U.S. patent application number 10/025167 was filed with the patent office on 2002-09-12 for reagents and methods useful for detecting diseases of the gastrointestinal tract.
Invention is credited to Billing-Medel, Patricia A., Cohen, Maurice, Colpitts, Tracey L., Friedman, Paula N., Hayden, Mark A., Klass, Michael R., Roberts-Rapp, Lisa, Russell, John C., Stroupe, Stephen D..
Application Number | 20020127693 10/025167 |
Document ID | / |
Family ID | 26727445 |
Filed Date | 2002-09-12 |
United States Patent
Application |
20020127693 |
Kind Code |
A1 |
Billing-Medel, Patricia A. ;
et al. |
September 12, 2002 |
Reagents and methods useful for detecting diseases of the
gastrointestinal tract
Abstract
A set of contiguous and partially overlapping cDNA sequences and
polypeptides encoded thereby, designated as CS193 and transcribed
from GI tract tissue, are described. These sequences are useful for
the detecting, diagnosing, staging, monitoring, prognosticating,
preventing or treating, or determining the predisposition of an
individual to diseases and conditions of the GI tract, such as GI
tract cancer. Also provided are antibodies which specifically bind
to CS193-encoded polypeptide or protein, and agonists or inhibitors
which prevent action of the tissue-specific CS193 polypeptide,
which molecules are useful for the therapeutic treatment of GI
tract diseases, tumors or metastases.
Inventors: |
Billing-Medel, Patricia A.;
(Grayslake, IL) ; Cohen, Maurice; (Highland Park,
IL) ; Colpitts, Tracey L.; (Round Lake, IL) ;
Friedman, Paula N.; (Deerfield, IL) ; Hayden, Mark
A.; (Ingleside, IL) ; Klass, Michael R.;
(Libertyville, IL) ; Roberts-Rapp, Lisa; (Gurnee,
IL) ; Russell, John C.; (Pleasant Prairie, WI)
; Stroupe, Stephen D.; (Libertyville, IL) |
Correspondence
Address: |
ABBOTT LABORATORIES
DEPT. 377 - AP6D-2
100 ABBOTT PARK ROAD
ABBOTT PARK
IL
60064-6050
US
|
Family ID: |
26727445 |
Appl. No.: |
10/025167 |
Filed: |
December 19, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10025167 |
Dec 19, 2001 |
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09049698 |
Mar 27, 1998 |
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6368792 |
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09049698 |
Mar 27, 1998 |
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08828856 |
Mar 31, 1997 |
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Current U.S.
Class: |
435/226 ;
435/320.1; 435/325; 435/6.16; 435/69.1; 536/23.2 |
Current CPC
Class: |
C12Q 2600/136 20130101;
C07K 2317/34 20130101; C12Q 2600/106 20130101; C07K 16/3046
20130101; C12Q 1/6886 20130101 |
Class at
Publication: |
435/226 ;
435/69.1; 435/325; 435/320.1; 536/23.2; 435/6 |
International
Class: |
C12Q 001/68; C07H
021/04; C12N 009/64; C12P 021/02; C12N 005/06 |
Claims
We claim:
1. A purified polynucleotide or fragment thereof derived from a
CS193 gene, wherein said polynucleotide is capable of selectively
hybridizing to the nucleic acid of said CS193 gene and has at least
50% identity to a sequence selected from the group consisting of
SEQUENCE ID NOS 1-18, and fragments or complements thereof.
2. The purified polynucleotide of claim 1, wherein said
polynucleotide is produced by recombinant techniques.
3. The purified polynucleotide of claim 1, wherein said
polynucleotide is produced by synthetic techniques.
4. The purified polynucleotide of claim 1, wherein said
polynucleotide comprises a sequence encoding at least one CS193
epitope.
5. A recombinant expression system comprising a nucleic acid
sequence that includes an open reading frame derived from CS193
operably linked to a control sequence compatible with a desired
host, wherein said nucleic acid sequence has at least 50% identity
to a sequence selected from the group consisting of SEQUENCE ID NOS
1-18 and fragments or complements thereof.
6. A cell transfected with the recombinant expression system of
claim 5.
7. A CS193 polypeptide having at least 60% identity with an amino
acid sequence selected from the group consisting of SEQUENCE ID NOS
41-49, and fragments thereof.
8. The polypeptide of claim 7, wherein said polypeptide is produced
by recombinant techniques.
9. The polypeptide of claim 7, wherein said polypeptide is produced
by synthetic techniques.
10. An antibody which specifically binds to at least one CS193
epitope, wherein said CS193 epitope is derived from an amino acid
sequence having at least 50% identity to an amino acid sequence
selected from the group consisting of SEQUENCE ID NOS 41-49, and
fragments thereof.
11. A cell transfected with a nucleic acid sequence encoding at
least one CS193 epitope, wherein said nucleic acid sequence is
selected from the group consisting of SEQUENCE ID NOS 1-18, and
fragments or complements thereof.
12. A method for producing a polypeptide comprising at least one
CS193 epitope, said method comprising incubating host cells that
have been transfected with an expression vector containing a
polynucleotide sequence encoding a polypeptide, wherein said
polypeptide comprises an amino acid sequence having at least 60%
identity with an amino acid sequence selected from the group
consisting of SEQUENCE ID NOS 41-49, and fragments thereof.
13. A method for producing antibodies which specifically bind to
CS193 antigen, said method comprising administering to an
individual an isolated immunogenic polypeptide or fragment thereof
in an amount sufficient to elicit in immune response, wherein said
immunogenic polypeptide comprises at least one CS193 epitope and
has at least 50% identity with a sequence selected from the group
consisting of SEQUENCE ID NOS 41-49, and fragments thereof.
14. A method for producing antibodies which specifically bind to
CS193 antigen, said method comprising administering to an
individual a plasmid comprising a polynucleotide sequence which
encodes at least one CS193 epitope derived from a polypeptide
having an amino acid sequence selected from the group consisting of
SEQUENCE ID NOS 41-49, and fragments thereof.
15. A composition of matter comprising a CS193 polynucleotide or
fragment thereof, wherein said polynucleotide has at least 50%
identity with a polynucleotide selected from the group consisting
of SEQUENCE ID NOS 1-18, and fragments or complements thereof.
16. A composition of matter comprising a polypeptide containing at
least one CS193 epitope, wherein said polypeptide has at least 60%
identity with a sequence selected from the group consisting of
SEQUENCE ID NOS 41-49, and fragments thereof.
17. A gene, or a fragment thereof, which codes for a CS193 protein
comprising an amino acid sequence that has at least 60% identity
with SEQUENCE ID NO 41.
18. A gene or fragment thereof comprising DNA having at least 50%
identity with SEQUENCE ID NO 16, SEQUENCE ID NO 17, or SEQUENCE ID
NO 18.
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application is a continuation-in-part of U.S.
application Ser. No. 08/828,856, filed Mar. 31, 1997, from which
priority is claimed pursuant to 35 U.S.C. .sctn.120 and which is
incorporated herein by reference in its entirety.
BACKGROUND OF THE INVENTION
[0002] The invention relates generally to detecting diseases of the
gastrointestinal tract organs, and more particularly, relates to
reagents such as polynucleotide sequences and the polypeptide
sequences encoded thereby, as well as methods which utilize these
sequences, which are useful for detecting, diagnosing, staging,
monitoring, prognosticating, preventing or treating, or determining
predisposition to diseases and conditions of the GI tract such as
cancer.
[0003] The organs of the GI tract include the esophagus, stomach,
small and large intestines, rectum and pancreas. Of the
approximately 225,900 new cases of GI tract cancer projected for
the United States during 1996, 131,200 will be due to colorectal
cancer. Further, GI tract cancers will account for approximately
127,070 related deaths (American Cancer Society statistics). In
addition to its high incidence, GI tract cancers can be extremely
lethal; for example, greater than 97% of pancreatic cancer patients
will die of the disease. H. J. Wanebo, et al., Cancer 78:580-91
(1996).
[0004] Generally, the early detection of GI tract cancers at a
pre-invasive stage dramatically reduces disease-related mortality.
However, only few GI tract cancers are detected at this stage. For
example, only 37% of colorectal cancers are detected at this stage
by screening for premalignant polyps which can be removed before
they progress to cancer. The primary methods used for colorectal
cancer screening are fecal occult blood testing (FOBT) and flexible
sigmoidoscopy. A. M. Cohen et al. In: Cancer: Principles and
Practice of Oncology, Fourth Edition, pp. 929-977, Philadelphia,
Pa.: J/B. Lippincott Co. (1993). Although FOBT is noninvasive,
simple and inexpensive, its sensitivity is low; for example,
sensitivity for detecting colorectal cancer was only 26% in one
study. D. A. Ahlquist et al., JAMA 269: 1262-1267 (1993). Further,
although flexible sigmoidoscopy is highly sensitive for detecting
early cancer and precursor polyps, it is invasive, costly, and too
technically demanding to be used for routine screening. D. F.
Ransohoff, et al., JAMA 269: 1278-1281 (1993). In addition, only
eight percent (8%) of pancreatic cancers and eighteen percent (18%)
of stomach cancers are detected at a pre-invasive stage (American
Cancer Society statistics). Thus, the need exists for improved
screening methods for detection of GI tract diseases such as
cancer.
[0005] The standard procedures currently used for establishing a
definitive diagnosis for a GI tract cancer include barium studies,
endoscopy, biopsy and computed tomography (CT). These procedures
are invasive and costly. Moreover, an erroneous diagnosis can
result from any of these procedures due to technical reasons, the
subjective interpretation of results, or lack of sensitivity of the
procedure. M. F. Brennan, et al. In: Cancer: Principles and
Practice of Oncology, Fourth Edition, pp. 849-882, Philadelphia,
Pa.: J.B. Lippincott Co. (1993).
[0006] After the diagnosis of a particular GI tract cancer is
confirmed, staging is performed to determine the anatomic extent of
the disease. Staging is performed by a pathologist on tissue
obtained by biopsy and/or surgery. Accurate staging is critical for
predicting patient outcome and providing criteria for designing
optimal therapy. Inaccurate staging can result in poor therapeutic
decisions and is a major clinical problem in colorectal cancer. A
need therefore exists for more sensitive diagnostic procedures for
staging GI tract cancers.
[0007] While surgical resection of the affected organ is typical
therapy for a majority of patients diagnosed with GI tract cancers,
some patients undergo radiation and/or chemotherapy. All of these
patients need to be monitored in order to evaluate their response
to therapy and to detect persistent or recurrent disease and
distant metastasis. A variety of markers including CEA and CA 19-9
can be assayed and the assay results used to monitor a patient's
progress in conjunction with radiological procedures and
colonoscopy. E. L. Jacobs, Curr. Probl. Cancer 15 (6):299-350
(1991). These monitoring techniques, however, have failed to
provide an accurate and effective means to monitor the progress of
these patients.
[0008] Assays based upon the appearance of various disease markers
in test samples such as blood, plasma or serum obtained by
minimally invasive techniques, could provide low-cost and accurate
information to aid the physician in diagnosing disease such as
cancer, in selecting a therapy protocol, and in monitoring the
success of the chosen therapy. Such markers have been placed into
several categories. The first category contains those markers which
are elevated in disease. Examples include human chorionic
gonadotropin (hCG) which is elevated in testicular cancer and
trophoblastic disease, and alpha fetoprotein (AFP) which is
elevated in hepato-cellular carcinoma (HCC). E. L. Jacobs, supra.
The second category includes qualitatively altered mRNA or protein
markers in disease. Examples include mRNA splice variants of CD 44
in bladder cancer and mutations in p53 protein in lung and
colorectal cancer. Y. Matsumura et al. Journal of Pathology
175(Suppl): 108A (1995); W. P. Bennett, Cancer Detection and
Prevention 19 (6): 503-511 (1995). The third category includes
those protein markers which are normally expressed in a specific
tissue, organ or organ system but which appear in an inappropriate
body compartment. For example, prostate specific antigen (PSA) is a
normal protein which is secreted at high levels into the seminal
fluid. PSA is present in very low levels in the blood of men with
normal prostates but markedly elevated in the blood of patients
with diseases of the prostate, including benign prostatic
hyperplasia (BPH) and adenocarcinoma of the prostate. At high
levels in the blood, PSA is a strong indicator of prostate disease.
P. H. Lange et al., Urology 33 (6 Suppl): 13 (1989). Similarly,
carcinoembryonic antigen (CEA) is a normal component of the inner
lining of the colon which is present in blood at low levels in
people without colon disease. E. L. Jacobs, supra. However, the CEA
concentration is markedly elevated in the blood, plasma or serum of
many patients diagnosed with colon disease including inflammatory
bowel disease and adeno-carcinoma of the colon, and is used as an
indicator of colorectal disease.
[0009] There are yet other examples of detecting disease markers in
an inappropriate bodily compartment. In the case of metastatic
cancer, the blood, bone marrow or lymph nodes may contain cells
which have originated from the primary tumor and which may express
mRNA or protein markers representative of the primary tumor. For
example, CEA and PSA have been demonstrated immunohistochemically
in lymph nodes or bone marrow of patients with metastatic
colorectal cancer and prostate cancer, respectively. B. R.
Davidson, et al., Cancer 65:967-970 (1990); J. L. Mansi, et al., J.
Urol., 139:545-548 (1988). In addition, RT-PCR has detected CEA and
PSA mRNAs at distant sites in patients with colon and prostate
cancer, suggesting the presence of metastatic cells. M. Gerhard, et
al., J. Clin. Oncol. 12:725-729 (1994); A. E. Katz, et al., Urology
43:765-775 (1994). Other compartments in which the inappropriate
appearance of normal gene products may be indicative of disease
include but are not limited to, whole blood, urine, saliva, and
stool. Currently, no universally acceptable marker(s) exist(s) for
the early detection of pancreatic, stomach, and esophageal cancers.
Further, improved markers are needed to detect colorectal
cancer.
[0010] It therefore would be advantageous to provide specific
methods and reagents for detecting, diagnosing, staging,
monitoring, prognosticating, preventing or treating, or determining
predisposition to diseases and conditions associated with the GI
tract or to indicate possible predisposition to these conditions.
Such methods would include assaying a test sample for products of a
gene which are overexpressed in GI tract diseases and conditions
such as cancer. Such methods may also include assaying a test
sample for products of a gene alteration associated with the GI
tract disease or condition. Such methods may further include
assaying a test sample for products of a gene whose distribution
among the various tissues and compartments of the body have been
altered by a GI tract-associated disease or condition such as
cancer. Useful reagents include polynucleotide(s), or fragment(s)
thereof which may be used in diagnostic methods such as reverse
transcriptase-polymerase chain reaction (RT-PCR), PCR, or
hybridization assays of mRNA extracted from biopsied tissue, blood
or other test samples; polypeptides or proteins which are the
translation products of such mRNAs; or antibodies directed against
these proteins. Drug treatment or gene therapy for diseases or
conditions of the GI tract then can be based on these identified
gene sequences or their expressed proteins, and efficacy of any
particular therapy can be monitored. Furthermore, it would be
advantageous to have available alternative, non-surgical diagnostic
methods capable of detecting early stage GI tract disease such as
cancer.
SUMMARY OF THE INVENTION
[0011] The present invention provides a method of detecting a
target CS193 polynucleotide in a test sample which comprises
contacting the test sample with at least one CS193-specific
polynucleotide and detecting the presence of the target CS193
polynucleotide in the test sample. The CS193-specific
polynucleotide has at least 50% identity with a polynucleotide
selected from the group consisting of SEQUENCE ID NO 1, SEQUENCE ID
NO 2, SEQUENCE ID NO 3, SEQUENCE ID NO 4, SEQUENCE ID NO 5,
SEQUENCE ID NO 6, SEQUENCE ID NO 7, SEQUENCE ID NO 8, SEQUENCE ID
NO 9, SEQUENCE ID NO 10, SEQUENCE ID NO 11, SEQUENCE ID NO 12,
SEQUENCE ID NO 13, SEQUENCE ID NO 14, SEQUENCE ID NO 15, SEQUENCE
ID NO 16, SEQUENCE ID NO 17, SEQUENCE ID NO 18 ("SEQUENCE ID NOS
1-18"), and fragments or complements thereof. Also, the
CS193-specific polynucleotide may be attached to a solid phase
prior to performing the method.
[0012] The present invention also provides a method for detecting
CS193 mRNA in a test sample, which comprises performing reverse
transcription (RT) with at least one primer in order to produce
cDNA, amplifying the cDNA so obtained using CS193 oligonucleotides
as sense and antisense primers to obtain CS193 amplicon, and
detecting the presence of the CS193 amplicon as an indication of
the presence of CS193 mRNA in the test sample, wherein the CS193
oligonucleotides have at least 50% identity to a sequence selected
from the group consisting of SEQUENCE ID NOS 1-18, and fragments or
complements thereof. Amplification can be performed by the
polymerase chain reaction. Also, the test sample can be reacted
with a solid phase prior to performing the method, prior to
amplification or prior to detection. This reaction can be a direct
or an indirect reaction. Further, the detection step can comprise
utilizing a detectable label capable of generating a measurable
signal. The detectable label can be attached to a solid phase.
[0013] The present invention further provides a method of detecting
a target CS193 polynucleotide in a test sample suspected of
containing target CS193 polynucleotides, which comprises (a)
contacting the test sample with at least one CS193 oligonucleotide
as a sense primer and at least one CS193 oligonucleotide as an
anti-sense primer, and amplifying same to obtain a first stage
reaction product; (b) contacting the first stage reaction product
with at least one other CS193 oligonucleotide to obtain a second
stage reaction product, with the proviso that the other CS193
oligonucleotide is located 3' to the CS193 oligonucleotides
utilized in step (a) and is complementary to the first stage
reaction product; and (c) detecting the second stage reaction
product as an indication of the presence of a target CS193
polynucleotide in the test sample. The CS193 oligonucleotides
selected as reagents in the method have at least 50% identity to a
sequence selected from the group consisting of SEQUENCE ID NOS
1-18, and fragments or complements thereof. Amplification may be
performed by the polymerase chain reaction. The test sample can be
reacted either directly or indirectly with a solid phase prior to
performing the method, or prior to amplification, or prior to
detection. The detection step also comprises utilizing a detectable
label capable of generating a measurable signal; further, the
detectable label can be attached to a solid phase. Test kits useful
for detecting target CS193 polynucleotides in a test sample are
also provided which comprise a container containing at least one
CS193-specific polynucleotide selected from the group consisting of
SEQUENCE ID NOS 1-18, and fragments or complements thereof. These
test kits further comprise containers with tools useful for
collecting test samples (such as, for example, blood, urine, saliva
and stool). Such tools include lancets and absorbent paper or cloth
for collecting and stabilizing blood; swabs for collecting and
stabilizing saliva; and cups for collecting and stabilizing urine
or stool samples. Collection materials, such as papers, cloths,
swabs, cups, and the like, may optionally be treated to avoid
denaturation or irreversible adsorption of the sample. The
collection materials also may be treated with or contain
preservatives, stabilizers or antimicrobial agents to help maintain
the integrity of the specimens.
[0014] The present invention also provides a purified
polynucleotide or fragment thereof derived from a CS193 gene. The
purified polynucleotide is capable of selectively hybridizing to
the nucleic acid of the CS193 gene, or a complement thereof. The
polynucleotide has at least 50% identity to a polynucleotide
selected from the group consisting of SEQUENCE ID NOS 1-18, and
fragments or complements thereof. Further, the purified
polynucleotide can be produced by recombinant and/or synthetic
techniques. The purified recombinant polynucleotide can be
contained within a recombinant vector. The invention further
comprises a host cell transfected with the recombinant vector.
[0015] The present invention further provides a recombinant
expression system comprising a nucleic acid sequence that includes
an open reading frame derived from CS193. The nucleic acid sequence
has at least 50% identity with a sequence selected from the group
consisting of SEQUENCE ID NOS 1-18, and fragments or complements
thereof. The nucleic acid sequence is operably linked to a control
sequence compatible with a desired host. Also provided is a cell
transfected with this recombinant expression system.
[0016] The present invention also provides a polypeptide encoded by
CS193. The polypeptide can be produced by recombinant technology,
provided in purified form, or produced by synthetic techniques. The
polypeptide comprises an amino acid sequence which has at least 60%
identity with an amino acid sequence selected from the group
consisting of SEQUENCE ID NO 41, SEQUENCE ID NO 42, SEQUENCE ID NO
43, SEQUENCE ID NO 44, SEQUENCE ID NO 45, SEQUENCE ID NO 46,
SEQUENCE ID NO 47, SEQUENCE ID NO 48, SEQUENCE ID NO 49 ("SEQUENCE
ID NOS 41-49"), and fragments thereof.
[0017] Also provided is al antibody which specifically binds to at
[cast one CS193 epitope. The antibody can be a polyclonal or
monoclonal antibody. The epitope is derived from an amino acid
sequence selected from the group consisting of SEQUENCE ID NOS
41-49, and fragments thereof. Assay kits for determining the
presence of CS193 antigen or anti-CS193 antibody in a test sample
are also included. In one embodiment, the assay kits comprise a
container containing at least one CS193 polypeptide having at least
50% identity to an amino acid sequence selected from the group
consisting of SEQUENCE ID NOS 41-49, and fragments thereof.
Further, the test kit can comprise a container with tools useful
for collecting test samples (such as blood, urine, saliva, and
stool). Such tools include lancets and absorbent paper or cloth for
collecting and stabilizing blood; swabs for collecting and
stabilizing saliva; and cups for collecting and stabilizing urine
or stool samples. Collection materials such as papers, cloths,
swabs, cups, and the like, may optionally be treated to avoid
denaturation or irreversible adsorption of the sample. These
collection materials also may be treated with or contain
preservatives, stabilizers or antimicrobial agents to help maintain
the integrity of the specimens. Also, the polypeptide can be
attached to a solid phase.
[0018] Another assay kit for determining the presence of CS193
antigen or anti-CS193 antibody in a test sample comprises a
container containing an antibody which specifically binds to a
CS193 antigen, wherein the CS193 antigen comprises at least one
CS193-encoded epitope. The CS193 antigen has at least about 60%
sequence similarity to a sequence of a CS193-encoded antigen
selected from the group consisting of SEQUENCE ID NOS 41-49, and
fragments thereof. These test kits can further comprise containers
with tools useful for collecting test samples (such as blood,
urine, saliva, and stool). Such tools include lancets and absorbent
paper or cloth for collecting and stabilizing blood; swabs for
collecting and stabilizing saliva; cups for collecting and
stabilizing urine or stool samples. Collection materials, papers,
cloths, swabs, cups and the like, may optionally be treated to
avoid denaturation or irreversible adsorption of the sample. These
collection materials also may be treated with, or contain,
preservatives, stabilizers or antimicrobial agents to help maintain
the integrity of the specimens. The antibody can be attached to a
solid phase.
[0019] A method for producing a polypeptide which contains at least
one epitope of CS193 is provided, which method comprises incubating
host cells that have been transfected with an expression vector.
This vector comprises a polynucleotide sequence encoding a
polypeptide, wherein the polypeptide comprises an amino acid
sequence having at least 60% identity to a CS193 amino acid
sequence selected from the group consisting of SEQUENCE ID NOS
41-49, and fragments thereof.
[0020] A method for detecting CS193 antigen in a test sample
suspected of containing CS193 antigen also is provided. The method
comprises contacting the test sample with an antibody or fragment
thereof which specifically binds to at least one epitope of CS193
antigen, for a time and under conditions sufficient for the
formation of antibody/antigen complexes; and detecting the presence
of such complexes containing the antibody as an indication of the
presence of CS193 antigen in the test sample. The antibody can be
attached to a solid phase and may be either a monoclonal or
polyclonal antibody. Furthermore, the antibody specifically binds
to at least one CS193 antigen selected from the group consisting of
SEQUENCE ID NOS 41-49, and fragments thereof.
[0021] Another method is provided which detects antibodies which
specifically bind to CS193 antigen in a test sample suspected of
containing these antibodies. The method comprises contacting the
test sample with a polypeptide which contains at least one CS193
epitope, wherein the CS193 epitope comprises an amino acid sequence
having at least 50% identity with an amino acid sequence encoded by
a CS193 polynucleotide, or a fragment thereof. Contacting is
carried out for a time and under conditions sufficient to allow
antigen/antibody complexes to form. The method further entails
detecting complexes which contain the polypeptide. The polypeptide
can be attached to a solid phase. Further, the polypeptide can be a
recombinant protein or a synthetic peptide having at least 50%
identity to an amino acid sequence selected from the group
consisting of SEQUENCE ID NOS 41-49, and fragments thereof.
[0022] The present invention provides a cell transfected with a
CS193 nucleic acid sequence that encodes at least one epitope of a
CS193 antigen or fragment thereof. The nucleic acid sequence is
selected from the group consisting of SEQUENCE ID NOS 1-18, and
fragments or complements thereof.
[0023] A method for producing antibodies to CS193 antigen also is
provided, which method comprises administering to an individual an
isolated immunogenic polypeptide or fragment thereof, wherein the
isolated immunogenic polypeptide comprises at least one CS193
epitope. The immunogenic polypeptide or fragment thereof is
administered in an amount sufficient to produce an immune response.
The isolated, immunogenic polypeptide comprises an amino acid
sequence selected from the group consisting of SEQUENCE ID NOS
41-49, and fragments thereof.
[0024] Another method for producing antibodies which specifically
bind to CS193 antigen is disclosed, which method comprises
administering to an individual a plasmid comprising a nucleic acid
sequence which encodes at least one CS193 epitope derived from an
amino acid sequence selected from the group consisting of SEQUENCE
ID NOS 41-49, and fragments thereof. The plasmid is administered in
an amount such that the plasmid is taken up by cells in the
individual and expressed at levels sufficient to produce an immune
response.
[0025] Also provided is a composition of matter that comprises a
CS193 polynucleotide of at least about 10-12 nucleotides having at
least 50% identity to a polynucleotide selected from the group
consisting of SEQUENCE ID NOS 1-18, and fragments or complements
thereof. The CS193 polynucleotide encodes an amino acid sequence
having at least one CS193 epitope. Another composition of matter
provided by the present invention comprises a polypeptide with at
least one CS193 epitope of about 8-10 amino acids. The polypeptide
comprises an amino acid sequence having at least 60% identity with
an amino acid sequence selected from the group consisting of
SEQUENCE ID NOS 41-49, and fragments thereof. Also provided is a
gene, or fragment thereof, coding for a CS193 polypeptide which has
at least 60% identity to SEQUENCE ID NO 41; and a gene, or a
fragment thereof, comprising DNA having at least 50% identity to
SEQUENCE ID NO 16, SEQUENCE ID NO 17, or SEQUENCE ID NO 18.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] FIGS. 1A-1G show the nucleotide alignment of clones 2767646
(SEQUENCE ID NO 1), 774134 (SEQUENCE ID NO 2), 775437 (SEQUENCE ID
NO 3), 1281329 (SEQUENCE ID NO 4), 1628677 (SEQUENCE ID NO 5),
1286372 (SEQUENCE ID NO 6), 774419 (SEQUENCE ID NO 7), 3233118
(SEQUENCE ID NO 8), 2733923 (SEQUENCE ID NO 9),906605 (SEQUENCE ID
NO 10), 2771475 (SEQUENCE ID NO 11), 1803247 (SEQUENCE ID NO 12),
1737526 (SEQUENCE ID NO 13), 2792957 (SEQUENCE ID NO 14), 1226186
(SEQUENCE ID NO 15); the consensus sequence (SEQUENCE ID NO 18)
derived therefrom; and the full-length sequences of clone 774134
(designated as clone 7741341H (SEQUENCE ID NO 16)) and clone 774419
(designated as clone 7744191H (SEQUENCE ID NO 17)).
