U.S. patent application number 11/537681 was filed with the patent office on 2008-09-18 for chemokine beta-15.
This patent application is currently assigned to Human Genome Sciences, Inc.. Invention is credited to Brent L. Kreider, Craig A. Rosen, Ying-Fei Wei.
Application Number | 20080226586 11/537681 |
Document ID | / |
Family ID | 26692668 |
Filed Date | 2008-09-18 |
United States Patent
Application |
20080226586 |
Kind Code |
A9 |
Wei; Ying-Fei ; et
al. |
September 18, 2008 |
Chemokine Beta-15
Abstract
The present invention concerns a member of the human chemokine
CC protein family. In particular, isolated nucleic acid molecules
are provided encoding the chemokine .beta.-15 protein. Chemokine
.beta.-15 polypeptides are also provided. The invention further
concerns diagnostic methods for detecting thymus disorders and
therapeutic methods for modulating bone marrow cell proliferation
and differentiation.
Inventors: |
Wei; Ying-Fei; (Berkeley,
CA) ; Kreider; Brent L.; (Bedford, MA) ;
Rosen; Craig A.; (Laytonsville, MD) |
Correspondence
Address: |
HUMAN GENOME SCIENCES INC.;INTELLECTUAL PROPERTY DEPT.
14200 SHADY GROVE ROAD
ROCKVILLE
MD
20850
US
|
Assignee: |
Human Genome Sciences, Inc.
Rockville
MD
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20070048256 A1 |
March 1, 2007 |
|
|
Family ID: |
26692668 |
Appl. No.: |
11/537681 |
Filed: |
October 2, 2006 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10263766 |
Oct 4, 2002 |
7135551 |
|
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11537681 |
Oct 2, 2006 |
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09272162 |
Mar 19, 1999 |
6503735 |
|
|
10263766 |
Oct 4, 2002 |
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08874460 |
Jun 16, 1997 |
5981231 |
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09272162 |
Mar 19, 1999 |
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60019837 |
Jun 17, 1996 |
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Current U.S.
Class: |
424/85.1 ;
435/320.1; 435/325; 435/69.5; 530/351; 530/388.23; 536/23.5 |
Current CPC
Class: |
C07K 14/523
20130101 |
Class at
Publication: |
424/085.1 ;
530/351; 536/023.5; 435/069.5; 435/320.1; 435/325; 530/388.23 |
International
Class: |
A61K 38/19 20070101
A61K038/19; C07K 14/52 20070101 C07K014/52; C07K 16/24 20070101
C07K016/24; C07H 21/04 20060101 C07H021/04; C12P 21/02 20060101
C12P021/02 |
Claims
1. An isolated nucleic acid molecule comprising a polynucleotide
having a nucleotide sequence at least 95% identical to a sequence
selected from the group consisting of: (a) a nucleotide sequence
encoding a polypeptide comprising amino acids from about -20 to
about 129 in SEQ ID NO:2; (b) a nucleotide sequence encoding a
polypeptide comprising amino acids from about -19 to about 129 in
SEQ ID NO:2; (c) a nucleotide sequence encoding a polypeptide
comprising amino acids from about 1 to about 129 in SEQ ID NO:2;
(d) a nucleotide sequence encoding a polypeptide having the amino
acid sequence encoded by the cDNA clone contained in ATCC.TM.
Deposit No. 97519; (e) a nucleotide sequence encoding the mature
chemokine .beta.-15 polypeptide having the amino acid sequence
encoded by the cDNA clone contained in ATCC.TM. Deposit No. 97519;
and (f) a nucleotide sequence complementary to any of the
nucleotide sequences in (a), (b), (c), (d), or (e).
2. The nucleic acid molecule of claim 1 wherein said polynucleotide
has the complete nucleotide sequence in SEQ ID NO:1.
3. The nucleic acid molecule of claim 1 wherein said polynucleotide
has the nucleotide sequence in SEQ ID NO:1 encoding the chemokine
.beta.-15 polypeptide having the complete amino acid sequence in
SEQ ID NO:2.
4. The nucleic acid molecule of claim 1 wherein said polynucleotide
has the nucleotide sequence in SEQ ID NO:1 encoding the mature
chemokine .beta.-15 polypeptide having the amino acid sequence in
SEQ ID NO:2.
5. The nucleic acid molecule of claim 1 wherein said polynucleotide
has the complete nucleotide sequence of the cDNA clone contained in
ATCC.TM. Deposit No. 97519.
6. The nucleic acid molecule of claim 1 wherein said polynucleotide
has the nucleotide sequence encoding the chemokine .beta.-15
polypeptide having the complete amino acid sequence encoded by the
cDNA clone contained in ATCC.TM. Deposit No. 97519.
7. The nucleic acid molecule of claim 1 wherein said polynucleotide
has the nucleotide sequence encoding the mature chemokine .beta.-15
polypeptide having the amino acid sequence encoded by the cDNA
clone contained in ATCC.TM. Deposit No. 97519.
8. An isolated nucleic acid molecule comprising a polynucleotide
which hybridizes under stringent hybridization conditions to a
polynucleotide having a nucleotide sequence identical to a
nucleotide sequence in (a), (b), (c), (d), (e), or (f) of claim 1
wherein said polynucleotide which hybridizes does not hybridize
under stringent hybridization conditions to a polynucleotide having
a nucleotide sequence consisting of only A residues or of only T
residues.
9. An isolated nucleic acid molecule comprising a polynucleotide
which encodes the amino acid sequence of an epitope-bearing portion
of a chemokine .beta.-15 polypeptide having an amino acid sequence
in (a), (b), (c), (d), or (e) of claim 1.
10. A method for making a recombinant vector comprising inserting
an isolated nucleic acid molecule of claim 1 into a vector.
11. A recombinant vector produced by the method of claim 10.
12. A method of making a recombinant host cell comprising
introducing the recombinant vector of claim 11 into a host
cell.
13. A recombinant host cell produced by the method of claim 12.
14. A recombinant method for producing a chemokine .beta.-15
polypeptide, comprising culturing the recombinant host cell of
claim 13 under conditions such that said polypeptide is expressed
and recovering said polypeptide.
15. An isolated chemokine .beta.-15 polypeptide having an amino
acid sequence at least 95 % identical to a sequence selected from
the group consisting of: (a) amino acids from about -20 to about
129 in SEQ ID NO:2; (b) amino acids from about -19 to about 129 in
SEQ ID NO:2; (c) amino acids from about 1 to about 129 in SEQ ID
NO:2; (d) the amino acid sequence of the chemokine .beta.-15
polypeptide having the amino acid sequence encoded by the cDNA
clone contained in ATCC.TM. Deposit No. 97519; (e) the amino acid
sequence of the mature chemokine .beta.-15 polypeptide having the
amino acid sequence encoded by the cDNA clone contained in ATCC.TM.
Deposit No. 97519; and (f) the amino acid sequence of an
epitope-bearing portion of any one of the polypeptides of (a), (b),
(c), (d), or (e).
16. An isolated antibody that binds specifically to a chemokine
.beta.-15 polypeptide of claim 15.
17. A method for treatment of an individual in need of an increased
level of chemokine .beta.-15 activity comprising administering to
said individual a composition comprising an isolated polypeptide of
claim 15.
18. A method useful during the diagnosis of a disorder of the
thymus in an individual comprising: (a) measuring chemokine
.beta.-15 gene expression level in cells or body fluid of said
individual; (b) comparing the chemokine .beta.-15 gene expression
level of said individual with a standard chemokine .beta.-15 gene
expression level, whereby an increase or decrease in the chemokine
.beta.-15 gene expression level of said individual compared to said
standard expression level is indicative of a thymus disorder.
Description
[0001] This application is a divisional of U.S. patent application
Ser. No. 10/263,766, filed Oct. 4, 2002, which is a divisional of
U.S. patent application Ser. No. 09/272,162, filed Mar. 19, 1999,
(now U.S. Pat. No. 6,503,735), which is a continuation of U.S.
patent application Ser. No. 08/874,460, filed Jun. 16, 1997 (now
U.S. Pat. No. 5,981,231), which claims the benefit under 35 U.S.C.
.sctn.119(e) of U.S. Provisional Application No. 60/019,837 filed
on Jun. 17, 1996, each of which is herein incorporated by reference
in its entirety.
BACKGROUND OF THE INVENTION
[0002] 1. Field of the Invention
[0003] The present invention relates to a human CC chemokine
protein (i.e., a cytokine having the first two of its four cysteine
residues adjacent as indicated by "CC") and to polynucleotides
encoding this protein.
[0004] 2. Background Information
[0005] The discovery of IL-8, in 1987, revealed the existence of a
novel class of small cytokines, now called chemokines, that are
widely studied because of their ability to activate leukocytes and
their potential role as mediators of inflammations. A number of
different human chemokines have been identified after IL-8, by
cloning or biochemical purification and amino acid sequencing. All
have four conserved cysteines that form characteristic disulfide
bonds, a short amino-terminal and a longer carboxy-terminal
sequence. Two subfamilies are distinguished by the arrangement of
the first two cysteines, which are either separated by one amino
acid (CXC chemokines) or are adjacent (CC chemokines.). Chemokine
cDNAs typically encode proteins of 92-99 amino acids in length that
are secreted after cleavage of a leader sequence of 20-25 amino
acids. Modeling on the basis of the NMR-derived structure of IL-8
suggests that CXC and CC chemokines are folded in a similar
manner.
[0006] The first human CC chemokine was identified by differential
hybridization cloning and was termed LD78 (Obaru, K. Fukuda, M.,
Maeda, S. and Shimada, K. (1986) J. Biochem. (Tokyo) 99, 885-894.)
Several cDNA isoforms of a closely related human chemokine, Act-2,
were later described (Miller, M. D. and Krangel, M. S. (1992) Crit.
Rev. Immunol. 12, 17-46), and two similar proteins, macrophage
inflammatory protein 1.alpha. (MIP-1.alpha.) and MIP-1.beta., were
purified form the culture medium of lipopolysaccharide
(LPS)-stimulated mouse macrophages (Wolpe, S. D., Davatelis, G.
Sherry, B. et al. (1988) J. Exp. Med. 167, 570-581). On the basis
of more than 70% amino acid identity, the murine and human proteins
are considered as homologs, and the terms human MIP-1.alpha. and
MIP-1.beta. are commonly used instead of LD78 and Act-2. The best
characterized CC chemokine is monocyte chemotactic protein 1
(MCP-1), which was purified and cloned from different sources
(Miller, M. D. and Krangel, M. S. (1992) Crit. Rev. Immunol. 12,
17-46; Yoshimure, T. Robinson, E. A. Tanaka, S. Appella, E. and
Leonardo, E. J. (1989) J. Immunol. 142, 1956-1962; Matsushima, K.,
Larsen, C. G., DuBois, G. C. and Oppenheim, J. J. (1989) J. Exp.
Med. 169, 1485-1490). Other CC chemokines, 1-309 (Miller, M. D.,
Hata, S., De Waal Malafyt, R. and Krangel, M. S. (1989) J. Immunol.
143, 2907-2916), RANTES (Schall, T. J. Jongstra, J., Dyer, B. J. et
al. (1988) J. Immunol. 141, 1018-1025) and HC14 (Chang, H. C., Hsu,
F., Freeman, G. J., Griffin, J. D. and Reinherz, E. L. (1989) Int.
Immunol. 1, 388-397), were purified or cloned as products of
activated T cells. HC14, termed MCP-2, was also isolated from
osteosarcoma cell cultures (Van Damme, J. Proost, P., Lenaerts,
J-P. and Opdenakker, G. (1992) J. Exp. Med. 176, 59-65), along with
a novel CC chemokine, MCP-3, which was subsequently cloned and
expressed (Minty, A. Chalon, P. Guillemot, J. C. et al. (1993) Eur.
Cytokine Netw. 4, 99-110; Opdenakker, G. Froyen, G. Fiten, P.,
Proost, P. and Van Damme, J.(1993) Biochem. Biophys. Res. Commun.
1991, 535-542). These CC chemokines share a sequence identify with
MCP-1 of between 29 and 71% (MCP-2 and MCP-3 have 62-71% identity
with MCP-1).
[0007] MCP-1, the prototype of the CC chemokine sub-family, is
chemotatic for monocytes but not for neutrophils (Yoshimure, T.
Robinson, E. A. Tanaka, S. Appella, E. and Leonardo, E. J. (1989)
J. Immunol. 142, 1956-1962; Matsushima, K., Larsen, C. G., DuBois,
G. C. and Oppenheim, J. J. (1989) J. Exp. Med. 169, 1485-1490) and
was initially considered to be a counterpart of IL-8. Indeed,
monocytes respond to all CC chemokines, as judged from
stimulus-dependent [Ca.sup.2+]i changes (Miller, M. D. and Krangel,
M. S. (1992) Crit. Rev. Immunol. 12, 17-46; Bioschoff, S. C.,
Krieger, M. Brunner, T. et al. (1993) Eur. J. Immunol. 23, 761-767;
McColl, S. R., Hachicha, M., Levasseur, S., Noete, K. and Schall,
T. J. (1993) J. Immunol. 150, 4550-4560). MCP-1, MCP-2 and MCP-3
induce monocyte infiltration on intradermal injection into rats and
rabbits (Van Damme, J. Proost, P., Lenaerts, J-P. and Opdenakker,
G. (1992) J. Exp. Med. 176, 59-65; Zacha, C. O. C., Anderson, A.
O., Thompson, H. L. et al. (1990) J. Exp. Med. 171, 2177-2182), and
MCP-1 also elicits in monocytes a respiratory burst (Miller, M. D.
and Krangel, M. S. (1992) Crit. Rev. Immunol. 12, 17-46) and the
expression of .beta.2 integrins (Jiang, Y., Beller, D. I., Frendl,
G. and Graves, D. T. (1992) J. Immunol. 148, 2423-2428).
[0008] While the view that CXC chemokines act on neutrophils and CC
chemokines act on monocytes apparently remains valid, recent
studies have revealed that CC chemokines have a much wider range of
biological activities since they can also activate some lymphocytes
and, in particular, basophil and eosinophil leukocytes. Thus, there
is a continuing need in the art for isolating novel CC
chemokines.
SUMMARY OF THE INVENTION
[0009] The present invention provides isolated nucleic acid
molecules comprising a polynucleotide encoding a human chemokine
.beta.-15 (CK.beta.-15) polypeptide having the amino acid sequence
in FIGS. 1A-C (SEQ ID NO:2) or the amino acid sequence encoded by
the cDNA clone deposited in a bacterial host as ATCC Deposit Number
97519 on Apr. 25, 1996. The nucleotide sequence determined by
sequencing the deposited CK.beta.-15 cDNA clone, which is shown in
FIGS. 1A-C (SEQ ID NO:1), contains an open reading frame encoding a
polypeptide of about 149 amino acid residues including an
initiation codon at positions 1-3, a leader sequence of about 20
amino acid residues and a deduced molecular weight of about 16 kDa.
The 129 amino acid sequence of the predicted mature CK.beta.-15
protein is shown in FIGS. 1A-C (amino acid residues from about 21
to about 149) and in SEQ ID NO:2 (amino acid residues from about 1
to about 129) and in SEQ ID NO:2 (amino acid residues from about
1-129).
[0010] Thus, one aspect of the invention provides isolated nucleic
acid molecules comprising a polynucleotide having a nucleotide
sequence selected from the group consisting of: (a) a nucleotide
sequence encoding the chemokine .beta.-15 polypeptide having the
complete amino acid sequence in SEQ ID NO:2; (b) a nucleotide
sequence encoding the chemokine .beta.-15 polypeptide having the
complete amino acid sequence in SEQ ID NO:2 but lacking the
N-terminal methionine residue; (c) a nucleotide sequence encoding
the mature chemokine .beta.-15 polypeptide having the amino acid
sequence at positions from about 1 to about 129 in SEQ ID NO:2; (d)
a nucleotide sequence encoding, the chemokine .beta.-15 polypeptide
having the complete amino acid sequence encoded by the cDNA clone
contained in ATCC.TM. Deposit No. 97519; (e) a nucleotide sequence
encoding the mature chemokine .beta.-15 polypeptide having the
amino acid sequence encoded by the cDNA clone contained in ATCC.TM.
Deposit No. 97519; and (f) a nucleotide sequence complementary to
any of the nucleotide sequences in (a), (b), (c), (d), or (e)
above. Preferably, the nucleic acid molecule will encode the mature
polypeptide in SEQ ID NO:2 or encoded by the above-described
deposited cDNA.
