U.S. patent application number 16/404204 was filed with the patent office on 2019-10-10 for cancer diagnosis, treatment selection and treatment.
This patent application is currently assigned to CHILDREN'S MEDICAL CENTER CORPORATION. The applicant listed for this patent is THE BRIGHAM AND WOMEN'S HOSPITAL, INC., CHILDREN'S MEDICAL CENTER CORPORATION, DANA-FARBER CANCER INSTITUTE, INC., THE TECHNICAL UNIVERSITY OF DENMARK. Invention is credited to Nicolai J. Birkbak, Andrea L. Richardson, Zoltan I. Szallasi, Zhigang Wang.
Application Number | 20190309373 16/404204 |
Document ID | / |
Family ID | 51625329 |
Filed Date | 2019-10-10 |
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United States Patent
Application |
20190309373 |
Kind Code |
A1 |
Szallasi; Zoltan I. ; et
al. |
October 10, 2019 |
CANCER DIAGNOSIS, TREATMENT SELECTION AND TREATMENT
Abstract
The present invention provides assays, methods and systems for
selecting an effective therapy for a subset of cancer patients
having cancer cells with increased expression of BML and FANCI
genes and/or having copy number increase in chromosome location
15q26 in the cancer cells and for treatment of such patients with
the effective therapy of cancer patients based on the personalized
cancer cell expression profile.
Inventors: |
Szallasi; Zoltan I.;
(Boston, MA) ; Richardson; Andrea L.; (Chestnut
Hill, MA) ; Birkbak; Nicolai J.; (Kobenhavn O,
DK) ; Wang; Zhigang; (Newton, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
CHILDREN'S MEDICAL CENTER CORPORATION
THE BRIGHAM AND WOMEN'S HOSPITAL, INC.
DANA-FARBER CANCER INSTITUTE, INC.
THE TECHNICAL UNIVERSITY OF DENMARK |
Boston
Boston
Boston
Lyngby |
MA
MA
MA |
US
US
US
DK |
|
|
Assignee: |
CHILDREN'S MEDICAL CENTER
CORPORATION
Boston
MA
THE BRIGHAM AND WOMEN'S HOSPITAL, INC.
Boston
MA
DANA-FARBER CANCER INSTITUTE, INC.
Boston
MA
THE TECHNICAL UNIVERSITY OF DENMARK
Lyngby
|
Family ID: |
51625329 |
Appl. No.: |
16/404204 |
Filed: |
May 6, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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14774772 |
Sep 11, 2015 |
10308986 |
|
|
PCT/US2014/025774 |
Mar 13, 2014 |
|
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16404204 |
|
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61784234 |
Mar 14, 2013 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 1/6886 20130101;
A61K 33/24 20130101; C12Q 2600/106 20130101; C12Q 2600/156
20130101; C12Q 2600/158 20130101; A61K 31/704 20130101; G01N
33/57415 20130101 |
International
Class: |
C12Q 1/6886 20060101
C12Q001/6886; A61K 31/704 20060101 A61K031/704; G01N 33/574
20060101 G01N033/574; A61K 33/24 20060101 A61K033/24 |
Goverment Interests
STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH
[0002] This invention was made with government support under Grant
No. 2P50 CA89393-06 awarded by the National Cancer Institute. The
Government has certain rights in the invention.
Claims
1. A method for treating cancer in a human subject in need thereof
comprising the step of administering an anthracycline-comprising
cancer therapy to the human subject when the cancer in the human
subject has been determined to have increased expression of BLM and
FANCI compared to a reference value.
2. A method of treating cancer in a human subject, comprising
administering an anthracycline-comprising cancer therapy to a human
subject when a cancer cell taken from the human subject has been or
is determined to carry a chromosome 15q26 copy number gain compared
to a reference value.
3. The method of claim 2, further comprising the steps of detecting
a chromosome 15q26 copy number in a sample comprising a cancer cell
taken from the subject; comparing the chromosome 15q26 copy number
to a reference value.
4. The method of claim 2, wherein the cancer is selected from
breast cancer, ovarian cancer and lung cancer.
5. The method of claim 2, wherein the subject's cancer is known to
not express a detectable quantity of ER, PgR, and HER2 receptor.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a Divisional of U.S. patent Ser. No.
14/774,772, filed Sep. 11, 2015, which is a 35 U.S.C. .sctn. 371
National Phase Entry Application of International Application No.
PCT/US2014/025774, filed Mar. 13, 2014, which designates the U.S.,
and which claims benefit under 35 U.S.C. .sctn. 119(e) of U.S.
Provisional Application No. 61/784,234, filed Mar. 14, 2013, the
contents of each of which are incorporated herein in their
entireties.
SEQUENCE LISTING
[0003] The instant application contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Nov. 18, 2015, is named 701039-075882-US_SL.txt and is 512 bytes
in size.
BACKGROUND
[0004] All publications herein are incorporated by reference to the
same extent as if each individual publication or patent application
was specifically and individually indicated to be incorporated by
reference. The following description includes information that may
be useful in understanding the present invention. It is not an
admission that any of the information provided herein is prior art
or relevant to the presently claimed invention, or that any
publication specifically or implicitly referenced is prior art.
[0005] Breast cancer is recognized as a collection of malignancies
that all arise in the breast but are remarkably heterogeneous. Gene
expression array experiments have defined at least 4 major
subtypes: 1) Luminal A; 2) Luminal B; 3) HER2+; and 4) Basal. There
is a strong correlation between clinically defined triple negative
breast cancer "TNBC", as defined by the absence of ER, PgR, and
HER2 by standard immunohistochemical staining, and the molecularly
defined basal subtype.
[0006] TN breast cancer accounts for only 10-15% of all incident
breast cancer cases in the U.S., but results in a disproportionate
number of breast cancer deaths. Women who are destined to develop
metastatic TN disease typically experience a short disease free
interval and have a higher degree of lung and brain involvement
than patients with luminal breast cancers. Furthermore, TN breast
cancer is overrepresented among patients who carry a deleterious
BRCA1 germline alteration, and among women of African ancestry.
[0007] From a clinical perspective, despite substantial efforts to
develop novel targeted agents, chemotherapy remains the mainstay of
therapy for TN breast cancer, as trials evaluating a number of
agents either in lieu of chemotherapy or in addition to
chemotherapy have failed to produce any new agent that is capable
of convincingly changing the natural history of the disease. In the
adjuvant setting, polychemotherapy regimens have been demonstrated
to improve both disease-free survival and overall survival. In the
neoadjuvant setting, a favorable response to chemotherapy is
associated with a low chance of relapse at 5 years. In contrast,
women who have a significant amount of residual disease after a
course of neoadjuvant chemotherapy have a particularly poor
prognosis, with at least half experiencing a recurrence and death
from TN breast cancer within 5 years. In the metastatic setting,
although patients may respond to chemotherapy, the responses tend
to be brief, and resistance tends to appear quickly.
[0008] Given the curative potential of chemotherapy in patients
presenting with stage I-III TN breast cancer, and the initial
responses (albeit often brief) seen with chemotherapy in the
metastatic setting, the general direction of targeted therapy
development for TN breast cancer has been to combine targeted
agents with chemotherapy. Thus, even with a growing number of
targeted therapies under investigation for TN breast cancer,
chemotherapy is likely to be a significant component of the
treatment of TN breast cancer for many years to come.
[0009] Across breast cancers as a whole, hormone receptor
dependence and tumor proliferation appear to be associated with
generic "chemosensitivity". Using the 70 gene signature as an
example, the current classifiers typically assign a "high-risk"
status to the vast majority of TN tumors, and are also unable to
define whether there may be differential benefit with one class of
chemotherapeutic agents over another. Thus, in both clinical
practice and in conventionally designed clinical trials, the
tendency is to layer new therapies directly atop existing
standards, increasing the risk of both overtreatment (because some,
but not all of the administered therapies are efficacious) or
undertreatment (because the tumor is not sensitive to any of the
specific chemotherapeutic agents contained in the treatment
regimen).
[0010] Accordingly, there exists a need in the art to identify the
best chemotherapy for each patient and to eliminate agents that are
inert and result in toxicity without benefit.
SUMMARY OF THE INVENTION
[0011] We provide novel methods, assays, systems and kits for
determining if a cancer patient is responsive to
platinum-comprising therapy or anthracyclin therapy. These methods,
assays, systems and kits provide a significant improvement to the
"trial-and-error"-therapies used in cancer therapy. The methods
allow one to personalize the treatment of a cancer patient based on
the cancer cells' specific protein/gene expression profile. In
other words, the methods apply the novel findings of a cancer cells
responses to cancer treatment methods and allow selection of the
most likely effective therapy without delay and thus significantly
improve the patient's quality of life. Avoiding use of ineffective
drugs will also provide a significant saving for the cost of
treatment for the cancer patient, as well avoiding exposure to side
effects of ineffective drugs.
[0012] The invention is based, at least in part, on the discovery
that patients having increased expression of BLM and/or FANCI genes
compared to a housekeeping gene or wild-type BRCA1 gene in their
cancer cells are likely to respond to platinum-comprising or
anthracyclin-comprising cancer therapy.
[0013] The following embodiments and aspects thereof are described
and illustrated in conjunction with compositions and methods which
are meant to be exemplary and illustrative, not limiting in
scope.
[0014] We provide an assay for selecting a therapy for a subject
having cancer, and optionally administering the therapy, the assay
comprising: subjecting a sample comprising a cancer cell taken from
the subject to an analysis for BLM and FANCI expression; comparing
the BLM and FANCI expression to a reference value; and selecting a
platinum-comprising cancer therapy for the subject when the BLM and
FANCI expression is increased compared to the reference value based
on the recognition that platinum-comprising cancer therapy is
effective in subjects whose cancer has increased expression of BLM
and FANCI, or selecting a non-platinum-comprising cancer therapy
for the subject when the BLM and FANCI expression is not increased
compared to the reference value based on the recognition that
platinum-comprising cancer therapy is not effective in subjects
whose cancer does not have increased BLM and FANCI expression
compared to the reference value.
[0015] The assay may further comprise assaying the BRCA1 and/or
BRCA2 status of the subject; and selecting the platinum-comprising
cancer therapy for the subject when the subject is negative for
BRCA1 and/or BRCA2 mutations, and the BLM and FANCI expression is
increased compared to the reference value based on the recognition
that platinum-comprising cancer therapy is effective in subjects
whose cancer has increased expression of BLM and FANCI and who are
negative for BRCA1 and/or BRCA2 mutations.
[0016] In some aspects of all the embodiments of the invention, the
subject is known to be or is determined to be negative for BRCA1
and/or BRCA2 mutations.
[0017] In some aspects of all the embodiments of the invention, the
assay further comprises assaying the estrogen receptor (ER),
progesterone receptor (PgR), and HER2 receptor status of the
subject's cancer; and selecting the platinum-comprising cancer
therapy for the subject when the subject's cancer does not express
a detectable quantity of ER, PgR, and HER2 receptor, and when the
BLM and FANCI expression is increased compared to the reference
value based on the recognition that platinum-comprising cancer
therapy is effective in subjects whose cancer has increased
expression of BLM and FANCI and whose cancer does not express a
detectable quantity of ER, PgR, and HER2 receptor.
[0018] In some aspects of all the embodiments of the invention, the
subject's cancer or cancer cell is known to not or is determined to
not express a detectable quantity of ER, PgR, and HER2
receptor.
[0019] In some aspects of all the embodiments of the invention, the
assay further comprises administering the selected therapy to the
subject.
[0020] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0021] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0022] In some aspects of all the embodiments of the invention, the
reference value is based on at least BRCA1 gene expression in the
cancer cell.
[0023] In some aspects of all the embodiments of the invention, the
reference value is based on at least one housekeeping gene
expression in the cancer cell.
[0024] We also provide a method for selecting platinum-comprising
therapy for a subject having cancer, and optionally administering
the platinum-comprising therapy, the method comprising: subjecting
a sample comprising a cancer cell taken from the subject to an
analysis for BLM and FANCI expression; detecting the BLM and FANCI
expression in the sample compared to a reference value; and
electing a platinum-comprising cancer therapy for the subject when
the BLM and FANCI expression compared to a reference value is
increased based on the recognition that platinum-comprising cancer
therapy is effective in patients whose cancer has increased BLM and
FANCI expression compared to the reference value.
[0025] In some aspects of all the embodiments of the invention, the
method further comprises administering to the subject the
platinum-comprising cancer therapy when the platinum-comprising
cancer therapy is selected. One can further select a therapy other
than platinum-comprising therapy when it is determined using the
assay that the cancer is not likely responsive to
platinum-comprising therapy.
[0026] In some aspects of all the embodiments of the invention, the
subject is known to be or is determined to be negative for BRCA1
and/or BRCA2 mutations.
[0027] In some aspects of all the embodiments of the invention, the
subject's cancer or cancer cell is known to not or determined to
not express a detectable quantity of ER, PgR, and HER2
receptor.
[0028] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0029] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0030] In some aspects of all the embodiments of the invention, the
reference value is based on at least BRCA1 gene expression in the
cancer cell.
[0031] In some aspects of all the embodiments of the invention, the
reference value is based on at least one housekeeping gene
expression in the cancer cell.
[0032] In some aspects of all the embodiments of the invention, the
housekeeping gene is selected from beta-actin, GAPDH, RPLP0, GUS,
TFRC and any combination thereof.
[0033] In some aspects of all the embodiments of the invention, the
housekeeping gene is RPLP0, and the BLM and/or FANCI expression is
increased by at least six-fold.
[0034] We further provide a method for selecting a
non-platinum-comprising therapy, and optionally administering the
non-platinum-comprising therapy, for a subject having cancer
comprising: subjecting a sample comprising a cancer cell taken from
the subject to an analysis for BLM and FANCI expression; detecting
the BLM and FANCI expression in the sample compared to a reference
value; and selecting the non-platinum-comprising cancer therapy for
the subject when the BLM and FANCI expression compared to the
reference value is not increased based on the recognition that
non-platinum-comprising cancer therapy is effective in patients
whose cancer does not have increased gene expression of BLM and
FANCI compared to the reference value.
[0035] In some aspects of all the embodiments of the invention, the
method further comprises administering to the subject the
non-platinum-comprising cancer therapy when non-platinum-comprising
cancer therapy is selected.
[0036] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0037] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0038] In some aspects of all the embodiments of the invention, the
reference value is based on at least BRCA1 gene expression in the
cancer cell.
[0039] In some aspects of all the embodiments of the invention, the
reference value is based on at least one housekeeping gene
expression in the cancer cell.
[0040] We provide an assay for selecting a therapy for a subject
having cancer, comprising: subjecting a sample comprising a cancer
cell taken from the subject to an analysis for BLM and FANCI
expression; comparing the BLM and FANCI expression to a reference
value; and selecting an anthracycline-comprising cancer therapy for
the subject when the BLM and FANCI expression is increased compared
to a reference value based on the recognition that
anthracycline-comprising cancer therapy is effective in subjects
whose cancer has increased expression of BLM and FANCI, or
selecting a non-anthracycline-comprising cancer therapy for the
subject when the BLM and FANCI expression is not increased compared
to a reference value based on the recognition that
anthracycline-comprising cancer therapy is not effective in
subjects whose cancer does not have increased BLM expression
compared to a reference value.
[0041] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0042] We provide a method for selecting an
anthracycline-comprising cancer therapy for a subject having cancer
and determined to be negative for BRCA1 and/or BRCA2 mutations,
comprising: subjecting a sample comprising a cancer cell taken from
the subject to an analysis for BLM and FANCI expression; comparing
the BLM and FANCI expression to a reference value; and selecting
the anthracycline-compri sing cancer therapy for the subject when
the BLM and FANCI expression compared to the reference value is
increased based on the recognition that anthracycline-comprising
cancer therapy is effective in patients whose cancer has increased
expression of BLM and FANCI compared to the reference value.
[0043] In some aspects of all the embodiments of the invention,
wherein the reference value is BRCA1 expression in the sample, and
the BLM and/or FANCI expression is increased by at least two-fold
compared to BRCA1 expression.
[0044] We further provide a method of treating cancer in a human
subject, comprising: detecting BLM and FANCI expression in a sample
comprising a cancer cell taken from the human subject; and
comparing the BLM and FANCI expression to a reference value; and
administering a platinum-comprising cancer therapy to the human
subject wherein an increase of BLM and FANCI expression compared to
the reference value is detected.
[0045] In some aspects of all the embodiments of the invention, the
human subject's cancer or cancer cell is known to not or is
determined to not express detectable quantities of estrogen
receptor (ER), progesterone receptor (PgR) and HER2 receptor.
[0046] In some aspects of all the embodiments of the invention, the
cancer is selected from breast, ovarian, and lung cancers.
[0047] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0048] In some aspects of all the embodiments of the invention, the
reference value is based on BRCA1 gene expression in the cancer
cell.
[0049] In some aspects of all the embodiments of the invention, the
reference value is based on a housekeeping gene expression in the
cancer cell.