[0027] FIG. 2 shows the contig map depicting the formation of the
consensus nucleotide sequence (SEQUENCE ID NO 18) from the
nucleotide alignment of overlapping clones 2767646 (SEQUENCE ID NO
1), 774134 (SEQUENCE ID NO 2), 775437 (SEQUENCE ID NO 3), 1281329
(SEQUENCE ID NO 4), 1628677 (SEQUENCE ID NO 5), 1286372 (SEQUENCE
ID NO 6), 774419 (SEQUENCE ID NO 7), 3233118 (SEQUENCE ID NO 8),
2733923 (SEQUENCE ID NO 9), 906605 (SEQUENCE ID NO 10), 2771475
(SEQUENCE ID NO 11), 1803247 (SEQUENCE ID NO 12), 1737526 (SEQUENCE
ID NO 13), 2792957 (SEQUENCE ID NO 14), 1226186 (SEQUENCE ID NO
15), 7741341H (SEQUENCE ID NO 16), and 7744191H (SEQUENCE ID NO
17).
DETAILED DESCRIPTION OF THE INVENTION
[0028] The present invention provides a gene, or a fragment
thereof, which codes for a CS193 polypeptide having at least about
60% identity to SEQUENCE ID NO 41. The present invention further
encompasses a CS193 gene, or a fragment thereof, comprising DNA
which has at least about 50% identity to SEQUENCE ID NO 16,
SEQUENCE ID NO 17, or SEQUENCE ID NO 18.
[0029] The present invention also provides methods for assaying a
test sample for products of a gastrointestinal tract (GI tract)
tissue gene designated as CS193, which method comprises making cDNA
from mRNA in the test sample and detecting the cDNA as an
indication of the presence of GI tract tissue gene CS193. The
method may include an amplification step, wherein one or more
portions of the mRNA from CS193 corresponding to the gene or
fragments thereof, is amplified. Methods also are provided for
assaying for the translation products of CS193. Test samples which
may be assayed by the methods provided herein include tissues,
cells, body fluids and secretions. The present invention also
provides reagents such as oligonucleotide primers and polypeptides
which are useful in performing these methods.
[0030] Portions of the nucleic acid sequences disclosed herein are
useful as primers for the reverse transcription of RNA or for the
amplification of cDNA or as probes to determine the presence of
certain mRNA sequences in test samples. Also disclosed are nucleic
acid sequences which permit the production of encoded polypeptide
sequences which are useful as standards or reagents in diagnostic
immunoassays, as targets for pharmaceutical screening assays and/or
as components or as target sites for various therapies. Monoclonal
and polyclonal antibodies directed against at least one epitope
contained within these polypeptide sequences are useful as delivery
agents for therapeutic agents as well as for diagnostic tests and
for screening for diseases or conditions associated with CS193,
especially GI tract cancer. Isolation of sequences of other
portions of the gene of interest can be accomplished utilizing
probes or PCR primers derived from these nucleic acid sequences.
This allows additional probes of the mRNA or cDNA of interest to be
established, as well as corresponding encoded polypeptide
sequences. These additional molecules are useful in detecting,
diagnosing, staging, monitoring, prognosticating, preventing or
treating, or determining the predisposition to diseases and
conditions of the GI tract, such as GI tract cancer, characterized
by CS193, as disclosed herein.
[0031] Techniques for determining amino acid sequence "similarity"
are well-known in the art. In general, "similarity" means the exact
amino acid to amino acid comparison of two or more polypeptides at
the appropriate place, where amino acids are identical or possess
similar chemical and/or physical properties such as charge or
hydrophobicity. A so-termed "percent similarity" then can be
determined between the compared polypeptide sequences. Techniques
for determining nucleic acid and amino acid sequence identity also
are well known in the art and include determining the nucleotide
sequence of the mRNA for that gene (usually via a cDNA
intermediate) and determining the amino acid sequence encoded
thereby, and comparing this to a second amino acid sequence. In
general, "identity" refers to an exact nucleotide to nucleotide or
amino acid to amino acid correspondence of two polynucleotides or
polypeptide sequences, respectively. Two or more polynucleotide
sequences can be compared by determining their "percent identity."
Two or more amino acid sequences likewise can be compared by
determining their "percent identity." The programs available in the
Wisconsin Sequence Analysis Package, Version 8 (available from
Genetics Computer Group, Madison, Wis.), for example, the GAP
program, are capable of calculating both the identity between two
polynucleotides and the identity and similarity between two
polypeptide sequences, respectively. Other programs for calculating
identity or similarity between sequences are known in the art.
[0032] The compositions and methods described herein will enable
the identification of certain markers as indicative of a GI tract
tissue disease or condition. The information obtained therefrom
will aid in the detecting, diagnosing, staging, monitoring,
prognosticating, preventing or treating, or determining diseases or
conditions associated with CS193, especially GI tract cancer. Test
methods include, for example, probe assays which utilize the
sequence(s) provided herein and which also may utilize nucleic acid
amplification methods such as the polymerase chain reaction (PCR),
the ligase chain reaction (LCR), and hybridization. In addition,
the nucleotide sequences provided herein contain open reading
frames from which an immunogenic epitope may be found. This epitope
is believed to be unique to the disease state or condition
associated with CS193. It also is thought that the polynucleotides
or polypeptides and protein encoded by the CS193 gene are useful as
a marker. This marker is either elevated in disease such as GI
tract cancer, altered in disease such as GI tract cancer, or
present as a normal protein but appearing in an inappropriate body
compartment. The uniqueness of the epitope may be determined by (i)
its immunological reactivity and specificity with antibodies
directed against proteins and polypeptides encoded by the CS193
gene, and (ii) its nonreactivity with any other tissue markers.
Methods for determining immunological reactivity are well-known and
include, but are not limited to, for example, radioimmunoassay
(RIA), enzyme-linked immunoabsorbent assay (ELISA),
hemagglutination (HA), fluorescence polarization immunoassay
(FPIA), chemiluminescent immunoassay (CLIA) and others. Several
examples of suitable methods are described herein.
[0033] Unless otherwise stated, the following terms shall have the
following meanings:
[0034] A polynucleotide "derived from" or "specific for" a
designated sequence refers to a polynucleotide sequence which
comprises a contiguous sequence of approximately at least about 6
nucleotides, preferably at least about 8 nucleotides, more
preferably at least about 10-12 nucleotides, and even more
preferably at least about 15-20 nucleotides corresponding, i.e.,
identical or complementary to, a region of the designated
nucleotide sequence. The sequence may be complementary or identical
to a sequence which is unique to a particular polynucleotide
sequence as determined by techniques known in the art. Comparisons
to sequences in databanks, for example, can be used as a method to
determine the uniqueness of a designated sequence. Regions from
which sequences may be derived, include but are not limited to,
regions encoding specific epitopes, as well as non-translated
and/or non-transcribed regions.
[0035] The derived polynucleotide will not necessarily be derived
physically from the nucleotide sequence of interest under study,
but may be generated in any manner, including, but not limited to,
chemical synthesis, replication, reverse transcription or
transcription, which is based on the information provided by the
sequence of bases in the region(s) from which the polynucleotide is
derived. As such, it may represent either a sense or an antisense
orientation of the original polynucleotide. In addition,
combinations of regions corresponding to that of the designated
sequence may be modified in ways known in the art to be consistent
with the intended use.
[0036] A "Fragment" of a specified polynucleotide refers to a
polynucleotide sequence which comprises a contiguous sequence of
approximately at least about 6 nucleotides, preferably at least
about 8 nucleotides, more preferably at least about 10-12
nucleotides, and even more preferably at least about 15-20
nucleotides corresponding, i.e., identical or complementary to, a
region of the specified nucleotide sequence.
[0037] The term "primer" denotes a specific oligonucleotide
sequence which is complementary to a target nucleotide sequence and
used to hybridize to the target nucleotide sequence. A primer
serves as an initiation point for nucleotide polymerization
catalyzed by either DNA polymerase, RNA polymerase or reverse
transcriptase.
[0038] The term "probe" denotes a defined nucleic acid segment (or
nucleotide analog segment, e.g., PNA as defined hereinbelow) which
can be used to identify a specific polynucleotide present in
samples bearing the complementary sequence.
[0039] "Encoded by" refers to a nucleic acid sequence which codes
for a polypeptide sequence, wherein the polypeptide sequence or a
portion thereof contains an amino acid sequence of at least 3 to 5
amino acids, more preferably at least 8 to 10 amino acids, and
even,more preferably at least 15 to 20 amino acids from a
polypeptide encoded by the nucleic acid sequence. Also encompassed
are polypeptide sequences which are immunologically identifiable
with a polypeptide encoded by the sequence. Thus, a "polypeptide,"
"protein," or "amino acid" sequence has at least about 50%
identity, preferably about 60% identity, more preferably about
75-85% identity, and most preferably about 90-95% or more identity
to a CS193 amino acid sequence. Further, the CS193 "polypeptide,"
"protein," or "amino acid" sequence may have at least about 60%
similarity, preferably at least about 75% similarity, more
preferably about 85% similarity, and most preferably about 95% or
more similarity to a polypeptide or amino acid sequence of CS193.
This amino acid sequence can be selected from the group consisting
of SEQUENCE ID NO 41, SEQUENCE ID NO 42, SEQUENCE ID NO 43,
SEQUENCE ID NO 44, SEQUENCE ID NO 45, SEQUENCE ID NO 46, SEQUENCE
ID NO 47, SEQUENCE ID NO 48, SEQUENCE ID NO 49, and fragments
thereof.
[0040] A "recombinant polypeptide," "recombinant protein," or "a
polypeptide produced by recombinant techniques," which terms may be
used interchangeably herein, describes a polypeptide which by
virtue of its origin or manipulation is not associated with all or
a portion of the polypeptide with which it is associated in nature
and/or is linked to a polypeptide other than that to which it is
linked in nature. A recombinant or encoded polypeptide or protein
is not necessarily translated from a designated nucleic acid
sequence. It also may be generated in any manner, including
chemical synthesis or expression of a recombinant expression
system.
[0041] The term "synthetic peptide" as used herein means a
polymeric form of amino acids of any length, which may be
chemically synthesized by methods well-known to the routineer.
These synthetic peptides are useful in various applications.
[0042] The term "polynucleotide," as used herein, means a polymeric
form of nucleotides of any length, either ribonucleotides or
deoxyribonucleotides. This term refers only to the primary
structure of the molecule. Thus, the term includes double- and
single-stranded DNA, as well as double- and single-stranded RNA. It
also includes modifications, such as methylation or capping and
unmodified forms of the polynucleotide. The terms "polynucleotide,"
"oligomer," "oligonucleotide," and "oligo" are used interchangeably
herein.
[0043] "A sequence corresponding to a cDNA" means that the sequence
contains a polynucleotide sequence that is identical or
complementary to a sequence in the designated DNA. The degree (or
"percent") of identity or complementarity to the cDNA will be
approximately 50% or greater, preferably at least about 70% or
greater, and more preferably at least about 90% or greater. The
sequence that corresponds to the identified cDNA will be at least
about 50 nucleotides in length, preferably at least about 60
nucleotides in length, and more preferably at least about 70
nucleotides in length. The correspondence between the gene or gene
fragment of interest and the cDNA can be determined by methods
known in the art and include, for example, a direct comparison of
the sequenced material with the cDNAs described, or hybridization
and digestion with single strand nucleases, followed by size
determination of the digested fragments.
[0044] "Purified polynucleotide" refers to a polynucleotide of
interest or fragment thereof which is essentially free, e.g.,
contains less than about 50%, preferably less than about 70%, and
more preferably less than about 90%, of the protein with which the
polynucleotide is naturally associated. Techniques for purifying
polynucleotides of interest are well-known in the art and include,
for example, disruption of the cell containing the polynucleotide
with a chaotropic agent and separation of the polynucleotide(s) and
proteins by ion-exchange chromatography, affinity chromatography
and sedimentation according to density.
[0045] "Purified polypeptide" or "purified protein" means a
polypeptide of interest or fragment thereof which is essentially
free of, e.g., contains less than about 50%, preferably less than
about 70%, and more preferably less than about 90%, cellular
components with which the polypeptide of interest is naturally
associated. Methods for purifying polypeptides of interest are
known in the art.
[0046] The term "isolated" means that the material is removed from
its original environment (e.g., the natural environment if it is
naturally occurring). For example, a naturally-occurring
polynucleotide or polypeptide present in a living animal is not
isolated, but the same polynucleotide or DNA or polypeptide, which
is separated from some or all of the coexisting materials in the
natural system, is isolated. Such polynucleotide could be part of a
vector and/or such polynucleotide or polypeptide could be part of a
composition, and still be isolated in that the vector or
composition is not part of its natural environment.
[0047] "Polypeptide" and "protein" are used interchangeably herein
and indicate at least one molecular chain of amino acids linked
through covalent and/or non-covalent bonds. The terms do not refer
to a specific length of the product. Thus peptides, oligopeptides
and proteins are included within the definition of polypeptide. The
terms include post-translational modifications of the polypeptide,
for example, glycosylations, acetylations, phosphorylations and the
like. In addition, protein fragments, analogs, mutated or variant
proteins, fusion proteins and the like are included within the
meaning of polypeptide.
[0048] A "fragment" of a specified polypeptide refers to an amino
acid sequence which comprises at least about 3-5 amino acids, more
preferably at least about 8-10 amino acids, and even more
preferably at least about 15-20 amino acids derived from the
specified polypeptide. "Recombinant host cells," "host cells,"
"cells," "cell lines," "cell cultures," and other such terms
denoting microorganisms or higher eukaryotic cell lines cultured as
unicellular entities refer to cells which can be, or have been,
used as recipients for recombinant vector or other transferred DNA,
and include the original progeny of the original cell which has
been transfected.
[0049] As used herein "replicon" means any genetic element, such as
a plasmid, a chromosome or a virus, that behaves as an autonomous
unit of polynucleotide replication within a cell.
[0050] A "vector" is a replicon in which another polynucleotide
segment is attached, such as to bring about the replication and/or
expression of the attached segment.
[0051] The term "control sequence" refers to a polynucleotide
sequence which is necessary to effect the expression of a coding
sequence to which it is ligated. The nature of such control
sequences differs depending upon the host organism. In prokaryotes,
such control sequences generally include a promoter, a ribosomal
binding site and terminators; in eukaryotes, such control sequences
generally include promoters, terminators and, in some instances,
enhancers. The term "control sequence" thus is intended to include
at a minimum all components whose presence is necessary for
expression, and also may include additional components whose
presence is advantageous, for example, leader sequences.
[0052] "Operably linked" refers to a situation wherein the
components described are in a relationship permitting them to
function in their intended manner. Thus, for example, a control
sequence "operably linked" to a coding sequence is ligated in such
a manner that expression of the coding sequence is achieved under
conditions compatible with the control sequence.
[0053] The term "open reading frame" or "ORF" refers to a region of
a polynucleotide sequence which encodes a polypeptide. This region
may represent a portion of a coding sequence or a total coding
sequence.
[0054] A "coding sequence" is a polynucleotide sequence which is
transcribed into mRNA and translated into a polypeptide when placed
under the control of appropriate regulatory sequences. The
boundaries of the coding sequence are determined by a translation
start codon at the 5'-terminus and a translation stop codon at the
3'-terminus. A coding sequence can include, but is not limited to,
mRNA, cDNA and recombinant polynucleotide sequences.
[0055] The term "immunologically identifiable with/as" refers to
the presence of epitope(s) and polypeptide(s) which also are
present in and are unique to the designated polypeptide(s).
Immunological identity may be determined by antibody binding and/or
competition in binding. These techniques are known to the routineer
and also are described herein. The uniqueness of an epitope also
can be determined by computer searches of known data banks, such as
GenBank, for the polynucleotide sequence which encodes the epitope
and by amino acid sequence comparisons with other known
proteins.
[0056] As used herein, "epitope" means an antigenic determinant of
a polypeptide or protein. Conceivably, an epitope can comprise
three amino acids in a spatial conformation which is unique to the
epitope. Generally, an epitope consists of at least five such amino
acids and more usually, it consists of at least eight to ten amino
acids. Methods of examining spatial conformation are known in the
art and include, for example, x-ray crystallography and
two-dimensional nuclear magnetic resonance.
[0057] A "conformational epitope" is an epitope that is comprised
of a specific juxtaposition of amino acids in an immunologically
recognizable structure, such amino acids being present on the same
polypeptide in a contiguous or non-contiguous order or present on
different polypeptides.
[0058] A polypeptide is "immunologically reactive" with an antibody
when it binds to an antibody due to antibody recognition of a
specific epitope contained within the polypeptide. Immunological
reactivity may be determined by antibody binding, more
particularly, by the kinetics of antibody binding, and/or by
competition in binding using as competitor(s) a known
polypeptide(s) containing an epitope against which the antibody is
directed. The methods for determining whether a polypeptide is
immunologically reactive with an antibody are known in the art.
[0059] As used herein, the term "immunogenic polypeptide containing
an epitope of interest" means naturally occurring polypeptides of
interest or fragments thereof, as well as polypeptides prepared by
other means, for example, by chemical synthesis or the expression
of the polypeptide in a recombinant organism.
[0060] The term "transfection" refers to the introduction of an
exogenous polynucleotide into a prokaryotic or eucaryotic host
cell, irrespective of the method used for the introduction. The
term "transfection" refers to both stable and transient
introduction of the polynucleotide, and encompasses direct uptake
of polynucleotides, transformation, transduction, and f-mating.
Once introduced into the host cell, the exogenous polynucleotide
may be maintained as a non-integrated replicon, for example, a
plasmid or alternatively, may be integrated into the host
genome.
[0061] "Treatment" refers to prophylaxis and/or therapy.
[0062] The term "individual" as used herein refers to vertebrates,
particularly members of the mammalian species and includes, but is
not limited to, domestic animals, sports animals, primates and
humans; more particularly, the term refers to humans.
[0063] The term "sense strand" or "plus strand" (or "+") as used
herein denotes a nucleic acid that contains the sequence that
encodes the polypeptide. The term "antisense strand" or "minus
strand" (or "-") denotes a nucleic acid that contains a sequence
that is complementary to that of the "plus" strand.
[0064] The term "test sample" refers to a component of an
individual's body which is the source of the analyte (such as
antibodies of interest or antigens of interest). These components
are well known in the art. A test sample is typically anything
suspected of containing a target sequence. Test samples can be
prepared using methodologies well known in the art such as by
obtaining a specimen from an individual and, if necessary,
disrupting any cells contained thereby to release target nucleic
acids. These test samples include biological samples which can be
tested by the methods of the present invention described herein and
include human and animal body fluids such as whole blood, serum,
plasma, cerebrospinal fluid, sputum, bronchial washing, bronchial
aspirates, urine, lymph fluids, and various external secretions of
the respiratory, intestinal and genitourinary tracts, tears,
saliva, milk, white blood cells, myelomas and the like; biological
fluids such as cell culture supernatants; tissue specimens which
may be fixed; and cell specimens which may be fixed.
[0065] "Purified product" refers to a preparation of the product
which has been isolated from the cellular constituents with which
the product is normally associated and from other types of cells
which may be present in the sample of interest.
[0066] "PNA" denotes a "peptide nucleic acid analog" which may be
utilized in a procedure such as an assay described herein to
determine the presence of a target. "MA" denotes a "morpholino
analog" which may be utilized in a procedure such as an assay
described herein to determine the presence of a target. See, for
example, U.S. Pat. No. 5,378,841, which is incorporated herein by
reference. PNAs are neutrally charged moieties which can be
directed against RNA targets or DNA. PNA probes used in assays in
place of, for example, the DNA probes of the present invention,
offer advantages not achievable when DNA probes are used. These
advantages include manufacturability, large scale labeling,
reproducibility, stability, insensitivity to changes in ionic
strength and resistance to enzymatic degradation which is present
in methods utilizing DNA or RNA. These PNAs can be labeled with
("attached to") such signal generating compounds as fluorescein,
radionucleotides, chemiluminescent compounds and the like. PNAs or
other nucleic acid analogs such as MAs thus can be used in assay
methods in place of DNA or RNA. Although assays are described
herein utilizing DNA probes, it is within the scope of the
routineer that PNAs or MAs can be substituted for RNA or DNA with
appropriate changes if and as needed in assay reagents.
[0067] "Analyte," as used herein, is the substance to be detected
which may be present in the test sample. The analyte can be any
substance for which there exists a naturally occurring specific
binding member (such as an antibody), or for which a specific
binding member can be prepared. Thus, an analyte is a substance
that can bind to one or more specific binding members in an assay.
"Analyte" also includes any antigenic substances, haptens,
antibodies and combinations thereof. As a member of a specific
binding pair, the analyte can be detected by means of naturally
occurring specific binding partners (pairs) such as the use of
intrinsic factor protein as a member of a specific binding pair for
the determination of Vitamin B12, the use of folate-binding protein
to determine folic acid, or the use of a lectin as a member of a
specific binding pair for the determination of a carbohydrate. The
analyte can include a protein, a polypeptide, an amino acid, a
nucleotide target and the like.
[0068] The terms "diseases of the GI tract," "GI tract disease,"
and "condition of the GI tract" are used interchangeably herein to
refer to any disease or condition of the esophagus, stomach, small
and large intestines, rectum and pancreas including, but not
limited to, Barret's esophagus, gastric ulcer, gastritis,
leiomyoma, polyps, Crohn's disease, ulcerative colitis,
pancreatitis and cancer.
[0069] "GI tract cancer," as used herein, refers to any malignant
disease of the gastrointestinal tract including, but not limited
to, adenocarcinoma, mucinous adenocarcinoma, carcinoid tumor,
squamous cell carcinoma, lymphoma, and sarcoma.
[0070] An "Expressed Sequence Tag" or "EST" refers to the partial
sequence of a cDNA insert which has been made by reverse
transcription of mRNA extracted from a tissue followed into a
vector.
[0071] A "transcript image" refers to a table or list giving the
quantitative distribution of ESTs in a library and represents the
genes active in the tissue from which the library was made.
[0072] The present invention provides assays which utilize specific
binding members. A "specific binding member," as used herein, is a
member of a specific binding pair. That is, two different molecules
where one of the molecules, through chemical or physical means,
specifically binds to the second molecule. Therefore, in addition
to antigen and antibody specific binding pairs of common
immunoassays, other specific binding pairs can include biotin and
avidin, carbohydrates and lectins, complementary nucleotide
sequences, effector and receptor molecules, cofactors and enzymes,
enzyme inhibitors, and enzymes and the like. Furthermore, specific
binding pairs can include members that are analogs of the original
specific binding members, for example, an analyte-analog.
Immunoreactive specific binding members include antigens, antigen
fragments, antibodies and antibody fragments, both monoclonal and
polyclonal and complexes thereof, including those formed by
recombinant DNA molecules.
[0073] The term "hapten," as used herein, refers to a partial
antigen or non-protein binding member which is capable of binding
to an antibody, but which is not capable of eliciting antibody
formation unless coupled to a carrier protein.
[0074] A "capture reagent," as used herein, refers to an unlabeled
specific binding member which is specific either for the analyte as
in a sandwich assay, for the indicator reagent or analyte as in a
competitive assay, or for an ancillary specific binding member,
which itself is specific for the analyte, as in an indirect assay.
The capture reagent can be directly or indirectly bound to a solid
phase material before the performance of the assay or during the
performance of the assay, thereby enabling the separation of
immobilized complexes from the test sample.
[0075] The "indicator reagent" comprises a "signal-generating
compound" ("label") which is capable of generating and generates a
measurable signal detectable by external means, conjugated
("attached") to a specific binding member. In addition to being all
antibody member of a specific binding pair, the indicator reagent
also can be a member of any specific binding pair, including either
hapten-anti-hapten systems such as biotin or anti-biotin, avidin or
biotin, a carbohydrate or a lectin, a complementary nucleotide
sequence, an effector or a receptor molecule, an enzyme cofactor
and an enzyme, an enzyme inhibitor or an enzyme and the like. An
immunoreactive specific binding member can be an antibody, an
antigen, or an antibody/antigen complex that is capable of binding
either to the polypeptide of interest as in a sandwich assay, to
the capture reagent as in a competitive assay, or to the ancillary
specific binding member as in an indirect assay. When describing
probes and probe assays, the term "reporter molecule" may be used.
A reporter molecule comprises a signal generating compound as
described hereinabove conjugated to a specific binding member of a
specific binding pair, such as carbazole or adamantane.
[0076] The various "signal-generating compounds" (labels)
contemplated include chromagens, catalysts such as enzymes,
luminescent compounds such as fluorescein and rhodamine,
chemiluminescent compounds such as dioxetanes, acridiniums,
phenanthridiniums and luminol, radioactive elements and direct
visual labels. Examples of enzymes include alkaline phosphatase,
horseradish peroxidase, beta-galactosidase and the like. The
selection of a particular label is not critical, but it,-Must be
capable of producing a signal either by itself or in conjunction
with one or more additional substances.
[0077] "Solid phases" ("solid supports") are known to those in the
art and include the walls of wells of a reaction tray, test tubes,
polystyrene beads, magnetic or non-magnetic beads, nitrocellulose
strips, membranes, microparticles such as latex particles, sheep
(or other animal) red blood cells and Duracytes.RTM. (red blood
cells "fixed" by pyruvic aldehyde and formaldehyde, available from
Abbott Laboratories, Abbott Park, Ill.) and others. The "solid
phase" is not critical and can be selected by one skilled in the
art. Thus, latex particles, microparticles, magnetic or
non-magnetic beads, membranes, plastic tubes, walls of microtiter
wells, glass or silicon chips, sheep (or other suitable animal's)
red blood cells and Duracytes.RTM. are all suitable examples.