[0011] Further embodiments of the invention include isolated
nucleic acid molecules that comprise a polynucleotide having a
nucleotide sequence at least 90% identical, and more preferably at
least 95%, 96%, 97%, 98% or 99% identical, to any of the nucleotide
sequences. in (a), (b), (c), (d), (e), or (f) above, or a
polynucleotide which hybridizes under stringent hybridization
conditions to a polynucleotide having a nucleotide sequence
identical to a nucleotide sequence in (a), (b), (c), (d), (e), or
(f), above. The polynucleotide which hybridizes does not hybridize
under stringent hybridization conditions to a polynucleotide having
a nucleotide sequence consisting of only A residues or of only T
residues. An additional nucleic acid embodiment of the invention
relates to an isolated nucleic acid molecule comprising a
polynucleotide which encodes the amino acid sequence of an
epitope-bearing portion of a chemokine .beta.-15 polypeptide having
an amino acid sequence in (a), (b), (c), (d), or (e), above.
[0012] The present invention also relates to recombinant vectors
which include the isolated nucleic acid molecules of the present
invention and to host cells containing the recombinant vectors, as
well as to methods of making such vectors and host cells and for
using them for production of CK.beta.-15 polypeptides or peptides
by recombinant techniques.
[0013] The invention further provides an isolated chemokine
.beta.-15 polypeptide having amino acid sequence selected from the
group consisting of: (a) a polypeptide comprising amino acids from
about -20 to about 129 in SEQ ID NO:2; (b) a polypeptide comprising
amino acids from about -19 to about 129 in SEQ ID NO:2; (c) a
polypeptide comprising amino acids from about 1 to about 129 in SEQ
ID NO:2; (d) the amino acid sequence of the chemokine .beta.-15
polypeptide having the complete amino acid sequence including the
leader encoded by the cDNA clone contained in ATCC.TM. Deposit No.
97519; and (e) the amino acid sequence of the mature chemokine
.beta.-15 polypeptide having the amino acid sequence encoded by the
cDNA clone contained in ATCC.TM. Deposit No. 97519. The
polypeptides of the present invention also include polypeptides
having an amino acid sequence with at least 90% similarity, more
preferably at least 95% similarity to those described in (a), (b),
(c), (d), or (e) above, as well as polypeptides having an amino
acid sequence at least 80% identical, more preferably at least 90%
identical, and still more preferably 95%, 96%, 97%, 98% or 99%
identical to those above.
[0014] An additional embodiment of this aspect of the invention
relates to a peptide or polypeptide which has the amino acid
sequence of an epitope-bearing portion of a chemokine .beta.-15
polypeptide having an amino acid sequence described in (a), (b),
(c), (d) or (e), above. Peptides or polypeptides having the amino
acid sequence of an epitope-bearing portion of a chemokine
.beta.-15 polypeptide of the invention include portions of such
polypeptides with at least six or seven, preferably at least nine,
and more preferably at least about 30 amino acids to about 50 amino
acids, although epitope-bearing polypeptides of any length up to
and including the entire amino acid sequence of a polypeptide of
the invention described above also are included in the invention.
In another embodiment the invention provides an isolated antibody
that binds specifically to a chemokine .beta.-15 polypeptide having
an amino acid sequence described in (a), (b), (c), (d) or (e)
above.
[0015] The present inventors have discovered that CK.beta.-15 is
expressed only in tissue of the thymus. FIG. 3. For a number of
thymus disorders, significantly higher or lower levels of
CK.beta.-15 gene expression can be detected in thymus tissue or
bodily fluids (e.g., serum, plasma, urine, synovial fluid or spinal
fluid) taken from an individual having such a disorder, relative to
a "standard" CK.beta.-15 gene expression level, i.e., the
CK.beta.-15 expression level in thymus tissue or bodily fluids from
an individual not having the thymus disorder. Thus, the invention
provides a diagnostic method useful during diagnosis of a thymus
disorder, which involves (a) assaying chemokine .beta.-15 gene
expression level in cells or body fluid of that individual; (b)
comparing that chemokine .beta.-15 gene expression level with a
standard chemokine .beta.-15 gene expression level, whereby an
increase or decrease in the assayed chemokine .beta.-15 gene
expression level compared to the standard expression level is
indicative of a thymus disorder. An additional aspect of the
invention is related to a method for treatment of an individual in
need of an increased level of chemokine .beta.-15 activity in the
body comprising administering to such an individual a composition
comprising an isolated chemokine .beta.-15 polypeptide of the
invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0016] FIGS. 1A-C show the nucleotide (SEQ ID NO:1) and deduced
amino acid (SEQ ID NO:2) sequences of the complete chemokine
.beta.-15 protein determined by sequencing of the DNA clone
contained in ATCC.TM. Deposit No. 97519. The protein has a leader
sequence of about 20 amino acid residues (underlined) and a deduced
molecular weight of about 16 kDa. The amino acid sequence of the
predicted mature CK.beta.-15 protein is shown in FIGS. 1A-C (last
129 amino acids) and in SEQ ID NO:2 (from amino acid residue 1 to
residue 129).
[0017] FIG. 2 shows the regions of similarity between the amino
acid sequences of the CK.beta.-15 protein and the mouse macrophage
inflammatory protein-related protein 2 (MMRP-2) [SEQ ID NO:3].
[0018] FIG. 3 shows a Northern blot assay for expression of mRNA
from the CK.beta.-15 gene in various human tissues. The panel
labeled "HTSEX82" shows hybridization to the CK.beta.-15 cDNA probe
which that labeled "ACTIN" shows hybridization of a cDNA encoding
actin which serves as a positive control indicating the presence of
intact RNA in each sample.
DETAILED DESCRIPTION OF THE INVENTION
[0019] The present invention provides isolated nucleic acid
molecules comprising a polynucleotide encoding the chemokine
.beta.-15 (CK.beta.-15) protein having the amino acid sequence
shown in FIGS. 1A-C (SEQ ID NO:2) which was determined by
sequencing a cloned cDNA. CK.beta.-15 is a novel member of the
.beta.-chemokine subfamily (CC) whose genes are on human chromosome
17 and on mouse chromosome 11 (Wilson, S. D., et al., J. Exp. Med.
171:1301(1990) and Modi, W. S., et al., Hum. Genet. 84:185 (1990)).
The CK.beta.-15 protein of the present invention shares sequence
homology with the mouse macrophage inflammatory protein-related
protein 2 (MMRP-2) (FIG. 2) (SEQ ID NO:3). The nucleotide sequence
shown in FIGS. 1A-C (SEQ ID NO:1) was obtained by sequencing the
HTSEX82 cDNA clone encoding a CK.beta.-15 polypeptide, which was
deposited on Apr. 25, 1996 at the American Type Culture Collection,
Patent Depository, 10801 University Boulevard, Manassas, Va.
20110-2209. The deposited clone is contained in the pBluescript.TM.
SK(-) plasmid (Stratagene, LaJolla, Calif.).
Nucleic Acid Molecules
[0020] Unless otherwise indicated, all nucleotide sequences
determined by sequencing a DNA molecule herein were determined
using an automated DNA sequencer (such as the Model 373 from
Applied Biosystems, Inc.), and all amino acid sequences of
polypeptides encoded by DNA molecules determined herein were
predicted by translation of a DNA sequence determined as above.
Therefore, as is known in the art for any DNA sequence determined
by this automated approach, any nucleotide sequence determined
herein may contain a some errors. Nucleotide sequences determined
by automation are typically at least about 90% identical, more
typically at least about 95% to at least about 99.9% identical to
the actual nucleotide sequence of the sequenced DNA molecule. The
actual sequence can be more precisely determined by other
approaches including manual DNA sequencing methods well known in
the art. As is also known in the art, a single insertion or
deletion in a determined nucleotide sequence compared to the actual
sequence will cause a frame shift in translation of the nucleotide
sequence such that the predicted amino acid sequence encoded by a
determined nucleotide sequence will be completely different from
the amino acid sequence actually encoded by the sequenced DNA
molecule, beginning at the point of such an insertion or
deletion.
[0021] Unless otherwise indicated, each "nucleotide sequence" set
forth herein is presented as a sequence of deoxyribonucleotides
(abbreviated A, G, C and T). However, by "nucleotide sequence" of a
nucleic acid molecule or polynucleotide is intended, for a DNA
molecule or polynucleotide, a sequence of deoxyribonucleotides, and
for an RNA molecule or polynucleotide, the corresponding sequence
of ribonucleotides (A, G, C and U) where each thymidine
deoxynucleotide (T) in the specified deoxynucleotide sequence in is
replaced by the ribonucleotide uridine (U). For instance, reference
to an RNA molecule having the sequence of SEQ ID NO:1 set forth
using deoxyribonucleotide abbreviations is intended to indicate an
RNA molecule having a sequence in which each deoxynucleotide A, G
or C of SEQ ID NO:1 has been replaced by the corresponding
ribonucleotide A, G or C, and each deoxynucleotide T has been
replaced by a ribonucleotide U.
[0022] Using the information provided herein, such as the
nucleotide sequence in FIGS. 1A-C, a nucleic acid molecule of the
present invention encoding a CK.beta.-15 polypeptide may be
obtained using standard cloning and screening procedures, such as
those for cloning cDNAs using mRNA as starting material.
Illustrative of the invention, the nucleic acid molecule described
in FIGS. 1A-C (SEQ ID NO:1) was discovered in a cDNA library
derived from human thymus tissue. The determined nucleotide
sequence of the CK.beta.-15 cDNA of FIGS. 1A-C contains an open
reading frame encoding a protein of about 149 amino acid residues
with an initiation codon at positions 1-3 of the nucleotide
sequence shown in FIGS. 1A-C (SEQ ID NO. 1), and a predicted leader
sequence of about 20 amino acid residues, and a deduced molecular
weight of about 16 kDa. The amino acid sequence of the predicted
mature CK.beta.-15 protein is shown in FIGS. 1A-C from amino acid
residue 21 to residue 149 and in SEQ ID NO:2 from amino acid
residue 1 to 129. The CK.beta.-15 protein shown in FIGS. 1A-C (SEQ
ID NO:2) is about 34% identical and about 53% similar to MMRP2
(FIG. 2).
[0023] The present invention also provides the mature form(s) of
the CK.beta.-15 polypeptide of the present invention. According to
the signal hypothesis, proteins secreted by mammalian cells have a
signal or secretory leader sequence which is cleaved from the
mature protein once export of the growing protein chain across the
rough endoplasmic reticulum has been initiated. Most mammalian
cells and even insect cells cleave secreted proteins with the same
specificity. However, in some cases, cleavage of a secreted protein
is not entirely uniform, which results in two or more mature
species on the protein. Further, it has long been known that the
cleavage specificity of a secreted protein is ultimately determined
by the primary structure of the complete protein, that is, it is
inherent in the amino acid sequence of the polypeptide. Therefore,
the present invention provides a nucleotide sequence encoding the
mature CK.beta.-15 polypeptides having the amino acid sequence
encoded by the cDNA clone contained in the host identified as
ATCC.TM. Deposit No.97519 and as shown in SEQ ID NO:2. By the
mature CK.beta.-15 protein having the amino acid sequence encoded
by the cDNA clone contained in the host identified as ATCC.TM.
Deposit No. 97519 is meant the mature form(s) of the CK.beta.-15
polypeptide produced by expression in a mammalian cell (e.g., COS
cells, as described below) of the complete open reading frame
encoded by the human DNA sequence of the clone contained in the
vector in the deposited host. As indicated below, the mature
CK.beta.-15 polypeptide having the amino acid sequence encoded by
the cDNA clone contained in ATCC.TM. Deposit No. 97519 may or may
not differ from the predicted "mature" CK.beta.-15 polypeptide
shown in SEQ ID NO:2 (amino acids from about 1 to about 129)
depending on the accuracy of the predicted cleavage site based on
computer analysis.
[0024] Methods for predicting whether a protein has a secretory
leader as well as the cleavage point for that leader sequence are
available. For instance, the methods of McGeoch, Virus Res. 3,
271-286 (1985) and von Heinje, Nucleic Acids Res. 14, 4683-4690
(1986) can be used. The accuracy of predicting the cleavage points
of known mammalian secretory proteins for each of these methods is
in the range of 75-80%. von Heinje, supra. However, the two methods
do not always produce the same predicted cleavage point(s) for a
given protein.
[0025] In the present case, the predicted amino acid sequence of
the complete CK.beta.-15 polypeptides of the present invention were
analyzed by a computer program (PSORT) (Nakai, K. and Kanehisa, M.
Genomics 14, 897-911 (1992)), which is an expert system for
predicting the cellular location of a protein based on the amino
acid sequence. As part of this computational prediction of
localization, the methods of McGeoch and von Heinje are
incorporated. The analysis by the PSORT program predicted the
cleavage site between amino acids -1 and 1 in SEQ ID NO:2.
Thereafter, the complete amino acid sequences were further analyzed
by visual inspection, applying a simple form of the (-1,-3) rule of
von Heinje. von Heinje, supra. Thus, the leader sequence for the
CK.beta.-15 polypeptide is predicted to consist of amino acid
residues from about -20 to about -1 in SEQ ID NO:2, while the
mature CK.beta.-15 polypeptide is predicted to consist of residues
from about 1 to about 129.
[0026] As one of ordinary skill would appreciate, due to the
possibilities of sequencing errors discussed above, as well as the
variability of cleavage sites for leaders in different known
proteins, the actual CK.beta.-15 polypeptide encoded by the
deposited cDNA comprises about 149 amino acids, but may be anywhere
in the range of 142-154 amino acids; and the actual leader sequence
of this protein is about 20 amino acids, but may be anywhere in the
range of about 15 to about 25 amino acids.
[0027] As indicated, nucleic acid molecules of the present
invention may be in the form of RNA, such as mRNA, or in the form
of DNA, including, for instance, cDNA and genomic DNA obtained by
cloning or produced synthetically. The DNA may be double-stranded
or single-stranded. Single-stranded DNA or RNA may be the coding
strand, also known as the sense strand, or it may be the non-coding
strand, also referred to as the anti-sense strand.
[0028] By "isolated" nucleic acid molecule(s) is intended a nucleic
acid molecule, DNA or RNA, which has been removed from its native
environment For example, recombinant DNA molecules contained in a
vector are considered isolated for the purposes of the present
invention. Further examples of isolated DNA molecules include
recombinant DNA molecules maintained in heterologous host cells or
purified (partially or substantially) DNA molecules in solution.
Isolated RNA molecules include in vivo or in vitro RNA transcripts
of the DNA molecules of the present invention. Isolated nucleic
acid molecules according to the present invention further include
such molecules produced synthetically.
[0029] Isolated nucleic acid molecules of the present invention
include DNA molecules comprising an open reading frame (ORF) with
an initiation codon at positions 1-3 of the nucleotide sequence
shown in FIGS. 1A-C (SEQ ID NO:1); DNA molecules comprising the
coding sequence for the mature CK.beta.-15 protein shown in FIGS.
1A-C (amino acid residues from about 21 to about 149) and SEQ ID
NO:2 (amino acid residues from about 1 to about 129); and DNA
molecules which comprise a sequence substantially different from
those described above but which, due to the degeneracy of the
genetic code, still encode the CK.beta.-15 protein. Of course, the
genetic code is well known in the art. Thus, it would be routine
for one skilled in the art to generate the degenerate variants
described above.
[0030] In another aspect, the invention provides isolated nucleic
acid molecules encoding the CK.beta.-15 polypeptide having an amino
acid sequence encoded by the cDNA clone contained in the plasmid
deposited as ATCC.TM. Deposit No. 97519 on Apr. 25, 1996.
Preferably, this nucleic acid molecule will encode the mature
polypeptide encoded by the above-described deposited cDNA clone. In
a further embodiment, nucleic acid molecules are provided encoding
the full-length CK.beta.-15 polypeptide lacking the N-terminal
methionine. The invention further provides an isolated nucleic acid
molecule having the nucleotide sequence shown in FIGS. 1A-C (SEQ ID
NO:1) or the nucleotide sequence of the CK.beta.-15 cDNA contained
in the above-described deposited clone, or nucleic acid molecule
having a sequence complementary to one of the above sequences. Such
isolated molecules, particularly DNA molecules, are useful as
probes for gene mapping by in situ hybridization with chromosomes
and for detecting expression of the CK.beta.-15 gene in human
tissue, for instance, by Northern blot analysis. As described in
detail below, detecting altered CK.beta.-15 gene expression in
certain tissues or bodily fluids is indicative of thymus
disorders.
[0031] The present invention is further directed to fragments of
the isolated nucleic acid molecules described herein. By a fragment
of an isolated nucleic acid molecule having the nucleotide sequence
of the deposited cDNA or the nucleotide sequence shown in SEQ ID
NO:1 is intended fragments at least about 15 nt, and more
preferably at least about 20 nt, still more preferably at least
about 30 nt, and even more preferably, at least about 40 nt in
length which are useful as diagnostic probes and primers as
discussed herein. Of course, larger fragments 50-500 nt in length
are also useful according to the present invention as are fragments
corresponding to most, if not all, of the nucleotide sequence of
the deposited cDNA or as shown in SEQ ID NO:1. By a fragment at
least 20 nt in length, for example, is intended fragments which
include 20 or more contiguous bases from the nucleotide sequence of
the deposited cDNA or the nucleotide sequence as shown in SEQ ID
NO:1. Preferred nucleic acid fragments of the present invention
include nucleic acid molecules encoding epitope-bearing portions of
the CK.beta.-15 protein.
