR kit (Perkin Elmer,
Norwalk, Conn.; Cat. No.: N8080205), with extension times of
approximately 10 minutes; and second, the Taq polymerase PCR kit
(Qiagen Inc., Valencia, Calif.; Cat. No.: 201223) was used under
high stringency conditions if smeared or multiple products were
observed with the XL PCR kit. The main PCR product from each
successful reactions was extracted from a 0.9% low melting agarose
gel and purified with the Geneclean DNA Purification kit prior to
sequencing.
[0485] Analysis
[0486] The identification and characterization of coding regions
was carried out as follows: First, repetitive sequences were masked
using RepeatMasker (A. F. A. Smit & P. Green,
http://ftp.genome.washington.edu/- RM/RM_details.html)which screens
DNA sequences in FastA format against a library of repetitive
elements and returns a masked query sequence. Repeats not masked
were identified by comparing the sequence to the GenBank database
using WUBLAST (Altschul, S & Gish, W., Methods Enzymol. 266:
460-480 (1996) and were masked manually.
[0487] Next, known genes were revealed by comparing the genomic
regions against Genentech's protein database using the WUBLAST2.0
algorithm and then annotated by aligning the genomic and cDNA
sequences for each gene, respectively, using a Needleman-Wunch
(Needleman and Wunsch, J. Mol. Biol. 48: 443453 (1970) algorithm to
find regions of local identity between sequences which are
otherwise largely dissimilar. The strategy results in detection of
all exons of the five known genes in the region, THPO, TRAP2,
elF4g, CLCN2 and hRPB17(Table 8).
10TABLE 8 Summary of known genes located in the 140 kb region
analyzed Known genes Man position eukaryotic translation initiation
factor 4 gamma 3q27-qter thrombopoietin 3q26-q27 chloride channel 2
3q26-qter TNF receptor associated protein 2 not previously mapped
RNA polymerase II subunit hRPB17 not previously mapped
[0488] Finally, novel transcription units were predicted using a
number of approaches. CpG islands (S. Cross & Bird, A., Curr.
Opin. Genet. Dev. 5: 109-314 (1995) islands were used to define
promoter regions and were identified as clusters of sites cleaved
by enzymes recognizing GC-rich, 6 or 8-mer palidromic sequences.
CpG islands are usually associated with promoter regions of genes.
WUBLAST2.0 analysis of short genomic regions (10-20 kb) versus
GenBank revealed matches to ESTs. The individual EST sequences (or
where possible, their sequence chromatogram files) were retrieved
and assembled with Sequencher to provide a theoretical cDNA
sequence (designated herein as DNA34415). GRAIL2 (ApoCom Inc.,
Knoxville, Tenn., command line version for the DEC alpha) was used
to predict a novel exon. The five known genes in the region served
as internal controls for the success of the GRAIL algorithm.
[0489] Isolation
[0490] Chordin cDNA clones were isolated from an oligo-dT-primed
human fetal lung library. Human fetal lung polyA.sup.+ RNA was
purchased from Clontech (cat #6528-1, lot #43777) and 5 mg used to
construct a cDNA library in pKR5B (Genentech, LIB26). The 3'-primer
(pGACTAGTTCTAGATCGCGAGCGGCCGCCCTTTTTTTTTTTTTTT) (SEQ ID NO:8) and
the 5'-linker (pCGGACGCGTGGGGCCTGCGCACCCAGCT) (SEQ ID NO:9) were
designed to introduce SalI and NotI restriction sites. Clones were
screened with oligonucleotide probes designed from the putative
human chordin cDNA sequence (DNA34415) deduced by manually
"splicing" together the proposed genomic exons of the gene. PCR
primers flanking the probes were used to confirm the identity of
the cDNA clones prior to sequencing.
[0491] The screening oligonucleotides probes were the
following:
11 The screening oligonucleotides probes were the following:
OLI5640 34415.p1 5'-GCCGCTCCCCGAACGGGCAGCGGCTCCTTCTCAGAA-3' (SEQ ID
NO:10) and OLI5642 34415.p2 5'-GGCGCACAGCACGCAGCGCATCACC-
CCGAATGGCTC-3' (SEQ ID NO:11); and the flanking probes used were
the following: OLI5639 34415.f1 5'-GTGCTGCCCATCCGTTCTGA- GAAGGA-3'
(SEQ ID NO:12) and OLI5643 34415.r 5'-GCAGGGTGCTCAAACAGGACAC-3'
(SEQ ID NO:13).
EXAMPLE 5
Northern Blot and in situ RNA Hybridization Analysis of PRO243
[0492] Expression of PRO243 mRNA in human tissues was examined by
Northern blot analysis. Human polyA+RNA blots derived from human
fetal and adult tissues (Clontech, Palo Alto, Calif.; Cat. Nos.
7760-1 and 7756-1) were hybridized to a .sup.32P-labelled cDNA
fragments probe based on the full length PRO243 cDNA. Blots were
incubated with the probes in hybridization buffer (5.times.SSPE; 2X
Denhardt's solution; 100 mg/mL denatured sheared salmon sperm DNA;
50% formamide; 2% SDS) for 60 hours at 42.degree. C. The blots were
washed several times in 2.times.SSC; 0.05% SDS for 1 hour at room
temperature, followed by a high stringency wash 30 minute wash in
0.1.times.SSC; 0.1% SDS at 50.degree. C and autoradiographed. The
blots were developed after overnight exposure by phosphorimager
analysis (Fuji).
[0493] PRO243 mRNA transcripts were detected. Analysis of the
expression pattern showed the strongest signal of the expected 4.0
kb transcript in adult and fetal liver and a very faint signal in
the adult kidney. Fetal brain, lung and kidney were negative, as
were adult heart, brain, lung and pancreas. Smaller transcripts
were observed in placenta (2.0 kb), adult skeletal muscle (1.8 kb)
and fetal liver (2.0 kb).
[0494] In situ hybridization of adult human tissue of PRO243 gave a
positive signal in the cleavage line of the developing synovial
joint forming between the femoral head and acetabulum. All other
tissues were negative. Additional sections of human fetal face,
head, limbs and mouse embryos were examined. Expression in human
fetal tissues was observed adjacent to developing limb and facial
bones in the perosteal msenchyme. The expression was highly
specific and was often adjacent to areas undergoing
vascularization. Expression was also observed in the developing
temporal and occipital lobes of the fetal brain, but was not
observed elsewhere in the brain. In addition, expression was seen
in the ganglia of the developing inner ear. No expression was seen
in any of the mouse tissues with the human probes.
[0495] In situ hybridization was performed using an optimized
protocol, using PCR-generating .sup.33P-labeled riboprobes. (Lu and
Gillett, Cell Vision 1: 169-176 (1994)). Formalin-fixed,
paraffin-embedded human fetal and adult tissues were sectioned,
deparaffinized, deproteinated in proteinase K (20 g/ml) for 15
minutes at 37.degree. C., and further processed for in situ
hybridization as described by Lu and Gillett (1994). A
[.sup.33P]-UTP-labeled antisense riboprobe was generated from a PCR
product and hybridized at 55.degree. C. overnight. The slides were
dipped in Kodak NTB2 nuclear track emulsion and exposed for 4
weeks.
EXAMPLE 6
Isolation of cDNA Clones Encoding Human PRO299
[0496] A cDNA sequence designated herein as DNA28847 (FIG. 7; SEQ
ID NO:18) was isolated as described in Example 2 above. After
further analysis, a 3' truncated version of DNA28847 was found and
is herein designated DNA35877 (FIG. 8; SEQ ID NO:19). Based on the
DNA35877 sequence, oligonucleotides were synthesized: 1) to
identify by PCR a cDNA library that contained the sequence of
interest, and 2) for use as probes to isolate a clone of the
full-length coding sequence for PRO299. Forward and reverse PCR
primers generally range from 20 to 30 nucleotides and are often
designed to give a PCR product of about 100-1000 bp in length. The
probe sequences are typically 40-55 bp in length. In some cases,
additional oligonucleotides are synthesized when the consensus
sequence is greater than about 1-1.5 kbp. In order to screen
several libraries for a full-length clone, DNA from the libraries
was screened by PCR amplification, as per Ausubel et al., Current
Protocols in Molecular Biology, with the PCR primer pair. A
positive library was then used to isolate clones encoding the gene
of interest using the probe oligonucleotide and one of the primer
pairs.
[0497] Forward and reverse PCR primers were synthesized:
12 forward PCR primer 5'-CTCTGGAAGGTCACGGCCACAGG-3' (SEQ ID NO:20)
reverse PCR primer 5'-CTCAGTTCGGTTGGCAAAGCTCTC-3' (SEQ ID
NO:21)
[0498] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the DNA35877 sequence which had the
following nucleotide sequence
13 hybridization probe 5'-CAGTGCTCCCTCATAGATGGACGAAAGTGTGA-
CCCCCCTTTCAGGCGAGAGCTTTGCCAACCG (SEQ ID NO:22) AACTGA-3'
[0499] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with one of the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO299 sequence using the probe oligonucleotide.
[0500] RNA for construction of the cDNA libraries was isolated from
human fetal brain tissue. The cDNA libraries used to isolate the
cDNA clones were constructed by standard methods using commercially
available reagents such as those from Invitrogen, San Diego, Calif.
The cDNA was primed with oligo dT containing a NotI site, linked
with blunt to SalI hemikinased adaptors, cleaved with NotI, sized
appropriately by gel electrophoresis, and cloned in a defined
orientation into a suitable cloning vector (such as pRKB or pRKD;
pRK5B is a precursor of pRK5D that does not contain the SfiI site;
see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique
XhoI and NotI sites.
[0501] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO299 [herein designated as
DNA39976-1215] (SEQ ID NO:14) and the derived protein sequence for
PRO299.
[0502] The entire nucleotide sequence of DNA39976-1215 is shown in
FIG. 5 (SEQ ID NO:14). Clone DNA39976-1215 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 111-113 and ending at the stop codon at
nucleotide positions 2322-2324 (FIG. 5). The predicted polypeptide
precursor is 737 amino acids long (FIG. 6). Important regions of
the polypeptide sequence encoded by clone DNA39976-1215 have been
identified and include the following: a signal peptide
corresponding to amino acids 1-28, a putative transmembrane region
corresponding to amino acids 638-662, 10 EGF repeats, corresponding
to amino acids 80-106, 121-203, 336-360, 378-415, 416-441, 454-490,
491-528, 529-548, 567-604, and 605-622, respectively, and 10
potential N-glycosylation sites, corresponding to amino acids
107-120, 204-207, 208-222, 223-285, 286-304, 361-374, 375-377,
442-453, 549-563, and respectively. Clone DNA39976-1215 has been
deposited with ATCC and is assigned ATCC deposit no. ATCC
209524.
[0503] Analysis of the amino acid sequence of the full-length
PRO299 polypeptide suggests that portions of it possess significant
homology to the notch protein, thereby indicating that PRO299 may
be a novel notch protein homolog and have activity typical of the
notch protein.
EXAMPLE 7
Isolation of cDNA Clones Encoding Human PRO323
[0504] A consensus DNA sequence was assembled relative to other EST
sequences as described in Example 1 above. This consensus sequence
is herein designated DNA30875. Based on the DNA30875 consensus
sequence, oligonucleotides were synthesized: 1) to identify by PCR
a cDNA library that contained the sequence of interest, and 2) for
use as probes to isolate a clone of the full-length coding sequence
for PRO323.
[0505] PCR primers (two forward and one reverse) were
synthesized:
14 forward PCR primer 1 5'-AGTTCTGGTCAGCCTATGTGCC-3' (SEQ ID NO:25)
forward PCR primer 2 5'-CGTGATGGTGTCTTTGTCCATGGG-3' (SEQ ID NO:26)
reverse PCR primer 5'-CTCCACCAATCCCGATGAACTTGG-- 3' (SEQ ID
NO:27)
[0506] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA30875 sequence which
had the following nucleotide sequence
15 hybridization probe 5'-GAGCAGATTGACCTCATACGCCGCATGTGTGC-
CTCCTATTCTGAGCTGGA-3' (SEQ ID NO:28)
[0507] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO323 gene using the probe oligonucleotide and one of the PCR
primers. RNA for construction of the cDNA libraries was isolated
from human fetal liver tissue (LIB6).
[0508] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO323 [herein designated as
DNA35595-12281] (SEQ ID NO:23) and the derived protein sequence for
PRO323.
[0509] The entire nucleotide sequence of DNA35595-1228 is shown in
FIG. 9 (SEQ ID NO:23). Clone DNA35595-1228 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 110-112 and ending at the stop codon at
nucleotide positions 1409-1411 (FIG. 9). The predicted polypeptide
precursor is 433 amino acids long (FIG. 10). The full-length PRO323
protein shown in FIG. 10 has an estimated molecular weight of about
47,787 daltons and a pI of about 6.11. Clone DNA35595-1228 has been
deposited with ATCC and is assigned ATCC deposit no. 209528.
[0510] Analysis of the amino acid sequence of the full-length
PRO323 polypeptide suggests that portions of it possess significant
homology to various dipeptidase proteins, thereby indicating that
PRO323 may be a novel dipeptidase protein.
EXAMPLE 8
Isolation of cDNA Clones Encoding Human PRO327
[0511] An expressed sequence tag (EST) DNA database (LIFESEQ.TM.,
Incyte Pharmaceuticals, Palo Alto, Calif.) was searched and various
EST sequences were identified which showed certain degrees of
homology to human prolactin receptor protein. Those EST sequences
were aligned using phrap and a consensus sequence was obtained.
This consensus DNA sequence was then extended using repeated cycles
of BLAST and phrap to extend the consensus sequence as far as
possible using the sources of EST sequences discussed above. The
extended assembly sequence is herein designated DNA38110. The above
searches were performed using the computer program BLAST or BLAST2
(Altshul et al., Methods in Enzymology 266:460-480 (1996)). Those
comparisons resulting in a BLAST score of 70 (or in some cases 90)
or greater that did not encode known proteins were clustered and
assembled into consensus DNA sequences with the program "phrap"
(Phil Green, University of Washington, Seattle, Wash.).
[0512] Based upon the DNA38110 consensus sequence obtained as
described above, oligonucleotides were synthesized: 1) to identify
by PCR a cDNA library that contained the sequence of interest, and
2) for use as probes to isolate a clone of the full-length coding
sequence for PRO327.
[0513] PCR primers (forward and reverse) were synthesized as
follows:
16 forward PCR primer 5'-CCCGCCCGACGTGCACGTGAGCC-3' (SEQ ID NO:33)
reverse PCR primer 5'-TGAGCCAGCCCAGGAACTGCTTG-3' (SEQ ID NO:34)
[0514] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA38110 consensus
sequence which had the following nucleotide sequence
17 hybridization probe 5'-CAAGTGCGCTGCAACCCCTTTGGCATCTATGG-
CTCCAAGAAAGCCGGGAT-3' (SEQ ID NO:35)
[0515] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with the PCR primer pair identified above. A positive
library was then used to isolate clones encoding the PRO327 gene
using the probe oligonucleotide and one of the PCR primers. RNA for
construction of the cDNA libraries was isolated from human fetal
lung tissue (LIB26).
[0516] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO327 [herein designated as
DNA38113-1230] (SEQ ID NO:16) and the derived protein sequence for
PRO327.
[0517] The entire nucleotide sequence of DNA38113-1230 is shown in
FIG. 13 (SEQ ID NO:31). Clone DNA38113-1230 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 119-121 and ending at the stop codon at
nucleotide positions 1385-1387 (FIG. 13). The predicted polypeptide
precursor is 422 amino acids long (FIG. 14). The full-length PRO327
protein shown in FIG. 14 has an estimated molecular weight of about
46,302 daltons and a pI of about 9.42. Clone DNA38113-1230 has been
deposited with ATCC and is assigned ATCC deposit no. ATCC
209530.
[0518] Analysis of the amino acid sequence of the full-length
PRO327 polypeptide suggests that it possess significant homology to
the human prolactin receptor protein, thereby indicating that
PRO327 may be a novel prolactin binding protein.
EXAMPLE 9
Isolation of cDNA Clones Encoding Human PRO233
[0519] A consensus DNA sequence was assembled relative to other EST
sequences as described in Example 1 above. This consensus sequence
is herein designated DNA30945. Based on the DNA30945 consensus
sequence, oligonucleotides were synthesized: 1) to identify by PCR
a cDNA library that contained the sequence of interest, and 2) for
use as probes to isolate a clone of the full-length coding sequence
for PRO233.
[0520] PCR primers were synthesized as followed:
18 forward PCR primer 5'-GGTGAAGGCAGAAATTGGAGATG-3' (SEQ ID NO:38)
reverse PCR primer 5'-ATCCCATGCATCAGCCTGTTTACC-3' (SEQ ID
NO:39)
[0521] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA30945 sequence which
had the following nucleotide sequence
19 hybridization probe 5'-GCTGGTGTAGTCTATACATCAGATTTGTTTGC-
TACACAAGATCCTCAG-3' (SEQ ID NO:40)
[0522] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with the PCR primer pair identified above. A positive
library was then used to isolate clones encoding the PRO233 gene
using the probe oligonucleotide. RNA for construction of the cDNA
libraries was isolated from human fetal brain tissue.
[0523] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO233 [herein designated as
DNA34436-1238] (SEQ ID NO:36) and the derived protein sequence for
PRO233.
[0524] The entire nucleotide sequence of DNA34436-1238 is shown in
FIG. 15 (SEQ ID NO:36). Clone DNA34436-1238 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 101-103 and ending at the stop codon at
nucleotide positions 1001-1003 (FIG. 15). The predicted polypeptide
precursor is 300 amino acids long (FIG. 16). The full-length PRO233
protein shown in FIG. 16 has an estimated molecular weight of about
32,964 daltons and a pI of about 9.52. In addition, regions of
interest including the signal peptide and a putative oxidoreductase
active site, are designated in FIG. 16. Clone DNA34436-1238 has
been deposited with ATCC and is assigned ATCC deposit no. ATCC
209523
[0525] Analysis of the amino acid sequence of the full-length
PRO233 polypeptide suggests that portions of it possess significant
homology to various reductase proteins, thereby indicating that
PRO233 may be a novel reductase.
EXAMPLE 10
Isolation of cDNA Clones Encoding Human PRO344
[0526] A consensus DNA sequence was assembled relative to other EST
sequences as described in Example 1 above. This consensus sequence
is herein designated DNA34398. Based on the DNA34398 consensus
sequences, oligonucleotides were synthesized: 1) to identify by PCR
a cDNA library that contained the sequence of interest, and 2) for
use as probes to isolate a clone of the full-length coding sequence
for PRO344.
[0527] Based on the DNA34398 consensus sequence, forward and
reverse PCR primers were synthesized as follows:
20 forward PCR primer (34398.f1) 5'-TACAGGCCCAGTCAGGACCAGGGG-3'
(SEQ ID NO:43) forward PCR primer (34398.f2)
5'-AGCCAGCCTCGCTCTCGG-3' (SEQ ID NO:44) forward PCR primer
(34398.f3) 5'-GTCTGCGATCAGGTCTGG-3' (SEQ ID NO:45) reverse PCR
primer (34398.r1) 5'-GAAAGAGGCAATGGATTCGC-3' (SEQ ID NO:46) reverse
PCR primer (34398.r2) 5'-GACTTACACTTGCCAGCACAGCAC-3- ' (SEQ ID
NO:47)
[0528] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the DNA34398 consensus sequence which
had the following nucleotide sequence
21 hybridization probe (34398.p1) 5'-GGAGCACCACCAACTGGAGG-
GTCCGGAGTAGCGAGCGCCCCGAAG-3' (SEQ ID NO:48)
[0529] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with one of the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO344 genes using the probe oligonucleotide and one of the PCR
primers. RNA for construction of the cDNA libraries was isolated
from human fetal kidney tissue.
[0530] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO344 [herein designated as
DNA40592-1242] (SEQ ID NO:41) and the derived protein sequence for
PRO344.
[0531] The entire nucleotide sequence of DNA40592-1242 is shown in
FIG. 17 (SEQ ID NO:41). Clone DNA40592-1242 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 227-229 and ending at the stop codon at
nucleotide positions 956-958 (FIG. 17). The predicted polypeptide
precursor is 243 amino acids long (FIG. 18). Important regions of
the native PRO344 amino acid sequence include the signal peptide,
the start of the mature protein, and two potential N-myristoylation
sites as shown in FIG. 18. Clone DNA40592-1242 has been deposited
with the ATCC and is assigned ATCC deposit no. ATCC 209492
[0532] Analysis of the amino acid sequence of the full-length
PRO344 polypeptides suggests that portions of them possess
significant homology to various human and murine complement
proteins, thereby indicating that PRO344 may be a novel complement
protein.
EXAMPLE 11
Isolation of cDNA Clones Encoding Human PRO347
[0533] A consensus DNA sequence was assembled relative to other EST
sequences as described in Example 1 above. This consensus sequence
is herein designated DNA39499. Based on the DNA39499 consensus
sequence, oligonucleotides were synthesized: 1) to identify by PCR
a cDNA library that contained the sequence of interest, and 2) for
use as probes to isolate a clone of the full-length coding sequence
for PRO347.
[0534] PCR primers (forward and reverse) were synthesized as
follows:
22 forward PCR primer 5'-AGGAACTTCTGGATCGGGCTCACC-3' (SEQ ID NO:51)
reverse PCR primer 5'-GGGTCTGGGCCAGGTGGAAGAGAG-3' (SEQ ID
NO:52)
[0535] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA39499 sequence which
had the following nucleotide sequence
23 hybridization probe 5'-GCCAAGGACTCCTTCCGCTGGGCCACAGGGGA-
GCACCAGGCCTTC-3' (SEQ ID NO:53)
[0536] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with the PCR primer pair identified above. A positive
library was then used to isolate clones encoding the PRO347 gene
using the probe oligonucleotide and one of the PCR primers. RNA for
construction of the cDNA libraries was isolated from human fetal
kidney tissue (LIB228).
[0537] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO347 [herein designated as
DNA44176-1244] (SEQ ID NO:49) and the derived protein sequence for
PRO347.
[0538] The entire nucleotide sequence of DNA44176-1244 is shown in
FIG. 19 (SEQ ID NO:49). Clone DNA44176-1244 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 123-125 and ending at the stop codon at
nucleotide positions 1488-1490 (FIG. 19). The predicted polypeptide
precursor is 455 amino acids long (FIG. 20). The full-length PRO347
protein shown in FIG. 20 has an estimated molecular weight of about
50,478 daltons and a pI of about 8.44. Clone DNA44176-1244 has been
deposited with ATCC and is assigned ATCC deposit no. ATCC
209532
[0539] Analysis of the amino acid sequence of the full-length
PRO347 polypeptide suggests that portions of it possess significant
homology to various cysteine-rich secretory proteins, thereby
indicating that PRO347 may be a novel cysteine-rich secretory
protein
EXAMPLE 12
Isolation of cDNA Clones Encoding Human PRO354
[0540] An expressed sequence tag (EST) DNA database (LIFESEQ.TM.,
Incyte Pharmaceuticals, Palo Alto, Calif.) was searched and various
EST sequences were identified which possessed certain degress of
homology with the inter-alpha-trypsin inhibitor heavy chain and
with one another. Those homologous EST sequences were then aligned
and a consensus sequence was obtained. The obtained consensus DNA
sequence was then extended using repeated cycles of BLAST and phrap
to extend the consensus sequence as far as possible using
homologous EST sequences derived from both public EST databases
(e.g., GenBank) and a proprietary EST DNA database (LIFESEQ.TM.,
Incyte Pharmaceuticals, Palo Alto, Calif.). The extended assembly
sequence is herein designated DNA39633. The above searches were
performed using the computer program BLAST or BLAST2 (Altshul et
al., Methods in Enzymology 266:460-480 (1996)). Those comparisons
resulting in a BLAST score of 70 (or in some cases 90) or greater
that did not encode known proteins were clustered and assembled
into consensus DNA sequences with the program "phrap" (Phil Green,
University of Washington, Seattle, Wash.).
[0541] Based on the DNA39633 consensus sequence, oligonucleotides
were synthesized: 1) to identify by PCR a cDNA library that
contained the sequence of interest, and 2) for use as probes to
isolate a clone of the full-length coding sequence for PRO354.
Forward and reverse PCR primers generally range from 20 to 30
nucleotides and are often designed to give a PCR product of about
100-1000 bp in length. The probe sequences are typically 40-55 bp
in length. In some cases, additional oligonucleotides are
synthesized when the consensus sequence is greater than about
1-1.5kbp. In order to screen several libraries for a full-length
clone, DNA from the libraries was screened by PCR amplification, as
per Ausubel et al., Current Protocols in Molecular Biology, with
the PCR primer pair. A positive library was then used to isolate
clones encoding the gene of interest using the probe
oligonucleotide and one of the primer pairs.
[0542] PCR primers were synthesized as follows:
24 forward PCR primer 1 (39633.f1) 5'-GTGGGAACCAAACTCCGGCAGACC-3'
(SEQ ID NO:56) forward PCR primer 2 (39633.f2)
5'-CACATCGAGCGTCTCTGG-3' (SEQ ID NO:57) reverse PCR primer
(39633.r1) 5'-AGCCGCTCCTTCTCCGGTTCATCG-3' (SEQ ID NO:58)
[0543] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA39633 sequence which
had the following nucleotide sequence
25 hybridization probe 5'-TGGAAGGACCACTTGATATCAGTCACTCCAGA-
CAGCATCAGGGATGGG-3' (SEQ ID NO:59)
[0544] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO354 gene using the probe oligonucleotide and one of the PCR
primers.
[0545] RNA for construction of the cDNA libraries was isolated from
human fetal kidney tissue (LIB227). The cDNA libraries used to
isolate the cDNA clones were constructed by standard methods using
commercially available reagents such as those from Invitrogen, San
Diego, Calif. The cDNA was primed with oligo dT containing a NotI
site, linked with blunt to SalI hemikinased adaptors, cleaved with
NotI, sized appropriately by gel electrophoresis, and cloned in a
defined orientation into a suitable cloning vector (such as pRKB or
pRKD; pRK5B is a precursor of pRK5D that does not contain the SfiI
site; see, Holmes et al., Science, 253:1278-1280 (1991)) in the
unique XhoI and NotI sites.
[0546] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO354 [herein designated as
DNA44192-12461] ((SEQ ID NO:54) and the derived protein sequence
for PRO354.
[0547] The entire nucleotide sequence of DNA44192-1246 is shown in
FIG. 21 (SEQ ID NO:54). Clone DNA44192-1246 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 72-74 and ending at the stop codon at
nucleotide positions 2154-2156 (FIG. 21). The predicted polypeptide
precursor is 694 amino acids long (FIG. 22). The full-length PRO354
protein shown in FIG. 22 has an estimated molecular weight of about
77,400 daltons and a pI of about 9.54. Clone DNA44192-1246 has been
deposited with ATCC and is assigned ATCC deposit no. ATCC
209531.
[0548] Analysis of the amino acid sequence of the full-length
PRO354 polypeptide suggests that it possess significant homology to
the inter-alpha-trypsin inhibitor heavy chain protein, thereby
indicating that PRO354 may be a novel inter-alpha-trypsin inhibitor
heavy chain protein homolog.
EXAMPLE 13
Isolation of cDNA Clones Encoding Human PRO355
[0549] A consensus DNA sequence was assembled relative to other EST
sequences using BLAST and phrap as described in Example 1 above.
This consensus sequence is herein designated DNA35702. Based on the
DNA35702 consensus sequence, oligonucleotides were synthesized: 1)
to identify by PCR a cDNA library that contained the sequence of
interest, and 2) for use as probes to isolate a clone of the
full-length coding sequence for PRO355.
[0550] Forward and reverse PCR primers were synthesized as
follows:
26 forward PCR primer 5'-GGCTTCTGCTGTTGCTCTTCTCCG-3' (SEQ ID NO:62)
forward PCR primer 5'-GTACACTGTGACCAGTCAGC-3' (SEQ ID NO:63)
forward PCR primer 5'-ATCATCACAGATTCCCGAGC-3' (SEQ ID NO:64)
reverse PCR primer 5'-TTCAATCTCCTCACCTTCCACCGC-- 3' (SEQ ID NO:65)
reverse PCR primer 5'-ATAGCTGTGTCTGCGTCTGCTGCG-3' (SEQ ID
NO:66)
[0551] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA35702 sequence which
had the following nucleotide sequence:
27 hybridization probe 5'-CGCGGCACTGATCCCCACAGGTGATGGGCAGA-
ATCTGTTTACGAAAGACG-3' (SEQ ID NO:67)
[0552] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with one of the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO355 gene using the probe oligonucleotide. RNA for construction
of the cDNA libraries was isolated from human fetal liver
tissue.
[0553] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO355 [herein designated as
DNA39518-1247] (SEQ ID NO:60) and the derived protein sequence for
PRO355.
[0554] The entire nucleotide sequence of DNA39518-1247 is shown in
FIG. 23 (SEQ ID NO:60). Clone DNA39518-1247 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 22-24 and ending at the stop codon at
nucleotide positions 1342-1344 (FIG. 23). The predicted polypeptide
precursor is 440 amino acids long (FIG. 24). The full-length PRO355
protein shown in FIG. 24 has an estimated molecular weight of about
48,240 daltons and a pI of about 4.93. In addition, regions of
interest including the signal peptide, Ig repeats in the
extracellular domain, potential N-glycosylation sites, and the
potential transmembrane domain, are designated in FIG. 24. Clone
DNA39518-1247 has been deposited with ATCC and is assigned ATCC
deposit no. ATCC 209529.
[0555] Analysis of the amino acid sequence of the full-length
PRO355 polypeptide suggests that portions of it possess significant
homology to the CRTAM protein, thereby indicating that PRO355 may
be CRTAM protein.
EXAMPLE 14
Isolation of cDNA Clones Encoding Human PRO357
[0556] The sequence expression tag clone no. "2452972" by Incyte
Pharmaceuticals, Palo Alto, Calif. was used to begin a data base
search. The extracellular domain (ECD) sequences (including the
secretion signal, if any) of from about 950 known secreted proteins
from the Swiss-Prot public protein database were used to search
expressed sequence tag (EST) databases which overlapped with a
portion of Incyte EST clone no. "2452972". The EST databases
included public EST databases (e.g., GenBank) and a proprietary EST
DNA database (LIFESEQ.TM., Incyte Pharmaceuticals, Palo Alto,
Calif.). The search was performed using the computer program BLAST
or BLAST2 (Altshul et al., Methods in Enzymology 266:460-480
(1996)) as a comparison of the ECD protein sequences to a 6 frame
translation of the EST sequence. Those comparisons resulting in a
BLAST score of 70 (or in some cases 90) or greater that did not
encode known proteins were clustered and assembled into consensus
DNA sequences with the program "phrap" (Phil Green, University of
Washington, Seattle, Wash.).
[0557] A consensus DNA sequence was then assembled relative to
other EST sequences using phrap. This consensus sequence is herein
designated DNA37162. In this case, the consensus DNA sequence was
extended using repeated cycles of BLAST and phrap to extend the
consensus sequence as far as possible using the sources of EST
sequences discussed above.
[0558] Based on the DNA37162 consensus sequence, oligonucleotides
were synthesized: 1) to identify by PCR a cDNA library that
contained the sequence of interest, and 2) for use as probes to
isolate a clone of the full-length coding sequence for PRO357.
Forward and reverse PCR primers generally range from 20 to 30
nucleotides and are often designed to give a PCR product of about
100-1000 bp in length. The probe sequences are typically 40-55 bp
in length. In some cases, additional oligonucleotides are
synthesized when the consensus sequence is greater than about 1-1.5
kbp. In order to screen several libraries for a full-length clone,
DNA from the libraries was screened by PCR amplification, as ber
Ausubel et al., Current Protocols in Molecular Biology, with the
PCR primer pair. A positive library was then used to isolate clones
encoding the gene of interest using the probe oligonucleotide and
one of the primer pairs.
[0559] PCR primers were synthesized as follows:
28 forward primer 1: 5'-CCCTCCACTGCCCCACCGACTG-3' (SEQ ID NO:70);
reverse primer 1: 5'-CGGTTCTGGGGACGTTAGGGCTCG-3' (SEQ ID NO:71);
and forward primer 2: 5'-CTGCCCACCGTCCACCTGCCTCAA- T-3' (SEQ ID
NO:72).
[0560] Additionally, two synthetic oligonucleotidehybridization
probes were constructed from the consensus DNA37162 sequence which
had the following nucleotide sequences:
29 hybridization probe 1: 5'-AGGACTGCCCACCGTCCACC-
TGCCTCAATGGGGGCACATGCCACC-3' (SEQ ID NO:73); and hybridization
probe 2: 5'-ACGCAAAGCCCTACATCTAAGCCAGAGAGAG- ACAGGGCAGCTGGG-3' (SEQ
ID NO:74).
[0561] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with a PCR primer pair identified above. A positive
library was then used to isolate clones encoding the PRO357 gene
using the probe oligonucleotide and one of the PCR primers.
[0562] RNA for construction of the cDNA libraries was isolated from
human fetal liver tissue. The cDNA libraries used to isolate the
cDNA clones were constructed by standard methods using commercially
available reagents such as those from Invitrogen, San Diego, Calif.
The cDNA was primed with oligo dT containing a NotI site, linked
with blunt to SalI hemikinased adaptors, cleaved with NotI, sized
appropriately by gel electrophoresis, and cloned in a defined
orientation into a suitable cloning vector (such as pRKB or pRKD;
pRK5B is a precursor of pRK5D that does not contain the SfiI site;
see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique
XhoI and NotI sites.
[0563] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO357 [herein designated as
DNA44804-1248] (SEQ ID NO:68) and the derived protein sequence for
PRO357.
[0564] The entire nucleotide sequence of DNA44804-1248 is shown in
FIG. 25 (SEQ ID NO:68). Clone DNA44804-1248 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 137-139 and ending at the stop codon at
nucleotide positions 1931-1933 (FIG. 25). The predicted polypeptide
precursor is 598 amino acids long (FIG. 26). Clone DNA44804-1248
has been deposited with ATCC and is assigned ATCC deposit no. ATCC
209527.
[0565] Analysis of the amino acid sequence of the full-length
PRO357 polypeptide therefore suggests that portions of it possess
significant homology to ALS, thereby indicating that PRO357 may be
a novel leucine rich repeat protein related to ALS.
EXAMPLE 15
Isolation of cDNA Clones Encoding Human PRO715
[0566] A proprietary EST DNA database (LIFESEQ.TM., Incyte
Pharmaceuticals, Palo Alto, Calif.) was searched for EST sequences
encoding polypeptides having homology to human TNF-.alpha.. This
search resulted in the identification of Incyte Expressed Sequence
Tag No. 2099855.
[0567] A consensus DNA sequence was then assembled relative to
other EST sequences using seqext and "phrap" (Phil Green,
University of Washington, Seattle, Wash.). This consensus sequence
is herein designated DNA52092. Based upon the alignment of the
various EST clones identified in this assembly, a single EST clone
from the Merck/Washington University EST set (EST clone no. 725887,
Accession No. AA292358) was obtained and its insert sequenced. The
full-length DNA52722-1229 sequence was then obtained from
sequencing the insert DNA from EST clone no. 725887.
[0568] The entire nucleotide sequence of DNA52722-1229 is shown in
FIG. 27 (SEQ ID NO:75). Clone DNA52722-1229 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 114-116 and ending at the stop codon at
nucleotide positions 864-866 (FIG. 27). The predicted polypeptide
is 250 amino acids long (FIG. 28). The full-length PRO715 protein
shown in FIG. 28 has an estimated molecular weight of about 27,433
daltons and a p1 of about 9.85.
[0569] Analysis of the amino acid sequence of the full-length
PRO715 polypeptide suggests that it possesses significant homology
to members of the tumor necrosis factor family of proteins, thereby
indicating that PRO715 is a novel tumor necrosis factor
protein.