Suitable methods for immobilizing peptides on solid phases include
ionic, hydrophobic, covalent interactions and the like. A "solid
phase," as used herein, refers to any material which is insoluble,
or can be made insoluble by a subsequent reaction. The solid phase
can be chosen for its intrinsic ability to attract and immobilize
the capture reagent. Alternatively, the solid phase can retain an
additional receptor which has the ability to attract and immobilize
the capture reagent. The additional receptor can include a charged
substance that is oppositely charged with respect to the capture
reagent itself or to a charged substance conjugated to the capture
reagent. As yet another alternative, the receptor molecule can be
any specific binding member which is immobilized upon (attached to)
the solid phase and which has the ability to immobilize the capture
reagent through a specific binding reaction. The receptor molecule
enables the indirect binding of the capture reagent to a solid
phase material before the performance of the assay or during the
performance of the assay. The solid phase thus can be a plastic,
derivatized plastic, magnetic or non-magnetic metal, glass or
silicon surface of a test tube, microtiter well, sheet, bead,
microparticle, chip, sheep (or other suitable animal's) red blood
cells, Duracytes.RTM. and other configurations known to those of
ordinary skill in the art.
[0078] It is contemplated and within the scope of the present
invention that the solid phase also can comprise any suitable
porous material with sufficient porosity to allow access by
detection antibodies and a suitable surface affinity to bind
antigens. Microporous structures generally are preferred, but
materials with a gel structure in the hydrated state may be used as
well. Such useful solid supports include, but are not limited to,
nitrocellulose and nylon. It is contemplated that such porous solid
supports described herein preferably are in the form of sheets of
thickness from about 0.01 to 0.5 mm, preferably about 0.1 mm. The
pore size may vary within wide limits and preferably is from about
0.025 to 15 microns, especially from about 0.15 to 15 microns. The
surface of such supports may be activated by chemical processes
which cause covalent linkage of the antigen or antibody to the
support. The irreversible binding of the antigen or antibody is
obtained, however, in general, by adsorption on the porous material
by poorly understood hydrophobic forces. Other suitable solid
supports are known in the art.
[0079] Reagents
[0080] The present invention provides reagents such as
polynucleotide sequences derived from a GI tract tissue of interest
and designated as CS193, polypeptides encoded thereby and
antibodies specific for these polypeptides. The present invention
also provides reagents such as oligonucleotide fragments derived
from the disclosed polynucleotides and nucleic acid sequences
complementary to these polynucleotides. The polynucleotides,
polypeptides, or antibodies of the present invention may be used to
provide information leading to the detecting, diagnosing, staging,
monitoring, prognosticating, preventing or treating of, or
determining the predisposition to, diseases and conditions of the
GI tract, such as GI tract cancer. The sequences disclosed herein
represent unique polynucleotides which can be used in assays or for
producing a specific profile of gene transcription activity. Such
assays are disclosed in European Patent Number 0373203B 1 and
International Publication No. WO 95/11995, which are hereby
incorporated by reference.
[0081] Selected CS193-derived polynucleotides can be used in the
methods described herein for the detection of normal or altered
gene expression. Such methods may employ CS193 polynucleotides or
oligonucleotides, fragments or derivatives thereof, or nucleic acid
sequences complementary thereto.
[0082] The polynucleotides disclosed herein, their complementary
sequences, or fragments of either, can be used in assays to detect,
amplify or quantify genes, nucleic acids, cDNAs or mRNAs relating
to GI tract tissue disease and conditions associated therewith.
They also can be used to identify an entire or partial coding
region of a CS193 polypeptide. They further can be provided in
individual containers in the form of a kit for assays, or provided
as individual compositions. If provided in a kit for assays, other
suitable reagents such as buffers, conjugates and the like may be
included.
[0083] The polynucleotide may be in the form of RNA or DNA.
Polynucleotides in the form of DNA, cDNA, genomic DNA, nucleic acid
analogs and synthetic DNA are within the scope of the present
invention. The DNA may be double-stranded or single-stranded, and
if single stranded, may be the coding (sense) strand or non-coding
(anti-sense) strand. The coding sequence which encodes the
polypeptide may be identical to the coding sequence provided herein
or may be a different coding sequence which coding sequence, as a
result of the redundancy or degeneracy of the genetic code, encodes
the same polypeptide as the DNA provided herein.
[0084] This polynucleotide may include only the coding sequence for
the polypeptide, or the coding sequence for the polypeptide and an
additional coding sequence such as a leader or secretory sequence
or a proprotein sequence, or the coding sequence for the
polypeptide (and optionally an additional coding sequence) and
non-coding sequence, such as a non-coding sequence 5' and/or 3' of
the coding sequence for the polypeptide.
[0085] In addition, the invention includes variant polynucleotides
containing modifications such as polynucleotide deletions,
substitutions or additions; and any polypeptide modification
resulting from the variant polynucleotide sequence. A
polynucleotide of the present invention also may have a coding
sequence which is a naturally occurring allelic variant of the
coding sequence provided herein.
[0086] In addition, the coding sequence for the polypeptide may be
fused in the same reading frame to a polynucleotide sequence which
aids in expression and secretion of a polypeptide from a host cell,
for example, a leader sequence which functions as a secretory
sequence for controlling transport of a polypeptide from the cell.
The polypeptide having a leader sequence is a preprotein and may
have the leader sequence cleaved by the host cell to form the
polypeptide. The polynucleotides may also encode for a proprotein
which is the protein plus additional 5' amino acid residues. A
protein having a prosequence is a proprotein and may, in some
cases, be an inactive form of the protein. Once the prosequence is
cleaved, an active protein remains. Thus, the polynucleotide of the
present invention may encode for a protein, or for a protein having
a prosequence, or for a protein having both a presequence (leader
sequence) and a prosequence.
[0087] The polynucleotides of the present invention may also have
the coding sequence fused in frame to a marker sequence which
allows for purification of the polypeptide of the present
invention. The marker sequence may be a hexa-histidine tag supplied
by a pQE-9 vector to provide for purification of the polypeptide
fused to the marker in the case of a bacterial host, or, for
example, the marker sequence may be a hemagglutinin (HA) tag when a
mammalian host, e.g. a COS-7 cell line, is used. The HA tag
corresponds to an epitope derived from the influenza hemagglutinin
protein. See, for example, I. Wilson et al., Cell 37:767
(1984).
[0088] It is contemplated that polynucleotides will be considered
to hybridize to the sequences provided herein if there is at least
50%, preferably at least 70%, and more preferably at least 90%
identity between the polynucleotide and the sequence.
[0089] The present invention also provides an antibody produced by
using a purified CS193 polypeptide of which at least a portion of
the polypeptide is encoded by a CS193 polynucleotide selected from
the polynucleotides provided herein. These antibodies may be used
in the methods provided herein for the detection of CS193 antigen
in test samples. The presence of CS193 antigen in the test samples
is indicative of the presence of a GI tract disease or condition.
The antibody also may be used for therapeutic purposes, for
example, in neutralizing the activity of CS193 polypeptide in
conditions associated with altered or abnormal expression.
[0090] The present invention further relates to a CS193 polypeptide
which has the deduced amino acid sequence as provided herein, as
well as fragments, analogs and derivatives of such polypeptide. The
polypeptide of the present invention may be a recombinant
polypeptide, a natural purified polypeptide or a synthetic
polypeptide. The fragment, derivative or analog of the CS193
polypeptide may be one in which one or more of the amino acid
residues is 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 it may be one in which one or more of the amino
acid residues includes a substituent group; or it may be one in
which the polypeptide is fused with another compound, such as a
compound to increase the half-life of the polypeptide (for example,
polyethylene glycol); or it may be one in which the additional
amino acids are fused to the polypeptide, such as a leader or
secretory sequence or a sequence which is employed for purification
of the polypeptide or a proprotein sequence. Such fragments,
derivatives and analogs are within the scope of the present
invention. The polypeptides and polynucleotides of the present
invention are provided preferably in an isolated form and
preferably purified.
[0091] Thus, a polypeptide of the present invention may have an
amino acid sequence that is identical to that of the naturally
occurring polypeptide or that is different by minor variations due
to one or more amino acid substitutions. The variation may be a
"conservative change" typically in the range of about 1 to 5 amino
acids, wherein the substituted amino acid has similar structural or
chemical properties, e.g., replacement of leucine with isoleucine
or threonine with serine. In contrast, variations may include
nonconservative changes, e.g., replacement of a glycine with a
tryptophan. Similar minor variations may also include amino acid
deletions or insertions, or both. Guidance in determining which and
how many amino acid residues may be substituted, inserted or
deleted without changing biological or immunological activity may
be found using computer programs well known in the art, for
example, DNASTAR software (DNASTAR Inc., Madison Wis.).
[0092] Probes constructed according to the polynucleotide sequences
of the present invention can be used in various assay methods to
provide various types of analysis. For example, such probes can be
used in fluorescent in situ hybridization (FISH) technology to
perform chromosomal analysis, and used to identify cancer-specific
structural alterations in the chromosomes, such as deletions or
translocations that are visible from chromosome spreads or
detectable using PCR-generated and/or allele specific
oligonucleotides probes, allele specific amplification or by direct
sequencing. Probes also can be labeled with radioisotopes,
directly- or indirectly- detectable haptens, or fluorescent
molecules, and utilized for in situ hybridization studies to
evaluate the mRNA expression of the gene comprising the
polynucleotide in tissue specimens or cells.
[0093] This invention also provides teachings as to the production
of the polynucleotides and polypeptides provided herein.
[0094] Probe Assays
[0095] The sequences provided herein may be used to produce probes
which can be used in assays for the detection of nucleic acids in
test samples. The probes may be designed from conserved nucleotide
regions of the polynucleotides of interest or from non-conserved
nucleotide regions of the polynucleotide of interest. The design of
such probes for optimization in assays is within the skill of the
routineer. Generally, nucleic acid probes are developed from
non-conserved or unique regions when maximum specificity is
desired, and nucleic acid probes are developed from conserved
regions when assaying for nucleotide regions that are closely
related to, for example, different members of a multi-gene family
or in related species like mouse and man.
[0096] The polymerase chain reaction (PCR) is a technique for
amplifying a desired nucleic acid sequence (target) contained in a
nucleic acid or mixture-thereof. In PCR, a pair of primers are
employed in excess to hybridize to the complementary strands of the
target nucleic acid. The primers are each extended by a polymerase
using the target nucleic acid as a template. The extension products
become target sequences themselves, following dissociation from the
original target strand. New primers then are hybridized and
extended by a polymerase, and the cycle is repeated to
geometrically increase the number of target sequence molecules. PCR
is disclosed in U.S. Pat. Nos. 4,683,195 and 4,683.202, which are
incorporated herein by reference.
[0097] The Ligase Chain Reaction (LCR) is an alternate method for
nucleic acid amplification. In LCR, probe pairs are used which
include two primary (first and second) and two secondary (third and
fourth) probes, all of which are employed in molar excess to
target. The first probe hybridizes to a first segment of the target
strand, and the second probe hybridizes to a second segment of the
target strand, the first and second segments being contiguous so
that the primary probes abut one another in 5' phosphate-3'
hydroxyl relationship, and so that a ligase can covalently fuse or
ligate the two probes into a fused product. In addition, a third
(secondary) probe can hybridize to a portion of the first probe and
a fourth (secondary) probe can hybridize to a portion of the second
probe in a similar abutting fashion. Of course, if the target is
initially double stranded, the secondary probes also will hybridize
to the target complement in the first instance. Once the ligated
strand of primary probes is separated from the target strand, it
will hybridize with the third and fourth probes which can be
ligated to form a complementary, secondary ligated product. It is
important to realize that the ligated products are functionally
equivalent to either the target or its complement. By repeated
cycles of hybridization and ligation, amplification of the target
sequence is achieved. This technique is described more completely
in EP-A-320 308 to K. Backman published Jun. 16, 1989 and EP-A-439
182 to K. Backman et al, published Jul. 31, 1991, both of which are
incorporated herein by reference.
[0098] For amplification of mRNAs, it is within the scope of the
present invention to reverse transcribe mRNA into cDNA followed by
polymerase chain reaction (RT-PCR); or, to use a single enzyme for
both steps as described in U.S. Pat. No. 5,322,770, which is
incorporated herein by reference; or reverse transcribe mRNA into
cDNA followed by asymmetric gap ligase chain reaction (RT-AGLCR) as
described by R. L. Marshall et al., PCR Methods and Applications 4:
80-84 (1994), which also is incorporated herein by reference.
[0099] Other known amplification methods which can be utilized
herein include but are not limited to the so-called "NASBA" or
"3SR" technique described by J. C. Guatelli et al., PNAS USA
87:1874-1878 (1990) and also described by J. Compton, Nature 350
(No. 6313):91-92 (1991); Q-beta amplification as described in
published European Patent Application (EPA) No. 4544610; strand
displacement amplification (as described in G. T. Walker et al.,
Clin. Chem. 42:9-13 [1996]) and European Patent Application No.
684315; and target mediated amplification, as described in
International Publication No. WO 93/22461.
[0100] Detection of CS193 may be accomplished using any suitable
detection method, including those detection methods which are
currently well known in the art, as well as detection strategies
which may evolve later. Examples of the foregoing presently known
detection methods are hereby incorporated herein by reference. See,
for example, Caskey et al., U.S. Pat. No. 5,582,989, Gelfand et
al., U.S. Pat. No. 5,210,015. Examples of such detection methods
include target amplification methods as well as signal
amplification technologies. An example of presently known detection
methods would include the nucleic acid amplification technologies
referred to as PCR, LCR, NASBA, SDA, RCR and TMA. See, for example,
Caskey et al., U.S. Pat. No. 5,582,989, Gelfand et al., U.S. Pat.
No. 5,210,015. All of the foregoing are hereby incorporated by
reference. Detection may also be accomplished using signal
amplification such as that disclosed in Snitman et al., U.S. Pat.
No. 5,273,882. While the amplification of target or signal is
preferred at present, it is contemplated and within the scope of
the present invention that ultrasensitive detection methods which
do not require amplification can be utilized herein.
[0101] Detection, both amplified and non-amplified, may be
(combined) carried out using a variety of heterogeneous and
homogeneous detection formats. Examples of heterogeneous detection
formats are disclosed in Snitman et al., U.S. Pat. No. 5,273,882,
Albarella et al. in EP-84114441.9, Urdea et al., U.S. Pat. No.
5,124,246, Ullman et al. U.S. Pat. Nos. 5,185,243 and Kourilsky et
al., U.S. Pat. 4,581,333. All of the foregoing are hereby
incorporated by reference. Examples of homogeneous detection
formats are disclosed in, Caskey et al., U.S. Pat. Nos. 5,582,989,
Gelfand et al., U.S. Pat. No. 5,210,015, which are incorporated
herein by reference. Also contemplated and within the scope of the
present invention is the use of multiple probes in the
hybridization assay, which use improves sensitivity and
amplification of the CS193 signal. See, for example, Caskey et al.,
U.S. Pat. Nos. 5,582,989, Gelfand et al., 5,210,015, which are
incorporated herein by reference.
[0102] In one embodiment, the present invention generally comprises
the steps of contacting a test sample suspected of containing a
target polynucleotide sequence with amplification fraction reagents
comprising an amplification primer, and a detection probe that can
hybridize with an internal region of the amplicon sequences. Probes
and primers employed according to the method provided herein are
labeled with capture and detection labels, wherein probes are
labeled with one type of label and primers are labeled with another
type of label. Additionally, the primers and probes are selected
such that the probe sequence has a lower melt temperature than the
primer sequences. The amplification reagents, detection reagents
and test sample are placed under amplification conditions whereby,
in the presence of target sequence, copies of the target sequence
(an amplicon) are produced. In the usual case, the amplicon is
double stranded because primers are provided to amplify a target
sequence and its complementary strand. The double stranded amplicon
then is thermally denatured to produce single stranded amplicon
members. Upon formation of the single stranded amplicon members,
the mixture is cooled to allow the formation of complexes between
the probes and single stranded amplicon members.
[0103] As the single stranded amplicon sequences and probe
sequences are cooled, the probe sequences preferentially bind the
single stranded amplicon members. This finding is counterintuitive
given that the probe sequences generally are selected to be shorter
than the primer sequences and therefore have a lower melt
temperature than the primers. Accordingly, the melt temperature of
the amplicon produced by the primers should also have a higher melt
temperature than the probes. Thus, as the mixture cools, the
re-formation of the double stranded amplicon would be expected. As
previously stated, however, this is not the case. The probes are
found to preferentially bind the single stranded amplicon members.
Moreover, this preference of probe/single stranded amplicon binding
exists even when the primer sequences are added in excess of the
probes.
[0104] After the probe/single stranded amplicon member hybrids are
formed, they are detected. Standard heterogeneous assay formats are
suitable for detecting the hybrids using the detection labels and
capture labels present on the primers and probes. The hybrids can
be bound to a solid phase reagent by virtue of the capture label
and detected by virtue of the detection label. In cases where the
detection label is directly detectable, the presence of the hybrids
on the solid phase can be detected by causing the label to produce
a detectable signal, if necessary, and detecting the signal. In
cases where the label is not directly detectable, the captured
hybrids can be contacted with a conjugate, which generally
comprises a binding member attached to a directly detectable label.
The conjugate becomes bound to the complexes and the conjugate's
presence on the complexes can be detected with the directly
detectable label. Thus, the presence of the hybrids on thy solid
phase reagent can be determined. Those skilled in the art will
recognize that wash steps may be employed to wash away unhybridized
amplicon or probe as well as unbound conjugate.
[0105] Although the target sequence is described as single
stranded, it also is contemplated to include the case where the
target sequence is actually double stranded but is merely separated
from its complement prior to hybridization with the amplification
primer sequences. In the case where PCR is employed in this method,
the ends of the target sequences are usually known. In cases where
LCR or a modification thereof is employed in the preferred method,
the entire target sequence is usually known. Typically, the target
sequence is a nucleic acid sequence such as, for example, RNA or
DNA.
[0106] The method provided herein can be used in well-known
amplification reactions that include thermal cycle reaction
mixtures, particularly in PCR and gap LCR (GLCR). Amplification
reactions typically employ primers to repeatedly generate copies of
a target nucleic acid sequence, which target sequence is usually a
small region of a much larger nucleic acid sequence. Primers are
themselves nucleic acid sequences that are complementary to regions
of a target sequence. Under amplification conditions, these primers
hybridize or bind to the complementary regions of the target
sequence. Copies of the target sequence typically are generated by
the process of primer extension and/or ligation which utilizes
enzymes with polymerase or ligase activity, separately or in
combination, to add nucleotides to the hybridized primers and/or
ligate adjacent probe pairs. The nucleotides that are added to the
primers or probes, as monomers or preformed oligomers, are also
complementary to the target sequence. Once the primers or probes
have been sufficiently extended and/or ligated, they are separated
from the target sequence, for example, by heating the reaction
mixture to a "melt temperature" which is one in which complementary
nucleic acid strands dissociate. Thus, a sequence complementary to
the target sequence is formed.
[0107] A new amplification cycle then can take place to further
amplify the number of target sequences by separating any double
stranded sequences, allowing primers or probes to hybridize to
their respective targets, extending and/or ligating the hybridized
primers or probes and re-separating. The complementary sequences
that are generated by amplification cycles can serve as templates
for primer extension or filling the gap of two probes to further
amplify the number of target sequences. Typically, a reaction
mixture is cycled between 20 and 100 times, more typically, a
reaction mixture is cycled between 25 and 50 times. The numbers of
cycles can be determined by the routineer. In this manner, multiple
copies of the target sequence and its complementary sequence are
produced. Thus, primers initiate amplification of the target
sequence when it is present under amplification conditions.
[0108] Generally, two primers which are complementary to a portion
of a target strand and its complement are employed in PCR. For LCR,
four probes, two of which are complementary to a target sequence
and two of which are similarly complementary to the target's
complement are generally employed. In addition to the primer sets
and enzymes previously mentioned, a nucleic acid amplification
reaction mixture may also comprise other reagents which are well
known and include but are not limited to: enzyme cofactors such as
manganese; magnesium; salts; nicotinamide adenine dinucleotide
(NAD); and deoxynucleotide triphosphates (dNTPs) such as, for
example, deoxyadenine triphosphate, deoxyguanine triphosphate,
deoxycytosine triphosphate and deoxythymine triphosphate.
[0109] While the amplification primers initiate amplification of
the target sequence, the detection (or hybridization) probe is not
involved in amplification. Detection probes are generally nucleic
acid sequences or uncharged nucleic acid analogs such as, for
example, peptide nucleic acids which are disclosed in International
Publication No. WO 92/20702; morpholino analogs which are described
in U.S. Pat. Nos. 5,185,444, 5,034,506 and 5,142,047; and the like.
Depending upon the type of label carried by the probe, the probe is
employed to capture or detect the amplicon generated by the
amplification reaction. The probe is not involved in amplification
of the target sequence and therefore may have to be rendered
"non-extendible" in that additional dNTPs cannot be added to the
probe. In and of themselves, analogs usually are non-extendible and
nucleic acid probes can be rendered non-extendible by modifying the
3' end of the probe such that the hydroxyl group is no longer
capable of participating in elongation. For example, the 3' end of
the probe can be functionalized with the capture or detection label
to thereby consume or otherwise block the hydroxyl group.
Alternatively, the 3' hydroxyl group simply can be cleaved,
replaced or modified. U.S. patent application Ser. No. 071049,061
filed Apr. 19, 1993 and incorporated herein by reference describes
modifications which can be used to render a probe
non-extendible.
[0110] The ratio of primers to probes is not important. Thus,
either the probes or primers can be added to the reaction mixture
in excess whereby the concentration of one would be greater than
the concentration of the other. Alternatively, primers and probes
can be employed in equivalent concentrations. Preferably, however,
the primers are added to the reaction mixture in excess of the
probes. Thus, primer to probe ratios of, for example, 5:1 and 20:1,
are preferred.
[0111] While the length of the primers and probes can vary, the
probe sequences are selected such that they have a lower melt
temperature than the primer sequences. Hence, the primer sequences
are generally longer than the probe sequences. Typically, the
primer sequences are in the range of between 20 and 50 nucleotides
long, more typically in the range of between 20 and 30 nucleotides
long. The typical probe is in the range of between 10 and 25
nucleotides long.
[0112] Various methods for synthesizing primers and probes are well
known in the art. Similarly, methods for attaching labels to
primers or probes are also well known in the art. For example, it
is a matter of routine to synthesize desired nucleic acid primers
or probes using conventional nucleotide phosphoramidite chemistry
and instruments available from Applied Biosystems, Inc., (Foster
City, Calif.), DuPont (Wilmington, Del.), or Milligen (Bedford
Mass.). Many methods have been described for labeling
oligonucleotides such as the primers or probes of the present
invention. Enzo Biochemical (New York, N.Y.) and Clontech (Palo
Alto, Calif.) both have described and commercialized probe labeling
techniques. For example, a primary amine can be attached to a 3'
oligo terminus using 3'-Amine-ON CPG.TM. (Clontech, Palo Alto,
Calif.). Similarly, a primary amine can be attached to a 5' oligo
terminus using Aminomodifier II.RTM. (Clontech). The amines can be
reacted to various haptens using conventional activation and
linking chemistries. In addition, copending applications U.S. Ser.
Nos. 625,566, filed Dec. 11, 1990 and 630,908, filed Dec. 20, 1990,
which are each incorporated herein by reference, teach methods for
labeling probes at their 5' and 3' termini, respectively.
International Publication NOS WO 92/10505, published Jun. 25, 1992,
and WO 92/11388, published Jul. 9, 1992, teach methods for labeling
probes at their 5' and 3' ends, respectively. According to one
known method for labeling an oligonucleotide, a
label-phosphoramidite reagent is prepared and used to add the label
to the oligonucleotide during its synthesis. See, for example, N.
T. Thuong et al., Tet. Letters 29(46):5905-5908 (1988); or J. S.
Cohen et al., published U.S. patent application Ser. No. 07/246,688
(NTIS ORDER No. PAT-APPL-7-246,688) (1989). Preferably, probes are
labeled at their 3' and 5' ends.
[0113] A capture label is attached to the primers or probes and can
be a specific binding member which forms a binding pair with the
solid phase reagent's specific binding member. It will be
understood that the primer or probe itself may serve as the capture
label. For example, in the case where a solid phase reagent's
binding member is a nucleic acid sequence, it may be selected such
that it binds a complementary portion of the primer or probe to
thereby immobilize the primer or probe to the solid phase. In cases
where the probe itself serves as the binding member, those skilled
in the art will recognize that the probe will contain a sequence or
"tail" that is not complementary to the single stranded amplicon
members. In the case where the primer itself serves as the capture
label, at least a portion of the primer will be free to hybridize
with a nucleic acid on a solid phase because the probe is selected
such that it is not fully complementary to the primer sequence.
[0114] Generally, probe/single stranded amplicon member complexes
can be detected using techniques commonly employed to perform
heterogeneous immunoassays. Preferably, in this embodiment,
detection is performed according to the protocols used by the
commercially available Abbott LCx.RTM. instrumentation (Abbott
Laboratories, Abbott Park, Ill.).
[0115] The primers and probes disclosed herein are useful in
typical PCR assays, wherein the test sample is contacted with a
pair of primers, amplification is performed, the hybridization
probe is added, and detection is performed.
[0116] Another method provided by the present invention comprises
contacting a test sample with a plurality of polynucleotides,
wherein at least one polynucleotide is a CS193 molecule as
described herein, hybridizing the test sample with the plurality of
polynucleotides and detecting hybridization complexes.
Hybridization complexes are identified and quantitated to compile a
profile which is indicative of GI tract tissue disease, such as GI
tract cancer. Expressed RNA sequences may further be detected by
reverse transcription and amplification of the DNA product by
procedures well-known in the art, including polymerase chain
reaction (PCR).
[0117] Drug Screening and Gene Therapy
[0118] The present invention also encompasses the use of gene
therapy methods for the introduction of anti-sense CS193 derived
molecules, such as polynucleotides or oligonucleotides of the
present invention, into patients with conditions associated with
abnormal expression of polynucleotides related to a GI tract tissue
disease or condition especially GI tract cancer. These molecules,
including antisense RNA and DNA fragments and ribozymes, are
designed to inhibit the translation of CS193-mRNA, and may be used
therapeutically in the treatment of conditions associated with
altered or abnormal expression of CS193 polynucleotide.
[0119] Alternatively, the oligonucleotides described above can be
delivered to cells by procedures known in the art such that the
anti-sense RNA or DNA may be expressed in vivo to inhibit
production of a CS193 polypeptide in the manner described above.
Antisense constructs to a CS193 polynucleotide, therefore, reverse
the action of CS193 transcripts and may be used for treating GI
tract tissue disease conditions, such as GI tract cancer. These
antisense constructs may also be used to treat tumor
metastases.
[0120] The present invention also provides a method of screening a
plurality of compounds for specific binding to CS193
polypeptide(s), or any fragment thereof, to identify at least one
compound which specifically binds the CS193 polypeptide. Such a
method comprises the steps of providing at least one compound;
combining the CS193 polypeptide with each compound under suitable
conditions for a time sufficient to allow binding; and detecting
the CS193 polypeptide binding to each compound.