[0050] We provide method of treating cancer in a human subject,
comprising: detecting BLM and FANCI expression in a sample
comprising a cancer cell taken from the human subject; and
comparing the BLM and FANCI expression to a reference value; and
administering an anthracycline-comprising cancer therapy to the
human subject wherein an increase of BLM and FANCI expression
compared to the reference value is detected.
[0051] In some aspects of all the embodiments of the invention, the
human subject's cancer or cancer cell is known to not or is
determined to not to express detectable quantities of estrogen
receptor (ER), progesterone receptor (PgR) and HER2 receptor.
[0052] In some aspects of all the embodiments of the invention, the
cancer is selected from breast, ovarian, and lung cancers.
[0053] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0054] In some aspects of all the embodiments of the invention, the
reference value is based on BRCA1 gene expression in the cancer
cell.
[0055] In some aspects of all the embodiments of the invention, the
reference value is based on a housekeeping gene expression in the
cancer cell.
[0056] We provide a method for assessing responsiveness of a cancer
cell to cancer therapy, comprising: assaying, in a cancer cell or
mRNA derived therefrom, BLM and FANCI expression; and comparing
said BLM and FANCI expression to a reference value, wherein the
cancer cell is assessed as responsive to a platinum-comprising
therapy if the BLM and FANCI expression is increased compared to
the reference value, or wherein the cancer cell is assessed as
poorly or not responsive to platinum-comprising cancer therapy
cancer if the BLM and FANCI expression is not increased.
[0057] In some aspects of all the embodiments of the invention, the
step of assaying comprises: contacting the cancer cell or mRNA
derived therefrom with at least one detectably labeled probe
capable of specifically binding to BLM mRNA, at least one
detectably probe capable of specifically binding to FANCI, at least
one detectably labeled probe capable of specifically binding to
BRCA1 and/or at least one housekeeping gene; and measuring the
expression of BLM and FANCI compared to the BRCA1 and/or the at
least one housekeeping gene.
[0058] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0059] We provide a method of predicting a cancer patient's
response to a cancer treatment regimen comprising platinum or
anthracycline, comprising: determining, in a cancer cell from the
cancer patient, BLM and FANCI expression; and correlating the
expression to a reference value, wherein when the expression is
increased the patient is predicted to respond well to a cancer
treatment regimen comprising platinum or anthracycline.
[0060] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0061] We also provide a method of predicting a cancer patient's
response to a cancer treatment regimen comprising platinum or
anthracycline, comprising: determining, in a cancer cell or mRNA
derived therefrom from said cancer patient, BLM and FANCI
expression; and correlating the expression to a reference value,
wherein when the expression is not increased the patient is
predicted to respond poorly to a cancer treatment regimen
comprising platinum or anthracycline.
[0062] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0063] We provide a method of treating cancer, comprising:
assaying, in a cancer cell from a cancer patient or mRNA obtained
therefrom, the BLM and FANCI expression compared to a reference
value; and administering to the cancer patient a cancer treatment
regimen comprising platinum or anthracycline if the BLM and FANCI
expression is increased compared to the reference value.
[0064] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0065] We also provide a use of platinum comprising cancer therapy
for treating a cancer patient that has been determined to have a
tumor comprising cancer cells wherein BLM and FANCI expression is
increased compared to a reference value.
[0066] In some aspects of all the embodiments of the invention, the
cancer patient has been determined to be negative for BRCA1 and/or
BRCA2 mutations.
[0067] In some aspects of all the embodiments of the invention, the
cancer patient's cancer or cancer cell is known to not or is
determined to not express detectable quantities of estrogen
receptor (ER), progesterone receptor (PgR) and HER2 receptor.
[0068] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0069] We provide a system for determining responsiveness of a
cancer cell to platinum-comprising therapy from a cancer cell of a
cancer patient, comprising: a sample analyzer configured to produce
a signal for the mRNA from each one of BLM and FANCI from a cancer
cell sample of a cancer patient; and a computer sub-system
programmed to calculate, based on the mRNA whether the signal is
greater or not than a reference value.
[0070] In some aspects of all the embodiments of the invention,
said computer sub-system is programmed to compare the mRNA to
determine a likelihood of responsiveness of said cancer cell to
platinum-comprising cancer therapy based on an algorithm that
classifies the patient as likely to respond to a
platinum-comprising therapy if the BLM and FANCI expression is
increased and as unlikely to respond to the platinum-comprising
therapy if the BLM and FANCI expression is not increased; or a
likelihood of responsiveness of said cancer cell to
anthracycline-comprising cancer therapy based on an algorithm that
classifies the patient as likely to respond to a
anthracycline-comprising therapy if the BLM and FANCI expression is
increased and as unlikely to respond to the
anthracycline-comprising therapy if the BLM and FANCI expression is
not increased.
[0071] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least two-fold compared to BRCA1
expression.
[0072] We provide a computer program product embodied in a computer
readable medium that, when executing on a computer, performs steps
comprising: detecting the BLM and FANCI gene expression in sample
comprising a cancer cell from a cancer patient; and comparing the
BLM and FANCI expression to a reference value.
[0073] In some aspects of all the embodiments of the invention, the
reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least two-fold compared to BRCA1
expression.
[0074] We provide a diagnostic kit for detecting a likelihood of a
cancer patient to respond to platinum- or anthracycline-comprising
comprising cancer therapy, comprising: no more than 10 probes
comprising a combination of detectably labeled probes or primers
for BLM and FANCI, and optionally for BRCA1 and/or at least one
housekeeping gene; and the computer program product of Claim
59.
[0075] We provide use of a plurality of oligonucleotides comprising
no more than 10 oligonucleotides capable of hybridizing to BLM and
FANCI, and optionally to BRCA1 and/or at least one housekeeping
gene, in a diagnostic kit for determining an increased likelihood
that a cancer patient will respond to cancer treatment regimen
comprising a platinum and/or anthracycline.
[0076] In some aspects of all the embodiments of the invention,
said anthracycline is epirubincin or doxorubicin.
[0077] In some aspects of all the embodiments of the invention,
said platinum comprising cancer therapy comprises cisplatinum or
cis-diamminedichloroplatinum, phenanthriplatin, carboplatin,
oxaliplatin, or a platinum complex that is activated by ultraviolet
A light.
[0078] We provide an assay for selecting a therapy for a subject
having cancer, and optionally administering the therapy, the assay
comprising: assaying a sample comprising a cancer cell taken from
the subject for a chromosome 15q26 copy number; comparing the
chromosome 15q26 copy number to a reference value; and selecting a
platinum-comprising cancer therapy for the subject if there is a
chromosome 15q26 copy number gain compared to the reference value,
or selecting a non-platinum-comprising cancer therapy for the
subject if there is not a chromosome 15q26 copy number gain, or if
there is a chromosome 15q26 copy number loss.
[0079] In some aspects of all the embodiments of the invention, the
assay further comprises: assaying the BRCA1 and/or BRCA2 status of
the subject; and selecting the platinum-comprising cancer therapy
for the subject when the subject is negative for BRCA1 and/or BRCA2
mutations, and there is a chromosome 15q26 copy number gain based
on the recognition that platinum-comprising cancer therapy is
effective in subjects who have a chromosome 15q26 copy number gain
who are negative for BRCA1 and/or BRCA2 mutations.
[0080] In some aspects of all the embodiments of the invention, the
subject is known to be or is determined to be negative for BRCA1
and/or BRCA2 mutations.
[0081] In some aspects of all the embodiments of the invention, the
assay further comprises: assaying the estrogen receptor (ER),
progesterone receptor (PgR), and HER2 receptor status of the
subject's cancer; and selecting the platinum-comprising cancer
therapy for the subject when the subject's cancer does not express
a detectable quantity of ER, PgR, and HER2 receptor, and when there
is a chromosome 15q26 copy number gain based on the recognition
that platinum-comprising cancer therapy is effective in subjects
who have a chromosome 15q26 copy number gain and whose cancer does
not express a detectable quantity of ER, PgR, and HER2
receptor.
[0082] In some aspects of all the embodiments of the invention, the
subject's cancer or cancer cell is known to not or is determined to
not express a detectable quantity of ER, PgR, and HER2
receptor.
[0083] In some aspects of all the embodiments of the invention, the
assay further comprises administering the selected therapy to the
subject.
[0084] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0085] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0086] We provide an assay for selecting a therapy for a subject
having cancer, and optionally administering the therapy, the assay
comprising: assaying a sample comprising a cancer cell taken from
the subject for a chromosome 15q26 copy number; comparing the
chromosome 15q26 copy number to a reference value; and selecting an
anthracycline-comprising cancer therapy for the subject if there is
a chromosome 15q26 copy number gain compared to the reference
value, or selecting a non-anthracycline-comprising cancer therapy
for the subject if there is not a chromosome 15q26 copy number
gain, or if there is a chromosome 15q26 copy number loss.
[0087] In some aspects of all the embodiments of the invention, the
assay further comprises: assaying the BRCA1 and/or BRCA2 status of
the subject; and selecting the anthracycline-comprising cancer
therapy for the subject when the subject is negative for BRCA1
and/or BRCA2 mutations, and there is a chromosome 15q26 copy number
gain based on the recognition that anthracycline-comprising cancer
therapy is effective in subjects who have a chromosome 15q26 copy
number gain who are negative for BRCA1 and/or BRCA2 mutations.
[0088] In some aspects of all the embodiments of the invention, the
subject is known to be or is determined to be negative for BRCA1
and/or BRCA2 mutations.
[0089] In some aspects of all the embodiments of the invention, the
assay further comprises assaying the estrogen receptor (ER),
progesterone receptor (PgR), and HER2 receptor status of the
subject's cancer; and selecting the anthracycline-comprising cancer
therapy for the subject when the subject's cancer does not express
a detectable quantity of ER, PgR, and HER2 receptor, and when there
is a chromosome 15q26 copy number gain based on the recognition
that anthracycline-comprising cancer therapy is effective in
subjects who have a chromosome 15q26 copy number gain and whose
cancer does not express a detectable quantity of ER, PgR, and HER2
receptor.
[0090] In some aspects of all the embodiments of the invention, the
subject's cancer or cancer cell is known to not or is determined to
not express a detectable quantity of ER, PgR, and HER2
receptor.
[0091] In some aspects of all the embodiments of the invention, the
assay further comprises administering the selected therapy to the
subject.
[0092] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0093] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0094] We provide a method of treating cancer in a human subject,
comprising: detecting a chromosome 15q26 copy number in a sample
comprising a cancer cell taken from the subject; comparing the
chromosome 15q26 copy number to a reference value; and
administering an platinum-comprising cancer therapy for the subject
if there is a chromosome 15q26 copy number gain compared to the
reference value, or administering a non-platinum-comprising cancer
therapy for the subject if there is not a chromosome 15q26 copy
number gain, or if there is a chromosome 15q26 copy number
loss.
[0095] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0096] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0097] In some aspects of all the embodiments of the invention, the
subject's cancer is known to not express a detectable quantity of
ER, PgR, and HER2 receptor.
[0098] We provide a method of treating cancer in a human subject,
comprising: detecting a chromosome 15q26 copy number in a sample
comprising a cancer cell taken from the subject; comparing the
chromosome 15q26 copy number to a reference value; and
administering an anthracycline-comprising cancer therapy for the
subject if there is a chromosome 15q26 copy number gain compared to
the reference value, or administering a
non-anthracycline-comprising cancer therapy for the subject if
there is not a chromosome 15q26 copy number gain, or if there is a
chromosome 15q26 copy number loss.
[0099] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0100] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0101] In some aspects of all the embodiments of the invention, the
subject's cancer or cancer cell is known to not or is determined to
not express a detectable quantity of ER, PgR, and HER2
receptor.
[0102] We provide a method for assessing responsiveness of a cancer
cell to a cancer therapy, and optionally administering the cancer
therapy, comprising: assaying a sample comprising a cancer cell
taken from the subject for a chromosome 15q26 copy number; and
comparing the chromosome 15q26 copy number to a reference value,
wherein the cancer cell is assessed as responsive to a
platinum-comprising therapy if there is a chromosome 15q26 copy
number gain compared to the reference value, or wherein the cancer
cell is assessed as poorly or not responsive to platinum-comprising
cancer therapy cancer if there is not a chromosome 15q26 copy
number gain or if there is a chromosome 15q26 copy number loss.
[0103] In some aspects of all the embodiments of the invention, the
reference value is copy number of chromosome 15.
[0104] In some aspects of all the embodiments of the invention, the
cancer is selected from breast cancer, ovarian cancer and lung
cancer.
[0105] In some aspects of all the embodiments of the invention, the
method further comprises administering the platinum-comprising
therapy if there is a chromosome 15q26 copy number gain.
[0106] We provide a method of predicting a cancer patient's
response to a cancer treatment regimen comprising platinum or
anthracycline, comprising: determining, in a cancer cell from the
cancer patient, chromosome 15q26 copy number; and correlating the
chromosome 15q26 copy number to a reference value, wherein when
there is a chromosome 15q26 copy number gain, the patient is
predicted to respond well to a cancer treatment comprising platinum
or anthracycline, or wherein when there is not a chromosome 15q26
copy number gain or a chromosome 15q26 copy number loss, the
patient is predicted respond poorly to a cancer treatment
comprising platinum or anthracycline.
[0107] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0108] We provide use of platinum comprising cancer therapy for
treating a cancer patient that has been determined to have a tumor
comprising cancer cells wherein a chromosome 15q26 copy gain is
detected compared to a reference value.
[0109] In some aspects of all the embodiments of the invention, the
cancer patient is known to be or is determined to be negative for
BRCA1 and/or BRCA2 mutations.
[0110] In some aspects of all the embodiments of the invention, the
cancer patient's cancer or cancer cell is known to not or is
determined to not express detectable quantities of estrogen
receptor (ER), progesterone receptor (PgR) and HER2 receptor.
[0111] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0112] We provide a system for determining responsiveness of a
cancer cell to platinum-comprising therapy from a cancer cell of a
cancer patient, comprising: a sample analyzer configured to produce
a signal for chromosome 15q26 copy number from a cancer cell sample
of a cancer patient; and a computer sub-system programmed to
calculate, based on the mRNA whether the signal is greater or not
than a reference value.
[0113] In some aspects of all the embodiments of the invention,
said computer sub-system is programmed to compare the mRNA to
determine a likelihood of responsiveness of said cancer cell to
platinum-comprising cancer therapy and/or or a
anthracycline-comprising cancer therapy based on an algorithm that
classifies the patient as likely to respond to a
platinum-comprising therapy if there is a chromosome 15q26 copy
number gain and as unlikely to respond to the platinum-comprising
therapy if there is not a chromosome 15q26 copy number gain or if
there is a chromosome 15q26 copy number loss.
[0114] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0115] We provide a computer program product embodied in a computer
readable medium that, when executing on a computer, performs steps
comprising: detecting chromosome 15q26 copy number in sample
comprising a cancer cell from a cancer patient; and comparing the
chromosome 15q26 copy number to a reference value.
[0116] In some aspects of all the embodiments of the invention, the
reference value is chromosome 15 centromere copy number in the
sample.
[0117] We provide a diagnostic kit for detecting a likelihood of a
cancer patient to respond to platinum- or anthracycline-comprising
cancer therapy, comprising: no more than 10 probes comprising a
combination of detectably labeled probes or primers for chromosome
15q26, and optionally for chromosome 15 centromere; and a computer
program as described herein.
[0118] We provide us of a plurality of oligonucleotides comprising
no more than 10 oligonucleotides capable of hybridizing to
chromosome 15q26, and optionally for chromosome 15 centromere, in a
diagnostic kit for determining an increased likelihood that a
cancer patient will respond to cancer treatment regimen comprising
a platinum and/or anthracycline.
[0119] In some aspects of all the embodiments of the invention,
said anthracycline is epirubincin or doxorubicin.
[0120] In some aspects of all the embodiments of the invention,
said platinum comprising cancer therapy comprises cisplatinum or
cis-diamminedichloroplatinum, phenanthriplatin, carboplatin,
oxaliplatin, or a platinum complex that is activated by ultraviolet
A light.
[0121] Other features and advantages of the invention will become
apparent from the following detailed description, taken in
conjunction with the accompanying drawings, which illustrate, by
way of example, various features of embodiments of the
invention.
BRIEF DESCRIPTION OF THE FIGURES
[0122] This patent or application file contains at least one
drawing executed in color. Copies of this patent or patent
application publication with color drawings will be provided by the
Office upon request and payment of the necessary fee.
[0123] Exemplary embodiments are illustrated in referenced figures.
It is intended that the embodiments and figures disclosed herein
are to be considered illustrative rather than restrictive.
[0124] FIGS. 1A and 1B show that GISTIC identifies 169 chromosomal
regions as either gained or lost. Several contained genes with
significantly different copy number between sensitive and resistant
cases. FIG. 1A shows data relating to the Cisplatin-1 clinical
trial. FIG. 1B shows data relating to the Cisplatin-2 clinical
trial.