EXAMPLE 16
Isolation of cDNA Clones Encoding Human PRO353
[0570] A consensus DNA sequence was assembled relative to other EST
sequences using phrap as described in Example 1 above. This
consensus sequences is herein designated DNA36363. The consensus
DNA sequence was extended using repeated cycles of BLAST and phrap
to extend the consensus sequence as far as possible using the
sources of EST sequences discussed above. Based on the DNA36363
consensus sequence, oligonucleotides were synthesized: 1) to
identify by PCR a cDNA library that contained the sequence of
interest, and 2) for use as probes to isolate a clone of the
full-length coding sequence for PRO353.
[0571] Based on the DNA36363 consensus sequence, forward and
reverse PCR primers were synthesized as follows:
30 forward PCR primer 5'-TACAGGCCCAGTCAGGACCAGGGG-3' (SEQ ID NO:79)
reverse PCR primer 5'-CTGAAGAAGTAGAGGCCGGGCACG-3' (SEQ ID
NO:80).
[0572] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the DNA36363 consensus sequence which
had the following nucleotide sequence:
31 hybridization probe 5'-CCCGGTGCTTGCGCTGCTGTGACCCCGGTACC-
TCCATGTACCCGG-3' (SEQ ID NO:81)
[0573] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with one of the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO353 gene using the probe oligonucleotide and one of the PCR
primers. RNA for construction of the cDNA libraries was isolated
from human fetal kidney tissue.
[0574] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO353 [herein designated as
DNA41234-1242] (SEQ ID NO:77) and the derived protein sequence for
PRO353.
[0575] The entire nucleotide sequence of DNA41234-1242 is shown in
FIG. 29 (SEQ ID NO:77). Clone DNA41234-1242 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 305-307 and ending at the stop codon at
nucleotide positions 1148-1150 (FIG. 29). The predicted polypeptide
precursor is 281 amino acids long (FIG. 30). Important regions of
the amino acid sequence encoded by PRO353 include the signal
peptide, corresponding to amino acids 1-26, the start of the mature
protein at amino acid position 27, a potential N-glycosylation
site, corresponding to amino acids 93-98 and a region which has
homology to a 30 kd adipocyte complement-related protein precursor,
corresponding to amino acids 99-281. Clone DNA41234-1242 has been
deposited with the ATCC and is assigned ATCC deposit no. ATCC
209618.
[0576] Analysis of the amino acid sequence of the full-length
PRO353 polypeptides suggests that portions of them possess
significant homology to portions of human and murine complement
proteins, thereby indicating that PRO353 may be a novel complement
protein.
EXAMPLE 17
Isolation of cDNA Clones Encoding Human PRO361
[0577] A consensus DNA sequence was assembled relative to other EST
sequences using phrap as described in Example 1 above. This
consensus sequence is herein designated DNA40654. Based on the
DNA40654 consensus sequence, oligonucleotides were synthesized: 1)
to identify by PCR a cDNA library that contained the sequence of
interest, and 2) for use as probes to isolate a clone of the
full-length coding sequence for PRO361.
[0578] Forward and reverse PCR primers were synthesized as
follows:
32 forward PCR primer 5'-AGGGAGGATTATCCTTGACCTTTGAAGACC-3' (SEQ ID
NO:84) forward PCR primer 5'-GAAGCAAGTGCCCAGCTC-3' (SEQ ID NO:85)
forward PCR primer 5'-CGGGTCCCTGCTCTTTGG-3' (SEQ ID NO:86) reverse
PCR primer 5'-CACCGTAGCTGGGAGCGCAC- TCAC-3' (SEQ ID NO:87) reverse
PCR primer 5'-AGTGTAAGTCAAGCTCCC-3' (SEQ ID NO:88)
[0579] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA40654 sequence which
had the following nucleotide sequence
33 hybridization probe 5'-GCTTCCTGACACTAAGGCTGTCTGCTAGTCAG-
AATTGCCTCAAAAAGAG-3' (SEQ ID NO:89)
[0580] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with one of the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO361 gene using the probe oligonucleotide. RNA for construction
of the cDNA libraries was isolated from human fetal kidney
tissue.
[0581] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO361 [herein designated as
DNA45410-1250] (SEQ ID NO:82) and the derived protein sequence for
PRO361.
[0582] The entire nucleotide sequence of DNA45410-1250 is shown in
FIG. 31 (SEQ ID NO:82). Clone DNA45410-1250 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 226-228 and ending at the stop codon at
nucleotide positions 1519-1521 (FIG. 31). The predicted polypeptide
precursor is 431 amino acids long (FIG. 32). The full-length PRO361
protein shown in FIG. 32 has an estimated molecular weight of about
46,810 daltons and a pI of about 6.45. In addition, regions of
interest including the transmembrane domain (amino acids 380-409)
and sequences typical of the arginase family of proteins (amino
acids 3-14 and 39-57) are designated in FIG. 32. Clone
DNA45410-1250 has been deposited with ATCC and is assigned ATCC
deposit no. ATCC 209621.
[0583] Analysis of the amino acid sequence of the full-length
PRO361 polypeptide suggests that portions of it possess significant
homology to the mucin and/or chitinase proteins, thereby indicating
that PRO361 may be a novel mucin and/or chitinase protein.
EXAMPLE 18
Isolation of cDNA Clones Encoding Human PRO365
[0584] A consensus DNA sequence was assembled relative to other EST
sequences using phrap as described in Example 1 above. This
consensus sequence is herein designated DNA35613. Based on the
DNA35613 consensus sequence, oligonucleotides were synthesized: 1)
to identify by PCR a cDNA library that contained the sequence of
interest, and 2) for use as probes to isolate a clone of the
full-length coding sequence for PRO365.
[0585] Forward and reverse PCR primers were synthesized as
follows:
34 forward PCR primer 5'-AATGTGACCACTGGACTCCC-3' (SEQ ID NO:92)
forward PCR primer 5'-AGGCTTGGAACTCCCTTC-3' (SEQ ID NO:93) reverse
PCR primer 5'-AAGATTCTTGAGCGATTCCAGCTG-3' (SEQ ID NO:94)
[0586] Additionally, a synthetic oligonucleotide hybridization
probe was constructed from the consensus DNA35613 sequence which
had the following nucleotide sequence
35 hybridization probe 5'-AATCCCTGCTCTTCATGGTGACCTATGACGAC-
GGAAGCACAAGACTG-3' (SEQ ID NO:95)
[0587] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with one of the PCR primer pairs identified above. A
positive library was then used to isolate clones encoding the
PRO365 gene using the probe oligonucleotide and one of the PCR
primers. RNA for construction of the cDNA libraries was isolated
from human fetal kidney tissue.
[0588] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO365 [herein designated as
DNA46777-1253] (SEQ ID NO:90) and the derived protein sequence for
PRO365.
[0589] The entire nucleotide sequence of DNA46777-1253 is shown in
FIG. 33 (SEQ ID NO:90). Clone DNA46777-1253 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 15-17 and ending at the stop codon at
nucleotide positions 720-722 (FIG. 33). The predicted polypeptide
precursor is 235 amino acids long (FIG. 34). Important regions of
the polypeptide sequence encoded by clone DNA46777-1253 have been
identified and include the following: a signal peptide
corresponding to amino acids 1-20, the start of the mature protein
corresponding to amino acid 21, and multiple potential
N-glycosylation sites as shown in FIG. 34. Clone DNA46777-1253 has
been deposited with ATCC and is assigned ATCC deposit no. ATCC
209619.
[0590] Analysis of the amino acid sequence of the full-length
PRO365 polypeptide suggests that portions of it possess significant
homology to the human 2-19 protein, thereby indicating that PRO365
may be a novel human 2-19 protein homolog.
EXAMPLE 19
Use of PRO Polypeptide-Encoding Nucleic Acid as Hybridization
Probes
[0591] The following method describes use of a nucleotide sequence
encoding PRO as a hybridization probe.
[0592] DNA comprising the coding sequence of full-length or mature
PRO as disclosed herein is employed as a probe to screen for
homologous DNAs (such as those encoding naturally-occurring
variants of PRO) in human tissue cDNA libraries or human tissue
genomic libraries.
[0593] Hybridization and washing of filters containing either
library DNAs is performed under the following high stringency
conditions. Hybridization of radiolabeled PRO-derived probe to the
filters is performed in a solution of 50% formamide, 5.times.SSC,
0.1% SDS, 0.1% sodium pyrophosphate, 50 mM sodium phosphate, pH
6.8, 2.times.Denhardt's solution, and 10% dextran sulfate at
42.degree. C. for 20 hours. Washing of the filters is performed in
an aqueous solution of 0.1.times.SSC and 0.1% SDS at 42.degree.
C.
[0594] DNAs having a desired sequence identity with the DNA
encoding full-length native sequence PRO can then be identified
using standard techniques known in the art.
EXAMPLE 20
Expression of PRO Polypeptides in E. coli
[0595] This example illustrates preparation of an unglycosylated
form of PRO by recombinant expression in E. coli.
[0596] The DNA sequence encoding PRO is initially amplified using
selected PCR primers. The primers should contain restriction enzyme
sites which correspond to the restriction enzyme sites on the
selected expression vector. A variety of expression vectors may be
employed. An example of a suitable vector is pBR322 (derived from
E. coli; see Bolivar et al., Gene 2:95 (1977)) which contains genes
for ampicillin and tetracycline resistance. The vector is digested
with restriction enzyme and dephosphorylated. The PCR amplified
sequences are then ligated into the vector. The vector will
preferably include sequences which encode for an antibiotic
resistance gene, a trp promoter, a polyhis leader (including the
first six STII codons, polyhis sequence, and enterokinase cleavage
site), the PRO coding region, lambda transcriptional terminator,
and an argU gene.
[0597] The ligation mixture is then used to transform a selected E.
coli strain using the methods described in Sambrook et al., supra.
Transformants are identified by their ability to grow on LB plates
and antibiotic resistant colonies are then selected. Plasmid DNA
can be isolated and confirmed by restriction analysis and DNA
sequencing.
[0598] Selected clones can be grown overnight in liquid culture
medium such as LB broth supplemented with antibiotics. The
overnight culture may subsequently be used to inoculate a larger
scale culture. The cells are then grown to a desired optical
density, during which the expression promoter is turned on.
[0599] After culturing the cells for several more hours, the cells
can be harvested by centrifugation. The cell pellet obtained by the
centrifugation can be solubilized using various agents known in the
art, and the solubilized PRO protein can then be purified using a
metal chelating column under conditions that allow tight binding of
the protein.
[0600] PRO may be expressed in E. coli in a poly-His tagged form,
using the following procedure. The DNA encoding PRO is initially
amplified using selected PCR primers. The primers will contain
restriction enzyme sites which correspond to the restriction enzyme
sites on the selected expression vector, and other useful sequences
providing for efficient and reliable translation initiation, rapid
purification on a metal chelation column, and proteolytic removal
with enterokinase. The PCR-amplified, poly-His tagged sequences are
then ligated into an expression vector, which is used to transform
an E. coli host based on strain 52 (W3110 fuhA(tonA) Ion galE
rpoHts(htpRts) clpP(lacIq). Transformants are first grown in LB
containing 50 mg/ml carbenicillin at 30.degree. C. with shaking
until an O.D.600 of 3-5 is reached. Cultures are then diluted
50-100 fold into CRAP media (prepared by mixing 3.57 g
(NH.sub.4).sub.2SO.sub.4, 0.71 g sodium citrateo.multidot.2H2O,
1.07 g KCl, 5.36 g Difco yeast extract, 5.36 g Sheffield hycase SF
in 500 mL water, as well as 110 mM MPOS, pH 7.3, 0.55% (w/v)
glucose and 7 mM MgSO.sub.4) and grown for approximately 20-30
hours at 30.degree. C. with shaking. Samples are removed to verify
expression by SDS-PAGE analysis, and the bulk culture is
centrifuged to pellet the cells. Cell pellets are frozen until
purification and refolding.
[0601] E. coli paste from 0.5 to 1 L fermentations (6-10 g pellets)
is resuspended in 10 volumes (w/v) in 7 M guanidine, 20 mM Tris, pH
8 buffer. Solid sodium sulfite and sodium tetrathionate is added to
make final concentrations of 0.1 M and 0.02 M, respectively, and
the solution is stirred overnight at 4 .degree. C. This step
results in a denatured protein with all cysteine residues blocked
by sulfitolization. The solution is centrifuged at 40,000 rpm in a
Beckman Ultracentifuge for 30 min. The supernatant is diluted with
3-5 volumes of metal chelate column buffer (6 M guanidine, 20 mM
Tris, pH 7.4) and filtered through 0.22 micron filters to clarify.
The clarified extract is loaded onto a 5 ml Qiagen Ni-NTA metal
chelate column equilibrated in the metal chelate column buffer. The
column is washed with additional buffer containing 50 mM imidazole
(Calbiochem, Utrol grade), pH 7.4. The protein is eluted with
buffer containing 250 mM imidazole. Fractions containing the
desired protein are pooled and stored at 4.degree. C. Protein
concentration is estimated by its absorbance at 280 nm using the
calculated extinction coefficient based on its amino acid
sequence.
[0602] The proteins are refolded by diluting the sample slowly into
freshly prepared refolding buffer consisting of: 20 mM Tris, pH
8.6, 0.3 M NaCl, 2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM
EDTA. Refolding volumes are chosen so that the final protein
concentration is between 50 to 100 micrograms/ml. The refolding
solution is stirred gently at 4.degree. C. for 12-36 hours. The
refolding reaction is quenched by the addition of TFA to a final
concentration of 0.4% (pH of approximately 3). Before further
purification of the protein, the solution is filtered through a
0.22 micron filter and acetonitrile is added to 2-10% final
concentration. The refolded protein is chromatographed on a Poros
R1/H reversed phase column using a mobile buffer of 0.1% TFA with
elution with a gradient of acetonitrile from 10 to 80%. Aliquots of
fractions with A280 absorbance are analyzed on SDS polyacrylamide
gels and fractions containing homogeneous refolded protein are
pooled. Generally, the properly refolded species of most proteins
are eluted at the lowest concentrations of acetonitrile since those
species are the most compact with their hydrophobic interiors
shielded from interaction with the reversed phase resin. Aggregated
species are usually eluted at higher acetonitrile concentrations.
In addition to resolving misfolded forms of proteins from the
desired form, the reversed phase step also removes endotoxin from
the samples.
[0603] Fractions containing the desired folded PRO polypeptide are
pooled and the acetonitrile removed using a gentle stream of
nitrogen directed at the solution. Proteins are formulated into 20
mM Hepes, pH 6.8 with 0.14 M sodium chloride and 4% mannitol by
dialysis or by gel filtration using G25 Superfine (Pharmacia)
resins equilibrated in the formulation buffer and sterile
filtered.
[0604] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
EXAMPLE 21
Expression of PRO Polypeptides in Mammalian Cells
[0605] This example illustrates preparation of a potentially
glycosylated form of PRO by recombinant expression in mammalian
cells.
[0606] The vector, pRK5 (see EP 307,247, published Mar. 15, 1989),
is employed as the expression vector. Optionally, the PRO DNA is
ligated into pRK5 with selected restriction enzymes to allow
insertion of the PRO DNA using ligation methods such as described
in Sambrook et al., supra. The resulting vector is called
pRK5-PRO.
[0607] In one embodiment, the selected host cells may be 293 cells.
Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue
culture plates in medium such as DMEM supplemented with fetal calf
serum and optionally, nutrient components and/or antibiotics. About
10 .mu.g pRK5-PRO DNA is mixed with about 1 .mu.g DNA encoding the
VA RNA gene [Thimmappaya et al., Cell, 31:543 (1982)] and dissolved
in 500 .mu.l of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCl.sub.2. To
this mixture is added, dropwise, 500 .mu.l of 50 mM HEPES (pH
7.35), 280 mM NaCl, 1.5 mM NaPO.sub.4, and a precipitate is allowed
to form for 10 minutes at 25.degree. C. The precipitate is
suspended and added to the 293 cells and allowed to settle for
about four hours at 37.degree. C. The culture medium is aspirated
off and 2 ml of 20% glycerol in PBS is added for 30 seconds. The
293 cells are then washed with serum free medium, fresh medium is
added and the cells are incubated for about 5 days.
[0608] Approximately 24 hours after the transfections, the culture
medium is removed and replaced with culture medium (alone) or
culture medium containing 200 .mu.Ci/ml .sup.35S-cysteine and 200
.mu.Ci/ml .sup.35S-methionine. After a 12 hour incubation, the
conditioned medium is collected, concentrated on a spin filter, and
loaded onto a 15% SDS gel. The processed gel may be dried and
exposed to film for a selected period of time to reveal the
presence of PRO polypeptide. The cultures containing transfected
cells may undergo further incubation (in serum free medium) and the
medium is tested in selected bioassays.
[0609] In an alternative technique, PRO may be introduced into 293
cells transiently using the dextran sulfate method described by
Somparyrac et al., Proc. Natl. Acad. Sci., 12:7575 (1981). 293
cells are grown to maximal density in a spinner flask and 700 .mu.g
pRK5-PRO DNA is added. The cells are first concentrated from the
spinner flask by centrifugation and washed with PBS. The
DNA-dextran precipitate is incubated on the cell pellet for four
hours. The cells are treated with 20% glycerol for 90 seconds,
washed with tissue culture medium, and re-introduced into the
spinner flask containing tissue culture medium, 5 .mu.g/ml bovine
insulin and 0.1 .mu.g/ml bovine transferrin. After about four days,
the conditioned media is centrifuged and filtered to remove cells
and debris. The sample containing expressed PRO can then be
concentrated and purified by any selected method, such as dialysis
and/or column chromatography.
[0610] In another embodiment, PRO can be expressed in CHO cells.
The pRK5-PRO can be transfected into CHO cells using known reagents
such as CaPO.sub.4 or DEAE-dextran. As described above, the cell
cultures can be incubated, and the medium replaced with culture
medium (alone) or medium containing a radiolabel such as
.sup.35S-methionine. After determining the presence of PRO
polypeptide, the culture medium may be replaced with serum free
medium. Preferably, the cultures are incubated for about 6 days,
and then the conditioned medium is harvested. The medium containing
the expressed PRO can then be concentrated and purified by any
selected method.
[0611] Epitope-tagged PRO may also be expressed in host CHO cells.
The PRO may be subcloned out of the pRK5 vector. The subclone
insert can undergo PCR to fuse in frame with a selected epitope tag
such as a poly-his tag into a Baculovirus expression vector. The
poly-his tagged PRO insert can then be subcloned into a SV40 driven
vector containing a selection marker such as DHFR for selection of
stable clones. Finally, the CHO cells can be transfected (as
described above) with the SV40 driven vector. Labeling may be
performed, as described above, to verify expression. The culture
medium containing the expressed poly-His tagged PRO can then be
concentrated and purified by any selected method, such as by
Ni.sup.2+-chelate affinity chromatography.
[0612] PRO may also be expressed in CHO and/or COS cells by a
transient expression procedure or in CHO cells by another stable
expression procedure.
[0613] Stable expression in CHO cells is performed using the
following procedure. The proteins are expressed as an IgG construct
(immunoadhesin), in which the coding sequences for the soluble
forms (e.g. extracellular domains) of the respective proteins are
fused to an IgGI constant region sequence containing the hinge, CH2
and CH2 domains and/or is a poly-His tagged form.
[0614] Following PCR amplification, the respective DNAs are
subcloned in a CHO expression vector using standard techniques as
described in Ausubel et al., Current Protocols of Molecular
Biology, Unit 3.16, John Wiley and Sons (1997). CHO expression
vectors are constructed to have compatible restriction sites 5' and
3' of the DNA of interest to allow the convenient shuttling of
cDNA's. The vector used expression in CHO cells is as described in
Lucas et al., Nucl. Acids Res. 24:9 (1774-1779 (1996), and uses the
SV40 early promoter/enhancer to drive expression of the cDNA of
interest and dihydrofolate reductase (DHFR). DHFR expression
permits selection for stable maintenance of the plasmid following
transfection.
[0615] Twelve micrograms of the desired plasmid DNA is introduced
into approximately 10 million CHO cells using commercially
available transfection reagents Superfect.RTM. (Quiagen),
Dosper.RTM. or Fugene.RTM. (Boehringer Mannheim). The cells are
grown as described in Lucas et al., supra. Approximately
3.times.10.sup.-7 cells are frozen in an ampule for further growth
and production as described below.
[0616] The ampules containing the plasmid DNA are thawed by
placement into water bath and mixed by vortexing. The contents are
pipetted into a centrifuge tube containing 10 mLs of media and
centrifuged at 1000 rpm for 5 minutes. The supernatant is aspirated
and the cells are resuspended in 10 mL of selective media (0.2
.mu.m filtered PS20 with 5% 0.2 .mu.m diafiltered fetal bovine
serum). The cells are then aliquoted into a 100 mL spinner
containing 90 mL of selective media. After 1-2 days, the cells are
transferred into a 250 mL spinner filled with 150 mL selective
growth medium and incubated at 37.degree. C. After another 2-3
days, 250 mL, 500 mL and 2000 mL spinners are seeded with
3.times.10.sup.5 cells/mL. The cell media is exchanged with fresh
media by centrifugation and resuspension in production medium.
Although any suitable CHO media may be employed, a production
medium described in U.S. Pat. No. 5,122,469, issued Jun. 16, 1992
may actually be used. A 3L production spinner is seeded at
1.2.times.10.sup.6 cells/mL. On day 0, the cell number pH ie
determined. On day 1, the spinner is sampled and sparging with
filtered air is commenced. On day 2, the spinner is sampled, the
temperature shifted to 33.degree. C., and 30 mL of 500 g/L glucose
and 0.6 mL of 10% antifoam (e.g., 35% polydimethylsiloxane
emulsion, Dow Corning 365 Medical Grade Emulsion) taken. Throughout
the production, the pH is adjusted as necessary to keep it at
around 7.2. After 10 days, or until the viability dropped below
70%, the cell culture is harvested by centrifugation and filtering
through a 0.22 .mu.m filter. The filtrate was either stored at
4.degree. C. or immediately loaded onto columns for
purification.
[0617] For the poly-His tagged constructs, the proteins are
purified using a Ni-NTA column (Qiagen). Before purification,
imidazole is added to the conditioned media to a concentration of 5
mM. The conditioned media is pumped onto a 6 ml Ni-NTA column
equilibrated in 20 mM Hepes, pH 7.4, buffer containing 0.3 M NaCl
and 5 mM imidazole at a flow rate of 4-5 ml/min. at 4.degree. C.
After loading, the column is washed with additional equilibration
buffer and the protein eluted with equilibration buffer containing
0.25 M imidazole. The highly purified protein is subsequently
desalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCl
and 4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia)
column and stored at -80.degree. C.
[0618] Immunoadhesin (Fc-containing) constructs are purified from
the conditioned media as follows. The conditioned medium is pumped
onto a 5 ml Protein A column (Pharmacia) which had been
equilibrated in 20 mM Na phosphate buffer, pH 6.8. After loading,
the column is washed extensively with equilibration buffer before
elution with 100 mM citric acid, pH 3.5. The eluted protein is
immediately neutralized by collecting 1 ml fractions into tubes
containing 275 .mu.L of 1 M Tris buffer, pH 9. The highly purified
protein is subsequently desalted into storage buffer as described
above for the poly-His tagged proteins. The homogeneity is assessed
by SDS polyacrylamide gels and by N-terminal amino acid sequencing
by Edman degradation.
[0619] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
EXAMPLE 22
Expression of PRO in Yeast
[0620] The following method describes recombinant expression of PRO
in yeast.
[0621] First, yeast expression vectors are constructed for
intracellular production or secretion of PRO from the ADH2/GAPDH
promoter. DNA encoding PRO and the promoter is inserted into
suitable restriction enzyme sites in the selected plasmid to direct
intracellular expression of PRO. For secretion, DNA encoding PRO
can be cloned into the selected plasmid, together with DNA encoding
the ADH2/GAPDH promoter, a native PRO signal peptide or other
mammalian signal peptide, or, for example, a yeast alpha-factor or
invertase secretory signal/leader sequence, and linker sequences
(if needed) for expression of PRO.
[0622] Yeast cells, such as yeast strain AB110, can then be
transformed with the expression plasmids described above and
cultured in selected fermentation media. The transformed yeast
supernatants can be analyzed by precipitation with 10%
trichloroacetic acid and separation by SDS-PAGE, followed by
staining of the gels with Coomassie Blue stain.
[0623] Recombinant PRO can subsequently be isolated and purified by
removing the yeast cells from the fermentation medium by
centrifugation and then concentrating the medium using selected
cartridge filters. The concentrate containing PRO may further be
purified using selected column chromatography resins.
[0624] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
EXAMPLE 23
Expression of PRO in Baculovirus-Infected Insect Cells
[0625] The following method describes recombinant expression of PRO
in Baculovirus-infected insect cells.
[0626] The sequence coding for PRO is fused upstream of an epitope
tag contained within a baculovirus expression vector. Such epitope
tags include poly-his tags and immunoglobulin tags (like Fc regions
of IgG). A variety of plasmids may be employed, including plasmids
derived from commercially available plasmids such as pVL1393
(Novagen). Briefly, the sequence encoding PRO or the desired
portion of the coding sequence of PRO such as the sequence encoding
the extracellular domain of a transmembrane protein or the sequence
encoding the mature protein if the protein is extracellular is
amplified by PCR with primers complementary to the 5' and 3'
regions. The 5' primer may incorporate flanking (selected)
restriction enzyme sites. The product is then digested with those
selected restriction enzymes and subcloned into the expression
vector.
[0627] Recombinant baculovirus is generated by co-transfecting the
above plasmid and BaculoGold.TM. virus DNA (Pharmingen) into
Spodoptera frugiperda ("Sf9") cells (ATCC CRL 1711) using
lipofectin (commercially available from GIBCO-BRL). After 4-5 days
of incubation at 28.degree. C., the released viruses are harvested
and used for further amplifications. Viral infection and protein
expression are performed as described by O'Reilley et al.,
Baculovirus expression vectors: A Laboratory Manual, Oxford: Oxford
University Press (1994).
[0628] Expressed poly-his tagged PRO can then be purified, for
example, by Ni.sup.2+-chelate affinity chromatography as follows.
Extracts are prepared from recombinant virus-infected Sf9 cells as
described by Rupert et al., Nature, 362:175-179 (1993). Briefly,
Sf9 cells are washed, resuspended in sonication buffer (25 mL
Hepes, pH 7.9; 12.5 mM MgCl.sub.2; 0.1 mM EDTA; 10% glycerol; 0.1%
NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice. The
sonicates are cleared by centrifugation, and the supernatant is
diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl,
10% glycerol, pH 7.8) and filtered through a 0.45 .mu.m filter. A
Ni.sup.2+-NTA agarose column (commercially available from Qiagen)
is prepared with a bed volume of 5 mL, washed with 25 mL of water
and equilibrated with 25 mL of loading buffer. The filtered cell
extract is loaded onto the column at 0.5 mL per minute. The column
is washed to baseline A.sub.280 with loading buffer, at which point
fraction collection is started. Next, the column is washed with a
secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% glycerol,
pH 6.0), which elutes nonspecifically bound protein. After reaching
A.sub.280 baseline again, the column is developed with a 0 to 500
mM Imidazole gradient in the secondary wash buffer. One mL
fractions are collected and analyzed by SDS-PAGE and silver
staining or Western blot with Ni.sup.2+-NTA-conjugated to alkaline
phosphatase (Qiagen). Fractions containing the eluted
His.sub.10-tagged PRO are pooled and dialyzed against loading
buffer.
[0629] Alternatively, purification of the IgG tagged (or Fc tagged)
PRO can be performed using known chromatography techniques,
including for instance, Protein A or protein G column
chromatography.
[0630] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
EXAMPLE 24
Preparation of Antibodies that Bind PRO
[0631] This example illustrates preparation of monoclonal
antibodies which can specifically bind PRO.
[0632] Techniques for producing the monoclonal antibodies are known
in the art and are described, for instance, in Goding, supra.
Immunogens that may be employed include purified PRO, fusion
proteins containing PRO, and cells expressing recombinant PRO on
the cell surface. Selection of the immunogen can be made by the
skilled artisan without undue experimentation.
[0633] Mice, such as Balb/c, are immunized with the PRO immunogen
emulsified in complete Freund's adjuvant and injected
subcutaneously or intraperitoneally in an amount from 1-100
micrograms. Alternatively, the immunogen is emulsified in MPL-TDM
adjuvant (Ribi Immunochemical Research, Hamilton, Mont.) and
injected into the animal's hind foot pads. The immunized mice are
then boosted 10 to 12 days later with additional immunogen
emulsified in the selected adjuvant. Thereafter, for several weeks,
the mice may also be boosted with additional immunization
injections. Serum samples may be periodically obtained from the
mice by retro-orbital bleeding for testing in ELISA assays to
detect anti-PRO antibodies.
[0634] After a suitable antibody titer has been detected, the
animals "positive" for antibodies can be injected with a final
intravenous injection of PRO. Three to four days later, the mice
are sacrificed and the spleen cells are harvested. The spleen cells
are then fused (using 35% polyethylene glycol) to a selected murine
myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL
1597. The fusions generate hybridoma cells which can then be plated
in 96 well tissue culture plates containing HAT (hypoxanthine,
aminopterin, and thymidine) medium to inhibit proliferation of
non-fused cells, myeloma hybrids, and spleen cell hybrids.
[0635] The hybridoma cells will be screened in an ELISA for
reactivity against PRO. Determination of "positive" hybridoma cells
secreting the desired monoclonal antibodies against PRO is within
the skill in the art.
[0636] The positive hybridoma cells can be injected
intraperitoneally into syngeneic Balb/c mice to produce ascites
containing the anti-PRO monoclonal antibodies. Alternatively, the
hybridoma cells can be grown in tissue culture flasks or roller
bottles. Purification of the monoclonal antibodies produced in the
ascites can be accomplished using ammonium sulfate precipitation,
followed by gel exclusion chromatography. Alternatively, affinity
chromatography based upon binding of antibody to protein A or
protein G can be employed.
EXAMPLE 25
Purification of PRO Polypeptides Using Specific Antibodies
[0637] Native or recombinant PRO polypeptides may be purified by a
variety of standard techniques in the art of protein purification.
For example, pro-PRO polypeptide, mature PRO polypeptide, or
pre-PRO polypeptide is purified by immunoaffinity chromatography
using antibodies specific for the PRO polypeptide of interest. In
general, an immunoaffinity column is constructed by covalently
coupling the anti-PRO polypeptide antibody to an activated
chromatographic resin.
[0638] Polyclonal immunoglobulins are prepared from immune sera
either by precipitation with ammonium sulfate or by purification on
immobilized Protein A (Pharmacia LKB Biotechnology, Piscataway,
N.J.). Likewise, monoclonal antibodies are prepared from mouse
ascites fluid by ammonium sulfate precipitation or chromatography
on immobilized Protein A. Partially purified immunoglobulin is
covalently attached to a chromatographic resin such as
CnBr-activated SEPHAROSE.TM. (Pharmacia LKB Biotechnology). The
antibody is coupled to the resin, the resin is blocked, and the
derivative resin is washed according to the manufacturer's
instructions.
[0639] Such an immunoaffinity column is utilized in the
purification of PRO polypeptide by preparing a fraction from cells
containing PRO polypeptide in a soluble form. This preparation is
derived by solubilization of the whole cell or of a subcellular
fraction obtained via differential centrifugation by the addition
of detergent or by other methods well known in the art.
Alternatively, soluble PRO polypeptide containing a signal sequence
may be secreted in useful quantity into the medium in which the
cells are grown.
[0640] A soluble PRO polypeptide-containing preparation is passed
over the immunoaffnity column, and the column is washed under
conditions that allow the preferential absorbance of PRO
polypeptide (e.g., high ionic strength buffers in the presence of
detergent). Then, the column is eluted under conditions that
disrupt antibody/PRO polypeptide binding (e.g., a low pH buffer
such as approximately pH 2-3, or a high concentration of a
chaotrope such as urea or thiocyanate ion), and PRO polypeptide is
collected.
EXAMPLE 26
Drug Screening
[0641] This invention is particularly useful for screening
compounds by using PRO polypeptides or binding fragment thereof in
any of a variety of drug screening techniques. The PRO polypeptide
or fragment employed in such a test may either be free in solution,
affixed to a solid support, borne on a cell surface, or located
intracellularly. One method of drug screening utilizes eukaryotic
or prokaryotic host cells which are stably transformed with
recombinant nucleic acids expressing the PRO polypeptide or
fragment. Drugs are screened against such transformed cells in
competitive binding assays. Such cells, either in viable or fixed
form, can be used for standard binding assays. One may measure, for
example, the formation of complexes between PRO polypeptide or a
fragment and the agent being tested. Alternatively, one can examine
the diminution in complex formation between the PRO polypeptide and
its target cell or target receptors caused by the agent being
tested.
[0642] Thus, the present invention provides methods of screening
for drugs or any other agents which can affect a PRO
polypeptide-associated disease or disorder. These methods comprise
contacting such an agent with an PRO polypeptide or fragment
thereof and assaying (I) for the presence of a complex between the
agent and the PRO polypeptide or fragment, or (ii) for the presence
of a complex between the PRO polypeptide or fragment and the cell,
by methods well known in the art. In such competitive binding
assays, the PRO polypeptide or fragment is typically labeled. After
suitable incubation, free PRO polypeptide or fragment is separated
from that present in bound form, and the amount of free or
uncomplexed label is a measure of the ability of the particular
agent to bind to PRO polypeptide or to interfere with the PRO
polypeptide/cell complex.
[0643] Another technique for drug screening provides high
throughput screening for compounds having suitable binding affinity
to a polypeptide and is described in detail in WO 84/03564,
published on Sep. 13, 1984. Briefly stated, large numbers of
different small peptide test compounds are synthesized on a solid
substrate, such as plastic pins or some other surface. As applied
to a PRO polypeptide, the peptide test compounds are reacted with
PRO polypeptide and washed. Bound PRO polypeptide is detected by
methods well known in the art. Purified PRO polypeptide can also be
coated directly onto plates for use in the aforementioned drug
screening techniques. In addition, non-neutralizing antibodies can
be used to capture the peptide and immobilize it on the solid
support.
[0644] This invention also contemplates the use of competitive drug
screening assays in which neutralizing antibodies capable of
binding PRO polypeptide specifically compete with a test compound
for binding to PRO polypeptide or fragments thereof. In this
manner, the antibodies can be used to detect the presence of any
peptide which shares one or more antigenic determinants with PRO
polypeptide.
EXAMPLE 27
Rational Drug Design
[0645] The goal of rational drug design is to produce structural
analogs of biologically active polypeptide of interest (i.e., a PRO
polypeptide) or of small molecules with which they interact, e.g.,
agonists, antagonists, or inhibitors. Any of these examples can be
used to fashion drugs which are more active or stable forms of the
PRO polypeptide or which enhance or interfere with the function of
the PRO polypeptide in vivo (cf., Hodgson, Bio/Technology, 9: 19-21
(1991)).
[0646] In one approach, the three-dimensional structure of the PRO
polypeptide, or of an PRO polypeptide-inhibitor complex, is
determined by x-ray crystallography, by computer modeling or, most
typically, by a combination of the two approaches. Both the shape
and charges of the PRO polypeptide must be ascertained to elucidate
the structure and to determine active site(s) of the molecule. Less
often, useful information regarding the structure of the PRO
polypeptide may be gained by modeling based on the structure of
homologous proteins. In both cases, relevant structural information
is used to design analogous PRO polypeptide-like molecules or to
identify efficient inhibitors. Useful examples of rational drug
design may include molecules which have improved activity or
stability as shown by Braxton and Wells, Biochemistry. 31:7796-7801
(1992) or which act as inhibitors, agonists, or antagonists of
native peptides as shown by Athauda et al., J. Biochem. 113:742-746
(1993).