[0032] In another aspect, the invention provides an isolated
nucleic acid molecule comprising a polynucleotide which hybridizes
under stringent hybridization conditions to a portion of the
polynucleotide in a nucleic acid molecule of the invention
described above, for instance, the cDNA clone contained in ATCC.TM.
Deposit 97519. By "stringent hybridization conditions" is intended
overnight incubation at 42.degree. C. in a solution comprising: 50%
formamide, 5.times.SSC (750 mM NaCl, 75 mM trisodium citrate), 50
mM sodium phosphate (pH7.6), 5.times. Denhardt's solution, 10%
dextran sulfate, and 20 .mu.g/ml denatured, sheared salmon sperm
DNA, followed by washing the filters in 0.1.times.SSC at about
65.degree. C. By a polynucleotide which hybridizes to a "portion"
of a polynucleotide is intended a polynucleotide (either DNA or
RNA) hybridizing to at least about 15 nucleotides (nt), and more
preferably at least about 20 nt, still more preferably at least
about 30 nt, and even more preferably about 30-70 nt of the
reference polynucleotide. These are useful as diagnostic probes and
primers as discussed above and in more detail below.
[0033] Of course, polynucleotides hybridizing to a larger portion
of the reference polynucleotide (e.g., the deposited cDNA clone),
for instance, a portion 50-750 nt in length, or even to the entire
length of the reference polynucleotide, also useful as probes
according to the present invention, as are polynucleotides
corresponding to most, if not all, of the nucleotide sequence of
the deposited cDNA or the nucleotide sequence as shown in FIGS.
1A-C (SEQ ID NO:1). By a portion of a polynucleotide of "at least
20 nt in length," for example, is intended 20 or more contiguous
nucleotides from the nucleotide sequence of the reference
polynucleotide, (e.g., the deposited cDNA or the nucleotide
sequence as shown in FIGS. 1A-C (SEQ ID NO:1)). As indicated, such
portions are useful diagnostically either as a probe according to
conventional DNA hybridization techniques or as primers for
amplification of a target sequence by the polymerase chain reaction
(PCR), as described, for instance, in Molecular Cloning, A
Laboratory Manual, 2nd. edition, edited by Sambrook, J., Fritsch,
E. F. and Maniatis, T., (1989), Cold Spring Harbor Laboratory
Press, the entire disclosure of which is hereby incorporated herein
by reference.
[0034] Since a CK.beta.-15 cDNA clone has been deposited and its
determined nucleotide sequence is provided in FIGS. 1A-C (SEQ ID
NO:1), generating polynucleotides which hybridize to a portion of
the CK.beta.-15 cDNA molecule would be routine to the skilled
artisan. For example, restriction endonuclease cleavage or shearing
by sonication of the CK.beta.-15 cDNA clone could easily be used to
generate DNA portions of various sizes which are polynucleotides
that hybridize to a portion of the CK.beta.-15 cDNA molecule.
Alternatively, the hybridizing polynucleotides of the present
invention could be generated synthetically according to known
techniques. Of course, a polynucleotide which hybridizes only to a
poly A sequence (such as the 3, terminal poly(A) tract of the
CK.beta.-15 cDNA shown in FIGS. 1A-C (SEQ ID NO:1)), or to a
complementary stretch of T (or U) resides, would not be included in
a polynucleotide of the invention used to hybridize to a portion of
a nucleic acid of the invention, since such a polynucleotide would
hybridize to any nucleic acid molecule contain a poly (A) stretch
or the complement thereof (e.g., practically any double-stranded
cDNA clone).
[0035] As indicated, nucleic acid molecules of the present
invention which encode the CK.beta.-15 protein polypeptide may
include, but are not limited to those encoding the amino acid
sequence of the mature polypeptide, by itself; the coding sequence
for the mature polypeptide and additional sequences, such as those
encoding the about 20 amino acid leader or secretory sequence, such
as a pre-, or pro- or prepro- protein sequence; the coding sequence
of the mature polypeptide, with or without the aforementioned
additional coding sequences, together with additional, non-coding
sequences, including for example, but not limited to introns and
non-coding 5' and 3' sequences, such as the transcribed,
non-translated sequences that play a role in transcription, mRNA
processing--including splicing and polyadenylation signals, for
example--ribosome binding and stability of mRNA; an additional
coding sequence which codes for additional amino acids, such as
those which provide additional functionalities. Thus, the sequence
encoding the polypeptide may be fused to a marker sequence, such as
a sequence encoding a peptide which facilitates purification of the
fused polypeptide. In certain preferred embodiments of this aspect
of the invention, the marker amino acid sequence is a
hexa-histidine peptide, such as the tag provided in a pQE vector
(Qiagen, Inc.), among others, many of which are commercially
available. As described in Gentz et al. (1989) Proc. Natl. Acad.
Sci., USA 86:821-824, for instance, hexa-histidine provides for
convenient purification of the fusion protein. The "HA" tag is
another peptide useful for purification which corresponds to an
epitope derived from the influenza hemagglutinin protein, which has
been described by Wilson et al., Cell 37: 767 (1984). As discussed
below, other such fusion proteins include the CK.beta.-15
polypeptide fused to Fc at the N- or C-terminus.
[0036] The present invention further relates to variants of the
nucleic acid molecules of the present invention, which encode
portions, analogs or derivatives of the CK.beta.-15 protein.
Variants may occur naturally, such as a natural allelic variant. By
an "allelic variant" is intended one of several alternate forms of
a gene occupying a given locus on a chromosome of an organism.
Genes II, Lewin, ed. Non-naturally occurring variants may be
produced using art-known mutagenesis techniques.
[0037] Such variants include those produced by nucleotide
substitutions, deletions or additions. The substitutions, deletions
or additions may involve one or more nucleotides. The variants may
be altered in coding or non-coding regions or both. Alterations in
the coding regions may produce conservative or non-conservative
amino acid substitutions, deletions or additions. Especially
preferred among these are silent substitutions, additions and
deletions, which do not alter the properties and activities of the
CK.beta.-15 protein or portions thereof. Also especially preferred
in this regard are conservative substitutions. Most highly
preferred are nucleic acid molecules encoding the mature
CK.beta.-15 protein having the amino acid sequence shown in FIGS.
1A-C (SEQ ID NO:2) or the mature CK.beta.-15 amino acid sequence
encoded by the deposited cDNA clone.
[0038] Further embodiments of the invention include isolated
nucleic acid molecules comprising a polynucleotide having a
nucleotide sequence at least 90% identical, and more preferably at
least 95%, 96%, 97%, 98% or 99% identical to (a) a nucleotide
sequence encoding the chemokine .beta.-15 polypeptide having the
complete amino acid sequence in SEQ ID NO:2; (b) a nucleotide
sequence encoding the chemokine .beta.-15 polypeptide having the
complete amino acid sequence in SEQ ID NO:2 but lacking the
N-terminal methionine residue; (c) a nucleotide sequence encoding
the mature chemokine .beta.-15 polypeptide having the amino acid
sequence at positions from about 1 to about 129 in SEQ ID NO:2; (d)
a nucleotide sequence encoding the chemokine .beta.-15 polypeptide
having the complete amino acid sequence encoded by the cDNA clone
contained in ATCC.TM. Deposit No. 97519; (e) a nucleotide sequence
encoding the mature chemokine .beta.-15 polypeptide having the
amino acid sequence encoded by the cDNA clone contained in ATCC.TM.
Deposit No. 97519; and (f) a nucleotide sequence complementary to
any of the nucleotide sequences in (a), (b), (c), (d), or (e)
above.
[0039] By a polynucleotide having a nucleotide sequence at least,
for example, 95% "identical" to a reference nucleotide sequence
encoding a chemokine .beta.-15 polypeptide is intended that the
nucleotide sequence of the polynucleotide is identical to the
reference sequence except that the polynucleotide sequence may
include up to five point mutations per each 100 nucleotides of the
reference nucleotide sequence encoding the chemokine .beta.-15
polypeptide. In other words, to obtain a polynucleotide having a
nucleotide sequence at least 95% identical to a reference
nucleotide sequence, up to 5% of the nucleotides in the reference
sequence may be deleted or substituted with another nucleotide, or
a number of nucleotides up to 5% of the total nucleotides in the
reference sequence may be inserted into the reference sequence.
These mutations of the reference sequence may occur at the 5' or 3'
terminal positions of the reference nucleotide sequence or anywhere
between those terminal positions, interspersed either individually
among nucleotides in the reference sequence or in one or more
contiguous groups within the reference sequence.
[0040] As a practical matter, whether any particular nucleic acid
molecule is at least 90%, 95%, 96%, 97%, 98% or 99% identical to,
for instance, the nucleotide sequence shown in FIGS. 1A-C or to the
nucleotides sequence of the deposited cDNA clone can be determined
conventionally using known computer programs such as the Bestfit
program (Wisconsin Sequence Analysis Package, Version 8 for Unix,
Genetics Computer Group, University Research Park, 575 Science
Drive, Madison, Wis. 53711). Bestfit uses the local homology
algorithm of Smith and Waterman (Advances in Applied Mathematics 2:
482-489, 1981) to find the best segment of homology between two
sequences. When using Bestfit or any other sequence alignment
program to determine whether a particular sequence is, for
instance, 95% identical to a reference sequence according to the
present invention, the parameters are set, of course, such that the
percentage of identity is calculated over the full length of the
reference nucleotide sequence and that gaps in homology of up to 5%
of the total number of nucleotides in the reference sequence are
allowed.
[0041] The present application is directed to nucleic acid
molecules at least 90%, 95%, 96%, 97%, 98% or 99% identical to the
nucleic acid sequence shown in FIGS. 1A-C (SEQ ID NO:1) or to the
nucleic acid sequence of the deposited cDNA, irrespective of
whether they encode a polypeptide having CK.beta.-15 activity. This
is because, even where a particular nucleic acid molecule does not
encode a polypeptide having CK.beta.-15 activity, one of skill in
the art would still know how to use the nucleic acid molecule, for
instance, as a hybridization probe or a polymerase chain reaction
(PCR) primer. Uses of the nucleic acid molecules of the present
invention that do not encode a polypeptide having CK.beta.-15
activity include, inter alia, (1) isolating the CK.beta.-15 gene or
allelic variants thereof in a cDNA library; (2) in situ
hybridization (e.g., "FISH") to metaphase chromosomal spreads to
provide precise chromosomal location of the CK.beta.-15 gene as
described in Verma et al., Human Chromosomes: a Manual of Basic
Techniques, Pergamon Press, New York (1988); and Northern Blot
analysis for detecting CK.beta.-15 mRNA expression in specific
tissues (e.g., thymus tissue).
[0042] Preferred, however, are nucleic acid molecules having
sequences at least 90%, 95%, 96%, 97%, 98% or 99% identical to the
nucleic acid sequence shown in FIGS. 1A-C (SEQ ID NO:1) or to the
nucleic acid sequence of the deposited cDNA which do, in fact,
encode a polypeptide having CK.beta.-15 protein activity. By "a
polypeptide having CK.beta.-15 activity" is intended polypeptides
exhibiting activity similar, but not necessarily identical, to an
activity of the CK.beta.-15 protein of the invention (either the
full-length protein or, preferably, the mature protein) as measured
in a particular biological assay. Like other CC cytokines,
CK.beta.-15 exhibits activity on monocytes, lymphocytes and
neutrophils. However, unlike other known CC cytokines, CK.beta.-15
has been shown to be expressed only in the thymus. Therefore,
CK.beta.-15 is particularly active in modulating activities of
cells in the thymus, particularly early thymocytes. For example,
stimulation of early thymocyte proliferation by CK.beta.-15 is
assayed in a standard proliferation assay (see, for instance, Spits
et al. (1987) J. Immunol. 139:1142; Dalloul et al. (1989) Eur. J.
Immunol. 19:1985; Murphy et al., (1992) Ped. Res. 32:269; Ruggiero
et al, (1996) J. Immunol. 156:3737). Briefly, the assay involves
purification of thymocytes from human thymus, plating them in media
with or without CK.beta.-15, and determining the change with
elapsed time in the rate of proliferation or the number of cells
compared to control cultures, by conventional means. Representative
cell lines could also be employed in such assays.
[0043] CK.beta.-15 also mediates the differentiation of intrathymic
T cell precursors into mature T-lymphocytes which are either
.alpha./.beta.+ or .gamma./.delta.+ T cell receptor lymphocytes (as
defined in Barcena et al. (1990) J. Exp. Med. 172:439). This effect
is mediated by modulating (either inducing or inhibiting) the
apoptosis of specific subsets of thymocytes within the thymus or by
directly inducing the differentiation of a specific subset. In
addition CK.beta.-15 also directs the homing of the immature
lymphocyte precursor to the thymus for proper maturation. This
activity is demonstrated by in vitro chemotaxis assays using
primary progenitors or representative cell lines. CK.beta.-15 also
mediates proper T-lymphocyte maturation via the thymic epithelial
cells, for example, by providing a co-stimulatory signal for
proliferation or differentiation, as shown by various in vitro
assays for human thymocyte proliferation or differentiation
(Ruggiero et al. (1996) J. Immunol. 156:3737; Barcena et al. (1990)
J. Exp. Med. 172:439; Singer et al. (1990) J. Immunol.
144:2931).
[0044] The CK.beta.-15 protein of the present invention also
modulates colony formation of bone marrow progenitor cells, as does
the macrophage inflammatory protein related protein-2 (MMRP-2). An
in vitro colony forming assay for measuring the extent of
inhibition of myeloid progenitor cells is described in Youn et al.,
The Journal of Immunology 155:2661-2667 (1995). Briefly, the assay
involves collecting human or mouse bone marrow cells and plating
the same on agar, adding one or more growth factors and either (1)
transfected host cell-supernatant containing CK.beta.-15 protein
(or a candidate polypeptide) or (2) nontransfected host
cell-supernatant control, and measuring the effect on colony
formation by murine and human CFU-granulocyte-macrophages (CFU-GM),
by human burst-forming unit-erythroid (BFU-E), or by human CFU
granulocyte-erythroid-macrophage-megakaryocyte (CFU-GEMM).
[0045] CK.beta.-15 protein modulates early thymocyte proliferation
and differentiation in a dose-dependent manner in the
above-described assays. Thus, "a polypeptide having CK.beta.-15
protein activity" includes polypeptides that also exhibit any of
the same thymocyte modulating activities in the above-described
assays in a dose-dependent manner. Although the degree of
dose-dependent activity need not be identical to that of the
CK.beta.-15 protein, preferably, "a polypeptide having CK.beta.-15
protein activity" will exhibit substantially similar
dose-dependence in a given activity as compared to the CK.beta.-15
protein (i.e., the candidate polypeptide will exhibit greater
activity or not more than about tenfold less and, preferably, not
more than about twofold less activity relative to the reference
CK.beta.-15 protein).
[0046] Of course, due to the degeneracy of the genetic code, one of
ordinary skill in the art will immediately recognize that a large
number of the nucleic acid molecules having a sequence at least
90%, 95%, 96%, 97%, 98%, or 99% identical to the nucleic acid
sequence of the deposited cDNA or the nucleic acid sequence shown
in FIGS. 1A-C (SEQ ID NO:1) will encode a polypeptide "having
CK.beta.-15 protein activity." In fact, since degenerate variants
of these nucleotide sequences all encode the same polypeptide, this
will be clear to the skilled artisan even without performing the
above described comparison assay. It will be further recognized in
the art that, for such nucleic acid molecules that are not
degenerate variants, a reasonable number will also encode a
polypeptide having CK.beta.-15 protein activity. This is because
the skilled artisan is fully aware of amino acid substitutions that
are either less likely or not likely to significantly effect
protein function (e.g., replacing one aliphatic amino acid with a
second aliphatic amino acid).
[0047] For example, guidance concerning how to make phenotypically
silent amino acid substitutions is provided in Bowie, J. U., et
al., "Deciphering the Message in Protein Sequences: Tolerance to
Amino Acid Substitutions," Science 247:1306-1310 (1990), wherein
the authors indicate that there are two main approaches for
studying the tolerance of an amino acid sequence to change. The
first method relies on the process of evolution, in which mutations
are either accepted or rejected by natural selection. The second
approach uses genetic engineering to introduce amino acid changes
at specific positions of a cloned gene and selections or screens to
identify sequences that maintain functionality. As the authors
state, these studies have revealed that proteins are surprisingly
tolerant of amino acid substitutions. The authors further indicate
which amino acid changes are likely to be permissive at a certain
position of the protein. For example, most buried amino acid
residues require nonpolar side chains, whereas few features of
surface side chains are generally conserved. Other such
phenotypically silent substitutions are described in Bowie, J. U.,
et al., supra, and the references cited therein.
