U.S. patent application number 11/071974 was filed with the patent office on 2005-07-21 for novel method of diagnosing, monitoring, staging, imaging and treating various cancers.
Invention is credited to Cafferkey, Robert, Recipon, Herve, Salceda, Susana, Sun, Yongming.
Application Number | 20050158241 11/071974 |
Document ID | / |
Family ID | 37848825 |
Filed Date | 2005-07-21 |
United States Patent
Application |
20050158241 |
Kind Code |
A1 |
Salceda, Susana ; et
al. |
July 21, 2005 |
Novel method of diagnosing, monitoring, staging, imaging and
treating various cancers
Abstract
The present invention provides a new method for detecting,
diagnosing, monitoring, staging, prognosticating, imaging and
treating selected cancers including gynecologic cancers such as
breast, ovarian, uterine and endometrial cancer and lung
cancer.
Inventors: |
Salceda, Susana; (San Jose,
CA) ; Sun, Yongming; (San Jose, CA) ; Recipon,
Herve; (San Francisco, CA) ; Cafferkey, Robert;
(San Jose, CA) |
Correspondence
Address: |
LICATA & TYRRELL P.C.
66 E. MAIN STREET
MARLTON
NJ
08053
US
|
Family ID: |
37848825 |
Appl. No.: |
11/071974 |
Filed: |
March 4, 2005 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11071974 |
Mar 4, 2005 |
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09763978 |
Apr 25, 2001 |
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09763978 |
Apr 25, 2001 |
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PCT/US99/19655 |
Sep 1, 1999 |
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Current U.S.
Class: |
424/1.49 ;
424/155.1; 435/7.23; 530/388.8 |
Current CPC
Class: |
C12Q 2600/158 20130101;
G01N 33/57442 20130101; A61P 35/00 20180101; G01N 33/57411
20130101; G01N 33/57415 20130101; C12Q 1/6886 20130101; C12Q
2600/16 20130101; A61P 43/00 20180101; Y10T 29/49108 20150115; A61P
35/04 20180101; G01N 33/57449 20130101 |
Class at
Publication: |
424/001.49 ;
424/155.1; 435/007.23; 530/388.8 |
International
Class: |
A61K 051/00; G01N
033/574; A61K 039/395; C07K 016/30 |
Claims
1. A method for detecting the presence of a selected cancer in a
patient comprising: (a) measuring levels of CSG in cells, tissues
or bodily fluids in a patient; and (b) comparing the measured
levels of CSG with levels of CSG in cells, tissues or bodily fluids
from a normal human control, wherein a change in measured levels of
CSG in said patient versus normal human control is associated with
the presence of a selected cancer.
2-5. (canceled)
6. The method of claim 1 wherein the CSG comprises SEQ ID NO:1, 10,
11, 12 or 13 and the selected cancer is a gynecologic cancer
selected from the group consisting of breast, ovarian, endometrial
and uterine cancer.
7. The method of claim 1 wherein the CSG comprises SEQ ID NO:2, 9
or 14 and the selected cancer is lung cancer or a gynecologic
cancer selected from the group consisting of ovarian, endometrial
and uterine cancer.
8. The method of claim 1 wherein the CSG comprises SEQ ID NO:1, 2,
3, 9, 10, 11, 12, 13 or 14 and the selected cancer is ovarian
cancer.
9. An antibody against a CSG wherein said CSG comprises SEQ ID
NO:1, 2, 3, 9, 10, 11, 12, 13 or 14.
10. A method of imaging or treating a selected cancer in a patient
comprising administering to the patient an antibody of claim 9.
11. The method of claim 10 wherein said antibody is labeled with
paramagnetic ions or a radioisotope.
12. (canceled)
13. The method of claim 10 wherein the antibody is conjugated to a
cytotoxic agent.
Description
FIELD OF THE INVENTION
[0001] This invention relates, in part, to newly developed assays
for detecting, diagnosing, monitoring, staging, prognosticating,
imaging and treating various cancers, particularly gynecologic
cancer including ovarian, uterine endometrial and breast cancer,
and lung cancer.
BACKGROUND OF THE INVENTION
[0002] The American Cancer Society has estimated that over 560,000
Americans will die this year from cancer. Cancer is the second
leading cause of death in the United States, exceeded only by heart
disease. It has been estimated that over one million new cancer
cases will be diagnosed in 1999 alone.
[0003] In women; gynecologic cancers account for more than
one-fourth of the malignancies.
[0004] Of the gynecologic cancers, breast cancer is the most
common. According to the Women's Cancer Network, 1 out of every 8
women in the United States is as risk of developing breast cancer,
and 1 out of every 28 women are at risk of dying from breast
cancer. Approximately 77% of women diagnosed with breast cancer are
over the age of 50. However, breast cancer is the leading cause of
death in women between the ages of 40 and 55.
[0005] Carcinoma of the ovary is another very common gynecologic
cancer. Approximately one in 70 women will develop ovarian cancer
during her lifetime. An estimated 14,500 deaths in 1995 resulted
from ovarian cancer. It causes more deaths than any other cancer of
the female reproductive system. Ovarian cancer often does not cause
any noticeable symptoms. Some possible warning signals, however,
are an enlarged abdomen due to an accumulation of fluid or vague
digestive disturbances (discomfort, gas or distention) in women
over 40; rarely there will be abnormal vaginal bleeding. Periodic,
complete pelvic examinations are important; a Pap test does not
detect ovarian cancer. Annual pelvic exams are recommended for
women over 40.
[0006] Also common in women is endometrial cancer or carcinoma of
the lining of the uterus. According to the Women's Cancer Center
endometrial cancer accounts for approximately 13% of all
malignancies in women. There are about 34,000 cases of endometrial
cancer diagnosed in the United States each year.
[0007] Uterine sarcoma is another type of uterine malignancy much
more rare as compared to other gynecologic cancers. In uterine
sarcoma, malignant cells start growing in the muscles or other
supporting tissues of the uterus. Sarcoma of the uterus is
different from cancer of the endometrium, a disease in which cancer
cells start growing in the lining of the uterus. This uterine
cancer usually begins after menopause. Women who have received
therapy with high-dose X-rays (external beam radiation therapy) to
their pelvis are at a higher risk to develop sarcoma of the uterus.
These X-rays are sometimes given to women to stop bleeding from the
uterus.
[0008] Lung cancer is the second most prevalent type of cancer for
both men and women in the United States and is the most common
cause of cancer death in both sexes. Lung cancer can result from a
primary tumor originating in the lung or a secondary tumor which
has spread from another organ such as the bowel or breast. Primary
lung cancer is divided into three main types; small cell lung
cancer non-small cell lung cancer; and mesothelioma. Small cell
lung cancer is also called "Oat Cell" lung cancer because the
cancer cells are a distinctive oat shape. There are three types of
non-small cell lung cancer. These are grouped together because they
behave in a similar way and respond to treatment differently to
small cell lung cancer. The three types are squamous cell
carcinoma, adenocarcinoma, and large cell carcinoma. Squamous cell
cancer is the most common type of lung cancer. It develops from the
cells that line the airways. Adenocarcinoma also develops from the
cells that line the airways. However, adenocarcinoma develops from
a particular type of cell that produces mucus (phlegm). Large cell
lung cancer has been thus named because the cells look large and
rounded when they are viewed under a microscope. Mesothelioma is a
rare type of cancer which affects the covering of the lung called
the pleura. Mesothelioma is often caused by exposure to
asbestos.
[0009] Procedures used for detecting, diagnosing, monitoring,
staging, and prognosticating each of these types of cancer are of
critical importance to the outcome of the patient. In all cases,
patients diagnosed early in development of the cancer generally
have a much greater five-year survival rate as compared to the
survival rate for patients diagnosed with a cancer which has
metastasized. New diagnostic methods which are more sensitive and
specific for early detection of various types of cancer are clearly
needed.
[0010] In the present invention methods are provided for detecting,
diagnosing, monitoring, staging, prognosticating, in vivo imaging
and treating selected cancers including, but not limited to,
gynecologic cancers such as ovarian, breast endometrial and/or
uterine cancer, and lung cancer via detection of a Cancer Specific
Genes (CSGs). Nine CGSs have been identified and refer, among other
things, to native proteins expressed by the genes comprising the
polynucleotide sequences of any of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7,
8 or 9. In the alternative, what is meant by the nine CSGs as used
herein, means the native mRNAs encoded by the genes comprising any
of the polynucleotide sequences of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7,
8 or 9 or it can refer to the actual genes comprising any of the
polynucleotide sequences of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8 or 9.
Fragments of the CSGs such as those depicted in SEQ ID NO:10, 11,
12, 13 or 14 can also be detected.
[0011] Other objects, features, advantages and aspects of the
present invention will become apparent to those of skill in the art
from the following description. It should be understood, however,
that the following description and the specific examples, while
indicating preferred embodiments of the invention are given by way
of illustration only. Various changes and modifications within the
spirit and scope of the disclosed invention will become readily
apparent to those skilled in the art from reading the following
description and from reading the other parts of the present
disclosure.
SUMMARY OF THE INVENTION
[0012] Toward these ends, and others, it is an object of the
present invention to provide a method for diagnosing the presence
of selected cancers by analyzing for changes in levels of CSG in
cells, tissues or bodily fluids compared with levels of CSG in
preferably the same cells, tissues, or bodily fluid type of a
normal human control, wherein a change in levels of CSG in the
patient versus the normal human control is associated with the
selected cancer. For the purposes of this invention, by "selected
dancer" it is meant to include gynecologic cancers such as ovarian,
breast, endometrial and uterine cancer, and lung dancer.
[0013] Further provided is a method of diagnosing metastatic cancer
in a patient having a selected cancer which is not known to have
metastasized by identifying a human patient suspected of having a
selected cancer that has metastasized; analyzing a sample of cells,
tissues, or bodily fluid from such patient for CSG; comparing the
CSG levels in such cells, tissues, or bodily fluid with levels of
CSG in preferably the same cells, tissues, or bodily fluid type of
a normal human control, wherein an increase in CSG levels in the
patient versus the normal human control is associated with a cancer
which has metastasized.
[0014] Also provided by the invention is a method of staging
selected cancers in a human patient by identifying a human patient
having such cancer; analyzing a sample of cells, tissues, or bodily
fluid from such patient for CSG; comparing CSG levels in such
cells, tissues, or bodily fluid with levels of CSG in preferably
the same cells, tissues, or bodily fluid type of a normal human
control sample, wherein an increase in CSG levels in the patient
versus the normal human control is associated with a cancer which
is progressing and a decrease in the levels of CSG is associated
with a cancer which is regressing or in remission.
[0015] Further provided is a method of monitoring selected cancers
in patients for the onset of metastasis. The method comprises
identifying a human patient having a selected cancer that is not
known to have metastasized; periodically analyzing a sample of
cells, tissues, or bodily fluid from such patient for CSG;
comparing the CSG levels in such cells, tissues, or bodily fluid
with levels of CSG in preferably the same cells, tissues, or bodily
fluid type of a normal human control sample, wherein an increase in
CSG levels in the patient versus the normal human control is
associated with a cancer which has metastasized.
[0016] Further provided is a method of monitoring the change in
stage of selected cancers in humans having such cancer by looking
at levels of CSG. The method comprises identifying a human patient
having a selected cancer; periodically analyzing a sample of cells,
tissues, or bodily fluid from such patient for CSG; comparing the
CSG levels in such cells, tissue, or bodily fluid with levels of
CSG in preferably the same cells, tissues, or bodily fluid type of
a normal human control sample, wherein an increase in CSG levels in
the patient versus the normal human control is associated with a
cancer which is progressing and a decrease in the levels of CSG is
associated with a cancer which is regressing or in remission.