[0647] It is also possible to isolate a target-specific antibody,
selected by functional assay, as described above, and then to solve
its crystal structure. This approach, in principle, yields a
pharmacore upon which subsequent drug design can be based. It is
possible to bypass protein crystallography altogether by generating
anti-idiotypic antibodies (anti-ids) to a functional,
pharmacologically active antibody. As a mirror image of a mirror
image, the binding site of the anti-ids would be expected to be an
analog of the original receptor. The anti-id could then be used to
identify and isolate peptides from banks of chemically or
biologically produced peptides. The isolated peptides would then
act as the pharmacore.
[0648] By virtue of the present invention, sufficient amounts of
the PRO polypeptide may be made available to perform such
analytical studies as X-ray crystallography. In addition, knowledge
of the PRO polypeptide amino acid sequence provided herein will
provide guidance to those employing computer modeling techniques in
place of or in addition to x-ray crystallography.
EXAMPLE 28
Gene Amplification
[0649] This example shows that the PRO327-, PRO344-, PRO347-,
PRO357- and PRO715-encoding genes are amplified in the genome of
certain human lung, colon and/or breast cancers and/or cell lines.
Amplification is associated with overexpression of the gene
product, indicating that the polypeptides are useful targets for
therapeutic intervention in certain cancers such as colon, lung,
breast and other cancers. Therapeutic agents may take the form of
antagonists of PRO327, PRO344, PRO347, PRO357 or PRO715
polypeptide, for example, murine-human chimeric, humanized or human
antibodies against a PRO327, PRO344, PRO347, PRO357 or PRO715
polypeptide. These amplifications also are useful as diagnostic
markers for the presence of a specific type of tumor type.
[0650] The starting material for the screen was genomic DNA
isolated from a variety cancers. The DNA is quantitated precisely,
e.g., fluorometrically. As a negative control, DNA was isolated
from the cells of ten normal healthy individuals which was pooled
and used as assay controls for the gene copy in healthy individuals
(not shown). The 5' nuclease assay (for example, TaqMan.TM.) and
real-time quantitative PCR (for example, ABI Prizm 7700 Sequence
Detection System.TM. (Perkin Elmer, Applied Biosystems Division,
Foster City, Calif.)), were used to find genes potentially
amplified in certain cancers. The results were used to determine
whether the DNA encoding PRO327, PRO344, PRO347, PRO357 or PRO715
is over-represented in any of the primary lung or colon cancers or
cancer cell lines or breast cancer cell lines that were screened.
The primary lung cancers were obtained from individuals with tumors
of the type and stage as indicated in Table 9. An explanation of
the abbreviations used for the designation of the primary tumors
listed in Table 9 and the primary tumors and cell lines referred to
throughout this example are given below.
[0651] The results of the TaqMan.TM. are reported in delta
(.DELTA.) Ct units. One unit corresponds to 1 PCR cycle or
approximately a 2-fold amplification relative to normal, two units
corresponds to 4-fold, 3 units to 8-fold amplification and so on.
Quantitation was obtained using primers and a TaqMan.TM.
fluorescent probe derived from the PRO327-, PRO344-, PRO347-,
PRO357- or PRO715-encoding gene. Regions of PRO327, PRO344, PRO347,
PRO357 or PRO715 which are most likely to contain unique nucleic
acid sequences and which are least likely to have spliced out
introns are preferred for the primer and probe derivation, e.g.,
3'-untranslated regions. The sequences for the primers and probes
(forward, reverse and probe) used for the PRO327, PRO344, PRO347,
PRO357 or PRO715 gene amplification analysis were as follows:
36 PRO327 (DNA38113-1230) forward 5'-CTCAAGAAGCACGCGTACTGC-- 3'
(SEQ ID NO:96) probe 5'-CCAACCTCAGCTTCCGCCTCTACGA-3' (SEQ ID NO:97)
reverse 5'-CATCCAGGCTCGCCACTG-3' (SEQ ID NO:98) PRO344
(DNA40592-1242) forward 5'-TGGCAAGGAATGGGAACAGT-3' (SEQ ID NO:99)
probe 5'-ATGCTGCCAGACCTGATCGCAGACA-3' (SEQ ID NO:100) reverse
5'-GGGCAGAAATCCAGCCACT-3' (SEQ ID NO:101) PRO347 (DNA44176-1244)
forward 5'-CCCTTCGCCTGCTTTTGA-3' (SEQ ID NO:102) probe
5'-GCCATCTAATTGAAGCCCATCTTCCCA-3' (SEQ ID NO:103) reverse
5'-CTGGCGGTGTCCTCTCCT-3' (SEQ ID NO:104) PRO357 (DNA44804-1248)
forward 5'-CCTCGGTCTCCTCATCTGTGA-3' (SEQ ID NO:105) probe
5'-TGGCCCAGCTGACGAGCCCT-3' (SEQ ID NO:106) reverse
5'-CTCATAGGCACTCGGTTCTGG-3' (SEQ ID NO:107) PRO715 (DNA52722-1229)
forward 5'-TGGCTCCCAGCTTGGAAGA-3' (SEQ ID NO:108) probe
5'-CAGCTCTTGGCTGTCTCCAGTATGTACCCA-3' (SEQ ID NO:109) reverse
5'-GATGCCTCTGTTCCTGCACAT-3' (SEQ ID NO:110)
[0652] The 5' nuclease assay reaction is a fluorescent PCR-based
technique which makes use of the 5' exonuclease activity of Taq DNA
polymerase enzyme to monitor amplification in real time. Two
oligonucleotide primers are used to generate an amplicon typical of
a PCR reaction. A third oligonucleotide, or probe, is designed to
detect nucleotide sequence located between the two PCR primers. The
probe is non-extendible by Taq DNA polymerase enzyme, and is
labeled with a reporter fluorescent dye and a quencher fluorescent
dye. Any laser-induced emission from the reporter dye is quenched
by the quenching dye when the two dyes are located close together
as they are on the probe. During the amplification reaction, the
Taq DNA polymerase enzyme cleaves the probe in a template-dependent
manner. The resultant probe fragments disassociate in solution, and
signal from the released reporter dye is free from the quenching
effect of the second fluorophore. One molecule of reporter dye is
liberated for each new molecule synthesized, and detection of the
unquenched reporter dye provides the basis for quantitative
interpretation of the data.
[0653] The 5' nuclease procedure is run on a real-time quantitative
PCR device such as the ABI Prism 7700TM Sequence Detection. The
system consists of a thermocycler, laser, charge-coupled device
(CCD) camera and computer. The system amplifies samples in a
96-well format on a thermocycler. During amplification,
laser-induced fluorescent signal is collected in real-time through
fiber optics cables for all 96 wells, and detected at the CCD. The
system includes software for running the instrument and for
analyzing the data.
[0654] 5' Nuclease assay data are initially expressed as Ct, or the
threshold cycle. This is defined as the cycle at which the reporter
signal accumulates above the background level of fluorescence. The
.DELTA.Ct values are used as quantitative measurement of the
relative number of starting copies of a particular target sequence
in a nucleic acid sample when comparing cancer DNA results to
normal human DNA results.
[0655] Table 9 describes the stage, T stage and N stage of various
primary tumors which were used to screen the PRO327, PRO344,
PRO347, PRO357 and PRO715 compounds of the invention.
37TABLE 9 Primary Lung and Colon Tumor Profiles Primary Tumor Stage
Stage Other Stage Dukes Stage T Stage N Stage Human lung tumor
AdenoCa (SRCC724) [LT1] IIA T1 N1 Human lung tumor SqCCa (SRCC725)
[LT1a] IIB T3 N0 Human lung tumor AdenoCa (SRCC726) [LT2] IB T2 N0
Human lung tumor AdenoCa (SRCC727) [LT3] IIIA T1 N2 Human lung
tumor AdenoCa (SRCC728) [LT4] IB T2 N0 Human lung tumor SqCCa
(SRCC729) [LT6] IB T2 N0 Human lung tumor Aden/SqCCa (SRCC730)
[LT7] IA T1 N0 Human lung tumor AdenoCa (SRCC731) [LT9] IB T2 N0
Human lung tumor SqCCa (SRCC732) [LTl0] IIB T2 N1 Human lung tumor
SqCCa (SRCC733) [LT11] IIA T1 N1 Human lung tumor AdenoCa (SRCC734)
[LT12] IV T2 N0 Human lung tumor AdenoSqCCa (SRCC735)[LT13] IB T2
N0 Human lung tumor SqCCa (SRCC736) [LT15] IB T2 N0 Human lung
tumor SqCCa (SRCC737) [LT16] IB T2 N0 Human lung tumor SqCCa
(SRCC738) [LT17] IIB T2 N1 Human lung tumor SqCCa (SRCC739) [LT18]
IB T2 N0 Human lung tumor SqCCa (SRCC740) [LT19] IB T2 N0 Human
lung tumor LCCa (SRCC741) [LT21] IIB T3 N1 Human lung AdenoCa
(SRCC811) [LT22] 1A T1 N0 Human colon AdenoCa (SRCC742) [CT2] M1 D
pT4 N0 Human colon AdenoCa (SRCC743) [CT3] B pT3 N0 Human colon
AdenoCa (SRCC744) [CT8] B T3 N0 Human colon AdenoCa (SRCC745)
[CT10] A pT2 N0 Human colon AdenoCa (SRCC746) [CT12] MO, R1 B T3 N0
Human colon AdenoCa (SRCC747) [CT14] pMO, RO B pT3 pN0 Human colon
AdenoCa (SRCC748) [CT15] M1, R2 D T4 N2 Human colon AdenoCa
(SRCC749) [CT16] pMO B pT3 pN0 Human colon AdenoCa (SRCC750) [CT17]
C1 pT3 pN1 Human colon AdenoCa (SRCC751) [CT1] MO, R1 B pT3 N0
Human colon AdenoCa (SRCC752) [CT4] B pT3 M0 Human colon AdenoCa
(SRCC753) [CT5] G2 C1 pT3 pN0 Human colon AdenoCa (SRCC754) [CT6]
pMO, RO B pT3 pN0 Human colon AdenoCa (SRCC755) [CT7] G1 A pT2 pN0
Human colon AdenoCa (SRCC756) [CT9] G3 D pT4 pN2 Human colon
AdenoCa (SRCC757) [CT11] B T3 N0 Human colon AdenoCa (SRCC758)
[CT18] MO, RO B pT3 pN0
[0656] DNA Preparation
[0657] DNA was prepared from cultured cell lines, primary tumors,
normal human blood. The isolation was performed using purification
kit, buffer set and protease and all from Quiagen, according to the
manufacturer's instructions and the description below.
[0658] Cell Culture Lysis
[0659] Cells were washed and trypsinized at a concentration of
7.5.times.10.sup.8 per tip and pelleted by centrifuging at 1000 rpm
for 5 minutes at 4.degree. C., followed by washing again with 1/2
volume of PBS recentrifugation. The pellets were washed a third
time, the suspended cells collected and washed 2.times. with PBS.
The cells were then suspended into 10 ml PBS Buffer C1 was
equilibrated at 4.degree. C. Qiagen protease #19155 was diluted
into 6.25 ml cold ddH.sub.2O to a final concentration of 20 mg/ml
and equilibrated at 4.degree. C. 10 ml of G2 Buffer was prepared by
diluting Qiagen RNAse A stock (100 mg/ml) to a final concentration
of 200 .mu.g/ml.
[0660] Buffer C1 (10 ml, 4.degree. C.) and ddH2O(40 ml, 4.degree.
C.) were then added to the 10 ml of cell suspension, mixed by
inverting and incubated on ice for 10 minutes. The cell nuclei were
pelleted by centrifuging in a Beckman swinging bucket rotor at 2500
rpm at 4.degree. C. for 15 minutes. The supernatant was discarded
and the nuclei were suspended with a vortex into 2 ml Buffer C1 (at
4.degree. C.) and 6 ml ddH.sub.2O, followed by a second 4.degree.
C. centrifugation at 2500 rpm for 15 minutes. The nuclei were then
resuspended into the residual buffer using 200 .mu.l per tip. G2
buffer (10 ml) was added to the suspended nuclei while gentle
vortexing was applied. Upon completion of buffer addition, vigorous
vortexing was applied for 30 seconds. Quiagen protease (200 .mu.l,
prepared as indicated above) was added and incubated at 50.degree.
C. for 60 minutes. The incubation and centrifugation was repeated
until the lysates were clear (e.g., incubating additional 30-60
minutes, pelleting at 3000.times.g for 10 min., 4.degree. C.)
[0661] Solid Human Tumor Sample Preparation and Lysis
[0662] Tumor samples were weighed and placed into 50 ml conical
tubes and held on ice. Processing was limited to no more than 250
mg tissue per preparation (1 tip/preparation). The protease
solution was freshly prepared by diluting into 6.25 ml cold
ddH.sub.2O to a final concentration of 20 mg/ml and stored at
4.degree. C. G2 buffer (20 ml) was prepared by diluting DNAse A to
a final concentration of 200 mg/ml (from 100 mg/ml stock). The
tumor tissue was homogenated in 19 ml G2 buffer for 60 seconds
using the large tip of the polytron in a laminar-flow TC hood in
order to avoid inhalation of aerosols, and held at room
temperature. Between samples, the polytron was cleaned by spinning
at 2.times.30 seconds each in 2L ddH.sub.2O, followed by G2 buffer
(50 ml). If tissue was still present on the generator tip, the
apparatus was disassembled and cleaned.
[0663] Quiagen protease (prepared as indicated above, 1.0 ml) was
added, followed by vortexing and incubation at 50.degree. C. for 3
hours. The incubation and centrifugation was repeated until the
lysates were clear (e.g., incubating additional 30-60 minutes,
pelleting at 3000.times.g for 10 min., 4.degree. C.).
[0664] Human Blood Preparation and Lysis
[0665] Blood was drawn from healthy volunteers using standard
infectious agent protocols and citrated into 10 ml samples per tip.
Quiagen protease was freshly prepared by dilution into 6.25 ml cold
ddH .sub.2O to a final concentration of 20 mg/ml and stored at
4.degree. C. G2 buffer was prepared by diluting RNAse A to a final
concentration of 200 .mu.g/ml from 100 mg/ml stock. The blood (10
ml) was placed into a 50 ml conical tube and 10 ml C1 buffer and 30
ml ddH.sub.2O (both previously equilibrated to 4.degree. C.) were
added, and the components mixed by inverting and held on ice for 10
minutes. The nuclei were pelleted with a Beckman swinging bucket
rotor at 2500 rpm, 4.degree. C. for 15 minutes and the supernatant
discarded. With a vortex, the nuclei were suspended into 2 ml C1
buffer (4.degree. C.) and 6 ml ddH.sub.2O (4.degree. C.). Vortexing
was repeated until the pellet was white. The nuclei were then
suspended into the residual buffer using a 200 .mu.l tip. G2 buffer
(10 ml) were added to the suspended nuclei while gently vortexing,
followed by vigorous vortexing for 30 seconds. Quiagen protease was
added (200 .mu.l) and incubated at 50.degree. C. for 60 minutes.
The incubation and centrifugation was repeated until the lysates
were clear (e.g., incubating additional 30-60 minutes, pelleting at
3000.times.g for 10 min., 4.degree. C.).
[0666] Purification of Cleared Lysates
[0667] (1) Isolation of Genomic DNA
[0668] Genomic DNA was equilibrated (1 sample per maxi tip
preparation) with 10 ml QBT buffer. QF elution buffer was
equilibrated at 50.degree. C. The samples were vortexed for 30
seconds, then loaded onto equilibrated tips and drained by gravity.
The tips were washed with 2.times.15 ml QC buffer. The DNA was
eluted into 30 ml silanized, autoclaved 30 ml Corex tubes with 15
ml QF buffer (50.degree. C.). Isopropanol (10.5 ml) was added to
each sample, the tubes covered with parafin and mixed by repeated
inversion until the DNA precipitated. Samples were pelleted by
centrifugation in the SS-34 rotor at 15,000 rpm for 10 minutes at
4.degree. C. The pellet location was marked, the supernatant
discarded, and 10 ml 70% ethanol (4.degree. C.) was added. Samples
were pelleted again by centrifugation on the SS-34 rotor at 10,000
rpm for 10 minutes at 4.degree. C. The pellet location was marked
and the supernatant discarded. The tubes were then placed on their
side in a drying rack and dried 10 minutes at 37.degree. C., taking
care not to overdry the samples.
[0669] After drying, the pellets were dissolved into 1.0 ml TE (pH
8.5) and placed at 50.degree. C. for 1-2 hours. Samples were held
overnight at 4.degree. C. as dissolution continued. The DNA
solution was then transferred to 1.5 ml tubes with a 26 gauge
needle on a tuberculin syringe. The transfer was repeated 5.times.
in order to shear the DNA. Samples were then placed at 50.degree. C
for 1-2 hours.
[0670] (2) Quantitation of Genomic DNA and Preparation for Gene
Amplification Assay
[0671] The DNA levels in each tube were quantified by standard
A.sub.260, A.sub.280 spectrophotometry on a 1:20 dilution (5 .mu.l
DNA+95 .mu.l ddH.sub.2O) using the 0.1 ml quartz cuvetts in the
Beckman DU640 spectrophotometer. A.sub.260/A.sub.280 ratios were in
the range of 1.8-1.9. Each DNA samples was then diluted further to
approximately 200 ng/ml in TE (pH 8.5). If the original material
was highly concentrated (about 700 ng/.mu.l), the material was
placed at 50.degree. C. for several hours until resuspended.
[0672] Fluorometric DNA quantitation was then performed on the
diluted material (20-600 ng/ml) using the manufacturer's guidelines
as modified below. This was accomplished by allowing a Hoeffer DyNA
Quant 200 fluorometer to warm-up for about 15 minutes. The Hoechst
dye working solution (#H33258, 10 .mu.l, prepared within 12 hours
of use) was diluted into 100 ml 1.times.TNE buffer. A 2 ml cuvette
was filled with the fluorometer solution, placed into the machine,
and the machine was zeroed. pGEM 3Zf(+) (2 .mu.l, lot #360851026)
was added to 2 ml of fluorometer solution and calibrated at 200
units. An additional 2 .mu.l of pGEM 3Zf(+) DNA was then tested and
the reading confirmed at 400+/-10 units. Each sample was then read
at least in triplicate. When 3 samples were found to be within 10%
of each other, their average was taken and this value was used as
the quantification value.
[0673] The fluorometricly determined concentration was then used to
dilute each sample to 10 ng/.mu.l in ddH.sub.2O. This was done
simultaneously on all template samples for a single TaqMan plate
assay, and with enough material to run 500-1000 assays. The samples
were tested in triplicate with Taqman.TM. primers and probe both
B-actin and GAPDH on a single plate with normal human DNA and
no-template controls. The diluted samples were used provided that
the CT value of normal human DNA subtracted from test DNA was +/-1
Ct. The diluted, lot-qualified genomic DNA was stored in 1.0 ml
aliquots at -80.degree. C. Aliquots which were subsequently to be
used in the gene amplification assay were stored at 4.degree. C.
Each 1 ml aliquot is enough for 8-9 plates or 64 tests.
[0674] Gene Amplification Assay
[0675] The PRO327, PRO344, PRO347, PRO357 and PRO715 compounds of
the invention were screened in the following primary tumors and the
resulting .DELTA.Ct values greater than or equal to 1.0 are
reported in Table 10.
38TABLE 10 .DELTA.Ct values in primary tumor and cell lines models
Primary Tumors PRO- PRO- PRO- PRO- PRO- or Cell Lines 327 344 347
357 715 LT1 -- -- 1.035 -- 1.625 LT1a 1.045 -- 1.865 1.18 1.045 1.0
2.47 1.93 LT3 1.135 -- 1.325 2.93 -- 1.2 LT6 1.395 -- 1.945 2.6 --
1.42 3.18 LT9 -- -- 2.645 3.47 1.005 2.91 LT10 1.305 -- 1.845 3.42
1.125 1.13 3.51 LT11 1.53 1.52 1.395 1.185 1.75 1.35 2.875 1.12
LT12 2.99 1.2 1.425 1.225 1.63 2.15 1.73 2.225 1.11 1.14 LT13 2.48
1.81 2.035 1.585 2.29 1.69 1.175 2.28 1.665 1.83 1.05 1.15 1.31
LT15 3.99 1.62 1.615 2.205 2.33 2.89 1.33 2.73 2.445 1.89 1.27 1.89
1.44 LT16 1.16 1.13 -- 2.605 1.2 2.65 1.09 1.1 LT17 1.76 1.46 1.24
1.275 1.95 1.09 2.855 1.33 1.01 LT18 -- -- -- 2.455 1.14 LT19 3.58
2.47 1.835 2.295 2.38 1.35 2.645 LT21 -- 1.09 1.14 2.675 -- CT2
3.645 1.84 2.1 2.01 1.675 1.605 1.605 CT3 1.125 -- 1.01 -- 1.135
1.105 CT8 1.645 -- 1.3 1.1 1.285 1.345 CT10 2.535 -- -- 1.42 2.155
1.785 CT12 1.885 -- -- -- -- CT14 2.515 1.16 1.39 1.5 1.265 1.45
1.575 CT15 1.305 1.17 1.3 1.25 1.585 1.475 CT16 1.475 -- 1.33 1.05
1.095 1.055 1.475 CT17 1.715 -- -- -- 1.245 1.375 CT1 1.375 1.245
1.045 1.045 1.285 1.6 1.085 CT4 2.225 1.465 -- 1.275 1.375 2.23
1.165 CT5 2.505 1.515 1.625 1.695 1.975 1.985 2.07 1.715 CT6 2.285
-- -- 1.085 1.305 1.73 1.245 CT7 -- -- -- 1.735 1.005 1.65 1.025
CT9 1.585 -- -- -- 1.0 CT11 3.335 1.355 1.315 1.835 2.185 1.525
2.54 CT18 1.075 -- -- -- 1.69 SRCC771 (H157) 1.65 -- -- -- --
SRCC772 (H441) 2.23 -- -- -- -- SRCC773 (H460) 1.12 -- -- -- --
SRCC774 (SKMES-1) 1.18 -- -- -- -- SRCC777 (SW620) 2.24 -- -- -- --
SRCC778 (Colo320) 1.01 -- -- -- -- SRCC830 (HCC2998) 1.23 -- -- --
-- SRCC831 (KM12) 1.61 -- -- -- -- SRCC832 (H522) 1.02 -- -- -- --
SRCC833 (H810) 1.11 -- -- -- --
[0676] PRO327
[0677] PRO327 (DNA38113-1230) was reexamined along with selected
tumors from the above initial screen with framework mapping. Table
11 describes the framework markers that were employed in
association with PRO327 (DNA38113-1230). The framework markers are
located approximately every 20 megabases along Chromosome 19, and
are used to control aneuploidy. The .DELTA.Ct values for the
described framework markers along Chromosome 19 relative to PRO327
(DNA38113-1230) are indicated for selected tumors in Table 13.
[0678] PRO327 (DNA38113-1230) was also reexamined along with
selected tumors from the above initial screen with epicenter
mapping. Table 12 describes the epicenter markers that were
employed in association with PRO327 (DNA38113-1230). These markers
are located in close proximity to DNA38113-1230 and are used to
assess the amplification status of the region of Chromosome 19 in
which DNA38113-1230 is located. The distance between markers is
measured in centirays (cR), which is a radiation breakage unit
approximately equal to a 1% chance of a breakage between two
markers. One cR is very roughly equivalent to 20 kilobases.
[0679] Table 14 indicates the .DELTA.Ct values for results of
epicenter mapping relative to DNA38113-1230, indicating the
relative amplification in the region more immediate to the actual
location of DNA38113-1230 along Chromosome 19.
39TABLE 11 Framework Markers Along Chromosome 19 Map Position on
Chromosome 19 Stanford Human Genome Center Marker Name S12
AFMa107xc9 S50 SHGC-31335 S105 SHGC-34102 S155 SHGC-16175
[0680]
40TABLE 12 Epicenter Markers Along Chromosome 19 used for
DNA38113-1230 Map Position Stanford Human Genome Distance to next
Marker on Chromosome 19 Center Marker Name (cR.sup.1) S42 WI-7289 5
S43 SHGC-32638 28 S44 SHGC-11753.sup.2 7 DNA38113-1230 -- -- S45
SHGC-14810 37 S46 AFM214YF6 15 S48 SHGC-36583 --
[0681]
41TABLE 13 Amplification of framework markers relative to
DNA38113-1230 (.DELTA.Ct) Framework Markers DNA38113- Tumor S12
1230 S50 S105 S155 LT1 0.16 -0.15 0.06 -0.42 0.11 LT1a 0.05 0.57
-0.27 0.17 0.40 LT2 0.48 0.57 0.41 0.52 0.13 LT3 0.27 0.77 0.83
0.11 0.50 LT4 0.48 0.08 0.67 0.20 0.56 LT6 0.72 0.33 0.74 0.32 0.35
LT7 0.82 0.29 0.85 0.95 0.95 LT9 0.72 -0.19 0.61 0.19 0.64 LT10
0.82 1.45 0.98 0.62 0.53 CT2 0.25 2.94 0.29 0.37 -0.02 CT3 -0.17
1.23 -0.10 0.34 -0.28 CT8 0.13 1.45 0.57 0.18 -0.16 CT10 0.15 1.72
0.51 -0.01 -0.81 CT12 0.13 1.60 0.57 0.41 0.20 CT14 0.40 2.03 0.39
0.45 0.36 CT15 -0.23 0.68 -0.30 -0.06 0.56 CT16 0.38 1.07 0.31 0.24
0.04 CT17 0.25 0.50 0.71 0.32 0.09
[0682]
42TABLE 14 Amplification of epicenter markers relative to
DNA38113-1230 (.DELTA.Ct) Tum- DNA38113- or S41 S42 S43 S44 1230
S45 S46 S48 LT1 -1.03 -0.25 -0.18 -0.11 -0.31 0.13 0.26 0.29 LT1a
0.14 -0.30 -0.11 -0.01 0.21 -0.44 0.45 -0.30 LT2 0.03 0.06 0.06
0.12 0.14 0.16 0.11 0.65 LT3 -1.08 -0.08 -0.01 0.11 0.43 -0.37 0.33
0.56 LT4 0.66 -0.14 -0.48 -0.79 -0.28 -0.31 0.04 0.09 LT6 -0.88
-0.08 -0.12 -1.00 0.20 -0.43 0.48 0.63 LT7 0.65 -0.19 -0.19 -0.04
-0.04 -0.42 0.43 0.57 LT9 0.66 -0.26 -0.01 -0.14 -0.06 -0.31 -16.48
0.16 LT10 1.16 -0.30 -0.11 -0.31 0.13 -0.33 0.34 0.50 LT11 0.46
0.01 -0.04 -0.86 0.67 0.23 0.24 -0.57 LT12 1.39 -0.01 -0.22 -1.33
1.57 -0.25 0.26 0.07 LT13 1.62 -0.03 0.00 -0.08 1.22 -0.08 0.48
0.14 LT15 1.09 0.20 0.47 0.62 2.47 0.38 0.01 0.44 LT16 1.51 0.04
-0.04 0.29 2.23 0.51 0.50 0.90 LT17 2.12 0.23 0.11 0.20 1.02 0.45
0.46 -0.41 LT18 1.80 -0.11 0.07 -0.70 0.9 0.10 0.00 -0.02 LT22
-0.12 0.06 0.41 -0.11 -0.06 0.34 0.03 0.52 CT1 -0.09 0.33 0.11 0.22
1.38 0.09 -0.25 -0.10 CT2 1.76 0.04 0.30 0.65 2.94 0.18 -0.04 0.01
CT3 1.10 -0.31 -0.24 0.16 1.23 -0.64 0.78 -0.17 CT4 1.63 0.22 0.32
-0.72 2.23 -0.04 0.44 0.72 CT5 2.22 0.02 0.21 0.10 2.51 0.02 0.18
0.24 CT6 0.48 0.20 0.22 -0.63 2.29 0.03 0.14 0.97 CT7 0.93 0.20
0.32 0.14 0.95 -0.01 0.20 0.54 CT8 1.15 -0.50 -0.14 0.15 1.45 -0.31
0.54 0.07 CT9 0.82 0.38 0.64 -0.71 1.59 1.04 0.26 0.93 CT10 1.57
-0.41 -0.03 -0.14 1.72 -0.27 0.04 0.10 CT11 1.49 -0.05 0.07 0.01
3.34 0.54 0.28 0.88 CT12 0.89 -0.09 -0.01 -0.62 1.6 -0.07 1.16 0.92
CT14 2.16 0.32 0.37 0.47 2.03 -0.07 1.21 0.44 CT15 0.64 -0.52 -0.21
-0.12 0.68 -0.61 1.01 0.32 CT16 1.75 -0.31 0.28 0.47 1.07 0.04 1.01
-0.29 CT17 0.77 -0.18 0.13 -0.04 0.5 -0.27 0.93 0.31 CT18 0.91 0.05
0.14 0.60 1.08 0.22 -0.59 0.61
[0683] PRO715 (DNA52722-1229)
[0684] PRO715 was also reexamined with both framework and epicenter
mapping. Table 15 indicates the chromosomal localizations of the
framework markers that were used for the procedure. The framework
markers are located approximately every 20 megabases and were used
to control aneuploidy. Table 16 indicates the epicenter mapping
markers that were used in the procedure. The epicenter markers were
located in close proximity to DNA52722-1229 and are used to
determine the relative DNA amplification in the immediate vicinity
of DNA52722-1229. The distance between individual markers is
measured in centirays, which is a radiation breakage unit
approximately equal to a 1% chance of a breakage between two
markers. One cR is very roughly equivalent to about 20 kilobases.
In Table 16, "BAC" means bacterial artificial chromosome. The ends
of a BAC clone which contained the gene of interest were sequenced.
TaqMan primers and probes were made from this sequence, which are
indicated in the table. BAC clones are typically 100 to 150 Kb, so
these primers and probes can be used as nearby markers to probe DNA
from tumors. In Table 16, the marker SHGC-31370 is the marker found
to be the closest to the location on chromosome 17 where
DNA52722-1229 maps.
43TABLE 15 Framework Markers Used Along Chromosome 17 for
DNA52722-1229 Stanford Human Map Position on Chromosome 17 Genome
Center Marker Name Q4 SHGC-31242 Q52 SHGC-35988 Q110 AFM200zf4 Q169
SHGC-32689 Q206 SHGC-11717 Q232 SHGC-32338
[0685]
44TABLE 16 Epicenter Markers Used on Chromosome 17 in Vicinity of
DNA52722-1229 Map Position on Stanford Human Genome Marker Distance
to next Chromosome 17 Name Marker (cR) Q33 SHGC-35547 18 cR to Q34
120F17FOR1 Marker from forward end of BAC sequence 120F17FOR2
Marker from forward end of BAC sequence DNA52722-1229 - - -
120F17REV1 Marker from reverse end of BAC sequence 120F17REV2
Marker from reverse end of BAC sequence Q34 SHGC-31370
[0686] Table 17 indicates the .DELTA.Ct values of the above
described framework markers along chromosome 17 relative to
DNA52722-1229 for selected tumors.
45TABLE 17 Amplification of Framework Markers Relative to
DNA52722-1229 Framework Marker DNA5272 Tumor Q4 Q52 2-1229 Q110
Q169 Q206 Q232 LT1 0.02 -0.50 -0.04 0.05 -0.32 -0.21 -0.34 LT1a
-0.01 -0.34 0.64 0.23 -0.20 -0.25 -0.15 LT2 0.25 0.15 0.19 0.05
-0.16 -0.14 -0.09 LT3 -0.08 -0.20 0.54 0.56 -0.06 0.32 0.05 LT4
-0.32 -0.45 0.31 0.19 -0.06 -0.12 0.04 LT6 -0.21 -0.38 0.31 0.13
-0.08 -0.30 0.01 LT7 -0.66 -1.02 0.02 0.62 -0.20 0.06 0.16 LT9
-0.03 -0.29 0.46 1.20 -1.75 -0.22 -0.13 LT10 -0.16 -0.09 0.58 0.11
0.01 -0.33 -0.45 LT11 -0.14 0.29 1.03 0.04 0.30 0.52 0.17 LT12
-0.25 -0.68 0.72 0.65 0.86 0.97 0.58 LT13 0.20 0.00 1.37 -0.15
-0.04 0.25 -0.01 LT15 0.11 -0.39 1.75 0.00 -0.02 0.43 -0.19 LT16
-0.07 -0.56 1.11 0.22 0.19 0.68 -0.55 LT17 0.41 -0.09 1.14 0.27
0.22 0.73 0.07 LT18 0.14 -0.22 1.04 0.27 0.35 0.48 -0.03 LT22 -0.07
-0.73 0.00 0.13 -0.02 0.41 0.05 CT2 0.12 -0.47 1.29 -0.19 0.32 --
0.18 CT3 0.05 0.17 1.06 -0.41 0.05 -- -0.06 CT8 0.44 0.14 1.08 0.02
-0.04 -- -0.11 CT10 0.35 0.26 1.60 -0.05 0.00 -- -0.02 CT12 -0.15
-0.46 0.52 -0.13 0.02 -- -0.20 CT14 0.26 -0.59 1.05 -0.01 0.68 --
0.48 CT15 0.55 -0.51 1.36 -0.69 0.11 -- -0.16 CT16 0.09 -0.14 1.06
0.00 0.00 -- -0.15 CT17 0.40 -0.16 1.00 -0.47 0.04 -- -0.29
[0687] Table 18 indicates the .DELTA.Ct values for the indicated
epicenter markers, indicating the relative amplification along
chromosome 17 in the immediate vicinity of DNA52722-1229.
46TABLE 18 Amplification of Epicenter Markers Relative to
DNA52722-1229 Epicenter marker 120F17FOR 120FL7FOR DNA5272 Tumor
Q33 1 2 2-1229 120F17REV1 120F17REV2 Q34 LT1 -0.18 0.11 0.00 0.20
-0.08 0.07 -0.36 LT1a 0.32 -0.06 0.00 0.68 -0.09 -0.20 0.32 LT2
0.06 0.14 0.00 0.27 -0.29 0.16 -0.16 LT3 0.08 -2.06 0.00 0.16 -0.84
-0.38 -0.16 LT4 -- -- -- -- -- -- -- LT6 -- -- -- -- -- -- -- LT7
-0.20 -0.51 0.00 0.23 -0.63 -0.37 -0.41 LT9 0.08 -0.17 0.00 0.59
0.02 -0.66 -0.01 LT10 0.09 0.05 0.00 0.59 -0.22 -0.12 0.36 LT11
0.75 0.09 0.00 1.07 0.43 -0.01 0.63 LT12 0.00 -0.45 0.00 0.63 -0.49
-0.82 0.18 LT13 0.72 -0.02 0.00 1.29 0.04 0.02 0.66 LT15 0.75 0.11
0.00 1.33 0.15 -0.19 0.90 LT16 0.34 -0.41 0.00 1.11 -0.39 -0.89
0.15 LT17 1.06 0.29 0.00 1.13 -0.26 -0.12 0.90 LT18 0.66 0.11 0.00
1.21 -0.28 0.11 0.47 LT19 -0.09 -0.37 0.00 0.12 -0.53 -0.48 -0.53
CT1 0.50 0.14 0.00 1.22 0.27 0.43 0.72 CT2 0.69 -0.47 0.00 0.95
-0.72 -0.17 0.77 CT3 0.87 0.08 0 1.19 -0.06 0.74 0.97 CT4 0.45
-0.11 0 1.26 0.43 0.38 0.79 CT5 0.36 -0.39 0 1.79 -0.48 0.09 0.95
CT6 0.41 0.08 0 1.71 -0.21 0.57 0.47 CT7 0.40 0.18 0 1.19 0.31 0.40
0.54 CT8 0.48 0.17 0 0.93 0.23 0.47 0.72 CT10 0.72 0.15 0 1.86 0.81
0.67 0.97 CT11 0.80 -0.09 0 2.29 0.20 0.25 0.85 CT12 0.01 -0.55 0
0.49 -0.43 -0.09 0.11 CT14 0.22 -0.36 0 1.05 0.63 0.41 0.40 CT15
1.06 -0.04 0 1.27 0.74 0.98 1.13 CT16 0.84 0.06 0 1.03 0.26 0.40
0.91 CT17 0.80 0.04 0 0.95 0.78 1.29 0.90 CT18 0.34 0.13 0 1.06
0.06 0.34 0.50
[0688] PRO357 (DNA44804-1248)
[0689] PRO357 was reexamined with selected tumors from the above
initial screen with framework mapping. Table 19 indicate the
chromosomal mapping of the framework markers that were used in the
present example. The framework markers are located approximately
every 20 megabases and were used to control aneuploidy.