[0125] FIG. 2 shows a 10 MB region with 59 genes on chr. 15q26.1-2
showed significant gain in sensitive samples.
[0126] FIG. 3 shows correlation between copy number and mRNA
expression, Genes on 15q26.1-2. 23 genes show significant
correlation.
[0127] FIG. 4 depicts leave-one-out analysis of gene expression
data.
[0128] FIGS. 5A-5B shows that expression of BLM and FANCI is only
associated with response to carboplatin, but not paclitaxel in
OVO1. (FIG. 5A) BLM expression; (FIG. 5B) FANCI Expression. Ahmed
et al., Cancer Cell 2007.
[0129] FIGS. 6A-6B depicts expression of BLM or FANCI is not
associated with response to multi-agent chemotherapy regimens in
triple negative breast cancer (TNBC). (FIG. 6A) BLM expression;
(FIG. 6B) FANCI Expression. .sup.1Hess et al., JCO 2006; Popovici
et al.; .sup.2Breast Cancer Res 2010; .sup.3Andre et al., Clin
Cancer Res 2009.
[0130] FIG. 7 shows that BLM is also associated with response to
single agent epirubicin. TOP trial, single agent epirubicin in
ER-negative breast cancer. .sup.1Desmedt et al., JCO 2011.
[0131] FIG. 8 depicts repair of cisplatin induced damage.
[0132] FIG. 9 depicts the metaphase spread, BRCA1 knock-out in
MEFs. BRCA1 is an essential part of the homologous repair system.
BRCA1 knock out cause high levels of quadrahelical chromosomes,
which is a prime substrate for the Bloom helicase. Gain of BLM is a
possible compensation mechanism for deficient HR. Silver D P et al,
Cell 2007.
[0133] FIGS. 10A-10B show gene signatures. FIG. 10A shows receiver
operating characteristic curves showing the ability of the
BRCA1-BLM-FANCI RNA 3-gene signature to predict for response to
cisplatin in the two cisplatin trials. FIG. 10B shows ROC curves
showing the ability of number of telomeric allelic imbalance
(NtAI)+3-gene mRNA signature to predict for sensitivity to
cisplatin in the combined trials.
[0134] FIG. 11 depicts ROC analysis of 3 gene signature to
determine cisplatin sensitivity in cisplatin 2 trial. Blue: all
cases; red; BRCA normal cases only.
[0135] FIG. 12 depicts functional modules of various embodiments of
the invention.
[0136] FIG. 13 depicts survival time with Kaplan-Meier plot,
showing over-all survival of patients from the TCGA squamous cell
lung cancer cohort, split by the median of the three gene signature
calculated as the ratio of BRCA1 expression over the mean of FANI
and BLM expression.
[0137] FIG. 14 shows the BLM+FANCI/BRCA1 signature. The Cisplatin-2
trial, separating resistant (MP 1-2-3) from sensitive (MP 4-5)
cases is optimized for qPCR data. Blue line is based on all
samples, while red is based on wtBRCA1. The optimum ratio is
calculated by ROC curve, and shows an optimum ratio of 5.5 for all
cases, on a log 2 scale. In un-logged values, this is equivalent of
45 fold.
[0138] FIG. 15 shows BLM/BRCA1 signature. The Cisplatin-2 trial,
separating resistant (MP 1-2-3) from sensitive (MP 4-5) cases is
optimized for qPCR data. The optimum ratio is 7.5 for all cases, on
a log 2 scale, which is equivalent of 180 fold or 7.5 cycles on a
PCR machine. This is a very large difference.
[0139] FIG. 16 shows FANCI/BRCA1 signature. The Cisplatin-2 trial,
separating resistant (MP 1-2-3) from sensitive (MP 4-5) cases is
optimized for qPCR data. The optimum ratio is 5.1 for all cases, on
a log 2 scale, which is equivalent of 34 fold.
[0140] FIG. 17 shows the BRCA1/RPLP0 signature. BRCA1 is compared
to a housekeeping gene, RPLP0. The optimum ratio here is -14 for
all cases, on a log 2 scale, which is approximately equivalent to
1/1600, or 14 cycles on a PCR machine. This is a very large
difference, but HK genes are expressed in very high numbers.
[0141] FIG. 18 shows BLM/RPLP0 signature. BLM is compared to a
housekeeping gene, RPLP0 The optimum ratio is higher, and
separation of sensitive/resistant cases is good.
[0142] FIG. 19 shows FANCI/RPLP0 signature. FANCI is compared to a
housekeeping gene, RPLP0. The optimum ratio is higher than BRCA1
alone.
[0143] FIGS. 20A and 20B show how the expression of each of the
three genes looks like in a large cohort of breast cancer patients
from the TCGA, and how their ratios is to RPLP0 and BRCA1. These
patients were not treated with platinum. This was focused on DNBC
cases (ER/HER2 negative), and the normal breast samples. The ratio
is much lower than using PCR data, yet there still appear to be a
clear increase in some cases. The normal samples have lower BLM and
BRCA1 expression, but that the ratio between these is inversed,
with higher BRCA1 than BLM, probably reflecting the normal balance
between these genes. FIG. 20A shows the expression of ESR1, BLM,
ERBB2, FANCI, BRCA1, and RPLP0 in DNBC, estrogen receptor negative
(ER), and HER2 receptor negative breast cancer patients and in
patients with metastases compared to normal breast samples. FIG.
20B shows data relating to (i) the 3-gene signature, (ii)
BRCA1/RPLP0 ratio, (iii) BLM/BRCA1 ratios, (iv) BLMIRPLP0 ratios,
(v) FANCI/BRCA1 ratios, and (vi) FANCI/RPLP0 ratios in the same
cohorts as FIG. 20A.
DETAILED DESCRIPTION
[0144] All references cited herein are incorporated by reference in
their entirety as though fully set forth. Unless defined otherwise,
technical and scientific terms used herein have the same meaning as
commonly understood by one of ordinary skill in the art to which
this invention belongs. Singleton et al., Dictionary of
Microbiology and Molecular Biology 3.sup.rd ed., J. Wiley &
Sons (New York, N.Y. 2001); March, Advanced Organic Chemistry
Reactions, Mechanisms and Structure 5.sup.th ed., J. Wiley &
Sons (New York, N.Y. 2001); and Sambrook and Russel, Molecular
Cloning: A Laboratory Manual 3rd ed., Cold Spring Harbor Laboratory
Press (Cold Spring Harbor, N.Y. 2001), provide one skilled in the
art with a general guide to many of the terms used in the present
application. For references on how to prepare antibodies, see D.
Lane, Antibodies: A Laboratory Manual (Cold Spring Harbor Press,
Cold Spring Harbor N.Y., 1988); Kohler and Milstein, (1976) Eur. J.
Immunol. 6: 511; Queen et al. U.S. Pat. No. 5,585,089; and
Riechmann et al., Nature 332: 323 (1988).
[0145] One skilled in the art will recognize many methods and
materials similar or equivalent to those described herein, which
could be used in the practice of the present invention. Indeed, the
present invention is in no way limited to the methods and materials
described.
[0146] To investigate whether specific genomic aberrations may
affect cancer sensitivity to cisplatin, the inventors generated
tumor DNA copy number profiles of 21 and 24 TNBC patients who
received pre-operative cisplatin-based chemotherapy in two separate
clinical trials. Using the GISTIC algorithm (1), the inventors
found that only a single region on chromosome 15q26 showed
consistent significant differential copy number in responders
versus non-responders, being preferentially lost in non-responders,
but preferentially gained in responders in both trials.
[0147] To see if genes on 15q26 were associated with platinum
sensitivity, the inventors acquired gene expression data from the
cisplatin TNBC trial (2), and from the carboplatin-only arm of an
ovarian cancer trial (3). The inventors then performed a
leave-one-out analysis, and found 9 genes significantly associated
with platinum response in at least 75% of all rounds in both
cohorts. These included BLM and FANCI located in the 15q26 region,
both showing higher expression in sensitive tumors, and known to be
involved in related DNA repair processes. To investigate if BLM and
FANCI were specifically associated with genotoxic chemotherapy
sensitivity, the inventors analyzed their expression in TNBCs from
three neoadjuvant trials of epirubicin alone (4) or
taxane-containing combination therapy (5, 6) and in ovarian cancers
from the taxane-only treatment arm (3). In the epirubicin trial,
BLM and FANCI expression was again significantly associated with
increased sensitivity to therapy. In contrast, there was no
association between either BLM or FANCI expression and TNBC
response to the taxane-containing regimen or ovarian cancer
response to single agent taxane treatment. These data suggest that
high expression of BLM and FANCI are associated with improved
response to DNA damaging agents, but not with response to other
types of chemotherapeutics. Furthermore, it suggests that the
patient subpopulations that respond to drugs such as anthracyclines
and taxanes are not overlapping, and that it will therefore be
difficult to robustly identify predictors of single agent response
based on multi-drug trials.
[0148] While not wishing to be bound by any particular theory, the
inventors believe that FANCI and BLM functions in multiple DNA
repair processes; increased FANCI and BLM is associated with
response to platinum-comprising therapy and
anthracycline-comprising therapy; low copy gain might be a
compensatory mechanism of HR deficient cells, trying to rescue some
DNA repair capacity; and if so, FANCI/BLM expression is a marker
for DNA repair deficiency, and increased sensitivity to genotoxic
chemotherapy drugs, such as platinum-comprising therapy and
anthracycline-comprising therapy.
[0149] Therefore, while the cancers specifically investigated for
their responses in the particular studies, such as breast cancer,
such as triple negative breast cancer, ovarian cancer and lung
cancer, Applicants believe that the finding of the association
between increased FANCI and BLM expression and responsiveness to
platinum-comprising therapy and anthracycline-comprising therapy is
applicable to most cancers.
[0150] The present invention is based, at least in part, on these
findings, and those further described herein and in the figures and
examples.
Selecting Therapy
[0151] Various embodiments provide for assays, methods and systems
for selecting an appropriate therapy for a subject based on an
analysis of the subject's BLM and FANCI expression, or based on the
subject's 15q26 copy number.
[0152] In various embodiments, the invention provide for an assay
for selecting a therapy, and optionally administering the therapy,
for a subject having cancer, the assay comprising: subjecting a
sample comprising a cancer cell taken from the subject to an
analysis for BLM and FANCI expression; comparing the BLM and FANCI
expression to a reference value; and selecting a
platinum-comprising cancer therapy for the subject when the BLM and
FANCI expression is increased compared to the reference value based
on the recognition that platinum-comprising cancer therapy is
effective in subjects whose cancer has increased expression of BLM
and FANCI, or selecting a non-platinum-comprising cancer therapy
for the subject when the BLM and FANCI expression is not increased
compared to the reference value based on the recognition that
platinum-comprising cancer therapy is not effective in subjects
whose cancer does not have increased BLM and FANCI expression
compared to the reference value.
[0153] In various embodiments, the assay further comprises:
assaying the BRCA1 and/or BRCA2 status of the subject; and
selecting the platinum-comprising cancer therapy for the subject
when the subject is negative for BRCA1 and/or BRCA2 mutations, and
the BLM and FANCI expression is increased compared to the reference
value based on the recognition that platinum-comprising cancer
therapy is effective in subjects whose cancer has increased
expression of BLM and FANCI and who are negative for BRCA1 and/or
BRCA2 mutations. In various embodiments, the subject is known to be
or is determined to be negative for BRCA1 and/or BRCA2 mutations.
The determination can be made before, concurrently with, or after
the analysis for BLM and FANCI expression.
[0154] In some aspects of all the embodiments of the invention, a
mutation that inactivates BRCA2 is highly predictive of
response.
[0155] In various embodiments, the assay further comprises:
assaying the estrogen receptor (ER), progesterone receptor (PgR),
and HER2 receptor status of the subject's cancer; and selecting the
platinum-comprising cancer therapy for the subject when the
subject's cancer does not express a detectable quantity of ER, PgR,
and HER2 receptor, and when the BLM and FANCI expression is
increased compared to the reference value based on the recognition
that platinum-comprising cancer therapy is effective in subjects
whose cancer has increased expression of BLM and FANCI and whose
cancer does not express a detectable quantity of ER, PgR, and HER2
receptor. In various embodiments, the subject's cancer or cancer
cell is known to not or is determined to not express a detectable
quantity of ER, PgR, and HER2 receptor. The determination can be
made before, concurrently with, or after analysis for BLM and FANCI
expression.
[0156] In various embodiments, the assay further comprises
administering the selected therapy to the subject.
[0157] In various embodiments, the cancer is selected from breast
cancer, ovarian cancer and lung cancer.
[0158] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0159] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold,
2.9-fold, 3-fold, 4-fold, 5-fold, or 6-fod, 10-20 fold, 20-50 fold
or higher, depending on the expression level of the gene used as a
standard, such as one or more housekeeping genes or BRCA1.
[0160] Typically, an increase in expression of at least 1.5 or at
least 2 fold is considered as a cut-off point for increased
expression if BRCA1 gene expression is used as a standard. Thus, in
certain embodiments, the reference value is BRCA1 expression, and
the BLM and/or FANCI expression is increased by at least two-fold
compared to BRCA1 expression.
[0161] For example, in our examples, we calculated the ratios, and
in cells expressing wild type BRCA1 (wtBRCA1) the ratio was around
6.6 for BLM+FANCI/BRCA1. Thus, is some aspects, the expression
level can be over 5, or over 6 or over 7 times that of BRCA1.
[0162] For analysis with qPCR, each of the analyzed genes is first
normalized to a housekeeping gene, such as RPLP0. For example, with
6 cycles of PCT, we calculated the optimum for BRCA1/BLM/FANCI
normalized to RPLP0, expression of which is typically very low. All
values are log 2, which means that a ratio of 6 reflects an amount
of 64 times higher than the reference gene, namely RPLP0.
[0163] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Examples of useful
housekeeping genes are described herein, e.g., in Table 1.
[0164] Various embodiments of the present invention provide for a
method for selecting platinum-comprising therapy, and optionally
administering the platinum-comprising therapy, for a subject having
cancer, comprising: subjecting a sample comprising a cancer cell
taken from the subject to an analysis for BLM and FANCI expression;
detecting the BLM and FANCI expression in the sample compared to a
reference value; and selecting a platinum-comprising cancer therapy
for the subject when the BLM and FANCI expression compared to a
reference value is increased based on the recognition that
platinum-comprising cancer therapy is effective in patients whose
cancer has increased BLM and FANCI expression compared to the
reference value.
[0165] In various embodiments, the method further comprises
administering to the subject the platinum-comprising cancer therapy
when the platinum-comprising cancer therapy is selected.
[0166] In various embodiments, the subject is known to be or is
determined to be negative for BRCA1 and/or BRCA2 mutations. The
determination can be made before, concurrently with, or after the
analysis for BLM and FANCI expression. In various embodiments, the
subject's cancer or cancer cell is known to not or is determined to
not express a detectable quantity of ER, PgR, and HER2 receptor.
The determination can be made before, concurrently with, or after
analysis for BLM and FANCI expression.
[0167] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0168] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold
2.9-fold or 3-fold compared to BRCA1 expression. In certain
embodiments, the reference value is BRCA1 expression, and the BLM
and/or FANCI expression is increased by at least or about two-fold
compared to BRCA1 expression. In certain embodiments, the BLM
and/or FANCI expression is increased by at least or about 6-fold
compared to BRCA1 expression.
[0169] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Housekeeping genes
are described herein.
[0170] In certain embodiments, the cancer is selected from breast
cancer, ovarian cancer and lung cancer.
[0171] Various embodiments of the present invention provide for a
method for selecting a non-platinum-comprising therapy, and
optionally administering the non-platinum-comprising therapy, for a
subject having cancer comprising: subjecting a sample comprising a
cancer cell taken from the subject to an analysis for BLM and FANCI
expression; detecting the BLM and FANCI expression in the sample
compared to a reference value; and selecting the
non-platinum-comprising cancer therapy for the subject when the BLM
and FANCI expression compared to the reference value is not
increased based on the recognition that non-platinum-comprising
cancer therapy is effective in patients whose cancer does not have
increased gene expression of BLM and FANCI compared to the
reference value.
[0172] In some aspects of all the embodiments of the invention a
dual assay allowing analysis of both BLM and FANCI expression to be
compared in the same assay is used. The dual assay may be based on
detecting RNA or protein. The assay may be specific for the dual
analysis of BLM and FANCI or may comprise reagents for assaying
one, two, three or more other biomolecules as well. In some aspects
of all the embodiments of the invention the one other biomolecule
is BRCA1.
[0173] In various embodiments, the method further comprises
administering to the subject the non-platinum-comprising cancer
therapy when non-platinum-comprising cancer therapy is
selected.
[0174] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0175] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold
2.9-fold or 3-fold compared to BRCA1 expression. In certain
embodiments, the reference value is BRCA1 expression, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0176] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Examples of
housekeeping genes are described herein although these genes are
well known to one of ordinary skill in the art.