[0017] Further provided are antibodies against CSG or fragments of
such antibodies which can be used to detect or image localization
of CSG in a patient for the purpose of detecting or diagnosing
selected cancers. Such antibodies can be polyclonal or monoclonal,
or prepared by molecular biology techniques. The term "antibody",
as used herein and throughout the instant specification is also
meant to include aptamers and single-stranded oligonucleotides such
as those derived from an in vitro evolution protocol referred to as
SELEX and well known to those skilled in the art. Antibodies can be
labeled with a variety of detectable labels including, but not
limited to, radioisotopes and paramagnetic metals. These antibodies
or fragments thereof can also be used as therapeutic agents in the
treatment of diseases characterized by expression of a CSG. In
therapeutic applications, the antibody can be used without or with
derivatization to a cytotoxic agent such as a radioisotope, enzyme,
toxin, drug or a prodrug.
[0018] Other objects, features, advantages and aspects of the
present invention will become apparent to those of skill in the art
from the following description. It should be understood, however,
that the following description and the specific examples, while
indicating preferred embodiments of the invention, are given by way
of illustration only. Various changes and modifications within the
spirit and scope of the disclosed invention will become readily
apparent to those skilled in the art from reading the following
description and from reading the other parts of the present
disclosure.
DETAILED DESCRIPTION OF THE INVENTION
[0019] The present invention relates to diagnostic assays and
methods, both quantitative and qualitative for detecting,
diagnosing, monitoring, staging and prognosticating selected
cancers by comparing levels of CSG with those of CSG in a normal
human control. What is meant by levels of CSG as used herein is
levels of the native protein expressed by the gene comprising the
polynucleotide sequence of any of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8
or 9. In the alternative, what is meant by levels of CSG as used
herein is levels of the native mRNA encoded by the gene comprising
any of the polynucleotide sequence of SEQ ID NO: 1, 2, 3, 4, 5, 6,
7, 8 or 9 or levels of the gene comprising any of the
polynucleotide sequences of SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8 or 9.
Fragments of CSGs such as those depicted in SEQ ID NO: 10, 11, 12,
13 and 14 can also be detected. Such levels are preferably measured
in at least one of cells, tissues and/or bodily fluids, including
determination of normal and abnormal levels. Thus, for instance, a
diagnostic assay in accordance with the invention for diagnosing
over-expression of CSG protein compared to normal control bodily
fluids, cells, or tissue samples may be used to diagnose the
presence of selected cancers. What is meant by "selected cancers"
as used herein is a gynecologic cancer such as ovarian, breast,
endometrial or uterine cancer, or lung case.
[0020] Any of the 9 CSGs can be measured alone in the methods of
the invention, or all together or any combination thereof. However,
for methods relating to gynecologic cancers including ovarian,
breast, endometrial and uterine cancer, it is preferred that levels
of CSG comprising SEQ ID NO:1 or a fragment thereof be determined.
Exemplary fragments of this CSG which can be detected are depicted
in SEQ ID NO: 10, 11, 12, and 13. For methods relating to lung
cancer and gynecologic cancers including ovarian, endometrial and
uterine, it is preferred that levels of CSG comprising SEQ ID NO:2
or 9 be determined. Fragments of this CSG such as that depicted in
SEQ ID NO:14 can also be detected. For methods relating to ovarian
cancer, determination of levels of CSG comprising SEQ ID NO:3 is
also preferred.
[0021] All the methods of the present invention may optionally
include measuring the levels of other cancer markers as well as
CSG. Other cancer markers, in addition to CSG, useful in the
present invention will depend on the cancer being tested and are
known to those of skill in the art.
[0022] Diagnostic Assays
[0023] The present invention provides methods for diagnosing the
presence of selected cancers by analyzing for changes in levels of
CSG in cells, tissues or bodily fluids compared with levels of CSG
in cells, tissues or bodily fluids of preferably the same type from
a normal human control, wherein a change in levels of CSG in the
patient versus the normal human control is associated with the
presence of a selected cancer.
[0024] Without limiting the instant invention, typically, for a
quantitative diagnostic assay a positive result indicating the
patient being tested has cancer is one in which cells, tissues or
bodily fluid levels of the cancer marker, such as CSG, are at least
two times higher, and most preferably are at least five times
higher, than in preferably the same cells, tissues or bodily fluid
of a normal human control.
[0025] The present invention also provides a method of diagnosing
metastases of selected cancers in a patient having a selected
cancer which has not yet metastasized for the onset of metastasis.
In the method of the present invention, a human cancer patient
suspected of having a selected cancer which may have metastasized
(but which was not previously known to have metastasized) is
identified. This is accomplished by a variety of means known to
those of skill in the art. For example, in the case of ovarian
cancer patients are typically diagnosed with ovarian cancer
following surgical staging and monitoring of CA125 levels.
Traditional detection methods are also available and well known for
other selected cancers which can be diagnosed by determination of
CSG levels in a patient.
[0026] In the present invention, determining the presence of CSG
levels in cells, tissues or bodily fluid, is particularly useful
for discriminating between a selected cancer which has not
metastasized and a selected cancer which has metastasized. Existing
techniques have difficulty discriminating between cancers which
have metastasized and cancers which have not metastasized and
proper treatment selection is often dependent upon such
knowledge.
[0027] In the present invention, the cancer marker levels measured
in such cells, tissues or bodily fluid is CSG, and are compared
with levels of CSG in preferably the same cells, tissue or bodily
fluid type of a normal human control. That is, if the cancer marker
being observed is CSG in serum, this level is preferably compared
with the level of CSG in serum of a normal human patient. An
increase in the CSG in the patient versus the normal human control
is associated with a cancer which has metastasized.
[0028] Without limiting the instant invention, typically, for a
quantitative diagnostic assay a positive result indicating the
cancer in the patient being tested or monitored has metastasized is
one in which cells, tissues or bodily fluid levels of the cancer
marker, such as CSG, are at least two times higher, and most
preferably are at least five times higher, than in preferably the
same cells, tissues or bodily fluid of a normal patient.
[0029] Normal human control as used herein includes a human patient
without cancer and/or non cancerous samples from the patient; in
the methods for diagnosing or monitoring for metastasis, normal
human control may also include samples from a human patient that is
determined by reliable methods to have a selected cancer which has
not metastasized.
[0030] Staging
[0031] The invention also provides a method of staging selected
cancers in human patients. The method comprises identifying a human
patient having a selected cancer and analyzing a sample of cells,
tissues or bodily fluid from such human patient for CSG. Then, the
method compares CSG levels in such cells, tissues or bodily fluid
with levels of CSG in preferably the same cells, tissues or bodily
fluid type of a normal human control sample, wherein an increase in
CSG levels in the human patient versus the normal human control is
associated with a cancer which is progressing and a decrease in the
levels of CSG is associated with a cancer which is regressing or in
remission.
[0032] Monitoring
[0033] Further provided is a method of monitoring selected cancers
in humans for the onset of metastasis. The method comprises
identifying a human patient having a selected cancer that is not
known to have metastasized; periodically analyzing a sample of
cells, tissues or bodily fluid from such human patient for CSG;
comparing the CSG levels in such cells, tissues or bodily fluid
with levels of CSG in preferably the same cells, tissues or bodily
fluid type of a normal human control sample, wherein an increase in
CSG levels in the human patient versus the normal human control is
associated with a cancer which has metastasized.
[0034] Further provided by this invention is a method of monitoring
the change in stage of selected cancers in humans having such
cancers. The method comprises identifying a human patient having a
selected cancer; periodically analyzing a sample of cells, tissues
or bodily fluid from such human patient for CSG; comparing the CSG
levels in such cells, tissues or bodily fluid with levels of CSG in
preferably the same cells, tissues or bodily fluid type of a normal
human control sample, wherein an increase in CSG levels in the
human patient versus the normal human control is associated with a
cancer which is progressing in stage and a decrease in the levels
of CSG is associated with a cancer which is regressing in stage or
in remission.
[0035] Monitoring such patient for onset of metastasis is periodic
and preferably done on a quarterly basis. However, this may be more
or less frequent depending on the cancer, the particular patient,
and the stage of the cancer.
[0036] Assay Techniques
[0037] Assay techniques that can be used to determine levels of
gene expression, such as CSG of the present invention, in a sample
derived from a patient are well known to those of skill in the art.
Such assay methods include radioimmunoassays, reverse transcriptase
PCR (RT-PCR) assays, immunohistochemistry assays, in situ
hybridization assays, competitive-binding assays, Western Blot
analyses, ELISA assays and proteomic approaches. Among these,
ELISAs are frequently preferred to diagnose a gene's expressed
protein in biological fluids.
[0038] An ELISA assay initially comprises preparing an antibody, if
not readily available from a commercial source, specific to CSG,
preferably a monoclonal antibody. In addition a reporter antibody
generally is prepared which binds specifically to CSG. The reporter
antibody is attached to a detectable reagent such as radioactive,
fluorescent or enzymatic reagent, for example horseradish
peroxidase enzyme or alkaline phosphatase.
[0039] To carry out the ELISA, antibody specific to CSG is
incubated on a solid support, e.g. a polystyrene dish, that binds
the antibody. Any free protein binding sites on the dish are then
covered by incubating with a non-specific protein such as bovine
serum albumin. Next, the sample to be analyzed is incubated in the
dish, during which time CSG binds to the specific antibody attached
to the polystyrene dish. Unbound sample is washed out with buffer.
A reporter antibody specifically directed to CSG and linked to
horseradish peroxidase is placed in the dish resulting in binding
of the reporter antibody to any monoclonal antibody bound to CSG.
Unattached reporter antibody is then washed out. Reagents for
peroxidase activity, including a calorimetric substrate are then
added to the dish. Immobilized peroxidase, linked to CSG
antibodies, produces a colored reaction product. The amount of
color developed in a given time period is proportional to the
amount of CSG protein present in the sample. Quantitative results
typically are obtained by reference to a standard curve.
[0040] A competition assay may be employed wherein antibodies
specific to CSG attached to a solid support and labeled CSG and a
sample derived from the host are passed over the solid support and
the amount of label detected attached to the solid support can be
correlated to a quantity of CSG in the sample.
[0041] Nucleic acid methods may be used to detect CSG mRNA as a
marker for selected cancers. Polymerase chain reaction (PCR) and
other nucleic acid methods, such as ligase chain reaction (LCR) and
nucleic acid sequence based amplification (NASABA), can be used to
detect malignant cells for diagnosis and monitoring of the various
selected malignancies. For example, reverse-transcriptase PCR
(RT-PCR) is a powerful technique which can be used to detect the
presence of a specific mRNA population in a complex mixture of
thousands of other mRNA species. In RT-PCR, an mRNA species is
first reverse transcribed to complementary DNA (cDNA) with use of
the enzyme reverse transcriptase; the cDNA is then amplified as in
a standard PCR reaction. RT-PCR can thus reveal by amplification
the presence of a single species of mRNA. Accordingly, if the mRNA
is highly specific for the cell that produces it, RT-PCR can be
used to identify the presence of a specific type of cell.
[0042] Hybridization to clones or oligonucleotides arrayed on a
solid support (i.e. gridding) can be used to both detect the
expression of and quantitate the level of expression of that gene.
In this approach, a cDNA encoding the CSG gene is fixed to a
substrate. The substrate may be of any suitable type including but
not limited to glass, nitrocellulose, nylon or plastic. At least a
portion of the DNA encoding the CSG gene is attached to the
substrate and then incubated with the analyte, which may be RNA or
a complementary DNA (cDNA) copy of the RNA, isolated from the
tissue of interest. Hybridization between the substrate bound DNA
and the analyte can be detected and quantitated by several means
including but not limited to radioactive labeling or fluorescence
labeling of the analyte or a secondary molecule designed to detect
the hybrid. Quantitation of the level of gene expression can be
done by comparison of the intensity of the signal from the analyte
compared with that determined from known standards. The standards
can be obtained by in vitro transcription of the target gene,
quantitating the yield, and then using that material to generate a
standard curve.