Vectors and Host Cells
[0048] The present invention also relates to vectors which include
the isolated DNA molecules of the present invention, host cells
which are genetically engineered with the recombinant vectors, and
the production of CK.beta.-15 polypeptides or portions thereof by
recombinant techniques.
[0049] Recombinant constructs may be introduced into host cells
using well known techniques such as infection, transduction,
transfection, transvection, electroporation and transformation. The
vector may be, for example, a phage, plasmid, viral or retroviral
vector. Retroviral vectors may be replication competent or
replication defective. In the latter case, viral propagation
generally will occur only in complementing host cells.
[0050] The polynucleotides may be joined to a vector containing a
selectable marker for propagation in a host. Generally, a plasmid
vector is introduced in a precipitate, such as a calcium phosphate
precipitate, or in a complex with a charged lipid. If the vector is
a virus, it may be packaged in vitro using an appropriate packaging
cell line and then transduced into host cells.
[0051] Preferred are vectors comprising cis-acting control regions
to the polynucleotide of interest. Appropriate trans-acting factors
may be supplied by the host, supplied by a complementing vector or
supplied by the vector itself upon introduction into the host.
[0052] In certain preferred embodiments in this regard, the vectors
provide for specific expression, which may be inducible and/or cell
type-specific. Particularly preferred among such vectors are those
inducible by environmental factors that are easy to manipulate,
such as temperature and nutrient additives.
[0053] Expression vectors useful in the present invention include
chromosomal-, episomal- and virus-derived vectors, e.g., vectors
derived from bacterial plasmids, bacteriophage, yeast episomes,
yeast chromosomal elements, viruses such as baculoviruses, papova
viruses, vaccinia viruses, adenoviruses, fowl pox viruses,
pseudorabies viruses and retroviruses, and vectors derived from
combinations thereof, such as cosmids and phagemids.
[0054] The DNA insert should be operatively linked to an
appropriate promoter, such as the phage lambda PL promoter, the E.
coli lac, trp and tac promoters, the SV40 early and late promoters
and promoters of retroviral LTRs, to name a few. Other suitable
promoters will be known to the skilled artisan. The expression
constructs will further contain sites for transcription initiation,
termination and, in the transcribed region, a ribosome binding site
for translation. The coding portion of the mature transcripts
expressed by the constructs will include a translation initiating
AUG at the beginning and a termination codon appropriately
positioned at the end of the polypeptide to be translated.
[0055] As indicated, the expression vectors will preferably include
at least one selectable marker. Such markers include dihydrofolate
reductase or neomycin resistance for eukaryotic cell culture and
tetracycline or ampicillin resistance genes for culturing in E.
coli and other bacteria. Representative examples of appropriate
hosts include bacterial cells, such as E. coli, Streptomyces and
Salmonella typhimurium cells; fungal cells, such as yeast cells;
insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal
cells such as CHO, COS and Bowes melanoma cells; and plant cells.
Appropriate culture media and conditions for the above-described
host cells are known in the art.
[0056] Among vectors preferred for use in bacteria include pA2,
pQE70, pQE60 and pQE-9, available from Qiagen; pBS vectors,
Phagescript vectors, Bluescript vectors, pNH8A, pNH16a, pNH18A,
pNH46A, available from Stratagene; and ptrc99a, pKK223-3, pKK233-3,
pDR540, pRIT5 available from Pharmacia. Among preferred eukaryotic
vectors are pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from
Stratagene; and pSVK3, pBPV, pMSG and pSVL available from
Pharmacia. Other suitable vectors will be readily apparent to the
skilled artisan.
[0057] Among known bacterial promoters suitable for use in the
present invention include the E. coli lacI and lacZ promoters, the
T3 and T7 promoters, the gpt promoter, the lambda PR and PL
promoters and the trp promoter. Suitable eukaryotic promoters
include the CMV immediate early promoter, the HSV thymidine kinase
promoter, the early and late SV40 promoters, the promoters of
retroviral LTRs, such as those of the Rous sarcoma virus (RSV), and
metallothionein promoters, such as the mouse metallothionein-I
promoter.
[0058] Introduction of the construct into the host cell can be
effected by calcium phosphate transfection, DEAE-dextran mediated
transfection, cationic lipid-mediated transfection,
electroporation, transduction, infection or other methods. Such
methods are described in many standard laboratory manuals, such as
Davis et al., BASIC METHODS IN MOLECULAR BIOLOGY, (1986).
[0059] Transcription of the DNA encoding the polypeptides of the
present invention 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 to increase transcriptional activity of a promoter in a given
host cell-type. Examples of enhancers include the SV40 enhancer,
which is located on the late side of the replication origin at bp
100 to 270, the cytomegalovirus early promoter enhancer, the
polyoma enhancer on the late side of the replication origin, and
adenovirus enhancers.
[0060] For secretion of the translated protein into the lumen of
the endoplasmic reticulum, into the periplasmic space or into the
extracellular environment, appropriate secretion signals may be
incorporated into the expressed polypeptide. The signals may be
endogenous to the polypeptide or they may be heterologous
signals.
[0061] The polypeptide may be expressed in a modified form, such as
a fusion protein, and may include not only secretion signals, but
also additional heterologous functional regions. Thus, for
instance, a region of additional amino acids, particularly charged
amino acids, may be added to the N-terminus of the polypeptide to
improve stability and persistence in the host cell, during
purification, or during subsequent handling and storage. Also,
peptide moieties may be added to the polypeptide to facilitate
purification. Such regions may be removed prior to final
preparation of the polypeptide. The addition of peptide moieties to
polypeptides to engender secretion or excretion, to improve
stability and to facilitate purification, among others, are
familiar and routine techniques in the art. A preferred fusion
protein comprises a heterologous region from immunoglobulin that is
useful to solubilize proteins. For example, EPA 0 464 533 (Canadian
counterpart 2045869) discloses fusion proteins comprising various
portions of constant region of immunoglobin molecules together with
another human protein or part thereof. In many cases, the Fc part
in a fusion protein is thoroughly advantageous for use in therapy
and diagnosis and thus results, for example, in improved
pharmacokinetic properties (EPA 0 232 262). On the other hand, for
some uses it would be desirable to be able to delete the Fc part
after the fusion protein has been expressed, detected and purified
in the advantageous manner described. This is the case when the Fc
portion proves to be a hindrance to use in therapy and diagnosis,
for example when the fusion protein is to be used as an antigen for
immunizations. In drug discovery, for example, human proteins, such
as the hIL5-receptor, have been fused with Fc portions for the
purpose of high-throughput screening assays to identify antagonists
of hIL-5. See, D. Bennett et al., J. of Molec. Recognition 8:52-58
(1995) and K. Johanson et al., J. Biol. Chem. 270:9459-9471
(1995).
[0062] The CK.beta.-15 protein can be recovered and purified from
recombinant cell cultures by well-known methods including ammonium
sulfate or ethanol precipitation, acid extraction, anion or cation
exchange chromatography, phosphocellulose chromatography,
hydrophobic interaction chromatography, affinity chromatography,
hydroxylapatite chromatography and lectin chromatography. Most
preferably, high performance liquid chromatography ("BPLC") is
employed for purification.
[0063] Polypeptides of the present invention include naturally
purified products, products of chemical synthetic procedures, and
products produced by recombinant techniques from a prokaryotic or
eukaryotic host, including, for example, bacterial, yeast, higher
plant, insect and mammalian cells. Depending upon the host employed
in a recombinant production procedure, the polypeptides of the
present invention may be glycosylated or may be non-glycosylated.
In addition, polypeptides of the invention may also include an
initial modified methionine residue, in some cases as a result of
host-mediated processes.
CK.beta.-15 Polypeptides and Peptides
[0064] The invention further provides an isolated CK.beta.-15
polypeptide having the amino acid sequence encoded by the deposited
cDNA, or the amino acid sequence in FIGS. 1A-C (SEQ ID NO:2), or a
peptide or polypeptide comprising a portion of the above
polypeptides. The terms "peptide" and "oligopeptide" are considered
synonymous (as is commonly recognized) and each term can be used
interchangeably as the context requires to indicate a chain of at
least two amino acids coupled by peptidyl linkages. The word
"polypeptide" is used herein for chains containing more than ten
amino acid residues. All oligopeptide and polypeptide formulas or
sequences herein are written from left to right and in the
direction from amino terminus to carboxy terminus.
[0065] It will be recognized in the art that some amino acid
sequence of the CK.beta.-15 polypeptide can be varied without
significant effect of the structure or function of the protein. If
such differences in sequence are contemplated, it should be
remembered that there will be critical areas on the protein which
determine activity. In general, it is possible to replace residues
which form the tertiary structure, provided that residues
performing a similar function are used. In other instances, the
type of residue may be completely unimportant if the alteration
occurs at a non-critical region of the protein.
[0066] Thus, the invention further includes variations of the
CK.beta.-15 polypeptide which show substantial CK.beta.-15
polypeptide activity or which include regions of CK.beta.-15
protein such as the protein portions discussed below. Such mutants
include deletions, insertions, inversions, repeats, and type
substitutions (for example, substituting one hydrophilic residue
for another, but not strongly hydrophilic for strongly hydrophobic
as a rule). Small changes or such "neutral" amino acid
substitutions will generally have little effect on activity.
[0067] Typically seen as conservative substitutions are the
replacements, one for another, among the aliphatic amino acids Ala,
Val, Leu and Ile; interchange of the hydroxyl residues Ser and Thr,
exchange of the acidic residues Asp and Glu, substitution between
the amide residues Asn and Gln, exchange of the basic residues Lys
and Arg and replacements among the aromatic residues Phe, Tyr.
[0068] As indicated in detail above, further guidance concerning
which amino acid changes are likely to be phenotypically silent
(i.e., are not likely to have a significant deleterious effect on a
function) can be found in Bowie, J. U., et al., "Deciphering the
Message in Protein Sequences: Tolerance to Amino Acid
Substitutions," Science 247:1306-1310 (1990).
[0069] Thus, the fragment, derivative or analog of the polypeptide
of SEQ ID NO:2, or that encoded by the deposited cDNA, may be (i)
one in which one or more of the amino acid residues are substituted
with a conserved or non-conserved amino acid residue (preferably a
conserved amino acid residue) and such substituted amino acid
residue may or may not be one encoded by the genetic code, or (ii)
one in which one or more of the amino acid residues includes a
substituent group, or (iii) one in which the mature polypeptide is
fused with another compound, such as a compound to increase the
half-life of the polypeptide (for example, polyethylene glycol), or
(iv) one in which the additional amino acids are fused to the
mature polypeptide, such as an IgG Fc fusion region peptide or
leader or secretory sequence or a sequence which is employed for
purification of the mature polypeptide or a proprotein sequence.
Such fragments, derivatives and analogs are deemed to be within the
scope of those skilled in the art from the teachings herein.
[0070] Of particular interest are substitutions of charged amino
acids with another charged amino acid and with neutral or
negatively charged amino acids. The latter results in proteins with
reduced positive charge to improve the characteristics of the
CK.beta.-15 protein. The prevention of aggregation is highly
desirable. Aggregation of proteins not only results in a loss of
activity but can also be problematic when preparing pharmaceutical
formulations, because they can be immunogenic. (Pinckard et al.,
Clin Exp. Immunol. 2:331-340 (1967); Robbins et al., Diabetes
36:838-845 (1987); Cleland et al., Crit. Rev. Therapeutic Drug
Carrier Systems 10:307-377 (1993)).
[0071] As indicated, changes are preferably of a minor nature, such
as conservative amino acid substitutions that do not significantly
affect the folding or activity of the protein (see Table 1).
TABLE-US-00001 TABLE 1 Conservative Amino Acid Substitutions.
Aromatic Phenylalanine Tryptophan Tyrosine Hydrophobic Leucine
Isoleucine Valine Polar Glutamine Asparagine Basic Arginine Lysine
Histidine Acidic Aspartic Acid Glutamic Acid Small Alanine Serine
Threonine Methionine Glycine
[0072] Amino acids in the CK.beta.-15 protein of the present
invention that are essential for function can be identified by
methods known in the art, such as site-directed mutagenesis or
alanine-scanning mutagenesis (Cunningham and Wells, Science
244:1081-1085 (1989)). The latter procedure introduces single
alanine mutations at every residue in the molecule. The resulting
mutant molecules are then tested for biological activity. Sites
that are critical for ligand-receptor binding can also be
determined by structural analysis such as crystallization, nuclear
magnetic resonance or photoaffinity labeling (Smith et al., J. Mol.
Biol. 224:899-904 (1992) and de Vos et al. Science 255:306-312
(1992)).
[0073] The polypeptides of the present invention are preferably
provided in an isolated form. By "isolated polypeptide" is intended
a polypeptide removed from its native environment. Thus, a
polypeptide produced and/or contained within a recombinant host
cell is considered isolated for purposes of the present invention.
Also intended as an "isolated polypeptide" are polypeptides that
have been purified, partially or substantially, from a recombinant
host cell. For example, a recombinantly produced version of the
CK.beta.-15 polypeptide can be substantially purified by the
one-step method described in Smith and Johnson, Gene 67:31-40
(1988).
[0074] The polypeptides of the present invention include the
polypeptide encoded by the deposited cDNA including the leader; the
mature polypeptide encoded by the deposited cDNA minus the leader
(i.e., the mature protein); a polypeptide comprising amino acids
from about -20 to about 129 in SEQ ID NO:2; a polypeptide
comprising amino acids from about -19 to about 129 in SEQ ID NO:2;
a polypeptide comprising amino acids from about 1 to about 129 in
SEQ ID NO:2; as well as polypeptides which are at least 80%
identical, more preferably at least 90% or 95% identical, still
more preferably at least 96%, 97%, 98% or 99% identical to the
polypeptides described above and also include portions of such
polypeptides with at least 30 amino acids and more preferably at
least 50 amino acids.
[0075] By "% similarity" for two polypeptides is intended a
similarity score produced by comparing the amino acid sequences of
the two polypeptides using the Bestfit program (Wisconsin Sequence
Analysis Package, Version 8 for Unix, Genetics Computer Group,
University Research Park, 575 Science Drive, Madison, Wis. 53711)
and the default settings for determining similarity. Bestfit uses
the local homology algorithm of Smith and Waterman (Advances in
Applied Mathematics 2: 482-489, 1981) to find the best segment of
similarity between two sequences.
[0076] By a polypeptide having an amino acid sequence at least, for
example, 95% "identical" to a reference amino acid sequence of a
chemokine .beta.-15 polypeptide is intended that the amino acid
sequence of the polypeptide is identical to the reference sequence
except that the polypeptide sequence may include up to five amino
acid alterations per each 100 amino acids of the reference amino
acid of the chemokine .beta.-15 polypeptide. In other words, to
obtain a polypeptide having an amino acid sequence at least 95%
identical to a reference amino acid sequence, up to 5% of the amino
acid residues in the reference sequence may be deleted or
substituted with another amino acid, or a number of amino acids up
to 5% of the total amino acid residues in the reference sequence
may be inserted into the reference sequence. These alterations of
the reference sequence may occur at the amino or carboxy terminal
positions of the reference amino acid sequence or anywhere between
those terminal positions, interspersed either individually among
residues in the reference sequence or in one or more contiguous
groups within the reference sequence.
[0077] As a practical matter, whether any particular polypeptide is
at least 90%, 95%, 96%, 97%, 98% or 99% identical to, for instance,
the amino acid sequence shown in FIGS. 1A-C (SEQ ID NO:2) or to the
amino acid sequence encoded by deposited cDNA clone can be
determined conventionally using known computer programs such the
Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for
Unix, Genetics Computer Group, University Research Park, 575
Science Drive, Madison, Wis. 53711. When using Bestfit or any other
sequence alignment program to determine whether a particular
sequence is, for instance, 95% identical to a reference sequence
according to the present invention, the parameters are set, of
course, such that the percentage of identity is calculated over the
full length of the reference amino acid sequence and that gaps in
homology of up to 5% of the total number of amino acid residues in
the reference sequence are allowed.
[0078] The polypeptide of the present invention are useful as a
molecular weight marker on SDS-PAGE gels or on molecular sieve gel
filtration columns using methods well known to those of skill in
the art.
[0079] As described in detail below, the polypeptides of the
present invention can be used to raise polyclonal and monoclonal
antibodies, which are useful in diagnostic assays for detecting
CK.beta.-15 protein expression as described below or as agonists
and antagonists capable of enhancing or inhibiting CK.beta.-15
protein function. Further, such polypeptides can be used in the
yeast two-hybrid system to "capture" CK.beta.-15 protein binding
proteins which are also candidate agonist and antagonist according
to the present invention. The yeast two hybrid system is described
in Fields and Song, Nature 340:245-246 (1989).
[0080] In another aspect, the invention provides a peptide or
polypeptide comprising an epitope-bearing portion of a polypeptide
of the invention. The epitope of this polypeptide portion is an
immunogenic or antigenic epitope of a polypeptide of the invention.