[0177] In various embodiments, the cancer is selected from breast
cancer, ovarian cancer and lung cancer.
[0178] Various embodiments of the present invention provide for an
assay for selecting a therapy for a subject having cancer,
comprising: subjecting a sample comprising a cancer cell taken from
the subject to an analysis for BLM and FANCI expression; comparing
the BLM and FANCI expression, optionally in a dual assay, to a
reference value; and selecting an anthracycline-comprising cancer
therapy for the subject when the BLM and FANCI expression is
increased compared to a reference value based on the recognition
that anthracycline-comprising cancer therapy is effective in
subjects whose cancer has increased expression of BLM and FANCI, or
selecting a non-anthracycline-comprising cancer therapy for the
subject when the BLM and FANCI expression is not increased compared
to a reference value based on the recognition that
anthracycline-comprising cancer therapy is not effective in
subjects whose cancer does not have increased BLM expression
compared to a reference value.
[0179] Various embodiments of the present invention provide for a
method for selecting an anthracycline-comprising cancer therapy for
a subject having cancer and determined to be negative for BRCA1 and
BRCA2 mutations, comprising: subjecting a sample comprising a
cancer cell taken from the subject to an analysis for BLM and FANCI
expression comparing the BLM and FANCI expression to a reference
value; and selecting the anthracycline-comprising cancer therapy
for the subject when the BLM and FANCI expression compared to the
reference value is increased based on the recognition that
anthracycline-comprising cancer therapy is effective in patients
whose cancer has increased expression of BLM and FANCI compared to
the reference value.
[0180] Various embodiments provide for an assay for selecting a
therapy for a subject having cancer, and optionally administering
the therapy, the assay comprising: assaying a sample comprising a
cancer cell taken from the subject for a chromosome 15q26 copy
number; comparing the chromosome 15q26 copy number to a reference
value; and selecting a platinum-comprising cancer therapy for the
subject if there is a chromosome 15q26 copy number gain compared to
the reference value, or selecting a non-platinum-comprising cancer
therapy for the subject if there is not a chromosome 15q26 copy
number gain, or if there is a chromosome 15q26 copy number
loss.
[0181] In various embodiments, the assay further comprises assaying
the BRCA1 and/or BRCA2 status of the subject; and selecting the
platinum-comprising cancer therapy for the subject when the subject
is negative for BRCA1 and/or BRCA2 mutations, and there is a
chromosome 15q26 copy number gain based on the recognition that
platinum-comprising cancer therapy is effective in subjects who
have a chromosome 15q26 copy number gain who are negative for BRCA1
and/or BRCA2 mutations. In various embodiments, the subject is
known to be or is determined to be negative for BRCA1 and/or BRCA2
mutations. The determination can be made before, concurrently with,
or after the analysis for BLM and FANCI expression.
[0182] In various embodiments, the assay further comprises assaying
the estrogen receptor (ER), progesterone receptor (PgR), and HER2
receptor status of the subject's cancer; and selecting the
platinum-comprising cancer therapy for the subject when the
subject's cancer does not express a detectable quantity of ER, PgR,
and HER2 receptor, and when there is a chromosome 15q26 copy number
gain based on the recognition that platinum-comprising cancer
therapy is effective in subjects who have a chromosome 15q26 copy
number gain and whose cancer does not express a detectable quantity
of ER, PgR, and HER2 receptor. In various embodiments, the
subject's cancer or cancer cell is known to not or is determined to
not express a detectable quantity of ER, PgR, and HER2 receptor.
The determination can be made before, concurrently with, or after
analysis for chromosome 15q26 copy number.
[0183] In various embodiments, the assay further comprises
administering the selected therapy to the subject.
[0184] In various embodiments, the cancer is selected from breast
cancer, ovarian cancer and lung cancer.
[0185] In various embodiments, the reference value is chromosome 15
centromere copy number.
[0186] Various embodiments of the present invention provide for an
assay for selecting a therapy for a subject having cancer, and
optionally administering the therapy, the assay comprising:
assaying a sample comprising a cancer cell taken from the subject
for a chromosome 15q26 copy number; comparing the chromosome 15q26
copy number to a reference value; and selecting an
anthracycline-comprising cancer therapy for the subject if there is
a chromosome 15q26 copy number gain compared to the reference
value, or selecting a non-anthracycline-comprising cancer therapy
for the subject if there is not a chromosome 15q26 copy number
gain, or if there is a chromosome 15q26 copy number loss.
[0187] In various embodiments, the assay further comprises assaying
the BRCA1 and/or BRCA2 status of the subject; and selecting the
anthracycline-comprising cancer therapy for the subject when the
subject is negative for BRCA1 and/or BRCA2 mutations, and there is
a chromosome 15q26 copy number gain based on the recognition that
anthracycline-comprising cancer therapy is effective in subjects
who have a chromosome 15q26 copy number gain and who are negative
for BRCA1 and/or BRCA2 mutations. In various embodiments, the
subject is known to be or is determined to be negative for BRCA1
and/or BRCA2 mutations. In some aspects of all the embodiments of
the invention, a mutation that inactivates BRCA2 is highly
predictive of response to platinum-comprising cancer therapy. The
determination can be made before, concurrently with, or after
analysis for chromosome 15q26 copy number.
[0188] In various embodiments, the assay further comprises assaying
the estrogen receptor (ER), progesterone receptor (PgR), and HER2
receptor status of the subject's cancer; and selecting the
anthracycline-comprising cancer therapy for the subject when the
subject's cancer does not express a detectable quantity of ER, PgR,
and HER2 receptor, and when there is a chromosome 15q26 copy number
gain based on the recognition that anthracycline-comprising cancer
therapy is effective in subjects who have a chromosome 15q26 copy
number gain and whose cancer does not express a detectable quantity
of ER, PgR, and HER2 receptor. In various embodiments, the
subject's cancer or cancer cell is known to not or is determined to
not express a detectable quantity of ER, PgR, and HER2 receptor.
The determination can be made before, concurrently with, or after
analysis for chromosome 15q26 copy number.
[0189] In various embodiments, the assay further comprises
administering the selected therapy to the subject.
[0190] In various embodiments, the cancer is selected from breast
cancer, ovarian cancer and lung cancer.
[0191] In various embodiments, the reference value is chromosome 15
centromere copy number.
Cancer Treatment
[0192] Various embodiments of the present invention provide for a
method of treating cancer in a human subject, comprising: detecting
BLM and FANCI expression in a sample comprising a cancer cell taken
from the human subject; and comparing the BLM and FANCI expression
to a reference value; and administering a platinum-comprising
cancer therapy to the human subject wherein an increase of BLM and
FANCI expression compared to the reference value is detected.
[0193] In various embodiments, the cancer is selected from breast,
ovarian, and lung cancers.
[0194] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0195] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold
2.9-fold or 3-fold compared to BRCA1 expression. In certain
embodiments, the reference value is BRCA1 expression, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0196] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Housekeeping genes
are described herein.
[0197] In certain embodiments, the human subject's cancer or cancer
cell is known to not or determined not to express detectable
quantities of estrogen receptor (ER), progesterone receptor (PgR)
and HER2 receptor. The determination can be made before,
concurrently with, or after analysis for chromosome 15q26 copy
number.
[0198] Various embodiments of the present invention provide for a
method of treating cancer in a human subject, comprising: detecting
BLM and FANCI expression in a sample comprising a cancer cell taken
from the human subject; and comparing the BLM and FANCI expression
to a reference value; and administering an anthracycline-comprising
cancer therapy to the human subject wherein an increase of BLM and
FANCI expression compared to the reference value is detected.
[0199] In various embodiments, the human subject's cancer is known
to not or determined to not express detectable quantities of
estrogen receptor (ER), progesterone receptor (PgR) and HER2
receptor. The determination can be made before, concurrently with,
or after analysis for chromosome 15q26 copy number.
[0200] In various embodiments, the cancer is selected from breast,
ovarian, and lung cancers.
[0201] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0202] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold
2.9-fold or 3-fold compared to BRCA1 expression. In certain
embodiments, the reference value is BRCA1 expression, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0203] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Housekeeping genes
are described herein, e.g., in Table 1.
[0204] Various embodiments of the present invention provide for a
method of treating cancer, comprising: assaying, in a cancer cell
from a cancer patient or mRNA obtained therefrom, the BLM and FANCI
expression compared to a reference value; and administering to the
cancer patient a cancer treatment regimen comprising platinum or
anthracycline if the BLM and FANCI expression is increased compared
to the reference value.
[0205] Various embodiments provide for a use of platinum comprising
cancer therapy for treating a cancer patient that has been
determined to have a tumor comprising cancer cells wherein BLM and
FANCI expression is increased compared to a reference value.
[0206] In various embodiments, the cancer patient is known to be or
is determined to be negative for BRCA1 and/or BRCA2 mutations. The
determination can be made before, concurrently with, or after the
analysis for BLM and FANCI expression. In certain embodiments, the
cancer patient's cancer or cancer cell is known to not or is
determined to not express detectable quantities of estrogen
receptor (ER), progesterone receptor (PgR) and HER2 receptor. The
determination can be made before, concurrently with, or after
analysis of BLM and FANCI expression.
[0207] Various embodiments of the present invention provide for a
method of treating cancer in a human subject whose cancer has
increased BLM and FANCI expression, comprising: identifying the
human subject whose cancer has increased BLM and FANCI expression;
and administering a platinum-comprising cancer therapy or an
anthracycline-comprising therapy to the human subject. In certain
embodiments, the human subject's cancer is known to not or is
determined to not express detectable quantities of estrogen
receptor (ER), progesterone receptor (PgR) and HER2 receptor. In
various embodiments, the human subject is known to be or is
determined to be negative for BRCA1 and/or BRCA2 mutations. These
determinations can be made before, concurrently with, or after
analysis of BLM and FANCI expression.
[0208] Various embodiments of the present invention provide for a
method of treating cancer in a human subject, comprising: detecting
a chromosome 15q26 copy number in a sample comprising a cancer cell
taken from the subject; comparing the chromosome 15q26 copy number
to a reference value; and administering an platinum-comprising
cancer therapy for the subject if there is a chromosome 15q26 copy
number gain compared to the reference value, or administering a
non-platinum-comprising cancer therapy for the subject if there is
not a chromosome 15q26 copy number gain, or if there is a
chromosome 15q26 copy number loss.
[0209] In various embodiments, the cancer is selected from breast
cancer, ovarian cancer and lung cancer. In various embodiments, the
reference value is chromosome 15 centromere copy number. In various
embodiments, the subject's cancer or cancer cell is known to not or
is determined to not express a detectable quantity of ER, PgR, and
HER2 receptor. The determination can be made before, concurrently
with, or after analysis of chromosome 15q26 copy number.
[0210] Various embodiments of the present invention provide for a
method of treating cancer in a human subject, comprising: detecting
a chromosome 15q26 copy number in a sample comprising a cancer cell
taken from the subject; comparing the chromosome 15q26 copy number
to a reference value; and administering an anthracycline-comprising
cancer therapy for the subject if there is a chromosome 15q26 copy
number gain compared to the reference value, or administering a
non-anthracycline-compri sing cancer therapy for the subject if
there is not a chromosome 15q26 copy number gain, or if there is a
chromosome 15q26 copy number loss.
[0211] In various embodiments, the cancer is selected from breast
cancer, ovarian cancer and lung cancer. In various embodiments, the
reference value is chromosome 15 centromere copy number. In various
embodiments, the subject's cancer or cancer cell is known to not or
is determined to not express a detectable quantity of ER, PgR, and
HER2 receptor. The determination can be made before, concurrently
with, or after analysis of chromosome 15q26 copy number.
Assessing and Predicting Responsiveness to Cancer Therapy
[0212] Various embodiments of the present invention provide for a
method for assessing responsiveness of a cancer cell to cancer
therapy, comprising: assaying, in a cancer cell or mRNA derived
therefrom, BLM and FANCI expression; and comparing said BLM and
FANCI expression to a reference value, wherein the cancer cell is
assessed as responsive to a platinum-comprising therapy if the BLM
and FANCI expression is increased compared to the reference value,
or wherein the cancer cell is assessed as poorly or not responsive
to platinum-comprising cancer therapy cancer if the BLM and FANCI
expression is not increased.
[0213] In various embodiments, the step of assaying comprises:
contacting the cancer cell or mRNA derived therefrom with at least
one detectably labeled probe capable of specifically binding to BLM
mRNA, at least one detectably probe capable of specifically binding
to FANCI, at least one detectably labeled probe capable of
specifically binding to BRCA1 and/or at least one housekeeping
gene; and measuring the expression of BLM and FANCI compared to the
BRCA1 and/or the at least one housekeeping gene.
[0214] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0215] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold
2.9-fold or 3-fold compared to BRCA1 expression. In certain
embodiments, the reference value is BRCA1 expression, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0216] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Housekeeping genes
are described herein, e.g., in Table 1.
[0217] Various embodiments of the present invention provide for a
method of predicting a cancer patient's response to a cancer
treatment regimen comprising platinum or anthracycline, comprising:
determining, in a cancer cell from the cancer patient, BLM and
FANCI expression; and correlating the expression to a reference
value, wherein when the expression is increased the patient is
predicted to respond well to a cancer treatment regimen comprising
platinum or anthracycline.
[0218] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0219] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold
2.9-fold or 3-fold compared to BRCA1 expression. In certain
embodiments, the reference value is BRCA1 expression, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0220] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Housekeeping genes
are described herein, e.g., in Table 1.
[0221] Various embodiments of the present invention provide for a
method of predicting a cancer patient's response to a cancer
treatment regimen comprising platinum or anthracycline, comprising:
determining, in a cancer cell or mRNA derived therefrom from said
cancer patient, BLM and FANCI expression; and correlating the
expression to a reference value, wherein when the expression is not
increased the patient is predicted to respond poorly to a cancer
treatment regimen comprising platinum or anthracycline.
[0222] In various embodiments, the reference value is based on
BRCA1 gene expression in the cancer cell. In various embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about 10, 20, 30, 40, 50,
60, 70, 80, or 90% compared to BRCA1 expression.
[0223] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold
2.9-fold or 3-fold compared to BRCA1 expression. In certain
embodiments, the reference value is BRCA1 expression, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression.
[0224] In various embodiments, the reference value is based on a
housekeeping gene expression in the cancer cell. Housekeeping genes
are described herein.
[0225] Various embodiments provide for a method for assessing
responsiveness of a cancer cell to a cancer therapy, and optionally
administering the cancer therapy, comprising: assaying a sample
comprising a cancer cell taken from the subject for a chromosome
15q26 copy number; and comparing the chromosome 15q26 copy number
to a reference value, wherein the cancer cell is assessed as
responsive to a platinum-comprising therapy if there is a
chromosome 15q26 copy number gain compared to the reference value,
or wherein the cancer cell is assessed as poorly or not responsive
to platinum-comprising cancer therapy cancer if there is not a
chromosome 15q26 copy number gain or if there is a chromosome 15q26
copy number loss.
[0226] In various embodiments, the reference value is chromosome 15
centromere copy number. In various embodiments, the cancer is
selected from breast cancer, ovarian cancer and lung cancer.
[0227] In various embodiments, the method further comprises
administering the platinum-comprising therapy if there is a
chromosome 15q26 copy number gain.
[0228] Various embodiments provide for a method of predicting a
cancer patient's response to a cancer treatment regimen comprising
platinum or anthracycline, comprising: determining, in a cancer
cell from the cancer patient, chromosome 15q26 copy number; and
correlating the chromosome 15q26 copy number to a reference value,
wherein when there is a chromosome 15q26 copy number gain, the
patient is predicted to respond well to a cancer treatment
comprising platinum or anthracycline, or wherein when there is not
a chromosome 15q26 copy number gain or a chromosome 15q26 copy
number loss, the patient is predicted respond poorly to a cancer
treatment comprising platinum or anthracycline.
[0229] In various embodiments, the reference value is chromosome 15
centromere copy number.
[0230] Various embodiments provide for the use of platinum
comprising cancer therapy for treating a cancer patient that has
been determined to have a tumor comprising cancer cells wherein a
chromosome 15q26 copy gain is detected compared to a reference
value. In various embodiments, cancer patient is known to be or is
determined to be negative for BRCA1 and/or BRCA2 mutations. The
determination can be made before, concurrently with, or after the
analysis for BLM and FANCI expression. In various embodiments, the
cancer patient is known to not or is determined to not express
detectable quantities of estrogen receptor (ER), progesterone
receptor (PgR) and HER2 receptor. In various embodiments, the
reference value is chromosome 15 centromere copy number.
Systems, Computers, Kits and Uses
[0231] Various embodiments of the present invention provide for a
system for determining responsiveness of a cancer cell to
platinum-comprising therapy from a cancer cell of a cancer patient,
comprising: a sample analyzer configured to produce a signal for
the mRNA from each one of BLM and FANCI from a cancer cell sample
of a cancer patient; and a computer sub-system programmed to
calculate, based on the mRNA whether the signal is greater or not
than a reference value.