[0043] Of the proteomic approaches, 2D electrophoresis is a
technique well known to those in the art. Isolation of individual
proteins from a sample such as serum is accomplished using
sequential separation of proteins by different characteristics
usually on polyacrylamide gels. First, proteins are separated by
size using an electric current. The current acts uniformly on all
proteins, so smaller proteins move farther on the gel than larger
proteins. The second dimension applies a current perpendicular to
the first and separates proteins not on the basis of size but on
the specific electric charge carried by each protein. Since no two
proteins with different sequences are identical on the basis of
both size and charge, the result of a 2D separation is a square gel
in which each protein occupies a unique spot. Analysis of the spots
with chemical or antibody probes, or subsequent protein
microsequencing can reveal the relative abundance of a given
protein and the identity of the proteins in the sample.
[0044] The above tests can be carried out on samples derived from a
variety of patients' cells, bodily fluids and/or tissue extracts
(homogenates or solubilized tissue) such as from tissue biopsy and
autopsy material. Bodily fluids useful in the present invention
include blood, urine, saliva or any other bodily secretion or
derivative thereof. Blood can include whole blood, plasma, serum or
any derivative of blood.
[0045] In Vivo Antibody Use
[0046] Antibodies against CSG can also be used in vivo in patients
suspected of suffering from a selected cancer including lung cancer
or gynecologic cancers such as ovarian, breast, endometrial or
uterine cancer. Specifically, antibodies against a CSG can be
injected into a patient suspected of having a selected cancer for
diagnostic and/or therapeutic purposes. The use of antibodies for
in vivo diagnosis is well known in the art. For example,
antibody-chelators labeled with Indium-111 have been described for
use in the radioimmunoscintographic imaging of carcinoembryonic
antigen expressing tumors (Sumerdbn et al. Nucl. Med. Biol. 1990
17: 247-254). In particular, these antibody-chelators have been
used in detecting tumors in patients suspected of having recurrent
colorectal cancer (Griffin et al. J. Clin. One. 1991 9: 631-640).
Antibodies with paramagnetic ions as labels for use in magnetic
resonance imaging have also been described (Lauffer, R. B. Magnetic
Resonance in Medicine 1991 22: 339-342). Antibodies directed
against CSGs can be used in a similar manner. Labeled antibodies
against a CSG can be injected into patients suspected of having a
selected cancer for the purpose of diagnosing or staging of the
disease status of the patient. The label used will be selected in
accordance with the imaging modality to be used. For example,
radioactive labels such as Indium-111, Technetium-99m or Iodine-131
can be used for planar scans or single photon emission computed
tomography (SPECT). Positron emitting labels such as Fluorine-19
can be used in positron emission tomography. Paramagnetic ions such
as Gadlinium (III) or anganese (II) can used in magnetic resonance
imaging (MRI). Localization of the label permits determination of
the spread of the cancer. The amount of label within an organ or
tissue also allows determination of the presence or absence of
cancer in that organ or tissue.
[0047] For patients diagnosed with a selected cancer, injection of
an antibody against a CSG can also have a therapeutic benefit. The
antibody may exert its therapeutic effect alone. Alternatively, the
antibody is conjugated to a cytotoxic agent such as a drug, toxin
or radionuclide to enhance its therapeutic effect. Drug monoclonal
antibodies have been described in the art for example by Garnett
and Baldwin, Cancer Research 1986 46: 2407-2412. The use of toxins
conjugated to monoclonal antibodies for the therapy of various
cancers has also been described by Pastan et al. Cell 1986 47:
641-648 Yttrium-90 labeled monoclonal antibodies have been
described for maximization of dose delivered to the tumor while
limiting toxicity to normal tissues (Goodwin and Meares Cancer
Supplement 1997 80: 2675-2680). Other cytotoxic radionuclides
including, but not limited to Copper-67, Iodine-131 and Rhenium-186
can also be used for labeling of antibodies against CSGs.
[0048] Antibodies which can be used in these in vivo methods
include both polyclonal and monoclonal antibodies and antibodies
prepared via molecular biology techniques. Antibody fragments and
aptamers and single-stranded oligonucleotides such as those derived
from an in vitro evolution protocol referred to as SELEX and well
known to those skilled in the art can also be used.
[0049] The present invention is further described by the following
examples. These examples are provided solely to illustrate the
invention by reference to specific embodiments. The
exemplifications, while illustrating certain aspects of the
invention, do not portray the limitations or circumscribe the scope
of the disclosed invention.
EXAMPLES
Example 1
[0050] Identification of CSGs were carried out by a systematic
analysis of data in the LIFESEQ database available from Incyte
Pharmaceuticals, Palo Alto, Calif., using the data mining Cancer
Leads Automatic Search Package (CLASP) developed by diaDexus LLC,
Santa Clara, Calif.
[0051] The CLASP performs the following steps: selection of highly
expressed organ specific genes based on the abundance level of the
corresponding EST in the targeted organ versus all the other
organs; analysis of the expression level of each highly expressed
organ specific genes in normal, tumor tissue, disease tissue and
tissue libraries associated with tumor or disease. Selection of the
candidates demonstrating component ESTs were exclusively or more
frequently found in tumor libraries. The CLASP allows the
identification of highly expressed organ and cancer specific genes.
A final manual in depth evaluation is then performed to finalize
the CSGs selection.
1TABLE 1 CSG Sequences SEQ ID NO: Clone ID Gene ID 1 16656542
234617 2 1283171 332459 3 1649377 481154 4 236044H1 none assigned 5
none assigned 255687 6 none assigned 251313 7 none assigned 12029 8
none assigned 251804
[0052] The following examples are carried out using standard
techniques, which are well known and routine to those of skill in
the art, except where otherwise described in detail. Routine
molecular biology techniques of the following example can be
carried out as described in standard laboratory manuals, such as
Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed.;
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
(1989).
Example 2
Relative Quantitation of Gene Expression
[0053] Real-Time quantitative PCR with fluorescent Taqman probes is
a quantitation detection system utilizing the 5'-3' nuclease
activity of Taq DNA polymerase. The method uses an internal
fluorescent oligonucleotide probe (Taqman) labeled with a 5'
reporter dye and a downstream, 3' quencher dye. During PCR, the
5'-3' nuclease activity of Taq DNA polymerase releases the
reporter, whose fluorescence can then be detected by the laser
detector of the Model 7700 Sequence Detection System (PE Applied
Biosystems, Foster-City, Calif., USA).
[0054] Amplification of an endogenous control is used to
standardize the amount of sample RNA added to the reaction and
normalize for Reverse Transcriptase (RT) efficiency. Either
cyclophilin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) or
18S ribosomal RNA (rRNA) is used as this endogenous control. To
calculate relative quantitation between all the samples studied,
the target RNA levels for one sample were used as the basis for
comparative results (calibrator). Quantitation relative to the
"calibrator" can be obtained using the standard curve method or the
comparative method (User Bulletin #2: ABI PRISM 7700 Sequence
Detection System).
[0055] The tissue distribution and the level of the target gene for
every example in normal and cancer tissue were evaluated. Total RNA
was extracted from normal tissues, cancer tissues, and from cancers
and the corresponding matched adjacent tissues. Subsequently, first
strand cDNA was prepared with reverse transcriptase and the
polymerase chain reaction was done using primers and Taqman probe
specific to each target gene. The results are analyzed using the
ABI PRISM 7700 Sequence Detector. The absolute numbers are relative
levels of expression of the target gene in a particular tissue
compared to the calibrator tissue.
[0056] Measurement of Ovr110; Clone ID16656542; Gene ID 234617 (SEQ
ID NO:1, 10, 11, 12 or 13)
[0057] The absolute numbers depicted in Table 2 are relative levels
of expression of Ovr110 (SEQ ID NO:1 or a fragment thereof as
depicted in SEQ ID NO:10, 11, 12, or 13) in 12 normal different
tissues. All the values are compared to normal stomach
(calibrator). These RNA samples are commercially available pools,
originated by pooling samples of a particular tissue from different
individuals.
2TABLE 2 Relative Levels of Ovr110 Expression in Pooled Samples
Tissue NORMAL colon 0.00 endometrium 8.82 kidney 7.19 liver 0.36
ovary 1.19 pancreas 21.41 prostate 2.79 small intestine 0.03 spleen
0.00 00000000000000stoma 1.00 testis 8.72 uterus 0.93
[0058] The relative levels of expression in Table 2 show that
Ovr110 is expressed at comparable levels in most of the normal
tissues analyzed. Pancreas, with a relative expression level of
21.41, endometrium (8.82), testis (8.72), and kidney (7.19) are the
only tissues expressing high levels of Ovr110 mRNA.
[0059] The absolute numbers in Table 2 were obtained analyzing
pools of samples of a particular tissue from different individuals.
They can not be compared to the absolute numbers originated from
RNA obtained from tissue samples of a single individual in Table
3.
[0060] The absolute numbers depicted in Table 3 are relative levels
of expression of Ovr110 in 73 pairs of matching samples. All the
values are compared to normal stomach (calibrator). A matching pair
is formed by mRNA from the cancer sample for a particular tissue
and mRNA from the normal adjacent sample for that same tissue from
the same individual. In addition, 15 unmatched cancer samples (from
ovary and mammary gland) and 14 unmatched normal samples (from
ovary and mammary gland) were also tested.