An "immunogenic epitope" is defined as a part of a protein that
elicits an antibody response when the whole protein is the
immunogen. These immunogenic epitopes are believed to be confined
to a few loci on the molecule. On the other hand, a region of a
protein molecule to which an antibody can bind is defined as an
"antigenic epitope." The number of immunogenic epitopes of a
protein generally is less than the number of antigenic epitopes.
See, for instance, Geysen, H. M., Meloen, R. H. and Barteling, S.
J. (1984) Use of peptide synthesis to probe viral antigens for
epitopes to a resolution of a single amino acid. Proc. Natl. Acad.
Sci. USA 81:3998-4002.
[0081] As to the selection of peptides or polypeptides bearing an
antigenic epitope (i.e., that contain a region of a protein
molecule to which an antibody can bind), it is well known in that
art that relatively short synthetic peptides that mimic part of a
protein sequence are routinely capable of eliciting an antiserum
that reacts with the partially mimicked protein. See, for instance,
Sutcliffe, J. G., Shinnick, T. M., Green, N. and Learner, R. A.
(1983) Antibodies that react with predetermined sites on proteins.
Science 219:660-666. Peptides capable of eliciting protein-reactive
sera are frequently represented in the primary sequence of a
protein, can be characterized by a set of simple chemical rules,
and are confined neither to immunodominant regions of intact
proteins (i.e., immunogenic epitopes) nor to the amino or carboxyl
terminals. Peptides that are extremely hydrophobic and those of six
or fewer residues generally are ineffective at inducing antibodies
that bind to the mimicked protein; longer, soluble peptides,
especially those containing proline residues, usually are
effective. Sutcliffe et al., supra, at 661. For instance, 18 of 20
peptides designed according to these guidelines, containing 8-39
residues covering 75% of the sequence of the influenza virus
hemagglutinin HA1 polypeptide chain, induced antibodies that
reacted with the HA1 protein or intact virus; and 12/12 peptides
from the MuLV polymerase and 18/18 from the rabies glycoprotein
induced antibodies that precipitated the respective proteins.
[0082] Antigenic epitope-bearing peptides and polypeptides of the
invention are therefore useful to raise antibodies, including
monoclonal antibodies, that bind specifically to a polypeptide of
the invention. Thus, a high proportion of hybridomas obtained by
fusion of spleen cells from donors immunized with an antigen
epitope-bearing peptide generally secrete antibody reactive with
the native protein. Sutcliffe et al., supra, at 663. The antibodies
raised by antigenic epitope-bearing peptides or polypeptides are
useful to detect the mimicked protein, and antibodies to different
peptides may be used for tracking the fate of various regions of a
protein precursor which undergoes posttranslation processing. The
peptides and anti-peptide antibodies may be used in a variety of
qualitative or quantitative assays for the mimicked protein, for
instance in competition assays since it has been shown that even
short peptides (e.g., about 9 amino acids) can bind and displace
the larger peptides in immunoprecipitation assays. See, for
instance, Wilson, I. A., Niman, H. L., Houghten, R. A., Cherenson,
A. R., Connolly, M. L. and Lerner, R. A. (1984) The structure of an
antigenic determinant in a protein. Cell 37:767-778 at 777. The
anti-peptide antibodies of the invention also are useful for
purification of the mimicked protein, for instance, by adsorption
chromatography using methods well known in the art.
[0083] Antigenic epitope-bearing peptides and polypeptides of the
invention designed according to the above guidelines preferably
contain a sequence of at least seven, more preferably at least nine
and most preferably between about 15 to about 30 amino acids
contained within the amino acid sequence of a polypeptide of the
invention. However, peptides or polypeptides comprising a larger
portion of an amino acid sequence of a polypeptide of the
invention, containing about 30 to about 50 amino acids, or any
length up to and including the entire amino acid sequence of a
polypeptide of the invention, also are considered epitope-bearing
peptides or polypeptides of the invention and also are useful for
inducing antibodies that react with the mimicked protein.
Preferably, the amino acid sequence of the epitope-bearing peptide
is selected to provide substantial solubility in aqueous solvents
(i.e., the sequence includes relatively hydrophilic residues and
highly hydrophobic sequences are preferably avoided); and sequences
containing proline residues are particularly preferred.
[0084] The epitope-bearing peptides and polypeptides of the
invention may be produced by any conventional means for making
peptides or polypeptides including recombinant means using nucleic
acid molecules of the invention. For instance, a short
epitope-bearing amino acid sequence may be fused to a larger
polypeptide which acts as a carrier during recombinant production
and purification, as well as during immunization to produce
anti-peptide antibodies. Epitope-bearing peptides also may be
synthesized using known methods of chemical synthesis. For
instance, Houghten has described a simple method for synthesis of
large numbers of peptides, such as 10-20 mg of 248 different 13
residue peptides representing single amino acid variants of a
segment of the HA1 polypeptide which were prepared and
characterized (by ELISA-type binding studies) in less than four
weeks. Houghten, R. A. (1985) General method for the rapid
solid-phase synthesis of large numbers of peptides: specificity of
antigen-antibody interaction at the level of individual amino
acids. Proc. Natl. Acad. Sci. USA 82:5131-5135. This "Simultaneous
Multiple Peptide Synthesis (SMPS)" process is further described in
U.S. Pat. No. 4,631,211 to Houghten et al. (1986). In this
procedure the individual resins for the solid-phase synthesis of
various peptides are contained in separate solvent-permeable
packets, enabling the optimal use of the many identical repetitive
steps involved in solid-phase methods. A completely manual
procedure allows 500-1000 or more syntheses to be conducted
simultaneously. Houghten et al., supra, at 5134.
[0085] Epitope-bearing peptides and polypeptides of the invention
are used to induce antibodies according to methods well known in
the art. See, for instance, Sutcliffe et al., supra; Wilson et al.,
supra; Chow, M., Yabrov, R., Bittle, J., Hogel, J. and Baltimore,
D., Proc. Natl. Acad. Sci. USA 82:910-914; and Bittle, F. J., Fry,
C. M., Rowlands, D. J., Brown, F., Bittle, J. L., Houghten, R. A.
and Lerner, R. A. (1985) J. Gen. Virol. 66:2347-2354. Generally,
animals may be immunized with free peptide; however, anti-peptide
antibody titer may be boosted by coupling of the peptide to a
macromolecular carrier, such as keyhole limpet hemacyanin (KLH) or
tetanus toxoid. For instance, peptides containing cysteine may be
coupled to carrier using a linker such as
m-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS), while other
peptides may be coupled to carrier using a more general linking
agent such as glutaraldehyde. Animals such as rabbits, rats and
mice are immunized with either free or carrier-coupled peptides,
for instance, by intraperitoneal and/or intradermal injection of
emulsions containing about 100 .mu.g peptide or carrier protein and
Freund's adjuvant. Several booster injections may be needed, for
instance, at intervals of about two weeks, to provide a useful
titer of anti-peptide antibody which can be detected, for example,
by ELISA assay using free peptide adsorbed to a solid surface. The
titer of anti-peptide antibodies in serum from an immunized animal
may be increased by selection of anti-peptide antibodies, for
instance, by adsorption to the peptide on a solid support and
elution of the selected antibodies according to methods well known
in the art.
[0086] Immunogenic epitope-bearing peptides of the invention, i.e.,
those parts of a protein that elicit an antibody response when the
whole protein is the immunogen, are identified according to methods
known in the art. For instance, Geysen et al., 1984, supra,
discloses a procedure for rapid concurrent synthesis on solid
supports of hundreds of peptides of sufficient purity to react in
an enzyme-linked immunosorbent assay. Interaction of synthesized
peptides with antibodies is then easily detected without removing
them from the support. In this manner a peptide bearing an
immunogenic epitope of a desired protein may be identified
routinely by one of ordinary skill in the art. For instance, the
immunologically important epitope in the coat protein of
foot-and-mouth disease virus was located by Geysen et al. with a
resolution of seven amino acids by synthesis of an overlapping set
of all 208 possible hexapeptides covering the entire 213 amino acid
sequence of the protein. Then, a complete replacement set of
peptides in which all 20 amino acids were substituted in turn at
every position within the epitope were synthesized, and the
particular amino acids conferring specificity for the reaction with
antibody were determined. Thus, peptide analogs of the
epitope-bearing peptides of the invention can be made routinely by
this method. U.S. Pat. No. 4,708,781 to Geysen (1987) further
describes this method of identifying a peptide bearing an
immunogenic epitope of a desired protein.
[0087] Further still, U.S. Pat. No. 5,194,392 to Geysen (1990)
describes a general method of detecting or determining the sequence
of monomers (amino acids or other compounds) which is a topological
equivalent of the epitope (i.e., a "mimotope") which is
complementary to a particular paratope (antigen binding site) of an
antibody of interest. More generally, U.S. Pat. No. 4,433,092 to
Geysen (1989) describes a method of detecting or determining a
sequence of monomers which is a topographical equivalent of a
ligand which is complementary to the ligand binding site of a
particular receptor of interest. Similarly, U.S. Pat. No. 5,480,971
to Houghten, R. A. et al. (1996) on Peralkylated Oligopeptide
Mixtures discloses linear C.sub.1-C.sub.7-alkyl peralkylated
oligopeptides and sets and libraries of such peptides, as well as
methods for using such oligopeptide sets and libraries for
determining the sequence of a peralkylated oligopeptide that
preferentially binds to an acceptor molecule of interest. Thus,
non-peptide analogs of the epitope-bearing peptides of the
invention also can be made routinely by these methods.
[0088] The entire disclosure of each document cited in this section
on "Polypeptides and Peptides" is hereby incorporated herein by
reference.
Thymus-Related Disorder Diagnosis
[0089] The present inventors have discovered that CK.beta.-15 is
expressed only in thymus tissue. For a number of thymus-related
disorders, substantially altered (increased or decreased) levels of
CK.beta.-15 gene expression can be detected in thymus tissue or
other cells or bodily fluids (e.g., sera, plasma, urine, synovial
fluid or spinal fluid) taken from an individual having such a
disorder, relative to a "standard" CK.beta.-15 gene expression
level, that is, the CK.beta.-15 expression level in thymus tissue
or bodily fluids from an individual not having the thymus disorder.
Thus, the invention provides a diagnostic method useful during
diagnosis of a thymus disorder, which involves measuring the
expression level of the gene encoding the CK.beta.-15 protein in
thymus tissue or other cells or body fluid from an individual and
comparing the measured gene expression level with a standard
CK.beta.-15 gene expression level, whereby an increase or decrease
in the gene expression level compared to the standard is indicative
of a thymus disorder.
[0090] By individual is intended mammalian individuals, preferably
humans. By "measuring the expression level of the gene encoding the
CK.beta.-15 protein" is intended qualitatively or quantitatively
measuring or estimating the level of the CK.beta.-15 protein or the
level of the mRNA encoding the CK.beta.-15 protein in a first
biological sample either directly (e.g., by determining or
estimating absolute protein level or mRNA level) or relatively
(e.g., by comparing to the CK.beta.-15 protein level or mRNA level
in a second biological sample). Preferably, the CK.beta.-15 protein
level or mRNA level in the first biological sample is measured or
estimated and compared to a standard CK.beta.-15 protein level or
mRNA level, the standard being taken from a second biological
sample obtained from an individual not having the disorder or being
determined by averaging levels from a population of individuals not
having a disorder of the thymus. As will be appreciated in the art,
once a standard CK.beta.-15 protein level or mRNA level is known,
it can be used repeatedly as a standard for comparison.
[0091] By "biological sample" is intended any biological sample
obtained from an individual, body fluid, cell line, tissue culture,
or other source which contains CK.beta.-15 protein or mRNA. As
indicated, biological samples include body fluids (such as sera,
plasma, urine, synovial fluid and spinal fluid) which contain
secreted mature CK.beta.-15 protein, thymus tissue, and other
tissue sources found to express CK.beta.-15 or a CK.beta.-15
receptor. Methods for obtaining tissue biopsies and body fluids
from mammals are well known in the art. Where the biological sample
is to include mRNA, a tissue biopsy is the preferred source.
[0092] The present invention is useful for diagnosis or treatment
of various thymus-related disorders in mammals, preferably humans.
Such disorders include the following tumors and cancers,
hypoactivity, hyperactivity, atrophy, enlargement of the thymus,
and the like. Other disorders include disregulation of T-lymphocyte
selection or activity and would include but not be limited to
disorders involving autoimmunity, arthritis, leukemias, lymphomas,
immunosuppression, sepsis, would healing, acute and chronic
inflammation, cell mediated immunity, humor immunity, TH1/TH2
imbalance, and the like.
[0093] Total cellular RNA can be isolated from a biological sample
using any suitable technique such as the single-step
guanidinium-thiocyanate-phenol-chloroform method described in
Chomczynski and Sacchi, Anal. Biochem. 162:156-159 (1987). Levels
of mRNA encoding the CK.beta.-15 protein are then assayed using any
appropriate method. These include Northern blot analysis, S1
nuclease mapping, the polymerase chain reaction (PCR), reverse
transcription in combination with the polymerase chain reaction
(RT-PCR), and reverse transcription in combination with the ligase
chain reaction (RT-LCR).
[0094] Northern blot analysis can be performed as described in
Harada et al., Cell 63:303-312 (1990). Briefly, total RNA is
prepared from a biological sample as described above. For the
Northern blot, the RNA is denatured in an appropriate buffer (such
as glyoxal/dimethyl sulfoxide/sodium phosphate buffer), subjected
to agarose gel electrophoresis, and transferred onto a
nitrocellulose filter. After the RNAs have been linked to the
filter by a UV linker, the filter is prehybridized in a solution
containing formamide, SSC, Denhardt's solution, denatured salmon
sperm, SDS, and sodium phosphate buffer. CK.beta.-15 protein cDNA
labeled according to any appropriate method (such as the
.sup.32P-multiprimed DNA labeling system (Amersham)) is used as
probe. After hybridization overnight, the filter is washed and
exposed to x-ray film. cDNA for use as probe according to the
present invention is described in the sections above and will
preferably at least 15 bp in length.
[0095] S1 mapping can be performed as described in Fujita et al.,
Cell 49:357-367 (1987). To prepare probe DNA for use in S1 mapping,
the sense strand of above-described cDNA is used as a template to
synthesize labeled antisense DNA. The antisense DNA can then be
digested using an appropriate restriction endonuclease to generate
further DNA probes of a desired length. Such antisense probes are
useful for visualizing protected bands corresponding to the target
mRNA (i.e., mRNA encoding the CK.beta.-15 protein). Northern blot
analysis can be performed as described above.
[0096] Preferably, levels of mRNA encoding the CK.beta.-15 protein
are assayed using the RT-PCR method described in Makino et al.,
Technique 2:295-301 (1990). By this method, the radioactivities of
the "amplicons" in the polyacrylamide gel bands are linearly
related to the initial concentration of the target mRNA. Briefly,
this method involves adding total RNA isolated from a biological
sample in a reaction mixture containing a RT primer and appropriate
buffer. After incubating for primer annealing, the mixture can be
supplemented with a RT buffer, dNTPs, DTT, RNase inhibitor and
reverse transcriptase. After incubation to achieve reverse
transcription of the RNA, the RT products are then subject to PCR
using labeled primers. Alternatively, rather than labeling the
primers, a labeled dNTP can be included in the PCR reaction
mixture. PCR amplification can be performed in a DNA thermal cycler
according to conventional techniques. After a suitable number of
rounds to achieve amplification, the PCR reaction mixture is
electrophoresed on a polyacrylamide gel. After drying the gel, the
radioactivity of the appropriate bands (corresponding to the mRNA
encoding the CK.beta.-15 protein) is quantified using an imaging
analyzer. RT and PCR reaction ingredients and conditions, reagent
and gel concentrations, and labeling methods are well known in the
art. Variations on the RT-PCR method will be apparent to the
skilled artisan.
[0097] Any set of oligonucleotide primers which will amplify
reverse transcribed target mRNA can be used and can be designed as
described in the sections above.
[0098] Assaying CK.beta.-15 protein levels in a biological sample
can occur using any art-known method. Preferred for assaying
CK.beta.-15 protein levels in a biological sample are
antibody-based techniques. For example, CK.beta.-15 protein
expression in tissues can be studied with classical
immunohistological methods. In these, the specific recognition is
provided by the primary antibody (polyclonal or monoclonal) but the
secondary detection system can utilize fluorescent, enzyme, or
other conjugated secondary antibodies. As a result, an
immunohistological staining of tissue section for pathological
examination is obtained. Tissues can also be extracted, e.g., with
urea and neutral detergent, for the liberation of CK.beta.-15
protein for Western-blot or dot/slot assay (Jalkanen, M., et al.,
J. Cell. Biol. 101:976-985 (1985)); Jalkanen, M., et al., J. Cell.
Biol. 105:3087-3096 (1987)). In this technique, which is based on
the use of cationic solid phases, quantitation of CK.beta.-15
protein can be accomplished using isolated CK.beta.-15 protein as a
standard. This technique can also be applied to body fluids. With
these samples, a molar concentration of CK.beta.-15 protein will
aid to set standard values of CK.beta.-15 protein content for
different body fluids, like serum, plasma, urine, synovial fluid,
spinal fluid, etc. The normal appearance of CK.beta.-15 protein
amounts can then be set using values from healthy individuals,
which can be compared to those obtained from a test subject.