[0121] The polypeptide or peptide fragment employed in such a test
may either be free in solution, affixed to a solid support, borne
on a cell surface or located intracellularly. One method of
screening utilizes eukaryotic or prokaryotic host cells which are
stably transfected with recombinant nucleic acids which can express
the polypeptide or peptide fragment. A drug, compound, or any other
agent may be screened against such transfected cells in competitive
binding assays. For example, the formation of complexes between a
polypeptide and the agent being tested can be measured in either
viable or fixed cells.
[0122] The present invention thus provides methods of screening for
drugs, compounds, or any other agent which can be used to treat
diseases associated with CS193. These methods comprise contacting
the agent with a polypeptide or fragment thereof and assaying for
either the presence of a complex between the agent and the
polypeptide, or for the presence of a complex between the
polypeptide and the cell. In competitive binding assays, the
polypeptide typically is labeled. After suitable incubation, free
(or uncomplexed) polypeptide or fragment thereof is separated from
that present in bound form, and the amount of free or uncomplexed
label is used as a measure of the ability of the particular agent
to bind to the polypeptide or to interfere with the
polypeptide/cell complex.
[0123] The present invention also encompasses the use of
competitive screening assays in which neutralizing antibodies
capable of binding polypeptide specifically compete with a test
agent for binding to the polypeptide or fragment thereof. In this
manner, the antibodies can be used to detect the presence of any
polypeptide in the test sample which shares one or more antigenic
determinants with a CS193 polypeptide as provided herein.
[0124] Another technique for screening provides high throughput
screening for compounds having suitable binding affinity to at
least one polypeptide of CS193 disclosed herein. Briefly, large
numbers of different small peptide test compounds are synthesized
on a solid phase, such as plastic pins or some other surface. The
peptide test compounds are reacted with polypeptide and washed.
Polypeptide thus bound to the solid phase is detected by methods
well-known in the art. Purified polypeptide can also be coated
directly onto plates for use in the screening techniques described
herein. In addition, non-neutralizing antibodies can be used to
capture the polypeptide and immobilize it on the solid support.
See, for example, EP 84/03564, published on Sep. 13, 1984, which is
incorporated herein by reference.
[0125] The goal of rational drug design is to produce structural
analogs of biologically active polypeptides of interest or of the
small molecules including agonists, antagonists, or inhibitors with
which they interact. Such structural analogs can be used to design
drugs which are more active or stable forms of the polypeptide or
which enhance or interfere with the function of a polypeptide in
vivo. J. Hodgson, Bio/Technology 9:19-21 (1991), incorporated
herein by reference.
[0126] For example, in one approach, the three-dimensional
structure of a polypeptide, or of a polypeptide-inhibitor complex,
is determined by x-ray crystallography, by computer modeling or,
most typically, by a combination of the two approaches. Both the
shape and charges of the polypeptide must be ascertained to
elucidate the structure and to determine active site(s) of the
molecule. Less often, useful information regarding the structure of
a polypeptide may be gained by modeling based on the structure of
homologous proteins. In both cases, relevant structural information
is used to design analogous polypeptide-like molecules or to
identify efficient inhibitors
[0127] Useful examples of rational drug design may include
molecules which have improved activity or stability as shown by S.
Braxton et al., Biochemistry 31:7796-7801 (1992), or which act as
inhibitors, agonists, or antagonists of native peptides as shown by
S. B. P. Athauda et al., J Biochem. (Tokyo) 113 (6):742-746 (1993),
incorporated herein by reference.
[0128] It also is possible to isolate a target-specific antibody
selected by an assay as described hereinabove, and then to
determine its crystal structure. In principle this approach yields
a pharmacophore upon which subsequent drug design can be based. It
further is possible to bypass protein crystallography altogether by
generating anti-idiotypic antibodies ("anti-ids") to a functional,
pharmacologically active antibody. As a mirror image of a mirror
image, the binding site of the anti-id is an analog of the original
receptor. The anti-id then can be used to identify and isolate
peptides from banks of chemically or biologically produced
peptides. The isolated peptides then can act as the pharmacophore
(that is, a prototype pharmaceutical drug).
[0129] A sufficient amount of a recombinant polypeptide of the
present invention may be made available to perform analytical
studies such as X-ray crystallography. In addition, knowledge of
the polypeptide amino acid sequence which is derivable from the
nucleic acid sequence provided herein will provide guidance to
those employing computer modeling techniques in place of, or in
addition to, x-ray crystallography.
[0130] Antibodies specific to a CS193 polypeptide (e.g., anti-CS193
antibodies) further may be used to inhibit the biological action of
the polypeptide by binding to the polypeptide. In this manner, the
antibodies may be used in therapy, for example, to treat GI tract
tissue diseases including GI tract cancer and its metastases.
[0131] Further, such antibodies can detect the presence or absence
of a CS193 polypeptide in a test sample and, therefore, are useful
as diagnostic markers for the diagnosis of a GI tract tissue
disease or condition especially GI tract cancer. Such antibodies
may also function as a diagnostic marker for GI tract tissue
disease conditions, such as GI tract cancer.
[0132] The present invention also is directed to antagonists and
inhibitors of the polypeptides of the present invention. The
antagonists and inhibitors are those which inhibit or eliminate the
function of the polypeptide. Thus, for example, an antagonist may
bind to a polypeptide of the present invention and inhibit or
eliminate its function. The antagonist, for example, could be an
antibody against the polypeptide which eliminates the activity of a
CS193 polypeptide by binding a CS193 polypeptide, or in some cases
the antagonist may be an oligonucleotide. Examples of small
molecule inhibitors include, but are not limited to, small peptides
or peptide-like molecules.
[0133] The antagonists and inhibitors may be employed as a
composition with a pharmaceutically acceptable carrier including,
but not limited to, saline, buffered saline, dextrose, water,
glycerol, ethanol and combinations thereof. Administration of CS193
polypeptide inhibitors is preferably systemic. The present
invention also provides an antibody which inhibits the action of
such a polypeptide.
[0134] Antisense technology can be used to reduce gene expression
through triple-helix formation or antisense DNA or RNA, both of
which methods are based on binding of a polynucleotide to DNA or
RNA. For example, the 5' coding portion of the polynucleotide
sequence, which encodes for the polypeptide of the present
invention, is used to design an antisense RNA oligonucleotide of
from 10 to 40 base pairs in length. A DNA oligonucleotide is
designed to be complementary to a region of the gene involved in
transcription, thereby preventing transcription and the production
of the CS193 polypeptide. For triple helix, see, for example, Lee
et al., Nuc. Acids Res. 6:3073 (1979); Cooney et al., Science
241:456 (1988); and Dervan et al., Science 251:1360 (1991) The
antisense RNA oligonucleotide hybridizes to the mRNA in vivo and
blocks translation of a mRNA molecule into the CS193 polypeptide.
For antisense, see, for example, Okano, J. Neurochem. 56:560
(1991); and "Oligodeoxynucleotides as Antisense Inhibitors of Gene
Expression," CRC Press, Boca Raton, Fla. (1988). Antisense
oligonucleotides act with greater efficacy when modified to contain
artificial internucleotide linkages which render the molecule
resistant to nucleolytic cleavage. Such artificial internucleotide
linkages include, but are not limited to, methylphosphonate,
phosphorothiolate and phosphoroamydate internucleotide
linkages.
[0135] Recombinant Technology
[0136] The present invention provides host cells and expression
vectors comprising CS193 polynucleotides of the present invention
and methods for the production of the polypeptide(s) they encode.
Such methods comprise culturing the host cells under conditions
suitable for the expression of the CS193 polynucleotide and
recovering the CS193 polypeptide from the cell culture.
[0137] The present invention also provides vectors which include
CS193 polynucleotides of the present invention, host cells which
are genetically engineered with vectors of the present invention
and the production of polypeptides of the present invention by
recombinant techniques.
[0138] Host cells are genetically engineered (transfected,
transduced or transformed) with the vectors of this invention which
may be cloning vectors or expression vectors. The vector may be in
the form of a plasmid, a viral particle, a phage, etc. The
engineered host cells can be cultured in conventional nutrient
media modified as appropriate for activating promoters, selecting
transfected cells, or amplifying CS193 gene(s). The culture
conditions, such as temperature, pH and the like, are those
previously used with the host cell selected for expression, and
will be apparent to the ordinarily skilled artisan.
[0139] The polynucleotides of the present invention may be employed
for producing a polypeptide by recombinant techniques. Thus, the
polynucleotide sequence may be included in any one of a variety of
expression vehicles, in particular, vectors or plasmids for
expressing a polypeptide. Such vectors include chromosomal,
nonchromosomal and synthetic DNA sequences; e.g., derivatives of
SV40; bacterial plasmids; phage DNA; yeast plasmids; vectors
derived from combinations of plasmids and phage DNA, viral DNA such
as vaccinia, adenovirus, fowl pox virus and pseudorabies. However,
any other plasmid or vector may be used so long as it is replicable
and viable in the host.
[0140] The appropriate DNA sequence may be inserted into the vector
by a variety of procedures. In general, the DNA sequence is
inserted into appropriate restriction endonuclease sites by
procedures known in the art. Such procedures and others are deemed
to be within the scope of those skilled in the art. The DNA
sequence in the expression vector is operatively linked to an
appropriate expression control sequence(s) (promoter) to direct
mRNA synthesis. Representative examples of such promoters include,
but are not limited to, the LTR or the SV40 promoter, the E. coli
lac or trp, the phage lambda P sub L promoter and other promoters
known to control expression of genes in prokaryotic or eukaryotic
cells or their viruses. The expression vector also contains a
ribosome binding site for translation initiation and a
transcription terminator. The vector may also include appropriate
sequences for amplifying expression. In addition, the expression
vectors preferably contain a gene to provide a phenotypic trait for
selection of transfected host cells such as dihydrofolate reductase
or neomycin resistance for eukaryotic cell culture, or such as
tetracycline or ampicillin resistance in E. coli.
[0141] The vector containing the appropriate DNA sequence as
hereinabove described, as well as an appropriate promoter or
control sequence, may be employed to transfect an appropriate host
to permit the host to express the protein. As representative
examples of appropriate hosts, there may be mentioned: bacterial
cells, such as E. coli, Salmonella typhimurium; Streptomyces sp.;
fungal cells, such as yeast; insect cells, such as Drosophila and
Sf9; animal cells, such as CHO, COS or Bowes melanoma; plant cells,
etc. The selection of an appropriate host is deemed to be within
the scope of those skilled in the art from the teachings provided
herein.
[0142] More particularly, the present invention also includes
recombinant constructs comprising one or more of the sequences as
broadly described above. The constructs comprise a vector, such as
a plasmid or viral vector, into which a sequence of the invention
has been inserted, in a forward or reverse orientation. In a
preferred aspect of this embodiment, the construct further
comprises regulatory sequences including, for example, a promoter,
operably linked to the sequence. Large numbers of suitable vectors
and promoters are known to those of skill in the art and are
commercially available. The following vectors are provided by way
of example. Bacterial: pINCY (Incyte Pharmaceuticals Inc., Palo
Alto, Calif.), pSPORT1 (Life Technologies, Gaithersburg, Md.),
pQE70, pQE60, pQE-9 (Qiagen) pBs, phagescript, psiX 174,
pBluescript SK, pBsKS, pNH8a, pNH16a, pNH 18a, pNH46a (Stratagene);
pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia); Eukaryotic:
pWLneo, pSV2cat, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG,
pSVL (Pharmacia). However, any other plasmid or vector may be used
as long as it is replicable and viable in the host.
[0143] Plasmid pINCY is generally identical to the plasmid pSPORT1
(available from Life Technologies, Gaithersburg, Md.) with the
exception that it has two modifications in the polylinker (multiple
cloning site). These modifications are (1) it lacks a HindIII
restriction site and (2) its EcoRI restriction site lies at a
different location. pINCY is created from pSPORT1 by cleaving
pSPORT1 with both HindIII and EcoRI and replacing the excised
fragment of the polylinker with synthetic DNA fragments (SEQUENCE
ID NO 19 and SEQUENCE ID NO 20). This replacement may be made in
any manner known to those of ordinary skill in the art. For
example, the two nucleotide sequences, SEQUENCE ID NO 19 and
SEQUENCE ID NO 20, may be generated synthetically with 5' terminal
phosphates, mixed together, and then ligated under standard
conditions for performing staggered end ligations into the pSPORT1
plasmid cut with HindIII and EcoRI. Suitable host cells (such as E.
coli DH5.mu. cells) then are transfected with the ligated DNA and
recombinant clones are selected for ampicillin resistance. Plasmid
DNA then is prepared from individual clones and subjected to
restriction enzyme analysis or DNA sequencing in order to confirm
the presence of insert sequences in the proper orientation. Other
cloning strategies known to the ordinary artisan also may be
employed.
[0144] Promoter regions can be selected from any desired gene using
CAT (chloramphenicol transferase) vectors or other vectors with
selectable markers. Two appropriate vectors are pKK232-8 and pCM7.
Particular named bacterial promoters include lac, lacZ, T3, SP6,
T7, gpt, lambda P sub R, P sub L and trp. Eukaryotic promoters
include cytomegalovirus (CMV) immediate early, herpes simplex virus
(HSV) thymidine kinase, early and late SV40, LTRs from retroviruses
and mouse metallothionein-I. Selection of the appropriate vector
and promoter is well within the level of ordinary skill in the
art.
[0145] In a further embodiment, the present invention provides host
cells containing the above-described construct. The host cell can
be a higher eukaryotic cell, such as a mammalian cell, or a lower
eukaryotic cell, such as a yeast cell, or the host cell can be a
prokaryotic cell, such as a bacterial cell. Introduction of the
construct into the host cell can be effected by calcium phosphate
transfection, DEAE-Dextran mediated transfection, or
electroporation (L. Davis et al., "Basic Methods in Molecular
Biology," 2nd edition, Appleton and Lang, Paramount Publishing,
East Norwalk, Conn. (1994)).
[0146] The constructs in host cells can be used in a conventional
manner to produce the gene product encoded by the recombinant
sequence. Alternatively, the polypeptides of the invention can be
synthetically produced by conventional peptide synthesizers.
[0147] Recombinant proteins can be expressed in mammalian cells,
yeast, bacteria, or other cells, under the control of appropriate
promoters. Cell-free translation systems can also be employed to
produce such proteins using RNAs derived from the DNA constructs of
the present invention. Appropriate cloning and expression vectors
for use with prokaryotic and eukaryotic hosts are described by
Sambrook et al., Molecular Cloning: A Laboratory Manual, Second
Edition, (Cold Spring Harbor, N.Y., 1989), which is hereby
incorporated by reference.
[0148] Transcription of a DNA encoding the polypeptide(s) of the
present invention by higher eukaryotes is increased by inserting an
enhancer sequence into the vector. Enhancers are cis-acting
elements of DNA, usually about from 10 to 300 bp, that act on a
promoter to increase its transcription. Examples include the SV40
enhancer on the late side of the replication origin (bp 100 to
270), a cytomegalovirus early promoter enhancer, a polyoma enhancer
on the late side of the replication origin and adenovirus
enhancers.
[0149] Generally, recombinant expression vectors will include
origins of replication and selectable markers permitting
transfection of the host cell, e.g., the ampicillin resistance gene
of E. coli and S. cerevisiae TRP1 gene, and a promoter derived from
a highly-expressed gene to direct transcription of a downstream
structural sequence. Such promoters can be derived from operons
encoding glycolytic enzymes such as 3-phosphoglycerate kinase
(PGK), alpha factor, acid phosphatase, or heat shock proteins,
among others. The heterologous structural sequence is assembled in
appropriate phase with translation initiation and termination
sequences, and preferably, a leader sequence capable of directing
secretion of translated protein into the periplasmic space or
extracellular medium. Optionally, the heterologous sequence can
encode a fusion protein including an N-terminal identification
peptide imparting desired characteristics, e.g., stabilization or
simplified purification of expressed recombinant product.
[0150] Useful expression vectors for bacterial use are constructed
by inserting a structural DNA sequence encoding a desired protein
together with suitable translation initiation and termination
signals in operable reading phase with a functional promoter. The
vector will comprise one or more phenotypic selectable markers and
an origin of replication to ensure maintenance of the vector and
to, if desirable, provide amplification within the host. Suitable
prokaryotic hosts for transfection include E. coli, Bacillus
subtilis, Salmonella typhimurium and various species within the
genera Pseudomonas, Streptomyces and Staphylococcus, although
others may also be employed as a routine matter of choice.
[0151] Useful expression vectors for bacterial use comprise a
selectable marker and bacterial origin of replication derived from
plasmids comprising genetic elements of the well-known cloning
vector pBR322 (ATCC 37017). Other vectors include but are not
limited to PKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and
GEM1 (Promega Biotec, Madison, Wis.). These pBR322 "backbone"
sections are combined with an appropriate promoter and the
structural sequence to be expressed.
[0152] Following transfection of a suitable host and growth of the
host to an appropriate cell density, the selected promoter is
derepressed by appropriate means (e.g., temperature shift or
chemical induction), and cells are cultured for an additional
period. Cells are typically harvested by centrifugation, disrupted
by physical or chemical means, and the resulting crude extract
retained for further purification. Microbial cells employed in
expression of proteins can be disrupted by any convenient method
including freeze-thaw cycling, sonication, mechanical disruption,
or use of cell lysing agents. Such methods are well-known to the
ordinary artisan.
[0153] Various mammalian cell culture systems can also be employed
to express recombinant protein. Examples of mammalian expression
systems include the COS-7 lines of monkey kidney fibroblasts
described by Gluzman, Cell 23:175 (1981), and other cell lines
capable of expressing a compatible vector, such as the C127,
HEK-293, 3T3, CHO, HeLa and BHK cell lines. Mammalian expression
vectors will comprise an origin of replication, a suitable promoter
and enhancer and also any necessary ribosome binding sites,
polyadenylation sites, splice donor and acceptor sites,
transcriptional termination sequences and 5' flanking
nontranscribed sequences. DNA sequences derived from the SV40 viral
genome, for example, SV40 origin, early promoter, enhancer, splice,
and polyadenylation sites may be used to provide the required
nontranscribed genetic elements. Representative, useful vectors
include pRc/CMV and pcDNA3 (available from Invitrogen, San Diego,
Calif.).
[0154] CS193 polypeptides are recovered and purified from
recombinant cell cultures by known methods including affinity
chromatography, ammonium sulfate or ethanol precipitation, acid
extraction, anion or cation exchange chromatography,
phosphocellulose chromatography, hydrophobic interaction
chromatography, hydroxyapatite chromatography or lectin
chromatography. It is preferred to have low concentrations
(approximately 0.1-5 mM) of calcium ion present during purification
(Price, et al., J. Biol. Chem. 244:917 (1969)). Protein refolding
steps can be used, as necessary, in completing configuration of the
polypeptide. Finally, high performance liquid chromatography (HPLC)
can be employed for final purification steps.
[0155] Thus, polypeptides of the present invention may be naturally
purified products expressed from a high expressing cell line, or a
product of chemical synthetic procedures, or produced by
recombinant techniques from a prokaryotic or eukaryotic host (for
example, by bacterial, yeast, higher plant, insect and mammalian
cells in culture). Depending upon the host employed in a
recombinant production procedure, the polypeptides of the present
invention may be glycosylated with mammalian or other eukaryotic
carbohydrates or may be non-glycosylated. The polypeptides of the
invention may also include an initial methionine amino acid
residue.
[0156] The starting plasmids can be constructed from available
plasmids in accord with published, known procedures. In addition,
equivalent plasmids to those described are known in the art and
will be apparent to one of ordinary skill in the art.
[0157] The following is the general procedure for the isolation and
analysis of cDNA clones. In a particular embodiment disclosed
herein, mRNA was isolated from GI tract tissue and used to generate
the cDNA library. GI tract tissue was obtained from patients by
surgical resection and was classified as tumor or non-tumor tissue
by a pathologist.
[0158] The cDNA inserts from random isolates of the GI tract tissue
libraries were sequenced in part, analyzed in detail as set forth
in the Examples and are disclosed in the Sequence Listing as
SEQUENCE ID NOS 1-15. Also analyzed in detail as set forth in the
Examples, and disclosed in the Sequence Listing, are the
full-length sequences of clones 774134 and 774419 (referred to as
clones 7741341H and 7744191H (SEQUENCE ID NOS 16 and 17,
respectively)). The consensus sequence of these inserts is
presented as SEQUENCE ID NO 18. These polynucleotides may contain
an entire open reading frame with or without associated regulatory
sequences for a particular gene, or they may encode only a portion
of the gene of interest. This is attributed to the fact that many
genes are several hundred and sometimes several thousand bases in
length and, with current technology, cannot be cloned in their
entirety because of vector limitations, incomplete reverse
transcription of the first strand, or incomplete replication of the
second strand. Contiguous, secondary clones containing additional
nucleotide sequences may be obtained using a variety of methods
known to those of skill in the art.
[0159] Methods for DNA sequencing are well known in the art.
Conventional enzymatic methods employ DNA polymerase, Klenow
fragment, Sequenase (US Biochemical Corp, Cleveland, Ohio) or Taq
polymerase to extend DNA chains from an oligonucleotide primer
annealed to the DNA template of interest. Methods have been
developed for the use of both single-stranded and double-stranded
templates. The chain termination reaction products may be
electrophoresed on urea/polyacrylamide gels and detected either by
autoradiography (for radionucleotide labeled precursors) or by
fluorescence (for fluorescent-labeled precursors). Recent
improvements in mechanized reaction preparation, sequencing and
analysis using the fluorescent detection method have permitted
expansion in the number of sequences that can be determined per day
using machines such as the Applied Biosystems 377 DNA Sequencers
(Applied Biosystems, Foster City, Calif.).
[0160] The reading frame of the nucleotide sequence can be
ascertained by several types of analyses. First, reading frames
contained within the coding sequence can be analyzed for the
presence of start codon ATG and stop codons TGA, TAA or TAG.
Typically, one reading frame will continue throughout the major
portion of a cDNA sequence while other reading frames tend to
contain numerous stop codons. In such cases, reading frame
determination is straightforward. In other more difficult cases,
further analysis is required.
[0161] Algorithms have been created to analyze the occurrence of
individual nucleotide bases at each putative codon triplet. See,
for example J. W. Fickett, Nuc. Acids Res. 10:5303 (1982). Coding
DNA for particular organisms (bacteria, plants and animals) tends
to contain certain nucleotides within certain triplet
periodicities, such as a significant preference for pyrimidines in
the third codon position. These preferences have been incorporated
into widely available software which can be used to determine
coding potential (and frame) of a given stretch of DNA. The
algorithm-derived information combined with start/stop codon
information can be used to determine proper frame with a high
degree of certainty. This, in turn, readily permits cloning of the
sequence in the correct reading frame into appropriate expression
vectors.
[0162] The nucleic acid sequences disclosed herein may be joined to
a variety of other polynucleotide sequences and vectors of interest
by means of well-established recombinant DNA techniques. See J.
Sambrook et al., supra. Vectors of interest include cloning
vectors, such as plasmids, cosmids, phage derivatives, phagemids,
as well as sequencing, replication and expression vectors, and the
like. In general, such vectors contain an origin of replication
functional in at least one organism, convenient restriction
endonuclease digestion sites and selectable markers appropriate for
particular host cells. The vectors can be transferred by a variety
of means known to those of skill in the art into suitable host
cells which then produce the desired DNA, RNA, or polypeptides.
[0163] Occasionally, sequencing or random reverse transcription
errors will mask the presence of the appropriate open reading frame
or regulatory element. In such cases, it is possible to determine
the correct reading frame by attempting to express the polypeptide
and determining the amino acid sequence by standard peptide mapping
and sequencing techniques. See, F. M. Ausubel et al., Current
Protocols in Molecular Biology, John Wiley & Sons, New York,
N.Y. (1989). Additionally, the actual reading frame of a given
nucleotide sequence may be determined by transfection of host cells
with vectors containing all three potential reading frames. Only
those cells with the nucleotide sequence in the correct reading
frame will produce a peptide of the predicted length.
[0164] The nucleotide sequences provided herein have been prepared
by current, state-of-the-art, automated methods and, as such, may
contain unidentified nucleotides. These will not present a problem
to those skilled in the art who wish to practice the invention.
Several methods employing standard recombinant techniques,
described in J. Sambrook (supra) or periodic updates thereof, may
be used to complete the missing sequence information. The same
techniques used for obtaining a full length sequence, as described
herein, may be used to obtain nucleotide sequences.
[0165] Expression of a particular cDNA may be accomplished by
subcloning the cDNA into an appropriate expression vector and
transfecting this vector into an appropriate expression host. The
cloning vector used for the generation of the GI tract tissue cDNA
library can be used for transcribing mRNA of a particular cDNA and
contains a promoter for beta-galactosidase, an amino-terminal met
and the subsequent seven amino acid residues of beta-galactosidase.
Immediately following these eight residues is an engineered
bacteriophage promoter useful for artificial priming and
transcription, as well as a number of unique restriction sites,
including EcoRI, for cloning. The vector can be transfected into an
appropriate host strain of E. coli.
[0166] Induction of the isolated bacterial strain with
isopropylthiogalactoside (IPTG) using standard methods will produce
a fusion protein which contains the first seven residues of
beta-galactosidase, about 15 residues of linker and the peptide
encoded within the cDNA. Since cDNA clone inserts are generated by
an essentially random process, there is one chance in three that
the included cDNA will lie in the correct frame for proper
translation. If the cDNA is not in the proper reading frame, the
correct frame can be obtained by deletion or insertion of an
appropriate number of bases by well known methods including in
vitro mutagenesis, digestion with exonuclease III or mung bean
nuclease, or oligonucleotide linker inclusion.
[0167] The cDNA can be shuttled into other vectors known to be
useful for expression of protein in specific hosts. Oligonucleotide
primers containing cloning sites and segments of DNA sufficient to
hybridize to stretches at both ends of the target cDNA can be
synthesized chemically by standard methods. These primers can then
be used to amplify the desired gene segments by PCR. The resulting
new gene segments can be digested with appropriate restriction
enzymes under standard conditions and isolated by gel
electrophoresis. Alternately, similar gene segments can be produced
by digestion of the cDNA with appropriate restriction enzymes and
filling in the missing gene segments with chemically synthesized
oligonucleotides. Segments of the coding sequence from more than
one gene can be ligated together and cloned in appropriate vectors
to optimize expression of recombinant sequence.
[0168] Suitable expression hosts for such chimeric molecules
include, but are not limited to, mammalian cells, such as Chinese
Hamster Ovary (CHO) and human embryonic kidney (HEK) 293 cells,
insect cells such as Sf9 cells, yeast cells, such as Saccharomyces
cerevisiae and bacteria, such as E. coli. For each of these cell
systems, a useful expression vector may also include an origin of
replication to allow propagation in bacteria and a selectable
marker such as the beta-lactamase antibiotic resistance gene to
allow selection in bacteria. In addition, the vectors may include a
second selectable marker, such as the neomycin phosphotransferase
gene, to allow selection in transfected eukaryotic host cells.