3TABLE 3 Relative Levels of Ovr110 Expression in Individual Samples
Matching Normal Sample ID Tissue Cancer Adjacent Normal Ovr103X
Ovary 1 86.22 0.53 Ovr1040O Ovary 2 168.31 Ovr1157 Ovary 3 528.22
Ovr63A Ovary 4 1.71 Ovr773O Ovary 5 464.65 Ovr1005O Ovary 6 18.32
Ovr1028 Ovary 7 7.78 Ovr1118 Ovary 8 0.00 Ovr130X Ovary 9 149.09
Ovr638A Ovary 10 3.14 OvrA1B Ovary 11 21.26 OvrA1C Ovary 12 1.83
OvrC360 Ovary 13 0.52 Ovr18GA Ovary 14 1.07 Ovr20GA Ovary 15 1.88
Ovr25GA Ovary 16 2.52 Ovr206I Ovary 17 2.51 Ovr32RA Ovary 18 3.01
Ovr35GA Ovary 19 5.17 Ovr40G Ovary 20 0.45 Ovr50GB Ovary 21 2.69
OvrC087 Ovary 22 0.47 OvrC179 Ovary 23 1.46 OvrC004 Ovary 24 4.99
OvrC007 Ovary 25 13.36 OvrC109 Ovary 26 6.61 MamS516 Mammary 16.39
13.74 Gland 1 MamS621 Mammary 826.70 4.60 Gland 2 MamS854 Mammary
34.60 18.30 Gland 3 Mam59X Mammary 721.57 27.00 Gland 4 MamS079
Mammary 80.73 5.10 Gland 5 MamS967 Mammary 6746.90 72.80 Gland 6
MamS127 Mammary 7.00 20.00 Gland 7 MamB011X Mammary 1042.00 29.00
Gland 8 Mam12B Mammary 1342.00 Gland 9 Mam82XI Mammary 507.00 Gland
10 MamS123 Mammary 24.85 4.24 Gland 11 MamS699 Mammary 84.74 5.54
Gland 12 MamS997 Mammary 482.71 11.84 Gland 13 Mam162X Mammary
15.73 10.59 Gland 14 MamA06X Mammary 1418.35 8.20 Gland 15 Mam603X
Mammary 294.00 Gland 16 Mam699F Mammary 567.40 86.60 Gland 17
Mam12X Mammary 425.00 31.00 Gland 18 MamA04 Mammary 2.00 Gland 19
Mam42DN Mammary 46.05 31.02 Gland 20 Utr23XU Uterus 1 600.49 27.95
Utr85XU Uterus 2 73.52 18.83 Utr135XO Uterus 3 178.00 274.00
Utr141XO Uterus 4 289.00 26.00 CvxNKS54 Cervix 1 2.47 0.61 CvxKS83
Cervix 2 1.00 2.00 CvxNKS18 Cervix 3 1.00 0.00 CvxNK23 Cervix 4
5.84 14.47 CvxNK24 Cervix 5 20.32 33.13 End68X Endometrium 1 167.73
544.96 End8963 Endometrium 2 340.14 20.89 End8XA Endometrium 3 1.68
224.41 End65RA Endometrium 4 303.00 5.00 End8911 Endometrium 5
1038.00 74.00 End3AX Endometrium 6 6.59 1.69 End4XA Endometrium 7
0.43 15.45 End5XA Endometrium 8 17.81 388.02 End10479 Endometrium 9
1251.60 31.10 End12XA Endometrium 312.80 33.80 10 Kid107XD Kidney 1
2.68 29.65 Kid109XD Kidney 2 81.01 228.33 Kid10XD Kidney 3 0.00
15.30 Kid6XD Kidney 4 18.32 9.06 Kid11XD Kidney 5 1.38 20.75 Kid5XD
Kidney 6 30.27 0.19 Liv15XA Liver 1 0.00 0.45 Liv42X Liver 2 0.81
0.40 Liv94XA Liver 3 12.00 2.16 Lng LC71 Lung 1 5.45 3.31 LngAC39
Lung 2 1.11 0.00 LngBR94 Lung 3 4.50 0.00 LngSQ45 Lung 4 15.03 0.76
LngC20X Lung 5 0.00 1.65 LngSQ56 Lung 6 91.77 8.03 ClnAS89 Colon 1
0.79 7.65 ClnC9XR Colon 2 0.03 0.00 ClnRC67 Colon 3 0.00 0.00
ClnSG36 Colon 4 0.81 0.35 ClnTX89 Colon 5 0.00 0.00 ClnSG45 Colon 6
0.00 0.06 ClnTX01 Colon 7 0.00 0.00 Pan77X Pancreas 1 0.89 2.62
Pan71XL Pancreas 2 3.99 0.12 Pan82XP Pancreas 3 59.92 28.44 Pan92X
Pancreas 4 17.21 0.00 StoAC93 Stomach 1 7.54 6.43 StoAC99 Stomach 2
19.49 3.19 StoAC44 Stomach 3 3.62 0.37 SmI21XA Small 0.00 0.00
Intestine 1 SmIH89 Small 0.00 0.00 Intestine 2 Bld32XK Bladder 1
0.00 0.21 Bld46XK Bladder 2 0.36 0.32 BldTR17 Bladder 3 0.28 0.00
Tst39X Testis 11.24 2.24 Pro84XB Prostate 1 2.60 24.30 Pro90XB
Prostate 2 1.40 2.00
[0061] 0.00=Negative
[0062] Table 2 and Table 3 represent a combined total of 187
samples in 16 different tissue types. In the analysis of matching
samples, the higher levels of expression were in mammary gland,
uterus, endometrium and ovary, showing a high degree of tissue
specificity for the gynecologic tissues. Of all the samples
different than those mentioned before analyzed, only a few samples
(Kid109XD, LngSQ56, and Pan82XP) showed high levels of expression
of Ovr110.
[0063] Furthermore, the level of mRNA expression was compared in
cancer samples and the isogenic normal adjacent tissue from the
same individual. This comparison provides an indication of
specificity for the cancer stage (e.g. higher levels of mRNA
expression in the cancer sample compared to the normal adjacent).
Table 3 shows overexpression of Ovr110 in 15 of 16 mammary gland
cancer tissues compared with their respective normal adjacent
(mammary gland samples MamS516, MamS621, MamS854, Mam59X, MamS079,
MamS967, MamB011X, MamS123, MamS699, MamS997, Mam162X, MamA06X,
Mam699F, Mam12X, and Mam42DN). There was overexpression in the
cancer tissue for 94% of the mammary gland matching samples
tested.
[0064] For uterus, Ovr110 is overexpressed in 3 of 4 matching
samples (uterus samples Utr23XU, Utr85XU, and Utr141XO). There was
overexpression in the cancer tissue for 75% of the uterus matching
samples analyzed.
[0065] For endometrium, Ovr110 is overexpressed in 6 of 10 matching
samples (endometrium samples End8963, End65RA, End8911, End3AX,
End10479, and End12XA). There was overexpression in the cancer
tissue for 60% of the endometrium matching samples.
[0066] For ovary, Ovr110 shows overexpression in 1 of 1 matching
sample. For the unmatched ovarian samples, 8 of 12 cancer samples
show expression values of Ovr110 higher than the median (2.52) for
the normal unmatched ovarian samples. There was overexpression in
the cancer tissue for 67% of the unmatched ovarian samples.
[0067] Altogether, the level of tissue specificity, plus the mRNA
overexpression in most of the matching samples tested are
indicative of Ovr110 (including SEQ ID NO:1, 10, 11, 12 or 13)
being a diagnostic marker for gynecologic cancers, specifically,
mammary gland or breast, uterine, ovarian and endometrial
cancer.
[0068] Measurement of Ovr114; Clone ID1649377; Gene ID 481154 (SEQ
ID NO:3)
[0069] The numbers depicted in Table 4 are relative levels of
expression in 12 normal tissues of Ovr114 compared to pancreas
(calibrator). These RNA samples were obtained commercially and were
generated by pooling samples from a particular tissue from
different individuals.
4TABLE 4 Relative Levels of Ovr114 Expression in Pooled Samples
Tissue Normal Colon 2.3 Endometrium 7.6 Kidney 0.5 Liver 0.6 Ovary
5.2 Pancreas 1.0 Prostate 2.1 Small Intestine 1.3 Spleen 2.4
Stomach 1.5 Testis 15.8 Uterus 8.8
[0070] The relative levels of expression in Table 4 show that
Ovr114 mRNA expression is detected in all the pools of normal
tissues analyzed.
[0071] The tissues shown in Table 4 are pooled samples from
different individuals. The tissues shown in Table 5 were obtained
from individuals and are not pooled. Hence the values for mRNA
expression levels shown in Table 4 cannot be directly compared to
the values shown in Table 5.
[0072] The numbers depicted in Table 5 are relative levels of
expression of Ovr114 compared to pancreas (calibrator), in 46 pairs
of matching samples and 27 unmatched tissue samples. Each matching
pair contains the cancer sample for a particular tissue and the
normal adjacent tissue sample for that same tissue from the same
individual. In cancers (for example, ovary) where it was not
possible to obtain normal adjacent samples from the same
individual, samples from a different normal individual were
analyzed.
5TABLE 5 Relative Levels of Ovr114 Expression in Individual Samples
Normal & Borderline Matching Normal Tissue Sample ID Cancer
Type Cancer Malignant Adjacent Ovary 1 Ovr1037O/1038O Papillary
serous 17.04 3.93 adenocarcinoma, G3 Ovary 2 OvrG021SPI/SN2
Papillary serous 1.62 4.34 adenocarcinoma Ovary 3 OvrG010SP/SN
Papillary serous 0.50 1.12 adenocarcinoma Ovary 4 OvrA081F/A082D
Mucinous tumor, low 0.84 0.96 malignant potential Ovary 5
OvrA084/A086 Mucinous tumor, grade G-B, 5.24 6.00 borderline Ovary
6 Ovr14604A1C Serous cystadenofibroma, 5.33 low malignancy Ovary 7
Ovr14638A1C Follicular cysts, low 8.11 malignant potential Ovary 8
Ovr1040O Papillary serous 13.27 adenocarcinoma, G2 Ovary 9 Ovr1157O
Papillary serous 106.08 adenocarcinoma Ovary 10 Ovr1005O Papillary
serous 77.04 endometricarcinoma Ovary 11 Ovr1028O Ovarian carcinoma
14.78 Ovary 12 Ovr14603A1D Adenocarcinoma 22.23 Ovary 13
Ovr9410C360 Endometrioid 4.74 adenocarcinoma Ovary 14 Ovr1305X
Papillary serous 96.49 adenocarcinoma Ovary 15 Ovr773O Papillary
serous 8.40 adenocarcinoma Ovary 16 Ovr988Z Papillary serous 6.40
adenocarcinoma Ovary 17 Ovr9702C018GA Normal Cystic 12.06 Ovary 18
Ovr2061 Normal left atrophic, 10.11 small cystic Ovary 19
Ovr9702C020GA Normal-multiple ovarian 12.70 cysts Ovary 20
Ovr9702C025GA Normal-hemorrhage CL cysts 22.09 Ovary 21
Ovr9701C050GB Normal-multiple ovarian 9.01 cysts Ovary 22
Ovr9701C087RA Normal-small follicle 1.86 cysts Ovary 23
Ovr9702C032RA 7.81 Ovary 24 Ovr9701C109RA Normal 1.50 Ovary 25
Ovr9411C057R Benign large endometriotic 5.22 cyst Ovary 26
Ovr9701C179a Normal 3.09 Ovary 27 Ovr1461O Serous cystadenofibroma,
3.53 no malignancy Ovary 28 Ovr9701C035GA Normal 6.32 Ovary 29
Ovr9702C007RA Normal 0 Ovary 30 Ovr9701C087RA Normal-small follicle
1.97 cysts Ovary 31 Ovr9411C109 Normal 9.49 Ovary 32 Ovr9701C177a
Normal-cystic follicles 3.85 Endometrium 1 End14863A1A/A2A
Moderately differ. Endome. 1.30 0.70 carcinoma/NAT Endometrium 2
End9709C056A/55A Endometrial 1.83 11.90 adenocarcinoma/NAT
Endometrium 3 End9704C281A/2A Endometrial 13.32 7.76
adenocarcinoma/NAT Endometrium 4 End9705A125A/6A Endometrial 3.62
3.34 adenocarcinoma/NAT Mammary Gland 1 Mam00042D01/N01 3.13 0.76
Mammary Gland 2 MamS99-522A/B 4.45 0.45 Mammary Gland 3
Mam1620F/1621F 0.74 1.91 Mammary Gland 4 Mam4003259a/g 3.48 2.00
Uterus 1 Utr850U/851U Stage 1 endometrial 46.96 11.96 cancer/NAT
Uterus 2 Utr233U96/234U96 Adenocarcinoma/NAT 20.02 5.90 Uterus 3
Utr1359O/1358O Tumor/NAT 10.23 7.74 Uterus 4 Utr1417O/1418O
Malignant tumor/NAT 7.52 4.92 Cervix 1 CvxVNM00083/83 Keratinizing
squamous cell 5.47 14.31 carcinoma Cervix 2 CvxIND00023D/N Large
cell nonkeratinizing 4.99 3.99 carcinoma Cervix 3 CvxIND00024D/N
Large cell nonkeratinizing 10.14 14.22 carcinoma Bladder 1
Bld665T/664T 1.43 4.03 Bladder 2 Bld327K/328K Papillary
transitional 1.15 0.99 cell carcinoma/NAT Kidney 1 Kid4003710C/F
0.03 0.35 Kidney 2 Kid1242D/1243D 1.61 0.14 Lung 1 Lng750C/751C
Metastatic osteogenic 2.44 5.73 sarcoma/NAT Lung 2 Lng8890A/8890B
Cancer/NAT 1.11 5.19 Lung 3 Lng9502C109R/10R 1.99 0.80 Liver 1
Liv1747/1743 Hepatocellular 0.67 1.07 carcinoma/NAT Liver 2
LivVNM00175/175 Cancer/NAT 15.46 2.85 Skin 1 Skn2S9821248A/B
Secondary malignant 2.83 0.70 melanoma Skin 2 Skn4005287A1/B2 0.91
4.02 Small Int. 1 SmI9802H008/009 0.87 0.82 Stomach 1
Sto4004864A4/B4 Adenocarcinoma/NAT 0.81 1.22 Stomach 2
StoS9822539A/B Adenocarcinoma/NAT 1.22 1.39 Stomach 3 StoS99728A/C
Malignant gastrointestinal 0.47 0.35 stromal tumor Prostate 1
Pro1012B/1013B Adenocarcinoma/NAT 2.39 2.61 Prostate 2
Pro1094B/1095B 0.10 0.38 Pancreas 1 Pan776p/777p Tumor/NAT 2.39
0.52 Pancreas 2 Pan824p/825p Cystic adenoma 1.66 1.22 Testis 1
Tst239X/240X Tumor/NAT 1.24 1.72 Colon 1 Cln9706c068ra/69ra
Adenocarcinoma/NAT 0.38 0.65 Colon 2 Cln4004732A7/B6
Adenocarcinoma/NAT 0.44 1.26 Colon 3 Cln4004695A9/B8 1.94 1.53
Colon 4 Cln9612B006/005 Asc. Colon, Cecum, 3.38 1.10 adenocarcinoma
Colon 5 Cln9704C024R/25R Adenocarcinoma/NAT 1.66 2.77
[0073] Table 4 and Table 5 represent a combined total of 129
samples in 17 human tissue types. Among 117 samples in Table 5
representing 16 different tissues high levels of expression are
seen only in ovarian cancer samples. The median expression of
Ovr114 is 14.03 (range: 0.5-106.08) in ovarian cancer and 4.34
(range: 0-22.09) in normal ovaries. In other words, the median
expression levels of Ovr114 in cancer samples is increased 3.5 fold
as compared with that of the normal ovarian samples. Five of 12
ovarian cancers (42%) showed increased expression relative to
normal ovary (with 95% specificity). The median expression of
Ovr114 in other gynecologic cancers is 4.99, and 2 out of 15
samples showed expression levels comparable with that in ovarian
cancer. The median of the expression levels of Ovr114 in the rest
of the cancer samples is 1.24, which is more than 11 fold less than
that detected in ovarian cancer samples. No individual showed an
expression level comparable to that of ovarian cancer samples
(except Liver 2; LivVNM00175/175).