[0099] Other antibody-based methods useful for detecting
CK.beta.-15 protein levels include immunoassays, such as the enzyme
linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA).
For example, CK.beta.-15 protein-specific monoclonal antibodies can
be used both as an immunoadsorbent and as an enzyme-labeled probe
to detect and quantify the CK.beta.-15 protein. The amount of
CK.beta.-15 protein present in the sample can be calculated by
reference to the amount present in a standard preparation using a
linear regression computer algorithm. Such an ELISA for detecting a
tumor antigen is described in Iacobelli et al., Breast Cancer
Research and Treatment 11:19-30 (1988). In another ELISA assay, two
distinct specific monoclonal antibodies can be used to detect
CK.beta.-15 protein in a body fluid. In this assay, one of the
antibodies is used as the immunoadsorbent and the other as the
enzyme-labeled probe.
[0100] The above techniques may be conducted essentially as a
"one-step" or "two-step" assay. The "one-step" assay involves
contacting CK.beta.-15 protein with immobilized antibody and,
without washing, contacting the mixture with the labeled antibody.
The "two-step" assay involves washing before contacting the mixture
with the labeled antibody. Other conventional methods may also be
employed as suitable. It is usually desirable to immobilize one
component of the assay system on a support, thereby allowing other
components of the system to be brought into contact with the
component and readily removed from the sample.
[0101] Suitable enzyme labels include, for example, those from the
oxidase group, which catalyze the production of hydrogen peroxide
by reacting with substrate. Glucose oxidase is particularly
preferred as it has good stability and its substrate (glucose) is
readily available. Activity of an oxidase label may be assayed by
measuring the concentration of hydrogen peroxide formed by the
enzyme-labeled antibody/substrate reaction. Besides enzymes, other
suitable labels include radioisotopes, such as iodine (.sup.125I,
.sup.121I), carbon (.sup.14C), sulfur (.sup.35S), tritium
(.sup.3H), indium (.sup.112In), and technetium (.sup.99mTc), and
fluorescent labels, such as fluorescein and rhodamine, and
biotin.
[0102] In addition to assaying CK.beta.-15 protein levels in a
biological sample obtained from an individual, CK.beta.-15 protein
can also be detected in vivo by imaging. Antibody labels or markers
for in vivo imaging of CK.beta.-15 protein include those detectable
by X-radiography, NMR or ESR. For X-radiography, suitable labels
include radioisotopes such as barium or cesium, which emit
detectable radiation but are not overtly harmful to the subject.
Suitable markers for NMR and ESR include those with a detectable
characteristic spin, such as deuterium, which may be incorporated
into the antibody by labeling of nutrients for the relevant
hybridoma.
[0103] A CK.beta.-15 protein-specific antibody or antibody portion
which has been labeled with an appropriate detectable imaging
moiety, such as a radioisotope (for example, .sup.131I, .sup.112In,
.sup.99mTc), a radio-opaque substance, or a material detectable by
nuclear magnetic resonance, is introduced (for example,
parenterally, subcutaneously or intraperitoneally) into the mammal
to be examined for a thymus disorder. It will be understood in the
art that the size of the subject and the imaging system used will
determine the quantity of imaging moieties needed to produce
diagnostic images. In the case of a radioisotope moiety, for a
human subject, the quantity of radioactivity injected will normally
range from about 5 to 20 millicuries of .sup.99mTc. The labeled
antibody or antibody portion will then preferentially accumulate at
the location of cells which contain CK.beta.-15 protein. In vivo
tumor imaging is described in S. W. Burchiel et al.,
"Immunopharmacokinetics of Radiolabeled Antibodies and Their
Portions" (Chapter 13 in Tumor Imaging: The Radiochemical Detection
of Cancer, eds., S. W. Burchiel and B. A. Rhodes, Masson Publishing
Inc. (1982)).
[0104] CK.beta.-15-protein specific antibodies for use in the
present invention can be raised against the intact CK.beta.-15
protein or an antigenic polypeptide portion thereof, which may
presented together with a carrier protein, such as an albumin, to
an animal system (such as rabbit or mouse) or, if it is long enough
(at least about 25 amino acids), without a carrier.
[0105] As used herein, the term "antibody" (Ab) or "monoclonal
antibody" (Mab) is meant to include intact molecules as well as
antibody portions (such as, for example, Fab and F(ab').sub.2
portions) which are capable of specifically binding to CK.beta.-15
protein. Fab and F(ab').sub.2 portions lack the Fc portion of
intact antibody, clear more rapidly from the circulation, and may
have less non-specific tissue binding of an intact antibody (Wahl
et al., J. Nucl. Med. 24:316-325 (1983)). Thus, these portions are
preferred.
[0106] The antibodies of the present invention may be prepared by
any of a variety of methods. For example, cells expressing the
CK.beta.-15 protein or an antigenic portion thereof can be
administered to an animal in order to induce the production of sera
containing polyclonal antibodies. In a preferred method, a
preparation of CK.beta.-15 protein is prepared and purified as
described above to render it substantially free of natural
contaminants. Such a preparation is then introduced into an animal
in order to produce polyclonal antisera of greater specific
activity.
[0107] In the most preferred method, the antibodies of the present
invention are monoclonal antibodies (or CK.beta.-15 protein binding
portions thereof). Such monoclonal antibodies can be prepared using
hybridoma technology (Kohler et al., Nature 256:495 (1975); Kohler
et al., Eur. J. Immunol. 6:511 (1976); Kohler et al., Eur. J.
Immunol. 6:292 (1976); Hammerling et al., In: Monoclonal Antibodies
and T-Cell Hybridomas, Elsevier, N.Y., pp. 563-681 (1981)). In
general, such procedures involve immunizing an animal (preferably a
mouse) with a CK.beta.-15 protein antigen or, more preferably, with
a CK.beta.-15 protein-expressing cell. Suitable cells can be
recognized by their capacity to bind anti-CK.beta.-15 protein
antibody. Such cells may be cultured in any suitable tissue culture
medium; however, it is preferable to culture cells in Earle's
modified Eagle's medium supplemented with 10% fetal bovine serum
(inactivated at about 56.degree. C.), and supplemented with about
10 .mu.g/l of nonessential amino acids, about 1,000 U/ml of
penicillin, and about 100 .mu.g/ml of streptomycin. The splenocytes
of such mice are extracted and fused with a suitable myeloma cell
line. Any suitable myeloma cell line may be employed in accordance
with the present invention; however, it is preferable to employ the
parent myeloma cell line (SP.sub.2O), available from the American
Type Culture Collection, Rockville, Md. After fusion, the resulting
hybridoma cells are selectively maintained in HAT medium, and then
cloned by limiting dilution as described by Wands et al.
(Gastroenterology 80:225-232 (1981)). The hybridoma cells obtained
through such a selection are then assayed to identify clones which
secrete antibodies capable of binding the CK.beta.-15 antigen.
[0108] Alternatively, additional antibodies capable of binding to
the CK.beta.-15 protein antigen may be produced in a two-step
procedure through the use of anti-idiotypic antibodies. Such a
method makes use of the fact that antibodies are themselves
antigens, and therefore it is possible to obtain an antibody which
binds to a second antibody. In accordance with this method,
CK.beta.-15 protein specific antibodies are used to immunize an
animal, preferably a mouse. The splenocytes of such an animal are
then used to produce hybridoma cells, and the hybridoma cells are
screened to identify clones which produce an antibody whose ability
to bind to the CK.beta.-15 protein-specific antibody can be blocked
by the CK.beta.-15 protein antigen. Such antibodies comprise
anti-idiotypic antibodies to the CK.beta.-15 protein-specific
antibody and can be used to immunize an animal to induce formation
of further CK.beta.-15 protein-specific antibodies.
[0109] It will be appreciated that Fab and F(ab').sub.2 and other
portions of the antibodies of the present invention may be used
according to the methods disclosed herein. Such portions are
typically produced by proteolytic cleavage, using enzymes such as
papain (to produce Fab portions) or pepsin (to produce F(ab').sub.2
portions). Alternatively, CK.beta.-15 protein-binding portions can
be produced through the application of recombinant DNA technology
or through synthetic chemistry.
[0110] Where in vivo imaging is used to detect enhanced levels of
CK.beta.-15 protein for diagnosis in humans, it may be preferable
to use "humanized" chimeric monoclonal antibodies. Such antibodies
can be produced using genetic constructs derived from hybridoma
cells producing the monoclonal antibodies described above. Methods
for producing chimeric antibodies are known in the art. See, for
review, Morrison, Science 229:1202 (1985); Oi et al., BioTechniques
4:214 (1986); Cabilly et al., U.S. Pat. No. 4,816,567; Taniguchi et
al., EP 171496; Morrison et al., EP 173494; Neuberger et al., WO
8601533; Robinson et al., WO 8702671; Boulianne et al., Nature
312:643 (1984); Neuberger et al., Nature 314:268 (1985).
[0111] Further suitable labels for the CK.beta.-15 protein-specific
antibodies of the present invention are provided below. Examples of
suitable enzyme labels include malate dehydrogenase, staphylococcal
nuclease, delta-S-steroid isomerase, yeast-alcohol dehydrogenase,
alpha-glycerol phosphate dehydrogenase, triose phosphate isomerase,
peroxidase, alkaline phosphatase, asparaginase, glucose oxidase,
beta-galactosidase, ribonuclease, urease, catalase,
glucose-6-phosphate dehydrogenase, glucoamylase, and acetylcholine
esterase.
[0112] Examples of suitable radioisotopic labels include .sup.3H,
.sup.111In, .sup.125I, .sup.131I, .sup.32P, .sup.35S, .sup.14C,
.sup.51Cr, .sup.57To, .sup.58Co, .sup.59Fe, .sup.75Se, .sup.152Eu,
.sup.90Y, .sup.67Cu, .sup.217Ci, .sup.211At, .sup.212Pb, .sup.47Sc,
.sup.109Pd, etc. .sup.111In is a preferred isotope where in vivo
imaging is used since its avoids the problem of dehalogenation of
the .sup.125I or .sup.131I-labeled monoclonal antibody by the
liver. In addition, this radionucleotide has a more favorable gamma
emission energy for imaging (Perkins et al., Eur. J. Nucl. Med.
10:296-301 (1985); Carasquillo et al., J. Nucl. Med. 28:281-287
(1987)). For example, illin coupled to monoclonal antibodies with
1-(P-isothiocyanatobenzyl)-DPTA has shown little uptake in
non-tumorous tissues, particularly the liver, and therefore
enhances specificity of tumor localization (Esteban et al., J.
Nucl. Med. 28:861-870 (1987)).
[0113] Examples of suitable non-radioactive isotopic labels include
.sup.157 Gd, .sup.55Mn, .sup.162Dy, .sup.52Tr, and .sup.56Fe.
[0114] Examples of suitable fluorescent labels include an
.sup.152Eu label, a fluorescein label, an isothiocyanate label, a
rhodamine label, a phycoerythrin label, a phycocyanin label, an
allophycocyanin label, an o-phthaldehyde label, and a
fluorescarnine label.
[0115] Examples of suitable toxin labels include diphtheria toxin,
ricin, and cholera toxin.
[0116] Examples of chemiluminescent labels include a luminal label,
an isoluminal label, an aromatic acridinium ester label, an
imidazole label, an acridinium salt label, an oxalate ester label,
a luciferin label, a luciferase label, and an aequorin label.
[0117] Examples of nuclear magnetic resonance contrasting agents
include heavy metal nuclei such as Gd, Mn, and Fe.
[0118] Typical techniques for binding the above-described labels to
antibodies are provided by Kennedy et al. (Clin. Chim. Acta 70:1-31
(1976)), and Schurs et al. (Clin. Chim. Acta 81:1-40 (1977)).
Coupling techniques mentioned in the latter are the glutaraldehyde
method, the periodate method, the dimaleimide method, the
m-maleimidobenzyl-N-hydroxy-succinimide ester method, all of which
methods are incorporated by reference herein.
Chromosome Assays
[0119] The nucleic acid molecules of the present invention are also
valuable for chromosome identification. The sequence is
specifically targeted to and can hybridize with a particular
location on an individual human chromosome. Moreover, there is a
current need for identifying particular sites on the chromosome.
Few chromosome marking reagents based on actual sequence data
(repeat polymorphisms) are presently available for marking
chromosomal location. The mapping of DNAs to chromosomes according
to the present invention is an important first step in correlating
those sequences with genes associated with disease.
[0120] In certain preferred embodiments in this regard, the cDNA
herein disclosed is used to clone genomic DNA of a CK.beta.-15
protein gene. This can be accomplished using a variety of well
known techniques and libraries, which generally are available
commercially. The genomic DNA then is used for in situ chromosome
mapping using well known techniques for this purpose. Typically, in
accordance with routine procedures for chromosome mapping, some
trial and error may be necessary to identify a genomic probe that
gives a good in situ hybridization signal.
[0121] In some cases, in addition, sequences can be mapped to
chromosomes by preparing PCR primers (preferably 15-25 bp) from the
cDNA. Computer analysis of the 3' untranslated region of the gene
is used to rapidly select primers that do not span more than one
exon in the genomic DNA, thus complicating the amplification
process. These primers are then used for PCR screening of somatic
cell hybrids containing individual human chromosomes. Only those
hybrids containing the human gene corresponding to the primer will
yield an amplified portion.
[0122] PCR mapping of somatic cell hybrids is a rapid procedure for
assigning a particular DNA to a particular chromosome. Using the
present invention with the same oligonucleotide primers,
sublocalization can be achieved with panels of portions from
specific chromosomes or pools of large genomic clones in an
analogous manner. Other mapping strategies that can similarly be
used to map to its chromosome include in situ hybridization,
prescreening with labeled flow-sorted chromosomes and preselection
by hybridization to construct chromosome specific-cDNA
libraries.
[0123] Fluorescence in situ hybridization ("FISH") of a cDNA clone
to a metaphase chromosomal spread can be used to provide a precise
chromosomal location in one step. This technique can be used with
probes from the cDNA as short as 50 or 60 bp. For a review of this
technique, see Verma et al., HUMAN CHROMOSOMES: A MANUAL OF BASIC
TECHNIQUES, Pergamon Press, New York (1988).
[0124] Once a sequence has been mapped to a precise chromosomal
location, the physical position of the sequence on the chromosome
can be correlated with genetic map data. Such data are found, for
example, in V. McKusick, MENDELIAN INHERITANCE IN MAN, available
on-line through Johns Hopkins University, Welch Medical Library.
The relationship between genes and diseases that have been mapped
to the same chromosomal region are then identified through linkage
analysis (coinheritance of physically adjacent genes).
[0125] Next, it is necessary to determine the differences in the
cDNA or genomic sequence between affected and unaffected
individuals. If a mutation is observed in some or all of the
affected individuals but not in any normal individuals, then the
mutation is likely to be the causative agent of the disease.
[0126] With current resolution of physical mapping and genetic
mapping techniques, a cDNA precisely localized to a chromosomal
region associated with the disease could be one of between 50 and
500 potential causative genes. (This assumes 1 megabase mapping
resolution and one gene per 20 kb).
Treatment of Thymus-Related Disorders
[0127] As noted above, unlike other known CC cytokines, CK.beta.-15
has been shown to be expressed only in the thymus. Therefore,
CK.beta.-15 is particularly active in modulating activities of
monocytes in the thymus, particularly those of early thymocytes,
such as the activities described above in relation to the
description of a "polypeptide having CK.beta.-15 activity." Given
the thymocyte activities modulated by CK.beta.-15, it is readily
apparent that a substantially altered (increased or decreased)
level of expression of CK.beta.-15 in an individual compared to the
standard or "normal" level produces pathological conditions such as
those described above in relation to diagnosis of thymus-related
disorders. It will also be appreciated by one of ordinary skill
that, since the CK.beta.-15 protein of the invention is translated
with a leader peptide suitable for secretion of the mature protein
from the cells which express CK.beta.-15, when CK.beta.-15 protein
(particularly the mature form) is added from an exogenous source to
cells, tissues or the body of an individual, the protein will exert
its modulating activities on any of its target cells of that
individual. Therefore, it will be appreciated that conditions
caused by a decrease in the standard or normal level of CK.beta.-15
activity in an individual, particularly disorders of the thymus,
can be treated be administration of CK.beta.-15 protein. Thus, the
invention also provides a method of treatment of an individual in
need of an increased level of CK.beta.-15 activity comprising
administering to such an individual a pharmaceutical composition
comprising an amount of an isolated CK.beta.-15 polypeptide of the
invention, particularly a mature form of the CK.beta.-15 protein of
the invention, effective to increase the CK.beta.-15 activity level
in such an individual.