[0232] In various embodiments, said computer sub-system is
programmed to compare the mRNA to determine a likelihood of
responsiveness of said cancer cell to platinum-comprising cancer
therapy based on an algorithm that classifies the patient as likely
to respond to a platinum-comprising therapy if the BLM and FANCI
expression is increased and as unlikely to respond to the
platinum-comprising therapy if the BLM and FANCI expression is not
increased; or a likelihood of responsiveness of said cancer cell to
anthracycline-comprising cancer therapy based on an algorithm that
classifies the patient as likely to respond to a
anthracycline-comprising therapy if the BLM and FANCI expression is
increased and as unlikely to respond to the
anthracycline-comprising therapy if the BLM and FANCI expression is
not increased.
[0233] Various embodiments of the present invention provide for a
system for determining responsiveness of a cancer cell to
platinum-comprising therapy from a cancer cell of a cancer patient,
comprising: a sample analyzer configured to produce a signal for
the protein from each one of BLM and FANCI from a cancer cell
sample of a cancer patient; and a computer sub-system programmed to
calculate, based on the protein whether the signal is greater or
not than a reference value.
[0234] In various embodiments, said computer sub-system is
programmed to compare the protein to determine a likelihood of
responsiveness of said cancer cell to platinum-comprising cancer
therapy based on an algorithm that classifies the patient as likely
to respond to a platinum-comprising therapy if the BLM and FANCI
expression is increased and as unlikely to respond to the
platinum-comprising therapy if the BLM and FANCI expression is not
increased; or a likelihood of responsiveness of said cancer cell to
anthracycline-comprising cancer therapy based on an algorithm that
classifies the patient as likely to respond to a
anthracycline-comprising therapy if the BLM and FANCI expression is
increased and as unlikely to respond to the
anthracycline-comprising therapy if the BLM and FANCI expression is
not increased.
[0235] Various embodiments of the present invention provide for a
computer program product embodied in a computer readable medium
that, when executing on a computer, performs steps comprising:
detecting the BLM and FANCI expression in sample comprising a
cancer cell from a cancer patient; and comparing the BLM and FANCI
expression to a reference value.
[0236] Various embodiments of the present invention provide for a
diagnostic kit for detecting a likelihood of a cancer patient to
respond to platinum- or anthracycline-compri sing comprising cancer
therapy, comprising: no more than 10 probes comprising a
combination of detectably labeled probes or primers for BLM and
FANCI, and optionally for BRCA1 and/or at least one housekeeping
gene; and the computer program product.
[0237] Various embodiments of the present invention provide for the
use of a plurality of oligonucleotides comprising no more than 10
oligonucleotides capable of hybridizing to BLM and FANCI, and
optionally to BRCA1 and/or at least one housekeeping gene, in a
diagnostic kit for determining an increased likelihood that a
cancer patient will respond to cancer treatment regimen comprising
a platinum and/or anthracycline.
[0238] Various embodiments provide for a system for determining
responsiveness of a cancer cell to platinum-comprising therapy from
a cancer cell of a cancer patient, comprising: a sample analyzer
configured to produce a signal for chromosome 15q26 copy number
from a cancer cell sample of a cancer patient; and a computer
sub-system programmed to calculate, based on the mRNA whether the
signal is greater or not than a reference value.
[0239] In various embodiments, the computer sub-system is
programmed to compare the mRNA to determine a likelihood of
responsiveness of said cancer cell to platinum-comprising cancer
therapy and/or or a anthracycline-comprising cancer therapy based
on an algorithm that classifies the patient as likely to respond to
a platinum-comprising therapy if there is a chromosome 15q26 copy
number gain and as unlikely to respond to the platinum-comprising
therapy if there is not a chromosome 15q26 copy number gain or if
there is a chromosome 15q26 copy number loss. In various
embodiments, the reference value is chromosome 15 centromere copy
number.
[0240] Various embodiments of the present invention provide for a
computer program product embodied in a computer readable medium
that, when executing on a computer, performs steps comprising:
detecting chromosome 15q26 copy number in sample comprising a
cancer cell from a cancer patient; and comparing the chromosome
15q26 copy number to a reference value. In various embodiments, the
reference value is chromosome 15 centromere copy number.
[0241] Various embodiments of the present invention provide for a
diagnostic kit for detecting a likelihood of a cancer patient to
respond to platinum- or anthracycline-compri sing cancer therapy,
comprising: no more than 10 probes comprising a combination of
detectably labeled probes or primers for chromosome 15q26, and
optionally for chromosome 15 centromere; and the computer program
product of described herein.
[0242] Various embodiments of the present invention provide for the
use of a plurality of oligonucleotides comprising no more than 10
oligonucleotides capable of hybridizing to chromosome 15q26, and
optionally for chromosome 15 centromere, in a diagnostic kit for
determining an increased likelihood that a cancer patient will
respond to cancer treatment regimen comprising a platinum and/or
anthracycline.
Reference Values
[0243] In various embodiments of the present invention, the
reference value is based on BRCA1 gene expression in the cancer
cell.
[0244] In various embodiments, the reference value for BLM
expression or FANCI expression is BRCA1 expression.
[0245] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90% compared to
BRCA1 expression.
[0246] In various embodiments, the reference value is BRCA1
expression, and the BLM and/or FANCI expression is increased by at
least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold,
1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold
2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold,
2.9-fold, or 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold
or 10-fold compared to BRCA1 expression. In certain embodiments,
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least or about two-fold to about
7-fold compared to BRCA1 expression.
[0247] In various embodiments of the present invention, the
reference value can be one or more housekeeping gene as described
herein. In certain embodiments, one or more housekeeping gene as
described herein, and the BLM and/or FANCI expression is increased
by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%
compared to the one or more housekeeping gene expression.
[0248] In certain embodiments, one or more housekeeping gene as
described herein, and the BLM and/or FANCI expression is increased
by at least or about 1-fold, 1.1-fold, 1.2-fold, 1.3-fold,
1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold,
2.1-fold 2.2-fold 2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold
2.8-fold 2.9-fold or 3-fold, 4-fold, 5-fold, 6-fold, 7-fold,
8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold,
60-fold or higher compared to the one or more housekeeping gene
expression depending on the level of the expression of the
housekeeping gene in the cell.
[0249] In various embodiments, the housekeeping gene can be
selected from the group consisting of beta-actin, GAPDH, RPLP0,
GUS, TFRC and combinations thereof. (See e.g., Cronin et al.,
Clinical Chemistry 53:6, 1084-1091 (2007), and ONCOTYPE DX
ASSAY.RTM., herein incorporated by reference in its entirety.)
Thus, in some embodiments, the house keeping gene is one of these
genes, and in other embodiments, the housekeeping gene is a
combination of 2, 3, 4, or all 5 of these genes. In particular
embodiments, the housekeeping gene is RPLP0, also called 36b4.
[0250] In various embodiments, the house keeping gene can be
selected from the genes listed in Table 1. Accordingly, in some
embodiments, the housekeeping gene is one of the genes from Table
1, and in other embodiments, the housekeeping gene is a combination
of any number or all of the genes from Table 1. (See e.g.,
Eisenberg and Levanon, Human housekeeping genes are compact. Trends
in Genetics, Volume 19, Issue 7, 362-365, 1 July 2003). Each gene
name/description is followed by its geometric average expression
level according to the data published by Su et al. Thus, based on
our experimental data on the RPLP0 housekeeping gene as a reference
gene, one of ordinary skill in the art can easily determine what
the cut-off points for increased expression for any one of these
genes is. For example, genes designated by asterisk are in popular
use as reference in real-time PCR or quantitative PCR (qPCR), which
is most often used in gene expression analysis.
[0251] In some aspects of all the embodiments on the invention, the
assays, methods, kits, and systems incorporate qPCR as the gene
expression analysis method to determine the amount compared to a
reference value.
TABLE-US-00001 TABLE 1 Housekeeping Genes. Accession No.
Description *NM_001101 Homo sapiens actin, beta (ACTB), mRNA 6988
*NM_000034 Homo sapiens aldolase A,fructose-bisphosphate (ALDOA),
mRNA 3425 *NM_002046 Homo sapiens glyceraldehyde-3-phosphate
dehydrogenase (GAPD), mRNA 828 *NM_000291 Homo sapiens
phosphoglycerate kinase 1 (PGK1), mRNA 2727 *NM_005566 Homo sapiens
lactate dehydrogenase A (LDHA), mRNA 2105 *NM_002954 Homo sapiens
ribosomal protein S27a (RPS27A), mRNA 4156 *NM_000981 Homo sapiens
ribosomal protein L19 (RPL19), mRNA 6997 *NM_000975 Homo sapiens
ribosomal protein L11 (RPL11), mRNA 6060 *NM_007363 Homo sapiens
non-POU domain containing, octamer- binding (NONO), mRNA 1708
*NM_004309 Homo sapiens Rho GDP dissociation inhibitor (GDI) alpha
(ARHGDIA), mRNA 1358 *NM_000994 Homo sapiens ribosomal protein L32
(RPL32), mRNA 9523 *NM_022551 Homo sapiens ribosomal protein S18
(RPS18), mRNA 11261 *NM_007355 Homo sapiens heat shock 90 kDa
protein 1, beta (HSPCB), mRNA 4119 NM_004515 Homo sapiens
interleukin enhancer binding factor 2, 45 kDa (ILF2), mRNA 1000
NM_004651 Homo sapiens ubiquitin specific protease 11 (USP11), mRNA
1950 NM_004888 Homo sapiens ATPase, H+ transporting, lysosomal 13
kDa, V1 subunit G isoform 1 (ATP6V1G1), mRNA 928 NM_003334 Homo
sapiens ubiquitin-activating enzyme El (A1S9T and BN75 temperature
sensitivity complementing) (UBE1), transcript variant 1, mRNA 1351
NM_001320 Homo sapiens casein kinase 2, beta polypeptide (CSNK2B),
mRNA 1233 NM_003915 Homo sapiens copine I (CPNE1), transcript
variant 3, mRNA 698 NM_001250 Homo sapiens tumor necrosis factor
receptor superfamily, member 5 (TNFRSF5), transcript variant 1,
mRNA 524 NM_001904 Homo sapiens catenin (cadherin-associated
protein), beta 1, 88 kDa (CTNNB1), mRNA 1165 NM_003753 Homo sapiens
eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67
kDa (EIF3S7), mRNA 1363 NM_004541 Homo sapiens NADH dehydrogenase
(ubiquinone) 1 alpha subcomplex, 1, 7.5 kDa (NDUFA1), nuclear gene
encoding mitochondrial protein, mRNA 2307 NM_001654 Homo sapiens
v-raf murine sarcoma 3611 viral oncogene homolog 1 (ARAF1), mRNA
846 NM_002967 Homo sapiens scaffold attachment factor B (SAFB),
mRNA 545 NM_001183 Homo sapiens ATPase, H+ transporting, lysosomal
interacting protein 1 (ATP6IP1), mRNA 1089 NM_003526 Homo sapiens
H2B histone family, member L (H2BFL), mRNA 2232 NM_004718 Homo
sapiens cytochrome c oxidase subunit VIIa polypeptide 2 like
(COX7A2L), nuclear gene encoding mitochondrial protein, mRNA 1013
NM_004436 Homo sapiens endosulfine alpha (ENSA), mRNA 659 NM_001207
Homo sapiens basic transcription factor 3 (BTF3), mRNA 3348
NM_004907 Homo sapiens immediate early protein (ETR101), mRNA 1249
NM_004889 Homo sapiens ATP synthase, H+ transporting, mitochondrial
F0 complex, subunit f, isoform 2 (ATP5J2), mRNA 1513 NM_003769 Homo
sapiens splicing factor, arginine/serine-rich 9 (SFRS9), mRNA 1207
NM_003910 Homo sapiens maternal G10 transcript (G10), mRNA 696
NM_000100 Homo sapiens cystatin B (stefin B) (CSTB), mRNA 1422
NM_004785 Homo sapiens solute carrier family 9 (sodium/hydrogen
exchanger), isoform 3 regulatory factor 2 (SLC9A3R2), mRNA 455
NM_001120 Homo sapiens tetracycline transporter-like protein
(TETRAN), mRNA 935 NM_000182 Homo sapiens hydroxyacyl-Coenzyme A
dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl- Coenzyme A
hydratase (trifunctional protein), alpha subunit (HADHA), mRNA 609
NM_003377 Homo sapiens vascular endothelial growth factor B
(VEGFB), mRNA 649 NM_003576 Homo sapiens serine/threonine kinase 24
(STE20 homolog, yeast) (STK24), mRNA 769 NM_000918 Homo sapiens
procollagen-proline, 2-oxoglutarate 4- dioxygenase (proline
4-hydroxylase), beta polypeptide (protein disulfide isomerase;
thyroid hormone binding protein p55) (P4HB), mRNA 2719 NM_004584
Homo sapiens RAD9 homolog (S. pombe) (RAD9), mRNA 860 NM_004952
Homo sapiens ephrin-A3 (EFNA3), mRNA 505 NM_004308 Homo sapiens Rho
GTPase activating protein 1 (ARHGAP1), mRNA 893 NM_003190 Homo
sapiens TAP binding protein (tapasin) (TAPBP), mRNA 1213 NM_004640