Vectors for use in eukaryotic expression hosts may require the
addition of 3' poly A tail if the sequence of interest lacks poly
A.
[0169] Additionally, the vector may contain promoters or enhancers
which increase gene expression. Such promoters are host specific
and include, but are not limited to, MMTV, SV40, or metallothionine
promoters for CHO cells; trp, lac, tac or T7 promoters for
bacterial hosts; or alpha factor, alcohol oxidase or PGH promoters
for yeast. Adenoviral vectors with or without transcription
enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be
used to drive protein expression in mammalian cell lines. Once
homogeneous cultures of recombinant cells are obtained, large
quantities of recombinantly produced protein can be recovered from
the conditioned medium and analyzed using chromatographic methods
well known in the art. An alternative method for the production of
large amounts of secreted protein involves the transfection of
mammalian embryos and the recovery of the recombinant protein from
milk produced by transgenic cows, goats, sheep, etc. Polypeptides
and closely related molecules may be expressed recombinantly in
such away as to facilitate protein purification. One approach
involves expression of a chimeric protein which includes one or
more additional polypeptide domains not naturally present on human
polypeptides. Such purification-facilitating domains include, but
are not limited to, metal-chelating peptides such as
histidine-tryptophan domains that allow purification on immobilized
metals, protein A domains that allow purification on immobilized
immunoglobulin and the domain utilized in the FLAGS
extension/affinity purification system (Immunex Corp, Seattle,
Wash.). The inclusion of a cleavable linker sequence such as Factor
XA or enterokinase from Invitrogen (San Diego, Calif.) between the
polypeptide sequence and the purification domain may be useful for
recovering the polypeptide.
[0170] Immunoassays
[0171] CS193 polypeptides, including fragments, derivatives, and
analogs thereof, or cells expressing such polypeptides, can be
utilized in a variety of assays, many of which are described
herein, for the detection of antibodies to GI tract tissue. They
also can be used as immunogens to produce antibodies. These
antibodies can be, for example, polyclonal or monoclonal
antibodies, chimeric, single chain and humanized antibodies, as
well as Fab fragments, or the product of an Fab expression library.
Various procedures known in the art may be used for the production
of such antibodies For example, antibodies generated against a
polypeptide comprising a sequence of the present invention can be
obtained by direct injection of the polypeptide into an animal or
by administering the polypeptide to an animal such as a mouse,
rabbit, goat or human. A mouse, rabbit or goat is preferred. The
polypeptide is selected from the group consisting of SEQUENCE ID
NOS 41-49, and fragments thereof. The antibody so obtained then
will bind the polypeptide itself. In this manner, even a sequence
encoding only a fragment of the polypeptide can be used to generate
antibodies that bind the native polypeptide. Such antibodies then
can be used to isolate the polypeptide from test samples such as
tissue suspected of containing that polypeptide. For preparation of
monoclonal antibodies, any technique which provides antibodies
produced by continuous cell line cultures can be used. Examples
include the hybridoma technique as described by Kohler and
Milstein, Nature 256:495-497 (1975), the trioma technique, the
human B-cell hybridoma technique as described by Kozbor et al,
Immun. Today 4:72 (1983) and the EBV-hybridoma technique to produce
human monoclonal antibodies as described by Cole et al., in
Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc, New
York, N.Y., pp. 77-96 (1985). Techniques described for the
production of single chain antibodies can be adapted to produce
single chain antibodies to immunogenic polypeptide products of this
invention. See, for example, U.S. Pat. No. 4,946,778, which is
incorporated herein by reference.
[0172] Various assay formats may utilize the antibodies of the
present invention, including "sandwich" immunoassays and probe
assays. For example, the antibodies of the present invention, or
fragments thereof, can be employed in various assay systems to
determine the presence, if any, of CS193 antigen in a test sample.
For example, in a first assay format, a polyclonal or monoclonal
antibody or fragment thereof, or a combination of these antibodies,
which has been coated on a solid phase, is contacted with a test
sample, to form a first mixture. This first mixture is incubated
for a time and under conditions sufficient to form antigen/antibody
complexes. Then, an indicator reagent comprising a monoclonal or a
polyclonal antibody or a fragment thereof, or a combination of
these antibodies, to which a signal generating compound has been
attached, is contacted with the antigen/antibody complexes to form
a second mixture. This second mixture then is incubated for a time
and under conditions sufficient to form antibody/antigen/antibody
complexes. The presence of CS193 antigen in the test sample and
captured on the solid phase, if any, is determined by detecting the
measurable signal generated by the signal generating compound. The
amount of CS193 antigen present in the test sample is proportional
to the signal generated.
[0173] In an alternative assay format, a mixture is formed by
contacting: (1) a polyclonal antibody, monoclonal antibody, or
fragment thereof, which specifically binds to CS193 antigen, or a
combination of such antibodies bound to a solid support; (2) the
test sample; and (3) an indicator reagent comprising a monoclonal
antibody, polyclonal antibody, or fragment thereof, which
specifically binds to a different CS193 antigen (or a combination
of these antibodies) to which a signal generating compound is
attached. This mixture is incubated for a time and under conditions
sufficient to form antibody/antigen/antibody complexes. The
presence, if any, of CS193 antigen present in the test sample and
captured on the solid phase is determined by detecting the
measurable signal generated by the signal generating compound. The
amount of CS193 antigen present in the test sample is proportional
to the signal generated.
[0174] In another assay format, one or a combination of at least
two monoclonal antibodies of the invention can be employed as a
competitive probe for the detection or antibodies to CS193 antigen.
For example, CS193 polypeptides such as the recombinant antigens
disclosed herein, either alone or in combination, are coated on a
solid phase. A test sample suspected of containing antibody to
CS193 antigen then is incubated with an indicator reagent
comprising a signal generating compound and at least one monoclonal
antibody of the invention for a time and under conditions
sufficient to form antigen/antibody complexes of either the test
sample and indicator reagent bound to the solid phase or the
indicator reagent bound to the solid phase. The reduction in
binding of the monoclonal antibody to the solid phase can be
quantitatively measured.
[0175] In yet another detection method, each of the monoclonal or
polyclonal antibodies of the present invention can be employed in
the detection of CS193 antigens in tissue sections, as well as in
cells, by immunohistochemical analysis. Cytochemical analysis
wherein these antibodies are labeled directly (with, for example,
fluorescein, colloidal gold, horseradish peroxidase, alkaline
phosphatase, etc.) or are labeled by using secondary labeled
anti-species antibodies (with various labels as exemplified herein)
to track the histopathology of disease also are within the scope of
the present invention.
[0176] In addition, these monoclonal antibodies can be bound to
matrices similar to CNBr-activated Sepharose and used for the
affinity purification of specific CS193 polypeptides from cell
cultures or biological tissues such as to purify recombinant and
native CS193 proteins.
[0177] The monoclonal antibodies of the invention also can be used
for the generation of chimeric antibodies for therapeutic use, or
other similar applications.
[0178] The monoclonal antibodies or fragments thereof can be
provided individually to detect CS193 antigens. Combinations of the
monoclonal antibodies (and fragments thereof) provided herein also
may be used together as components in a mixture or "cocktail" of at
least one CS193 antibody of the invention, along with antibodies
which specifically bind to other CS193 regions, each antibody
having different binding specificities. Thus, this cocktail can
include the monoclonal antibodies of the invention which are
directed to CS193 polypeptides disclosed herein and other
monoclonal antibodies specific to other antigenic determinants of
CS193 antigens or other related proteins.
[0179] The polyclonal antibody or fragment thereof which can be
used in the assay formats should specifically bind to a CS193
polypeptide or other CS193 polypeptides additionally used in the
assay. The polyclonal antibody used preferably is of mammalian
origin such as, human, goat, rabbit or sheep polyclonal antibody
which binds CS193 polypeptide. Most preferably, the polyclonal
antibody is of rabbit origin. The polyclonal antibodies used in the
assays can be used either alone or as a cocktail of polyclonal
antibodies. Since the cocktails used in the assay formats are
comprised of either monoclonal antibodies or polyclonal antibodies
having different binding specificity to CS193 polypeptides, they
are useful for the detecting, diagnosing, staging, monitoring,
prognosticating, preventing or treating, or determining the
predisposition to, diseases and conditions of the GI tract, such as
GI tract cancer.
[0180] It is contemplated and within the scope of the present
invention that CS193 antigen may be detectable in assays by use of
a recombinant antigen as well as by use of a synthetic peptide or
purified peptide, which peptide comprises an amino acid sequence of
CS193. The amino acid sequence of such a polypeptide is selected
from the group consisting of SEQUENCE ID NOS 41-49, and fragments
thereof. It also is within the scope of the present invention that
different synthetic, recombinant or purified peptides, identifying
different epitopes of CS193, can be used in combination in an assay
for the detecting, diagnosing, staging, monitoring,
prognosticating, preventing or treating, or determining the
predisposition to diseases and conditions of the GI tract, such as
GI tract cancer. In this case, all of these peptides can be coated
onto one solid phase. Alternatively, each separate peptide may be
coated onto separate solid phases, such as microparticles, and then
combined to form a mixture of peptides which can be later used in
assays. Furthermore, it is contemplated that multiple peptides
which define epitopes from different antigens may be used for the
detection, diagnosis, staging, monitoring, prognosis, prevention or
treatment of, or determining the predisposition to, diseases and
conditions of the GI tract such as GI tract cancer. Peptides coated
on solid phases or labeled with detectable labels are then allowed
to compete with those present in a patient sample (if any) for a
limited amount of antibody. A reduction in binding of the
synthetic, recombinant, or purified peptides to the antibody (or
antibodies) is an indication of the presence of CS193 antigen in
the patient sample. The presence of CS193 antigen indicates the
presence of GI tract tissue disease, especially GI tract cancer, in
the patient. Variations of assay formats are known to those of
ordinary skill in the art and many are discussed herein below.
[0181] In another assay format, the presence of anti-CS193 antibody
and/or CS193 antigen can be detected in a simultaneous assay, as
follows. A test sample is simultaneously contacted with a capture
reagent of a first analyte, wherein said capture reagent comprises
a first binding member specific for a first analyte attached to a
solid phase and a capture reagent for a second analyte, wherein
said capture reagent comprises a first binding member for a second
analyte attached to a second solid phase, to thereby form a
mixture. This mixture is incubated for a time and under conditions
sufficient to form capture reagent/first analyte and capture
reagent/second analyte complexes. These so-formed complexes then
are contacted with an indicator reagent comprising a member of a
binding pair specific for the first analyte labeled with a signal
generating compound and an indicator reagent comprising a member of
a binding pair specific for the second analyte labeled with a
signal generating compound to form a second mixture. This second
mixture is incubated for a time and under conditions sufficient to
form capture reagent/first analyte/indicator reagent complexes and
capture reagent/second analyte/indicator reagent complexes. The
presence of one or more analytes is determined by detecting a
signal generated in connection with the complexes formed on either
or both solid phases as an indication of the presence of one or
more analytes in the test sample. In this assay format, recombinant
antigens derived from the expression systems disclosed herein may
be utilized, as well as monoclonal antibodies produced from the
proteins derived from the expression systems as disclosed herein.
For example, in this assay system, CS193 antigen can be the first
analyte. Such assay systems are described in greater detail in EP
Publication No. 0473065.
[0182] In yet other assay formats, the polypeptides disclosed
herein may be utilized to detect the presence of antibody against
CS193 antigen in test samples. For example, a test sample is
incubated with a solid phase to which at least one polypeptide such
as a recombinant protein or synthetic peptide has been attached.
The polypeptide is selected from the group consisting of SEQUENCE
ID NOS 41-49, and fragments thereof. These are reacted for a time
and under conditions sufficient to form antigen/antibody complexes.
Following incubation, the antigen/antibody complex is detected.
Indicator reagents may be used to facilitate detection, depending
upon the assay system chosen.
[0183] In another assay format, a test sample is contacted with a
solid phase to which a recombinant protein produced as described
herein is attached, and also is contacted with a monoclonal or
polyclonal antibody specific for the protein, which preferably has
been labeled with an indicator reagent. After incubation for a time
and under conditions sufficient for antibody/antigen complexes to
form, the solid phase is separated from the free phase, and the
label is detected in either the solid or free phase as an
indication of the presence of antibody against CS193 antigen. Other
assay formats utilizing the recombinant antigens disclosed herein
are contemplated. These include contacting a test sample with a
solid phase to which at least one antigen from a first source has
been attached, incubating the solid phase and test sample for a
time and under conditions sufficient to form antigen/antibody
complexes, and then contacting the solid phase with a labeled
antigen, which antigen is derived from a second source different
from the first source. For example, a recombinant protein derived
from a first source such as E. coli is used as a capture antigen on
a solid phase, a test sample is added to the so-prepared solid
phase, and following standard incubation and washing steps as
deemed or required, a recombinant protein derived from a different
source (i.e., non-E. coli) is utilized as a part of an indicator
reagent which subsequently is detected. Likewise, combinations of a
recombinant antigen on a solid phase and synthetic peptide in the
indicator phase also are possible. Any assay format which utilizes
an antigen specific for CS193 produced or derived from a first
source as the capture antigen and an antigen specific for CS193
from a different second source is contemplated. Thus, various
combinations of recombinant antigens, as well as the use of
synthetic peptides, purified proteins and the like, are within the
scope of this invention. Assays such as this and others are
described in U.S. Pat. No. 5,254,458, which enjoys common ownership
and is incorporated herein by reference.
[0184] Other embodiments which utilize various other solid phases
also are contemplated and are within the scope of this invention.
For example, ion capture procedures for immobilizing an
immobilizable reaction complex with a negatively charged polymer
(described in EP publication 0326100 and EP publication No.
0406473), can be employed according to the present invention to
effect a fast solution-phase immunochemical reaction. An
immobilizable immune complex is separated from the rest of the
reaction mixture by ionic interactions between the negatively
charged poly-anion/immune complex and the previously treated,
positively charged porous matrix and detected by using various
signal generating systems previously described, including those
described in chemiluminescent signal measurements as described in
EPO Publication No. 0 273,115.
[0185] Also, the methods of the present invention can be adapted
for use in systems which utilize microparticle technology including
automated and semi-automated systems wherein the solid phase
comprises a microparticle (magnetic or non-magnetic). Such systems
include those described in, for example, published EPO applications
NOS. EP 0 425 633 and EP 0 424 634, respectively.
[0186] The use of scanning probe microscopy (SPM) for immunoassays
also is a technology to which the monoclonal antibodies of the
present invention are easily adaptable. In scanning probe
microscopy, particularly in atomic force microscopy, the capture
phase, for example, at least one of the monoclonal antibodies of
the invention, is adhered to a solid phase and a scanning probe
microscope is utilized to detect antigen/antibody complexes which
may be present on the surface of the solid phase. The use of
scanning tunneling microscopy eliminates the need for labels which
normally must be utilized in many immunoassay systems to detect
antigen/antibody complexes. The use of SPM to monitor specific
binding reactions can occur in many ways. In one embodiment, one
member of a specific binding partner (analyte specific substance
which is the monoclonal antibody of the invention) is attached to a
surface suitable for scanning. The attachment of the analyte
specific substance may be by adsorption to a test piece which
comprises a solid phase of a plastic or metal surface, following
methods known to those of ordinary skill in the art. Or, covalent
attachment of a specific binding partner (analyte specific
substance) to a test piece which test piece comprises a solid phase
of derivatized plastic, metal, silicon, or glass may be utilized.
Covalent attachment methods are known to those skilled in the art
and include a variety of means to irreversibly link specific
binding partners to the test piece. If the test piece is silicon or
glass, the surface must be activated prior to attaching the
specific binding partner. Also, polyelectrolyte interactions may be
used to immobilize a specific binding partner on a surface of a
test piece by using techniques and chemistries. The preferred
method of attachment is by covalent means. Following attachment of
a specific binding member, the surface may be further treated with
materials such as serum, proteins, or other blocking agents to
minimize non-specific binding. The surface also may be scanned
either at the site of manufacture or point of use to verify its
suitability for assay purposes. The scanning process is not
anticipated to alter the specific binding properties of the test
piece.
[0187] While the present invention discloses the preference for the
use of solid phases, it is contemplated that the reagents such as
antibodies, proteins and peptides of the present invention can be
utilized in non-solid phase assay systems. These assay systems are
known to those skilled in the art, and are considered to be within
the scope of the present invention.
[0188] It is contemplated that the reagent employed for the assay
can be provided in the form of a test kit with one or more
containers such as vials or bottles, with each container containing
a separate reagent such as a probe, primer, monoclonal antibody or
a cocktail of monoclonal antibodies, or a polypeptide (e.g.
recombinantly, synthetically produced or purified) employed in the
assay. The polypeptide is selected from the group consisting of
SEQUENCE ID NOS 4149, and fragments thereof. Other components such
as buffers, controls and the like, known to those of ordinary skill
in art, may be included in such test kits. It also is contemplated
to provide test kits which have means for collecting test samples
comprising accessible body fluids, e.g., blood, urine, saliva and
stool. Such tools useful for collection ("collection materials")
include lancets and absorbent taper or cloth for collecting and
stabilizing blood; swabs for collecting and stabilizing saliva;
cups for collecting and stabilizing urine or stool samples.
Collection materials, cloths, swabs, cups and the like, may
optionally be treated to avoid denaturation or irreversible
adsorption of the sample. The collection materials also may be
treated with or contain preservatives, stabilizers or antimicrobial
agents to help maintain the integrity of the specimens. Test kits
designed for the collection, stabilization and preservation of test
specimens obtained by surgery or needle biopsy are also useful. It
is contemplated that all kits may be configured in two components
which can be provided separately; one component for collection and
transport of the specimen and the other component for the analysis
of the specimen. The collection component, for example, can be
provided to the open market user while the components for analysis
can be provided to others such as laboratory personnel for
determination of the presence, absence or amount of analyte.
Further, kits for the collection, stabilization and preservation of
test specimens may be configured for use by untrained personnel and
may be available in the open market for use at home with subsequent
transportation to a laboratory for analysis of the test sample.
[0189] E. coli bacterium (clone 774134 and clone 774419) were
deposited with the Americas Type Culture Collection (A.T.C.C.),
12301 Parklawn Drive, Rockville, Md. 20852, on Sep. 12, 1997 and
Jun. 25, 1997, respectively, under the terms of the Budapest
Treaty, and will be maintained for a period of thirty (30) years
from the date of deposit, or for five (5) years after the last
request for the deposit, or for the enforceable period of the U.S.
patent. whichever is longer. These deposits, and any other
deposited material described herein, are provided for convenience
only and are not required to practice the present invention in view
of the teachings provided herein. The cDNA sequence in all of the
deposited material is incorporated herein by reference. Clones
774134 and 774419 were accorded A.T.C.C. Deposit NOS. 98543 and
98484, respectively.
[0190] The present invention will now be described by way of
examples, which are meant to illustrate, but not to limit, the
scope of the present invention.
EXAMPLES
Example 1
Identification of Gastrointestinal Tract Tissue Library CS193
Gene-Specific Clones
[0191] A. Library Comparison of Expressed Sequence Tags (ESTs) or
Transcript Images. Partial sequences of cDNA clone inserts,
so-called "expressed sequence tags" (ESTs), were derived from cDNA
libraries made from GI tract tumor tissues, GI tract non-tumor
tissues and numerous other tissues, both tumor and non-tumor and
entered into a database (LIFESEQ.TM. database, available from
Incyte Pharmaceuticals, Palo Alto, Calif.) as gene transcript
images. See International Publication No. WO 95/20681. (A
transcript image is a listing of the number of EST's for each of
the represented genes in a given tissue library. ESTs sharing
regions of mutual sequence overlap are classified into clusters. A
cluster is assigned a cone number from a representative 5' EST.
Often, a cluster of interest can be extended by comparing its
consensus sequence with sequences of other EST's which did not meet
the criteria for automated clustering. The alignment of all
available clusters and single ESTs represent a contig from which a
consensus sequence is derived.) The transcript images then were
evaluated to identify EST sequences that were representative
primarily of the GI tract tissue libraries. These target clones
then were ranked according to their abundance (occurrence) in the
target libraries and their absence from background libraries.
Higher abundance clones with low background occurrence were given
higher study priority. ESTs corresponding to the consensus sequence
of CS193 (SEQUENCE ID NO 18, and fragments or complements thereof)
were found in 28.6% (10 of 35) of GI tract tissue libraries. ESTs
corresponding to the consensus sequence of CS193 (SEQUENCE ID NO
18, and fragments or complements thereof) were found in 0.35% (I of
288) of the other, non-GI tract, libraries of the data base.
Therefore, the consensus sequence or fragment thereof was found
more than 82 times more often in GI tract than non-GI tract
tissues. Overlapping clones 2767646 (SEQUENCE ID NO 1), 774134
(SEQUENCE ID NO 2), 775437 (SEQUENCE ID NO 3), 1281329 (SEQUENCE ID
NO 4), 1628677 (SEQUENCE ID NO 5), 1286372 (SEQUENCE ID NO 6),
774419 (SEQUENCE ID NO 7), 3233118 (SEQUENCE ID NO 8), 2733923
(SEQUENCE ID NO 9), 906605 (SEQUENCE ID NO 10), 2771475 (SEQUENCE
ID NO 11), 1803247 (SEQUENCE ID NO 12), 1737526 (SEQUENCE ID NO
13), 2792957 (SEQUENCE ID NO 14), and 1226186 (SEQUENCE ID NO 15)
were identified for further study. These represented the minimum
number of clones that were needed to form the contig and from
which, along with the full-length sequence clones 774134IH and
774419IH (SEQUENCE ID NO 16 and SEQUENCE ID NO 17, respectively),
the consensus sequence provided herein (SEQUENCE ID NO 18) was
derived.
[0192] B. Generation of a Consensus Sequence. The nucleotide
sequences of clones 2767646 (SEQUENCE ID NO 1), 774134 (SEQUENCE ID
NO 2), 775437 (SEQUENCE ID NO 3),1281329 (SEQUENCE ID NO 4),1628677
(SEQUENCE ID NO 5),1286372 (SEQUENCE ID NO 6),774419 (SEQUENCE ID
NO 7), 3233118 (SEQUENCE ID NO 8),2733923 (SEQUENCE ID NO 9),906605
(SEQUENCE ID NO 10), 2771475 (SEQUENCE ID NO 11), 1803247 (SEQUENCE
ID NO 12), 1737526 (SEQUENCE ID NO 13),2792957 (SEQUENCE ID NO
14),1226186 (SEQUENCE ID NO 15), 7741341H (SEQUENCE ID NO 16), and
7744191H (SEQUENCE ID 17) were entered in the Sequencher.TM.
Program (available from Gene Codes Corporation, Ann Arbor, Mich.,
in order to generate a nucleotide alignment (contig map) and then
generate their consensus sequence (SEQUENCE ID NO 18). FIGS. 1A-G
show the nucleotide sequence alignment of these clones and their
resultant nucleotide consensus sequence (SEQUENCE ID NO 18). FIG. 2
presents the contig map depicting the clones 2767646 (SEQUENCE ID
NO 1), 774134 (SEQUENCE ID NO 2), 775437 (SEQUENCE ID NO 3),
1281329 (SEQUENCE ID NO 4), 1628677 (SEQUENCE ID NO 5),1286372
(SEQUENCE ID NO 6),774419 (SEQUENCE ID NO 7), 3233118 (SEQUENCE ID
NO 8), 2733923 (SEQUENCE ID NO 9), 906605 (SEQUENCE ID NO 10),
2771475 (SEQUENCE ID NO 11), 1803247 (SEQUENCE ID NO 12),1737526
(SEQUENCE ID NO 13),2792957 (SEQUENCE ID NO 14), 1226186 (SEQUENCE
ID NO 15), 7741341H (SEQUENCE ID NO 16), and 7744191H (SEQUENCE ID
17), which form overlapping regions of the CS193 gene, and the
resultant consensus nucleotide sequence (SEQUENCE ID NO 18) of
these clones in a graphic display. Following this, a three-frame
translation was performed oil the consensus sequence (SEQUENCE ID
NO 18). The first forward frame was found to have an open reading
frame encoding a 917 residue amino acid sequence which is presented
as SEQUENCE ID NO 41. The 917 residue polypeptide sequence depicted
in SEQUENCE ID NO 41 was compared with published sequences using
software and techniques known to those skilled in the art. The
polypeptide sequence of a bovine epithelial chloride channel
protein was found to be partially homologous to the CS193
polypeptide of SEQUENCE ID NO 41. This bovine chloride channel
protein is described by S. Cunningham et al. J. Biol. Chem.
270:31016-31026 (1995).
Example 2
Sequencing of CS193 EST-Specific Clones
[0193] The full-length DNA sequences of clones 774134 and 774419 of
the CS193 gene contig were determined using dideoxy termination
sequencing with dye terminators following known methods (F. Sanger
et al., PNAS U.S.A. 74:5463 (1977). These full-length sequences are
referred to herein as clones 7741341H (SEQUENCE ID NO 16) and
7744191H (SEQUENCE ID 17), respectively.
[0194] Because the pINCY vector (available from Incyte
Pharmaceuticals, Inc., Palo Alto, Calif.) contains universal
priming sites just adjacent to the 3' and 5' ligation junctions of
the inserts, approximately 300 bases of the insert were sequenced
in both directions using two universal primers (SEQUENCE ID NO 21
and SEQUENCE ID NO 22, available from New England Biolabs, Beverly,
Mass., and Applied Biosystems Inc, Foster City, Calif.). The
sequencing reactions were run on a polyacrylamide denaturing gel,
and the sequences were determined by an Applied Biosystems 377
Sequencer (available from Applied Biosystems, Foster City, Calif.).
Additional sequencing primers (SEQUENCE ID NOS 23-38) were designed
from sequence information determined by the initial sequencing
reactions near the 3'-ends of the two DNA strands. These primers
then were used to determine the remaining DNA sequence of the
cloned insert from each DNA strand, as previously described.
Example 3
Nucleic Acid
[0195] A. RNA Extraction from Tissue. Total RNA is isolated from GI
tract tissues and from non-GI tract tissues. Various methods are
utilized, including but not limited to the lithium chloride/urea
technique, known in the art and described by Kato et al. (J. Virol.
61:2182-2191, 1987), and TRIzol.TM. (Gibco-BRL, Grand Island,
N.Y.).