[0128] In addition, since the CK.beta.-15 protein suppresses
myeloid cell growth when administered to an individual, the
invention provides methods for suppressing myeloid cell
proliferation in an individual, which involve administering a
myelosuppressive amount of CK.beta.-15 either alone or together
with one or more chemokines selected from the group consisting of
Macrophage Inflammatory Protein-1.alpha. (MIP-1.alpha.), Macrophage
Inflammatory Protein-2.alpha. (MIP-2.alpha.), Platelet Factor 4
(PF4), Interleukin-8 (IL-8), Macrophage Chemotactic and Activating
Factor (MCAF), and Macrophage Inflammatory Protein-Related
Protein-2 (MRP-2). The myelosuppressive compositions of the present
invention thus provide myeloprotective effects and are useful in
conjunction with therapies that have an adverse affect on myeloid
cells. This is because the myelosuppressive compositions of the
present invention place myeloid cells in a slow-cycling state
thereby providing protection against cell damage caused by, for
example, radiation therapy or chemotherapy using cell-cycle active
drugs, such as cytosine arabinoside and hydroxyurea.
[0129] The myelosuppressive pharmaceutical compositions of the
present invention are also useful in the treatment of leukemia,
which causes a hyperproliferative myeloid cell state. Thus, the
invention further provides methods for treating leukemia, which
involve administering to a leukemia patient a myelosuppressive
amount of CK.beta.-15 either alone or together with one or more
chemokines selected from the group consisting of MIP-1.alpha.,
MIP-2.alpha., PF4, IL-8, MCAF, and MRP-2.
[0130] By "suppressing myeloid cell proliferation" is intended
decreasing the cell proliferation of myeloid cells and/or
increasing the percentage of myeloid cells in the slow-cycling
phase. As above, by "individual" is intended mammalian individuals,
preferably humans. Preincubation of the myelosuppressive
compositions of the present invention with acetonitrile (ACN)
significantly enhances the specific activity of these chemokines
for suppression of myeloid progenitor cells. Thus, preferably,
prior to administration, the myelosuppresive compositions of the
present invention are pretreated with ACN as described in Broxmeyer
H. E., et al., Ann-Hematol. 71(5):235-46(1995) and PCT Publication
WO 94/13321, the entire disclosures of which are hereby
incorporated herein by reference.
[0131] The myelosuppressive compositions of the present invention
may be used in combination with a variety of chemotherapeutic
agents including alkylating agents such as nitrogen mustards,
ethylenimines, methylmelamines, alkyl sulfonates, nitrosuoureas,
and triazenes; antimetabolites such as folic acid analogs,
pyrimidine analogs, in particular fluorouracil and cytosine
arabinoside, and purine analogs; natural products such as vinca
alkaloids, epipodophyllotoxins, antibiotics, enzymes and biological
response modifiers; and miscellaneous products such as platinum
coordination complexes, anthracenedione, substituted urea such as
hydroxyurea, methyl hydrazine derivatives, and adrenocorticoid
suppressant.
[0132] Chemotherapeutic agents can be administered at known
concentrations according to known techniques. The myelosuppressive
compositions of the present invention can be co-administered with a
chemotherapeutic agent, or administered separately, either before
or after chemotherapeutic administration.
[0133] Certain chemokines, such as MIP-1.beta., MIP-2.beta. and
GRO-.alpha., inhibit (at least partially block) the myeloid
suppressive affects of the myelosuppresive compositions of the
present invention. Thus, in a further embodiment, the invention
provides methods for inhibiting myelosuppression, which involves
administering an effective amount of a myelosuppressive inhibitor
selected from the group consisting of MIP-1.beta., MIP-2.beta. and
GRO-.alpha. to a mammal previously exposed to the myelosuppresive
agent CK.beta.-15 either alone or together with one or more of
MIP-1.alpha., MIP-2.alpha., PF4, IL-8, MCAF, and MRP-2.
[0134] One of ordinary skill will appreciate that effective amounts
of the CK.beta.-15 polypeptides for treating an individual in need
of an increased level of CK.beta.-15 activity (including amounts of
CK.beta.-15 polypeptides effective for myelosuppression with or
without myelosuppressive agents or myelosuppressive inhibitors) can
be determined empirically for each condition where administration
of CK.beta.-15 is indicated. The polypeptide having CK.beta.-15
activity my be administered in pharmaceutical compositions in
combination with one or more pharmaceutically acceptable
excipients. It will be understood that, when administered to a
human patient, the total daily usage of the pharmaceutical
compositions of the present invention will be decided by the
attending physician within the scope of sound medical judgment. The
specific therapeutically effective dose level for any particular
patient will depend upon a variety of factors including the type
and degree of the response to be achieved; the specific composition
an other agent, if any, employed; the age, body weight, general
health, sex and diet of the patient; the time of administration,
route of administration, and rate of excretion of the composition;
the duration of the treatment; drugs, (such as a chemotherapeutic
agent) used in combination or coincidental with the specific
composition; and like factors well known in the medical arts.
[0135] For example, satisfactory results are obtained by oral
administration of a polypeptide having CK.beta.-15 activity in
dosages on the order of from 0.05 to 10 mg/kg/day, preferably 0.1
to 7.5 mg/kg/day, more preferably 0.1 to 2 mg/kg/day, administered
once or, in divided doses, 2 to 4 times per day. On administration
parenterally, for example by i.v. drip or infusion, dosages on the
order of from 0.01 to 5 mg/kg/day, preferably 0.05 to 1.0 mg/kg/day
and more preferably 0. 1 to 1.0 mg/kg/day can be used. Suitable
daily dosages for patients are thus on the order of from 2.5 to 500
mg p.o., preferably 5 to 250 mg p.o., more preferably 5 to 100 mg
p.o., or on the order of from 0.5 to 250 mg i.v., preferably 2.5 to
125 mg i.v. and more preferably 2.5 to 50 mg i.v.
[0136] Dosaging may also be arranged in a patient specific manner
to provide a predetermined concentration of an CK.beta.-15 activity
in the blood, as determined by an RIA technique, for instance. Thus
patient dosaging may be adjusted to achieve regular on-going trough
blood levels, as measured by RIA, on the order of from 50 to 1000
ng/ml, preferably 150 to 500 ng/ml.
[0137] Pharmaceutical compositions of the invention may be
administered orally, rectally, parenterally, intracistemally,
intravaginally, intraperitoneally, topically (as by powders,
ointments, drops or transdermal patch), bucally, or as an oral or
nasal spray. By "pharmaceutically acceptable carrier" is meant a
non-toxic solid, semisolid or liquid filler, diluent, encapsulating
material or formulation auxiliary of any type. The term
"parenteral" as used herein refers to modes of administration which
include intravenous, intramuscular, intraperitoneal, intrastemal,
subcutaneous and intraarticular injection and infusion.
[0138] Pharmaceutical compositions of the present invention for
parenteral injection can comprise pharmaceutically acceptable
sterile aqueous or nonaqueous solutions, dispersions, suspensions
or emulsions as well as sterile powders for reconstitution into
sterile injectable solutions or dispersions just prior to use.
Examples of suitable aqueous and nonaqueous carriers, diluents,
solvents or vehicles include water, ethanol, polyols (such as
glycerol, propylene glycol, polyethylene glycol, and the like),
carboxymethylceuulose and suitable mixtures thereof, vegetable oils
(such as olive oil), and injectable organic esters such as ethyl
oleate. Proper fluidity can be maintained, for example, by the use
of coating materials such as lecithin, by the maintenance of the
required particle size in the case of dispersions, and by the use
of surfactants.
[0139] The compositions of the present invention may also contain
adjuvants such as preservatives, wetting agents, emulsifying
agents, and dispersing agents. Prevention of the action of
microorganisms may be ensured by the inclusion of various
antibacterial and antifungal agents, for example, paraben,
chlorobutanol, phenol sorbic acid, and the like. It may also be
desirable to include isotonic agents such as sugars, sodium
chloride, and the like. Prolonged absorption of the injectable
pharmaceutical form may be brought about by the inclusion of agents
which delay absorption such as aluminum monostearate and
gelatin.
[0140] In some cases, in order to prolong the effect of the
pharmaceutical composition, it is desirable to slow the absorption
of the drug from subcutaneous or intramuscular injection. This may
be accomplished by the use of a liquid suspension of crystalline or
amorphous material with poor water solubility. The rate of
absorption of the drug then depends upon its rate of dissolution
which, in turn, may depend upon crystal size and crystalline form.
Alternatively, delayed absorption of a parenterally administered
drug form is accomplished by dissolving or suspending the drug in
an oil vehicle.
[0141] Injectable depot forms are made by forming microencapsuled
matrices of the drug in biodegradable polymers such as
polylactide-polyglycolide. Depending upon the ratio of drug to
polymer and the nature of the particular polymer employed, the rate
of drug release can be controlled. Examples of other biodegradable
polymers include poly(orthoesters) and poly(anhydrides). Depot
injectable formulations are also prepared by entrapping the drug in
liposomes or microemulsions which are compatible with body
tissues.
[0142] The injectable formulations can be sterilized, for example,
by filtration through a bacterial-retaining filter, or by
incorporating sterilizing agents in the form of sterile solid
compositions which can be dissolved or dispersed in sterile water
or other sterile injectable medium just prior to use.
[0143] Solid dosage forms for oral administration include capsules,
tablets, pills, powders, and granules. In such solid dosage forms,
the active compounds are mixed with at least one item
pharmaceutically acceptable excipient or carrier such as sodium
citrate or dicalcium phosphate and/or a) fillers or extenders such
as starches, lactose, sucrose, glucose, mannitol, and silicic acid,
b) binders such as, for example, carboxymethylcerulose, alginates,
gelatin, polyvinylpyrrolidone, sucrose, and acacia, c) humectants
such as glycerol, d) disintegrating agents such as agar-agar,
calcium carbonate, potato or tapioca starch, alginic acid, certain
silicates, and sodium carbonate, e) solution retarding agents such
as paraffin, f)absorption accelerators such as quaternary ammonium
compounds, g) wetting agents such as, for example, cetyl alcohol
and glycerol monostearate, h)absorbents such as kaolin and
bentonite clay, and I) lubricants such as talc, calcium stearate,
magnesium stearate, solid polyethylene glycols, sodium lauryl
sulfate, and mixtures thereof. In the case of capsules, tablets and
pills, the dosage form may also comprise buffering agents.
[0144] Solid compositions of a similar type may also be employed as
fillers in soft and hard filled gelatin capsules using such
excipients as lactose or milk sugar as well as high molecular
weight polyethylene glycols and the like.
[0145] The solid dosage forms of tablets, dragees, capsules, pills,
and granules can be prepared with coatings and shells such as
enteric coatings and other coatings well known in the
pharmaceutical formulating art. They may optionally contain
opacifying agents and can also be of a composition that they
release the active ingredient(s) only, or preferentially, in a
certain part of the intestinal tract, optionally, in a delayed
manner. Examples of embedding compositions which can be used
include polymeric substances and waxes.
[0146] The active compounds can also be in micro-encapsulated form,
if appropriate, with one or more of the above-mentioned
excipients.
[0147] Liquid dosage forms for oral administration include
pharmaceutically acceptable emulsions, solutions, suspensions,
syrups and elixirs. In addition to the active compounds, the liquid
dosage forms may contain inert diluents commonly used in the art
such as, for example, water or other solvents, solubilizing agents
and emulsifiers such as ethyl alcohol, isoptopyl alcohol, ethyl
carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate,
propylene glycol, 1,3-butylene glycol, dimethyl formamide, oils (in
particular, cottonseed, groundnut, corn, germ, olive, castor, and
sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene
glycols and fatty acid esters of sorbitan, and mixtures
thereof.
[0148] Besides inert diluents, the oral compositions can also
include adjuvants such as wetting agents, emulsifying and
suspending agents, sweetening, flavoring, and perfuming agents.
[0149] Suspensions, in addition to the active compounds, may
contain suspending agents as, for example, ethoxylated isostearyl
alcohols, polyoxyethylene sorbitol and sorbitan esters,
microcrystalline cellulose, aluminum metahydroxide, bentonite,
agar-agar, and tragacanth, and mixtures thereof.
[0150] The active polypeptide can also be administered in the form
of liposomes. As is known in the art, liposomes are generally
derived from phospholipids or other lipid substances. Liposomes are
formed by mono- or multi-lamellar hydrated liquid crystals that are
dispersed in an aqueous medium. Any non-toxic, physiologically
acceptable and metabolizable lipid capable of forming liposomes can
be used. The present compositions in liposome form can contain, in
addition to the agent or inhibitor, stabilizers, preservatives,
excipients, and the like. The preferred lipids are the
phospholipids and the phosphatidyl cholates (lecithins), both
natural and synthetic. Methods to form liposomes are known in the
art. See, for example, Prescott, Ed., Methods in Cell Biology,
Volume XIV, Academic Press, New York, N.Y. (1976), p. 33 et
seq.
[0151] Having generally described the invention, the same will be
more readily understood by reference to the following examples,
which are provided by way of illustration and are not intended as
limiting.
EXAMPLES
Example 1
Expression and Purification of CK.beta.-15 in E. coli
[0152] The DNA sequence encoding the mature CK.beta.-15 protein in
the deposited cDNA clone was amplified using PCR oligonucleotide
primers specific to the amino terminal sequences of the CK.beta.-15
protein and to vector sequences 3' to the gene. Additional
nucleotides containing restriction sites to facilitate cloning were
added to the 5' and 3' sequences respectively.
[0153] The 5' oligonucleotide primer had the sequence 5' GCC GTC
GAC GTC CAC ACC CAA GGT GTC 3' (SEQ ID NO:4) containing the
underlined SalI restriction site, which encodes 18 nucleotides of
the CK.beta.-15 protein coding sequence in FIGS. 1A-C (SEQ ID NO:1)
beginning immediately after the signal peptide.
[0154] The 3' primer had the sequence 5' GCC TCT AGA GGA GCC CAG
AAA TGA GCC GGC 3' [SEQ ID NO:5] containing the underlined XbaI
restriction site followed by 21 nucleotides complementary to the
last 21 nucleotides immediately after the CK.beta.-15 protein
coding sequence in FIGS. 1A-C.
[0155] The restriction sites were convenient to restriction enzyme
sites in the bacterial expression vector pD10 (pQE9), which were
used for bacterial expression in these examples. (Qiagen, Inc. 9259
Eton Avenue, Chatsworth, Calif., 91311). [pD10]pQE9 encodes
ampicillin antibiotic resistance ("Amp.sup.r") and contains a
bacterial origin of replication ("ori"), an IPTG inducible
promoter, a ribosome binding site ("RBS"), a 6-His tag and
restriction enzyme sites.
[0156] The amplified CK.beta.-15 protein DNA and the vector pQE9
both were digested with SalI and XbaI and the digested DNAs were
then ligated together. Insertion of the CK.beta.-15 protein DNA
into the restricted pQE9 vector placed the CK.beta.-15 protein
coding region downstream of and operably linked to the vector's
IPTG-inducible promoter and in-frame with an initiating AUG
appropriately positioned for translation of CK.beta.-15
protein.
[0157] The ligation mixture was transformed into competent E. coli
cells using standard procedures. Such procedures are described in
Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed.;
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
(1989). E. coli strain M15/rep4, containing multiple copies of the
plasmid pREP4, which expresses lac repressor and confers kanamycin
resistance ("Kan.sup.r"), was used in carrying out the illustrative
example described here. This strain, which is only one of many that
are suitable for expressing CK.beta.-15 protein, is available
commercially from Qiagen.
[0158] Transformants were identified by their ability to grow on LB
plates in the presence of ampicillin and kanamycin. Plasmid DNA was
isolated from resistant colonies and the identity of the cloned DNA
was confirmed by restriction analysis.
[0159] Clones containing the desired constructs were grown
overnight ("O/N") in liquid culture in LB media supplemented with
both ampicillin (100 .mu.g/ml) and kanamycin (25 .mu.g/ml).
[0160] The O/N culture is used to inoculate a large culture, at a
dilution of approximately 1:100 to 1:250. The cells are grown to an
optical density at 600 nm ("OD600") of between 0.4 and 0.6.
Isopropyl-B-D-thiogalactopyranoside ("IPTG") is then added to a
final concentration of 1 mM to induce transcription from lac
repressor sensitive promoters, by inactivating the lacI repressor.