[0074] The 3.5 fold increase in expression in 42% of the individual
ovarian cancer samples and no compatible expression in other
non-gynecologic cancers is indicative of Ovr114 being a diagnostic
marker for detection of ovarian cancer cells. It is believed that
the Ovr114 marker may also be useful in detection of additional
gynecologic cancers.
[0075] Measurement of Ovr115; Clone ID1283171; Gene ID 332459 (SEQ
ID NO:2 or 14)
[0076] The numbers depicted in Table 6 are relative levels of
expression Ovr115 compared to their respective calibrators. The
numbers are relative levels of expression in 12 normal tissues of
ovaries compared to Testis (calibrator). These RNA samples were
obtained commercially and were generated by pooling samples from a
particular tissue from different individuals.
6TABLE 6 Relative Levels of Ovr115 Expression in Pooled Samples
Tissue Normal Colon 858.10 Endometrium 12.34 Kidney 3.76 Liver 0.00
Ovary 0.43 Pancreas 0.00 Prostate 8.91 Small Intestine 62.25 Spleen
0.00 Stomach 37.53 Testis 1.00 Uterus 47.67
[0077] The relative levels of expression in Table 6 show that
Ovr115 mRNA expression is detected in all the 12 normal tissue
pools analyzed.
[0078] The tissues shown in Table 6 are pooled samples from
different individuals. The tissues shown in Table 7 were obtained
from individuals and are not pooled. Hence the values for mRNA
expression levels shown in Table 6 cannot be directly compared to
the values shown in Table 7.
[0079] The numbers depicted in Table 7 are relative levels of
expression of Ovr115 compared to testis (calibrator), in 46 pairs
of matching samples and 27 unmatched tissue samples. Each matching
pair contains the cancer sample for a particular tissue and the
normal adjacent tissue sample for that same tissue from the same
individual. In cancers (for example, ovary) where it was not
possible to obtain normal adjacent samples from the same
individual, samples from a different normal individual were
analyzed.
7TABLE 7 Relative Levels of Ovr115 Expression in Individual Samples
Normal & Borderline Matching Normal Tissue Sample ID Cancer
Type Cancer Malignant Adjacent Ovary 1 Ovr1037O/1038O Papillary
serous 193.34 0.24 adenocarcinoma, G3 Ovary 3 OvrG021SPI/SN2
Papillary serous 0.38 0.31 adenocarcinoma Ovary 4 OvrG010SP/SN
Papillary serous 231.25 0.45 adenocarcinoma Ovary 2 OvrA084/A086
Mucinous tumor, grade G- 143.34 16.65 B, borderline Ovary 5
OvrA081F/A082D Mucinous tumor, low 314.13 0 malignant potential
Ovary 19 Ovr14604A1C Serous cystadenofibroma, 299.87 low malignancy
Ovary 26 Ovr14638A1C Follicular cysts, low 1278.32 malignant
potential Ovary 6 Ovr1040O Papillary serous 144.25 adenocarcinoma,
G2 Ovary 22 Ovr9410C360 Endometrioid 0.29 adenocarcinoma Ovary 23
Ovr1305X Papillary serous 157.41 adenocarcinoma Ovary 27 Ovr773O
Papillary serous 340.04 adenocarcinoma Ovary 28 Ovr988Z Papillary
serous 464.75 adenocarcinoma Ovary 7 Ovr1157O Papillary serous
432.07 adenocarcinoma Ovary 8 Ovr1005O Papillary serous 74.23
endometricarcinoma Ovary 9 Ovr1028O Ovarian carcinoma 1408.79 Ovary
10 Ovr14603A1D Adenocarcinoma 0.00 Ovary 11 Ovr9702C018GA Normal
Cystic 0.16 Ovary 12 Ovr2061 Normal left atrophic, 0.00 small
cystic Ovary 13 Ovr9702C020GA Normal-multiple ovarian 0.00 cysts
Ovary 14 Ovr9702C025GA Normal-hemorrhage CL 0.00 cysts Ovary 15
Ovr9701C050GB Normal-multiple ovarian 0.91 cysts Ovary 16
Ovr9701C087RA Normal-small follicle 0.00 cysts Ovary 17
Ovr9702C032RA 0.28 Ovary 18 Ovr9701C109RA Normal 0.00 Ovary 20
Ovr9411C057R Benign large 38.87 endometriotic cyst Ovary 21
Ovr9701C179a Normal 0.08 Ovary 24 Ovr1461O Serous cystadenofibroma,
0.00 no malignancy Ovary 25 Ovr9701C035GA Normal 0.00 Ovary 29
Ovr9702C007RA Normal 0.00 Ovary 30 Ovr9701C087RA Normal-small
follicle 0.00 cysts Ovary 31 Ovr9411C109 Normal 0.00 Ovary 32
Ovr9701C177a Normal-cystic follicles 0.00 Uterus 1 Utr850U/851U
Stage 1 endometrial 39.95 13.60 cancer/NAT Uterus 2
Utr233U96/234U96 Adenocarcinoma/NAT 140.37 22.67 Uterus 3
Utr1359O/1358) Tumor/NAT 16.45 32.50 Uterus 4 Utr1417O/1418O
Malignant tumor/NAT 288.52 5.29 Endometrium 1 End14863A1A/A2A
Moderately differ. 2.61 6.24 Endome. carcinoma/NAT Endometrium 2
End9709C056A/55A Endometrial 2.10 49.40 adenocarcinoma/NAT
Endometrium 3 End9704C281A/2A Endometrial 480.77 19.22
adenocarcinoma/NAT Endometrium 4 End9705A125A/6A Endometrial 322.07
31.08 adenocarcinoma/NAT Lung 1 Lng750C/751C Metastatic osteogenic
38.81 7.36 sarcoma/NAT Lung 2 Lng8890A/8890B Cancer/NAT 690.12
14.71 Lung 3 Lng9502C109R/10R 1756.90 2.86 Skin 1 Skn2S9821248A/B
Secondary malignant 10.56 0.00 melanoma Skin 2 Skn4005287A1/B2
331.30 47.23 Prostate 1 Pro1012B/1013B Adenocarcinoma/NAT 14.64
4.39 Prostate 2 Pro1094B/1095B 0.09 2.54 Bladder 1 B1d665T/664T
404.56 90.20 Bladder 2 B1d327K/328K Papillary transitional 77.35
177.37 cell carcinoma/NAT Kidney 1 Kid4003710C/F 0.17 12.72 Kidney
2 Kid1242D/1243D 0.00 13.74 Mammary Gland 1 Mam1620F/1621F 0.27
0.12 Mammary Gland 2 Mam4003259a/g 5.71 0.00 Liver 1 Liv1747/1743
Hepatocellular 0.14 0.69 carcinoma/NAT Liver 2 LivVNM00175/175
Cancer/NAT 0.00 0.00 Small Int. 1 SmI9802H008/009 128.44 151.38
Stomach 1 Sto4004864A4/B4 Adenocarcinoma/NAT 303.01 116.72 Stomach
2 StoS9822539A/B Adenocarcinoma/NAT 24.12 17.76 Stomach 3
StoS99728A/C Malignant 0.00 9.10 gastrointestinal stromal tumor
Pancreas 1 Pan776p/777p Tumor/NAT 0.00 0.43 Pancreas 2 Pan824p/825p
Cystic adenoma 0.00 3.17 Testis 1 Tst239X/240X Tumor/NAT 24.05 1.37
Colon 1 Cln9706c068ra/69ra Adenocarcinoma/NAT 605.60 169.77 Colon 2
Cln4004732A7/B6 Adenocarcinoma/NAT 367.20 281.32 Colon 3
Cln4004695A9/B8 316.15 295.77 Colon 4 Cln9612B006/005 Asc. Colon.
Cecum, 820.89 543.52 adenocarcinoma Colon 5 Cln9704C024R/25R
Adenocarcinoma/NAT 161.18 150.07 Cervix 1 CvxVNM00083/83
Keratinizing squamous 738.17 1195.88 cell carcinoma Cervix 2
CvxIND00023D/N Large cell 1473.04 1229.80 nonkeratinizing carcinoma
Cervix 3 CvxIND00024D/N Large cell 2877.48 1275.02 nonkeratinizing
carcinoma
[0080] Table 6 and Table 7 represent a combined total of 129
samples in 17 human tissue types. Comparisons of the level of mRNA
expression in ovarian cancer samples and the normal adjacent tissue
from the same individuals or normal tissues from other individuals
are shown in Table 7. Ovr115 was expressed at higher levels in 9 of
12 cancer tissues (75%), relative to the maximum level detected in
all 21 normal or normal adjacent ovarian samples. All 4 of 4 (100%)
ovarian tumors with borderline malignancy had elevated Ovr115
expression. The median expression in ovarian cancers (including the
ones with borderline malignancy) was 212.30 while the median
expression in normal ovaries was 0. When compared with their own
normal adjacent tissue samples, expression levels of Ovr115 were
also elevated in 3 of 3 (100%) lung cancers, 3 of 4 (75%) uterus
cancers and 2 of 4 (50%) endometrial cancers.