Homo sapiens HLA-B associated transcript 1 (BAT1), transcript
variant 1, mRNA 1022 NM_001064 Homo sapiens transketolase
(Wernicke-Korsakoff syndrome) (TKT), mRNA 1139 NM_002117 Homo
sapiens major histocompatibility complex, class I, C (HLA-C), mRNA
4696 NM_004161 Homo sapiens RAB1A, member RAS oncogene family
(RAB1A), mRNA 2163 NM_003339 Homo sapiens ubiquitin-conjugating
enzyme E2D 2 (UBC4/5 homolog, yeast) (UBE2D2), mRNA 514 NM_003969
Homo sapiens ubiquitin-conjugating enzyme E2M (UBC12 homolog,
yeast) (UBE2M), mRNA 1197 NM_000516 Homo sapiens GNAS complex locus
(GNAS), transcript variant 1, mRNA 4358 NM_002819 Homo sapiens
polypyrimidine tract binding protein 1 (PTBP1), transcript variant
1, mRNA 1138 NM_001001 Homo sapiens ribosomal protein L36a-like
(RPL36AL), mRNA 1740 NM_004649 Homo sapiens chromosome 21 open
reading frame 33 (C21orf33), mRNA 585 NM_000175 Homo sapiens
glucose phosphate isomerase (GPI), mRNA 1633 NM_001867 Homo sapiens
cytochrome c oxidase subunit VIIc (COX7C), nuclear gene encoding
mitochondrial protein, mRNA 3004 NM_001967 Homo sapiens eukaryotic
translation initiation factor 4A, isoform 2 (EIF4A2), mRNA 2935
NM_001863 Homo sapiens cytochrome c oxidase subunit VIb (COX6B),
nuclear gene encoding mitochondrial protein, mRNA 1719 NM_001997
Homo sapiens Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV)
ubiquitously expressed (fox derived); ribosomal protein S30 (FAU),
mRNA 3898 NM_002088 Homo sapiens glutamate receptor, ionotropic,
kainate 5 (GRIK5), mRNA 535 NM_001862 Homo sapiens cytochrome c
oxidase subunit Yb (COX5B), nuclear gene encoding mitochondrial
protein, mRNA 1087 NM_004255 Homo sapiens cytochrome c oxidase
subunit Va (COX5A), nuclear gene encoding mitochondrial protein,
mRNA 853 NM_001788 Homo sapiens CDC10 cell division cycle 10
homolog (S. cerevisiae) (CDC10), mRNA 1340 NM_004781 Homo sapiens
vesicle-associated membrane protein 3 (cellubrevin) (VAMP3), mRNA
684 NM_003801 Homo sapiens GPAA1P anchor attachment protein 1
homolog (yeast) (GPAA1), mRNA 776 NM_004643 Homo sapiens poly(A)
binding protein, nuclear 1 (PABPN1), mRNA 502 NM_001537 Homo
sapiens heat shock factor binding protein 1 (HSBP1), mRNA 874
NM_003680 Homo sapiens tyrosyl-tRNA synthetase (YARS), mRNA 535
NM_003345 Homo sapiens ubiquitin-conjugating enzyme E21 (UBC9
homolog, yeast) (UBE2I), mRNA 1283 NM_002568 Homo sapiens poly(A)
binding protein, cytoplasmic 1 (PABPC1), mRNA 3199 NM_001487 Homo
sapiens GCN5 general control of amino-acid synthesis 5-like 1
(yeast) (GCN5L1), mRNA 313 NM_001861 Homo sapiens cytochrome c
oxidase subunit IV isoform 1 (COX4I1), nuclear gene encoding
mitochondrial protein, mRNA2 738 NM_004890 Homo sapiens sperm
associated antigen 7 (SPAG7), mRNA 618 NM_002812 Homo sapiens
proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 (PSMD8),
mRNA 942 NM_004926 Homo sapiens zinc finger protein 36, C3H
type-like 1 (ZFP36L1), mRNA 1168 NM_002539 Homo sapiens ornithine
decarboxylase 1 (ODC1), mRNA 1361 NM_000979 Homo sapiens ribosomal
protein L18 (RPL18), mRNA 4417 NM_000977 Homo sapiens ribosomal
protein L13 (RPL13), transcript variant 1, mRNA 6407 NM_001015 Homo
sapiens ribosomal protein S11 (RPS11), mRNA 7614 NM_001760 Homo
sapiens cyclin D3 (CCND3), mRNA 676 NM_003973 Homo sapiens
ribosomal protein L14 (RPL14), mRNA 3135 NM_002815 Homo sapiens
proteasome (prosome, macropain) 26S subunit, non-ATPase, 11
(PSMD11), mRNA 536 NM_000367 Homo sapiens thiopurine
S-methyltransferase (TPMT), mRNA 1574 NM_000973 Homo sapiens
ribosomal protein L8 (RPL8), transcript variant 1, mRNA 8138
NM_004689 Homo sapiens metastasis associated 1 (MTA1), mRNA 506
NM_001848 Homo sapiens collagen, type VI, alpha 1 (COL6A1), mRNA
757 NM_004068 Homo sapiens adaptor-related protein complex 2, mu 1
subunit (AP2M1), mRNA 2188 NM_001687 Homo sapiens ATP synthase, H+
transporting, mitochondrial F1 complex, delta subunit (ATP5D), mRNA
1167 NM_004197 Homo sapiens serine/threonine kinase 19 (STK19),
transcript variant 1, mRNA 574 NM_001028 Homo sapiens ribosomal
protein S25 (RPS25), mRNA 4683 NM_001022 Homo sapiens ribosomal
protein S19 (RPS19), mRNA 6683 NM_004759 Homo sapiens
mitogen-activated protein kinase-activated protein kinase 2
(MAPKAPK2), transcript variant 1, mRNA 641 NM_001623 Homo sapiens
allograft inflammatory factor 1 (AIF1), transcript variant 3, mRNA
497 NM_004894 Homo sapiens chromosome 14 open reading frame 2
(C14orf2), mRNA 704 NM_002375 Homo sapiens microtubule-associated
protein 4 (MAP4), transcript variant 1, mRNA 717 NM_001013 Homo
sapiens ribosomal protein S9 (RPS9), mRNA 6868 NM_003779 Homo
sapiens UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase,
polypeptide 3 (B4GALT3), mRNA 565 NM_001296 Homo sapiens chemokine
binding protein 2 (CCBP2), mRNA 394 NM_001009 Homo sapiens
ribosomal protein S5 (RPS5), mRNA 6739 NM_003021 Homo sapiens small
glutamine-rich tetratricopeptide repeat (TPR)-containing (SGT),
mRNA 488 NM_004285 Homo sapiens hexose-6-phosphate dehydrogenase
(glucose 1-dehydrogenase) (H6PD), mRNA 646 NM_004142 Homo sapiens
matrix metalloproteinase-like 1 (MMPL1), mRNA 695 NM_001950 Homo
sapiens E2F transcription factor 4, p107/p130- binding (E2F4), mRNA
956 NM_003815 Homo sapiens a disintegrin and metalloproteinase
domain 15 (metargidin) (ADAM15), mRNA 771 NM_001119 Homo sapiens
adducin 1 (alpha) (ADD1), transcript variant 1, mRNA 1356 NM_001111
Homo sapiens adenosine deaminase, RNA-specific (ADAR), transcript
variant ADAR-a, mRNA 1036 NM_003466 Homo sapiens paired box gene 8
(PAX8), transcript variant PAX8A, mRNA 901 NM_001155 Homo sapiens
annexin A6 (ANXA6), transcript variant 1, mRNA 718 NM_003465 Homo
sapiens chitinase 1 (chitotriosidase) (CHIT1), mRNA 561 NM_003186
Homo sapiens transgelin (TAGLN), mRNA 1209 NM_000802 Homo sapiens
folate receptor 1 (adult) (FOLR1), transcript variant 2, mRNA 514
NM_004924 Homo sapiens actinin, alpha 4 (ACTN4), mRNA 1187
NM_002931 Homo sapiens ring finger protein 1 (RING 1), mRNA 576
NM_000020 Homo sapiens activin A receptor type II-like 1 (ACVRL1),
mRNA 849 NM_001785 Homo sapiens cytidine deaminase (CDA), mRNA 391
NM_004339 Homo sapiens pituitary tumor-transforming 1 interacting
protein (PTTG1 IP), mRNA 1200 NM_003860 Homo sapiens Breakpoint
cluster region protein, uterine leiomyoma, 1; barrier to
autointegration factor (BCRP1), mRNA 1303 NM_000214 Homo sapiens
jagged 1 (Alagille syndrome) (JAGO, mRNA 536
NM_002167 Homo sapiens inhibitor of DNA binding 3, dominant
negative helix-loop-helix protein (ID3), mRNA 1192 NM_001664 Homo
sapiens ras homolog gene family, member A (ARHA), mRNA 4050
NM_003166 Homo sapiens sulfotransferase family, cytosolic, 1A,
phenol-preferring, member 3 (SULT1A3), mRNA 461 NM_001746 Homo
sapiens calnexin (CANX), mRNA 1923 NM_001662 Homo sapiens
ADP-ribosylation factor 5 (ARF5), mRNA 724 NM_001660 Homo sapiens
ADP-ribosylation factor 4 (ARF4), mRNA 1014 NM_001658 Homo sapiens
ADP-ribosylation factor 1 (ARF1), mRNA 2195 NM_003313 Homo sapiens
tissue specific transplantation antigen P35B (TSTA3), mRNA 440
NM_001494 Homo sapiens GDP dissociation inhibitor 2 (GDI2), mRNA
1352 NM_003145 Homo sapiens signal sequence receptor, beta
(translocon- associated protein beta) (SSR2), mRNA 1265 NM_001619
Homo sapiens adrenergic, beta, receptor kinase 1 (ADRBK1), mRNA 695
NM_001420 Homo sapiens ELAV (embryonic lethal, abnormal vision,
Drosophila)-like 3 (Hu antigen C) (ELAVL3), mRNA 1070 NM_004930
Homo sapiens capping protein (actin filament) muscle Z- line, beta
(CAPZB), mRNA 1183 NM_004596 Homo sapiens small nuclear
ribonucleoprotein polypeptide A (SNRPA), mRNA 734 NM_004168 Homo
sapiens succinate dehydrogenase complex, subunit A, flavoprotein
(Fp) (SDHA), nuclear gene encoding mitochondrial protein, mRNA 1106
NM_004156 Homo sapiens protein phosphatase 2 (formerly 2A),
catalytic subunit, beta isoform (PPP2CB), mRNA 1195 NM_004910 Homo
sapiens phosphatidylinositol transfer protein, membrane-associated
(PITPNM), mRNA 869 NM_004517 Homo sapiens integrin-linked kinase
(ILK), mRNA 654 NM_004494 Homo sapiens hepatoma-derived growth
factor (high- mobility group protein 1-like) (HDGF), mRNA 1385
NM_004121 Homo sapiens gamma-glutamyltransferase-like activity 1
(GGTLA1), mRNA 412 NM_004404 Homo sapiens neural precursor cell
expressed, developmentally down-regulated 5 (NEDD5), mRNA 1571
NM_004394 Homo sapiens death-associated protein (DAP), mRNA 623
NM_004383 Homo sapiens c-src tyrosine kinase (CSK), mRNA 899
NM_004074 Homo sapiens cytochrome c oxidase subunit VIII (COX8),
nuclear gene encoding mitochondrial protein, mRNA 3188 NM_004039
Homo sapiens annexin A2 (ANXA2), mRNA 2417 NM_001053 Homo sapiens
somatostatin receptor 5 (SSTR5), mRNA 423 NM_001328 Homo sapiens
C-terminal binding protein 1 (CTBP1), mRNA 798 NM_001273 Homo
sapiens chromodomain helicase DNA binding protein 4 (CHD4), mRNA
775 NM_003430 Homo sapiens zinc finger protein 91 (HPF7, HTF10)
(ZNF91), mRNA 716 NM_003314 Homo sapiens tetratricopeptide repeat
domain 1 (TTC1), mRNA 651 NM_003217 Homo sapiens testis enhanced
gene transcript (TEGT), mRNA 1766 NM_003132 Homo sapiens spermidine
synthase (SRM), mRNA 1093 NM_000199 Homo sapiens N-sulfoglucosamine
sulfohydrolase (sulfamidase) (SGSH), mRNA 565 NM_002818 Homo
sapiens proteasome (prosome, macropain) activator subunit 2 (PA28
beta) (PSME2), mRNA 697 NM_002733 Homo sapiens protein kinase,
AMP-activated, gamma 1 non-catalytic subunit (PRKAG1), mRNA 497
NM_002631 Homo sapiens phosphogluconate dehydrogenase (PGD), mRNA
1009 NM_002574 Homo sapiens peroxiredoxin 1 (PRDX1), mRNA 2241
NM_002512 Homo sapiens non-metastatic cells 2, protein (NM23B)
expressed in (NME2), nuclear gene encoding mitochondrial protein,
mRNA 2553 NM_002455 Homo sapiens metaxin 1 (MTX1), mRNA 845
NM_002444 Homo sapiens moesin (MSN), mRNA 1798 NM_000529 Homo
sapiens melanocortin 2 receptor (adrenocorticotropic hormone)
(MC2R), mRNA 420 NM_003573 Homo sapiens latent transforming growth
factor beta binding protein 4 (LTBP4), mRNA 740 NM_002315 Homo
sapiens LIM_domain only 1 (rhombotin 1) (LMO1), mRNA 469 NM_000884
Homo sapiens IMP (inosine monophosphate) dehydrogenase 2 (IMPDH2),
mRNA 1288 NM_003641 Homo sapiens interferon induced transmembrane
protein 1 (9-27) (IFITM1), mRNA 4898 NM_000841 Homo sapiens
glutamate receptor, metabotropic 4 (GRM4), mRNA 1369 NM_002070 Homo
sapiens guanine nucleotide binding protein (G protein), alpha
inhibiting activity polypeptide 2 (GNAI2), mRNA 1877 NM_001493 Homo
sapiens GDP dissociation inhibitor 1 (GDI1), mRNA 1387 NM_002048
Homo sapiens growth arrest-specific 1 (GAS1), mRNA 940 NM_002032
Homo sapiens ferritin, heavy polypeptide 1 (FTH1), mRNA 2616
NM_001418 Homo sapiens eukaryotic translation initiation factor 4
gamma, 2 (EIF4G2), mRNA 3646 NM_001350 Homo sapiens
death-associated protein 6 (DAXX), mRNA 510 NM_001843 Homo sapiens
contactin 1 (CNTN1), mRNA 535 NM_001728 Homo sapiens basigin (BSG),
mRNA 1508 NM_001667 Homo sapiens ADP-ribosylation factor-like 2
(ARL2), mRNA 965 NM_001659 Homo sapiens ADP-ribosylation factor 3
(ARF3), mRNA 1327 NM_003746 Homo sapiens dynein, cytoplasmic, light
polypeptide 1 (DNCL1), mRNA 2758 NM_002127 Homo sapiens HLA-G
histocompatibility antigen, class I, G (HLA-G), mRNA 1090 NM_004712
Homo sapiens hepatocyte growth factor-regulated tyrosine kinase
substrate (HGS), mRNA 505 NM_003475 Homo sapiens chromosome 11 open
reading frame 13 (C11orf13), mRNA 413 NM_004046 Homo sapiens ATP
synthase, H+ transporting, mitochondrial F1 complex, alpha subunit,
isoform 1, cardiac muscle (ATP5A1), mRNA 1348 NM_001894 Homo
sapiens casein kinase 1, epsilon (CSNK1E), transcript variant 2,
mRNA 613 NM_003795 Homo sapiens sorting nexin 3 (SNX3), transcript
variant 1, mRNA 1426 NM_001909 Homo sapiens cathepsin D (lysosomal
aspartyl protease) (CTSD), mRNA 1512 NM_002792 Homo sapiens
proteasome (prosome, macropain) subunit, alpha type, 7 (PSMA7),
transcript variant 1, mRNA 728 NM_002799 Homo sapiens proteasome
(prosome, macropain) subunit, beta type, 7 (PSMB7), mRNA 545
NM_002300 Homo sapiens lactate dehydrogenase B (LDHB), mRNA 4144
NM_004176 Homo sapiens sterol regulatory element binding
transcription factor 1 (SREBF1), mRNA 632 NM_002796 Homo sapiens
proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4), mRNA
1229 NM_002794 Homo sapiens proteasome (prosome, macropain)
subunit, beta type, 2 (PSMB2), mRNA 1304 NM_002793 Homo sapiens
proteasome (prosome, macropain) subunit, beta type, 1 (PSMB1), mRNA
2084 NM_002473 Homo sapiens myosin, heavy polypeptide 9, non-muscle
(MYH9), mRNA 1381 NM_001810 Homo sapiens centromere protein B, 80
kDa (CENPB), mRNA 532 NM_002624 Homo sapiens prefoldin 5 (PFDN5),
transcript variant 1, mRNA 1718 NM_004710 Homo sapiens synaptogyrin
2 (SYNGR2), mRNA 1414 NM_001127 Homo sapiens adaptor-related
protein complex 1, beta 1 subunit (AP1B1), transcript variant 1,
mRNA 873 NM_002107 Homo sapiens H3 histone, family 3A (H3F3A), mRNA
9328 NM_003899 Homo sapiens Rho guanine nucleotide exchange factor
(GEF) 7 (ARHGEF7), transcript variant 1, mRNA 558 NM_003406 Homo
sapiens tyrosine 3-monooxygenase/tryptophan 5- monooxygenase
activation protein, zeta polypeptide (YWHAZ), transcript variant 1,
mRNA 2008 NM_002419 Homo sapiens mitogen-activated protein kinase
kinase kinase 11 (MAP3K11), mRNA 535 NM_001130 Homo sapiens