Cells subsequently are incubated further for 3 to 4 hours. Cells
then are harvested by centrifugation and disrupted, by standard
methods. Inclusion bodies are purified from the disrupted cells
using routine collection techniques, and protein is solubilized
from the inclusion bodies into 8M urea. The 8M urea solution
containing the solubilized protein is passed over a PD-10 column in
2.times. phosphate-buffered saline ("PBS"), thereby removing the
urea, exchanging the buffer and refolding the protein. The protein
is purified by a further step of chromatography to remove
endotoxin. Then, it is sterile filtered. The sterile filtered
protein preparation is stored in 2.times. PBS at a concentration of
95 .mu./ml.
[0161] Analysis of the preparation by standard methods of
polyacrylamide gel electrophoresis reveals that the preparation
contains about 95% monomer CK.beta.-15 protein having the expected
molecular weight of approximately 16.7 kDa.
Example 2
Cloning and Expression of CK.beta.-15 Protein in a Baculovirus
Expression System
[0162] The cDNA sequence encoding the full length CK.beta.-15
protein in the deposited clone is amplified using PCR
oligonucleotide primers corresponding to the 5' and 3' sequences of
the gene:
[0163] The 5' primer has the sequence 5' GCC TCT AGA GCC ATC ATG
AAC CTG TGG CTC CTG GCC 3' (SEQ ID NO:6) containing the underlined
XbaI restriction enzyme site followed by 21 bases of the sequence
of CK.beta.-15 protein in FIGS. 1A-C. Inserted into an expression
vector, as described below, the 5' end of the amplified fragment
encoding CK.beta.-15 provides an efficient signal peptide. An
efficient signal for initiation of translation in eukaryotic cells,
as described by Kozak, M., J. Mol. Biol. 196: 947-950 (1987) is
appropriately located in the vector portion of the construct.
[0164] The 3' primer has the sequence 5' GCC TCT AGA GGA GCC CAG
AAA TGA CCC GGC 3' (SEQ ID NO:7) containing the underlined XbaI
restriction site followed by nucleotides complementary to the last
21 nucleotides of the CK[-15 coding sequence set out in FIGS.
1A-C.
[0165] The amplified fragment is isolated from a 1% agarose gel
using a commercially available kit ("Geneclean," BIO 101 Inc., La
Jolla, Calif.). The fragment then is digested with XbaI and again
is purified on a 1% agaroae gel. This fragment is designated herein
F2.
[0166] The vector pA2 is used to express the CK.beta.-15 protein in
the baculovirus expression system, using standard methods, as
described in Summers et al, A MANUAL OF METHODS FOR BACULOVIRUS
VECTORS AND INSECT CELL CULTURE PROCEDURES, Texas Agricultural
Experimental Station Bulletin No. 1555 (1987). This expression
vector contains the strong polyhedrin promoter of the Autographa
californica nuclear polyhedrosis virus (AcMNPV) followed by
convenient restriction sites such as BamHI and Asp718. The
polyadenylation site of the simian virus 40 ("SV40") is used for
efficient polyadenylation. For easy selection of recombinant virus,
the plasmid contains the beta-galactosidase gene from E. coli under
control of a weak Drosophila promoter in the same orientation,
followed by the polyadenylation signal of the polyhedrin gene. The
inserted genes are flanked on both sides by viral sequences for
cell-mediated homologous recombination with wild-type viral DNA to
generate viable virus that express the cloned polynucleotide.
[0167] Many other baculovirus vectors could be used in place of
pA2, such as pAc373, pVL941 and pAcIM1 provided, as those of skill
readily will appreciate, that construction provides appropriately
located signals for transcription, translation, trafficking and the
like, such as an in-frame AUG and a signal peptide, as required.
Such vectors are described in Luckow et al., Virology 170:31-39,
among others.
[0168] The plasmid is digested with the restriction enzyme XbaI and
then is dephosphorylated using calf intestinal phosphatase, using
routine procedures known in the art. The DNA is then isolated from
a 1% agarose gel using a commercially available kit ("Geneclean"
BIO 101 Inc., La Jolla, Calif.). This vector DNA is designated
herein "V2".
[0169] Fragment F2 and the dephosphorylated plasmid V2 are ligated
together with T4 DNA ligase. E. coli BB 101 cells are transformed
with ligation mix and spread on culture plates. Bacteria are
identified that contain the plasmid with the human CK.beta.-15 gene
by digesting DNA from individual colonies using XbaI and then
analyzing the digestion product by gel electrophoresis. The
sequence of the cloned fragment is confirmed by DNA sequencing.
This plasmid is designated herein pBacCK.beta.-15.
[0170] 5 .mu.g of the plasmid pBacCK.beta.-15 is co-transfected
with 1.0 .mu.g of a commercially available linearized baculovirus
DNA ("BaculoGold.TM. baculovirus DNA", Pharmingen, San Diego,
Calif.), using the lipofection method described by Felgner et al.,
Proc. Natl. Acad. Sci. USA 84: 7413-7417 (1987). 1 .mu.g of
BaculoGold.TM. virus DNA and 5 .mu.g of the plasmid pBacCK.beta.-15
are mixed in a sterile well of a microtiter plate containing 50
.mu.l of serum-free Grace's medium (Life Technologies Inc.,
Gaithersburg, Md.). Afterwards 10 .mu.l Lipofectin plus 90 .mu.l
Grace's medium are added, mixed and incubated for 15 minutes at
room temperature. Then the transfection mixture is added drop-wise
to Sf9 insect cells (ATCC.TM. CRL 1711) seeded in a 35 mm tissue
culture plate with 1 ml Grace's medium without serum. The plate is
rocked back and forth to mix the newly added solution. The plate is
then incubated for 5 hours at 27.degree. C. After 5 hours the
transfection solution is removed from the plate and 1 ml of Grace's
insect medium supplemented with 10% fetal calf serum is added. The
plate is put back into an incubator and cultivation is continued at
27.degree. C. for four days.
[0171] After four days the supernatant is collected and a plaque
assay is performed, as described by Summers and Smith, cited above.
An agarose gel with "Blue Gal" (Life Technologies Inc.,
Gaithersburg) is used to allow easy identification and isolation of
gal-expressing clones, which produce blue-stained plaques. (A
detailed description of a "plaque assay" of this type can also be
found in the user's guide for insect cell culture and
baculovirology distributed by Life Technologies Inc., Gaithersburg,
page 9-10).
[0172] Four days after serial dilution, the virus is added to the
cells. After appropriate incubation, blue stained plaques are
picked with the tip of an Eppendorf pipette. The agar containing
the recombinant viruses is then resuspended in an Eppendorf tube
containing 200 .mu.l of Grace's medium. The agar is removed by a
brief centrifugation and the supernatant containing the recombinant
baculovirus is used to infect Sf9 cells seeded in 35 mm dishes.
Four days later the supernatants of these culture dishes are
harvested and then they are stored at 4.degree. C. A clone
containing properly inserted hESSB I, II and III is identified by
DNA analysis including restriction mapping and sequencing. This is
designated herein as V-CK.beta.-15.
[0173] Sf9 cells are grown in Grace's medium supplemented with 10%
heat-inactivated FBS. The cells are infected with the recombinant
baculovirus V-CK.beta.-15 at a multiplicity of infection ("MOI") of
about 2 (about 1 to about 3). Six hours later the medium is removed
and is replaced with SF900 II medium minus methionine and cysteine
(available from Life Technologies Inc., Gaithersburg). 42 hours
later, 5 .mu.Ci of .sup.35S-methionine and 5 .mu.Ci
.sup.35S-cysteine (available from Amersham) are added. The cells
are further incubated for 16 hours and then they are harvested by
centrifugation, lysed and the labeled proteins are visualized by
SDS-PAGE and autoradiography.
Example 3
Expression in Mammalian Cells (COS)
[0174] The expression plasmid, pCK.beta.-15 HA, is made by cloning
a cDNA encoding CK.beta.-15 into the expression vector pcDNAI/Amp
(which can be obtained from Invitrogen, Inc.).
[0175] The expression vector pcDNAI/amp contains: (1) an E. coli
origin of replication effective for propagation in E. coli and
other prokaryotic cells; (2) an ampicillin resistance gene for
selection of plasmid-containing prokaryotic cells; (3) an SV40
origin of replication for propagation in eukaryotic cells; (4) a
CMV promoter, a polylinker, an SV40 intron, and a polyadenylation
signal arranged so that a cDNA conveniently can be placed under
expression control of the CMV promoter and operably linked to the
SV40 intron and the polyadenylation signal by means of restriction
sites in the polylinker.
[0176] A DNA fragment encoding the entire CK.beta.-15 precursor and
an HA tag fused in frame to its 3' end is cloned into the
polylinker region of the vector so that recombinant protein
expression is directed by the CMV promoter. The HA tag corresponds
to an epitope derived from the influenza hemagglutinin protein
described by Wilson et al., Cell 37: 767 (1984). The fusion of the
HA tag to the target protein allows easy detection of the
recombinant protein with an antibody that recognizes the HA
epitope.
[0177] The plasmid construction strategy is as follows.
[0178] The CK.beta.-15 cDNA of the deposited clone is amplified
using primers that contain convenient restriction sites, much as
described above regarding the construction of expression vectors
for expression of CK.beta.-15 in E. coli. To facilitate detection,
purification and characterization of the expressed CK.beta.-15, one
of the primers contains a hemagglutinin tag ("HA tag") as described
above.
[0179] Suitable primers include that following, which are used in
this example. The 5' primer, containing the underlined HindIII
site, an AUG start codon and 6 codons of the 5' coding region has
the following sequence: 5' GCG AAG CTT ATG AAC CTG TGG CTC CTG GCC
3' [SEQ ID NO:8].
[0180] The 3' primer, containing the underlined XhoI site, a stop
codon, 9 codons thereafter forming the hemagglutinin HA tag, and 22
bp of 3' coding sequence (at the 3' end) has the following
sequence: 5' GCG CTC GAG TCA AGC GTA GTC TGG GAC GTC GTA TGG GTA
CAG TCC TGA ATT AGC TGA TAT C 3' [SEQ ID NO:9].
[0181] The PCR amplified DNA fragment and the vector, pcDNAI/Amp,
are digested with HindIII and XhoI and then ligated. The ligation
mixture is transformed into E. coli strain SURE (available from
Stratagene Cloning Systems, 11099 North Torrey Pines Road, La
Jolla, Calif. 92037) the transformed culture is plated on
ampicillin media plates which then are incubated to allow growth of
ampicillin resistant colonies. Plasmid DNA is isolated from
resistant colonies and examined by restriction analysis and gel
sizing for the presence of the CB.beta.-15-encoding fragment.
[0182] For expression of recombinant CK.beta.-15, COS cells are
transfected with an expression vector, as described above, using
DEAE-DEXTRAN, as described, for instance, in Sambrook et al.,
MOLECULAR CLONING: A LABORATORY MANUAL, Cold Spring Laboratory
Press, Cold Spring Harbor, N.Y. (1989). Cells are incubated under
conditions for expression of CK.beta.-15 by the vector.
[0183] Expression of the CK.beta.-15 HA fusion protein is detected
by radiolabelling and immunoprecipitation, using methods described
in, for example Harlow et al., ANTIBODIES: A LABORATORY MANUAL, 2nd
Ed.; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
(1988). To this end, two days after transfection, the cells are
labeled by incubation in media containing .sup.35S-cysteine for 8
hours. The cells and the media are collected, and the cells are
washed and the lysed with detergent-containing RIPA buffer: 150 mM
NaCl, 1% NP-40, 0.1% SDS, 1% NP-40, 0.5% DOC, 50 mM TRIS, pH 7.5,
as described by Wilson et al. cited above. Proteins are
precipitated from the cell lysate and from the culture media using
an HA-specific monoclonal antibody. The precipitated proteins then
are analyzed by SDS-PAGE gels and autoradiography. An expression
product of the expected size is seen in the cell lysate, which is
not seen in negative controls.
Example 4
Tissue Distribution of CK.beta.-15 Protein Expression
[0184] Northern blot analysis was carried out to examine the levels
of expression of CK.beta.-15 protein in human tissues, using
methods described by, among others, Sambrook et al, cited above.
PolyA.sup.+ was purchased from Clontech (1020 East Meadow Circle,
Palo Alto, Calif. 94303).
[0185] About 1 .mu.g of PolyA.sup.+ RNA was size resolved by
electrophoresis through a 1% agarose gel under strongly denaturing
conditions. RNA was blotted from the gel onto a nylon filter, and
the filter then was prepared for hybridization to a detectably
labeled polynucleotide probe.
[0186] As a probe to detect mRNA that encodes CK.beta.-15 protein,
the antisense strand of the coding region of the cDNA insert in the
deposited clone was labeled to a high specific activity. The cDNA
was labeled by primer extension, using the Prime-It kit, available
from Stratagene. The reaction was carried out using 50 ng of the
cDNA, following the standard reaction protocol as recommended by
the supplier. The labeled polynucleotide was purified away from
other labeled reaction components by column chromatography using a
Select-G-50 column, obtained from 5-Prime -3-Prime, Inc. of 5603
Arapahoe Road, Boulder, Colo. 80303.
[0187] The labeled probe was hybridized to the filter, at a
concentration of 1,000,000 cpm/ml, as described in Kreider et al.,
Molecular and Cellular Biology, September 1990, pp. 4846-4853.
Thereafter the probe solution was drained and the filter was washed
twice at room temperature and twice at 65.degree. C. with
0.1.times.SSC, 0.1% SDS. The filter then was then dried and exposed
to film at -70.degree. C. overnight with an intensifying screen.
The results of a typical Nothern blot using the CK.beta.-15 cDNA
probe are shown in FIG. 3.
Example 5
Gene Therapeutic Expression of Human CK.beta.-15 Protein
[0188] Fibroblasts are obtained from a subject by skin biopsy. The
resulting tissue is placed in tissue-culture medium and separated
into small pieces. Small chunks of the tissue are placed on a wet
surface of a tissue culture flask, approximately ten pieces are
placed in each flask. The flask is turned upside down, closed tight
and left at room temperature overnight. After 24 hours at room
temperature, the flask is inverted--the chunks of tissue remain
fixed to the bottom of the flask--and fresh media is added (e.g.,
Ham's F12 media, with 10% FBS, penicillin and streptomycin). The
tissue is then incubated at 37.degree. C. for approximately one
week. At this time, fresh media is added and subsequently changed
every several days. After an additional two weeks in culture, a
monolayer of fibroblasts emerges. The monolayer is trypsinized and
scaled into larger flasks.
[0189] A vector for gene therapy is digested with restriction
enzymes for cloning a portion to be expressed. The digested vector
is treated with calf intestinal phosphatase to prevent
self-ligation. The dephosphorylated, linear vector is fractionated
on an agarose gel and purified.
[0190] CK.beta.-15 protein cDNA capable of expressing active
CK.beta.-15 protein, is isolated. The ends of the portion are
modified, if necessary, for cloning into the vector. For instance,
5'overhanging may be treated with DNA polymerase to create blunt
ends. 3' overhanging ends may be removed using S1 nuclease. Linkers
may be ligated to blunt ends with T4 DNA ligase.
[0191] Equal quantities of the Moloney murine leukemia virus linear
backbone and the CK.beta.-15 protein portion are mixed together and
joined using T4 DNA ligase. The ligation mixture is used to
transform E. coli and the bacteria are then plated onto
agar-containing kanamycin. Kanamycin phenotype and restriction
analysis confirm that the vector has the properly inserted
gene.
[0192] Packaging cells are grown in tissue culture to confluent
density in Dulbecco's Modified Eagles Medium (DMEM) with 10% calf
serum (CS), penicillin and streptomycin. The vector containing the
CK.beta.-15 protein gene is introduced into the packaging cells by
standard techniques. Infectious viral particles containing the
CK.beta.-15 protein gene are collected from the packaging cells,
which now are called producer cells.
[0193] Fresh media is added to the producer cells, and after an
appropriate incubation period media is harvested from the plates of
confluent producer cells. The media, containing the infectious
viral particles, is filtered through a Millipore filter to remove
detached producer cells. The filtered media then is used to infect
fibroblast cells. Media is removed from a sub-confluent plate of
fibroblasts and quickly replaced with the filtered media. Polybrene
(Aldrich) may be included in the media to facilitate transduction.
After appropriate incubation, the media is removed and replaced
with fresh media. If the titer of virus is high, then virtually all
fibroblasts will be infected and no selection is required. If the
titer is low, then it is necessary to use a retroviral vector that
has a selectable marker, such as neo or his, to select out
transduced cells for expansion.
[0194] Transformed fibroblasts then may be injected into rats,
either alone or after having been grown to confluence on
microcarrier beads, such as cytodex 3 beads. The injected
fibroblasts produce CK.beta.-15 protein product, and the biological
actions of the protein are conveyed to the host.
[0195] It will be clear that the invention may be practiced
otherwise than as particularly described in the foregoing
description and examples.
[0196] Numerous modifications and variations of the present
invention are possible in light of the above teachings and,
therefore, are within the scope of the appended claims.
[0197] The disclosures of all patents, patent applications, and
publications referred to herein are hereby incorporated by
reference.
Sequence CWU 1
1
* * * * *