[0690] PRO357 was also examined with epicenter mapping. The markers
indicated in Table 20 are located in close proximity (in the
genome) to DNA44804-1248 and are used to assess the relative
amplification in the immediate vicinity of chromosome16 wherein
DNA44804-1248 is located. The distance between individual markers
is measured in centirays (cR), which is a radiation breakage unit
approximately equal to a 1% chance of a breakage between the two
markers. One cR is very roughly equivalent to 20 kilobases. The
marker SHGC-6154 is the marker found to be the closest to the
location on chromosome 16 where DNA44804-1248 maps.
47TABLE 19 Framework markers for DNA44804-1248 Stanford Human Map
Position on Chromosome 16 Genome Center Marker Name P7 SHGC-2835
P55 SHGC-9643 P99 GATA7BO2 P154 SHGC-33727 P208 SHGC-13577
[0691]
48TABLE 20 Epicenter markers for DNA44804-1248 along chromosome 16
Map position on Stanford Human Genome Distance to next Marker
chromosome 16 Center Marker Name (cR) P1 AFMA139WG1 6 P3 SHGC-32420
170 (gap) P4 SHGC-14817 40 P5 SHGC-12265 4 P6 SHGC-6154 33
DNA44804-1248 -- -- P7 SHGC-2835 10 P8 S HGC-2850 9 P9 AFM297yg5 67
P15 CHLC.GATA70B04 --
[0692] The .DELTA.Ct values of the above described framework
markers along chromosome 16 relative to DNA44804-1248 is described
in Table 21.
49TABLE 21 Amplification of Framework Markers relative to
DNA44804-1248 (.DELTA.Ct) Framework marker DNA44804- Tumor 1248 P7
P55 P99 P154 208 LT1 0.25 0.22 -0.17 0.42 0.04 0.43 LT1a 0.90 0.09
-0.10 -0.38 0.29 0.93 LT2 -0.16 0.03 0.19 -0.18 0.18 0.54 LT3 1.15
0.68 0.57 -0.34 -0.03 0.86 LT4 0.19 0.58 0.36 -0.31 0.08 1.14 LT6
0.28 0.27 -0.11 -0.74 -0.13 0.22 LT7 0.58 0.63 0.14 0.82 0.09 -0.21
LT9 0.68 0.63 0.14 0.82 0.09 -0.21 LT10 1.21 0.52 0.40 -0.39 -0.15
0.77 LT11 1.71 -0.79 1.31 0.73 -0.08 0.90 LT12 1.96 -0.95 0.94 0.00
-0.63 0.18 LT13 2.32 -0.97 0.94 0.88 -0.04 0.70 LT15 3.01 -0.54
0.60 0.12 0.14 1.15 LT16 0.67 -0.27 0.57 -0.39 0.08 1.04 LT17 1.64
0.25 1.10 0.28 0.10 0.23 LT18 0.34 0.09 0.51 0.33 -0.20 -0.09 LT19
3.03 -0.82 0.63 0.06 0.09 0.55 LT21 1.33 -1.19 1.01 0.11 0.34
0.07
[0693] Table 22 indicates the .DELTA.Ct values for the results of
epicenter mapping relative to DNA44804-1248, indicating the
relative amplification in the region more immediate to the actual
location of DNA44804-1248 along chromosome 16.
50TABLE 22 Amplification of epicenter markers relative to
DNA44804-1248 Epicenter marker DNA4480 Tumor P1 P3 P4 P5 P6 4-1248
P7 P8 P9 P15 LT1 0.31 -0.30 0.65 0.05 -0.33 0.16 -0.41 0.20 0.1
0.17 LT1a -0.23 -17.67 0.97 -0.65 -1.83 0.56 -0.65 -0.28 -0.27
-0.07 LT2 0.18 -0.06 0.33 -0.11 -0.38 -0.32 -1.08 -0.31 -0.53 -0.05
LT3 0.00 0.25 1.07 -0.23 -0.11 0.70 -0.71 -0.12 -0.17 -0.01 LT4
0.07 -0.25 0.55 -1.15 -1.78 -0.09 -0.82 -0.07 -0.34 -0.07 LT6 0.24
0.07 0.48 -0.55 -0.34 -0.07 -1.33 -0.41 -0.7 -0.27 LT7 0.07 -0.07
0.61 -0.19 -0.36 0.29 -0.96 -0.09 -0.26 -0.08 LT9 0.16 -0.16 0.64
-0.33 -0.14 0.43 -1.01 -0.19 -0.36 -0.21 LT10 0.47 0.76 -0.30 0.80
-0.09 0.00 -0.85 -0.17 -0.28 -0.07 LT11 0.14 0.14 0.96 -0.02 0.37
1.27 -0.23 0.09 -0.33 -0.07 LT12 -0.12 -0.04 0.84 -1.52 -0.28 1.42
-0.39 -0.38 -1.21 -0.25 LT13 0.41 -0.02 1.19 -0.34 0.14 1.67 -0.87
-0.22 -0.72 -0.33 LT15 0.01 0.21 1.30 -0.48 -0.35 2.36 -0.96 -0.36
-0.54 -0.22 LT16 -0.38 -0.07 0.41 -0.32 -1.22 -0.08 -0.45 -0.25
-0.52 -0.31 LT17 0.36 0.23 1.39 -1.39 01.37 1.17 -0.39 -0.13 0.52
0.01 LT18 0.17 -0.27 0.04 -0.04 0.18 -0.39 -0.59 -0.25 -0.21 -0.22
LT19 0.11 -0.02 1.27 -0.12 1.27 2.49 -0.30 -0.36 -0.82 -0.40 LT21
0.28 -0.18 0.85 0.09 0.66 0.85 -0.49 -0.35 -0.27 -0.16
[0694] Conclusion
[0695] The .DELTA.Ct values for the above DNAs in a variety of
tumors are reported. A .DELTA.Ct of >1 was typically used as the
threshold value for amplification scoring, as this represents a
doubling of gene copy. The above data indicates that significant
amplification of the tested nucleic acids occurred in primary lung
tumors and/or primary colon tumors: Amplification has been
confirmed by framework mapping. The framework markers analysis
reports the relative amplification of particular chromosomal
regions in the indicated tumors, while the epicenter markers
analysis gives a more precise reading of the relative amplification
in the region immediately in the vicinity of the gene of
interest.
[0696] Amplification has been confirmed by epicenter mapping and
the data evidenced significant amplification in primary colon
tumors and/or primary lung tumors: Amplification of the closest
known epicenter markers does not occur to a greater extent than
that of the DNAs tested. This strongly suggests that the DNAs
tested are responsible for the amplification of the particular
region on the respective chromosome.
[0697] Because amplification of the DNAs tested occurs in various
lung and colon tumors, it is highly probable that these DNAs play a
significant role in tumor formation or growth. As a result,
antagonists (e.g., antibodies) directed against the proteins
encoded by the DNAs tested would be expected to have utility in
cancer therapy and as useful diagnostic reagents. The polypeptides
encoded by the DNAs tested have utility as diagnostic markers for
determining the presence of tumor cells in lung and/or colon tissue
samples. The nucleic acid sequences encoding these polypeptides
have utility as sources of nucleic acid probes for carrying out the
above diagnostic procedures.
EXAMPLE 29
Ability of PRO241 to Stimulate the Release of Proteoglycans from
Cartilage (Assay 97)
[0698] The ability of PRO241 to stimulate the release of
proteoglycans from cartilage tissue was tested as follows. A
positive result in this assay evidences that the polypeptide is
expected to be useful in the therapeutic treatment of various
cartilage and/or bone injuries or disorders including, for example,
arthritis.
[0699] The metacarphophalangeal joint of 4-6 month old pigs was
aseptically dissected, and articular cartilage was removed by free
hand slicing being careful to avoid the underlying bone. The
cartilage was minced and cultured in bulk for 24 hours in a
humidified atmosphere of 95% air, 5% CO.sub.2 in serum free (SF)
media (DME/F12 1:1) woth 0.1% BSA and 100 U/ml penicillin and 100
.mu.g/ml streptomycin. After washing three times, approximately 100
mg of articular cartilage was aliquoted into micronics tubes and
incubated for an additional 24 hours in the above SF media. PRO241
polypeptides were then added at 1% either alone or in combination
with 18 ng/ml interleukin-l1.alpha., a known stimulator of
proteoglycan release from cartilage tissue. The supernatant was
then harvested and assayed for the amount of proteoglycans using
the 1,9-dimethyl-methylene blue (DMB) colorimetric assay (Farndale
and Buttle, Biochem. Biophys. Acta 883:173-177 (1985)). A positive
result in this assay indicates that the test polypeptide will find
use, for example, in the treatment of sports-related joint
problems, articular cartilage defects, osteoarthritis or rheumatoid
arthritis.
[0700] When PRO241 polypeptides were tested in the above assay, the
polypeptides demonstrated a marked ability to stimulate release of
proteoglycans from cartilage tissue both basally and after
stimulation with interleukin- 1.alpha. and at 24 and 72 hours after
treatment, thereby indicating that PRO241 polypeptides are useful
for stimulating proteoglycan release from cartilage tissue. As
such, PRO241 polypeptides are useful for the treatment of
sports-related joint problems, articular cartilage defects,
osteoarthritis or rheumatoid arthritis.
EXAMPLE 30
In Vitro Antitumor Assay with PRO344 (Assay 161)
[0701] The antiproliferative activity of the PRO344 polypeptide was
determined in the investigational, disease-oriented in vitro
anti-cancer drug discovery assay of the National Cancer Institute
(NCI), using a sulforhodamine B(SRB) dye binding assay essentially
as described by Skehan et al., J. Natl. Cancer Inst. 82:1107-1112
(1990). The 60 tumor cell lines employed in this study ("the NCI
panel"), as well as conditions for their maintenance and culture in
vitro have been described by Monks et al., J. Natl. Cancer Inst.
83:757-766 (199 1). The purpose of this screen is to initially
evaluate the cytotoxic and/or cytostatic activity of the test
compounds against different types of tumors (Monks et al., supra;
Boyd, Cancer: Princ. Pract. Oncol. Update 3(10):1-12 [1989]).
[0702] Cells from approximately 60 human tumor cell lines were
harvested with trypsin/EDTA (Gibco), washed once, resuspended in
IMEM and their viability was determined. The cell suspensions were
added by pipet (100 .mu.L volume) into separate 96-well microtiter
plates. The cell density for the 6-day incubation was less than for
the 2-day incubation to prevent overgrowth. Inoculates were allowed
a preincubation period of 24 hours at 37.degree. C. for
stabilization. Dilutions at twice the intended test concentration
were added at time zero in 100 .mu.L aliquots to the microtiter
plate wells (1:2 dilution). Test compounds were evaluated at five
half-log dilutions (1000 to 100,000-fold). Incubations took place
for two days and six days in a 5% CO.sub.2 atmosphere and 100%
humidity.
[0703] After incubation, the medium was removed and the cells were
fixed in 0.1 ml of 10% trichloroacetic acid at 40.degree. C. The
plates were rinsed five times with deionized water, dried, stained
for 30 minutes with 0.1 ml of 0.4% sulforhodamine B dye (Sigma)
dissolved in 1% acetic acid, rinsed four times with 1% acetic acid
to remove unbound dye, dried, and the stain was extracted for five
minutes with 0.1 ml of 10 mM Tris base
[tris(hydroxymethyl)aminomethane], pH 10.5. The absorbance (OD) of
sulforhodamine B at 492 nm was measured using a
computer-interfaced, 96-well microtiter plate reader.
[0704] A test sample is considered positive if it shows at least
50% growth inhibitory effect at one or more concentrations. The
results are shown in the following Table 23, where the
abbreviations are as follows: NSCL=non-small cell lung carcinoma
CNS=central nervous system
51TABLE 23 Tumor Cell Cell Line Test compound Concentration Days
Line Type Designation PR0344 1.2 nM 2 Leukemia HL-60 (TB) PR0344
1.2 nM 6 Renal UO-31 and CAKI-1 PR0344 14.9 nM 2 Colon KM-12 PR0344
14.9 nM 2 CNS SF-268 PR0344 14.9 nM 2 Ovarian OVCAR-4 PR0344 14.9
nM 2 Renal CAKI-1 PR0344 14.9 nM 2 Breast MDA-MB-435 PR0344 14.9 nM
6 Leukemia HL-60 (TB) PR0344 14.9 nM 6 Colon KM-12 PR0344 14.9 nM 6
CNS SF-295 PR0344 14.9 nM 6 NSCL HOP62
[0705] The results of these assays demonstrate that PRO344
polypeptides are useful for inhibiting neoplastic growth in a
number of different tumor cell types and may be used
therapeutically therefor. Antibodies against PRO344 are useful for
affinity purification of this useful polypeptide. Nucleic acids
encoding PRO344 polypeptides are useful for the recombinant
preparation of these polypeptides.
EXAMPLE 31
Inhibition of Vascular Endothelial Growth Factor (VEGF) Stimulated
Proliferation of Endothelial Cell Growth (Assay 9)
[0706] The ability of various PRO polypeptides to inhibit VEGF
stimulated proliferation of endothelial cells was tested.
Polypeptides testing positive in this assay are useful for
inhibiting endothelial cell growth in mammals where such an effect
would be beneficial, e.g., for inhibiting tumor growth.
[0707] Specifically, bovine adrenal cortical capillary endothelial
cells (ACE) (from primary culture, maximum of 12-14 passages) were
plated in 96-well plates at 500 cells/well per 100 microliter.
Assay media included low glucose DMEM, 10% calf serum, 2 mM
glutamine, and 1X penicillin/streptomycin/fungizone. Control wells
included the following: (1) no ACE cells added; (2) ACE cells
alone; (3) ACE cells plus 5 ng/ml FGF; (4) ACE cells plus 3 ng/ml
VEGF; (5) ACE cells plus 3 ng/ml VEGF plus 1 ng/ml TGF-beta; and
(6) ACE cells plus 3 ng/ml VEGF plus 5 ng/ml LIF. The test samples,
poly-his tagged PRO polypeptides (in 100 microliter volumes), were
then added to the wells (at dilutions of 1%, 0.1% and 0.01%,
respectively). The cell cultures were incubated for 6-7 days at
37.degree. C./5% CO.sub.2. After the incubation, the media in the
wells was aspirated, the cells were washed 1.times. with PBS. An
acid phosphatase reaction mixture (100 microliter; 0.1 M sodium
acetate, pH 5.5, 0.1% Triton X-100, 10 mM p-nitrophenyl phosphate)
was then added to each well. After a 2 hour incubation at
37.degree. C., the reaction was stopped by addition of 10
microliters 1N NaOH. Optical density (OD) was measured on a
microplate reader at 405 nm.
[0708] The activity of PRO polypeptides was calculated as the
percent inhibition of VEGF (3 ng/ml) stimulated proliferation (as
determined by measuring acid phosphatase activity at OD 405 nm)
relative to the cells without stimulation. TGF-beta was employed as
an activity reference at 1 ng/ml, since TGF-beta blocks 70-90% of
VEGF-stimulated ACE cell proliferation. The results are indicative
of the utility of the PRO polypeptides in cancer therapy and
specifically in inhibiting tumor angiogenesis. Numerical values
(relative inhibition) are determined by calculating the percent
inhibition of VEGF stimulated proliferation by the PRO polypeptides
relative to cells without stimulation and then dividing that
percentage into the percent inhibition obtained by TGF-.beta. at 1
ng/ml which is known to block 70-90% of VEGF stimulated cell
proliferation. The results are considered positive if the PRO
polypeptide exhibits 30% or greater inhibition of VEGF stimulation
of endothelial cell growth (relative inhibition 30% or
greater).
[0709] The following polypeptide tested positive in this assay:
PRO323.
EXAMPLE 32
Rod Photoreceptor Cell Survival (Assay 56)
[0710] This assay shows that certain polypeptides of the invention
act to enhance the survival/proliferation of rod photoreceptor
cells and, therefore, are useful for the therapeutic treatment of
retinal disorders or injuries including, for example, treating
sight loss in mammals due to retinitis pigmentosum, AMD, etc.
Sprague Dawley rat pups at 7 day postnatal (mixed population: glia
and retinal neuronal cell types) are killed by decapitation
following CO.sub.2 anesthesis and the eyes are removed under
sterile conditions. The neural retina is dissected away form the
pigment epithelium and other ocular tissue and then dissociated
into a single cell suspension using 0.25% trypsin in Ca.sup.2+,
Mg.sup.2+-free PBS. The retinas are incubated at 37.degree. C. for
7-10 minutes after which the trypsin is inactivated by adding 1 ml
soybean trypsin inhibitor. The cells are plated at 100,000 cells
per well in 96 well plates in DMEM/F12 supplemented with N.sub.2.
Cells for all experiments are grown at 37.degree. C. in a water
saturated atmosphere of 5% CO.sub.2. After 2-3 days in culture,
cells are fixed using 4% paraformaldehyde, and then stained using
CellTracker Green CMFDA. Rho 4D2 (ascites or IgG 1:100), a
monoclonal antibody directed towards the visual pigment rhodopsin
is used to detect rod photoreceptor cells by indirect
immunofluorescence. The results are calculated as % survival: total
number of calcein--rhodopsin positive cells at 2-3 days in culture,
divided by the total number of rhodopsin positive cells at time 2-3
days in culture. The total cells (fluorescent) are quantified at
20.times.objective magnification using a CCD camera and NIH image
software for MacIntosh. Fields in the well are chosen at
random.
[0711] The following polypeptides tested positive in this assay:
PRO243.
EXAMPLE 33
Pericyte c-Fos Induction (Assay 93)
[0712] This assay shows that certain polypeptides of the invention
act to induce the expression of c-fos in pericyte cells and,
therefore, are useful not only as diagnostic markers for particular
types of pericyte-associated tumors but also for giving rise to
antagonists which would be expected to be useful for the
therapeutic treatment of pericyte-associated tumors. Specifically,
on day 1, pericytes are received from VEC Technologies and all but
5 ml of media is removed from flask. On day 2, the pericytes are
trypsinized, washed, spun and then plated onto 96 well plates. On
day 7, the media is removed and the pericytes are treated with 100
.mu.l of PRO polypeptide test samples and controls (positive
control=DME+5% serum +/-PDGF at 500 ng/ml; negative control=protein
32). Replicates are averaged and SD/CV are determined. Fold
increase over Protein 32 (buffer control) value indicated by
chemiluminescence units (RLU) luminometer reading verses frequency
is plotted on a histogram Two-fold above Protein 32 value is
considered positive for the assay. ASY Matrix: Growth media=low
glucose DMEM=20% FBS + 1.times.pen strep+1.times.fungizone. Assay
Media=low glucose DMEM +5% FBS.
[0713] The following polypeptides tested positive in this assay:
PRO241.
EXAMPLE 34
Inhibitory Activity in Mixed Lymphocyte Reaction (MLR) Assay (Assay
67)
[0714] This example shows that one or more of the polypeptides of
the invention are active as inhibitors of the proliferation of
stimulated T-lymphocytes. Compounds which inhibit proliferation of
lymphocytes are useful therapeutically where suppression of an
immune response is beneficial.
[0715] The basic protocol for this assay is described in Current
Protocols in Immunology, unit 3.12; edited by J E Coligan, A M
Kruisbeek, D H Marglies, E M Shevach, W Strober, National Insitutes
of Health, Published by John Wiley & Sons, Inc.
[0716] More specifically, in one assay variant, peripheral blood
mononuclear cells (PBMC) are isolated from mammalian individuals,
for example a human volunteer, by leukopheresis (one donor will
supply stimulator PBMCs, the other donor will supply responder
PBMCs). If desired, the cells are frozen in fetal bovine serum and
DMSO after isolation. Frozen cells may be thawed overnight in assay
media (37.degree. C., 5% CO.sub.2) and then washed and resuspended
to 3.times.10.sup.6 cells/ml of assay media (RPMI; 10% fetal bovine
serum, 1% penicillin/streptomycin, 1% glutamine, 1% HEPES, 1%
non-essential amino acids, 1% pyruvate). The stimulator PBMCs are
prepared by irradiating the cells (about 3000 Rads).
[0717] The assay is prepared by plating in triplicate wells a
mixture of:
[0718] 100:1 of test sample diluted to 1% or to 0. 1%,
[0719] 50:1 of irradiated stimulator cells, and
[0720] 50:1 of responder PBMC cells.
[0721] 100 microliters of cell culture media or 100 microliter of
CD4-IgG is used as the control. The wells are then incubated at
37.degree. C., 5% CO.sub.2 for 4 days. On day 5, each well is
pulsed with tritiated thymidine (1.0 mC/well; Amersham). After 6
hours the cells are washed 3 times and then the uptake of the label
is evaluated.
[0722] In another variant of this assay, PBMCs are isolated from
the spleens of Balb/c mice and C57B6 mice. The cells are teased
from freshly harvested spleens in assay media (RPMI; 10% fetal
bovine serum, 1% penicillin/streptomycin, 1% glutamine, 1% HEPES,
1% non-essential amino acids, 1% pyruvate) and the PBMCs are
isolated by overlaying these cells over Lympholyte M (Organon
Teknika), centrifuging at 2000 rpm for 20 minutes, collecting and
washing the mononuclear cell layer in assay media and resuspending
the cells to 1.times.10.sup.7 cells/ml of assay media. The assay is
then conducted as described above.
[0723] Any decreases below control is considered to be a positive
result for an inhibitory compound, with decreases of less than or
equal to 80% being preferred. However, any value less than control
indicates an inhibitory effect for the test protein.
[0724] The following polypeptide tested positive in this assay:
PRO361.
EXAMPLE 35
Tissue Expression Distribution
[0725] Oligonucleotide probes were constructed from the PRO
polypeptide-cncoding nucleotide sequences shown in the accompanying
figures for use in quantitative PCR amplification reactions. The
oligonucleotide probes were chosen so as to give an approximately
200-600 base pair amplified fragment from the 3' end of its
associated template in a standard PCR reaction. The oligonucleotide
probes were employed in standard quantitative PCR amplification
reactions with cDNA libraries isolated from different human adult
and/or fetal tissue sources and analyzed by agarose gel
electrophoresis so as to obtain a quantitative determination of the
level of expression of the PRO polypeptide-encoding nucleic acid in
the various tissues tested. Knowledge of the expression pattern or
the differential expression of the PRO polypeptide-encoding nucleic
acid in various different human tissue types provides a diagnostic
marker useful for tissue typing, with or without other
tissue-specific markers, for determining the primary tissue source
of a metastatic tumor, and the like. The results of these assays
are shown in Table 24 below.
52TABLE 24 Not Significantly Nucleic Acid Significantly Expressed
In Expressed In DNA34392-1170 liver, kidney, brain, lung placenta
DNA39976-1215 brain lung DNA35595-1228 pancreas, brain, kidney,
liver DNA34436-1238 lung, placenta, brain testis DNA44176-1244
liver brain, lung DNA44192-1246 kidney liver DNA44804-1248 lung,
brain DNA41234-1242 lung, liver, kidney brain DNA45410-1250 lung,
brain, kidney, liver DNA46777-1253 liver, placenta, brain
EXAMPLE 36
Fetal Hemoglobin Induction in an Erythroblastic Cell Line (Assay
107)
[0726] This assay is useful for screening PRO polypeptides for the
ability to induce the switch from adult hemoglobin to fetal
hemoglobin in an erythroblastic cell line. Molecules testing
positive in this assay are expected to be useful for
therapeutically treating various mammalian hemoglobin-associated
disorders such as the various thalassemias. The assay is performed
as follows. Erythroblastic cells are plated in standard growth
medium at 1000 cells/well in a 96 well format. PRO polypeptides are
added to the growth medium at a concentration of 0.2% or 2% and the
cells are incubated for 5 days at 37.degree. C. As a positive
control, cells are treated with 100 .mu.M hemin and as a negative
control, the cells are untreated. After 5 days, cell lysates are
prepared and analyzed for the expression of gamma globin (a fetal
marker). A positive in the assay is a gamma globin level at least
2-fold above the negative control.
[0727] The following polypeptide tested positive in this assay:
PRO243.
EXAMPLE 37
In situ Hybridization
[0728] In situ hybridization is a powerful and versatile technique
for the detection and localization of nucleic acid sequences within
cell or tissue preparations. It may be useful, for example, to
identify sites of gene expression, analyze the tissue distribution
of transcription, identify and localize viral infection, follow
changes in specific mRNA synthesis and aid in chromosome
mapping.
[0729] In situ hybridization was performed following an optimized
version of the protocol by Lu and Gillett, Cell Vision 1:169-176
(1994), using PCR-generated .sup.33P-labeled riboprobes. Briefly,
formalin-fixed, paraffin-embedded human tissues were sectioned,
deparaffinized, deproteinated in proteinase K (20 g/ml) for 15
minutes at 37.degree. C., and further processed for in situ
hybridization as described by Lu and Gillett, supra. A [.sup.33-P]
UTP-labeled antisense riboprobe was generated from a PCR product
and hybridized at 55.degree. C. overnight. The slides were dipped
in Kodak NTB2 nuclear track emulsion and exposed for 4 weeks.
[0730] .sup.33P-Riboprobe Synthesis
[0731] 6.0 .mu.l (125 mCi) of .sup.33P-UTP (Amersham BF 1002,
SA<2000 Ci/mmol) were speed vac dried. To each tube containing
dried .sup.33P-UTP, the following ingredients were added:
[0732] 2.0 .mu.l 5.times.transcription buffer
[0733] 1.0 .mu.l DTT (100 mM)
[0734] 2.0 .mu.l NTP mix (2.5 mM: 10.mu.; each of 10 mM GTP, CTP
& ATP+10 .mu.l H.sub.2O)
[0735] 1.0 .mu.l UTP (50 .mu.M)
[0736] 1.0 .mu.l Rnasin
[0737] 1.0 .mu.l DNA template (1 .mu.g)
[0738] 1.0 .mu.l H.sub.2O
[0739] 1.0 .mu.l RNA polymerase (for PCR products T3=AS, T7=S,
usually)
[0740] The tubes were incubated at 37.degree. C. for one hour. 1.0
.mu.l RQ1 DNase were added, followed by incubation at 37.degree. C.
for 15 minutes. 90 .mu.l TE (10 mM Tris pH 7.6/1 mM EDTA pH 8.0)
were added, and the mixture pipetted onto DE81 paper. The remaining
solution was loaded in a Microcon-50 ultrafiltration unit, and spun
using program 10(6 minutes). The filtration unit was inverted over
a second tube and spun using program 2 (3 minutes). After the final
recovery spin, 100 .mu.l TE were added. 1 .mu.l of the final
product was pipetted on DE81 paper and counted in 6 ml of Biofluor
II.
[0741] The probe was run on a TBE/urea gel. 1-3 .mu.l of the probe
or 5 .mu.l of RNA Mrk III were added to 3 .mu.l of loading buffer.
After heating on a 95 .degree. C. heat block for three minutes, the
gel was immediately placed on ice. The wells of gel were flushed,
the sample loaded, and run at 180-250 volts for 45 minutes. The gel
was wrapped in saran wrap and exposed to XAR film with an
intensifying screen in -70.degree. C. freezer one hour to
overnight.
[0742] .sup.33P-Hybridization
[0743] A. Pretreatment of Frozen Sections
[0744] The slides were removed from the freezer, placed on
aluminium trays and thawed at room temperature for 5 minutes. The
trays were placed in 55.degree. C. incubator for five minutes to
reduce condensation. The slides were fixed for 10 minutes in 4%
paraformaldehyde on ice in the fume hood, and washed in
0.5.times.SSC for 5 minutes, at room temperature (25 ml
20.times.SSC+975 ml SQ H.sub.2O). After deproteination in 0.5
.mu.g/ml proteinase K for 10 minutes at 37.degree. C. (12.5 .mu.l
of 10 mg/ml stock in 250 ml prewarmed RNase-free RNAse buffer), the
sections were washed in 0.5.times.SSC for 10 minutes at room
temperature. The sections were dehydrated in 70%, 95%, 100%
ethanol, 2 minutes each.
[0745] B. Pretreatment of Paraffin-embedded Sections
[0746] The slides were deparaffinized, placed in SQ H.sub.2O, and
rinsed twice in 2.times.SSC at room temperature, for 5 minutes each
time. The sections were deproteinated in 20 .mu.g/ml proteinase K
(500 .mu.l of 10 mg/ml in 250 ml RNase-free RNase buffer;
37.degree. C., 15 minutes)--human embryo, or 8.times.proteinase K
(100 .mu.l in 250 ml Rnase buffer, 37.degree. C., 30
minutes)--formalin tissues. Subsequent rinsing in 0.5.times.SSC and
dehydration were performed as described above.
[0747] C. Prehybridization
[0748] The slides were laid out in a plastic box lined with Box
buffer (4.times.SSC, 50% formamide)--saturated filter paper. The
tissue was covered with 50 .mu.l of hybridization buffer (3.75g
Dextran Sulfate +6 ml SQ H.sub.2O), vortexed and heated in the
microwave for 2 minutes with the cap loosened. After cooling on
ice, 18.75 ml formamide, 3.75 ml 20.times.SSC and 9 ml SQ H.sub.2O
were added, the tissue was vortexed well, and incubated at
42.degree. C. for 1-4 hours.
[0749] D. Hybridization
[0750] 1.0.times.10.sup.6 cpm probe and 1.0 .mu.l tRNA (50 mg/ml
stock) per slide were heated at 95.degree. C. for 3 minutes. The
slides were cooled on ice, and 48 .mu.l hybridization buffer were
added per slide. After vortexing, 50 .mu.l .sup.33P mix were added
to 50 .mu.l prehybridization on slide. The slides were incubated
overnight at 55.degree. C.
[0751] E. Washes
[0752] Washing was done 2.times.10 minutes with 2.times.SSC, EDTA
at room temperature (400 ml 20.times.SSC +16 ml 0.25M EDTA,
V.sub.f=4L), followed by RNaseA treatment at 37.degree. C. for 30
minutes (500 .mu.l of 10 mg/ml in 250 ml Rnase buffer=20 .mu.g/ml),
The slides were washed 2.times.10 minutes with 2.times.SSC, EDTA at
room temperature. The stringency wash conditions were as follows: 2
hours at 55.degree. C., 0.1.times.SSC, EDTA (20 ml 20.times.SSC+16
ml EDTA, V.sub.f=4L).
[0753] F. Oligonucleotides
[0754] In situ analysis was performed on a variety of DNA sequences
disclosed herein. The oligonucleotides employed for these analyses
are as follows.
53 (1) DNA44804-1248 (PRO357) p1 5'-GGATTCTAATACGACTCACTAT-
AGGGCTGCCCGCAACCCCTTCAACTG-3' (SEQ ID NO:111) p2
5'-CTATGAAATTAACCCTCACTAAAGGGACCGCAGCTGGGTGACCGTGTA-3' (SEQ lD
NO:112) (2) DNA52722-1229 (PRO715) p1 5'-GGATTCTAATACGACTCACT-
ATAGGGCCGCCCCGCCACCTCCT-3' (SEQ ID NO:113) p2
5'-CTATGAAATTAACCCTCACTAAAGGGACTCGAGACACCACCTGACCCA-3' (SEQ ID
NO:114) p3 5'-GGATTCTAATACGACTCACTATAGGGCCCAAGGAAGGCAGGAGACTCT-3'
(SEQ ID NO:115) p4
5'-CTATGAAATTAACCCTCACTAAAGGGACTAGGGGGTGGGAATGAAAAG-3' (SEQ ID
NO:116) (3) DNA38113-1230 (PRO327) p1
5'-GGATTCTAATACGACTCACTATAGGGCCCCCCTGAGCTCTCCCGTGTA-3' (SEQ ID
NO:117) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAAGGCTCGCCACTGGTCGTAGA-3'
(SEQ ID NO:118) (4) DNA35917-1207 (PRO243) p1
5'-GGATTCTAATACGACTCACTATAGGGCAAGGAGCCGGGACCCAGGAGA-3' (SEQ ID
NO:119) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAGGGGGCCCTTGGTGCTGAGT-3'
(SEQ ID NO:120)
[0755] G. Results
[0756] In situ analysis was performed on a variety of DNA sequences
disclosed herein. The results from these analyses are as
follows.
[0757] (1) DNA44804-1248 (PRO357)
[0758] Low to moderate level expression at sites of bone formation
in fetal tissues and in the malignant cells of an osteosarcoma.
Possible signal in placenta and cord. All other tissues
negative.
[0759] Fetal tissues examined (E12-E16 weeks) include: liver,
kidney, adrenals, lungs, heart, great vessels, oesophagus, stomach,
spleen, gonad, brain, spinal cord and body wall.
[0760] Adult human tissues examined: liver, kidney, stomach,
spleen, adrenal, pancreas, lung, colonic carcinoma, renal cell
carcinoma and osteosarcoma. Acetominophen induced liver injury and
hepatic cirrhosis.
[0761] Chimp Tissues examined: thyroid, parathyroid, lymph node,
nerve, tongue, thymus, adrenal, gastric mucosa and salivary
gland.
[0762] Rhesus Monkey: cerebrum and cerebellum.
[0763] (2) DNA52722-1229 (PRO715)
[0764] Generalized high signal seen over many tissues--highest
signal seen over placenta, osteoblasts, injured renal tubules,
injured liver, colorectal liver metastasis and gall bladder.
[0765] Fetal tissues examined (E12-E16 weeks) include: placenta,
umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart,
great vessels, oesophagus, stomach, small intestine, spleen,
thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and
lower limb.
[0766] Adult human tissues examined: liver, kidney, adrenal,
myocardium, aorta, spleen, lung, skin, chondrosarcoma, eye,
stomach, colon, colonic carcinoma, prostate, bladder mucosa and
gall bladder. Acetominophen induced liver injury and hepatic
cirrhosis.
[0767] Rhesus Tissues examined: cerebral cortex (rm), hippocampus
(rm)
[0768] Chimp Tissues examined: thyroid, parathyroid, lymph node,
nerve, tongue, thymus, adrenal, gastric mucosa and salivary
gland.
[0769] (3) DNA38113-1230 (PRO327)
[0770] High level of expression observed in developing mouse and
human fetal lung. Normal human adult lung, including bronchial
epithelium, was negative. Expression in submucosa of human fetal
trachea, possibly in smooth muscle cells. Expression also observed
in non-trophoblastic cells of uncertain histogenesis in the human
placenta. In the mouse expression was observed in the developing
snout and in the developing tongue. All other tissues were
negative. Speculated function: Probable role in bronchial
development.
[0771] Fetal tissues examined (E12-E16 weeks) include: placenta,
umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart,
great vessels, oesophagus, stomach, small intestine, spleen,
thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and
lower limb.
[0772] Adult tissues examined: liver, kidney, adrenal, myocardium,
aorta, spleen, lymph node, pancreas, lung, skin, cerebral cortex
(rm), hippocampus (rm), cerebellum (rm), penis, eye, bladder,
stomach, gastric carcinoma, colon, colonic carcinoma, thyroid
(chimp), parathyroid (chimp) ovary (chimp) and chondrosarcoma.
[0773] (4) DNA35917-1207 (PRO243)
[0774] Cornelia de Lange syndrome (CdLS) is a congenital syndrome.