amino-terminal enhancer of split (AES), mRNA 2395 NM_003379 Homo
sapiens villin 2 (ezrin) (VIL2), mRNA 1356 NM_002636 Homo sapiens
PHD finger protein 1 (PHF1), transcript variant 1, mRNA 640
NM_002622 Homo sapiens prefoldin 1 (PFDN1), mRNA 658 NM_001823 Homo
sapiens creatine kinase, brain (CKB), mRNA 1407 NM_003405 Homo
sapiens tyrosine 3-monooxygenase/tryptophan 5- monooxygenase
activation protein, eta polypeptide (YWHAH), mRNA 2195 NM_002939
Homo sapiens ribonuclease/angiogenin inhibitor (RNH), mRNA 726
NM_003562 Homo sapiens solute carrier family 25 (mitochondrial
carrier; oxoglutarate carrier), member 11 (SLC25A11), mRNA 517
NM_001916 Homo sapiens cytochrome c-1 (CYC1), mRNA 895 NM_002823
Homo sapiens prothymosin, alpha (gene sequence 28) (PTMA), mRNA
3723 NM_003096 Homo sapiens small nuclear ribonucleoprotein
polypeptide G (SNRPG), mRNA 687 NM_003321 Homo sapiens Tu
translation elongation factor, mitochondrial (TUFM), mRNA 1543
NM_003404 Homo sapiens tyrosine 3-monooxygenase/tryptophan 5-
monooxygenase activation protein, beta polypeptide (YWHAB),
transcript variant 1, mRNA 1144 NM_002946 Homo sapiens replication
protein A2, 32 kDa (RPA2), mRNA 537 NM_004356 Homo sapiens CD81
antigen (target of antiproliferative antibody 1) (CD81), mRNA 3638
NM_001743 Homo sapiens calmodulin 2 (phosphorylase kinase, delta)
(CALM2), mRNA 4675 NM_004231 Homo sapiens ATPase, H+ transporting,
lysosomal 14 kDa, V1 subunit F (ATP6V1F), mRNA 997 NM_004893 Homo
sapiens H2A histone family, member Y (H2AFY), transcript variant 2,
mRNA 788 NM_004146 Homo sapiens NADH dehydrogenase (ubiquinone) 1
beta subcomplex, 7, 18 kDa (NDUFB7), mRNA 967 NM_002128 Homo
sapiens high-mobility group box 1 (HMGB1), mRNA 1295 NM_002002 Homo
sapiens Fc fragment of IgE, low affinity II, receptor for (CD23A)
(FCER2), mRNA 969 NM_000858 Homo sapiens guanylate kinase 1 (GUK1),
mRNA 1166 NM_001469 Homo sapiens thyroid autoantigen 70 kDa (Ku
antigen) (G22P1), mRNA 1684 NM_003766 Homo sapiens beclin 1
(coiled-coil, myosin-like BCL2 interacting protein) (BECN1), mRNA
948 NM_003906 Homo sapiens MCM3 minichromosome maintenance
deficient 3 (S. cerevisiae) associated protein (MCM3AP), mRNA 430
NM_000757 Homo sapiens colony stimulating factor 1 (macrophage)
(CSF1), mRNA 797 NM_002149 Homo sapiens hippocalcin-like 1
(HPCAL1), transcript variant 1, mRNA 1026 NM_001694 Homo sapiens
ATPase, H+ transporting, lysosomal 16 kDa, V0 subunit c (ATP6V0C),
mRNA 2105 NM_004047 Homo sapiens ATPase, H+ transporting, lysosomal
21 kDa, V0 subunit c'' (ATP6V0B), mRNA 1212 NM_001696 Homo sapiens
ATPase, H+ transporting, lysosomal 31 kDa, V1 subunit E isoform 1
(ATP6V1E1), mRNA 784 NM_001865 Homo sapiens cytochrome c oxidase
subunit VIIa polypeptide 2 (liver) (COX7A2), nuclear gene encoding
mitochondrial protein, mRNA 1818 NM_004373 Homo sapiens cytochrome
c oxidase subunit VIa polypeptide 1 (COX6A1), nuclear gene encoding
mitochondrial protein, mRNA 5529 NM_000801 Homo sapiens FK506
binding protein 1A, 12 kDa (FKBP1A), transcript variant 12B, mRNA
4273 NM_000992 Homo sapiens ribosomal protein L29 (RPL29), mRNA
6060 NM_000988 Homo sapiens ribosomal protein L27 (RPL27), mRNA
6101 NM_001004 Homo sapiens ribosomal protein, large P2 (RPLP2),
mRNA 5924 NM_001003 Homo sapiens ribosomal protein, large, P1
(RPLP1), mRNA 10300 NM_000405 Homo sapiens GM2 ganglioside
activator protein (GM2A), mRNA 1250 NM_000967 Homo sapiens
ribosomal protein L3 (RPL3), mRNA 7416 NM_001428 Homo sapiens
enolase 1, (alpha) (ENO1), mRNA 3668 NM_000999 Homo sapiens
ribosomal protein L38 (RPL38), mRNA 8302 NM_000997 Homo sapiens
ribosomal protein L37 (RPL37), mRNA 6689 NM_000995 Homo sapiens
ribosomal protein L34 (RPL34), transcript variant 1, mRNA 5424
NM_002948 Homo sapiens ribosomal protein L15 (RPL15), mRNA 5450
NM_002952 Homo sapiens ribosomal protein S2 (RPS2), mRNA 8825
NM_001026 Homo sapiens ribosomal protein S24 (RP524), transcript
variant 2, mRNA 5701 NM_001020 Homo sapiens ribosomal protein S16
(RPS16), mRNA 7477 NM_001018 Homo sapiens ribosomal protein S15
(RPS15), mRNA 6261
NM_001017 Homo sapiens ribosomal protein S13 (RPS13), mRNA 5430
NM_000969 Homo sapiens ribosomal protein L5 (RPL5), mRNA 4653
NM_000985 Homo sapiens ribosomal protein L17 (RPL17), mRNA 4369
NM_000937 Homo sapiens polymerase (RNA) II (DNA directed)
polypeptide A, 220 kDa (POLR2A), mRNA 753 NM_001016 Homo sapiens
ribosomal protein S12 (RPS12), mRNA 8265 NM_002140 Homo sapiens
heterogeneous nuclear ribonucleoprotein K (HNRPK), transcript
variant 1, mRNA 2429 NM_002138 Homo sapiens heterogeneous nuclear
ribonucleoprotein D (AU-rich element RNA binding protein 1, 37 kDa)
(HNRPD), transcript variant 3, mRNA 1157 NM_004499 Homo sapiens
heterogeneous nuclear ribonucleoprotein A/B (HNRPAB), transcript
variant 2, mRNA 654 NM_001014 Homo sapiens ribosomal protein S10
(RPS10), mRNA 8074 NM_002383 Homo sapiens MYC-associated zinc
finger protein (purine-binding transcription factor) (MAZ), mRNA
2580 NM_002467 Homo sapiens v-myc myelocytomatosis viral oncogene
homolog (avian) (MYC), mRNA 537 NM_001436 Homo sapiens fibrillarin
(FBL), mRNA 1408 NM_004069 Homo sapiens adaptor-related protein
complex 2, sigma 1 subunit (AP2S1), transcript variant AP17, mRNA
979 NM_001614 Homo sapiens actin, gamma 1 (ACTG1), mRNA 6560
NM_002355 Homo sapiens mannose-6-phosphate receptor (cation
dependent) (M6PR), mRNA 388 NM_004597 Homo sapiens small nuclear
ribonucleoprotein D2 polypeptide 16.5 kDa (SNRPD2), mRNA 1136
NM_002308 Homo sapiens lectin, galactoside-binding, soluble, 9
(galectin 9) (LGALS9), transcript variant short, mRNA 888 NM_000398
Homo sapiens diaphorase (NADH) (cytochrome b-5 reductase) (DIA1),
nuclear gene encoding mitochondrial protein, transcript variant M,
mRNA 2190 NM_000754 Homo sapiens catechol-O-methyltransferase
(COMT), transcript variant MB-COMT, mRNA 845 NM_002406 Homo sapiens
mannosyl (alpha-1,3-)-glycoprotein beta-
1,2-N-acetylglucosaminyltransferase (MGAT1), mRNA 893 NM_003752
Homo sapiens eukaryotic translation initiation factor 3, subunit 8,
110 kDa (EIF3S8), mRNA 1871 NM_001355 Homo sapiens D-dopachrome
tautomerase (DDT), mRNA 631 NM_004960 Homo sapiens fusion, derived
from t(12; 16) malignant liposarcoma (FUS), mRNA 1019 NM_004729
Homo sapiens Ac-like transposable element (ALTE), mRNA 963
NM_004587 Homo sapiens ribosome binding protein 1 homolog 180 kDa
(dog) (RRBP1), mRNA 658 NM_004552 Homo sapiens NADH dehydrogenase
(ubiquinone) Fe--S protein 5, 15 kDa (NADH-coenzyme Q reductase)
(NDUFS5), mRNA 936 NM_004450 Homo sapiens enhancer of rudimentary
homolog (Drosophila) (ERH), mRNA 1028 NM_004048 Homo sapiens
beta-2-microglobulin (B2M), mRNA 4992 NM_000239 Homo sapiens
lysozyme (renal amyloidosis) (LYZ), mRNA 796 NM_000269 Homo sapiens
non-metastatic cells 1, protein (NM23A) expressed in (NME1), mRNA
887 NM_000431 Homo sapiens mevalonate kinase (mevalonic aciduria)
(MVK), mRNA 753 NM_001247 Homo sapiens ectonucleoside triphosphate
diphosphohydrolase 6 (putative function) (ENTPD6), mRNA 495
NM_003365 Homo sapiens ubiquinol-cytochrome c reductase core
protein I (UQCRC1), mRNA 1026 NM_003329 Homo sapiens thioredoxin
(TXN), mRNA 1002 NM_001069 Homo sapiens tubulin, beta polypeptide
(TUBB), mRNA 1013 NM_000356 Homo sapiens Treacher
Collins-Franceschetti syndrome 1 (TCOF1), mRNA 673 NM_003134 Homo
sapiens signal recognition particle 14 kDa (homologous Alu RNA
binding protein) (SRP14), mRNA 2911 NM_003131 Homo sapiens serum
response factor (c-fos serum response element-binding transcription
factor) (SRF), mRNA 664 NM_000454 Homo sapiens superoxide dismutase
1, soluble (amyotrophic lateral sclerosis 1 (adult)) (SOD1), mRNA
1739 NM_003091 Homo sapiens small nuclear ribonucleoprotein
polypeptides B and B1 (SNRPB), mRNA 1609 NM_003089 Homo sapiens
small nuclear ribonucleoprotein 70 kDa polypeptide (RNP antigen)
(SNRP70), mRNA 1672 NM_003016 Homo sapiens splicing factor,
arginine/serine-rich 2 (SFRS2), mRNA 1476 NM_003952 Homo sapiens
ribosomal protein S6 kinase, 70 kDa, polypeptide 2 (RPS6KB2), mRNA
476 NM_002950 Homo sapiens ribophorin I (RPN1), mRNA 495 NM_002743
Homo sapiens protein kinase C substrate 80 K-H (PRKCSH), mRNA 691
NM_002686 Homo sapiens phenylethanolamine N-methyltransferase
(PNMT), mRNA 501 NM_002654 Homo sapiens pyruvate kinase, muscle
(PKM2), mRNA 2474 NM_002648 Homo sapiens pim-1 oncogene (PIM1),
mRNA 1052 NM_002635 Homo sapiens solute carrier family 25
(mitochondrial carrier; phosphate carrier), member 3 (SLC25A3),
nuclear gene encoding mitochondrial protein, transcript variant 1b,
mRNA 2310 NM_002494 Homo sapiens NADH dehydrogenase (ubiquinone) 1,
subcomplex unknown, 1, 6 kDa (NDUFC1), mRNA 2247 NM_002488 Homo
sapiens NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8
kDa (NDUFA2), mRNA 689 NM_002434 Homo sapiens N-methylpurine-DNA
glycosylase (MPG), mRNA 1808 NM_002415 Homo sapiens macrophage
migration inhibitory factor (glycosylation-inhibiting factor)
(MIF), mRNA 3774 NM_002227 Homo sapiens Janus kinase 1 (a protein
tyrosine kinase) (JAK1), mRNA 990 NM_001536 Homo sapiens HMT1 hnRNP
methyltransferase-like 2 (S. cerevisiae) (HRMT1L2), mRNA 832
NM_000183 Homo sapiens hydroxyacyl-Coenzyme A
dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl- Coenzyme A
hydratase (trifunctional protein), beta subunit (HADHB), mRNA 1087
NM_002085 Homo sapiens glutathione peroxidase 4 (phospholipid
hydroperoxidase) (GPX4), mRNA 1279 NM_001502 Homo sapiens
glycoprotein 2 (zymogen granule membrane) (GP2), mRNA 572 NM_002080
Homo sapiens glutamic-oxaloacetic transaminase 2, mitochondrial
(aspartate aminotransferase 2) (GOT2), nuclear gene encoding
mitochondrial protein, mRNA 1000 NM_001440 Homo sapiens exostoses
(multiple)-like 3 (EXTL3), mRNA 592 NM_003754 Homo sapiens
eukaryotic translation initiation factor 3, subunit 5 epsilon, 47
kDa (EIF3S5), mRNA 1585 NM_003755 Homo sapiens eukaryotic
translation initiation factor 3, subunit 4 delta, 44 kDa (EIF3S4),
mRNA 1085 NM_003757 Homo sapiens eukaryotic translation initiation
factor 3, subunit 2 beta, 36 kDa (EIF3S2), mRNA 622 NM_001360 Homo
sapiens 7-dehydrocholesterol reductase (DHCR7), mRNA 653 NM_001344
Homo sapiens defender against cell death 1 (DAD1), mRNA 812
NM_001914 Homo sapiens cytochrome b-5 (CYB5), nuclear gene encoding
mitochondrial protein, mRNA 667 NM_001834 Homo sapiens clathrin,
light polypeptide (Lcb) (CLTB), transcript variant nonbrain, mRNA
447 NM_001833 Homo sapiens clathrin, light polypeptide (Lca)
(CLTA), transcript variant nonbrain, mRNA 1315 NM_001281 Homo
sapiens cytoskeleton-associated protein 1 (CKAP1), mRNA 1066
NM_001749 Homo sapiens calpain, small subunit 1 (CAPNS1), mRNA 1308
NM_001697 Homo sapiens ATP synthase, H+ transporting, mitochondrial
F1 complex, O subunit (oligomycin sensitivity conferring protein)
(ATP5O), mRNA 1155 NM_001689 Homo sapiens ATP synthase, H+
transporting, mitochondrial F0 complex, subunit c (subunit 9)
isoform 3 (ATP5G3), mRNA 1152 NM_001675 Homo sapiens activating
transcription factor 4 (tax- responsive enhancer element B67)
(ATF4), mRNA 1392 NM_001642 Homo sapiens amyloid beta (A4)
precursor-like protein 2 (APLP2), mRNA 1341 NM_014724 Homo sapiens
zinc finger protein 305 (ZNF305), mRNA 719 NM_005494 Homo sapiens
DnaJ (Hsp40) homolog, subfamily B, member 6 (DNAJB6), transcript
variant 2, mRNA 923 NM_006597 Homo sapiens heat shock 70 kDa
protein 8 (HSPA8), transcript variant 1, mRNA 1650 NM_006623 Homo
sapiens phosphoglycerate dehydrogenase (PHGDH), mRNA 888 NM_015646
Homo sapiens RAP1B, member of RAS oncogene family (RAP1B), mRNA 736
NM_016532 Homo sapiens skeletal muscle and kidney enriched inositol
phosphatase (SKIP), transcript variant 1, mRNA 1529 NM_015292 Homo
sapiens likely ortholog of mouse membrane bound C2 domain
containing protein (MBC2), mRNA 475 NM_005870 Homo sapiens
sin3-associated polypeptide, 18 kDa (SAP18), mRNA 1651 NM_006833
Homo sapiens COP9 subunit 6 (MOV34 homolog, 34 kD) (COPS6), mRNA
1338 NM_005718 Homo sapiens actin related protein 2/3 complex,
subunit 4, 20 kDa (ARPC4), mRNA 433 NM_005719 Homo sapiens actin
related protein 2/3 complex, subunit 3, 21 kDa (ARPC3), mRNA 949
NM_006372 Homo sapiens NS1-associated protein 1 (NSAP1), mRNA 704
NM_005180 Homo sapiens B lymphoma Mo-MLV insertion region (mouse)
(BMI1), mRNA 732 NM_018975 Homo sapiens telomeric repeat binding
factor 2, interacting protein (TERF2IP), mRNA 684 NM_005731 Homo
sapiens actin related protein 2/3 complex, subunit 2, 34 kDa
(ARPC2), transcript variant 2, mRNA 2262 NM_020151 Homo sapiens
START domain containing 7 (STARD7), transcript variant 1, mRNA 1562
NM_005103 Homo sapiens fasciculation and elongation protein zeta 1
(zygin I) (FEZ1), transcript variant 1, mRNA 672 NM_012179 Homo
sapiens F-box only protein 7 (FBXO7), mRNA 865 NM_020360 Homo
sapiens phospholipid scramblase 3 (PLSCR3), mRNA 3645 NM_014891
Homo sapiens PDGFA associated protein 1 (PDAP1), mRNA 1045
NM_005745 Homo sapiens accessory protein BAP31 (DX51357E), mRNA
1525 NM_005418 Homo sapiens suppression of tumorigenicity 5 (ST5),
transcript variant 1, mRNA 2305 NM_006262 Homo sapiens peripherin
(PRPH), mRNA 484 NM_133476 Homo sapiens zinc finger protein 384
(ZNF384), mRNA 448 NM_006570 Homo sapiens Ras-related GTP-binding
protein (RAGA), mRNA 903 NM_006333 Homo sapiens nuclear DNA-binding
protein (CID), mRNA 740 NM_007285 Homo sapiens GABA(A)
receptor-associated protein-like 2 (GABARAPL2), mRNA 1265 NM_006354