[0081] The relatively high expression levels of Ovr115 in ovarian
and other selected cancer samples is indicative of Ovr115 being a
diagnostic marker for detection of ovarian, lung, uterine and
endometrial cancer.
[0082] A homolog of Ovr115 has also been identified in public data
base; g2597613 as
gi.vertline.2507612.vertline.gb.vertline.U75329.1.vertline.HS-
U75329 Human serine protease mRNA, complete CDS. This homolog is
depicted herein as SEQ ID NO:9. It is believed that SEQ ID NO:9 or
the protein encoded thereby (SEQ ID NO:15) may also be useful as a
diagnostic marker for detection of ovarian, lung, uterine and
endometrial cancer in human patients.
Sequence CWU 1
1
16 1 2587 DNA Homo sapien 1 ggaaggcagc gggcagctcc actcagccag
tacccagata cgctgggaac cttccccagc 60 catggcttcc ctggggcaga
tcctcttctg gagcataatt agcatcatca ttattctggc 120 tggagcaatt
gcactcatca ttggctttgg tatttcaggg agacactcca tcacagtcac 180
tactgtcgcc tcagctggga acattgggga ggatggaatc ctgagctgca cttttgaacc
240 tgacatcaaa ctttctgata tcgtgataca atggctgaag gaaggtgttt
taggcttggt 300 ccatgagttc aaagaaggca aagatgagct gtcggagcag
gatgaaatgt tcagaggccg 360 gacagcagtg tttgctgatc aagtgatagt
tggcaatgcc tctttgcggc tgaaaaacgt 420 gcaactcaca gatgctggca
cctacaaatg ttatatcatc acttctaaag gcaaggggaa 480 tgctaacctt
gagtataaaa ctggagcctt cagcatgccg gaagtgaatg tggactataa 540
tgccagctca gagaccttgc ggtgtgaggc tccccgatgg ttcccccagc ccacagtggt
600 ctgggcatcc caagttgacc agggagccaa cttctcggaa gtctccaata
ccagctttga 660 gctgaactct gagaatgtga ccatgaaggt tgtgtctgtg
ctctacaatg ttacgatcaa 720 caacacatac tcctgtatga ttgaaaatga
cattgccaaa gcaacagggg atatcaaagt 780 gacagaatcg gagatcaaaa
ggcggagtca cctacagctg ctaaactcaa aggcttctct 840 gtgtgtctct
tctttctttg ccatcagctg ggcacttctg cctctcagcc cttacctgat 900
gctaaaataa tgtgccttgg ccacaaaaaa gcatgcaaag tcattgttac aacagggatc
960 tacagaacta tttcaccacc agatatgacc tagttttata tttctgggag
gaaatgaatt 1020 catatctaga agtctggagt gagcaaacaa gagcaagaaa
caaaaagaag ccaaaagcag 1080 aaggctccaa tatgaacaag ataaatctat
cttcaaagac atattagaag ttgggaaaat 1140 aattcatgtg aactagacaa
gtgtgttaag agtgataagt aaaatgcacg tggagacaag 1200 tgcatcccca
gatctcaggg acctccccct gcctgtcacc tggggagtga gaggacagga 1260
tagtgcatgt tctttgtctc tgaattttta gttatatgtg ctgtaatgtt gctctgagga
1320 agcccctgga aagtctatcc caacatatcc acatcttata ttccacaaat
taagctgtag 1380 tatgtaccct aagacgctgc taattgactg ccacttcgca
actcaggggc ggctgcattt 1440 tagtaatggg tcaaatgatt cactttttat
gatgcttcca aaggtgcctt ggcttctctt 1500 cccaactgac aaatgccaaa
gttgagaaaa atgatcataa ttttagcata aacagagcag 1560 tcggcgacac
cgattttata aataaactga gcaccttctt tttaaacaaa caaatgcggg 1620
tttatttctc agatgatgtt catccgtgaa tggtccaggg aaggaccttt caccttgact
1680 atatggcatt atgtcatcac aagctctgag gcttctcctt tccatcctgc
gtggacagct 1740 aagacctcag ttttcaatag catctagagc agtgggactc
agctggggtg atttcgcccc 1800 ccatctccgg gggaatgtct gaagacaatt
ttggttacct caatgaggga gtggaggagg 1860 atacagtgct actaccaact
agtggataaa ggccagggat gctgctcaac ctcctaccat 1920 gtacaggacg
tctccccatt acaactaccc aatccgaagt gtcaactgtg tcaggactaa 1980
gaaaccctgg ttttgagtag aaaagggcct ggaaagaggg gagccaacaa atctgtctgc
2040 ttctcacatt agtcattggc aaataagcat tctgtctctt tggctgctgc
ctcagcacag 2100 agagccagaa ctctatcggg caccaggata acatctctca
gtgaacagag ttgacaaggc 2160 ctatgggaaa tgcctgatgg gattatcttc
agcttgttga gcttctaagt ttctttccct 2220 tcattctacc ctgcaagcca
agttctgtaa gagaaatgcc tgagttctag ctcaggtttt 2280 cttactctga
atttagatct ccagaccctt cctggccaca attcaaatta aggcaacaaa 2340
catatacctt ccatgaagca cacacagact tttgaaagca aggacaatga ctgcttgaat
2400 tgaggccttg aggaatgaag ctttgaagga aaagaatact ttgtttccag
cccccttccc 2460 acactcttca tgtgttaacc actgccttcc tggaccttgg
agccacggtg actgtattac 2520 atgttgttat agaaaactga ttttagagtt
ctgatcgttc aagagaatga ttaaatatac 2580 atttcct 2587 2 2070 DNA Homo
sapien 2 cacagagaga ggcagcagct tgctcagcgg acaaggatgc tgggcgtgag
ggaccaaggc 60 ctgccctgca ctcgggcctc ctccagccag tgctgaccag
ggacttctga cctgctggcc 120 agccaggacc tgtgtgggga ggccctcctg
ctgccttggg gtgacaatct cagctccagg 180 ctacagggag accgggagga
tcacagagcc agcatgttac aggatcctga cagtgatcaa 240 cctctgaaca
gcctcgatgt caaacccctg cgcaaacccc gtatccccat ggagaccttc 300
agaaaggtgg ggatccccat catcatagca ctactgagcc tggcgagtat catcattgtg
360 gttgtcctca tcaaggtgat tctggataaa tactacttcc tctgcgggca
gcctctccac 420 ttcatcccga ggaagcagct gtgtgacgga gagctggact
gtcccttggg ggaggacgag 480 gagcactgtg tcaagagctt ccccgaaggg
cctgcagtgg cagtccgcct ctccaaggac 540 cgatccacac tgcaggtgct
ggactcggcc acagggaact ggttctctgc ctgtttcgac 600 aacttcacag
aagctctcgc tgagacagcc tgtaggcaga tgggctacag cagcaaaccc 660
actttcagag ctgtggagat tggcccagac caggatctgg atgttgttga aatcacagaa
720 aacagccagg agcttcgcat gcggaactca agtgggccct gtctctcagg
ctccctggtc 780 tccctgcact gtcttgcctg tgggaagagc ctgaagaccc
cccgtgtggt gggtggggag 840 gaggcctctg tggattcttg gccttggcag
gtcagcatcc agtacgacaa acagcacgtc 900 tgtggaggga gcatcctgga
cccccactgg gtcctcacgg gcagcccact gcttcaggaa 960 acataccgat
gtgttcaact ggaaggtgcg ggcaggctca gacaaactgg gcagcttccc 1020
atccctggct gtggccaaga tcatcatcat tgaattcaac cccatgtacc ccaaagacaa
1080 tgacatcgcc ctcatgaagc tgcagttccc actcactttc tcaggcacag
tcaggcccat 1140 ctgtctgccc ttctttgatg aggagctcac tccagccacc
ccactctgga tcattggatg 1200 gggctttacg aagcagaatg gagggaagat
gtctgacata ctgctgcagg cgtcagtcca 1260 ggtcattgac agcacacggt
gcaatgcaga cgatgcgtac cagggggaag tcaccgagaa 1320 gatgatgtgt
gcaggcatcc cggaaggggg tgtggacacc tgccagggtg acagtggtgg 1380
gcccctgatg taccaatctg accagtggca tgtggtgggc atcgttagct ggggctatgg
1440 ctgcgggggc ccgagcaccc caggagtata caccaaggtc tcagcctatc
tcaactggat 1500 ctacaatgtc tggaaggctg agctgtaatg ctgctgcccc
tttgcagtgc tgggagccgc 1560 ttccttcctg ccctgcccac ctggggatcc
cccaaagtca gacacagagc aagagtcccc 1620 ttgggtacac ccctctgccc
acagcctcag catttcttgg agcagcaaag ggcctcaatt 1680 cctataagag
accctcgcag cccagaggcg cccagaggaa gtcagcagcc ctagctcggc 1740
cacacttggt gctcccagca tcccagggag agacacagcc cactgaacaa ggtctcaggg
1800 gtattgctaa gccaagaagg aactttccca cactactgaa tggaagcagg
ctgtcttgta 1860 aaagcccaga tcactgtggg ctggagagga gaaggaaagg
gtctgcgcca gccctgtccg 1920 tcttcaccca tccccaagcc tactagagca
agaaaccagt tgtaatataa aatgcactgc 1980 cctactgttg gtatgactac
cgttacctac tgttgcattg ttattacagc tatggccact 2040 attattaaag
agctgtgtaa catctctggc 2070 3 1709 DNA Homo sapien 3 agcagactca
caccagaact acattccctg gccccctgcc tgtgtgcttc tggccaggcc 60
ttggttggca agtctgaccc gagaaaagga tctgcagaaa atcagactat gggatcactt
120 tgtttgtgca ttgggaatga cattctttcc caccccagga aaacctttgg
gactttcaga 180 gacattgtgg ctagccaacc acatggtcag cctcaaagtt
gagaggctca gtaaccctcc 240 tatccctaga gaattccaaa gtgtggatgt
aatttaacta gaaagccatt ggtgactatc 300 tgtgatcctc tggaagtatg
ctatgttgtg tatatcttgc atccaaagcc agagggaacc 360 acaatgacta
gtaaaacggt ggtctcaatg cccacttagc ctctgcctct gaatttgacc 420
atagtggcgt tcagctgata gagcgggaag aagaaatatg cattttttat gaaaaaataa
480 atatccaaga gaagatgaaa ctaaatggag aaattgaaat acatctactg
gaagaaaaga 540 tccaattcct gaaaatgaag attgctgaga agcaaagaca
aatttgtgtg acccagaaat 600 tactgccagc caagaggtcc ctggatgccg
acctagctgt gctccaaatt cagttttcac 660 agtgtacaga cagaattaaa
gacctggaga aacagttcgt aaagcctgat ggtgagaata 720 gagctcgctt
ccttccaggg aaagatctga ccgaaaaaga aatgatccaa aaattagaca 780
agctggaact acaactggcc aagaaggagg agaagctgct ggagaaggat ttcatctatg
840 agcaggtctc caggctcaca gacaggctct gcagcaaaac tcagggctgc
aagcaggaca 900 cactgctctt agccaagaag atgaatggct atcaaagaag
gatcaaaaat gcaactgaga 960 aaatgatggc tcttgttgct gagctgtcca
tgaaacaagc cctaaccatt gaactccaaa 1020 aggaagtcag ggagaaagaa