That means it is present from birth. CdLS is a disorder that causes
a delay in physical, intellectual, and langauge development. The
vast majority of children with CdLS are mentally retarded, with the
degree of mental retardation ranging from mild to severe. Reported
IQ's from 30 to 85. The average IQ is 53. The head and facial
features include small head size, thin eyebrows which often meet at
the midline, long eyelashes, short upturned nose, thin downturned
lips, lowset ears and high arched palate or cleft palate. Other
characteristics may include language delay, even in the most mildly
affected, delayed growth and small stature, low pitched cry, small
hands and feet, incurved fifth fingers, simian creases, and
excessive body hair. Diagnosis depends on the presence of a
combination of these characteristics. Many of these characteristics
appear in varying degrees. In some cases these characteristics may
not be present or be so mild that they will be recognized only when
observed by a trained geneticist or other person familar with the
syndrome. Although much is known about CdLS, recent reports suggest
that there is much more to be learned.
[0775] In this study additional sections of human fetal face, head,
limbs and mouse embryos were examined. No expression was seen in
any of the mouse tissues. Expression was only seen with the
antisense probe.
[0776] Expression was observed adjacent to developing limb and
facial bones in the perosteal mesenchyme. The expression was highly
specific and was often adjacent to areas undergoing
vascularization. The distribution is consistent with the observed
skeletal abnormalities in the Cornelia de Lange syndrome.
Expression was also observed in the developing temporal and
occipital lobes of the fetal brain, but was not observed elsewhere.
In addition, expression was seen in the ganglia of the developing
inner ear; the significance of this finding is unclear.
[0777] Though these data do not provide functional information, the
distribution is consistent with the sites that are known to be
affected most severely in this syndrome.
[0778] Additionally, faint expression was observed at the cleavage
line in the developing synovial joint forming between the femoral
head and acetabulum (hip joint). If this pattern of expression were
observed at sites of joint formation elsewhere, it might explain
the facial and limb abnormalities observed in the Cornelia de Lange
syndrome.
EXAMPLE 38
Activity of PRO243 mRNA in Xenopus Oocytes
[0779] In order to demonstrate that the human chordin clone
(DNA35917-1207) encoding PRO243 is functional and acts in a manner
predicted by the Xenopus chordin and Drosophila sog genes,
supercoiled plasmid DNA from DNA35917-1207 was prepared by Qiagen
and used for injection into Xenopus laevis embryos. Micro-injection
of Xenopus chordin mRNA into ventrovegetal blastomeres induces
secondary (twinned) axes (Sasai et al., Cell 79:779-790 (1994)) and
Drosophila sog also induces a secondary axis when ectopically
expresed on the ventral side of the Xenopus embryo (Holley et al.,
Nature 376:249-253 (1995) and Schmidt et al., Development
121:4319-4328 (1995)). The ability of sog to function in Xenopus
ooctyes suggests that the processes involved in dorsoventral
patterning have been conserved during evolution.
[0780] Methods
[0781] Manipulation of Xenopus Embryos
[0782] Adult female frogs were boosted with 200 I.U. pregnant mare
serum 3 days before use and with 800 I.U. of human chorionic
gonadotropin the night before injection. Fresh oocytes were
squeezed out from female frogs the next morning and in vitro
fertilization of oocytes was performed by mixing oocytes with
minced testis from sacrificed male frogs. Developing embryos were
maintained and staged according to Nieuwkoop and Faber, Normal
Table of Xenopus laevis, N.-H. P. Co., ed. (Amsterdam, 1967).
[0783] Fertilized eggs were dejellied with 2% cysteine (pH 7.8) for
10 minutes, washed once with distilled water and transferred to
0.1.times.MBS with 5% Ficoll. Fertilized eggs were lined on
injection trays in 0.1.times.MBS with 5% Ficoll. Two-cell stage
developing Xenopus embryos were injected with 200 pg of pRK5
containing wild type chordin (DNA35917-1207) or 200 pg of pRK5
without an insert as a control. Injected embryos were kept on trays
for another 6 hours, after which they were transferred to
0.1.times.MBS with 50 mg/ml gentamycin until reaching Nieukwkoop
stage 37-38.
[0784] Results
[0785] Injection of human chordin cDNA into single blastomeres
resulted in the ventralization of the tadpole. The ventralization
of the tadpole is visible in the shortening and kinking of the tail
and the expansion of the cement gland. The ability of human chordin
to function as a ventralizing agent in Xenopus shows that the
protein encoded by DNA35917-1207 is functional and influences
dorsal-ventral patterning in frogs and suggests that the processes
involved in dorsoventral patterning have been conserved during
evolution, with mechanisms in common between humans, flies and
frogs.
[0786] Deposit of Material
[0787] The following materials have been deposited with the
American Type Culture Collection, 10801 University Blvd., Manassas,
Va. 20110-2209, USA (ATCC):
54 Material ATCC Dep. No. Deposit Date DNA34392-1170 ATCC 209526
December 10, 1997 DNA35917-1207 ATCC 209508 December 3, 1997
DNA39976-1215 ATCC 209524 December 10, 1997 DNA35595-1228 ATCC
209528 December 10, 1997 DNA38113-1230 ATCC 209530 December 10,
1997 DNA34436-1238 ATCC 209523 December 10, 1997 DNA40592-1242 ATCC
209492 November 21, 1997 DNA44176-1244 ATCC 209532 December 10,
1997 DNA44192-1246 ATCC 209531 December 10, 1997 DNA39518-1247 ATCC
209529 December 10, 1997 DNA44804-1248 ATCC 209527 December 10,
1997 DNA52722-1229 ATCC 209570 January 7, 1998 DNA41234-1242 ATCC
209618 February 5, 1998 DNA45410-1250 ATCC 209621 February 5, 1998
DNA46777-1253 ATCC 209619 February 5, 1998
[0788] These deposit were made under the provisions of the Budapest
Treaty on the International Recognition of the Deposit of
Microorganisms for the Purpose of Patent Procedure and the
Regulations thereunder (Budapest Treaty). This assures maintenance
of a viable culture of the deposit for 30 years from the date of
deposit. The deposits will be made available by ATCC under the
terms of the Budapest Treaty, and subject to an agreement between
Genentech, Inc. and ATCC, which assures permanent and unrestricted
availability of the progeny of the culture of the deposit to the
public upon issuance of the pertinent U.S. patent or upon laying
open to the public of any U.S. or foreign patent application,
whichever comes first, and assures availability of the progeny to
one determined by the U.S. Commissioner of Patents and Trademarks
to be entitled thereto according to 35 USC .sctn.122 and the
Commissioner's rules pursuant thereto (including 37 CFR .sctn.1.14
with particular reference to 886 OG 638).
[0789] The assignee of the present application has agreed that if a
culture of the materials on deposit should die or be lost or
destroyed when cultivated under suitable conditions, the materials
will be promptly replaced on notification with another of the same.
Availability of the deposited material is not to be construed as a
license to practice the invention in contravention of the rights
granted under the authority of any government in accordance with
its patent laws.
[0790] The foregoing written specification is considered to be
sufficient to enable one skilled in the art to practice the
invention. The present invention is not to be limited in scope by
the construct deposited, since the deposited embodiment is intended
as a single illustration of certain aspects of the invention and
any constructs that are functionally equivalent are within the
scope of this invention. The deposit of material herein does not
constitute an admission that the written description herein
contained is inadequate to enable the practice of any aspect of the
invention, including the best mode thereof, nor is it to be
construed as limiting the scope of the claims to the specific
illustrations that it represents. Indeed, various modifications of
the invention in addition to those shown and described herein will
become apparent to those skilled in the art from the foregoing
description and fall within the scope of the appended claims.
Sequence CWU 1
1
120 1 2454 DNA Homo Sapien 1 ggactaatct gtgggagcag tttattccag
tatcacccag ggtgcagcca 50 caccaggact gtgttgaagg gtgttttttt
tcttttaaat gtaatacctc 100 ctcatctttt cttcttacac agtgtctgag
aacatttaca ttatagataa 150 gtagtacatg gtggataact tctactttta
ggaggactac tctcttctga 200 cagtcctaga ctggtcttct acactaagac
accatgaagg agtatgtgct 250 cctattattc ctggctttgt gctctgccaa
acccttcttt agcccttcac 300 acatcgcact gaagaatatg atgctgaagg
atatggaaga cacagatgat 350 gatgatgatg atgatgatga tgatgatgat
gatgaggaca actctctttt 400 tccaacaaga gagccaagaa gccatttttt
tccatttgat ctgtttccaa 450 tgtgtccatt tggatgtcag tgctattcac
gagttgtaca ttgctcagat 500 ttaggtttga cctcagtccc aaccaacatt
ccatttgata ctcgaatgct 550 tgatcttcaa aacaataaaa ttaaggaaat
caaagaaaat gattttaaag 600 gactcacttc actttatggt ctgatcctga
acaacaacaa gctaacgaag 650 attcacccaa aagcctttct aaccacaaag
aagttgcgaa ggctgtatct 700 gtcccacaat caactaagtg aaataccact
taatcttccc aaatcattag 750 cagaactcag aattcatgaa aataaagtta
agaaaataca aaaggacaca 800 ttcaaaggaa tgaatgcttt acacgttttg
gaaatgagtg caaaccctct 850 tgataataat gggatagagc caggggcatt
tgaaggggtg acggtgttcc 900 atatcagaat tgcagaagca aaactgacct
cagttcctaa aggcttacca 950 ccaactttat tggagcttca cttagattat
aataaaattt caacagtgga 1000 acttgaggat tttaaacgat acaaagaact
acaaaggctg ggcctaggaa 1050 acaacaaaat cacagatatc gaaaatggga
gtcttgctaa cataccacgt 1100 gtgagagaaa tacatttgga aaacaataaa
ctaaaaaaaa tcccttcagg 1150 attaccagag ttgaaatacc tccagataat
cttccttcat tctaattcaa 1200 ttgcaagagt gggagtaaat gacttctgtc
caacagtgcc aaagatgaag 1250 aaatctttat acagtgcaat aagtttattc
aacaacccgg tgaaatactg 1300 ggaaatgcaa cctgcaacat ttcgttgtgt
tttgagcaga atgagtgttc 1350 agcttgggaa ctttggaatg taataattag
taattggtaa tgtccattta 1400 atataagatt caaaaatccc tacatttgga
atacttgaac tctattaata 1450 atggtagtat tatatataca agcaaatatc
tattctcaag tggtaagtcc 1500 actgacttat tttatgacaa gaaatttcaa
cggaattttg ccaaactatt 1550 gatacataag gggttgagag aaacaagcat
ctattgcagt ttcctttttg 1600 cgtacaaatg atcttacata aatctcatgc
ttgaccattc ctttcttcat 1650 aacaaaaaag taagatattc ggtatttaac
actttgttat caagcacatt 1700 ttaaaaagaa ctgtactgta aatggaatgc
ttgacttagc aaaatttgtg 1750 ctctttcatt tgctgttaga aaaacagaat
taacaaagac agtaatgtga 1800 agagtgcatt acactattct tattctttag
taacttgggt agtactgtaa 1850 tatttttaat catcttaaag tatgatttga
tataatctta ttgaaattac 1900 cttatcatgt cttagagccc gtctttatgt
ttaaaactaa tttcttaaaa 1950 taaagccttc agtaaatgtt cattaccaac
ttgataaatg ctactcataa 2000 gagctggttt ggggctatag catatgcttt
ttttttttta attattacct 2050 gatttaaaaa tctctgtaaa aacgtgtagt
gtttcataaa atctgtaact 2100 cgcattttaa tgatccgcta ttataagctt
ttaatagcat gaaaattgtt 2150 aggctatata acattgccac ttcaactcta
aggaatattt ttgagatatc 2200 cctttggaag accttgcttg gaagagcctg
gacactaaca attctacacc 2250 aaattgtctc ttcaaatacg tatggactgg
ataactctga gaaacacatc 2300 tagtataact gaataagcag agcatcaaat
taaacagaca gaaaccgaaa 2350 gctctatata aatgctcaga gttctttatg
tatttcttat tggcattcaa 2400 catatgtaaa atcagaaaac agggaaattt
tcattaaaaa tattggtttg 2450 aaat 2454 2 379 PRT Homo Sapien 2 Met
Lys Glu Tyr Val Leu Leu Leu Phe Leu Ala Leu Cys Ser Ala 1 5 10 15
Lys Pro Phe Phe Ser Pro Ser His Ile Ala Leu Lys Asn Met Met 20 25
30 Leu Lys Asp Met Glu Asp Thr Asp Asp Asp Asp Asp Asp Asp Asp 35
40 45 Asp Asp Asp Asp Asp Glu Asp Asn Ser Leu Phe Pro Thr Arg Glu
50 55 60 Pro Arg Ser His Phe Phe Pro Phe Asp Leu Phe Pro Met Cys
Pro 65 70 75 Phe Gly Cys Gln Cys Tyr Ser Arg Val Val His Cys Ser
Asp Leu 80 85 90 Gly Leu Thr Ser Val Pro Thr Asn Ile Pro Phe Asp
Thr Arg Met 95 100 105 Leu Asp Leu Gln Asn Asn Lys Ile Lys Glu Ile
Lys Glu Asn Asp 110 115 120 Phe Lys Gly Leu Thr Ser Leu Tyr Gly Leu
Ile Leu Asn Asn Asn 125 130 135 Lys Leu Thr Lys Ile His Pro Lys Ala
Phe Leu Thr Thr Lys Lys 140 145 150 Leu Arg Arg Leu Tyr Leu Ser His
Asn Gln Leu Ser Glu Ile Pro 155 160 165 Leu Asn Leu Pro Lys Ser Leu
Ala Glu Leu Arg Ile His Glu Asn 170 175 180 Lys Val Lys Lys Ile Gln
Lys Asp Thr Phe Lys Gly Met Asn Ala 185 190 195 Leu His Val Leu Glu
Met Ser Ala Asn Pro Leu Asp Asn Asn Gly 200 205 210 Ile Glu Pro Gly
Ala Phe Glu Gly Val Thr Val Phe His Ile Arg 215 220 225 Ile Ala Glu
Ala Lys Leu Thr Ser Val Pro Lys Gly Leu Pro Pro 230 235 240 Thr Leu
Leu Glu Leu His Leu Asp Tyr Asn Lys Ile Ser Thr Val 245 250 255 Glu
Leu Glu Asp Phe Lys Arg Tyr Lys Glu Leu Gln Arg Leu Gly 260 265 270
Leu Gly Asn Asn Lys Ile Thr Asp Ile Glu Asn Gly Ser Leu Ala 275 280
285 Asn Ile Pro Arg Val Arg Glu Ile His Leu Glu Asn Asn Lys Leu 290
295 300 Lys Lys Ile Pro Ser Gly Leu Pro Glu Leu Lys Tyr Leu Gln Ile
305 310 315 Ile Phe Leu His Ser Asn Ser Ile Ala Arg Val Gly Val Asn
Asp 320 325 330 Phe Cys Pro Thr Val Pro Lys Met Lys Lys Ser Leu Tyr
Ser Ala 335 340 345 Ile Ser Leu Phe Asn Asn Pro Val Lys Tyr Trp Glu
Met Gln Pro 350 355 360 Ala Thr Phe Arg Cys Val Leu Ser Arg Met Ser
Val Gln Leu Gly 365 370 375 Asn Phe Gly Met 3 20 DNA Artificial
Sequence Synthetic Oligonucleotide Probe 3 ggaaatgagt gcaaaccctc 20
4 24 DNA Artificial Sequence Synthetic Oligonucleotide Probe 4
tcccaagctg aacactcatt ctgc 24 5 50 DNA Artificial Sequence
Synthetic Oligonucleotide Probe 5 gggtgacggt gttccatatc agaattgcag
aagcaaaact gacctcagtt 50 6 3441 DNA Homo Sapien 6 cggacgcgtg
ggcggacgcg tgggcccgcs gcaccgcccc cggcccggcc 50 ctccgccctc
cgcactcgcg cctccctccc tccgcccgct cccgcgccct 100 cctccctccc
tcctccccag ctgtcccgtt cgcgtcatgc cgagcctccc 150 ggccccgccg
gccccgctgc tgctcctcgg gctgctgctg ctcggctccc 200 ggccggcccg
cggcgccggc ccagagcccc ccgtgctgcc catccgttct 250 gagaaggagc
cgctgcccgt tcggggagcg gcaggctgca ccttcggcgg 300 gaaggtctat
gccttggacg agacgtggca cccggaccta gggcagccat 350 tcggggtgat
gcgctgcgtg ctgtgcgcct gcgaggcgcc tcagtggggt 400 cgccgtacca
ggggccctgg cagggtcagc tgcaagaaca tcaaaccaga 450 gtgcccaacc
ccggcctgtg ggcagccgcg ccagctgccg ggacactgct 500 gccagacctg
cccccaggag cgcagcagtt cggagcggca gccgagcggc 550 ctgtccttcg
agtatccgcg ggacccggag catcgcagtt atagcgaccg 600 cggggagcca
ggcgctgagg agcgggcccg tggtgacggc cacacggact 650 tcgtggcgct
gctgacaggg ccgaggtcgc aggcggtggc acgagcccga 700 gtctcgctgc
tgcgctctag cctccgcttc tctatctcct acaggcggct 750 ggaccgccct
accaggatcc gcttctcaga ctccaatggc agtgtcctgt 800 ttgagcaccc
tgcagccccc acccaagatg gcctggtctg tggggtgtgg 850 cgggcagtgc
ctcggttgtc tctgcggctc cttagggcag aacagctgca 900 tgtggcactt
gtgacactca ctcacccttc aggggaggtc tgggggcctc 950 tcatccggca
ccgggccctg gctgcagaga ccttcagtgc catcctgact 1000 ctagaaggcc
ccccacagca gggcgtaggg ggcatcaccc tgctcactct 1050 cagtgacaca
gaggactcct tgcatttttt gctgctcttc cgagggctgc 1100 tggaacccag
gagtggggga ctaacccagg ttcccttgag gctccagatt 1150 ctacaccagg
ggcagctact gcgagaactt caggccaatg tctcagccca 1200 ggaaccaggc
tttgctgagg tgctgcccaa cctgacagtc caggagatgg 1250 actggctggt
gctgggggag ctgcagatgg ccctggagtg ggcaggcagg 1300 ccagggctgc
gcatcagtgg acacattgct gccaggaaga gctgcgacgt 1350 cctgcaaagt
gtcctttgtg gggctgatgc cctgatccca gtccagacgg 1400 gtgctgccgg
ctcagccagc ctcacgctgc taggaaatgg ctccctgatc 1450 tatcaggtgc
aagtggtagg gacaagcagt gaggtggtgg ccatgacact 1500 ggagaccaag
cctcagcgga gggatcagcg cactgtcctg tgccacatgg 1550 ctggactcca
gccaggagga cacacggccg tgggtatctg ccctgggctg 1600 ggtgcccgag
gggctcatat gctgctgcag aatgagctct tcctgaacgt 1650 gggcaccaag
gacttcccag acggagagct tcgggggcac gtggctgccc 1700 tgccctactg
tgggcatagc gcccgccatg acacgctgcc cgtgccccta 1750 gcaggagccc
tggtgctacc ccctgtgaag agccaagcag cagggcacgc 1800 ctggctttcc
ttggataccc actgtcacct gcactatgaa gtgctgctgg 1850 ctgggcttgg
tggctcagaa caaggcactg tcactgccca cctccttggg 1900 cctcctggaa
cgccagggcc tcggcggctg ctgaagggat tctatggctc 1950 agaggcccag
ggtgtggtga aggacctgga gccggaactg ctgcggcacc 2000 tggcaaaagg
catggcctcc ctgatgatca ccaccaaggg tagccccaga 2050 ggggagctcc
gagggcaggt gcacatagcc aaccaatgtg aggttggcgg 2100 actgcgcctg
gaggcggccg gggccgaggg ggtgcgggcg ctgggggctc 2150 cggatacagc
ctctgctgcg ccgcctgtgg tgcctggtct cccggcccta 2200 gcgcccgcca
aacctggtgg tcctgggcgg ccccgagacc ccaacacatg 2250 cttcttcgag
gggcagcagc gcccccacgg ggctcgctgg gcgcccaact 2300 acgacccgct
ctgctcactc tgcacctgcc agagacgaac ggtgatctgt 2350 gacccggtgg
tgtgcccacc gcccagctgc ccacacccgg tgcaggctcc 2400 cgaccagtgc
tgccctgttt gccctgagaa acaagatgtc agagacttgc 2450 cagggctgcc
aaggagccgg gacccaggag agggctgcta ttttgatggt 2500 gaccggagct
ggcgggcagc gggtacgcgg tggcaccccg ttgtgccccc 2550 ctttggctta
attaagtgtg ctgtctgcac ctgcaagggg ggcactggag 2600 aggtgcactg
tgagaaggtg cagtgtcccc ggctggcctg tgcccagcct 2650 gtgcgtgtca
accccaccga ctgctgcaaa cagtgtccag tggggtcggg 2700 ggcccacccc
cagctggggg accccatgca ggctgatggg ccccggggct 2750 gccgttttgc
tgggcagtgg ttcccagaga gtcagagctg gcacccctca 2800 gtgccccctt
ttggagagat gagctgtatc acctgcagat gtggggcagg 2850 ggtgcctcac
tgtgagcggg atgactgttc actgccactg tcctgtggct 2900 cggggaagga
gagtcgatgc tgttcccgct gcacggccca ccggcggccc 2950 ccagagacca
gaactgatcc agagctggag aaagaagccg aaggctctta 3000 gggagcagcc
agagggccaa gtgaccaaga ggatggggcc tgagctgggg 3050 aaggggtggc
atcgaggacc ttcttgcatt ctcctgtggg aagcccagtg 3100 cctttgctcc
tctgtcctgc ctctactccc acccccacta cctctgggaa 3150 ccacagctcc
acaaggggga gaggcagctg ggccagaccg aggtcacagc 3200 cactccaagt
cctgccctgc caccctcggc ctctgtcctg gaagccccac 3250 ccctttcctc
ctgtacataa tgtcactggc ttgttgggat ttttaattta 3300 tcttcactca
gcaccaaggg cccccgacac tccactcctg ctgcccctga 3350 gctgagcaga
gtcattattg gagagttttg tatttattaa aacatttctt 3400 tttcagtcaa
aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa a 3441 7 954 PRT Homo Sapien 7 Met
Pro Ser Leu Pro Ala Pro Pro Ala Pro Leu Leu Leu Leu Gly 1 5 10 15
Leu Leu Leu Leu Gly Ser Arg Pro Ala Arg Gly Ala Gly Pro Glu 20 25
30 Pro Pro Val Leu Pro Ile Arg Ser Glu Lys Glu Pro Leu Pro Val 35
40 45 Arg Gly Ala Ala Gly Cys Thr Phe Gly Gly Lys Val Tyr Ala Leu
50 55 60 Asp Glu Thr Trp His Pro Asp Leu Gly Gln Pro Phe Gly Val
Met 65 70 75 Arg Cys Val Leu Cys Ala Cys Glu Ala Pro Gln Trp Gly
Arg Arg 80 85 90 Thr Arg Gly Pro Gly Arg Val Ser Cys Lys Asn Ile
Lys Pro Glu 95 100 105 Cys Pro Thr Pro Ala Cys Gly Gln Pro Arg Gln
Leu Pro Gly His 110 115 120 Cys Cys Gln Thr Cys Pro Gln Glu Arg Ser
Ser Ser Glu Arg Gln 125 130 135 Pro Ser Gly Leu Ser Phe Glu Tyr Pro
Arg Asp Pro Glu His Arg 140 145 150 Ser Tyr Ser Asp Arg Gly Glu Pro
Gly Ala Glu Glu Arg Ala Arg 155 160 165 Gly Asp Gly His Thr Asp Phe
Val Ala Leu Leu Thr Gly Pro Arg 170 175 180 Ser Gln Ala Val Ala Arg
Ala Arg Val Ser Leu Leu Arg Ser Ser 185 190 195 Leu Arg Phe Ser Ile
Ser Tyr Arg Arg Leu Asp Arg Pro Thr Arg 200 205 210 Ile Arg Phe Ser
Asp Ser Asn Gly Ser Val Leu Phe Glu His Pro 215 220 225 Ala Ala Pro
Thr Gln Asp Gly Leu Val Cys Gly Val Trp Arg Ala 230 235 240 Val Pro
Arg Leu Ser Leu Arg Leu Leu Arg Ala Glu Gln Leu His 245 250 255 Val
Ala Leu Val Thr Leu Thr His Pro Ser Gly Glu Val Trp Gly 260 265 270
Pro Leu Ile Arg His Arg Ala Leu Ala Ala Glu Thr Phe Ser Ala 275 280
285 Ile Leu Thr Leu Glu Gly Pro Pro Gln Gln Gly Val Gly Gly Ile 290
295 300 Thr Leu Leu Thr Leu Ser Asp Thr Glu Asp Ser Leu His Phe Leu
305 310 315 Leu Leu Phe Arg Gly Leu Leu Glu Pro Arg Ser Gly Gly Leu
Thr 320 325 330 Gln Val Pro Leu Arg Leu Gln Ile Leu His Gln Gly Gln
Leu Leu 335 340 345 Arg Glu Leu Gln Ala Asn Val Ser Ala Gln Glu Pro
Gly Phe Ala 350 355 360 Glu Val Leu Pro Asn Leu Thr Val Gln Glu Met
Asp Trp Leu Val 365 370 375 Leu Gly Glu Leu Gln Met Ala Leu Glu Trp
Ala Gly Arg Pro Gly 380 385 390 Leu Arg Ile Ser Gly His Ile Ala Ala
Arg Lys Ser Cys Asp Val 395 400 405 Leu Gln Ser Val Leu Cys Gly Ala
Asp Ala Leu Ile Pro Val Gln 410 415 420 Thr Gly Ala Ala Gly Ser Ala
Ser Leu Thr Leu Leu Gly Asn Gly 425 430 435 Ser Leu Ile Tyr Gln Val
Gln Val Val Gly Thr Ser Ser Glu Val 440 445 450 Val Ala Met Thr Leu
Glu Thr Lys Pro Gln Arg Arg Asp Gln Arg 455 460 465 Thr Val Leu Cys
His Met Ala Gly Leu Gln Pro Gly Gly His Thr 470 475 480 Ala Val Gly
Ile Cys Pro Gly Leu Gly Ala Arg Gly Ala His Met 485 490 495 Leu Leu
Gln Asn Glu Leu Phe Leu Asn Val Gly Thr Lys Asp Phe 500 505 510 Pro
Asp Gly Glu Leu Arg Gly His Val Ala Ala Leu Pro Tyr Cys 515 520 525
Gly His Ser Ala Arg His Asp Thr Leu Pro Val Pro Leu Ala Gly 530 535
540 Ala Leu Val Leu Pro Pro Val Lys Ser Gln Ala Ala Gly His Ala 545
550 555 Trp Leu Ser Leu Asp Thr His Cys His Leu His Tyr Glu Val Leu
560 565 570 Leu Ala Gly Leu Gly Gly Ser Glu Gln Gly Thr Val Thr Ala
His 575 580 585 Leu Leu Gly Pro Pro Gly Thr Pro Gly Pro Arg Arg Leu
Leu Lys 590 595 600 Gly Phe Tyr Gly Ser Glu Ala Gln Gly Val Val Lys
Asp Leu Glu 605 610 615 Pro Glu Leu Leu Arg His Leu Ala Lys Gly Met
Ala Ser Leu Met 620 625 630 Ile Thr Thr Lys Gly Ser Pro Arg Gly Glu
Leu Arg Gly Gln Val 635 640 645 His Ile Ala Asn Gln Cys Glu Val Gly
Gly Leu Arg Leu Glu Ala 650 655 660 Ala Gly Ala Glu Gly Val Arg Ala
Leu Gly Ala Pro Asp Thr Ala 665 670 675 Ser Ala Ala Pro Pro Val Val
Pro Gly Leu Pro Ala Leu Ala Pro 680 685 690 Ala Lys Pro Gly Gly Pro
Gly Arg Pro Arg Asp Pro Asn Thr Cys 695 700 705 Phe Phe Glu Gly Gln
Gln Arg Pro His Gly Ala Arg Trp Ala Pro 710 715 720 Asn Tyr Asp Pro
Leu Cys Ser Leu Cys Thr Cys Gln Arg Arg Thr 725 730 735 Val Ile Cys
Asp Pro Val Val Cys Pro Pro Pro Ser Cys Pro His 740 745 750 Pro Val
Gln Ala Pro Asp Gln Cys Cys Pro Val Cys Pro Glu Lys 755 760 765 Gln
Asp
Val Arg Asp Leu Pro Gly Leu Pro Arg Ser Arg Asp Pro 770 775 780 Gly
Glu Gly Cys Tyr Phe Asp Gly Asp Arg Ser Trp Arg Ala Ala 785 790 795
Gly Thr Arg Trp His Pro Val Val Pro Pro Phe Gly Leu Ile Lys 800 805
810 Cys Ala Val Cys Thr Cys Lys Gly Gly Thr Gly Glu Val His Cys 815
820 825 Glu Lys Val Gln Cys Pro Arg Leu Ala Cys Ala Gln Pro Val Arg
830 835 840 Val Asn Pro Thr Asp Cys Cys Lys Gln Cys Pro Val Gly Ser
Gly 845 850 855 Ala His Pro Gln Leu Gly Asp Pro Met Gln Ala Asp Gly
Pro Arg 860 865 870 Gly Cys Arg Phe Ala Gly Gln Trp Phe Pro Glu Ser
Gln Ser Trp 875 880 885 His Pro Ser Val Pro Pro Phe Gly Glu Met Ser
Cys Ile Thr Cys 890 895 900 Arg Cys Gly Ala Gly Val Pro His Cys Glu
Arg Asp Asp Cys Ser 905 910 915 Leu Pro Leu Ser Cys Gly Ser Gly Lys
Glu Ser Arg Cys Cys Ser 920 925 930 Arg Cys Thr Ala His Arg Arg Pro
Pro Glu Thr Arg Thr Asp Pro 935 940 945 Glu Leu Glu Lys Glu Ala Glu
Gly Ser 950 8 44 DNA Artificial Sequence Synthetic Oligonucleotide
probe 8 gactagttct agatcgcgag cggccgccct tttttttttt tttt 44 9 28
DNA Artificial Sequence Synthetic oligonucleotide probe 9
cggacgcgtg gggcctgcgc acccagct 28 10 36 DNA Artificial Sequence
Synthetic oligonucleotide probe 10 gccgctcccc gaacgggcag cggctccttc
tcagaa 36 11 36 DNA Artificial Sequence Synthetic oligonucleotide
probe 11 ggcgcacagc acgcagcgca tcaccccgaa tggctc 36 12 26 DNA
Artificial Sequence Synthetic Oligonucleotide Probe 12 gtgctgccca
tccgttctga gaagga 26 13 22 DNA Artificial Sequence Synthetic
oligonucleotide probe 13 gcagggtgct caaacaggac ac 22 14 3231 DNA
Homo Sapien 14 ggcggagcag ccctagccgc caccgtcgct ctcgcagctc
tcgtcgccac 50 tgccaccgcc gccgccgtca ctgcgtcctg gctccggctc
ccgcgccctc 100 ccggccggcc atgcagcccc gccgcgccca ggcgcccggt
gcgcagctgc 150 tgcccgcgct ggccctgctg ctgctgctgc tcggagcggg
gccccgaggc 200 agctccctgg ccaacccggt gcccgccgcg cccttgtctg