[0196] Briefly, tissue is placed in a sterile conical tube on ice
and 10-15 volumes of 3 M LiCl, 6 M urea, 5 mM EDTA, 0.1 M
P-mercaptoethanol, 50 mM Tris-HCl (pH 7.5) are added. The tissue is
homogenized with a Polytrone homogenizer (Brinkman Instruments,
Inc., Westbury, N.Y.) for 30-50 sec on ice. The solution is
transferred to a 15 ml plastic centrifuge tube and placed overnight
at -20.degree. C. The tube is centrifuged for 90 min at
9,000.times.g at 0-4.degree. C. and the supernatant is immediately
decanted. Ten ml of 3 M LiCl are added and the tube is vortexed for
5 sec. The tube is centrifuged for 45 min at 11,000.times.g at
0-4.degree. C. The decanting, resuspension in LiCl, and
centrifugation is repeated and the final pellet is air dried and
suspended in 2 ml of 1 mM EDTA, 0.5% SDS, 10 mM Tris (pH 7.5).
Twenty microliters (20 .mu.l) of Proteinase K (20 mg/ml) are added,
and the solution is incubated for 30 min at 37.degree. C. with
occasional mixing. One-tenth volume (0.22-0.25 ml) of 3 M NaCl is
added and the solution is vortexed before transfer into another
tube containing 2 ml of phenol/chloroform/isoamyl alcohol (PCI).
The tube is vortexed for 1-3 sec and centrifuged for 20 min at
3,000.times.g at 10.degree. C. The PCI extraction is repeated and
followed by two similar extractions with chloroform/isoamyl alcohol
(CI). The final aqueous solution is transferred to a prechilled 15
ml Corex glass tube containing 6 ml of absolute ethanol, the tube
is covered with parafilm, and placed at -20.degree. C. overnight.
The tube is centrifuged for 30 min at 10,000.times.g at 0-4.degree.
C. and the ethanol supernatant is decanted immediately. The RNA
pellet is washed four times with 10 ml of 75% ice-cold ethanol and
the final pellet is air dried for 15 min at room temperature. The
RNA is suspended in 0.5 ml of 10 mM TE (pH 7.6, 1 mM EDTA) and its
concentration is determined spectrophotometrically. RNA samples are
aliquoted and stored at -70.degree. C. as ethanol precipitates.
[0197] The quality of the RNA is determined by agarose gel
electrophoresis (see Example 5, Northern Blot Analysis) and
staining with 0.5 .mu.g/ml ethidium bromide for one hour. RNA
samples that do not contain intact rRNAs are excluded from the
study.
[0198] Alternatively, for RT-PCR analysis, 1 ml of Ultraspec RNA
reagent is added to 120 mg of pulverized tissue in a 2.0 ml
polypropylene microfuge tube, homogenized with a Polytron.RTM.
homogenizer (Brinkman Instruments, Inc., Westbury, N.Y.) for 50 sec
and placed on ice for 5 min. Then, 0.2 ml of chloroform is added to
each sample, followed by vortexing for 15 sec. The sample is placed
on ice for another 5 min, followed by centrifugation at
12,000.times.g for 15 min at 4.degree. C. The upper layer is
collected and transferred to another RNase-free 2.0 ml microfuge
tube. An equal volume of isopropanol is added to each sample, and
the solution is placed on ice for 10 min. The sample is centrifuged
at 12,000.times.g for 10 min at 4.degree. C., and the supernatant
is discarded. The remaining pellet is washed twice with cold 75%
ethanol, resuspended by vortexing, and the resuspended material is
then pelleted by centrifugation at 7500.times.g for 5 min at
4.degree. C. Finally, the RNA pellet is dried in a Speedvac
(Savant, Farmingdale, N.Y.) for 5 min and reconstituted in
RNase-free water.
[0199] B. RNA Extraction from Blood Mononuclear Cells. Mononuclear
cells are isolated from blood samples from patients by
centrifugation using Ficoll-Hypaque as follows. A 10 ml volume of
whole blood is mixed with an equal volume of RPMI Medium
(Gibco-BRL, Grand Island, N.Y.). This mixture is then underlayed
with 10 ml of Ficoll-Hypaque (Pharmacia, Piscataway, N.J.) and
centrifuged for 30 minutes at 200.times.g. The buffy coat
containing the mononuclear cells is removed, diluted to 50 ml with
Dulbecco's PBS (Gibco-BRL, Grand Island, N.Y.) and the mixture
centrifuged for 10 minutes at 200.times.g. After two washes, the
resulting pellet is resuspended in Dulbecco's PBS to a final volume
of 1 ml.
[0200] RNA is prepared from the isolated mononuclear cells as
described by N. Kato et al., J. Virology 61: 2182-2191 (1987).
Briefly, the pelleted mononuclear cells are brought to a final
volume of 1 ml and then are resuspended in 250 .mu.L of PBS and
mixed with 2.5 ml of 3 M LiCl, 6 M urea, 5 mM EDTA, 0.1 M
2-mercaptoethanol, 50 mM Tris-HCl (pH 7.5). The resulting mixture
is homogenized and incubated at -20.degree. C. overnight. The
homogenate is centrifuged at 8,000 RPM in a Beckman J2-21M rotor
for 90 minutes at 0-4.degree. C. The pellet is resuspended in 10 ml
of 3 M LiCl by vortexing and then centrifuged at 10,000 RPM in a
Beckman J2-21M rotor centrifuge for 45 minutes at 0-4.degree. C.
The resuspending and pelleting steps then are repeated. The pellet
is resuspended in 2 ml of 1 mM EDTA, 0.5% SDS, 10 mM Tris (pH 7.5)
and 400 .mu.g Proteinase K with vortexing and then it is incubated
at 37.degree. C. for 30 minutes with shaking. One tenth volume of 3
M NaCl then is added and the mixture is vortexed.
[0201] Proteins are removed by two cycles of extraction with
phenol/chloroform/isoamyl alcohol (PCI) followed by one extraction
will chloroform/isoamyl alcohol (CI). RNA is precipitated by the
addition of 6 ml of absolute ethanol followed by overnight
incubation at -20.degree. C. After the precipitated RNA is
collected by centrifugation, the pellet is washed 4 times in 75%
ethanol. The pelleted RNA is then dissolved in solution containing
1 mM EDTA, 10 mM Tris-HCl (pH 7.5).
[0202] Non-GI tract tissues are used as negative controls. The mRNA
can be further purified from total RNA by using commercially
available kits such as oligo dT cellulose spin columns (RediCol.TM.
from Pharmacia, Uppsala, Sweden) for the isolation of
poly-adenylated RNA. Total RNA or mRNA can be dissolved in lysis
buffer (5M guanidine thiocyanate, 0.1 M EDTA, pH 7.0) for analysis
in the ribonuclease protection assay.
[0203] C. RNA Extraction from polysomes. Tissue is minced in saline
at 4.degree. C. and mixed with 2.5 volumes of 0.8 M sucrose in a
TK.sub.150M solution (150 mM KCl, 5 mM MgCl.sub.2, 50 mM Tris-HCl,
pH 7.4) containing 6 mM 2-mercaptoethanol. The tissue is
homogenized in a Teflon-glass Potter homogenizer with five strokes
at 100-200 rpm followed by six strokes in a Dounce homogenizer, as
described by B. Mechler, Methods in Enzymology 152:241-248 (1987).
The homogenate then is centrifuged at 12,000.times.g for 15 min at
4.degree. C. to sediment the nuclei. The polysomes are isolated by
mixing 2 ml of the supernatant with 6 ml of 2.5 M sucrose in
TK.sub.150M and layering this mixture over 4 ml of 2.5 M sucrose in
TK.sub.150M in a 38 ml polyallomer tube. Two additional sucrose
TK.sub.150M solutions are successively layered onto the extract
fraction, a first layer of 13 ml 2.05 M sucrose, followed by a
second layer of 6 ml of 1.3 M sucrose. The polysomes are isolated
by centrifuging the gradient at 90,000.times.g for 5 hr at
4.degree. C. The fraction then is taken from the 1.3 M sucrose/2.05
M sucrose interface with a siliconized pasteur, pipette and diluted
in an equal volume of TE (10 mM Tris-HCl, pH 7.4, 1 mM EDTA). An
equal volume of 90.degree. C. SDS buffer (1% SDS, 200 mM NaCl, 20
mM Tris-HCl, pH 7.4) is added and the solution is incubated in a
boiling water bath for 2 min. Proteins next are digested with a
Proteinase-K digestion (50 mg/ml) for 15 min at 37.degree. C. The
mRNA is purified with 3 equal volumes of phenol-chloroform
extractions followed by precipitation with 0.1 volume of 2 M sodium
acetate (pH 5.2) and 2 volumes of 100% ethanol at -20.degree. C.
overnight. The precipitated RNA is recovered by centrifugation at
12,000.times.g for 10 min at 4.degree. C. The RNA is dried and
resuspended in TE (pH 7.4) or distilled water. The resuspended RNA
then can be used in a slot blot or dot blot hybridization assay to
check for the presence of CS193 mRNA (see Example 6).
[0204] The quality of nucleic acid and proteins is dependent on the
method of preparation used. Each sample may require a different
preparation technique to maximize isolation efficiency of the
target molecule. These preparation techniques are within the skill
of the ordinary artisan.
Example 4
Ribonuclease Protection Assay
[0205] A. Synthesis of Labeled Complementary RNA (cRNA)
Hybridization Probe and Unlabeled Sense Strand. Labeled antisense
and unlabeled sense riboprobes are transcribed from the CS193 gene
cDNA sequence which contains a 5' RNA polymerase promoter such as
SP6 or T7. The sequence may be from a vector containing the
appropriate CS193 cDNA insert, or from a PCR-generated product of
the insert using PCR primers which incorporate a 5' RNA polymerase
promoter sequence. For example, the described plasmid, clones
774134 or 774419 or another comparable clone, containing the CS193
gene cDNA sequence, flanked by opposed SP6 and T7 polymerase
promoters, is purified using Qiagen Plasmid Purification Kit
(Qiagen, Chatsworth, Calif.). Then 10 .mu.g of the plasmid are
linearized by cutting with 10 U DdeI restriction enzyme for 1 hr at
37.degree. C. The linearized plasmid is purified using QIAprep kits
(Qiagen, Chatsworth, Calif.) and used for the synthesis of
antisense transcript from the appropriate SP6 or T7 promoter using
the Riboprobe.RTM. in vitro Transcription System (Promega
Corporation, Madison, Wis.), as described by the supplier's
instructions, incorporating either 6.3 .mu.M (alpha.sup.32P) UTP
(Amersham Life Sciences, Inc. Arlington Heights, Ill.) or 100-500
.mu.M biotinylated UTP as a label. To generate the sense strand, 10
.mu.g of the purified plasmid are cut with restriction enzymes 10 U
XbaI and 10 U NotI, and transcribed as above from the appropriate
SP6 or T7 promoter. Both sense and antisense strands are isolated
by spin column chromatography. Unlabeled sense strand is
quantitated by UV absorption at 260 nm.
[0206] B. Hybridization of Labeled Probe to Target. Frozen tissue
is pulverized to powder under liquid nitrogen and 100-500 mg are
dissolved in 1 ml of lysis buffer, available as a component of the
Direct Protect.TM. Lysate RNase Protection kit (Ambion, Inc.,
Austin, Tex.). Further dissolution can be achieved using a tissue
homogenizer. In addition, a dilution series of a known amount of
sense strand in mouse liver lysate is made for use as a positive
control. Finally, 45 .mu.l of solubilized tissue or diluted sense
strand is mixed directly with either 1) 1.times.10.sup.5 cpm of
radioactively labeled probe or 2) 250 pg of non-isotopically
labeled probe in 5 .mu.l of lysis buffer. Hybridization is allowed
to proceed overnight at 37.degree. C. Sec, T. Kaabache et al.,
Anal. Biochem. 232:225-230 (1995).
[0207] C. RNase Digestion. RNA that is not hybridized to probe is
removed from the reaction as per the Direct Protect.TM. protocol
using a solution of RNase A and RNase T1 for 30 min at 37.degree.
C., followed by removal of RNase by Proteinase-K digestion in the
presence of sodium sarcosyl. Hybridized fragments protected from
digestion are then precipitated by the addition of an equal volume
of isopropanol and placed at -70.degree. C. for 3 hr. The
precipitates are collected by centrifugation at 12,000.times.g for
20 min.
[0208] D. Fragment Analysis. The precipitates are dissolved in
denaturing gel loading dye (80% formamide, 10 mM EDTA (pH 8.0), 1
mg/ml xylene cyanol, 1 mg/ml bromophenol blue), heat denatured, and
electrophoresed in 6% polyacrylamide TBE, 8 M urea denaturing gels.
The gels are imaged and analyzed using the STORM.TM. storage
phosphor autoradiography system (Molecular Dynamics, Sunnyvale,
Calif.). Quantitation of protected fragment bands, expressed in
femtograms (fg), is achieved by comparing the peak areas obtained
from the test samples to those from the known dilutions of the
positive control sense strand (see Section B, supra). The results
are expressed in molecules of CS193 RNA/cell and as a image rating
score. In cases where non-isotopic labels are used, hybrids are
transferred from the gels to membranes (nylon or nitrocellulose) by
blotting and then analyzed using detection systems that employ
streptavidin alkaline phosphatase conjugates and chemiluminesence
or chemifluoresence reagents.
[0209] Detection of a product comprising a sequence selected from
the group consisting of SEQUENCE ID NOS ]-18, and fragments or
complements thereof, is indicative of the presence of CS193
mRNA(s), suggesting a diagnosis of a GI tract tissue disease or
condition, such as GI tract cancer.
Example 5
Northern Blotting
[0210] The northern blot technique is used to identify a specific
size RNA fragment from a complex population of RNA using gel
electrophoresis and nucleic acid hybridization. Northern blotting
is well-known technique in the art. Briefly, 5-10 .mu.g of total
RNA (see Example 3) are incubated in 15 .mu.l of a solution
containing 40 mM morphilinopropanesulfonic acid (MOPS) (pH 7.0), 10
mM sodium acetate, 1 mM EDTA, 2.2 M formaldehyde, 50% v/v formamide
for 15 min at 65.degree. C. The denatured RNA is mixed with 2 .mu.l
of loading buffer (50% glycerol, 1 mM EDTA, 0.4% bromophenol blue,
0.4% xylene cyanol) and loaded into a denaturing 1.0% agarose gel
containing 40 mM MOPS (ply 7.0), 10 mM sodium acetate, 1 mM EDTA
and 2.2 M formaldehyde. The gel is electrophoresed at 60 V for 1.5
h and rinsed in RNAse free water. RNA is transferred from the gel
onto nylon membranes (Brightstar-Plus, Ambion, Inc., Austin, Tex.)
for 1.5 hours using the downward alkaline capillary transfer method
(Chomczynski, Anal. Biochem. 201:134-139, 1992). The filter is
rinsed with 1.times.SSC, and RNA is crosslinked to the filter using
a Stratalinker (Stratagene, Inc., La Jolla, Calif.) on the
autocrosslinking mode and dried for 15 min. The membrane is then
placed into a hybridization tube containing 20 ml of preheated
prehybridization solution (5.times.SSC, 50% formamide,
5.times.Denhardt's solution, 100 .mu.g/ml denatured salmon sperm
DNA) and incubated in a 42.degree. C. hybridization oven for at
least 3 hr. While the blot is prehybridizing, a .sup.32P-labeled
random-primed probe is generated using the CS193 insert fragment
(obtained by digesting clones 774134 or 774419 or another
comparable clone with XbaI and NotI) using Random Primer DNA
Labeling System (Life Technologies, Inc., Gaithersburg, Md.)
according to the manufacturer's instructions. Half of the probe is
boiled for 10 min, quick chilled on ice and added to the
hybridization tube. Hybridization is carried out at 42.degree. C.
for at least 12 hr. The hybridization solution is discarded and the
filter is washed in 30 ml of 3.times.SSC, 0.1% SDS at 42.degree. C.
for 15 min, followed by 30 ml of 3.times.SSC, 0. 1% SDS at
42.degree. C. for 15 min. The filter is wrapped in saran wrap,
exposed to Kodak XAR-Omat film for 8-96 hr, and the film is
developed for analysis.
[0211] Detection of a product comprising a sequence selected from
the group consisting of SEQUENCE ID NOS 1-18, and fragments or
complements thereof, is indicative of the presence of CS193
mRNA(s), suggesting a diagnosis of a GI tract tissue disease or
condition, such as GI tract cancer.
Example 6
Dot Blot/Slot Blot
[0212] Dot and slot blot assays are quick methods to evaluate the
presence of a specific nucleic acid sequence in a complex mix of
nucleic acid. To perform such assays, up to 50 .mu.g of RNA are
mixed in 50 .mu.l of 50% formamide, 7% formaldehyde, 1.times.SSC,
incubated 15 min at 68.degree. C., and then cooled on ice. Then,
100 .mu.l of 20.times.SSC are added to the RNA mixture and loaded
under vacuum onto a manifold apparatus that has a prepared
nitrocellulose or nylon membrane. The membrane is soaked in water,
20.times.SSC for 1 hour, placed on two sheets of 20.times.SSC
prewet Whatman #3 filter paper, and loaded into a slot blot or dot
blot vacuum manifold apparatus. The slot blot is analyzed with
probes prepared and labeled as described in Example 4, supra.
Detection of a product comprising a sequence selected from the
group consisting of SEQUENCE ID NOS 1-18, and fragments or
complements thereof, is indicative of the presence of CS193
mRNA(s), suggesting a diagnosis of a GI tract tissue disease or
condition, Such as GI tract cancer.
[0213] Other methods and buffers which can be utilized in the
methods described in Examples 5 and 6, but not specifically
detailed herein, are known in the art and are described in J.
Sambrook et al, supra which is incorporated herein by
reference.
Example 7
In Situ Hybridization
[0214] This method is useful to directly detect specific target
nucleic acid sequences in cells using detectable nucleic acid
hybridization probes.
[0215] Tissues are prepared with cross-linking fixative agents such
as paraformaldehyde or glutaraldehyde for maximum cellular RNA
retention. See, L. Angerer et al., Methods in Cell Biol. 35:37-71
(1991). Briefly, the tissue is placed in greater than 5 volumes of
1% glutaraldehyde in 50 mM sodium phosphate, pH 7.5 at 4.degree. C.
for 30 min. The solution is changed with fresh glutaraldehyde
solution (1% glutaraldehyde in 50 mM sodium phosphate, pH 7.5) for
a further 30 min fixing. The fixing solution should have an
osmolality of approximately 0.375% NaCl. The tissue is washed once
in isotonic NaCl to remove the phosphate.
[0216] The fixed tissues then are embedded in paraffin as follows.
The tissue is dehydrated though a series of increasing ethanol
concentrations for 15 min each: 50% (twice), 70% (twice), 85%, 90%
and then 100% (twice). Next, the tissue is soaked in two changes of
xylene for 20 min each at room temperature. The tissue is then
soaked in two changes of a 1:1 mixture of xylene and paraffin for
20 min each at 60.degree. C.; and then in three final changes of
paraffin for 15 min each.
[0217] Next, the tissue is cut in 5 .mu.m sections using a standard
microtome and placed on a slide previously treated with a tissue
adhesive such as 3-aminopropyltriethoxysilane.
[0218] Paraffin is removed from the tissue by two 10 min xylene
soaks and rehydrated in a series of decreasing ethanol
concentrations: 99% (twice), 95%, 85%, 70%, 50%, 30%, and then
distilled water (twice). The sections are pre-treated with 0.2 M
HCl for 10 min and permeabilized with 2 .mu.g/ml Proteinase-K at
37.degree. C. for 15 min.
[0219] Labeled Riboprobes transcribed from the CS193 gene plasmid
(see Example 4) are hybridized to the prepared tissue sections and
incubated overnight at 56.degree. C. in 3.times.standard saline
extract and 50% formamide. Excess probe is removed by washing in
2.times.standard saline citrate and 50% formamide followed by
digestion with 100 .mu.g/ml RNase A at 37.degree. C. for 30 min.
Fluorescence probe is visualized by illumination with ultraviolet
(UV) light under a microscope. Fluorescence in the cytoplasm is
indicative of CS193 mRNA. Alternatively, the sections can be
visualized by autoradiography.
[0220] Detection of a product comprising a sequence selected from
the group consisting of SEQUENCE ID NOS 1-18, and fragments or
complements thereof, is indicative of the presence of CS193
mRNA(s), suggesting a diagnosis of a GI tract tissue disease or
condition, such as GI tract cancer.
Example 8
Reverse Transcription PCR
[0221] A. One Step RT-PCR Assay. Target-specific primers are
designed to detect the above-described target sequences by reverse
transcription PCR using methods known in the art. One step RT-PCR
is a sequential procedure that performs both RT and PCR in a single
reaction mixture. The procedure is performed in a 200 .mu.l
reaction mixture containing 50 mM
(N,N,-bis[2-Hydroxyethyl]glycine), pH 8.15, 81.7 mM KOAc, 33.33 mM
KOH, 0.01 mg/ml bovine serum albumin, 0.1 mM ethylene
diaminetetraacetic acid, 0.02 mg/ml NaN.sub.3, 8% w/v glycerol, 150
.mu.M each of dNTP, 0.25 .mu.M each primer, 5 U rTth polymerase,
3.25 mM Mn(OAc).sub.2 and 5 .mu.l of target RNA (see Example 3).
Since RNA and the rTth polymerase enzyme are unstable in the
presence of Mn(OAc).sub.2, the Mn(OAc).sub.2 should be added just
before target addition. Optimal conditions for cDNA synthesis and
thermal cycling readily can be determined by those skilled in the
art. The reaction is incubated in a Perkin-Elmer Thermal Cycler
480. Optimal conditions for cDNA synthesis and thermal cycling can
readily be determined by those skilled in the art. Conditions which
may be found useful include cDNA synthesis at 60.degree.-70.degree.
C. for 15-45 min and 30-45 amplification cycles at 94.degree. C., 1
min; 55.degree.-70.degree. C., 1 min; 72.degree. C., 2 min. One
step RT-PCR also may be performed by using a dual enzyme procedure
with Taq polymerase and a reverse transcriptase enzyme, such as
MMLV or AMV RT enzymes.
[0222] B. Traditional RT-PCR. A traditional two-step RT-PCR
reaction was performed, as described by K. Q. Hu et al., Virology
181:721-726 (1991). Briefly, 0.5 .mu.g of extracted mRNA (see
Example 3) was reverse transcribed in a 20 .mu.l reaction mixture
containing 1.times.PCR II buffer (Perkin-Elmer), 5 MM MgCl.sub.2, 1
mM dNTP, 20 U RNasin, 2.5 .mu.M random hexamers, and 50 U MMLV
(Moloney murine leukemia virus) reverse transcriptase (RT). Reverse
transcription was performed at room temperature for 10 min,
42.degree. C. for 60 min in a PE-480 thermal cycler, followed by
further incubation at 95.degree. C. for 5 min to inactivate the RT.
PCR was performed using 2 .mu.l of the cDNA reaction in a final PCR
reaction volume of 50 .mu.l containing 10 mM Tris-HCl (pH 8.3), 50
mM KCl, 1.5 mM MgCl.sub.2, 200 .mu.M dNTP, 0.4 .mu.M of each sense
and antisense primer, SEQUENCE ID NO 39 and SEQUENCE ID NO 40,
respectively, and 2.5 U of Taq polymerase. The reaction was
incubated in and MJ Research Model PTC-200 as follows: Denaturation
at 94.degree. C. for 2 min., followed by 35 cycles of amplification
(94.degree. C., 45 sec; 55.degree. C, 45 sec; and 72.degree. C, 2
min); a final extension (72.degree. C., 5 min); and a soak at
4.degree. C.
[0223] C. PCR Fragment Analysis. The correct products then can be
verified by size determination using gel electrophoresis with
SYBR.RTM. Green I nucleic acid gel stain (Molecular Probes, Eugene,
Oreg.) and imaged using a STORM imaging system, or also verified by
Southern, dot or slot blot analysis using a labeled probe against
the internal sequences of the PCR product. The probes also may be
polynucleotides analogs, such as morpholinos or peptide nucleic
acids analogs (PNAs).
[0224] Detection of a product comprising a sequence selected from
the group consisting of SEQUENCE ID NOS 1-18, and fragments or
complements thereof, is indicative of the presence of CS193
mRNA(s), suggesting a diagnosis of a GI tract tissue disease or
condition, such as GI tract cancer.
Example 9
OH-PCR
[0225] A. Probe selection and Labeling. Target-specific primers and
probes are designed to detect the above-described target sequences
by oligonucleotide hybridization PCR. International Publication NOS
WO 92/10505, published Jun. 25, 1992, and WO 92/11388, published
Jul. 9, 1992, teach methods for labeling oligonucleotides at their
5' and 3' ends, respectively. According to one known method for
labeling an oligonucleotide, a label-phosphoramidite reagent is
prepared and used to add the label to the oligonucleotide during
its synthesis. For example, see N. T. Thuong et al., Tet. Letters
29(46):5905-5908 (1988); or J. S. Cohen et al., published U.S.
patent application Ser. No. 07/246,688 (NTIS ORDER No.
PAT-APPL-7-246,688) (1989). Preferably, probes are labeled at their
3' end to prevent participation in PCR and the formation of
undesired extension products. For one step OH-PCR, the probe should
have a T.sub.M at least 15.degree. C. below the T.sub.M of the
primers. The primers and probes are utilized as specific binding
members, with or without detectable labels, using standard
phosphoramidite chemistry and/or post-synthetic labeling methods
which are well-known to one skilled in the art.
[0226] B. One Step Oligo Hybridization PCR. OH-PCR is performed on
a 200 .mu.l reaction containing 50 mM
(N,N,-bis[2-Hydroxyethyl]glycine), pH 8.15, 81.7 mM KOAc, 33.33 mM
KOH, 0.01 mg/ml bovine serum albumin, 0.1 mM ethylene
diaminetetraacetic acid, 0.02 mg/ml NaN.sub.3, 8% w/v glycerol, 150
.mu.M each of dNTP, 0.25 .mu.M each primer, 3.75 nM probe, 5U rTth
polymerase, 3.25 mM Mn(OAc).sub.2 and 5 .mu.l blood equivalents of
target (see Example 3). Since RNA and the rTth polymerase enzyme
are unstable in the presence of Mn(OAc).sub.2, the Mn(OAc).sub.2
should be added just before target addition. The reaction is
incubated in a Perkin-Elmer Thermal Cycler 480. Optimal conditions
for cDNA synthesis and thermal cycling can be readily determined by
those skilled in the art. Conditions which may be found useful
include cDNA synthesis (60.degree. C., 30 min), 30-45 amplification
cycles (94.degree. C., 40 sec; 55-70.degree. C., 60 sec),
oligo-hybridization (97.degree. C., 5 min; 15.degree. C., 5 min;
15.degree. C. soak). The correct reaction product contains at least
one of the strands of the PCR product and an internally hybridized
probe.