gacttcatct tcacttgcaa ttccaggata gaaaaaggtc 1080 tgccactcaa
taaggaaatt gagaaagaat ggttgaaagt ccttcgagat gaagaaatgc 1140
acgccttggc catcgctgaa aagtctcagg agttcttgga agcagataat cgccagctgc
1200 ccaatggtgt ttacacaact gcagagcagc gtccgaatgc ctacatccca
gaagcagatg 1260 ccactcttcc tttgccaaaa ccttatggtg ctttggctcc
ttttaaaccc agtgaacctg 1320 gagccaatat gaggcacata aggaaacctg
ttataaagcc agttgaaatc tgaatatgtg 1380 aacaaatcca ggcctctcaa
ggaaaagact tcaaccaggc ttccttgtac ccacaggtga 1440 aaaatgtgag
cataatactt ctaatattat tgataagtaa ggtaaccaca attagtcagc 1500
aacagagtac aacagggttt ctatttaccc accaactact atacctttca tgacgttgaa
1560 tgggacatag aactgtccta catttatgtc aaagtatata tttgaatcgc
ttatattttc 1620 tttttcactc tttatattga gtacattcca gaaatttgta
gtaggcaagg tgctataaaa 1680 atgcactaaa aataaatctg ttctcaatg 1709 4
257 DNA Homo sapien 4 ttaatgggta agtatttttt atatgcttta gctatagcta
aagaaaactg atacttaaca 60 aagttgaata gtattattca ctggtgctcc
taaaatattg tttttcagtg taaaatatgc 120 atatcttcta tatttaatat
gaaagtcttg aaatgtatca gacagaaggg gatttcagtt 180 tgcaaataat
gagcaatgta gcaattttaa cacatttcat aaatatatat tttgtcattg 240
gtggagagca ccatttg 257 5 359 DNA Homo sapien 5 gcctgagagc
acttagcgtt catgagtgtc cccaccatgg cctggatgat gcttctcctc 60
ggactccttg cttatggatc aggtcaggga gtggattctc agactgtggt gacccaagag
120 ccatcgttat cagtgtcccc tggagggaca gtcacactca cttgtggctt
ggcctctgac 180 tcagtctcta ctaatttctt ccccacctgg taccagcaga
ccccaggcca ggctccacgc 240 acgctcatct acagcacaag cactcgctct
tctggggtcc ctgatcgttt ctctggctcc 300 atccttggga acaaagctgc
cctcaccatt acgggggccc aggcagatga tgaatctga 359 6 1372 DNA Homo
sapien misc_feature (6)..(6) n = a, c, g or t 6 ccttanagnc
ttggttgcca aacagaatgc ccatatccgt cttacttgtg aggaagcttg 60
ccttgggcgc cctctgctgg ccctcctgaa gctaacaggg gcgagtgctc ggtggtttac
120 aaattgcctc catgcagact atgaaactgt tcagcctgct atagttagat
ctctggcact 180 ggcccaggag gtcttgcaga tttgcagatc aaggagaacc
caggagtttc aaagaagcgg 240 ctagtaaagg tctctgagat ccttgcacta
gctacatcct cagggtagga ggaagatggc 300 ttccagaagc atgcggctgc
tcctattgct gagctgcctg gccaaaacag gagtcctggg 360 tgatatcatc
atgagaccca gctgtgctcc tgggatggtt ttaccacaag tccaattgct 420
atggttactt caggaagctg aggaactggt ctgatgccga gctcgagtgt cagtcttacg
480 gaaacggagc ccacctggca tctatcctga gtttaaagga agccagcacc
atagcagagt 540 acataagtgg ctatcagaga agccagccga tatggattgg
cctgcacgac ccacagaaga 600 ggcagcagtg gcagtggatt gatggggcca
tgtatctgta cagatcctgg tctggcaagt 660 ccatgggtgg gaacaagcac
tgtgctgaga tgagctccaa taacaacttt ttaacttgga 720 gcagcaacga
atgcaacaag cgccaacact tcctgtgcaa gtaccgacca tagagcaaga 780
atcaagattc tgctaactcc tgcacagccc cgtcctcttc ctttctgcta gcctggctaa
840 atctgctcat tatttcagag gggaaaccta gcaaactaag agtgataagg
gccctactac 900 actggctttt ttaggcttag agacagaaac tttagcattg
gcccagtagt ggcttctagc 960 tctaaatgtt tgccccgcca tccctttcca
cagtatcctt cttccctcct cccctgtctc 1020 tggctgtctc gagcagtcta
gaagagtgca tctccagcct atgaaacagc tgggtctttg 1080 gccataagaa
gtaaagattt gaagacagaa ggaagaaact caggagtaag cttctagccc 1140
ccttcagctt ctacaccctt ctgccctctc tccattgcct gcaccccacc ccagccactc
1200 aactcctgct tgtttttcct ttggccatgg gaaggtttac cagtagaatc
cttgctaggt 1260 tgatgtgggc catacattcc tttaataaac cattgtgtac
ataagaggtt gctgtgttcc 1320 agttcagtaa atggtgaatg tggaaaagtg
aaataagacc aagaaataca aa 1372 7 291 DNA Homo sapien misc_feature
(277)..(277) n= a, c, g, or t 7 agaatggtag tagtaagaag aagaaaaata
gaggatctga atgtattttg aaggtagagt 60 ccactggact tagagatgga
ttgaatgtgg aagattaagg aaagggagaa atgaaagata 120 gtcttaggtt
tcatcttcag atgactgggt gaacagcagt gttctttgct aagatgggga 180
agactaggga aaagagccag ttctgtattg agcatattat atttaagaca atcccatctg
240 ggtccaaaga caatgttgat tttttttctt agatacntgc cctttagacc t 291 8
1275 DNA Homo sapien misc_feature (410)..(410) n= a, c, g, or t 8
attctagaac atatgtataa gctaaaaaca gtattttact cagatcagta gttatcgtgt
60 ctatcagcta taaaaaaaat caactgccag ccaagaactt taaaacttta
agctgtgtat 120 tatagaaccg ttttgtgtag cattggaata ttgtccattt
tgtaagtcat tgtgaatgtt 180 cttaattatc agcttgaagg tatttttgta
ttaaaagttg acattgaaga acctaagtgg 240 atgatgggat ttggggccag
tagtgaaagt atgtttcctc taaaatattt ccctaaacag 300 tggtatacat
ggttatttta ttatgagatt tgtatatgtt ctgtgtttct ctgtgaacaa 360
tgtttcagtc tctctgtcac catatgtaag gggaagtcca caaatatagn actacattgc
420 acaaaactaa aattgttaat tacaagaaaa tataggtgct taccttttga
aggtttatta 480 atacatatgg ttgtcacaat acgtatatat gataaatggt
gtacatatac agatgtttat 540 ggtgtataaa tttttctata cccaattaga
attatcttcc tgattcttta ttcaataaca 600 tgctaattcc tcttctatgt
tctatagtga cagaatgcta acttttctta taccctggca 660 gaggacagag
gagtctggtc taggatgggg aactgaattt ttgaacgaaa aggaaagaga 720
aaggatgnnn nnnnnnnnnn nnnnnnnnnn nnnnnntaat gtttcttagt cattttgatt
780 ggccatttga acagtctaca agtttaacgt tatttccagt gaagtaggat
ggctgaccta 840 gcaatacatg tttcttcaaa agggtaaaca tgctttagtg
acctaaagct aaattttgta 900 catttgacat caggggtgtt ataagtactg
cacttaatac aaagctattt ctcaatngtg 960 ttatttttga gacaaatttt
tcttcaccat taacttcttg ttggtagctt tttgttttgt 1020 aaaaattgag
agatggcaat gcttatctca accagattat ccatctgcag aattaaggta 1080
tgcaactggt aaataaaaga caaatgctcc agtttgtctt tctcaacctt tgagttctta
1140 acctttgagt taaaacctag tctaaatagt gggaatgtct tggtttacag
taaggttttc 1200 ttgggaagga tcttggtttt gtgatctatt tgtgaattaa
ggagtagatg ttaaccatta 1260 ttttatagat aagtg 1275 9 2479 DNA Homo
sapien 9 gtcatattga acattccaga tacctatcat tactcgatgc tgttgataac
agcaagatgg 60 ctttgaactc agggtcacca ccagctattg gaccttacta
tgaaaaccat ggataccaac 120 cggaaaaccc ctatcccgca cagcccactg
tggtccccac tgtctacgag gtgcatccgg 180 ctcagtacta cccgtccccc
gtgccccagt acgccccgag ggtcctgacg caggcttcca 240 accccgtcgt
ctgcacgcag cccaaatccc catccgggac agtgtgcacc tcaaagacta 300
agaaagcact gtgcatcacc ttgaccctgg ggaccttcct cgtgggagct gcgctggccg
360 ctggcctact ctggaagttc atgggcagca agtgctccaa ctctgggata
gagtgcgact 420 cctcaggtac ctgcatcaac ccctctaact ggtgtgatgg
cgtgtcacac tgccccggcg 480 gggaggacga gaatcggtgt gttcgcctct
acggaccaaa cttcatcctt cagatgtact 540 catctcagag gaagtcctgg
caccctgtgt gccaagacga ctggaacgag aactacgggc 600 gggcggcctg
cagggacatg ggctataaga ataattttta ctctagccaa ggaatagtgg 660
atgacagcgg atccaccagc tttatgaaac tgaacacaag tgccggcaat gtcgatatct
720 ataaaaaact gtaccacagt gatgcctgtt cttcaaaagc agtggtttct
ttacgctgtt 780 tagcctgcgg ggtcaacttg aactcaagcc gccagagcag
gatcgtgggc ggtgagagcg 840 cgctcccggg ggcctggccc tggcaggtca
gcctgcacgt ccagaacgtc cacgtgtgcg 900 gaggctccat catcaccccc
gagtggatcg tgacagccgc ccactgcgtg gaaaaacctc 960 ttaacaatcc
atggcattgg acggcatttg cggggatttt gagacaatct ttcatgttct 1020
atggagccgg ataccaagta caaaaagtga tttctcatcc aaattatgac tccaagacca
1080 agaacaatga cattgcgctg atgaagctgc agaagcctct gactttcaac
gacctagtga 1140 aaccagtgtg tctgcccaac ccaggcatga tgctgcagcc
agaacagctc tgctggattt 1200 ccgggtgggg ggccaccgag gagaaaggga
agacctcaga agtgctgaac gctgccaagg 1260 tgcttctcat tgagacacag
agatgcaaca gcagatatgt ctatgacaac ctgatcacac 1320 cagccatgat
ctgtgccggc ttcctgcagg ggaacgtcga ttcttgccag ggtgacagtg 1380
gagggcctct ggtcacttcg aacaacaata tctggtggct gataggggat acaagctggg
1440 gttctggctg tgccaaagct tacagaccag gagtgtacgg gaatgtgatg
gtattcacgg 1500 actggattta tcgacaaatg aaggcaaacg gctaatccac
atggtcttcg tccttgacgt 1560 cgttttacaa gaaaacaatg gggctggttt
tgcttccccg tgcatgattt actcttagag 1620 atgattcaga ggtcacttca
tttttattaa acagtgaact tgtctggctt tggcactctc 1680 tgccatactg
tgcaggctgc agtggctccc ctgcccagcc tgctctccct aaccccttgt 1740
ccgcaagggg tgatggccgg ctggttgtgg gcactggcgg tcaattgtgg aaggaagagg
1800 gttggaggct gcccccattg agatcttcct gctgagtcct ttccaggggc
caattttgga 1860 tgagcatgga gctgtcactt ctcagctgct ggatgacttg