cgcccgggcc 250 gtgcgccgcg cagccctgcc ggaatggggg tgtgtgcacc
tcgcgccctg 300 agccggaccc gcagcacccg gcccccgccg gcgagcctgg
ctacagctgc 350 acctgccccg ccgggatctc cggcgccaac tgccagcttg
ttgcagatcc 400 ttgtgccagc aacccttgtc accatggcaa ctgcagcagc
agcagcagca 450 gcagcagcga tggctacctc tgcatttgca atgaaggcta
tgaaggtccc 500 aactgtgaac aggcacttcc cagtctccca gccactggct
ggaccgaatc 550 catggcaccc cgacagcttc agcctgttcc tgctactcag
gagcctgaca 600 aaatcctgcc tcgctctcag gcaacggtga cactgcctac
ctggcagccg 650 aaaacagggc agaaagttgt agaaatgaaa tgggatcaag
tggaggtgat 700 cccagatatt gcctgtggga atgccagttc taacagctct
gcgggtggcc 750 gcctggtatc ctttgaagtg ccacagaaca cctcagtcaa
gattcggcaa 800 gatgccactg cctcactgat tttgctctgg aaggtcacgg
ccacaggatt 850 ccaacagtgc tccctcatag atggacgaag tgtgaccccc
cttcaggctt 900 cagggggact ggtcctcctg gaggagatgc tcgccttggg
gaataatcac 950 tttattggtt ttgtgaatga ttctgtgact aagtctattg
tggctttgcg 1000 cttaactctg gtggtgaagg tcagcacctg tgtgccgggg
gagagtcacg 1050 caaatgactt ggagtgttca ggaaaaggaa aatgcaccac
gaagccgtca 1100 gaggcaactt tttcctgtac ctgtgaggag cagtacgtgg
gtactttctg 1150 tgaagaatac gatgcttgcc agaggaaacc ttgccaaaac
aacgcgagct 1200 gtattgatgc aaatgaaaag caagatggga gcaatttcac
ctgtgtttgc 1250 cttcctggtt atactggaga gctttgccag tccaagattg
attactgcat 1300 cctagaccca tgcagaaatg gagcaacatg catttccagt
ctcagtggat 1350 tcacctgcca gtgtccagaa ggatacttcg gatctgcttg
tgaagaaaag 1400 gtggacccct gcgcctcgtc tccgtgccag aacaacggca
cctgctatgt 1450 ggacggggta cactttacct gcaactgcag cccgggcttc
acagggccga 1500 cctgtgccca gcttattgac ttctgtgccc tcagcccctg
tgctcatggc 1550 acgtgccgca gcgtgggcac cagctacaaa tgcctctgtg
atccaggtta 1600 ccatggcctc tactgtgagg aggaatataa tgagtgcctc
tccgctccat 1650 gcctgaatgc agccacctgc agggacctcg ttaatggcta
tgagtgtgtg 1700 tgcctggcag aatacaaagg aacacactgt gaattgtaca
aggatccctg 1750 cgctaacgtc agctgtctga acggagccac ctgtgacagc
gacggcctga 1800 atggcacgtg catctgtgca cccgggttta caggtgaaga
gtgcgacatt 1850 gacataaatg aatgtgacag taacccctgc caccatggtg
ggagctgcct 1900 ggaccagccc aatggttata actgccactg cccgcatggt
tgggtgggag 1950 caaactgtga gatccacctc caatggaagt ccgggcacat
ggcggagagc 2000 ctcaccaaca tgccacggca ctccctctac atcatcattg
gagccctctg 2050 cgtggccttc atccttatgc tgatcatcct gatcgtgggg
atttgccgca 2100 tcagccgcat tgaataccag ggttcttcca ggccagccta
tgaggagttc 2150 tacaactgcc gcagcatcga cagcgagttc agcaatgcca
ttgcatccat 2200 ccggcatgcc aggtttggaa agaaatcccg gcctgcaatg
tatgatgtga 2250 gccccatcgc ctatgaagat tacagtcctg atgacaaacc
cttggtcaca 2300 ctgattaaaa ctaaagattt gtaatctttt tttggattat
ttttcaaaaa 2350 gatgagatac tacactcatt taaatatttt taagaaaata
aaaagcttaa 2400 gaaatttaaa atgctagctg ctcaagagtt ttcagtagaa
tatttaagaa 2450 ctaattttct gcagctttta gtttggaaaa aatattttaa
aaacaaaatt 2500 tgtgaaacct atagacgatg ttttaatgta ccttcagctc
tctaaactgt 2550 gtgcttctac tagtgtgtgc tcttttcact gtagacacta
tcacgagacc 2600 cagattaatt tctgtggttg ttacagaata agtctaatca
aggagaagtt 2650 tctgtttgac gtttgagtgc cggctttctg agtagagtta
ggaaaaccac 2700 gtaacgtagc atatgatgta taatagagta tacccgttac
ttaaaaagaa 2750 gtctgaaatg ttcgttttgt ggaaaagaaa ctagttaaat
ttactattcc 2800 taacccgaat gaaattagcc tttgccttat tctgtgcatg
ggtaagtaac 2850 ttatttctgc actgttttgt tgaactttgt ggaaacattc
tttcgagttt 2900 gtttttgtca ttttcgtaac agtcgtcgaa ctaggcctca
aaaacatacg 2950 taacgaaaag gcctagcgag gcaaattctg attgatttga
atctatattt 3000 ttctttaaaa agtcaagggt tctatattgt gagtaaatta
aatttacatt 3050 tgagttgttt gttgctaaga ggtagtaaat gtaagagagt
actggttcct 3100 tcagtagtga gtatttctca tagtgcagct ttatttatct
ccaggatgtt 3150 tttgtggctg tatttgattg atatgtgctt cttctgattc
ttgctaattt 3200 ccaaccatat tgaataaatg tgatcaagtc a 3231 15 737 PRT
Homo Sapien 15 Met Gln Pro Arg Arg Ala Gln Ala Pro Gly Ala Gln Leu
Leu Pro 1 5 10 15 Ala Leu Ala Leu Leu Leu Leu Leu Leu Gly Ala Gly
Pro Arg Gly 20 25 30 Ser Ser Leu Ala Asn Pro Val Pro Ala Ala Pro
Leu Ser Ala Pro 35 40 45 Gly Pro Cys Ala Ala Gln Pro Cys Arg Asn
Gly Gly Val Cys Thr 50 55 60 Ser Arg Pro Glu Pro Asp Pro Gln His
Pro Ala Pro Ala Gly Glu 65 70 75 Pro Gly Tyr Ser Cys Thr Cys Pro
Ala Gly Ile Ser Gly Ala Asn 80 85 90 Cys Gln Leu Val Ala Asp Pro
Cys Ala Ser Asn Pro Cys His His 95 100 105 Gly Asn Cys Ser Ser Ser
Ser Ser Ser Ser Ser Asp Gly Tyr Leu 110 115 120 Cys Ile Cys Asn Glu
Gly Tyr Glu Gly Pro Asn Cys Glu Gln Ala 125 130 135 Leu Pro Ser Leu
Pro Ala Thr Gly Trp Thr Glu Ser Met Ala Pro 140 145 150 Arg Gln Leu
Gln Pro Val Pro Ala Thr Gln Glu Pro Asp Lys Ile 155 160 165 Leu Pro
Arg Ser Gln Ala Thr Val Thr Leu Pro Thr Trp Gln Pro 170 175 180 Lys
Thr Gly Gln Lys Val Val Glu Met Lys Trp Asp Gln Val Glu 185 190 195
Val Ile Pro Asp Ile Ala Cys Gly Asn Ala Ser Ser Asn Ser Ser 200 205
210 Ala Gly Gly Arg Leu Val Ser Phe Glu Val Pro Gln Asn Thr Ser 215
220 225 Val Lys Ile Arg Gln Asp Ala Thr Ala Ser Leu Ile Leu Leu Trp
230 235 240 Lys Val Thr Ala Thr Gly Phe Gln Gln Cys Ser Leu Ile Asp
Gly 245 250 255 Arg Ser Val Thr Pro Leu Gln Ala Ser Gly Gly Leu Val
Leu Leu 260 265 270 Glu Glu Met Leu Ala Leu Gly Asn Asn His Phe Ile
Gly Phe Val 275 280 285 Asn Asp Ser Val Thr Lys Ser Ile Val Ala Leu
Arg Leu Thr Leu 290 295 300 Val Val Lys Val Ser Thr Cys Val Pro Gly
Glu Ser His Ala Asn 305 310 315 Asp Leu Glu Cys Ser Gly Lys Gly Lys
Cys Thr Thr Lys Pro Ser 320 325 330 Glu Ala Thr Phe Ser Cys Thr Cys
Glu Glu Gln Tyr Val Gly Thr 335 340 345 Phe Cys Glu Glu Tyr Asp Ala
Cys Gln Arg Lys Pro Cys Gln Asn 350 355 360 Asn Ala Ser Cys Ile Asp
Ala Asn Glu Lys Gln Asp Gly Ser Asn 365 370 375 Phe Thr Cys Val Cys
Leu Pro Gly Tyr Thr Gly Glu Leu Cys Gln 380 385 390 Ser Lys Ile Asp
Tyr Cys Ile Leu Asp Pro Cys Arg Asn Gly Ala 395 400 405 Thr Cys Ile
Ser Ser Leu Ser Gly Phe Thr Cys Gln Cys Pro Glu 410 415 420 Gly Tyr
Phe Gly Ser Ala Cys Glu Glu Lys Val Asp Pro Cys Ala 425 430 435 Ser
Ser Pro Cys Gln Asn Asn Gly Thr Cys Tyr Val Asp Gly Val 440 445 450
His Phe Thr Cys Asn Cys Ser Pro Gly Phe Thr Gly Pro Thr Cys 455 460
465 Ala Gln Leu Ile Asp Phe Cys Ala Leu Ser Pro Cys Ala His Gly 470
475 480 Thr Cys Arg Ser Val Gly Thr Ser Tyr Lys Cys Leu Cys Asp Pro
485 490 495 Gly Tyr His Gly Leu Tyr Cys Glu Glu Glu Tyr Asn Glu Cys
Leu 500 505 510 Ser Ala Pro Cys Leu Asn Ala Ala Thr Cys Arg Asp Leu
Val Asn 515 520 525 Gly Tyr Glu Cys Val Cys Leu Ala Glu Tyr Lys Gly
Thr His Cys 530 535 540 Glu Leu Tyr Lys Asp Pro Cys Ala Asn Val Ser
Cys Leu Asn Gly 545 550 555 Ala Thr Cys Asp Ser Asp Gly Leu Asn Gly
Thr Cys Ile Cys Ala 560 565 570 Pro Gly Phe Thr Gly Glu Glu Cys Asp
Ile Asp Ile Asn Glu Cys 575 580 585 Asp Ser Asn Pro Cys His His Gly
Gly Ser Cys Leu Asp Gln Pro 590 595 600 Asn Gly Tyr Asn Cys His Cys
Pro His Gly Trp Val Gly Ala Asn 605 610 615 Cys Glu Ile His Leu Gln
Trp Lys Ser Gly His Met Ala Glu Ser 620 625 630 Leu Thr Asn Met Pro
Arg His Ser Leu Tyr Ile Ile Ile Gly Ala 635 640 645 Leu Cys Val Ala
Phe Ile Leu Met Leu Ile Ile Leu Ile Val Gly 650 655 660 Ile Cys Arg
Ile Ser Arg Ile Glu Tyr Gln Gly Ser Ser Arg Pro 665 670 675 Ala Tyr
Glu Glu Phe Tyr Asn Cys Arg Ser Ile Asp Ser Glu Phe 680 685 690 Ser
Asn Ala Ile Ala Ser Ile Arg His Ala Arg Phe Gly Lys Lys 695 700 705
Ser Arg Pro Ala Met Tyr Asp Val Ser Pro Ile Ala Tyr Glu Asp 710 715
720 Tyr Ser Pro Asp Asp Lys Pro Leu Val Thr Leu Ile Lys Thr Lys 725
730 735 Asp Leu 16 43 DNA Artificial Sequence Synthetic
Oligonucleotide Probe 16 tgtaaaacga cggccagtta aatagacctg
caattattaa tct 43 17 41 DNA Artificial Sequence Synthetic
Oligonucleotide Probe 17 caggaaacag ctatgaccac ctgcacacct
gcaaatccat t 41 18 508 DNA Homo Sapien 18 ctctggaagg tcacggccac
aggattccaa cagtgctccc tcatagatgg 50 acgaaagtgt gacccccctt
tcaggctttc agggggactg gtcctcctgg 100 aggagatgct cgccttgggg
aataatcact ttattggttt tgtgaatgat 150 tctgtgacta agtctattgt
ggctttgcgc ttaactctgg tggtgaaggt 200 cagcacctgt gtgccggggg
agagtcacgc aaatgacttg gagtgttcag 250 gaaaaggaaa atgcaccacg
aagccgtcag aggcaacttt ttcctgtacc 300 tgtgaggagc agtacgtggg
tactttctgt gaagaatacg atgcttgcca 350 gaggaaacct tgccaaaaca
acgcgagctg tattgatgca aatgaaaagc 400 aagatgggag caatttcacc
tgtgtttgcc ttcctggtta tactggagag 450 ctttgccaac cgaactgaga
ttggagcgaa cgacctacac cgaactgaga 500 taggggag 508 19 508 DNA Homo
Sapien 19 ctctggaagg tcacggccac aggattccaa cagtgctccc tcatagatgg 50
acgaaagtgt gacccccctt tcaggctttc agggggactg gtcctcctgg 100
aggagatgct cgccttgggg aataatcact ttattggttt tgtgaatgat 150
tctgtgacta agtctattgt ggctttgcgc ttaactctgg tggtgaaggt 200
cagcacctgt gtgccggggg agagtcacgc aaatgacttg gagtgttcag 250
gaaaaggaaa atgcaccacg aagccgtcag aggcaacttt ttcctgtacc 300
tgtgaggagc agtacgtggg tactttctgt gaagaatacg atgcttgcca 350
gaggaaacct tgccaaaaca acgcgagctg tattgatgca aatgaaaagc 400
aagatgggag caatttcacc tgtgtttgcc ttcctggtta tactggagag 450
ctttgccaac cgaactgaga ttggagcgaa cgacctacac cgaactgaga 500 taggggag
508 20 23 DNA Artificial Sequence Synthetic Oligonucleotide Probe
20 ctctggaagg tcacggccac agg 23 21 24 DNA Artificial Sequence
Synthetic oligonucleotide probe 21 ctcagttcgg ttggcaaagc tctc 24 22
69 DNA Artificial Sequence Synthetic oligonucleotide probe 22
cagtgctccc tcatagatgg acgaaagtgt gacccccctt tcaggcgaga 50
gctttgccaa ccgaactga 69 23 1520 DNA Homo Sapien 23 gctgagtctg
ctgctcctgc tgctgctgct ccagcctgta acctgtgcct 50 acaccacgcc
aggccccccc agagccctca ccacgctggg cgcccccaga 100 gcccacacca
tgccgggcac ctacgctccc tcgaccacac tcagtagtcc 150 cagcacccag
ggcctgcaag agcaggcacg ggccctgatg cgggacttcc 200 cgctcgtgga
cggccacaac gacctgcccc tggtcctaag gcaggtttac 250 cagaaagggc
tacaggatgt taacctgcgc aatttcagct acggccagac 300 cagcctggac
aggcttagag atggcctcgt gggcgcccag ttctggtcag 350 cctatgtgcc
atgccagacc caggaccggg atgccctgcg cctcaccctg 400 gagcagattg
acctcatacg ccgcatgtgt gcctcctatt ctgagctgga 450 gcttgtgacc
tcggctaaag ctctgaacga cactcagaaa ttggcctgcc 500 tcatcggtgt
agagggtggc cactcgctgg acaatagcct ctccatctta 550 cgtaccttct
acatgctggg agtgcgctac ctgacgctca cccacacctg 600 caacacaccc
tgggcagaga gctccgctaa gggcgtccac tccttctaca 650 acaacatcag
cgggctgact gactttggtg agaaggtggt ggcagaaatg 700 aaccgcctgg
gcatgatggt agacttatcc catgtctcag atgctgtggc 750 acggcgggcc
ctggaagtgt cacaggcacc tgtgatcttc tcccactcgg 800 ctgcccgggg
tgtgtgcaac agtgctcgga atgttcctga tgacatcctg 850 cagcttctga
agaagaacgg tggcgtcgtg atggtgtctt tgtccatggg 900 agtaatacag
tgcaacccat cagccaatgt gtccactgtg gcagatcact 950 tcgaccacat
caaggctgtc attggatcca agttcatcgg gattggtgga 1000 gattatgatg
gggccggcaa attccctcag gggctggaag acgtgtccac 1050 atacccggtc
ctgatagagg agttgctgag tcgtggctgg agtgaggaag 1100 agcttcaggg
tgtccttcgt ggaaacctgc tgcgggtctt cagacaagtg 1150 gaaaaggtac
aggaagaaaa caaatggcaa agccccttgg aggacaagtt 1200 cccggatgag
cagctgagca gttcctgcca ctccgacctc tcacgtctgc 1250 gtcagagaca
gagtctgact tcaggccagg aactcactga gattcccata 1300 cactggacag
ccaagttacc agccaagtgg tcagtctcag agtcctcccc 1350 ccacatggcc
ccagtccttg cagttgtggc caccttccca gtccttattc 1400 tgtggctctg
atgacccagt tagtcctgcc agatgtcact gtagcaagcc 1450 acagacaccc
cacaaagttc ccctgttgtg caggcacaaa tatttcctga 1500 aataaatgtt
ttggacatag 1520 24 433 PRT Homo Sapien 24 Met Pro Gly Thr Tyr Ala
Pro Ser Thr Thr Leu Ser Ser Pro Ser 1 5 10 15 Thr Gln Gly Leu Gln
Glu Gln Ala Arg Ala Leu Met Arg Asp Phe 20 25 30 Pro Leu Val Asp
Gly His Asn Asp Leu Pro Leu Val Leu Arg Gln 35 40 45 Val Tyr Gln
Lys Gly Leu Gln Asp Val Asn Leu Arg Asn Phe Ser 50 55 60 Tyr Gly
Gln Thr
Ser Leu Asp Arg Leu Arg Asp Gly Leu Val Gly 65 70 75 Ala Gln Phe
Trp Ser Ala Tyr Val Pro Cys Gln Thr Gln Asp Arg 80 85 90 Asp Ala
Leu Arg Leu Thr Leu Glu Gln Ile Asp Leu Ile Arg Arg 95 100 105 Met
Cys Ala Ser Tyr Ser Glu Leu Glu Leu Val Thr Ser Ala Lys 110 115 120
Ala Leu Asn Asp Thr Gln Lys Leu Ala Cys Leu Ile Gly Val Glu 125 130
135 Gly Gly His Ser Leu Asp Asn Ser Leu Ser Ile Leu Arg Thr Phe 140
145 150 Tyr Met Leu Gly Val Arg Tyr Leu Thr Leu Thr His Thr Cys Asn
155 160 165 Thr Pro Trp Ala Glu Ser Ser Ala Lys Gly Val His Ser Phe
Tyr 170 175 180 Asn Asn Ile Ser Gly Leu Thr Asp Phe Gly Glu Lys Val
Val Ala 185 190 195 Glu Met Asn Arg Leu Gly Met Met Val Asp Leu Ser
His Val Ser 200 205 210 Asp Ala Val Ala Arg Arg Ala Leu Glu Val Ser
Gln Ala Pro Val 215 220 225 Ile Phe Ser His Ser Ala Ala Arg Gly Val
Cys Asn Ser Ala Arg 230 235 240 Asn Val Pro Asp Asp Ile Leu Gln Leu
Leu Lys Lys Asn Gly Gly 245 250 255 Val Val Met Val Ser Leu Ser Met
Gly Val Ile Gln Cys Asn Pro 260 265 270 Ser Ala Asn Val Ser Thr Val
Ala Asp His Phe Asp His Ile Lys 275 280 285 Ala Val Ile Gly Ser Lys
Phe Ile Gly Ile Gly Gly Asp Tyr Asp 290 295 300 Gly Ala Gly Lys Phe
Pro Gln Gly Leu Glu Asp Val Ser Thr Tyr 305 310 315 Pro Val Leu Ile
Glu Glu Leu Leu Ser Arg Gly Trp Ser Glu Glu 320 325 330 Glu Leu Gln
Gly Val Leu Arg Gly Asn Leu Leu Arg Val Phe Arg 335 340 345 Gln Val
Glu Lys Val Gln Glu Glu Asn Lys Trp Gln Ser Pro Leu 350 355 360 Glu
Asp Lys Phe Pro Asp Glu Gln Leu Ser Ser Ser Cys His Ser 365 370 375
Asp Leu Ser Arg Leu Arg Gln Arg Gln Ser Leu Thr Ser Gly Gln 380 385
390 Glu Leu Thr Glu Ile Pro Ile His Trp Thr Ala Lys Leu Pro Ala 395
400 405 Lys Trp Ser Val Ser Glu Ser Ser Pro His Met Ala Pro Val Leu
410 415 420 Ala Val Val Ala Thr Phe Pro Val Leu Ile Leu Trp Leu 425
430 25 22 DNA Artificial Sequence Synthetic oligonucleotide probe
25 agttctggtc agcctatgtg cc 22 26 24 DNA Artificial Sequence
Synthetic oligonucleotide probe 26 cgtgatggtg tctttgtcca tggg 24 27
24 DNA Artificial Sequence Synthetic oligonucleotide probe 27
ctccaccaat cccgatgaac ttgg 24 28 50 DNA Artificial Sequence
Synthetic oligonucleotide probe 28 gagcagattg acctcatacg ccgcatgtgt
gcctcctatt ctgagctgga 50 29 1416 DNA Homo Sapien 29 aaaacctata
aatattccgg attattcata ccgtcccacc atcgggcgcg 50 gatccgcggc
cgcgaattct aaaccaacat gccgggcacc tacgctccct 100 cgaccacact
cagtagtccc agcacccagg gcctgcaaga gcaggcacgg 150 gccctgatgc
gggacttccc gctcgtggac ggccacaacg acctgcccct 200 ggtcctaagg
caggtttacc agaaagggct acaggatgtt aacctgcgca 250 atttcagcta
cggccagacc agcctggaca ggcttagaga tggcctcgtg 300 ggcgcccagt
tctggtcagc ctatgtgcca tgccagaccc aggaccggga 350 tgccctgcgc
ctcaccctgg agcagattga cctcatacgc cgcatgtgtg 400 cctcctattc
tgagctggag cttgtgacct cggctaaagc tctgaacgac 450 actcagaaat
tggcctgcct catcggtgta gagggtggcc actcgctgga 500 caatagcctc
tccatcttac gtaccttcta catgctggga gtgcgctacc 550 tgacgctcac
ccacacctgc aacacaccct gggcagagag ctccgctaag 600 ggcgtccact
ccttctacaa caacatcagc gggctgactg actttggtga 650 gaaggtggtg
gcagaaatga accgcctggg catgatggta gacttatccc 700 atgtctcaga
tgctgtggca cggcgggccc tggaagtgtc acaggcacct 750 gtgatcttct
cccactcggc tgcccggggt gtgtgcaaca gtgctcggaa 800 tgttcctgat
gacatcctgc agcttctgaa gaagaacggt ggcgtcgtga 850 tggtgtcttt
gtccatggga gtaatacagt gcaacccatc agccaatgtg 900 tccactgtgg
cagatcactt cgaccacatc aaggctgtca ttggatccaa 950 gttcatcggg
attggtggag attatgatgg ggccggcaaa ttccctcagg 1000 ggctggaaga
cgtgtccaca tacccggtcc tgatagagga gttgctgagt 1050 cgtggctgga
gtgaggaaga gcttcagggt gtccttcgtg gaaacctgct 1100 gcgggtcttc
agacaagtgg aaaaggtaca ggaagaaaac aaatggcaaa 1150 gccccttgga
ggacaagttc ccggatgagc agctgagcag ttcctgccac 1200 tccgacctct
cacgtctgcg tcagagacag agtctgactt caggccagga 1250 actcactgag
attcccatac actggacagc caagttacca gccaagtggt 1300 cagtctcaga
gtcctccccc caccctgaca aaactcacac atgcccaccg 1350 tgcccagcac
ctgaactcct ggggggaccg tcagtcttcc tcttcccccc 1400 aaaacccaag gacacc
1416 30 446 PRT Homo Sapien 30 Met Pro Gly Thr Tyr Ala Pro Ser Thr
Thr Leu Ser Ser Pro Ser 1 5 10 15 Thr Gln Gly Leu Gln Glu Gln Ala
Arg Ala Leu Met Arg Asp Phe 20 25 30 Pro Leu Val Asp Gly His Asn
Asp Leu Pro Leu Val Leu Arg Gln 35 40 45 Val Tyr Gln Lys Gly Leu
Gln Asp Val Asn Leu Arg Asn Phe Ser 50 55 60 Tyr Gly Gln Thr Ser
Leu Asp Arg Leu Arg Asp Gly Leu Val Gly 65 70 75 Ala Gln Phe Trp
Ser Ala Tyr Val Pro Cys Gln Thr Gln Asp Arg 80 85 90 Asp Ala Leu
Arg Leu Thr Leu Glu Gln Ile Asp Leu Ile Arg Arg 95 100 105 Met Cys
Ala Ser Tyr Ser Glu Leu Glu Leu Val Thr Ser Ala Lys 110 115 120 Ala
Leu Asn Asp Thr Gln Lys Leu Ala Cys Leu Ile Gly Val Glu 125 130 135
Gly Gly His Ser Leu Asp Asn Ser Leu Ser Ile Leu Arg Thr Phe 140 145
150 Tyr Met Leu Gly Val Arg Tyr Leu Thr Leu Thr His Thr Cys Asn 155
160 165 Thr Pro Trp Ala Glu Ser Ser Ala Lys Gly Val His Ser Phe Tyr
170 175 180 Asn Asn Ile Ser Gly Leu Thr Asp Phe Gly Glu Lys Val Val
Ala 185 190 195 Glu Met Asn Arg Leu Gly Met Met Val Asp Leu Ser His
Val Ser 200 205 210 Asp Ala Val Ala Arg Arg Ala Leu Glu Val Ser Gln
Ala Pro Val 215 220 225 Ile Phe Ser His Ser Ala Ala Arg Gly Val Cys
Asn Ser Ala Arg 230 235 240 Asn Val Pro Asp Asp Ile Leu Gln Leu Leu
Lys Lys Asn Gly Gly 245 250 255 Val Val Met Val Ser Leu Ser Met Gly
Val Ile Gln Cys Asn Pro 260 265 270 Ser Ala Asn Val Ser Thr Val Ala
Asp His Phe Asp His Ile Lys 275 280 285 Ala Val Ile Gly Ser Lys Phe
Ile Gly Ile Gly Gly Asp Tyr Asp 290 295 300 Gly Ala Gly Lys Phe Pro
Gln Gly Leu Glu Asp Val Ser Thr Tyr 305 310 315 Pro Val Leu Ile Glu
Glu Leu Leu Ser Arg Gly Trp Ser Glu Glu 320 325 330 Glu Leu Gln Gly
Val Leu Arg Gly Asn Leu Leu Arg Val Phe Arg 335 340 345 Gln Val Glu
Lys Val Gln Glu Glu Asn Lys Trp Gln Ser Pro Leu 350 355 360 Glu Asp
Lys Phe Pro Asp Glu Gln Leu Ser Ser Ser Cys His Ser 365 370 375 Asp
Leu Ser Arg Leu Arg Gln Arg Gln Ser Leu Thr Ser Gly Gln 380 385 390
Glu Leu Thr Glu Ile Pro Ile His Trp Thr Ala Lys Leu Pro Ala 395 400
405 Lys Trp Ser Val Ser Glu Ser Ser Pro His Pro Asp Lys Thr His 410
415 420 Thr Cys Pro Pro Cys Pro Ala Pro Glu Leu Leu Gly Gly Pro Ser
425 430 435 Val Phe Leu Phe Pro Pro Lys Pro Lys Asp Thr 440 445 31
1790 DNA Homo Sapien 31 cgcccagcga cgtgcgggcg gcctggcccg cgccctcccg
cgcccggcct 50 gcgtcccgcg ccctgcgcca ccgccgccga gccgcagccc
gccgcgcgcc 100 cccggcagcg ccggccccat gcccgccggc cgccggggcc
ccgccgccca 150 atccgcgcgg cggccgccgc cgttgctgcc cctgctgctg
ctgctctgcg 200 tcctcggggc gccgcgagcc ggatcaggag cccacacagc
tgtgatcagt 250 ccccaggatc ccacgcttct catcggctcc tccctgctgg
ccacctgctc 300 agtgcacgga gacccaccag gagccaccgc cgagggcctc
tactggaccc 350 tcaacgggcg ccgcctgccc cctgagctct cccgtgtact
caacgcctcc 400 accttggctc tggccctggc caacctcaat gggtccaggc
agcggtcggg 450 ggacaacctc gtgtgccacg cccgtgacgg cagcatcctg
gctggctcct 500 gcctctatgt tggcctgccc ccagagaaac ccgtcaacat
cagctgctgg 550 tccaagaaca tgaaggactt gacctgccgc tggacgccag
gggcccacgg 600 ggagaccttc ctccacacca actactccct caagtacaag
cttaggtggt 650 atggccagga caacacatgt gaggagtacc acacagtggg
gccccactcc 700 tgccacatcc ccaaggacct ggctctcttt acgccctatg
agatctgggt 750 ggaggccacc aaccgcctgg gctctgcccg ctccgatgta
ctcacgctgg 800 atatcctgga tgtggtgacc acggaccccc cgcccgacgt
gcacgtgagc 850 cgcgtcgggg gcctggagga ccagctgagc gtgcgctggg
tgtcgccacc 900 cgccctcaag gatttcctct ttcaagccaa ataccagatc
cgctaccgag 950 tggaggacag tgtggactgg aaggtggtgg acgatgtgag
caaccagacc 1000 tcctgccgcc tggccggcct gaaacccggc accgtgtact
tcgtgcaagt 1050 gcgctgcaac ccctttggca tctatggctc caagaaagcc
gggatctgga 1100 gtgagtggag ccaccccaca gccgcctcca ctccccgcag
tgagcgcccg 1150 ggcccgggcg gcggggcgtg cgaaccgcgg ggcggagagc
cgagctcggg 1200 gccggtgcgg cgcgagctca agcagttcct gggctggctc
aagaagcacg 1250 cgtactgctc caacctcagc ttccgcctct acgaccagtg
gcgagcctgg 1300 atgcagaagt cgcacaagac ccgcaaccag gacgagggga
tcctgccctc 1350 gggcagacgg ggcacggcga gaggtcctgc cagataagct
gtaggggctc 1400 aggccaccct ccctgccacg tggagacgca gaggccgaac
ccaaactggg 1450 gccacctctg taccctcact tcagggcacc tgagccaccc
tcagcaggag 1500 ctggggtggc ccctgagctc caacggccat aacagctctg
actcccacgt 1550 gaggccacct ttgggtgcac cccagtgggt gtgtgtgtgt
gtgtgagggt 1600 tggttgagtt gcctagaacc cctgccaggg ctgggggtga
gaaggggagt 1650 cattactccc cattacctag ggcccctcca aaagagtcct
tttaaataaa 1700 tgagctattt aggtgctgtg attgtgaaaa aaaaaaaaaa
aaaaaaaaaa 1750 aaaaaaaaaa aaaaaaaaaa aaaaacaaaa aaaaaaaaaa 1790 32
422 PRT Homo Sapien 32 Met Pro Ala Gly Arg Arg Gly Pro Ala Ala Gln
Ser Ala Arg Arg 1 5 10 15 Pro Pro Pro Leu Leu Pro Leu Leu Leu Leu
Leu Cys Val Leu Gly 20 25 30 Ala Pro Arg Ala Gly Ser Gly Ala His
Thr Ala Val Ile Ser Pro 35 40 45 Gln Asp Pro Thr Leu Leu Ile Gly
Ser Ser Leu Leu Ala Thr Cys 50 55 60 Ser Val His Gly Asp Pro Pro
Gly Ala Thr Ala Glu Gly Leu Tyr 65 70 75 Trp Thr Leu Asn Gly Arg
Arg Leu Pro Pro Glu Leu Ser Arg Val 80 85 90 Leu Asn Ala Ser Thr
Leu Ala Leu Ala Leu Ala Asn Leu Asn Gly 95 100 105 Ser Arg Gln Arg
Ser Gly Asp Asn Leu Val Cys His Ala Arg Asp 110 115 120 Gly Ser Ile
Leu Ala Gly Ser Cys Leu Tyr Val Gly Leu Pro Pro 125 130 135 Glu Lys
Pro Val Asn Ile Ser Cys Trp Ser Lys Asn Met Lys Asp 140 145 150 Leu
Thr Cys Arg Trp Thr Pro Gly Ala His Gly Glu Thr Phe Leu 155 160 165
His Thr Asn Tyr Ser Leu Lys Tyr Lys Leu Arg Trp Tyr Gly Gln 170 175
180 Asp Asn Thr Cys Glu Glu Tyr His Thr Val Gly Pro His Ser Cys 185
190 195 His Ile Pro Lys Asp Leu Ala Leu Phe Thr Pro Tyr Glu Ile Trp
200 205 210 Val Glu Ala Thr Asn Arg Leu Gly Ser Ala Arg Ser Asp Val
Leu 215 220 225 Thr Leu Asp Ile Leu Asp Val Val Thr Thr Asp Pro Pro
Pro Asp 230 235 240 Val His Val Ser Arg Val Gly Gly Leu Glu Asp Gln
Leu Ser Val 245 250 255 Arg Trp Val Ser Pro Pro Ala Leu Lys Asp Phe
Leu Phe Gln Ala 260 265 270 Lys Tyr Gln Ile Arg Tyr Arg Val Glu Asp
Ser Val Asp Trp Lys 275 280 285 Val Val Asp Asp Val Ser Asn Gln Thr
Ser Cys Arg Leu Ala Gly 290 295 300 Leu Lys Pro Gly Thr Val Tyr Phe
Val Gln Val Arg Cys Asn Pro 305 310 315 Phe Gly Ile Tyr Gly Ser Lys
Lys Ala Gly Ile Trp Ser Glu Trp 320 325 330 Ser His Pro Thr Ala Ala
Ser Thr Pro Arg Ser Glu Arg Pro Gly 335 340 345 Pro Gly Gly Gly Ala
Cys Glu Pro Arg Gly Gly Glu Pro Ser Ser 350 355 360 Gly Pro Val Arg
Arg Glu Leu Lys Gln Phe Leu Gly Trp Leu Lys 365 370 375 Lys His Ala
Tyr Cys Ser Asn Leu Ser Phe Arg Leu Tyr Asp Gln 380 385 390 Trp Arg
Ala Trp Met Gln Lys Ser His Lys Thr Arg Asn Gln Asp 395 400 405 Glu
Gly Ile Leu Pro Ser Gly Arg Arg Gly Thr Ala Arg Gly Pro 410 415 420
Ala Arg 33 23 DNA Artificial Sequence Synthetic oligonucleotide
probe 33 cccgcccgac gtgcacgtga gcc 23 34 23 DNA Artificial Sequence
Synthetic oligonucleotide probe 34 tgagccagcc caggaactgc ttg 23 35
50 DNA Artificial Sequence Synthetic oligonucleotide probe 35
caagtgcgct gcaacccctt tggcatctat ggctccaaga aagccgggat 50 36 1771
DNA Homo Sapien 36 cccacgcgtc cgctggtgtt agatcgagca accctctaaa
agcagtttag 50 agtggtaaaa aaaaaaaaaa acacaccaaa cgctcgcagc
cacaaaaggg 100 atgaaatttc ttctggacat cctcctgctt ctcccgttac
tgatcgtctg 150 ctccctagag tccttcgtga agctttttat tcctaagagg
agaaaatcag 200 tcaccggcga aatcgtgctg attacaggag ctgggcatgg
aattgggaga 250 ctgactgcct atgaatttgc taaacttaaa agcaagctgg
ttctctggga 300 tataaataag catggactgg aggaaacagc tgccaaatgc
aagggactgg 350 gtgccaaggt tcataccttt gtggtagact gcagcaaccg
agaagatatt 400 tacagctctg caaagaaggt gaaggcagaa attggagatg
ttagtatttt 450 agtaaataat gctggtgtag tctatacatc agatttgttt
gctacacaag 500 atcctcagat tgaaaagact tttgaagtta atgtacttgc
acatttctgg 550 actacaaagg catttcttcc tgcaatgacg aagaataacc
atggccatat 600 tgtcactgtg gcttcggcag ctggacatgt ctcggtcccc
ttcttactgg 650 cttactgttc aagcaagttt gctgctgttg gatttcataa
aactttgaca 700 gatgaactgg ctgccttaca aataactgga gtcaaaacaa
catgtctgtg 750 tcctaatttc gtaaacactg gcttcatcaa aaatccaagt
acaagtttgg 800 gacccactct ggaacctgag gaagtggtaa acaggctgat
gcatgggatt 850 ctgactgagc agaagatgat ttttattcca tcttctatag
cttttttaac 900 aacattggaa aggatccttc ctgagcgttt cctggcagtt
ttaaaacgaa 950 aaatcagtgt taagtttgat gcagttattg gatataaaat
gaaagcgcaa 1000 taagcaccta gttttctgaa aactgattta ccaggtttag
gttgatgtca 1050 tctaatagtg ccagaatttt aatgtttgaa cttctgtttt
ttctaattat 1100 ccccatttct tcaatatcat ttttgaggct ttggcagtct
tcatttacta 1150 ccacttgttc tttagccaaa agctgattac atatgatata
aacagagaaa 1200 tacctttaga ggtgacttta aggaaaatga agaaaaagaa