[0227] C. OH-PCR Product Analysis. Amplified reaction products are
detected on an LCx.RTM. analyzer system (available from Abbott
Laboratories, Abbott Park, Ill.). Briefly, the correct reaction
product is captured by an antibody labeled microparticle at a
capturable site on either the PCR product strand or the
hybridization probe, and the complex is detected by binding of a
detectable antibody conjugate to either a detectable site on the
probe or the PCR strand. Only a complex containing a PCR strand
hybridized with the internal probe is detectable. The detection of
this complex then is indicative of the presence of CS193 mRNA,
suggesting a diagnosis of a GI tract disease or condition, such as
GI tract cancer.
[0228] Many other detection formats exist which can be used and/or
modified by those skilled in the art to detect the presence of
amplified or non-amplified CS193-derived nucleic acid sequences
including but not limited to, ligase chain reaction (LCR, Abbott
Laboratories, Abbott Park, Ill.); Q-beta replicase (Gene-Trak.TM.,
Naperville, Ill.), branched chain reaction (Chiron, Emeryville,
Calif.) and strand displacement assays (Becton Dickinson, Research
Triangle Park, N.C.).
[0229] Detection of a product comprising a sequence selected from
the group consisting of SEQUENCE ID NOS 1-18, and fragments or
complements thereof, is indicative of the presence of CS193
mRNA(s), suggesting a diagnosis of a GI tract tissue disease or
condition, such as GI tract cancer.
Example 10
Synthetic Peptide Production
[0230] Synthetic peptides were modeled and then prepared based upon
the predicted amino acid sequence of the CS193 polypeptide
consensus sequence (see Example 1). In particular, a number of
CS193 peptides modeled from SEQUENCE ID NO 41, including the
peptides of SEQUENCE ID NOS 42-49. Of these, a number of peptides
were prepared, including the peptides of SEQUENCE ID NO 42,
SEQUENCE ID NO 43, SEQUENCE ID NO 44, and SEQUENCE ID NO 45. All
peptides were synthesized on a Symphony Peptide Synthesizer
(available from Rainin Instrument Co, Emeryville, Calif.) using
FMOC chemistry, standard cycles and in-situ HBTU activation.
Cleavage and deprotection conditions were as follows: a volume of
2.5 ml of cleavage reagent (77.5% v/v trifluoroacetic acid, 15% v/v
ethanedithiol, 2.5% v/v water, 5% v/v thioanisole, 1-2% w/v phenol)
were added to the resin, and agitated at room temperature for 2-4
hours. The filtrate was then removed, and the peptide was
precipitated from the cleavage reagent with cold diethyl ether.
Each peptide was filtered, purified via reverse-phase preparative
HPLC using a water/acetonitrile/0.1% TFA gradient, and lyophilized.
The product was confirmed by mass spectrometry (see Example
12).
[0231] The purified peptides were used to immunize animals (see
Example 14).
Example 11a
Expression of Protein in a Cell Line Using Plasmid 577
[0232] A. Construction of a CS193 Expression Plasmid. Plasmid 577,
described in U.S. patent application Ser. No. 08/478,073, filed
Jun. 7, 1995 and incorporated herein by reference, has been
constructed for the expression of secreted antigens in a permanent
cell line. This plasmid contains the following DNA segments: (a) a
2.3 Kb fragment of pBR322 containing bacterial beta-lactamase and
origin of DNA replication; (b) a 1.8 Kb cassette directing
expression of a neomycin resistance gene under control of HSV-1
thymidine kinase promoter and poly-A addition signals; (c) a 1.9 Kb
cassette directing expression of a dihydrofolate reductase gene
under the control of an SV-40 promoter and poly-A addition signals;
(d) a 3.5 Kb cassette directing expression of a rabbit
immunoglobulin heavy chain signal sequence fused to a modified
hepatitis C virus (HCV) E2 protein under the control of the Simian
Virus 40 T-Ag promoter and transcription enhancer, the hepatitis B
virus surface antigen (HBsAg) enhancer I followed by a fragment of
Herpes Simplex Virus-1 (HSV-1) genome providing poly-A addition
signals; and (e) a residual 0.7 Kb fragment of Simian Virus 40
genome late region of no function in this plasmid. All of the
segments of the vector were assembled by standard methods known to
those skilled in the art of molecular biology.
[0233] Plasmids for the expression of secretable CS193 proteins are
constructed by replacing the hepatitis C virus E2 protein coding
sequence in plasmid 577 with that of a CS193 polynucleotide
sequence selected from the group consisting of SEQUENCE ID NOS
1-18, and fragments or complements thereof, as follows. Digestion
of plasmid 577 with XbaI releases the hepatitis C Virus E2 gene
fragment. The resulting plasmid backbone allows insertion of the
CS193 cDNA insert downstream of the rabbit immunoglobulin heavy
chain signal sequence which directs the expressed proteins into the
secretory pathway of the cell. The CS193 cDNA fragment is generated
by PCR using standard procedures. Encoded in the sense PCR primer
sequence is an XbaI site, immediately followed by a 12 nucleotide
sequence that encodes the amino acid sequence Ser-Asn-Glu-Leu
("SNEL") to promote signal protease processing, efficient secretion
and final product stability in culture fluids. Immediately
following this 12 nucleotide sequence the primer contains
nucleotides complementary to template sequences encoding amino
acids of the CS193 gene. The antisense primer incorporates a
sequence encoding the following eight amino acids just before the
stop codons: Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys (SEQUENCE ID NO 50).
Within this sequence is incorporated a recognition site to aid in
analysis and purification of the CS193 protein product. A
recognition site (termed "FLAG") that is recognized by a
commercially available monoclonal antibody designated anti-FLAG M2
(Eastman Kodak, Co., New Haven, Conn.) can be utilized, as well as
other comparable sequences and their corresponding antibodies. For
example, PCR is performed using GeneAmp.RTM. reagents obtained from
Perkin-Elmer-Cetus, as directed by the supplier's instructions. PCR
primers are used at a final concentration of 0.5 .mu.M. PCR is
performed on the CS193 plasmid template in a 100 .mu.l reaction for
35 cycles (94.degree. C., 30 seconds; 55.degree. C., 30 seconds;
72.degree. C., 90 seconds) followed by an extension cycle of
72.degree. C. for 10 min.
[0234] B. Transfection of Dihydrofolate Reductase Deficient Chinese
Hamster Ovary Cells. The plasmid described supra is transfected
into CHO/dhfr- cells (DXB-111, Uriacio et al., PNAS 77:4451-4466
(1980)). These cells are available from the
[0235] A.T.C.C., 12301 Parklawn Drive, Rockville, Md. 20852, under
Accession No. CRL 9096. Transfection is carried out using the
cationic liposome-mediated procedure described by P. L. Felgner et
al., PNAS 84:7413-7417 (1987). Particularly, CHO/dhfr-cells are
cultured in Ham's F-12 media supplemented with 10% fetal calf
serum, L-glutamine (1 mM) and freshly seeded into a flask at a
density of 5-8.times.10.sup.5 cells per flask. The cells are grown
to a confluency of between 60 and 80% for transfection. Twenty
micrograms (20 kg) of plasmid DNA is added to 1.5 ml of Opti-MEM I
medium and 100 .mu.l of Lipofectin Reagent (Gibco-BRL; Grand
Island, N.Y.) are added to a second 1.5 ml portion of Opti-MEM I
media. The two solutions are mixed and incubated at room
temperature for 20 min. After the culture medium is removed from
the cells, the cells are rinsed 3 times with 5 ml of Opti-MEM I
medium. The Opti-MEM I-Lipofection-plasmid DNA solution then is
overlaid onto the cells. The cells are incubated for 3 h at
37.degree. C., after which time the Opti-MEM I-Lipofectin-DNA
solution is replaced with culture medium for an additional 24 h
prior to selection.
[0236] C. Selection and Amplification. One day after transfection,
cells are passaged 1:3 and incubated with dhfr/G418 selection
medium (hereafter, "F-12 minus medium G"). Selection medium is
Ham's F-12 with L-glutamine and without hypoxanthine, thymidine and
glycine (JRH Biosciences, Lenexa, Kans.) and 300 .mu.g per ml G418
(Gibco-BRL; Grand Island, N.Y.). Media volume-to-surface area
ratios of 5 ml per 25 cm.sup.2 are maintained. After approximately
two weeks, DHFR/G418 cells are expanded to allow passage and
continuous maintenance in F-12 minus medium G.
[0237] Amplification of each of the transfected CS193 cDNA
sequences is achieved by stepwise selection of DHFR.sup.+,
G418.sup.+ cells with methotrexate (reviewed by R. Schimke, Cell
37:705-713 [1984]). Cells are incubated with F-12 minus medium G
containing 150 nM methotrexate (MTX) (Sigma, St. Louis, Mo.) for
approximately two weeks until resistant colonies appear. Further
gene amplification is achieved by selection of 150 nM adapted cells
with 5 .mu.M MTX.
[0238] D. Antigen Production. F-12 minus medium G supplemented with
5 .mu.M MTX is overlaid onto just confluent monolayers for 12 to 24
h at 37.degree. C. in 5% CO.sub.2. The growth medium is removed and
the cells are rinsed 3 times with Dulbecco's phosphate buffered
saline (PBS) with calcium and magnesium (Gibco-BRL; Grand Island,
N.Y.) to remove the remaining media/serum which may be present.
Cells then are incubated with VAS custom medium (VAS custom
formulation with L-glutamine with HEPES without phenol red,
available from JRH Bioscience; Lenexa, Kans., product number
52-08678P), for 1 h at 37.degree. C. in 5% CO.sub.2. Cells then are
overlaid with VAS for production at 5 ml per T flask. Medium is
removed after seven days of incubation, retained, and then frozen
to await purification with harvests 2, 3 and 4. The monolayers are
overlaid with VAS for 3 more seven day harvests.
[0239] E. Analysis of GI Tract Tissue Gene CS193 Antigen
Expression. Aliquots of VAS supernatants from the cells expressing
the CS193 protein construct are analyzed, either by
SDS-polyacrylamide gel electrophoresis (SDS-PAGE) using standard
methods and reagents known in the art (Laemmli discontinuous gels),
or by mass spectrometry.
[0240] F. Purification. Purification of the CS193 protein
containing the FLAG sequence is performed by immunoaffinity
chromatography using an affinity matrix comprising anti-FLAG M2
monoclonal antibody covalently attached to agarose by hydrazide
linkage (Eastman Kodak Co., New Haven, Conn.). Prior to affinity
purification, protein in pooled VAS medium harvests from roller
bottles is exchanged into 50 mM Tris-HCl (pH 7.5), 150 mM NaCl
buffer using a Sephadex G-25 (Pharmacia Biotech Inc., Uppsala,
Sweden) column. Protein in this buffer is applied to the anti-FLAG
M2 antibody affinity column. Non-binding protein is eluted by
washing the column with 50 mM Tris-HCl (pH 7.5), 150 mM NaCl
buffer. Bound protein is eluted using an excess of FLAG peptide in
50 mM Tris-HCl (pH 7.5), 150 mM NaCl. The excess FLAG peptide can
be removed from the purified CS193 protein by gel electrophoresis
or HPLC.
[0241] Although plasmid 577 is utilized in this example, it is
known to those skilled in the art that other comparable expression
systems, such as CMV, can be utilized herein with appropriate
modifications in reagent and/or techniques and are within the skill
of the ordinary artisan.
[0242] The largest cloned insert containing the coding region of
the CS193 gene is then sub-cloned into either (i) a eukaryotic
expression vector which may contain, for example, a cytomegalovirus
(CMV) promoter and/or protein fusible sequences which aid in
protein expression and detection, or (ii) a bacterial expression
vector containing a superoxide-dismutase (SOD) and CMP-KDO
synthetase (CKS) or other protein fusion gene for expression of the
protein sequence. Methods and vectors which are useful for the
production of polypeptides which contain fusion sequences of SOD
are described in EPO 0 196056, published Oct. 1, 1986, which is
incorporated herein by reference and those containing fusion
sequences of CKS are described in EPO Publication No. 0331961,
published Sep. 13, 1989, which publication is also incorporated
herein by reference. This so-purified protein can be used in a
variety of techniques, including, but not limited to animal
immunization studies, solid phase immunoassays, etc.
Example 11b
Expression of Protein in a Cell Line Using pcDNA3.1/Myc-His
[0243] A. Construction of a CS193 Expression Plasmid. Plasmid
pcDNA3.1/Myc-His (Cat. # V855-20, Invitrogen, Carlsbad, Calif.) has
been constructed, in the past, for the expression of secreted
antigens by most mammalian cell lines. Expressed protein inserts
are fused to a myc-his peptide tag. The myc-his tag is a 21 residue
amino acid sequence having the following sequence:
Glu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-Leu-Asn-Met-H-
is-Thr-Glu-His-His-His-His-His-His (SEQUENCE ID NO 51) and
comprises a myc epitope and a polyhistidine sequence which are
useful for the purification of an expressed fusion protein using
either anti-myc or anti-his affinity columns, or metalloprotein
binding columns.
[0244] Plasmids for the expression of secretable CS193 proteins are
constructed by inserting an CS193 polynucleotide sequence selected
from the group consisting of SEQUENCE ID NOS 1-18, and fragments or
complements thereof. Prior to construction of an CS193 expression
plasmid, the CS193 cDNA sequence is first cloned into a
pCR.RTM.-Blunt vector as follows.
[0245] The CS193 cDNA fragment is generated by PCR using standard
procedures. For example, PCR is performed using Stratagene.RTM.
reagents obtained from Stratagene, La Jolla, Calif., as directed by
the supplier's instructions. PCR primers are used at a final
concentration of 0.5 .mu.M. PCR using 5 U of pfu polymerase
(Stratagene) is performed on the CS193 plasmid template (see
Example 2) in a 50 .mu.l reaction for 30 cycles (94.degree. C., 1
min; 65.degree. C., 1.5 min; 72.degree. C., 3 min) followed by an
extension cycle at 72.degree. C. for 8 min. The sense PCR primer
sequence comprises nucleotides which are either complementary to
the pINCY vector directly upstream of the CS193 gene insert or
which incorporate a 5' EcoRI restriction site, an adjacent
downstream protein translation consensus initiator, and a 3'
nucleic acid sequence which is the same sense as the 5'-most end of
the CS193 cDNA insert. The antisense primer incorporates a 5' NotI
restriction sequence and a sequence complementary to the 3' end of
the CS193 cDNA insert just upstream of the 3'-most, in-frame stop
codon. Five microliters (5 .mu.l) of the resulting blunt-ended PCR
product are ligated into 25 ng of linearized pCR.RTM.-Blunt vector
(Invitrogen, Carlsbad, Calif.) interrupting the lethal ccdB gene of
the vector. The resulting ligated vector is transfected into TOP 10
E. coli (Invitrogen , Carlsbad, Calif.) using a One Shot.TM.
transformation kit (Invitrogen , Carlsbad, Calif.) following the
supplier's directions. The transfected cells are grown on LB-Kan
(50 .mu.g/ml kanamycin) selection plates at 37.degree. C. Only
cells containing a plasmid with an interrupted ccdB gene will grow
after transfection (Grant, S. G. N., PNAS USA 87:4645-4649 (1990)).
Transfected colonies are picked and grown up in 3 ml of LB-Kan
broth at 37.degree. C. Plasmid DNA is isolated using a QIAprep.RTM.
(Qiagen Inc., Santa Clarita, Calif.) procedure, as directed by the
supplier's instructions. The DNA is cut with EcoRI or SnaBI, and
NotI restriction enzymes to release the CS193 insert fragment. The
fragment is run on 1% Seakem.RTM. LE agarose/0.5 .mu.g/ml ethidium
bromide/TE gel, visualized by UV irradiation, excised and purified
using QiAquick.TM. (Qiagen Inc., Santa Clarita, Calif.) procedures,
as directed by the supplier's instructions.
[0246] The pcDNA3.1/Myc-His plasmid DNA is linearized by digestion
with EcoRI or SnaBI, and NotI in the polylinker region of the
plasmid DNA. The resulting plasmid DNA backbone allows insertion of
the CS193 purified cDNA fragment, supra, downstream of a CMV
promoter which directs expression of the proteins in mammalian
cells. The ligated plasmid is transfected into DH5 alpha.TM. cells
(GibcoBRL, Gaithersburg, Md.) as directed by the supplier's
instructions. Briefly, 10 ng of pcDNA3.1/Myc-His containing an
CS193 insert is added to 50 .mu.l of competent DH5 alpha cells, and
the contents are mixed gently. The mixture is incubated on ice for
30 mill, heat shocked for 20 sec at 37.degree. C., and placed on
ice for an additional 2 min. Upon addition of 0.95 ml of LB medium,
the mixture is incubated for 1 h at 37.degree. C. while shaking at
225 rpm. The transfected cells are then plated onto 100 mm LB/Amp
(50 .mu.g/ml ampicillin) plates and grown at 37.degree. C. Colonies
are picked and grown in 3 ml of LB/Amp broth. Plasmid DNA is
purified using a QIAprep.RTM. kit. Presence of the insert is
confirmed using techniques known to those skilled in the art
including, but not limited to, restriction digestion and gel
analysis. See, e.g., J. Sambrook et al., supra.
[0247] B. Transfection of Human Embryonic Kidney 293 Cells. The
CS193 expression plasmid described supra is purified from the DH5
alpha cells using a QIAfilter.TM. Maxi kit (Qiagen, Chatsworth,
Calif.), and then transfected into HEK293 cells (F. L. Graham et
al., J. Gen. Vir. 36:59-72 (1977)). These cells are available from
the A.T.C.C., 12301 Parklawn Drive, Rockville, Md. 20852, under
Accession No. CRL 1573. Transfection is carried out using the
cationic lipofectamine-mediated procedure described by P.
Hawley-Nelson et al., Focus 15:73 (1993). Particularly, HEK293
cells are cultured in 10 ml DMEM media supplemented with 10% fetal
bovine serum (FBS), L-glutamine (2 mM) and freshly seeded into 100
mm culture plates at a density of 9.times.10.sup.6 cells per plate.
The cells are grown at 37.degree. C. to a confluency of between 70%
and 80% for transfection. Eight micrograms (8 .mu.g) of plasmid DNA
is added to 800 .mu.l of Opti-MEM I.RTM. medium (Gibco-BRL Grand
Island, N.Y.), and 48-96 .mu.l of Lipofectamine.TM. Reagent
(Gibco-BRL, Grand Island, N.Y.) is added to a second 800 .mu.l
portion of Opti-MEM I.RTM. media. The two solutions are mixed and
incubated at room temperature for 15-30 min. After the culture
medium is removed from the cells, the cells are washed once with 10
ml of serum-free DMEM. The Opti-MEM I.RTM.-Lipofectamine-pla- smid
DNA solution is diluted in 6.4 ml of serum-free DMEM and then
overlaid onto the cells. The cells are incubated for 5 h at
37.degree. C., after which time, an additional 8 ml of DMEM with
20% FBS is added. After 18-24 h, the old medium is aspirated, and
the cells are overlaid with 5 ml of fresh DMEM with 10% FBS.
Supernatants and cell extracts are analyzed for CS193 gene activity
72 h after transfection.
[0248] C. Analysis of GI Tract Tissue Gene CS193 Antigen
Expression. The culture supernatant, supra, is transferred to
cryotubes and stored on ice. HEK293 cells are harvested by washing
twice with 10 ml cold Dulbecco's PBS and lysing by addition of 1.5
ml of CAT lysis buffer (Boehringer Mannheim, Indianapolis, Ind.),
followed by incubation for 30 min at room temperature. Lysate is
transferred to 1.7 ml polypropylene microfuge tubes and centrifuged
at 1000.times.g for 10 min. The supernatant is transferred to new
cryotubes and stored on ice. Aliquots of cell supernatants and the
lysate of the cells expressing the CS193 protein construct are
analyzed for the presence of CS193 recombinant protein. The
aliquots can be analyzed using SDS-polyacrylamide gel
electrophoresis (SDS-PAGE), using standard methods and reagents
known in the art. See, e.g., J. Sambrook et al., supra. The gels
can then be blotted onto a solid medium such as nitrocellulose,
nytran, or the like, and the CS193 protein band can be visualized
using western blotting techniques with anti-myc epitope or
anti-histidine monoclonal antibodies (Invitrogen, Carlsbad, Calif.)
or CS193 polyclonal serum (see Example 14). Alternatively, the
expressed CS193 recombinant protein can be analyzed by mass
spectrometry (see Example 12).
[0249] D. Purification. Purification of the CS193 recombinant
protein containing the myc-his sequence is performed using the
Xpress.RTM. affinity chromatography system (Invitrogen, Carlsbad,
Calif.) containing a nickel-charged agarose resin which
specifically binds polyhistidine residues. Supernatants from
10.times.100 mm plates, prepared as described supra, are pooled and
passed over the nickel-charged column. Non-binding protein is
eluted by washing the column with 50 mM Tris-HCl (pH 7.5)/150 mM
NaCl buffer, leaving only the myc-his fusion proteins. Bound CS193
recombinant protein then is eluted from the column using either an
excess of imidazole or histidine, or a low pH buffer.
Alternatively, the recombinant protein can also be purified by
binding at the myc-his sequence to an affinity column consisting of
either anti-myc or anti-histidine monoclonal antibodies conjugated
through a hydrazide or other linkage to an agarose resin and
eluting with an excess of myc peptide or histidine,
respectively.
[0250] The purified recombinant protein can then be covalently
cross-linked to a solid phase, such as
N-hydroxysuccinimide-activated sepharose columns (Pharmacia
Biotech, Piscataway, N.J.), as directed by supplier's instructions.
These columns containing covalently linked CS193 recombinant
protein, can then be used to purify anti-CS193 antibodies from
rabbit or-mouse sera (see Examples 13 and 14).
[0251] E. Coating Microtiter Plates with CS193 Expressed Proteins.
Supernatant from a 100 mm plate, as described supra, is diluted in
an appropriate volume of PBS. 100 .mu.l of the resulting mixture is
placed into each well of a Reacti-Bind.TM. metal chelate microtiter
plate (Pierce, Rockford, Ill.), incubated at room temperature while
shaking, and followed by three washes with 200 .mu.l each of PBS
with 0.05% Tween 20. The prepared microtiter plate can then be used
to screen polyclonal antisera for the presence of CS193 antibodies
(see Example 17).
[0252] Although pcDNA3.1/Myc-His is utilized in this example, it is
known to those skilled in the art that other comparable expression
systems can be utilized herein with appropriate modifications in
reagent and/or techniques and are within the skill of one of
ordinary skill in the art. The largest cloned insert containing the
coding region of the CS193 gene is sub-cloned into either (i) a
eukaryotic expression vector which may contain, for example, a
cytomegalovirus (CMV) promoter and/or protein fusible sequences
which aid in protein expression and detection, or (ii) a bacterial
expression vector containing a superoxide-dismutase (SOD) and
CMP-KDO synthetase (CKS) or other protein fusion gene for
expression of the protein sequence. Methods and vectors which are
useful for the production of polypeptides which contain fusion
sequences of SOD are described in European patent application No.
EP 0 196 056, published Oct. 1, 1986, which is incorporated herein
by reference, and vectors containing fusion sequences of CKS are
described in European patent application No. EP 0 331 961,
published Sep. 13, 1989, which publication is also incorporated
herein by reference. The purified protein can be used in a variety
of techniques, including but not limited to, animal immunization
studies, solid phase immunoassays, etc.
Example 12
Chemical Analysis of GI tract Tissue Proteins
[0253] A. Analysis of Tryptic Peptide Fragments Using MS. Sera from
patients with GI tract disease, such as GI tract cancer, sera from
patients with no GI tract disease, extracts of GI tract tissues or
cells from patients with GI tract disease, such as GI tract cancer,
extracts of GI tract tissues or cells from patients with no GI
tract disease, and extracts of tissues or cells from other
non-diseased or diseased organs of patients, are run on a
polyacrylamide gel using standard procedures and stained with
Coomassie Blue. Sections of the gel suspected of containing the
unknown polypeptide are excised and subjected to an in-gel
reduction, acetamidation and tryptic digestion. P. Jeno et al,
Anal. Bio. 224:451-455 (1995) and J. Rosenfeld et al, Anal. Bio.
203:173-179 (1992). The gel sections are washed with 100 mM
NH.sub.4HCO.sub.3 and acetonitrile. The shrunken gel pieces are
swollen in digestion buffer (50 mM NH.sub.4HCO.sub.3, 5 mM
CaCl.sub.2 and 12.5 .mu.l-ml trypsin) at 4.degree. C. for 45 min.
The supernatant is aspirated and replaced with 5 to 10 .mu.l of
digestion buffer without trypsin and allowed to incubate overnight
at 37.degree. C. Peptides are extracted with 3 changes of 5% formic
acid and acetonitrile and evaporated to dryness. The peptides are
adsorbed to approximately 0.1 .mu.l of POROS R2 sorbent (Perseptive
Biosystems, Framingham, Mass.) trapped in the tip of a drawn gas
chromatography capillary tube by dissolving them in 10 .mu.l of 5%
formic acid and passing it through the capillary. The adsorbed
peptides are washed with water and eluted with 5% formic acid in
60% methanol. The eluant is passed directly into the spraying
capillary of an API III mass spectrometer (Perkin-Elmer Sciex,
Thornhill, Ontario, Canada) for analysis by nano-electrospray mass
spectrometry. M. Wilm et al., Int. J. Mass Spectrom. Ion Process
136:167-180 (1994) and M. Wilm et al., Anal. Chem. 66:1-8 (1994).
The masses of the tryptic peptides are determined from the mass
spectrum obtained off the first quadrupole. Masses corresponding to
predicted peptides can be further analyzed in MS/MS mode to give
the amino acid sequence of the peptide.
[0254] B. Peptide Fragment Analysis Using LC/MS. The presence of
polypeptides predicted from mRNA sequences found in hyperplastic
disease tissues also can be confirmed using liquid
chromatography/tandem mass spectrometry (LC/MS/MS). D. Hess et al.,
METHODS, A Companion to Methods in Enzymology 6:227-238 (1994). The
serum specimen or tumor extract from the patient is denatured with
SDS and reduced with dithiothreitol (1.5 mg/ml) for 30 min at
90.degree. C. followed by alkylation with iodoacetamide (4 mg/ml)
for 15 min at 25.degree. C. Following acrylamide electrophoresis,
the polypeptides are electroblotted to a cationic membrane and
stained with Coomassie Blue. Following staining, the membranes are
washed and sections thought to contain the unknown polypeptides are
cut out and dissected into small pieces. The membranes are placed
in 500 .mu.l microcentrifuge tubes and immersed in 10 to 20 .mu.l
of proteolytic digestion buffer (100 mM Tris-HCl, pH 8.2,
containing 0.1 M NaCl, 10% acetonitrile, 2 mM CaCl.sub.2 and 5
.mu.g/ml trypsin) (Sigma, St. Louis, Mo.). After 15 h at 37.degree.