agatgaaaaa ggagagacat 1920 ggaaagggag acagccaggt ggcacctgca
gcggctgccc tctggggcca cttggtagtg 1980 tccccagcct acttcacaag
gggattttgc tgatgggttc ttagagcctt agcagccctg 2040 gatggtggcc
agaaataaag ggaccagccc ttcatgggtg gtgacgtggt agtcacttgt 2100
aaggggaaca gaaacatttt tgttcttatg gggtgagaat atagacagtg cccttggtgc
2160 gagggaagca attgaaaagg aacttgccct gagcactcct ggtgcaggtc
tccacctgca 2220 cattgggtgg ggctcctggg agggagactc agccttcctc
ctcatcctcc ctgaccctgc 2280 tcctagcacc ctggagagtg aatgcccctt
ggtccctggc agggcgccaa gtttggcacc 2340 atgtcggcct cttcaggcct
gatagtcatt ggaaattgag gtccatgggg gaaatcaagg 2400 atgctcagtt
taaggtacac tgtttccatg ttatgtttct acacattgat ggtggtgacc 2460
ctgagttcaa agccatctt 2479 10 576 DNA Homo sapien 10 ttcaaagaca
tattagaagt tgggaaaata attcatgtga actagacaag tgtgttaaga 60
gtgataagta aaatgcacgt ggagacaagt gcatccccag atctcaggga cctccccctg
120 cctgtcacct ggggagtgag aggacaggat agtgcatgtt ctttgtctct
gaatttttag 180 ttatatgtgc tgtaatgttg ctctgaggaa gcccctggaa
agtctatccc aacatatcca 240 catcttatat tccacaaatt aagctgtagt
atgtacccta agacgctgct aattgactgc 300 cacttcgcaa ctcaggggcg
gctgcatttt agtaatgggt caaatgattc actttttatg 360 atgcttccaa
aggtgccttg gcttctcttc ccaactgaca aatgccaaag ttgagaaaaa 420
tgatcataat tttagcataa acagagcagt cggcgacacc gattttataa ataaactgag
480 caccttcttt ttaaacaaac aaatgcgggt ttatttctca gatgatgttc
atccgtgaat 540 ggtccaggga aggacctttc accttgacta tatggc 576 11 890
DNA Homo sapien 11 caagctctga ggcttctcct ttccatcctg cgtggacagc
taagacctca gttttcaata 60 gcatctagag cagtgggact cagctggggt
gatttcgccc cccatctccg ggggaatgtc 120 tgaagacaat tttggttacc
tcaatgaggg agtggaggag gatacagtgc tactaccaac 180 tagtggataa
aggccaggga tgctgctcaa cctcctacca tgtacaggga cgtctcccca 240
ttacaactac ccaatccgaa gtgtcaactg tgtcaggact aagaaaccct ggttttgagt
300 agaaaagggc ctggaaagag gggagccaac aaatctgtct gcttcctcac
attagtcatt 360 ggcaaataag cattctgtct ctttggctgc tgcctcagca
cagagagcca gaactctatc 420 gggcaccagg ataacatctc tcagtgaaca
gagttgacaa ggcctatggg aaatgcctga 480 tgggattatc ttcagcttgt
tgagcttcta agtttctttc ccttcattct accctgcaag 540 ccaagttctg
taagagaaat gcctgagttc tagctcaggt tttcttactc tgaatttaga 600
tctccagacc cttcctggcc acaattcaaa ttaaggcaac aaacatatac cttccatgaa
660 gcacacacag acttttgaaa gcaaggacaa tgactgcttg aattgaggcc
ttgaggaatg 720 aagctttgaa ggaaaagaat actttgtttc cagccccctt
cccacactct tcatgtgtta 780 accactgcct tcctggacct tggagccacg
gtgactgtat tacatgttgt tatagaaaac 840 tgattttaga gttctgatcg
ttcaagagaa tgattaaata tacatttcct 890 12 406 DNA Homo sapien
misc_feature (30)..(30) n= a, c, g, or t 12 gtgaatgtgg actataatgc
cagctcagan accttgcggt gtgaggctcc ccgatggttc 60 ccccagccca
cagtggtctg ggcatcccaa gttgaccagg gagccaactt ctcggaagtc 120
tccaatacca gctttgagct gaactctgag aatgtgacca tgaaggttgt gtctgtgctc
180 tacaatgtta cgatcaacaa cacatactcc tgtatgattg aaaatgacat
tgccaaagca 240 acaggggnta tcaaagtgac agaatcggag atcaaaaggc
ggagtcacct acagctgcta 300 aactcaaagg cttctctgtg tgtctcttct
ttctttgcca tcagctgggc acttctgcct 360 ctcagccctt acctgatgct
aanataatgt gccttggcca caaaaa 406 13 462 DNA Homo sapien 13
ggaaggcagc ggcagctcca
ctcagccagt acccagatac gctgggaacc ttccccagcc 60 atggcttccc
tggggcagat cctcttctgg agcataatta gcatcatcat tattctggct 120
ggagcaattg cactcatcat tggctttggt atttcaggga gacactccat cacagtcact
180 actgtcgcct cagctgggaa cattggggag gatggaatcc tgagctgcac
ttttgaacct 240 gacatcaaac tttctgatat cgtgatacaa tggctgaagg
aaggtgtttt aggcttggtc 300 catgagttca aagaaggcaa agatgagctg
tcggagcagg atgaaatgtt cagaggccgg 360 acagcagtgt ttgctgatca
agtgatagtt ggcaatgcct ctttgcggct gaaaaacgtg 420 caactcacag
atgctggcac ctacaaatgt tatatcatca ct 462 14 272 DNA Homo sapien 14
gcagcttgct cagcggacaa ggatgctggg cgtgagggac caaggcctgc cctgcactcg
60 ggcctcctcc agccagtgct gaccagggac ttctgacctg ctggccagcc
aggacctgtg 120 tggggaggcc ctcctgctgc cttggggtga caatctcagc
tccaggctac agggagaccg 180 ggaggatcac agagccagca tggatcctga
cagtgatcaa cctctgaaca gcctcgtcaa 240 ggtgattctg gataaatact
acttcctctg cg 272 15 492 PRT Homo sapien 15 Met Ala Leu Asn Ser Gly
Ser Pro Pro Ala Ile Gly Pro Tyr Tyr Glu 1 5 10 15 Asn His Gly Tyr
Gln Pro Glu Asn Pro Tyr Pro Ala Gln Pro Thr Val 20 25 30 Val Pro
Thr Val Tyr Glu Val His Pro Ala Gln Tyr Tyr Pro Ser Pro 35 40 45
Val Pro Gln Tyr Ala Pro Arg Val Leu Thr Gln Ala Ser Asn Pro Val 50
55 60 Val Cys Thr Gln Pro Lys Ser Pro Ser Gly Thr Val Cys Thr Ser
Lys 65 70 75 80 Thr Lys Lys Ala Leu Cys Ile Thr Leu Thr Leu Gly Thr
Phe Leu Val 85 90 95 Gly Ala Ala Leu Ala Ala Gly Leu Leu Trp Lys
Phe Met Gly Ser Lys 100 105 110 Cys Ser Asn Ser Gly Ile Glu Cys Asp
Ser Ser Gly Thr Cys Ile Asn 115 120 125 Pro Ser Asn Trp Cys Asp Gly
Val Ser His Cys Pro Gly Gly Glu Asp 130 135 140 Glu Asn Arg Cys Val
Arg Leu Tyr Gly Pro Asn Phe Ile Leu Gln Met 145 150 155 160 Tyr Ser
Ser Gln Arg Lys Ser Trp His Pro Val Cys Gln Asp Asp Trp 165 170 175
Asn Glu Asn Tyr Gly Arg Ala Ala Cys Arg Asp Met Gly Tyr Lys Asn 180
185 190 Asn Phe Tyr Ser Ser Gln Gly Ile Val Asp Asp Ser Gly Ser Thr
Ser 195 200 205 Phe Met Lys Leu Asn Thr Ser Ala Gly Asn Val Asp Ile
Tyr Lys Lys 210 215 220 Leu Tyr His Ser Asp Ala Cys Ser Ser Lys Ala
Val Val Ser Leu Arg 225 230 235 240 Cys Leu Ala Cys Gly Val Asn Leu
Asn Ser Ser Arg Gln Ser Arg Ile 245 250 255 Val Gly Gly Glu Ser Ala
Leu Pro Gly Ala Trp Pro Trp Gln Val Ser 260 265 270 Leu His Val Gln
Asn Val His Val Cys Gly Gly Ser Ile Ile Thr Pro 275 280 285 Glu Trp
Ile Val Thr Ala Ala His Cys Val Glu Lys Pro Leu Asn Asn 290 295 300
Pro Trp His Trp Thr Ala Phe Ala Gly Ile Leu Arg Gln Ser Phe Met 305
310 315 320 Phe Tyr Gly Ala Gly Tyr Gln Val Gln Lys Val Ile Ser His
Pro Asn 325 330 335 Tyr Asp Ser Lys Thr Lys Asn Asn Asp Ile Ala Leu
Met Lys Leu Gln 340 345 350 Lys Pro Leu Thr Phe Asn Asp Leu Val Lys
Pro Val Cys Leu Pro Asn 355 360 365 Pro Gly Met Met Leu Gln Pro Glu
Gln Leu Cys Trp Ile Ser Gly Trp 370 375 380 Gly Ala Thr Glu Glu Lys
Gly Lys Thr Ser Glu Val Leu Asn Ala Ala 385 390 395 400 Lys Val Leu
Leu Ile Glu Thr Gln Arg Cys Asn Ser Arg Tyr Val Tyr 405 410 415 Asp
Asn Leu Ile Thr Pro Ala Met Ile Cys Ala Gly Phe Leu Gln Gly 420 425
430 Asn Val Asp Ser Cys Gln Gly Asp Ser Gly Gly Pro Leu Val Thr Ser
435 440 445 Asn Asn Asn Ile Trp Trp Leu Ile Gly Asp Thr Ser Trp Gly
Ser Gly 450 455 460 Cys Ala Lys Ala Tyr Arg Pro Gly Val Tyr Gly Asn
Val Met Val Phe 465 470 475 480 Thr Asp Trp Ile Tyr Arg Gln Met Lys
Ala Asn Gly 485 490 16 890 DNA Homo sapien misc_feature
(168)..(237) n=a, c, g or t 16 caagctctga ggcttctcct ttccatcctg
cgtggacagc taagacctca gttttcaata 60 gcatctagag cagtgggact
cagctggggt gatttcgccc cccatctccg ggggaatgtc 120 tgaagacaat
tttggttacc tcaatgaggg agtggaggag gatacagnnn nnnnnnnnnn 180
nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnncat
240 tacaactacc caatccgaag tgtcaactgt gtcaggacta agaaaccctg
gttttgagta 300 gaaaagggcc tgggaaagag gggagccaac aaatctgtct
gcttcctcac attagtcatt 360 ggcaaataag cattctgtct ctttggctgc
tgcctcagca cagagagcca gaactctatc 420 gggcaccagg ataacatctc
tcagtgaaca gagttgacaa ggcctatggg aaatgcctga 480 tgggattatc
ttcagcttgt tgagcttcta agtttctttc ccttcattct accctgcaag 540
ccaagttctg taagagaaat gcctgagttc tagctcaggt tttcttactc tgaatttaga
600 tctccagacc ctgcctggcc acaattcaaa ttaaggcaac aaacatatac
cttccatgaa 660 gcacacacag acttttgaaa gcaaggacaa tgactgcttg
aattgaggcc ttgaggaatg 720 aagctttgaa ggaaaagaat actttgtttc
cagccccctt cccacactct tcatgtgtta 780 accactgcct tcctggacct
tggagccacg gtgactgtat tacatgttgt tatagaaaac 840 tgattttaga
gttctgatcg ttcaagagaa tgattaaata tacatttcct 890
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