ccaaaatgac 1250 tttattaaaa taatttccaa gattatttgt ggctcacctg
aaggctttgc 1300 aaaatttgta ccataaccgt ttatttaaca tatattttta
tttttgattg 1350 cacttaaatt ttgtataatt tgtgtttctt tttctgttct
acataaaatc 1400 agaaacttca agctctctaa ataaaatgaa ggactatatc
tagtggtatt 1450 tcacaatgaa tatcatgaac tctcaatggg taggtttcat
cctacccatt 1500 gccactctgt ttcctgagag atacctcaca ttccaatgcc
aaacatttct 1550 gcacagggaa gctagaggtg gatacacgtg ttgcaagtat
aaaagcatca 1600 ctgggattta aggagaattg agagaatgta cccacaaatg
gcagcaataa 1650 taaatggatc acacttaaaa aaaaaaaaaa aaaaaaaaaa
aaaaaaaaaa 1700 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
aaaaaaaaaa 1750 aaaaaaaaaa
aaaaaaaaaa a 1771 37 300 PRT Homo Sapien 37 Met Lys Phe Leu Leu Asp
Ile Leu Leu Leu Leu Pro Leu Leu Ile 1 5 10 15 Val Cys Ser Leu Glu
Ser Phe Val Lys Leu Phe Ile Pro Lys Arg 20 25 30 Arg Lys Ser Val
Thr Gly Glu Ile Val Leu Ile Thr Gly Ala Gly 35 40 45 His Gly Ile
Gly Arg Leu Thr Ala Tyr Glu Phe Ala Lys Leu Lys 50 55 60 Ser Lys
Leu Val Leu Trp Asp Ile Asn Lys His Gly Leu Glu Glu 65 70 75 Thr
Ala Ala Lys Cys Lys Gly Leu Gly Ala Lys Val His Thr Phe 80 85 90
Val Val Asp Cys Ser Asn Arg Glu Asp Ile Tyr Ser Ser Ala Lys 95 100
105 Lys Val Lys Ala Glu Ile Gly Asp Val Ser Ile Leu Val Asn Asn 110
115 120 Ala Gly Val Val Tyr Thr Ser Asp Leu Phe Ala Thr Gln Asp Pro
125 130 135 Gln Ile Glu Lys Thr Phe Glu Val Asn Val Leu Ala His Phe
Trp 140 145 150 Thr Thr Lys Ala Phe Leu Pro Ala Met Thr Lys Asn Asn
His Gly 155 160 165 His Ile Val Thr Val Ala Ser Ala Ala Gly His Val
Ser Val Pro 170 175 180 Phe Leu Leu Ala Tyr Cys Ser Ser Lys Phe Ala
Ala Val Gly Phe 185 190 195 His Lys Thr Leu Thr Asp Glu Leu Ala Ala
Leu Gln Ile Thr Gly 200 205 210 Val Lys Thr Thr Cys Leu Cys Pro Asn
Phe Val Asn Thr Gly Phe 215 220 225 Ile Lys Asn Pro Ser Thr Ser Leu
Gly Pro Thr Leu Glu Pro Glu 230 235 240 Glu Val Val Asn Arg Leu Met
His Gly Ile Leu Thr Glu Gln Lys 245 250 255 Met Ile Phe Ile Pro Ser
Ser Ile Ala Phe Leu Thr Thr Leu Glu 260 265 270 Arg Ile Leu Pro Glu
Arg Phe Leu Ala Val Leu Lys Arg Lys Ile 275 280 285 Ser Val Lys Phe
Asp Ala Val Ile Gly Tyr Lys Met Lys Ala Gln 290 295 300 38 23 DNA
Artificial Sequence Synthetic oligonucleotide probe 38 ggtgaaggca
gaaattggag atg 23 39 24 DNA Artificial Sequence Synthetic
oligonucleotide probe 39 atcccatgca tcagcctgtt tacc 24 40 48 DNA
Artificial Sequence Synthetic oligonucleotide probe 40 gctggtgtag
tctatacatc agatttgttt gctacacaag atcctcag 48 41 1377 DNA Homo
Sapien 41 gactagttct cttggagtct gggaggagga aagcggagcc ggcagggagc 50
gaaccaggac tggggtgacg gcagggcagg gggcgcctgg ccggggagaa 100
gcgcgggggc tggagcacca ccaactggag ggtccggagt agcgagcgcc 150
ccgaaggagg ccatcgggga gccgggaggg gggactgcga gaggaccccg 200
gcgtccgggc tcccggtgcc agcgctatga ggccactcct cgtcctgctg 250
ctcctgggcc tggcggccgg ctcgccccca ctggacgaca acaagatccc 300
cagcctctgc ccggggcacc ccggccttcc aggcacgccg ggccaccatg 350
gcagccaggg cttgccgggc cgcgatggcc gcgacggccg cgacggcgcg 400
cccggggctc cgggagagaa aggcgagggc gggaggccgg gactgccggg 450
acctcgaggg gaccccgggc cgcgaggaga ggcgggaccc gcggggccca 500
ccgggcctgc cggggagtgc tcggtgcctc cgcgatccgc cttcagcgcc 550
aagcgctccg agagccgggt gcctccgccg tctgacgcac ccttgccctt 600
cgaccgcgtg ctggtgaacg agcagggaca ttacgacgcc gtcaccggca 650
agttcacctg ccaggtgcct ggggtctact acttcgccgt ccatgccacc 700
gtctaccggg ccagcctgca gtttgatctg gtgaagaatg gcgaatccat 750
tgcctctttc ttccagtttt tcggggggtg gcccaagcca gcctcgctct 800
cggggggggc catggtgagg ctggagcctg aggaccaagt gtgggtgcag 850
gtgggtgtgg gtgactacat tggcatctat gccagcatca agacagacag 900
caccttctcc ggatttctgg tgtactccga ctggcacagc tccccagtct 950
ttgcttagtg cccactgcaa agtgagctca tgctctcact cctagaagga 1000
gggtgtgagg ctgacaacca ggtcatccag gagggctggc ccccctggaa 1050
tattgtgaat gactagggag gtggggtaga gcactctccg tcctgctgct 1100
ggcaaggaat gggaacagtg gctgtctgcg atcaggtctg gcagcatggg 1150
gcagtggctg gatttctgcc caagaccaga ggagtgtgct gtgctggcaa 1200
gtgtaagtcc cccagttgct ctggtccagg agcccacggt ggggtgctct 1250
cttcctggtc ctctgcttct ctggatcctc cccaccccct cctgctcctg 1300
gggccggccc ttttctcaga gatcactcaa taaacctaag aaccctcata 1350
aaaaaaaaaa aaaaaaaaaa aaaaaaa 1377 42 243 PRT Homo Sapien 42 Met
Arg Pro Leu Leu Val Leu Leu Leu Leu Gly Leu Ala Ala Gly 1 5 10 15
Ser Pro Pro Leu Asp Asp Asn Lys Ile Pro Ser Leu Cys Pro Gly 20 25
30 His Pro Gly Leu Pro Gly Thr Pro Gly His His Gly Ser Gln Gly 35
40 45 Leu Pro Gly Arg Asp Gly Arg Asp Gly Arg Asp Gly Ala Pro Gly
50 55 60 Ala Pro Gly Glu Lys Gly Glu Gly Gly Arg Pro Gly Leu Pro
Gly 65 70 75 Pro Arg Gly Asp Pro Gly Pro Arg Gly Glu Ala Gly Pro
Ala Gly 80 85 90 Pro Thr Gly Pro Ala Gly Glu Cys Ser Val Pro Pro
Arg Ser Ala 95 100 105 Phe Ser Ala Lys Arg Ser Glu Ser Arg Val Pro
Pro Pro Ser Asp 110 115 120 Ala Pro Leu Pro Phe Asp Arg Val Leu Val
Asn Glu Gln Gly His 125 130 135 Tyr Asp Ala Val Thr Gly Lys Phe Thr
Cys Gln Val Pro Gly Val 140 145 150 Tyr Tyr Phe Ala Val His Ala Thr
Val Tyr Arg Ala Ser Leu Gln 155 160 165 Phe Asp Leu Val Lys Asn Gly
Glu Ser Ile Ala Ser Phe Phe Gln 170 175 180 Phe Phe Gly Gly Trp Pro
Lys Pro Ala Ser Leu Ser Gly Gly Ala 185 190 195 Met Val Arg Leu Glu
Pro Glu Asp Gln Val Trp Val Gln Val Gly 200 205 210 Val Gly Asp Tyr
Ile Gly Ile Tyr Ala Ser Ile Lys Thr Asp Ser 215 220 225 Thr Phe Ser
Gly Phe Leu Val Tyr Ser Asp Trp His Ser Ser Pro 230 235 240 Val Phe
Ala 43 24 DNA Artificial Sequence Synthetic oligonucleotide probe
43 tacaggccca gtcaggacca gggg 24 44 18 DNA Artificial Sequence
Synthetic oligonucleotide probe 44 agccagcctc gctctcgg 18 45 18 DNA
Artificial Sequence Synthetic oligonucleotide probe 45 gtctgcgatc
aggtctgg 18 46 20 DNA Artificial Sequence Synthetic oligonucleotide
probe 46 gaaagaggca atggattcgc 20 47 24 DNA Artificial Sequence
Synthetic oligonucleotide probe 47 gacttacact tgccagcaca gcac 24 48
45 DNA Artificial Sequence Synthetic oligonucleotide probe 48
ggagcaccac caactggagg gtccggagta gcgagcgccc cgaag 45 49 1876 DNA
Homo Sapien 49 ctcttttgtc caccagccca gcctgactcc tggagattgt
gaatagctcc 50 atccagcctg agaaacaagc cgggtggctg agccaggctg
tgcacggagc 100 acctgacggg cccaacagac ccatgctgca tccagagacc
tcccctggcc 150 gggggcatct cctggctgtg ctcctggccc tccttggcac
cacctgggca 200 gaggtgtggc caccccagct gcaggagcag gctccgatgg
ccggagccct 250 gaacaggaag gagagtttct tgctcctctc cctgcacaac
cgcctgcgca 300 gctgggtcca gccccctgcg gctgacatgc ggaggctgga
ctggagtgac 350 agcctggccc aactggctca agccagggca gccctctgtg
gaatcccaac 400 cccgagcctg gcatccggcc tgtggcgcac cctgcaagtg
ggctggaaca 450 tgcagctgct gcccgcgggc ttggcgtcct ttgttgaagt
ggtcagccta 500 tggtttgcag aggggcagcg gtacagccac gcggcaggag
agtgtgctcg 550 caacgccacc tgcacccact acacgcagct cgtgtgggcc
acctcaagcc 600 agctgggctg tgggcggcac ctgtgctctg caggccagac
agcgatagaa 650 gcctttgtct gtgcctactc ccccggaggc aactgggagg
tcaacgggaa 700 gacaatcatc ccctataaga agggtgcctg gtgttcgctc
tgcacagcca 750 gtgtctcagg ctgcttcaaa gcctgggacc atgcaggggg
gctctgtgag 800 gtccccagga atccttgtcg catgagctgc cagaaccatg
gacgtctcaa 850 catcagcacc tgccactgcc actgtccccc tggctacacg
ggcagatact 900 gccaagtgag gtgcagcctg cagtgtgtgc acggccggtt
ccgggaggag 950 gagtgctcgt gcgtctgtga catcggctac gggggagccc
agtgtgccac 1000 caaggtgcat tttcccttcc acacctgtga cctgaggatc
gacggagact 1050 gcttcatggt gtcttcagag gcagacacct attacagagc
caggatgaaa 1100 tgtcagagga aaggcggggt gctggcccag atcaagagcc
agaaagtgca 1150 ggacatcctc gccttctatc tgggccgcct ggagaccacc
aacgaggtga 1200 ctgacagtga cttcgagacc aggaacttct ggatcgggct
cacctacaag 1250 accgccaagg actccttccg ctgggccaca ggggagcacc
aggccttcac 1300 cagttttgcc tttgggcagc ctgacaacca cgggctggtg
tggctgagtg 1350 ctgccatggg gtttggcaac tgcgtggagc tgcaggcttc
agctgccttc 1400 aactggaacg accagcgctg caaaacccga aaccgttaca
tctgccagtt 1450 tgcccaggag cacatctccc ggtggggccc agggtcctga
ggcctgacca 1500 catggctccc tcgcctgccc tgggagcacc ggctctgctt
acctgtctgc 1550 ccacctgtct ggaacaaggg ccaggttaag accacatgcc
tcatgtccaa 1600 agaggtctca gaccttgcac aatgccagaa gttgggcaga
gagaggcagg 1650 gaggccagtg agggccaggg agtgagtgtt agaagaagct
ggggcccttc 1700 gcctgctttt gattgggaag atgggcttca attagatggc
gaaggagagg 1750 acaccgccag tggtccaaaa aggctgctct cttccacctg
gcccagaccc 1800 tgtggggcag cggagcttcc ctgtggcatg aaccccacgg
ggtattaaat 1850 tatgaatcag ctgaaaaaaa aaaaaa 1876 50 455 PRT Homo
Sapien 50 Met Leu His Pro Glu Thr Ser Pro Gly Arg Gly His Leu Leu
Ala 1 5 10 15 Val Leu Leu Ala Leu Leu Gly Thr Thr Trp Ala Glu Val
Trp Pro 20 25 30 Pro Gln Leu Gln Glu Gln Ala Pro Met Ala Gly Ala
Leu Asn Arg 35 40 45 Lys Glu Ser Phe Leu Leu Leu Ser Leu His Asn
Arg Leu Arg Ser 50 55 60 Trp Val Gln Pro Pro Ala Ala Asp Met Arg
Arg Leu Asp Trp Ser 65 70 75 Asp Ser Leu Ala Gln Leu Ala Gln Ala
Arg Ala Ala Leu Cys Gly 80 85 90 Ile Pro Thr Pro Ser Leu Ala Ser
Gly Leu Trp Arg Thr Leu Gln 95 100 105 Val Gly Trp Asn Met Gln Leu
Leu Pro Ala Gly Leu Ala Ser Phe 110 115 120 Val Glu Val Val Ser Leu
Trp Phe Ala Glu Gly Gln Arg Tyr Ser 125 130 135 His Ala Ala Gly Glu
Cys Ala Arg Asn Ala Thr Cys Thr His Tyr 140 145 150 Thr Gln Leu Val
Trp Ala Thr Ser Ser Gln Leu Gly Cys Gly Arg 155 160 165 His Leu Cys
Ser Ala Gly Gln Thr Ala Ile Glu Ala Phe Val Cys 170 175 180 Ala Tyr
Ser Pro Gly Gly Asn Trp Glu Val Asn Gly Lys Thr Ile 185 190 195 Ile
Pro Tyr Lys Lys Gly Ala Trp Cys Ser Leu Cys Thr Ala Ser 200 205 210
Val Ser Gly Cys Phe Lys Ala Trp Asp His Ala Gly Gly Leu Cys 215 220
225 Glu Val Pro Arg Asn Pro Cys Arg Met Ser Cys Gln Asn His Gly 230
235 240 Arg Leu Asn Ile Ser Thr Cys His Cys His Cys Pro Pro Gly Tyr
245 250 255 Thr Gly Arg Tyr Cys Gln Val Arg Cys Ser Leu Gln Cys Val
His 260 265 270 Gly Arg Phe Arg Glu Glu Glu Cys Ser Cys Val Cys Asp
Ile Gly 275 280 285 Tyr Gly Gly Ala Gln Cys Ala Thr Lys Val His Phe
Pro Phe His 290 295 300 Thr Cys Asp Leu Arg Ile Asp Gly Asp Cys Phe
Met Val Ser Ser 305 310 315 Glu Ala Asp Thr Tyr Tyr Arg Ala Arg Met
Lys Cys Gln Arg Lys 320 325 330 Gly Gly Val Leu Ala Gln Ile Lys Ser
Gln Lys Val Gln Asp Ile 335 340 345 Leu Ala Phe Tyr Leu Gly Arg Leu
Glu Thr Thr Asn Glu Val Thr 350 355 360 Asp Ser Asp Phe Glu Thr Arg
Asn Phe Trp Ile Gly Leu Thr Tyr 365 370 375 Lys Thr Ala Lys Asp Ser
Phe Arg Trp Ala Thr Gly Glu His Gln 380 385 390 Ala Phe Thr Ser Phe
Ala Phe Gly Gln Pro Asp Asn His Gly Leu 395 400 405 Val Trp Leu Ser
Ala Ala Met Gly Phe Gly Asn Cys Val Glu Leu 410 415 420 Gln Ala Ser
Ala Ala Phe Asn Trp Asn Asp Gln Arg Cys Lys Thr 425 430 435 Arg Asn
Arg Tyr Ile Cys Gln Phe Ala Gln Glu His Ile Ser Arg 440 445 450 Trp
Gly Pro Gly Ser 455 51 24 DNA Artificial Sequence Synthetic
oligonucleotide probe 51 52 24 DNA Artificial Sequence Synthetic
oligonucleotide probe 52 53 45 DNA Artificial Sequence Synthetic
oligonucleotide probe 53 54 2331 DNA Homo Sapien 54 cggacgcgtg
ggctgggcgc tgcaaagcgt gtcccgccgg gtccccgagc 50 gtcccgcgcc
ctcgccccgc catgctcctg ctgctggggc tgtgcctggg 100 gctgtccctg
tgtgtggggt cgcaggaaga ggcgcagagc tggggccact 150 cttcggagca
ggatggactc agggtcccga ggcaagtcag actgttgcag 200 aggctgaaaa
ccaaaccttt gatgacagaa ttctcagtga agtctaccat 250 catttcccgt
tatgccttca ctacggtttc ctgcagaatg ctgaacagag 300 cttctgaaga
ccaggacatt gagttccaga tgcagattcc agctgcagct 350 ttcatcacca
acttcactat gcttattgga gacaaggtgt atcagggcga 400 aattacagag
agagaaaaga agagtggtga tagggtaaaa gagaaaagga 450 ataaaaccac
agaagaaaat ggagagaagg ggactgaaat attcagagct 500 tctgcagtga
ttcccagcaa ggacaaagcc gcctttttcc tgagttatga 550 ggagcttctg
cagaggcgcc tgggcaagta cgagcacagc atcagcgtgc 600 ggccccagca
gctgtccggg aggctgagcg tggacgtgaa tatcctggag 650 agcgcgggca
tcgcatccct ggaggtgctg ccgcttcaca acagcaggca 700 gaggggcagt
gggcgcgggg aagatgattc tgggcctccc ccatctactg 750 tcattaacca
aaatgaaaca tttgccaaca taatttttaa acctactgta 800 gtacaacaag
ccaggattgc ccagaatgga attttgggag actttatcat 850 tagatatgac
gtcaatagag aacagagcat tggggacatc caggttctaa 900 atggctattt
tgtgcactac tttgctccta aagaccttcc tcctttaccc 950 aagaatgtgg
tattcgtgct tgacagcagt gcttctatgg tgggaaccaa 1000 actccggcag
accaaggatg ccctcttcac aattctccat gacctccgac 1050 cccaggaccg
tttcagtatc attggatttt ccaaccggat caaagtatgg 1100 aaggaccact
tgatatcagt cactccagac agcatcaggg atgggaaagt 1150 gtacattcac
catatgtcac ccactggagg cacagacatc aacggggccc 1200 tgcagagggc
catcaggctc ctcaacaagt acgtggccca cagtggcatt 1250 ggagaccgga
gcgtgtccct catcgtcttc ctgacggatg ggaagcccac 1300 ggtcggggag
acgcacaccc tcaagatcct caacaacacc cgagaggccg 1350 cccgaggcca
agtctgcatc ttcaccattg gcatcggcaa cgacgtggac 1400 ttcaggctgc
tggagaaact gtcgctggag aactgtggcc tcacacggcg 1450 cgtgcacgag
gaggaggacg caggctcgca gctcatcggg ttctacgatg 1500 aaatcaggac
cccgctcctc tctgacatcc gcatcgatta tccccccagc 1550 tcagtggtgc
aggccaccaa gaccctgttc cccaactact tcaacggctc 1600 ggagatcatc
attgcgggga agctggtgga caggaagctg gatcacctgc 1650 acgtggaggt
caccgccagc aacagtaaga aattcatcat cctgaagaca 1700 gatgtgcctg
tgcggcctca gaaggcaggg aaagatgtca caggaagccc 1750 caggcctgga
ggcgatggag agggggacac caaccacatc gagcgtctct 1800 ggagctacct
caccacaaag gagctgctga gctcctggct gcaaagtgac 1850 gatgaaccgg
agaaggagcg gctgcggcag cgggcccagg ccctggctgt 1900 gagctaccgc
ttcctcactc ccttcacctc catgaagctg agggggccgg 1950 tcccacgcat
ggatggcctg gaggaggccc acggcatgtc ggctgccatg 2000 ggacccgaac
cggtggtgca gagcgtgcga ggagctggca cgcagccagg 2050 acctttgctc
aagaagccaa actccgtcaa aaaaaaacaa aacaaaacaa 2100 aaaaaagaca
tgggagagat ggtgtttttc ctctccacca cctggggata 2150 cgatgagaag
atggccacct gcaagccagg aagacggccc tcaccagaca 2200 ccatgtctgc
tggcaccttg atcttggacc tcccagcctc cagaactgtg 2250 agaaataaat
gtgttttgtt taagctaaaa aaaaaaaaaa aaaaaaaaaa 2300 aaaaaaaaaa
aaaaaaaaaa aaaaaaaaaa a 2331 55 694 PRT Homo Sapien 55 Met Leu Leu
Leu Leu Gly Leu Cys Leu Gly Leu Ser Leu Cys Val 1 5 10 15 Gly Ser
Gln Glu Glu Ala Gln Ser Trp Gly His Ser Ser Glu Gln 20 25 30 Asp
Gly Leu Arg Val Pro Arg Gln Val Arg Leu Leu Gln Arg Leu 35 40
45 Lys Thr Lys Pro Leu Met Thr Glu Phe Ser Val Lys Ser Thr Ile 50
55 60 Ile Ser Arg Tyr Ala Phe Thr Thr Val Ser Cys Arg Met Leu Asn
65 70 75 Arg Ala Ser Glu Asp Gln Asp Ile Glu Phe Gln Met Gln Ile
Pro 80 85 90 Ala Ala Ala Phe Ile Thr Asn Phe Thr Met Leu Ile Gly
Asp Lys 95 100 105 Val Tyr Gln Gly Glu Ile Thr Glu Arg Glu Lys Lys
Ser Gly Asp 110 115 120 Arg Val Lys Glu Lys Arg Asn Lys Thr Thr Glu
Glu Asn Gly Glu 125 130 135 Lys Gly Thr Glu Ile Phe Arg Ala Ser Ala
Val Ile Pro Ser Lys 140 145 150 Asp Lys Ala Ala Phe Phe Leu Ser Tyr
Glu Glu Leu Leu Gln Arg 155 160 165 Arg Leu Gly Lys Tyr Glu His Ser
Ile Ser Val Arg Pro Gln Gln 170 175 180 Leu Ser Gly Arg Leu Ser Val
Asp Val Asn Ile Leu Glu Ser Ala 185 190 195 Gly Ile Ala Ser Leu Glu
Val Leu Pro Leu His Asn Ser Arg Gln 200 205 210 Arg Gly Ser Gly Arg
Gly Glu Asp Asp Ser Gly Pro Pro Pro Ser 215 220 225 Thr Val Ile Asn
Gln Asn Glu Thr Phe Ala Asn Ile Ile Phe Lys 230 235 240 Pro Thr Val
Val Gln Gln Ala Arg Ile Ala Gln Asn Gly Ile Leu 245 250 255 Gly Asp
Phe Ile Ile Arg Tyr Asp Val Asn Arg Glu Gln Ser Ile 260 265 270 Gly
Asp Ile Gln Val Leu Asn Gly Tyr Phe Val His Tyr Phe Ala 275 280 285
Pro Lys Asp Leu Pro Pro Leu Pro Lys Asn Val Val Phe Val Leu 290 295
300 Asp Ser Ser Ala Ser Met Val Gly Thr Lys Leu Arg Gln Thr Lys 305
310 315 Asp Ala Leu Phe Thr Ile Leu His Asp Leu Arg Pro Gln Asp Arg
320 325 330 Phe Ser Ile Ile Gly Phe Ser Asn Arg Ile Lys Val Trp Lys
Asp 335 340 345 His Leu Ile Ser Val Thr Pro Asp Ser Ile Arg Asp Gly
Lys Val 350 355 360 Tyr Ile His His Met Ser Pro Thr Gly Gly Thr Asp
Ile Asn Gly 365 370 375 Ala Leu Gln Arg Ala Ile Arg Leu Leu Asn Lys
Tyr Val Ala His 380 385 390 Ser Gly Ile Gly Asp Arg Ser Val Ser Leu
Ile Val Phe Leu Thr 395 400 405 Asp Gly Lys Pro Thr Val Gly Glu Thr
His Thr Leu Lys Ile Leu 410 415 420 Asn Asn Thr Arg Glu Ala Ala Arg
Gly Gln Val Cys Ile Phe Thr 425 430 435 Ile Gly Ile Gly Asn Asp Val
Asp Phe Arg Leu Leu Glu Lys Leu 440 445 450 Ser Leu Glu Asn Cys Gly
Leu Thr Arg Arg Val His Glu Glu Glu 455 460 465 Asp Ala Gly Ser Gln
Leu Ile Gly Phe Tyr Asp Glu Ile Arg Thr 470 475 480 Pro Leu Leu Ser
Asp Ile Arg Ile Asp Tyr Pro Pro Ser Ser Val 485 490 495 Val Gln Ala
Thr Lys Thr Leu Phe Pro Asn Tyr Phe Asn Gly Ser 500 505 510 Glu Ile
Ile Ile Ala Gly Lys Leu Val Asp Arg Lys Leu Asp His 515 520 525 Leu
His Val Glu Val Thr Ala Ser Asn Ser Lys Lys Phe Ile Ile 530 535 540
Leu Lys Thr Asp Val Pro Val Arg Pro Gln Lys Ala Gly Lys Asp 545 550
555 Val Thr Gly Ser Pro Arg Pro Gly Gly Asp Gly Glu Gly Asp Thr 560
565 570 Asn His Ile Glu Arg Leu Trp Ser Tyr Leu Thr Thr Lys Glu Leu
575 580 585 Leu Ser Ser Trp Leu Gln Ser Asp Asp Glu Pro Glu Lys Glu
Arg 590 595 600 Leu Arg Gln Arg Ala Gln Ala Leu Ala Val Ser Tyr Arg
Phe Leu 605 610 615 Thr Pro Phe Thr Ser Met Lys Leu Arg Gly Pro Val
Pro Arg Met 620 625 630 Asp Gly Leu Glu Glu Ala His Gly Met Ser Ala
Ala Met Gly Pro 635 640 645 Glu Pro Val Val Gln Ser Val Arg Gly Ala
Gly Thr Gln Pro Gly 650 655 660 Pro Leu Leu Lys Lys Pro Asn Ser Val
Lys Lys Lys Gln Asn Lys 665 670 675 Thr Lys Lys Arg His Gly Arg Asp
Gly Val Phe Pro Leu His His 680 685 690 Leu Gly Ile Arg 56 24 DNA
Artificial Sequence Synthetic oligonucleotide probe 56 gtgggaacca
aactccggca gacc 24 57 18 DNA Artificial Sequence Synthetic
oligonucleotide probe 57 cacatcgagc gtctctgg 18 58 24 DNA
Artificial Sequence Synthetic oligonucleotide probe 58 agccgctcct
tctccggttc atcg 24 59 48 DNA Artificial Sequence Synthetic
oligonucleotide probe 59 tggaaggacc acttgatatc agtcactcca
gacagcatca gggatggg 48 60 1413 DNA Homo Sapien 60 cggacgcgtg
gggtgcccga catggcgagt gtagtgctgc cgagcggatc 50 ccagtgtgcg
gcggcagcgg cggcggcggc gcctcccggg ctccggcttc 100 tgctgttgct
cttctccgcc gcggcactga tccccacagg tgatgggcag 150 aatctgttta
cgaaagacgt gacagtgatc gagggagagg ttgcgaccat 200 cagttgccaa
gtcaataaga gtgacgactc tgtgattcag ctactgaatc 250 ccaacaggca
gaccatttat ttcagggact tcaggccttt gaaggacagc 300 aggtttcagt
tgctgaattt ttctagcagt gaactcaaag tatcattgac 350 aaacgtctca
atttctgatg aaggaagata cttttgccag ctctataccg 400 atcccccaca
ggaaagttac accaccatca cagtcctggt cccaccacgt 450 aatctgatga
tcgatatcca gaaagacact gcggtggaag gtgaggagat 500 tgaagtcaac
tgcactgcta tggccagcaa gccagccacg actatcaggt 550 ggttcaaagg
gaacacagag ctaaaaggca aatcggaggt ggaagagtgg 600 tcagacatgt
acactgtgac cagtcagctg atgctgaagg tgcacaagga 650 ggacgatggg
gtcccagtga tctgccaggt ggagcaccct gcggtcactg 700 gaaacctgca
gacccagcgg tatctagaag tacagtataa gcctcaagtg 750 cacattcaga
tgacttatcc tctacaaggc ttaacccggg aaggggacgc 800 gcttgagtta
acatgtgaag ccatcgggaa gccccagcct gtgatggtaa 850 cttgggtgag
agtcgatgat gaaatgcctc aacacgccgt actgtctggg 900 cccaacctgt
tcatcaataa cctaaacaaa acagataatg gtacataccg 950 ctgtgaagct
tcaaacatag tggggaaagc tcactcggat tatatgctgt 1000 atgtatacga
tccccccaca actatccctc ctcccacaac aaccaccacc 1050 accaccacca
ccaccaccac caccatcctt accatcatca cagattcccg 1100 agcaggtgaa
gaaggctcga tcagggcagt ggatcatgcc gtgatcggtg 1150 gcgtcgtggc
ggtggtggtg ttcgccatgc tgtgcttgct catcattctg 1200 gggcgctatt
ttgccagaca taaaggtaca tacttcactc atgaagccaa 1250 aggagccgat
gacgcagcag acgcagacac agctataatc aatgcagaag 1300 gaggacagaa
caactccgaa gaaaagaaag agtacttcat ctagatcagc 1350 ctttttgttt
caatgaggtg tccaactggc cctatttaga tgataaagag 1400 acagtgatat tgg
1413 61 440 PRT Homo Sapien 61 Met Ala Ser Val Val Leu Pro Ser Gly
Ser Gln Cys Ala Ala Ala 1 5 10 15 Ala Ala Ala Ala Ala Pro Pro Gly
Leu Arg Leu Leu Leu Leu Leu 20 25 30 Phe Ser Ala Ala Ala Leu Ile
Pro Thr Gly Asp Gly Gln Asn Leu 35 40 45 Phe Thr Lys Asp Val Thr
Val Ile Glu Gly Glu Val Ala Thr Ile 50 55 60 Ser Cys Gln Val Asn
Lys Ser Asp Asp Ser Val Ile Gln Leu Leu 65 70 75 Asn Pro Asn Arg
Gln Thr Ile Tyr Phe Arg Asp Phe Arg Pro Leu 80 85 90 Lys Asp Ser
Arg Phe Gln Leu Leu Asn Phe Ser Ser Ser Glu Leu 95 100 105 Lys Val
Ser Leu Thr Asn Val Ser Ile Ser Asp Glu Gly Arg Tyr 110 115 120 Phe
Cys Gln Leu Tyr Thr Asp Pro Pro Gln Glu Ser Tyr Thr Thr 125 130 135
Ile Thr Val Leu Val Pro Pro Arg Asn Leu Met Ile Asp Ile Gln 140 145
150 Lys Asp Thr Ala Val Glu Gly Glu Glu Ile Glu Val Asn Cys Thr 155
160 165 Ala Met Ala Ser Lys Pro Ala Thr Thr Ile Arg Trp Phe Lys Gly
170 175 180 Asn Thr Glu Leu Lys Gly Lys Ser Glu Val Glu Glu Trp Ser
Asp 185 190 195 Met Tyr Thr Val Thr Ser Gln Leu Met Leu Lys Val His
Lys Glu 200 205 210 Asp Asp Gly Val Pro Val Ile Cys Gln Val Glu His
Pro Ala Val 215 220 225 Thr Gly Asn Leu Gln Thr Gln Arg Tyr Leu Glu
Val Gln Tyr Lys 230 235 240 Pro Gln Val His Ile Gln Met Thr Tyr Pro
Leu Gln Gly Leu Thr 245 250 255 Arg Glu Gly Asp Ala Leu Glu Leu Thr
Cys Glu Ala Ile Gly Lys 260 265 270 Pro Gln Pro Val Met Val Thr Trp
Val Arg Val Asp Asp Glu Met 275 280 285 Pro Gln His Ala Val Leu Ser
Gly Pro Asn Leu Phe Ile Asn Asn 290 295 300 Leu Asn Lys Thr Asp Asn
Gly Thr Tyr Arg Cys Glu Ala Ser Asn 305 310 315 Ile Val Gly Lys Ala
His Ser Asp Tyr Met Leu Tyr Val Tyr Asp 320 325 330 Pro Pro Thr Thr
Ile Pro Pro Pro Thr Thr Thr Thr Thr Thr Thr 335 340 345 Thr Thr Thr
Thr Thr Thr Ile Leu Thr Ile Ile Thr Asp Ser Arg 350 355 360 Ala Gly
Glu Glu Gly Ser Ile Arg Ala Val Asp His Ala Val Ile 365 370 375 Gly
Gly Val Val Ala Val Val Val Phe Ala Met Leu Cys Leu Leu 380 385 390
Ile Ile Leu Gly Arg Tyr Phe Ala Arg His Lys Gly Thr Tyr Phe 395 400
405 Thr His Glu Ala Lys Gly Ala Asp Asp Ala Ala Asp Ala Asp Thr 410
415 420 Ala Ile Ile Asn Ala Glu Gly Gly Gln Asn Asn Ser Glu Glu Lys
425 430 435 Lys Glu Tyr Phe Ile 440 62 24 DNA Artificial Sequence
Synthetic oligonucleotide probe 62 ggcttctgct gttgctcttc tccg 24 63
20 DNA Artificial Sequence Synthetic oligonucleotide probe 63
gtacactgtg accagtcagc 20 64 20 DNA Artificial Sequence Synthetic
oligonucleotide probe 64 atcatcacag attcccgagc 20 65 24 DNA
Artificial Sequence Synthetic oligonucleotide probe 65 ttcaatctcc
tcaccttcca ccgc 24 66 24 DNA Artificial Sequence Synthetic
oligonucleotide probe 66 atagctgtgt ctgcgtctgc tgcg 24 67 50 DNA
Artificial Sequence Synthetic oligonucleotide probe 67 cgcggcactg
atccccacag gtgatgggca gaatctgttt acgaaagacg 50 68 2555 DNA Homo
Sapien 68 ggggcgggtg gacgcggact cgaacgcagt tgcttcggga cccaggaccc 50
cctcgggccc gacccgccag gaaagactga ggccgcggcc tgccccgccc 100
ggctccctgc gccgccgccg cctcccggga cagaagatgt gctccagggt 150
ccctctgctg ctgccgctgc tcctgctact ggccctgggg cctggggtgc 200
agggctgccc atccggctgc cagtgcagcc agccacagac agtcttctgc 250
actgcccgcc aggggaccac ggtgccccga gacgtgccac ccgacacggt 300
ggggctgtac gtctttgaga acggcatcac catgctcgac gcaagcagct 350
ttgccggcct gccgggcctg cagctcctgg acctgtcaca gaaccagatc 400
gccagcctgc gcctgccccg cctgctgctg ctggacctca gccacaacag 450
cctcctggcc ctggagcccg gcatcctgga cactgccaac gtggaggcgc 500
tgcggctggc tggtctgggg ctgcagcagc tggacgaggg gctcttcagc 550
cgcttgcgca acctccacga cctggatgtg tccgacaacc agctggagcg 600
agtgccacct gtgatccgag gcctccgggg cctgacgcgc ctgcggctgg 650
ccggcaacac ccgcattgcc cagctgcggc ccgaggacct ggccggcctg 700
gctgccctgc aggagctgga tgtgagcaac ctaagcctgc aggccctgcc 750
tggcgacctc tcgggcctct tcccccgcct gcggctgctg gcagctgccc 800
gcaacccctt caactgcgtg tgccccctga gctggtttgg cccctgggtg 850
cgcgagagcc acgtcacact ggccagccct gaggagacgc gctgccactt 900
cccgcccaag aacgctggcc ggctgctcct ggagcttgac tacgccgact 950
ttggctgccc agccaccacc accacagcca cagtgcccac cacgaggccc 1000
gtggtgcggg agcccacagc cttgtcttct agcttggctc ctacctggct 1050
tagccccaca gcgccggcca ctgaggcccc cagcccgccc tccactgccc 1100
caccgactgt agggcctgtc ccccagcccc aggactgccc accgtccacc 1150
tgcctcaatg ggggcacatg ccacctgggg acacggcacc acctggcgtg 1200
cttgtgcccc gaaggcttca cgggcctgta ctgtgagagc cagatggggc 1250
aggggacacg gcccagccct acaccagtca cgccgaggcc accacggtcc 1300
ctgaccctgg gcatcgagcc ggtgagcccc acctccctgc gcgtggggct 1350
gcagcgctac ctccagggga gctccgtgca gctcaggagc ctccgtctca 1400