C., 3 .mu.l of saturated urea and 1 .mu.l of 100 .mu.g/ml trypsin
cue added and incubated for an additional 5 h at 37.degree. C. The
digestion mixture is acidified with 3 .mu.l of 10% trifluoroacetic
acid and centrifuged to separate supernatant from membrane. The
supernatant is injected directly onto a microbore, reverse phase
HPLC column and eluted with a linear gradient of acetonitrile in
0.05% trifluoroacetic acid. The eluate is fed directly into an
electrospray mass spectrometer, after passing though a stream
splitter if necessary to adjust the volume of material. The data is
analyzed following the procedures set forth in Example 12, Section
A.
Example 13
Gene Immunization Protocol
[0255] A. In Vivo Antigen Expression. Gene immunization circumvents
protein purification steps by directly expressing an antigen in
vivo after inoculation of the appropriate expression vector. Also,
production of antigen by this method may allow correct protein
folding and glycosylation since the protein is produced in
mammalian tissue. The method utilizes insertion of the gene
sequence into a plasmid which contains a CMV promoter, expansion
and purification of the plasmid and injection of the plasmid DNA
into the muscle tissue of an animal. Preferred animals include mice
and rabbits. See, for example, H. Davis et al., Human Molecular
Genetics 2:1847-1851 (1993). After one or two booster
immunizations, the animal can then be bled, ascites fluid
collected, or the animal's spleen can be harvested for production
of hybridomas.
[0256] B. Plasmid Preparation and Purification. CS193 cDNA
sequences are generated from the CS193 cDNA-containing vector using
appropriate PCR primers containing suitable 5' restriction sites
following the procedures described in Example 11. The PCR product
is cut with appropriate restriction enzymes and inserted into a
vector which contains the CMV promoter (for example, pRc/CMV or
pcDNA3 vectors from Invitrogen, San Diego, Calif.). This plasmid
then is expanded in the appropriate bacterial strain and purified
from the cell lysate using a CsCl gradient or a Qiagen plasmid DNA
purification column. All these techniques are familiar to one of
ordinary skill in the art of molecular biology.
[0257] C. Immunization Protocol. Anesthetized animals are immunized
intramuscularly with 0.1-100 .mu.g of the purified plasmid diluted
in PBS or other DNA uptake enhancers (Cardiotoxin, 25% sucrose).
See, for example, H. Davis et al, Human Gene Therapy 4:733-740
(1993); and P. W. Wolff et al, Biotechniques 11:474-485 (1991). One
to two booster injections are given at monthly intervals.
[0258] D. Testing and Use of Antiserum. Animals are bled and the
resultant sera tested for antibody using peptides synthesized from
the known gene sequence (see Example 16) using techniques known in
the art, such as western blotting or ETA techniques. Antisera
produced by this method can then be used to detect the presence of
the antigen in a patient's tissue or cell extract or in a patient's
serum by ELISA or Western blotting techniques, such as those
described in Examples 15 through 18.
Example 14
Production of Antibodies Against CS193
[0259] A. Production of Polyclonal Antisera. Antiserum against
CS193 was prepared by injecting rabbits with peptides whose
sequences were derived from that of the predicted amino acid
sequence of the CS193 consensus sequence (SEQUENCE ID NO 18). The
synthesis of peptides is described in Example 10. Unconjugated
peptides, SEQUENCE ID NO 42, SEQUENCE ID NO 43, SEQUENCE ID NO 44,
and SEQUENCE ID NO 45, were used as immunogens [i.e., peptides were
not conjugated to a carrier such as keyhole limpet hemocyanine
(KLH)].
[0260] Animal Immunization. Female white New Zealand rabbits
weighing 2 kg or more were used for raising polyclonal antiserum.
One animal was immunized per unconjugated peptide (SEQUENCE ID NO
42, SEQUENCE ID NO 43, SEQUENCE ID NO 44, and SEQUENCE ID NO 45).
One week prior to the first immunization, 5 to 10 ml of blood were
obtained from the animal to serve as a non-immune prebleed
sample.
[0261] Unconjugated peptides, SEQUENCE ID NO 42, SEQUENCE ID NO 43,
SEQUENCE ID NO 44, and SEQUENCE ID NO 45, were used to prepare the
primary immunogen by emulsifying 0.5 ml of the peptide at a
concentration of 2 mg/ml in PBS (pH 7.2) which contained 0.5 ml of
complete Freund's adjuvant (CFA) (Difco, Detroit, Mich.). The
immunogen was injected into several sites of the animal via
subcutaneous, intraperitoneal, and intramuscular routes of
administration. Four weeks following the primary immunization, a
booster immunization was administered. The immunogen used for the
booster immunization dose was prepared by emulsifying 0.5 ml of the
same unconjugated peptide used for the primary immunogen, except
that the peptide now was diluted to 1 mg/ml with 0.5 ml of
incomplete Freund's adjuvant (IFA) (Difco, Detroit, Mich.). Again,
the booster dose was administered into several sites via
subcutaneous, intraperitoneal and intramuscular types of
injections. The animals were bled (5 ml) two weeks after the
booster immunizations and each serum was tested for
immunoreactivity to the peptide as described below. The booster and
bleed schedule was repeated at 4 week intervals until an adequate
titer was obtained. The titer or concentration of antiserum was
determined by using unconjugated peptides in a microtiter ETA as
described in Example 17, below. An antibody titer of 1:500 or
greater was considered an adequate titer for further use and
study.
1TABLE 1 Titer of rabbit anti-CS193 peptide antisera (13 week
bleed) Peptide Immunogen Titer SEQUENCE ID NO 42 12,000 SEQUENCE ID
NO 43 12,000 SEQUENCE ID NO 44 2,100 SEQUENCE ID NO 45 42,000
[0262] B. Production of Monoclonal Antibody.
[0263] 1. Immunization Protocol. Mice are immunized using peptides
which can either be conjugated to a carrier such KLH, prepared as
described hereinbelow, or unconjugated (i.e., not conjugated to a
carrier such as KLH), except that the amount of the unconjugated or
conjugated peptide for monoclonal antibody production in mice is
one-tenth the amount used to produce polyclonal antisera in
rabbits. Thus, the primary immunogen consists of 100 .mu.g of
unconjugated or conjugated peptide in 0.1 ml of CFA emulsion; while
the immunogen used for booster immunizations consists of 50 .mu.g
of unconjugated or conjugated peptide in 0.1 ml of IFA. Hybridomas
for the generation of monoclonal antibodies are prepared and
screened using standard techniques. The methods used for monoclonal
antibody development follow procedures known in the art such as
those detailed in Kohler and Milstein, Nature 256:494 (1975) and
reviewed in J. G. R. Hurrel, ed., Monoclonal Hybridoma Antibodies:
Techniques and Applications, CRC Press, Inc., Boca Raton, Fla.
(1982). Another method of monoclonal antibody development which is
based on the Kohler and Milstein method is that of L. T. Mimms et
al., Virology 176:604-619 (1990), which is incorporated herein by
reference.
[0264] The immunization regimen (per mouse) consists of a primary
immunization with additional booster immunizations. The primary
immunogen used for the primary immunization consists of 100 .mu.g
of unconjugated or conjugated peptide in 50 .mu.l of PBS (pH 7.2)
previously emulsified in 50 .mu.l of CFA. Booster immunizations
performed at approximately two weeks and four weeks post primary
immunization consist of 50 .mu.g of unconjugated or conjugated
peptide in 50 .mu.l of PBS (pH 7.2) emulsified with 50 .mu.l IFA. A
total of 100 .mu.l of this immunogen is inoculated
intraperitoneally and subcutaneously into each mouse. Individual
mice are screened for immune response by microtiter plate enzyme
immunoassay (EIA) as described in Example 17 approximately four
weeks after the third immunization. Mice are inoculated either
intravenously, intrasplenically or intraperitoneally with 50 .mu.g
of unconjugated or conjugated peptide in PBS (pH 7.2) approximately
fifteen weeks after the third immunization.
[0265] Three days after this intravenous boost, splenocytes are
fused with, for example, Sp2/0-Ag 14 myeloma cells (Milstein
Laboratories, England) using the polyethylene glycol (PEG) method.
The fusions are cultured in Iscove's Modified Dullbecco's Medium
(IMDM) containing 10% fetal calf serum (FCS), plus 1% hypoxanthine,
aminopterin and thymidine (HAT). Bulk cultures were screened by
microtiter plate EIA following the protocol in Example 17. Clones
reactive with the peptide used an immunogen and non-reactive with
other peptides (i.e., peptides of CS193 not used as the immunogen)
are selected for final expansion. Clones thus selected are
expanded, aliquoted and frozen in IMDM containing 10% FCS and 10%
dimethyl-sulfoxide.
[0266] 2. Peptide Conjugation. Peptide is conjugated to maleimide
activated keyhole limpet hemocyanine (KLH, commercially available
as Imject.RTM., available from Pierce Chemical Company, Rockford,
Ill.). Imject.RTM. contains about 250 moles of reactive maleimide
groups per mole of hemocyanine. The activated KLH is dissolved in
phosphate buffered saline (PBS, pH 8.4) at a concentration of about
7.7 mg/ml. The peptide is conjugated through cysteines occurring in
the peptide sequence, or to a cysteine previously added to the
synthesized peptide in order to provide a point of attachment. The
peptide is dissolved in dimethyl sulfoxide (DMSO, Sigma Chemical
Company, St. Louis, Mo.) and reacted with the activated KLH at a
mole ratio of about 1.5 moles of peptide per mole of reactive
maleimide attached to the KLH. A procedure for the conjugation of
peptide (SEQUENCE ID NO 42) is provided hereinbelow. It is known to
the ordinary artisan that the amounts, times and conditions of such
a procedure can be varied to optimize peptide conjugation.
[0267] The conjugation reaction described hereinbelow is based on
obtaining 3 mg of KLH peptide conjugate ("conjugated peptide"),
which contains about 0.77 .mu.moles of reactive maleimide groups.
This quantity of peptide conjugate usually is adequate for one
primary injection and four booster injections for production of
polyclonal antisera in a rabbit. Briefly, peptide (SEQUENCE ID NO
42) is dissolved in DMSO at a concentration of 1.16 .mu.moles/100
.mu.l of DMSO. One hundred microliters (100 .mu.l) of the DMSO
solution is added to 380 .mu.l of the activated KLH solution
prepared as described hereinabove, and 20 .mu.l of PBS (pH 8.4) is
added to bring the volume to 500 .mu.l. The reaction is incubated
overnight at room temperature with stirring. The extent of reaction
is determined by measuring the amount of unreacted thiol in the
reaction mixture. The difference between the starting concentration
of thiol and the final concentration is assumed to be the
concentration of peptide which has coupled to the activated KLH.
The amount of remaining thiol is measured using Ellman's reagent
(5,5'-dithiobis(2-nitrobenzoic acid), Pierce Chemical Company,
Rockford, Ill.). Cysteine standards are made at a concentration of
0, 0.1, 0.5, 2, 5 and 20 mM by dissolving 35 mg of cysteine HCl
(Pierce Chemical Company, Rockford, Ill.) in 10 ml of PBS (pH 7.2)
and diluting the stock solution to the desired concentration(s).
The photometric determination of the concentration of thiol is
accomplished by placing 200 .mu.l of PBS (pH 8.4) in each well of
an Immulon 2.RTM. microwell plate (Dynex Technologies, Chantilly,
Va.). Next, 10 .mu.l of standard or reaction mixture is added to
each well. Finally, 20 .mu.l of Ellman's reagent at a concentration
of 1 mg/ml in PBS (pH 8.4) is added to each well. The wells are
incubated for 10 minutes at room temperature, and the absorbance of
all wells is read at 415 nm with a microplate reader (such as the
BioRad Model 3550, BioRad, Richmond, Calif.). The absorbance of the
standards is used to construct a standard curve and the thiol
concentration of the reaction mixture is determined from the
standard curve. A decrease in the concentration of free thiol is
indicative of a successful conjugation reaction. Unreacted peptide
is removed by dialysis against PBS (pH 7.2) at room temperature for
6 hours. The conjugate is stored at 2-8.degree. C. if it is to be
used immediately; otherwise, it is stored at -20.degree. C. or
colder.
[0268] 3. Production of Ascites Fluid Containing Monoclonal
Antibodies. Frozen hybridoma cells prepared as described
hereinabove are thawed and placed into expansion culture. Viable
hybridoma cells are inoculated intraperitoneally into Pristane
treated mice. Ascitic fluid is removed from the mice, pooled,
filtered through a 0.2.mu. filter and subjected to an
immunoglobulin class G (IgG) analysis to determine the volume of
the Protein A column required for the purification.
[0269] 4. Purification of Monoclonal Antibodies From Ascites Fluid.
Briefly, filtered and thawed ascites fluid is mixed with an equal
volume of Protein A sepharose binding buffer (1.5 M glycine, 3.0 M
NaCl, pH 8.9) and refiltered through a 0.2.mu. filter. The volume
of the Protein A column is determined by the quantity of IgG
present in the ascites fluid. The eluate then is dialyzed against
PBS (pH 7.2) overnight at 2-8.degree. C. The dialyzed monoclonal
antibody is sterile filtered and dispensed in aliquots. The
immunoreactivity of the purified monoclonal antibody is confirmed
by determining its ability to specifically bind to the peptide used
as the immunogen by use of the EIA microtiter plate assay procedure
of Example 17. The specificity of the purified monoclonal antibody
is confirmed by determining its lack of binding to irrelevant
peptides such as peptides of CS193 not used as the immunogen. The
purified anti-CS193 monoclonal thus prepared and characterized is
placed at either 2-8.degree. C. for short term storage or at
-80.degree. C. for long term storage.
[0270] 5. Further Characterization of Monoclonal Antibody. The
isotype and subtype of the monoclonal antibody produced as
described hereinabove can be determined using commercially
available kits (available from Amersham. Inc., Arlington Heights,
Ill.). Stability testing also can be performed on the monoclonal
antibody by placing an aliquot of the monoclonal antibody in
continuous storage at 2-8.degree. C. and assaying optical density
(OD) readings throughout the course of a given period of time.
[0271] C. Use of Recombinant Proteins as Immunogens. It is within
the scope of the present invention that recombinant proteins made
as described herein can be utilized as immunogens in the production
of polyclonal and monoclonal antibodies, with corresponding changes
in reagents and techniques known to those skilled in the art.
Example 15
Purification of Serum Antibodies Which Specifically Bind to CS193
Peptides
[0272] Immune sera, obtained as described hereinabove in Examples
13 and/or 14, is affinity purified using immobilized synthetic
peptides prepared as described in Example 10, or recombinant
proteins prepared as described in Example 11. An IgG fraction of
the antiserum is obtained by passing the diluted, crude antiserum
over a Protein A column (Affi-Gel protein A, Bio-Rad, Hercules,
Calif.). Elution with a buffer (Binding Buffer, supplied by the
manufacturer) removes substantially all proteins that are not
immunoglobulins. Elution with 0.1M buffered glycine (pH 3) gives an
immunoglobulin preparation that is substantially free of albumin
and other serum proteins.
[0273] Immunoaffinity chromatography is performed to obtain a
preparation with a higher fraction of specific antigen-binding
antibody. The peptide used to raise the antiserum is immobilized on
a chromatography resin, and the specific antibodies directed
against its epitopes are adsorbed to the resin. After washing away
non-binding components, the specific antibodies are eluted with 0.1
M glycine buffer, pH 2.3. Antibody fractions are immediately
neutralized with 1.0M Tris buffer (pH 8.0) to preserve
immunoreactivity. The chromatography resin chosen depends on the
reactive groups present in the peptide. If the peptide has an amino
group, a resin such as Affi-Gel 10 or Affi-Gel 15 is used (Bio-Rad,
Hercules, Calif.). If coupling through a carboxy group on the
peptide is desired, Affi-Gel 102 can be used (Bio-Rad, Hercules,
Calif.). If the peptide has a free sulfhlydryl group, an
organomercurial resin such as Affi-Gel 501 can be used (Bio-Rad,
Hercules, Calif.).
[0274] Alternatively, spleens can be harvested and used in the
production of hybridomas to produce monoclonal antibodies following
routine methods known in the art as described hereinabove.
Example 16
Western Blotting of Tissue Samples
[0275] Protein extracts are prepared by homogenizing tissue samples
in 0.1M Tris-HCl (pH 7.5), 15% (w/v) glycerol, 0.2 mM EDTA, 1.0 mM
1,4-dithiothreitol, 10 .mu.g/ml leupeptin and 1.0 mM
phenylmethylsulfonylfluoride (Kain et al., Biotechniques, 17:982
(1994)). Following homogenization, the homogenates are centrifuged
at 4.degree. C. for 5 minutes to separate supernate from debris.
For protein quantitation, 3-10 .mu.l of supernate are added to 1.5
ml of bicinchoninic acid reagent (Sigma, St. Louis, Mo.), and the
resulting absorbance at 562 nm is measured.
[0276] For SDS-PAGE, samples are adjusted to desired protein
concentration with Tricine Buffer (Novex, San Diego, Calif.), mixed
with an equal volume of 2.times.Tricine sample buffer (Novex, San
Diego, Calif.), and heated for 5 minutes at 100.degree. C. in a
thermal cycler. Samples are then applied to a Novex 10-20% Precast
Tricine Gel for electrophoresis. Following electrophoresis, samples
are transferred from the gels to nitrocellulose membranes in Novex
Tris-Glycine Transfer buffer. Membranes are then probed with
specific anti-peptide antibodies using the reagents and procedures
provided in the Western Lights or Western Lights Plus (Tropix,
Bedford, Mass.) chemiluminesence detection kits. Chemiluminescent
bands are visualized by exposing the developed membranes to
Hyperfilm ECL (Amersham, Arlington Heights, Ill.).
[0277] Competition experiments are carried out in an analogous
manner as above, with the following exception; the primary
antibodies (anti-peptide polyclonal antisera) are pre-incubated for
30 minutes at room temperature with varying concentrations of
peptide immunogen prior to exposure to the nitrocellulose filter.
Development of the Western is performed as above.
[0278] After visualization of the bands on film, the bands can also
be visualized directly on the membranes by the addition and
development of a chromogenic substrate such as
5-bromo-4-chloro-3-indolyl phosphate (BCIP). This chromogenic
solution contains 0.016% BCIP in a solution containing 100 mM NaCl,
5 mM MgCl.sub.2 and 100 mM Tris-HCl (pH 9.5). The filter is
incubated in the solution at room temperature until the bands
develop to the desired intensity. Molecular mass determination is
made based upon the mobility of pre-stained molecular weight
standards (Novex, San Diego, Calif.) or biotinylated molecular
weight standards (Tropix, Bedford, Mass.).
Example 17
EIA Microtiter Plate Assay
[0279] The immunoreactivity of antiserum obtained from rabbits as
described in Example 14 was determined by means of a microtiter
plate EIA, as follows. Briefly, synthetic peptides, SEQUENCE ID NO
42, SEQUENCE ID NO 43, SEQUENCE ID NO 44, and SEQUENCE ID NO 45,
prepared as described in Example 10, were dissolved in carbonate
buffer (50 mM, pH 9.6) to a final concentration of 2 .mu.g/ml.
Next, 100 .mu.l of the peptide or protein solution were placed in
each well of an Immulon 2.RTM. microtiter plate (Dynex
Technologies, Chantilly, Va.). The plate was incubated overnight at
room temperature and then washed four times with deionized water.
The wells were blocked by adding 125 .mu.L of a suitable protein
blocking agent, such as Superblock.RTM. (Pierce Chemical Company,
Rockford, Ill.), to each well and then immediately discarding the
solution. This blocking procedure was performed three times.
Antiserum obtained from immunized rabbits, prepared as previously
described, was diluted in a protein blocking agent (e.g., a 3%
Superblock.RTM. solution) in PBS containing 0.05% Tween-20.RTM.
(monolaurate polyoxyethylene ether) (Sigma Chemical Company, St.
Louis, Mo.) and 0.05% sodium azide at dilutions of 1:100, 1:500,
1:2500, 1:12,500, and 1:62,500 and placed in each well of the
coated microtiter plate. The wells were then incubated for three
hours at room temperature. Each well was washed four times with
deionized water. One hundred microliters of alkaline
phosphatase-conjugated goat anti-rabbit IgG antiserum (Southern
Biotech, Birmingham, Ala.) diluted 1:2000 in 3% Superblock.RTM.
solution in phosphate buffered saline containing 0.05% Tween
20.RTM. and 0.05% sodium azide, were added to each well. The wells
were incubated for two hours at room temperature. Next, each well
was washed four times with deionized water. One hundred microliters
of paranitrophenyl phosphate substrate (Kirkegaard and Perry
Laboratories, Gaithersburg, Md.) then were added to each well. The
wells were incubated for thirty minutes at room temperature. The
absorbance at 405 nm was read in each well. Positive reactions were
identified by an increase in absorbance at 405 nm in the test well
above that absorbance given by a non-immune serum (negative
control). A positive reaction was indicative of the presence of
detectable anti-CS193 antibodies. Titers of the anti-peptide
antisera were calculated from the previously described dilutions of
antisera and defined as the calculated dilution, where A.sub.405
nm=0.5 OD.
Example 18
Coating of Solid Phase Particles
[0280] A. Coating of Microparticles with Antibodies Which
Specifically Bind to CS193 Antigen. Affinity purified antibodies
which specifically bind to CS193 protein (see Example 15) are
coated onto microparticles of polystyrene, carboxylated
polystyrene, polymethylacrylate or similar particles having a
radius in the range of about 0.1 to 20 .mu.m. Microparticles may be
either passively or actively coated. One coating method comprises
coating EDAC (1-(3-dimethylaminopropyl)-3-ethylcarbodiim- ide
hydrochloride (Aldrich Chemical Co., Milwaukee, Wis.) activated
carboxylated latex microparticles with antibodies which
specifically bind to CS193 protein, as follows. Briefly, a final
0.375% solid suspension of resin washed carboxylated latex
microparticles (available from Bangs Laboratories, Carmel, Ind. or
Scrodyn, Indianapolis, Ind.) are mixed in a solution containing 50
mM MES buffer, pH 4.0 and 150 mg/l of affinity purified anti-CS193
antibody (see Example 14) for 15 min in an appropriate container.
EDAC coupling agent is added to a final concentration of 5.5
.mu.g/ml to the mixture and mixed for 2.5 h at room
temperature.
[0281] The microparticles then are washed with 8 volumes of a Tween
20.RTM./sodium phosphate wash buffer (pH 7.2) by tangential flow
filtration using a 0.2 .mu.m Microgon Filtration module. Washed
microparticles are stored in an appropriate buffer which usually
contains a dilute surfactant and irrelevant protein as a blocking
agent, until needed.
[0282] B. Coating of 1/4 Inch Beads. Antibodies which specifically
bind to CS193-antigen also may be coated on the surface of 1/4 inch
polystyrene beads by routine methods known in the art (Snitman et
al, U.S. Pat. No. 5,273,882, incorporated herein by reference) and
used in competitive binding or EIA sandwich assays.
[0283] Polystyrene beads first are cleaned by ultrasonicating them
for about 15 seconds in 10 mM NaHCO.sub.3 buffer at pH 8.0. The
beads then are washed in deionized water until all fines are
removed. Beads then are immersed in an antibody solution in 10 mM
carbonate buffer, pH 8 to 9.5. The antibody solution can be as
dilute as 1 .mu.g/ml in the case of high affinity monoclonal
antibodies or as concentrated as about 500 .mu.g/ml for polyclonal
antibodies which have not been affinity purified. Beads are coated
for at least 12 hours at room temperature, and then they are washed
with deionized water. Beads may be air dried or stored wet (in PBS,
pH 7.4). They also may be overcoated with protein stabilizers (such
as sucrose) or protein blocking agents used as non-specific binding
blockers (such as irrelevant proteins, Carnation skim milk,
Superblock.RTM., or the like).
Example 19
Microparticle Enzyme Immunoassay (MEIA)
[0284] CS193 antigens are detected in patient test samples by
performing a standard antigen competition EIA or antibody sandwich
EIA and utilizing a solid phase such as microparticles (MEIA). The
assay can be performed on an automated analyzer such as the
IMx.RTM. Analyzer (Abbott Laboratories, Abbott Park, Ill.).
[0285] A. Antibody Sandwich EIA. Briefly, samples suspected of
containing CS193 antigen are incubated in the presence of
anti-CS193 antibody-coated microparticles (prepared as described in
Example 17) in order to form antigen/antibody complexes.
[0286] The microparticles then are washed and an indicator reagent
comprising an antibody conjugated to a signal generating compound
(i.e., enzymes such as alkaline phosphatase or horseradish
peroxide) is added to the antigen/antibody complexes or the
microparticles and incubated. The microparticles are washed and the
bound antibody/antigen/antibody complexes are detected by adding a
substrate (e.g., 4-methyl umbelliferyl phosphate (MUP), or
OPD/peroxide, respectively), that reacts with the signal generating
compound to generate a measurable signal. An elevated signal in the
test sample, compared to the signal generated by a negative
control, detects the presence of CS193 antigen. The presence of
CS193 antigen in the test sample is indicative of a diagnosis of a
GI tract disease or condition, such as GI tract cancer.
[0287] B. Competitive Binding Assay. The competitive binding assay
uses a peptide or protein that generates a measurable signal when
the labeled peptide is contacted with an anti-peptide antibody
coated microparticle. This assay can be performed on the IMx.RTM.
Analyzer (available from Abbott Laboratories, Abbott Park, Ill.).
The labeled peptide is added to the CS193 antibody-coated
microparticles (prepared as described in Example 17) in the
presence of a test sample suspected of containing CS193 antigen,
and incubated for a time and under conditions sufficient to form
labeled CS193 peptide (or labeled protein)/bound antibody complexes
and/or patient CS193 antigen/bound antibody complexes. The CS193
antigen in the test sample competes with the labeled CS193 peptide
(or CS193 protein) for binding sites on the microparticle. CS193
antigen in the test sample results in a lowered binding of labeled
peptide and antibody coated microparticles in the assay since
antigen in the test sample and the CS193 peptide or CS193 protein
compete for antibody binding sites. A lowered signal (compared to a
control) indicates the presence of CS193 antigen in the test
sample. The presence of CS193 antigen suggests the diagnosis of a
GI tract disease or condition, such as GI tract cancer.
[0288] The CS193 polynucleotides and the proteins encoded thereby
which are provided and discussed hereinabove are useful as markers
of GI tract tissue disease, especially GI tract cancer. Tests based
upon the appearance of this marker in a test sample such as blood,
plasma or serum can provide low cost, non-invasive, diagnostic
information to aid the physician to make a diagnosis of cancer, to
help select a therapy protocol, or to monitor the success of a
chosen therapy. This marker may appear in readily accessible body
fluids such as blood, urine or stool as antigens derived from the
diseased tissue which are detectable by immunological methods. This
marker may be elevated in a disease state, altered in a disease
state, or be a normal protein of the GI tract which appears in an
inappropriate body compartment.
Sequence CWU 1
1
* * * * *