cctatcgcaa cctatcgggc cctgataagc ggctggtgac gctgcgactg 1450
cctgcctcgc tcgctgagta cacggtcacc cagctgcggc ccaacgccac 1500
ttactccgtc tgtgtcatgc ctttggggcc cgggcgggtg ccggagggcg 1550
aggaggcctg cggggaggcc catacacccc cagccgtcca ctccaaccac 1600
gccccagtca cccaggcccg cgagggcaac ctgccgctcc tcattgcgcc 1650
cgccctggcc gcggtgctcc tggccgcgct ggctgcggtg ggggcagcct 1700
actgtgtgcg gcgggggcgg gccatggcag cagcggctca ggacaaaggg 1750
caggtggggc caggggctgg gcccctggaa ctggagggag tgaaggtccc 1800
cttggagcca ggcccgaagg caacagaggg cggtggagag gccctgccca 1850
gcgggtctga gtgtgaggtg ccactcatgg gcttcccagg gcctggcctc 1900
cagtcacccc tccacgcaaa gccctacatc taagccagag agagacaggg 1950
cagctggggc cgggctctca gccagtgaga tggccagccc cctcctgctg 2000
ccacaccacg taagttctca gtcccaacct cggggatgtg tgcagacagg 2050
gctgtgtgac cacagctggg ccctgttccc tctggacctc ggtctcctca 2100
tctgtgagat gctgtggccc agctgacgag ccctaacgtc cccagaaccg 2150
agtgcctatg aggacagtgt ccgccctgcc ctccgcaacg tgcagtccct 2200
gggcacggcg ggccctgcca tgtgctggta acgcatgcct gggccctgct 2250
gggctctccc actccaggcg gaccctgggg gccagtgaag gaagctcccg 2300
gaaagagcag agggagagcg ggtaggcggc tgtgtgactc tagtcttggc 2350
cccaggaagc gaaggaacaa aagaaactgg aaaggaagat gctttaggaa 2400
catgttttgc ttttttaaaa tatatatata tttataagag atcctttccc 2450
atttattctg ggaagatgtt tttcaaactc agagacaagg actttggttt 2500
ttgtaagaca aacgatgata tgaaggcctt ttgtaagaaa aaataaaaaa 2550 aaaaa
2555 69 598 PRT Homo Sapien 69 Met Cys Ser Arg Val Pro Leu Leu Leu
Pro Leu Leu Leu Leu Leu 1 5 10 15 Ala Leu Gly Pro Gly Val Gln Gly
Cys Pro Ser Gly Cys Gln Cys 20 25 30 Ser Gln Pro Gln Thr Val Phe
Cys Thr Ala Arg Gln Gly Thr Thr 35 40 45 Val Pro Arg Asp Val Pro
Pro Asp Thr Val Gly Leu Tyr Val Phe 50 55 60 Glu Asn Gly Ile Thr
Met Leu Asp Ala Ser Ser Phe Ala Gly Leu 65 70 75 Pro Gly Leu Gln
Leu Leu Asp Leu Ser Gln Asn Gln Ile Ala Ser 80 85 90 Leu Arg Leu
Pro Arg Leu Leu Leu Leu Asp Leu Ser His Asn Ser 95 100 105 Leu Leu
Ala Leu Glu Pro Gly Ile Leu Asp Thr Ala Asn Val Glu 110 115 120 Ala
Leu Arg Leu Ala Gly Leu Gly Leu Gln Gln Leu Asp Glu Gly 125 130 135
Leu Phe Ser Arg Leu Arg Asn Leu His Asp Leu Asp Val Ser Asp 140 145
150 Asn Gln Leu Glu Arg Val Pro Pro Val Ile Arg Gly Leu Arg Gly 155
160 165 Leu Thr Arg Leu Arg Leu Ala Gly Asn Thr Arg Ile Ala Gln Leu
170 175 180 Arg Pro Glu Asp Leu Ala Gly Leu Ala Ala Leu Gln Glu Leu
Asp 185 190 195 Val Ser Asn Leu Ser Leu Gln Ala Leu Pro Gly Asp Leu
Ser Gly 200 205 210 Leu Phe Pro Arg Leu Arg Leu Leu Ala Ala Ala Arg
Asn Pro Phe 215 220 225 Asn Cys Val Cys Pro Leu Ser Trp Phe Gly Pro
Trp Val Arg Glu 230 235 240 Ser His Val Thr Leu Ala Ser Pro Glu Glu
Thr Arg Cys His Phe 245 250 255 Pro Pro Lys Asn Ala Gly Arg Leu Leu
Leu Glu Leu Asp Tyr Ala 260 265 270 Asp Phe Gly Cys Pro Ala
Thr Thr Thr Thr Ala Thr Val Pro Thr 275 280 285 Thr Arg Pro Val Val
Arg Glu Pro Thr Ala Leu Ser Ser Ser Leu 290 295 300 Ala Pro Thr Trp
Leu Ser Pro Thr Ala Pro Ala Thr Glu Ala Pro 305 310 315 Ser Pro Pro
Ser Thr Ala Pro Pro Thr Val Gly Pro Val Pro Gln 320 325 330 Pro Gln
Asp Cys Pro Pro Ser Thr Cys Leu Asn Gly Gly Thr Cys 335 340 345 His
Leu Gly Thr Arg His His Leu Ala Cys Leu Cys Pro Glu Gly 350 355 360
Phe Thr Gly Leu Tyr Cys Glu Ser Gln Met Gly Gln Gly Thr Arg 365 370
375 Pro Ser Pro Thr Pro Val Thr Pro Arg Pro Pro Arg Ser Leu Thr 380
385 390 Leu Gly Ile Glu Pro Val Ser Pro Thr Ser Leu Arg Val Gly Leu
395 400 405 Gln Arg Tyr Leu Gln Gly Ser Ser Val Gln Leu Arg Ser Leu
Arg 410 415 420 Leu Thr Tyr Arg Asn Leu Ser Gly Pro Asp Lys Arg Leu
Val Thr 425 430 435 Leu Arg Leu Pro Ala Ser Leu Ala Glu Tyr Thr Val
Thr Gln Leu 440 445 450 Arg Pro Asn Ala Thr Tyr Ser Val Cys Val Met
Pro Leu Gly Pro 455 460 465 Gly Arg Val Pro Glu Gly Glu Glu Ala Cys
Gly Glu Ala His Thr 470 475 480 Pro Pro Ala Val His Ser Asn His Ala
Pro Val Thr Gln Ala Arg 485 490 495 Glu Gly Asn Leu Pro Leu Leu Ile
Ala Pro Ala Leu Ala Ala Val 500 505 510 Leu Leu Ala Ala Leu Ala Ala
Val Gly Ala Ala Tyr Cys Val Arg 515 520 525 Arg Gly Arg Ala Met Ala
Ala Ala Ala Gln Asp Lys Gly Gln Val 530 535 540 Gly Pro Gly Ala Gly
Pro Leu Glu Leu Glu Gly Val Lys Val Pro 545 550 555 Leu Glu Pro Gly
Pro Lys Ala Thr Glu Gly Gly Gly Glu Ala Leu 560 565 570 Pro Ser Gly
Ser Glu Cys Glu Val Pro Leu Met Gly Phe Pro Gly 575 580 585 Pro Gly
Leu Gln Ser Pro Leu His Ala Lys Pro Tyr Ile 590 595 70 22 DNA
Artificial Sequence Synthetic oligonucleotide probe 70 ccctccactg
ccccaccgac tg 22 71 24 DNA Artificial Sequence Synthetic
oligonucleotide probe 71 cggttctggg gacgttaggg ctcg 24 72 25 DNA
Artificial Sequence Synthetic oligonucleotide probe 72 ctgcccaccg
tccacctgcc tcaat 25 73 45 DNA Artificial Sequence Synthetic
oligonucleotide probe 73 aggactgccc accgtccacc tgcctcaatg
ggggcacatg ccacc 45 74 45 DNA Artificial Sequence Synthetic
Oligonucleotide Probe 74 acgcaaagcc ctacatctaa gccagagaga
gacagggcag ctggg 45 75 1077 DNA Homo Sapien 75 ggcactagga
caaccttctt cccttctgca ccactgcccg tacccttacc 50 cgccccgcca
cctccttgct accccactct tgaaaccaca gctgttggca 100 gggtccccag
ctcatgccag cctcatctcc tttcttgcta gcccccaaag 150 ggcctccagg
caacatgggg ggcccagtca gagagccggc actctcagtt 200 gccctctggt
tgagttgggg ggcagctctg ggggccgtgg cttgtgccat 250 ggctctgctg
acccaacaaa cagagctgca gagcctcagg agagaggtga 300 gccggctgca
ggggacagga ggcccctccc agaatgggga agggtatccc 350 tggcagagtc
tcccggagca gagttccgat gccctggaag cctgggagaa 400 tggggagaga
tcccggaaaa ggagagcagt gctcacccaa aaacagaaga 450 agcagcactc
tgtcctgcac ctggttccca ttaacgccac ctccaaggat 500 gactccgatg
tgacagaggt gatgtggcaa ccagctctta ggcgtgggag 550 aggcctacag
gcccaaggat atggtgtccg aatccaggat gctggagttt 600 atctgctgta
tagccaggtc ctgtttcaag acgtgacttt caccatgggt 650 caggtggtgt
ctcgagaagg ccaaggaagg caggagactc tattccgatg 700 tataagaagt
atgccctccc acccggaccg ggcctacaac agctgctata 750 gcgcaggtgt
cttccattta caccaagggg atattctgag tgtcataatt 800 ccccgggcaa
gggcgaaact taacctctct ccacatggaa ccttcctggg 850 gtttgtgaaa
ctgtgattgt gttataaaaa gtggctccca gcttggaaga 900 ccagggtggg
tacatactgg agacagccaa gagctgagta tataaaggag 950 agggaatgtg
caggaacaga ggcatcttcc tgggtttggc tccccgttcc 1000 tcacttttcc
cttttcattc ccacccccta gactttgatt ttacggatat 1050 cttgcttctg
ttccccatgg agctccg 1077 76 250 PRT Homo Sapien 76 Met Pro Ala Ser
Ser Pro Phe Leu Leu Ala Pro Lys Gly Pro Pro 1 5 10 15 Gly Asn Met
Gly Gly Pro Val Arg Glu Pro Ala Leu Ser Val Ala 20 25 30 Leu Trp
Leu Ser Trp Gly Ala Ala Leu Gly Ala Val Ala Cys Ala 35 40 45 Met
Ala Leu Leu Thr Gln Gln Thr Glu Leu Gln Ser Leu Arg Arg 50 55 60
Glu Val Ser Arg Leu Gln Gly Thr Gly Gly Pro Ser Gln Asn Gly 65 70
75 Glu Gly Tyr Pro Trp Gln Ser Leu Pro Glu Gln Ser Ser Asp Ala 80
85 90 Leu Glu Ala Trp Glu Asn Gly Glu Arg Ser Arg Lys Arg Arg Ala
95 100 105 Val Leu Thr Gln Lys Gln Lys Lys Gln His Ser Val Leu His
Leu 110 115 120 Val Pro Ile Asn Ala Thr Ser Lys Asp Asp Ser Asp Val
Thr Glu 125 130 135 Val Met Trp Gln Pro Ala Leu Arg Arg Gly Arg Gly
Leu Gln Ala 140 145 150 Gln Gly Tyr Gly Val Arg Ile Gln Asp Ala Gly
Val Tyr Leu Leu 155 160 165 Tyr Ser Gln Val Leu Phe Gln Asp Val Thr
Phe Thr Met Gly Gln 170 175 180 Val Val Ser Arg Glu Gly Gln Gly Arg
Gln Glu Thr Leu Phe Arg 185 190 195 Cys Ile Arg Ser Met Pro Ser His
Pro Asp Arg Ala Tyr Asn Ser 200 205 210 Cys Tyr Ser Ala Gly Val Phe
His Leu His Gln Gly Asp Ile Leu 215 220 225 Ser Val Ile Ile Pro Arg
Ala Arg Ala Lys Leu Asn Leu Ser Pro 230 235 240 His Gly Thr Phe Leu
Gly Phe Val Lys Leu 245 250 77 2849 DNA Homo Sapien 77 cactttctcc
ctctcttcct ttactttcga gaaaccgcgc ttccgcttct 50 ggtcgcagag
acctcggaga ccgcgccggg gagacggagg tgctgtgggt 100 gggggggacc
tgtggctgct cgtaccgccc cccaccctcc tcttctgcac 150 tgccgtcctc
cggaagacct tttcccctgc tctgtttcct tcaccgagtc 200 tgtgcatcgc
cccggacctg gccgggagga ggcttggccg gcgggagatg 250 ctctaggggc
ggcgcgggag gagcggccgg cgggacggag ggcccggcag 300 gaagatgggc
tcccgtggac agggactctt gctggcgtac tgcctgctcc 350 ttgcctttgc
ctctggcctg gtcctgagtc gtgtgcccca tgtccagggg 400 gaacagcagg
agtgggaggg gactgaggag ctgccgtcgc ctccggacca 450 tgccgagagg
gctgaagaac aacatgaaaa atacaggccc agtcaggacc 500 aggggctccc
tgcttcccgg tgcttgcgct gctgtgaccc cggtacctcc 550 atgtacccgg
cgaccgccgt gccccagatc aacatcacta tcttgaaagg 600 ggagaagggt
gaccgcggag atcgaggcct ccaagggaaa tatggcaaaa 650 caggctcagc
aggggccagg ggccacactg gacccaaagg gcagaagggc 700 tccatggggg
cccctgggga gcggtgcaag agccactacg ccgccttttc 750 ggtgggccgg
aagaagccca tgcacagcaa ccactactac cagacggtga 800 tcttcgacac
ggagttcgtg aacctctacg accacttcaa catgttcacc 850 ggcaagttct
actgctacgt gcccggcctc tacttcttca gcctcaacgt 900 gcacacctgg
aaccagaagg agacctacct gcacatcatg aagaacgagg 950 aggaggtggt
gatcttgttc gcgcaggtgg gcgaccgcag catcatgcaa 1000 agccagagcc
tgatgctgga gctgcgagag caggaccagg tgtgggtacg 1050 cctctacaag
ggcgaacgtg agaacgccat cttcagcgag gagctggaca 1100 cctacatcac
cttcagtggc tacctggtca agcacgccac cgagccctag 1150 ctggccggcc
acctcctttc ctctcgccac cttccacccc tgcgctgtgc 1200 tgaccccacc
gcctcttccc cgatccctgg actccgactc cctggctttg 1250 gcattcagtg
agacgccctg cacacacaga aagccaaagc gatcggtgct 1300 cccagatccc
gcagcctctg gagagagctg acggcagatg aaatcaccag 1350 ggcggggcac
ccgcgagaac cctctgggac cttccgcggc cctctctgca 1400 cacatcctca
agtgaccccg cacggcgaga cgcgggtggc ggcagggcgt 1450 cccagggtgc
ggcaccgcgg ctccagtcct tggaaataat taggcaaatt 1500 ctaaaggtct
caaaaggagc aaagtaaacc gtggaggaca aagaaaaggg 1550 ttgttatttt
tgtctttcca gccagcctgc tggctcccaa gagagaggcc 1600 ttttcagttg
agactctgct taagagaaga tccaaagtta aagctctggg 1650 gtcaggggag
gggccggggg caggaaacta cctctggctt aattctttta 1700 agccacgtag
gaactttctt gagggatagg tggaccctga catccctgtg 1750 gccttgccca
agggctctgc tggtctttct gagtcacagc tgcgaggtga 1800 tgggggctgg
ggccccaggc gtcagcctcc cagagggaca gctgagcccc 1850 ctgccttggc
tccaggttgg tagaagcagc cgaagggctc ctgacagtgg 1900 ccagggaccc
ctgggtcccc caggcctgca gatgtttcta tgaggggcag 1950 agctccttgg
tacatccatg tgtggctctg ctccacccct gtgccacccc 2000 agagccctgg
ggggtggtct ccatgcctgc caccctggca tcggctttct 2050 gtgccgcctc
ccacacaaat cagccccaga aggccccggg gccttggctt 2100 ctgtttttta
taaaacacct caagcagcac tgcagtctcc catctcctcg 2150 tgggctaagc
atcaccgctt ccacgtgtgt tgtgttggtt ggcagcaagg 2200 ctgatccaga
ccccttctgc ccccactgcc ctcatccagg cctctgacca 2250 gtagcctgag
aggggctttt tctaggcttc agagcagggg agagctggaa 2300 ggggctagaa
agctcccgct tgtctgtttc tcaggctcct gtgagcctca 2350 gtcctgagac
cagagtcaag aggaagtaca cgtcccaatc acccgtgtca 2400 ggattcactc
tcaggagctg ggtggcagga gaggcaatag cccctgtggc 2450 aattgcagga
ccagctggag cagggttgcg gtgtctccac ggtgctctcg 2500 ccctgcccat
ggccacccca gactctgatc tccaggaacc ccatagcccc 2550 tctccacctc
accccatgtt gatgcccagg gtcactcttg ctacccgctg 2600 ggcccccaaa
cccccgctgc ctctcttcct tccccccatc ccccacctgg 2650 ttttgactaa
tcctgcttcc ctctctgggc ctggctgccg ggatctgggg 2700 tccctaagtc
cctctcttta aagaacttct gcgggtcaga ctctgaagcc 2750 gagttgctgt
gggcgtgccc ggaagcagag cgccacactc gctgcttaag 2800 ctcccccagc
tctttccaga aaacattaaa ctcagaattg tgttttcaa 2849 78 281 PRT Homo
Sapien 78 Met Gly Ser Arg Gly Gln Gly Leu Leu Leu Ala Tyr Cys Leu
Leu 1 5 10 15 Leu Ala Phe Ala Ser Gly Leu Val Leu Ser Arg Val Pro
His Val 20 25 30 Gln Gly Glu Gln Gln Glu Trp Glu Gly Thr Glu Glu
Leu Pro Ser 35 40 45 Pro Pro Asp His Ala Glu Arg Ala Glu Glu Gln
His Glu Lys Tyr 50 55 60 Arg Pro Ser Gln Asp Gln Gly Leu Pro Ala
Ser Arg Cys Leu Arg 65 70 75 Cys Cys Asp Pro Gly Thr Ser Met Tyr
Pro Ala Thr Ala Val Pro 80 85 90 Gln Ile Asn Ile Thr Ile Leu Lys
Gly Glu Lys Gly Asp Arg Gly 95 100 105 Asp Arg Gly Leu Gln Gly Lys
Tyr Gly Lys Thr Gly Ser Ala Gly 110 115 120 Ala Arg Gly His Thr Gly
Pro Lys Gly Gln Lys Gly Ser Met Gly 125 130 135 Ala Pro Gly Glu Arg
Cys Lys Ser His Tyr Ala Ala Phe Ser Val 140 145 150 Gly Arg Lys Lys
Pro Met His Ser Asn His Tyr Tyr Gln Thr Val 155 160 165 Ile Phe Asp
Thr Glu Phe Val Asn Leu Tyr Asp His Phe Asn Met 170 175 180 Phe Thr
Gly Lys Phe Tyr Cys Tyr Val Pro Gly Leu Tyr Phe Phe 185 190 195 Ser
Leu Asn Val His Thr Trp Asn Gln Lys Glu Thr Tyr Leu His 200 205 210
Ile Met Lys Asn Glu Glu Glu Val Val Ile Leu Phe Ala Gln Val 215 220
225 Gly Asp Arg Ser Ile Met Gln Ser Gln Ser Leu Met Leu Glu Leu 230
235 240 Arg Glu Gln Asp Gln Val Trp Val Arg Leu Tyr Lys Gly Glu Arg
245 250 255 Glu Asn Ala Ile Phe Ser Glu Glu Leu Asp Thr Tyr Ile Thr
Phe 260 265 270 Ser Gly Tyr Leu Val Lys His Ala Thr Glu Pro 275 280
79 24 DNA Artificial Sequence Synthetic oligonucleotide probe 79
tacaggccca gtcaggacca gggg 24 80 24 DNA Artificial Sequence
Synthetic oligonucleotide probe 80 ctgaagaagt agaggccggg cacg 24 81
45 DNA Artificial Sequence Synthetic oligonucleotide probe 81
cccggtgctt gcgctgctgt gaccccggta cctccatgta cccgg 45 82 2284 DNA
Homo Sapien 82 gcggagcatc cgctgcggtc ctcgccgaga cccccgcgcg
gattcgccgg 50 tccttcccgc gggcgcgaca gagctgtcct cgcacctgga
tggcagcagg 100 ggcgccgggg tcctctcgac gccagagaga aatctcatca
tctgtgcagc 150 cttcttaaag caaactaaga ccagagggag gattatcctt
gacctttgaa 200 gaccaaaact aaactgaaat ttaaaatgtt cttcggggga
gaagggagct 250 tgacttacac tttggtaata atttgcttcc tgacactaag
gctgtctgct 300 agtcagaatt gcctcaaaaa gagtctagaa gatgttgtca
ttgacatcca 350 gtcatctctt tctaagggaa tcagaggcaa tgagcccgta
tatacttcaa 400 ctcaagaaga ctgcattaat tcttgctgtt caacaaaaaa
catatcaggg 450 gacaaagcat gtaacttgat gatcttcgac actcgaaaaa
cagctagaca 500 acccaactgc tacctatttt tctgtcccaa cgaggaagcc
tgtccattga 550 aaccagcaaa aggacttatg agttacagga taattacaga
ttttccatct 600 ttgaccagaa atttgccaag ccaagagtta ccccaggaag
attctctctt 650 acatggccaa ttttcacaag cagtcactcc cctagcccat
catcacacag 700 attattcaaa gcccaccgat atctcatgga gagacacact
ttctcagaag 750 tttggatcct cagatcacct ggagaaacta tttaagatgg
atgaagcaag 800 tgcccagctc cttgcttata aggaaaaagg ccattctcag
agttcacaat 850 tttcctctga tcaagaaata gctcatctgc tgcctgaaaa
tgtgagtgcg 900 ctcccagcta cggtggcagt tgcttctcca cataccacct
cggctactcc 950 aaagcccgcc acccttctac ccaccaatgc ttcagtgaca
ccttctggga 1000 cttcccagcc acagctggcc accacagctc cacctgtaac
cactgtcact 1050 tctcagcctc ccacgaccct catttctaca gtttttacac
gggctgcggc 1100 tacactccaa gcaatggcta caacagcagt tctgactacc
acctttcagg 1150 cacctacgga ctcgaaaggc agcttagaaa ccataccgtt
tacagaaatc 1200 tccaacttaa ctttgaacac agggaatgtg tataacccta
ctgcactttc 1250 tatgtcaaat gtggagtctt ccactatgaa taaaactgct
tcctgggaag 1300 gtagggaggc cagtccaggc agttcctccc agggcagtgt
tccagaaaat 1350 cagtacggcc ttccatttga aaaatggctt cttatcgggt
ccctgctctt 1400 tggtgtcctg ttcctggtga taggcctcgt cctcctgggt
agaatccttt 1450 cggaatcact ccgcaggaaa cgttactcaa gactggatta
tttgatcaat 1500 gggatctatg tggacatcta aggatggaac tcggtgtctc
ttaattcatt 1550 tagtaaccag aagcccaaat gcaatgagtt tctgctgact
tgctagtctt 1600 agcaggaggt tgtattttga agacaggaaa atgccccctt
ctgctttcct 1650 tttttttttt ggagacagag tcttgctctg ttgcccaggc
tggagtgcag 1700 tagcacgatc tcggctctca ccgcaacctc cgtctcctgg
gttcaagcga 1750 ttctcctgcc tcagcctcct aagtatctgg gattacaggc
atgtgccacc 1800 acacctgggt gatttttgta tttttagtag agacggggtt
tcaccatgtt 1850 ggtcaggctg gtctcaaact cctgacctag tgatccaccc
tcctcggcct 1900 cccaaagtgc tgggattaca ggcatgagcc accacagctg
gcccccttct 1950 gttttatgtt tggtttttga gaaggaatga agtgggaacc
aaattaggta 2000 attttgggta atctgtctct aaaatattag ctaaaaacaa
agctctatgt 2050 aaagtaataa agtataattg ccatataaat ttcaaaattc
aactggcttt 2100 tatgcaaaga aacaggttag gacatctagg ttccaattca
ttcacattct 2150 tggttccaga taaaatcaac tgtttatatc aatttctaat
ggatttgctt 2200 ttctttttat atggattcct ttaaaactta ttccagatgt
agttccttcc 2250 aattaaatat ttgaataaat cttttgttac tcaa 2284 83 431
PRT Homo Sapien 83 Met Phe Phe Gly Gly Glu Gly Ser Leu Thr Tyr Thr
Leu Val Ile 1 5 10 15 Ile Cys Phe Leu Thr Leu Arg Leu Ser Ala Ser
Gln Asn Cys Leu 20 25 30 Lys Lys Ser Leu Glu Asp Val Val Ile Asp
Ile Gln Ser Ser Leu 35 40 45 Ser Lys Gly Ile Arg Gly Asn Glu Pro
Val Tyr Thr Ser Thr Gln 50 55 60 Glu Asp Cys Ile Asn Ser Cys Cys
Ser Thr Lys Asn Ile Ser Gly 65 70 75 Asp Lys Ala Cys Asn Leu Met
Ile Phe Asp Thr Arg Lys Thr Ala 80 85 90 Arg Gln Pro Asn Cys Tyr
Leu Phe Phe Cys Pro Asn Glu Glu Ala 95 100 105 Cys Pro Leu Lys Pro
Ala Lys Gly Leu Met Ser Tyr Arg Ile Ile 110 115 120 Thr Asp Phe Pro
Ser Leu Thr Arg Asn Leu Pro Ser Gln Glu Leu 125
130 135 Pro Gln Glu Asp Ser Leu Leu His Gly Gln Phe Ser Gln Ala Val
140 145 150 Thr Pro Leu Ala His His His Thr Asp Tyr Ser Lys Pro Thr
Asp 155 160 165 Ile Ser Trp Arg Asp Thr Leu Ser Gln Lys Phe Gly Ser
Ser Asp 170 175 180 His Leu Glu Lys Leu Phe Lys Met Asp Glu Ala Ser
Ala Gln Leu 185 190 195 Leu Ala Tyr Lys Glu Lys Gly His Ser Gln Ser
Ser Gln Phe Ser 200 205 210 Ser Asp Gln Glu Ile Ala His Leu Leu Pro
Glu Asn Val Ser Ala 215 220 225 Leu Pro Ala Thr Val Ala Val Ala Ser
Pro His Thr Thr Ser Ala 230 235 240 Thr Pro Lys Pro Ala Thr Leu Leu
Pro Thr Asn Ala Ser Val Thr 245 250 255 Pro Ser Gly Thr Ser Gln Pro
Gln Leu Ala Thr Thr Ala Pro Pro 260 265 270 Val Thr Thr Val Thr Ser
Gln Pro Pro Thr Thr Leu Ile Ser Thr 275 280 285 Val Phe Thr Arg Ala
Ala Ala Thr Leu Gln Ala Met Ala Thr Thr 290 295 300 Ala Val Leu Thr
Thr Thr Phe Gln Ala Pro Thr Asp Ser Lys Gly 305 310 315 Ser Leu Glu
Thr Ile Pro Phe Thr Glu Ile Ser Asn Leu Thr Leu 320 325 330 Asn Thr
Gly Asn Val Tyr Asn Pro Thr Ala Leu Ser Met Ser Asn 335 340 345 Val
Glu Ser Ser Thr Met Asn Lys Thr Ala Ser Trp Glu Gly Arg 350 355 360
Glu Ala Ser Pro Gly Ser Ser Ser Gln Gly Ser Val Pro Glu Asn 365 370
375 Gln Tyr Gly Leu Pro Phe Glu Lys Trp Leu Leu Ile Gly Ser Leu 380
385 390 Leu Phe Gly Val Leu Phe Leu Val Ile Gly Leu Val Leu Leu Gly
395 400 405 Arg Ile Leu Ser Glu Ser Leu Arg Arg Lys Arg Tyr Ser Arg
Leu 410 415 420 Asp Tyr Leu Ile Asn Gly Ile Tyr Val Asp Ile 425 430
84 30 DNA Artificial Sequence Synthetic oligonucleotide probe 84
agggaggatt atccttgacc tttgaagacc 30 85 18 DNA Artificial Sequence
Synthetic oligonucleotide probe 85 gaagcaagtg cccagctc 18 86 18 DNA
Artificial Sequence Synthetic oligonucleotide probe 86 cgggtccctg
ctctttgg 18 87 24 DNA Artificial Sequence Synthetic oligonucleotide
probe 87 caccgtagct gggagcgcac tcac 24 88 18 DNA Artificial
Sequence Synthetic oligonucleotide probe 88 agtgtaagtc aagctccc 18
89 49 DNA Artificial Sequence Synthetic oligonucleotide probe 89
gcttcctgac actaaggctg tctgctagtc agaattgcct caaaaagag 49 90 957 DNA
Homo Sapien 90 cctggaagat gcgcccattg gctggtggcc tgctcaaggt
ggtgttcgtg 50 gtcttcgcct ccttgtgtgc ctggtattcg gggtacctgc
tcgcagagct 100 cattccagat gcacccctgt ccagtgctgc ctatagcatc
cgcagcatcg 150 gggagaggcc tgtcctcaaa gctccagtcc ccaaaaggca
aaaatgtgac 200 cactggactc cctgcccatc tgacacctat gcctacaggt
tactcagcgg 250 aggtggcaga agcaagtacg ccaaaatctg ctttgaggat
aacctactta 300 tgggagaaca gctgggaaat gttgccagag gaataaacat
tgccattgtc 350 aactatgtaa ctgggaatgt gacagcaaca cgatgttttg
atatgtatga 400 aggcgataac tctggaccga tgacaaagtt tattcagagt
gctgctccaa 450 aatccctgct cttcatggtg acctatgacg acggaagcac
aagactgaat 500 aacgatgcca agaatgccat agaagcactt ggaagtaaag
aaatcaggaa 550 catgaaattc aggtctagct gggtatttat tgcagcaaaa
ggcttggaac 600 tcccttccga aattcagaga gaaaagatca accactctga
tgctaagaac 650 aacagatatt ctggctggcc tgcagagatc cagatagaag
gctgcatacc 700 caaagaacga agctgacact gcagggtcct gagtaaatgt
gttctgtata 750 aacaaatgca gctggaatcg ctcaagaatc ttatttttct
aaatccaaca 800 gcccatattt gatgagtatt ttgggtttgt tgtaaaccaa
tgaacatttg 850 ctagttgtat caaatcttgg tacgcagtat ttttatacca
gtattttatg 900 tagtgaagat gtcaattagc aggaaactaa aatgaatgga
aattcttaaa 950 aaaaaaa 957 91 235 PRT Homo Sapien 91 Met Arg Pro
Leu Ala Gly Gly Leu Leu Lys Val Val Phe Val Val 1 5 10 15 Phe Ala
Ser Leu Cys Ala Trp Tyr Ser Gly Tyr Leu Leu Ala Glu 20 25 30 Leu
Ile Pro Asp Ala Pro Leu Ser Ser Ala Ala Tyr Ser Ile Arg 35 40 45
Ser Ile Gly Glu Arg Pro Val Leu Lys Ala Pro Val Pro Lys Arg 50 55
60 Gln Lys Cys Asp His Trp Thr Pro Cys Pro Ser Asp Thr Tyr Ala 65
70 75 Tyr Arg Leu Leu Ser Gly Gly Gly Arg Ser Lys Tyr Ala Lys Ile
80 85 90 Cys Phe Glu Asp Asn Leu Leu Met Gly Glu Gln Leu Gly Asn
Val 95 100 105 Ala Arg Gly Ile Asn Ile Ala Ile Val Asn Tyr Val Thr
Gly Asn 110 115 120 Val Thr Ala Thr Arg Cys Phe Asp Met Tyr Glu Gly
Asp Asn Ser 125 130 135 Gly Pro Met Thr Lys Phe Ile Gln Ser Ala Ala
Pro Lys Ser Leu 140 145 150 Leu Phe Met Val Thr Tyr Asp Asp Gly Ser
Thr Arg Leu Asn Asn 155 160 165 Asp Ala Lys Asn Ala Ile Glu Ala Leu
Gly Ser Lys Glu Ile Arg 170 175 180 Asn Met Lys Phe Arg Ser Ser Trp
Val Phe Ile Ala Ala Lys Gly 185 190 195 Leu Glu Leu Pro Ser Glu Ile
Gln Arg Glu Lys Ile Asn His Ser 200 205 210 Asp Ala Lys Asn Asn Arg
Tyr Ser Gly Trp Pro Ala Glu Ile Gln 215 220 225 Ile Glu Gly Cys Ile
Pro Lys Glu Arg Ser 230 235 92 20 DNA Artificial Sequence Synthetic
oligonucleotide probe 92 aatgtgacca ctggactccc 20 93 18 DNA
Artificial Sequence Synthetic oligonucleotide probe 93 aggcttggaa
ctcccttc 18 94 24 DNA Artificial Sequence Synthetic oligonucleotide
probe 94 aagattcttg agcgattcca gctg 24 95 47 DNA Artificial
Sequence Synthetic oligonucleotide probe 95 aatccctgct cttcatggtg
acctatgacg acggaagcac aagactg 47 96 21 DNA Artificial Sequence
Synthetic oligonucleotide probe 96 ctcaagaagc acgcgtactg c 21 97 25
DNA Artificial Sequence Synthetic oligonucleotide probe 97
ccaacctcag cttccgcctc tacga 25 98 18 DNA Artificial Sequence
Synthetic oligonucleotide probe 98 catccaggct cgccactg 18 99 20 DNA
Artificial Sequence Synthetic oligonucleotide probe 99 tggcaaggaa
tgggaacagt 20 100 25 DNA Artificial Sequence Synthetic
oligonucleotide probe 100 atgctgccag acctgatcgc agaca 25 101 19 DNA
Artificial Sequence Synthetic oligonucleotide probe 101 gggcagaaat
ccagccact 19 102 18 DNA Artificial Sequence Synthetic
oligonucleotide probe 102 cccttcgcct gcttttga 18 103 27 DNA
Artificial Sequence Synthetic oligonucleotide probe 103 gccatctaat
tgaagcccat cttccca 27 104 19 DNA Artificial Sequence Synthetic
oligonucleotide probe 104 ctggcggtgt cctctcctt 19 105 21 DNA
Artificial Sequence Synthetic oligonucleotide probe 105 cctcggtctc
ctcatctgtg a 21 106 20 DNA Artificial Sequence Synthetic
oligonucleotide probe 106 tggcccagct gacgagccct 20 107 21 DNA
Artificial Sequence Synthetic oligonucleotide probe 107 ctcataggca
ctcggttctg g 21 108 19 DNA Artificial Sequence Synthetic
oligonucleotide probe 108 tggctcccag cttggaaga 19 109 30 DNA
Artificial Sequence Synthetic oligonucleotide probe 109 cagctcttgg
ctgtctccag tatgtaccca 30 110 21 DNA Artificial Sequence Synthetic
oligonucleotide probe 110 gatgcctctg ttcctgcaca t 21 111 48 DNA
Artificial Sequence Synthetic oligonucleotide probe 111 ggattctaat
acgactcact atagggctgc ccgcaacccc ttcaactg 48 112 48 DNA Artificial
Sequence Synthetic oligonucleotide probe 112 ctatgaaatt aaccctcact
aaagggaccg cagctgggtg accgtgta 48 113 43 DNA Artificial Sequence
Synthetic oligonucleotide probe 113 ggattctaat acgactcact
atagggccgc cccgccacct cct 43 114 48 DNA Artificial Sequence
Synthetic oligonucleotide probe 114 ctatgaaatt aaccctcact
aaagggactc gagacaccac ctgaccca 48 115 48 DNA Artificial Sequence
Synthetic oligonucleotide probe 115 ggattctaat acgactcact
atagggccca aggaaggcag gagactct 48 116 48 DNA Artificial Sequence
Synthetic Oligonucleotide probe 116 ctatgaaatt aaccctcact
aaagggacta gggggtggga atgaaaag 48 117 48 DNA Artificial Sequence
Synthetic oligonucleotide probe 117 ggattctaat acgactcact
atagggcccc cctgagctct cccgtgta 48 118 48 DNA Artificial Sequence
Synthetic oligonucleotide probe 118 ctatgaaatt aaccctcact
aaagggaagg ctcgccactg gtcgtaga 48 119 48 DNA Artificial Sequence
Synthetic oligonucleotide probe 119 ggattctaat acgactcact
atagggcaag gagccgggac ccaggaga 48 120 47 DNA Artificial Sequence
Synthetic oligonucleotide probe 120 ctatgaaatt aaccctcact
aaagggaggg ggcccttggt gctgagt 47
* * * * *
References