Homo sapiens transcriptional adaptor 3-like (TADA3L) transcript
variant 1, mRNA 1060 NM_014302 Homo sapiens Sec61 gamma (SEC61G),
mRNA 644 NM_006118 Homo sapiens HS1 binding protein (HAX1), mRNA
1493 NM_012100 Homo sapiens aspartyl aminopeptidase (DNPEP), mRNA
419 NM_015680 Homo sapiens hypothetical protein CGI-57 (CGI-57),
mRNA 976 NM_030796 Homo sapiens hypothetical protein DKFZp564K0822
(DKFZP564K0822), mRNA 572 NM_024069 Homo sapiens hypothetical
protein MGC2749 (MGC2749), mRNA 573 NM_013234 Homo sapiens muscle
specific gene (M9), mRNA 1056 NM_013310 Homo sapiens hypothetical
protein AF038169 (AF038169), mRNA 1319 NM_018507 Homo sapiens
hypothetical protein PRO1843 (PRO1843), mRNA 1081 NM_017670 Homo
sapiens hypothetical protein FLJ20113 (FLJ20113), mRNA 999
NM_016292 Homo sapiens heat shock protein 75 (TRAP1), mRNA 615
NM_014916 Homo sapiens KIAA1079 protein (KIAA1079), mRNA 772
NM_014696 Homo sapiens KIAA0514 gene product (KIAA0514), mRNA 746
NM_014630 Homo sapiens KIAA0211 gene product (KIAA0211), mRNA 750
NM_014761 Homo sapiens KIAA0174 gene product (KIAA0174), mRNA 679
NM_007286 Homo sapiens synaptopodin (KIAA1029), mRNA 1349 NM_007263
Homo sapiens coatomer protein complex, subunit epsilon (COPE), mRNA
1272 NM_006349 Homo sapiens putative cyclin G1 interacting protein
(CG1I), mRNA 591 NM_006004 Homo sapiens ubiquinol-cytochrome c
reductase hinge protein (UQCRH), mRNA 1285 NM_005787 Homo sapiens
Not56 (D. melanogaster)-like protein (NOT56L), mRNA 458
NM_012412 Homo sapiens histone H2A.F/Z variant (H2AV), transcript
variant 1, mRNA 1070 NM_012401 Homo sapiens plexin B2 (PLXNB2),
mRNA 929 NM_007262 Homo sapiens RNA-binding protein regulatory
subunit (DJ-1), mRNA 1514 NM_007273 Homo sapiens repressor of
estrogen receptor activity (REA), mRNA 1804 NM_021009 Homo sapiens
ubiquitin C (UBC), mRNA 8892 NM_023009 Homo sapiens macrophage
myristoylated alanine-rich C kinase substrate (MACMARCKS), mRNA
2025 NM_015456 Homo sapiens cofactor of BRCA1 (COBRA1), mRNA 848
NM_005053 Homo sapiens RAD23 homolog A (S. cerevisiae) (RAD23A),
mRNA 1015 NM_006830 Homo sapiens ubiquinol-cytochrome c reductase
(6.4 kD) subunit (UQCR), mRNA 1489 NM_005682 Homo sapiens G
protein-coupled receptor 56 (GPR56), mRNA 742 NM_012102 Homo
sapiens arginine-glutamic acid dipeptide (RE) repeats (RERE), mRNA
940 NM_005550 Homo sapiens kinesin family member C3 (KIFC3), mRNA
603 NM_021960 Homo sapiens myeloid cell leukemia sequence 1 (BCL2-
related) (MCL1), mRNA 961 NM_021959 Homo sapiens protein
phosphatase 1, regulatory (inhibitor) subunit 11 (PPP1R11), mRNA
462 NM_014730 Homo sapiens KIAA0152 gene product (KIAA0152), mRNA
713 NM_014402 Homo sapiens low molecular mass ubiquinone-binding
protein (9.5 kD) (QP-C), mRNA 2805 NM_007067 Homo sapiens histone
acetyltransferase (HBOA), mRNA 510 NM_006086 Homo sapiens tubulin,
beta, 4 (TUBB4), mRNA 2239 NM_014972 Homo sapiens KIAA1049 protein
(KIAA1049), mRNA 1011 NM_024092 Homo sapiens hypothetical protein
MGC5508 (MGC5508), mRNA 749 NM_021983 Homo sapiens major
histocompatibility complex, class II, DR beta 4 (HLA-DRB4), mRNA
1095 NM_006510 Homo sapiens ret finger protein (RFP), transcript
variant alpha, mRNA 420 NM_006711 Homo sapiens RNA binding protein
Si, serine-rich domain (RNPS1), transcript variant 1, mRNA 1376
NM_006145 Homo sapiens DnaJ (Hsp40) homolog, subfmaily B, member 1
(DNAJB1), mRNA 667 NM_033142 Homo sapiens chorionic gonadotropin,
beta polypeptide 7 (CGB7), mRNA 773 NM_006351 Homo sapiens
translocase of inner mitochondrial membrane 44 homolog (yeast)
(TIM1V144), mRNA 717 NM_014281 Homo sapiens fuse-binding
protein-interacting repressor (SIABBP1), transcript variant 2, mRNA
632 NM_012106 Homo sapiens binder of Arl Two (BART1), mRNA 760
NM_021975 Homo sapiens v-rel reticuloendotheliosis viral oncogene
homolog A, nuclear factor of kappa light polypeptide gene enhancer
in B-cells 3, p65 (avian) (RELA), mRNA 767 NM_014874 Homo sapiens
mitofusin 2 (MFN2), mRNA 453 NM_006796 Homo sapiens AFG3 ATPase
family gene 3-like 2 (yeast) (AFG3L2), nuclear gene encoding
mitochondrial protein, mRNA 724 NM_006666 Homo sapiens RuvB-like 2
(E. coli) (RUVBL2), mRNA 690 NM_005219 Homo sapiens diaphanous
homolog 1 (Drosophila) (DIAPH1), mRNA 592 NM_033546 Homo sapiens
myosin regulatory light chain (MLC-B), mRNA 1231 NM_032348 Homo
sapiens hypothetical protein MGC3047 (MGC3047), mRNA 553 NM_024798
Homo sapiens hypothetical protein FLJ13952 (FLJ13952), mRNA 2142
NM_021103 Homo sapiens thymosin, beta 10 (TMSB10), mRNA 1890
NM_020195 Homo sapiens HCDI protein (HCDI), mRNA 612 NM_017432 Homo
sapiens prostate tumor over expressed gene 1 (PTOV1), mRNA 1509
NM_014901 Homo sapiens KIAA1100 protein (KIAA1100), mRNA 1999
NM_014694 Homo sapiens KIAA0605 gene product (KIAA0605), mRNA 532
NM_007369 Homo sapiens G-protein coupled receptor (RE2), mRNA 963
NM_006156 Homo sapiens neural precursor cell expressed,
developmentally down-regulated 8 (NEDD8), mRNA 867 NM_006429 Homo
sapiens chaperonin containing TCP1, subunit 7 (eta) (CCT7), mRNA
1434 NM_006513 Homo sapiens seryl-tRNA synthetase (SARS), mRNA 1130
NM_005022 Homo sapiens profilin 1 (PFN1), mRNA 2793 NM_014654 Homo
sapiens syndecan 3 (N-syndecan) (SDC3), mRNA 1082 NM_007209 Homo
sapiens ribosomal protein L35 (RPL35), mRNA 3463 NM_006082 Homo
sapiens tubulin, alpha, ubiquitous (K-ALPHA-1), mRNA 4261 NM_006362
Homo sapiens nuclear RNA export factor 1 (NXF1), mRNA 729 NM_014228
Homo sapiens solute carrier family 6 (neurotransmitter transporter,
L-proline), member 7 (SLC6A7), mRNA 1037 NM_006411 Homo sapiens
1-acylglycerol-3-phosphate O- acyltransferase 1 (lysophosphatidic
acid acyltransferase, alpha) (AGPAT1), mRNA 742 NM_021134 Homo
sapiens mitochondrial ribosomal protein L23 (MRPL23), mRNA 771
NM_021974 Homo sapiens polymerase (RNA) II (DNA directed)
polypeptide F (POLR2F), mRNA 1169 NM_006808 Homo sapiens protein
translocation complex beta (SEC61B), mRNA 679 NM_005617 Homo
sapiens ribosomal protein S14 (RPS14), mRNA 7764 NM_005520 Homo
sapiens heterogeneous nuclear ribonucleoprotein H1 (H) (HNRPH1),
mRNA 2234 NM_006755 Homo sapiens transaldolase 1 (TALDO1), mRNA 874
NM_006010 Homo sapiens arginine-rich, mutated in early stage tumors
(ARMET), mRNA 617 NM_005088 Homo sapiens DNA segment on chromosome
X and Y (unique) 155 expressed sequence (DXYS155E), mRNA 524
NM_014754 Homo sapiens phosphatidylserine synthase 1 (PTDSS1), mRNA
930 NM_021953 Homo sapiens forkhead box M1 (FOXM1), mRNA 567
NM_006908 Homo sapiens ras-related C3 botulinum toxin substrate 1
(rho family, small GTP binding protein Rac1) (RAC1), transcript
variant Rac1, mRNA 1978 NM_014231 Homo sapiens vesicle-associated
membrane protein 1 (synaptobrevin 1) (VAMP1), transcript variant
VAMP- 1A, mRNA 745 NM_014833 Homo sapiens KIAA0618 gene product
(KIAA0618), mRNA 607 NM_005157 Homo sapiens v-abl Abelson murine
leukemia viral oncogene homolog 1 (ABL1), transcript variant a,
mRNA 777 NM_006325 Homo sapiens RAN, member RAS oncogene family
(RAN), mRNA 3100 NM_007245 Homo sapiens ataxin 2 related protein
(A2LP), transcript variant 1, mRNA 564 NM_007008 Homo sapiens
reticulon 4 (RTN4), mRNA 1267 NM_006782 Homo sapiens zinc finger
protein-like 1 (ZFPL1), mRNA 712 NM_006694 Homo sapiens jumping
translocation breakpoint (JTB), mRNA 2394 NM_006703 Homo sapiens
nudix (nucleoside diphosphate linked moiety X)-type motif 3
(NUDT3), mRNA 566 NM_006032 Homo sapiens copine VI (neuronal)
(CPNE6), mRNA 1540 NM_012227 Homo sapiens Pseudoautosomal
GTP-binding protein- like (PGPL), mRNA 494 NM_014604 Homo sapiens
Tax interaction protein 1 (TIP-1), mRNA 748 NM_021642 Homo sapiens
Fc fragment of IgG, low affinity Ha, receptor for (CD32) (FCGR2A),
mRNA 772 NM_005354 Homo sapiens jun D proto-oncogene (JUND), mRNA
4967 NM_020529 Homo sapiens nuclear factor of kappa light
polypeptide gene enhancer in B-cells inhibitor, alpha (NFKBIA),
mRNA 922 NM_005561 Homo sapiens lysosomal-associated membrane
protein 1 (LAMP1), mRNA 2865 NM_014774 Homo sapiens KIAA0494 gene
product (KIAA0494), mRNA 604 NM_014390 Homo sapiens EBNA-2
co-activator (100 kD) (p100), mRNA 867 NM_014623 Homo sapiens
male-enhanced antigen (MEA), mRNA 548 NM_014453 Homo sapiens
putative breast adenocarcinoma marker (32 kD) (BC-2), mRNA 597
NM_012127 Homo sapiens Cip1-interacting zinc finger protein (CIZ1),
mRNA 1051 NM_012099 Homo sapiens CD3-epsilon-associated protein;
antisense to ERCC-1 (ASE-1), mRNA 472 NM_006888 Homo sapiens
calmodulin 1 (phosphorylase kinase, delta) (CALM1), mRNA 2161
NM_006867 Homo sapiens RNA-binding protein gene with multiple
splicing (RBPMS), mRNA 1255 NM_006743 Homo sapiens RNA binding
motif protein 3 (RBM3), mRNA 2949 NM_006688 Homo sapiens
C1q-related factor (CRF), mRNA 3604 NM_006295 Homo sapiens
valyl-tRNA synthetase 2 (VARS2), mRNA 721 NM_006283 Homo sapiens
transforming, acidic coiled-coil containing protein 1 (TACC1), mRNA
867 NM_006221 Homo sapiens protein (peptidyl-prolyl cis/trans
isomerase) NIMA-interacting 1 (PIN1), mRNA 561 NM_006148 Homo
sapiens LIM_and SH3 protein 1 (LASP1), mRNA 1067 NM_005954 Homo
sapiens metallothionein 3 (growth inhibitory factor (neurotrophic))
(MT3), mRNA 2311 NM_006003 Homo sapiens ubiquinol-cytochrome c
reductase, Rieske iron-sulfur polypeptide 1 (UQCRFS1), nuclear gene
encoding mitochondrial protein, mRNA 951 NM_005998 Homo sapiens
chaperonin containing TCP1, subunit 3 (gamma) (CCT3), mRNA 1098
NM_005997 Homo sapiens transcription factor-like 1 (TCFL1), mRNA
505 NM_005629 Homo sapiens solute carrier family 6
(neurotransmitter transporter, creatine), member 8 (SLC6A8), mRNA
628 NM_005548 Homo sapiens lysyl-tRNA synthetase (KARS), mRNA 1193
NM_005545 Homo sapiens immunoglobulin superfamily containing
leucine-rich repeat (ISLR), mRNA 796 NM_005507 Homo sapiens cofilin
1 (non-muscle) (CFL1), mRNA 5155 NM_005381 Homo sapiens nucleolin
(NCL), mRNA 2043 NM_005439 Homo sapiens myeloid leukemia factor 2
(MLF2), mRNA 697 NM_006445 Homo sapiens PRP8 pre-mRNA processing
factor 8 homolog (yeast) (PRPF8), mRNA 1384 NM_019059 Homo sapiens
homolog of Tom7 (S. cerevisiae) (TOM7), mRNA 2364 NM_006039 Homo
sapiens mannose receptor, C type 2 (MRC2), mRNA 564 NM_006066 Homo
sapiens aldo-keto reductase family 1, member A1 (aldehyde
reductase) (AKR1A1), transcript variant 1, mRNA 879 NM_013318 Homo
sapiens hypothetical protein LQFBS-1 (LQFBS-1), mRNA 485 NM_006098
Homo sapiens guanine nucleotide binding protein (G protein), beta
polypeptide 2-like 1 (GNB2L1), mRNA 7556 NM_007359 Homo sapiens
M1LN51 protein (M1LN51), mRNA 975 NM_017510 Homo sapiens gp25L2
protein (HSGP25L2G), mRNA 1032 NM_015399 Homo sapiens breast cancer
metastasis-suppressor 1 (BRMS1), mRNA 476 NM_014508 Homo sapiens
apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C
(APOBEC3C), mRNA 816 NM_018955 Homo sapiens ubiquitin B (UBB), mRNA
6074 NM_006368 Homo sapiens cAMP responsive element binding protein
3 (luman) (CREB3), mRNA 533 NM_015024 Homo sapiens RAN binding
protein 16 (RANBP16), mRNA 559 NM_031420 Homo sapiens mitochondrial
ribosomal protein L9 (MRPL9), nuclear gene encoding mitochondrial
protein, mRNA 476 NM_013232 Homo sapiens programmed cell death 6
(PDCD6), mRNA 816 NM_005917 Homo sapiens malate dehydrogenase 1,
NAD (soluble) (MDH1), mRNA 1724 NM_032801 Homo sapiens junctional
adhesion molecule 3 (JAM3), mRNA 624 NM_030662 Homo sapiens
mitogen-activated protein kinase kinase 2 (MAP2K2), mRNA 663
NM_006268 Homo sapiens requiem, apoptosis response zinc finger gene
(REQ), mRNA 784 NM_006826 Homo sapiens tyrosine
3-monooxygenase/tryptophan 5- monooxygenase activation protein,
theta polypeptide (YWHAQ), mRNA 1917 NM_144582 Homo sapiens
hypothetical protein MGC32043 (MGC32043), mRNA 712 NM_144565 Homo
sapiens hypothetical protein FLJ32334 (FLJ32334), mRNA 5319
NM_005984 Homo sapiens solute carrier family 25 (mitochondrial
carrier; citrate transporter), member 1 (SLC25A1), mRNA 620
NM_017828 Homo sapiens hypothetical protein FLJ20452 (FLJ20452),
mRNA 546 NM_020150 Homo sapiens SARI protein (SARI), mRNA 581
NM_014610 Homo sapiens alpha glucosidase II alpha subunit (G2AN),
mRNA 1293 NM_014225 Homo sapiens protein phosphatase 2 (formerly
2A), regulatory subunit A (PR 65), alpha isoform (PPP2R1A), mRNA
1687 NM_006937 Homo sapiens SMT3 suppressor of mif two 3 homolog 2
(yeast) (SMT3H2), mRNA 2940 NM_005726 Homo sapiens Ts translation
elongation factor, mitochondrial (TSFM), mRNA 408 NM_005347 Homo
sapiens heat shock 70 kDa protein 5 (glucose- regulated protein, 78
kDa) (HSPA5), mRNA 1111 NM_014255 Homo sapiens transmembrane
protein 4 (TMEM4), mRNA 505 NM_006815 Homo sapiens coated vesicle
membrane protein (RNP24), mRNA 1642 NM_005456 Homo sapiens
mitogen-activated protein kinase 8 interacting protein 1
(MAPK8IP1), mRNA 885 NM_005273 Homo sapiens guanine nucleotide
binding protein (G protein), beta polypeptide 2 (GNB2), mRNA 1478
NM_007260 Homo sapiens lysophospholipase II (LYPLA2), mRNA 2000
NM_007103 Homo sapiens NADH dehydrogenase (ubiquinone) flavoprotein
1, 51 kDa (NDUFV1), mRNA 803 NM_017797 Homo sapiens BTB (POZ)
domain containing 2 (BTBD2), mRNA 1030 NM_016237 Homo sapiens
anaphase promoting complex subunit 5 (ANAPC5), mRNA 935 NM_005801
Homo sapiens putative translation initiation factor (SUI1), mRNA
1058 NM_005216 Homo sapiens
dolichyl-diphosphooligosaccharide-protein glycosyltransferase
(DDOST), mRNA 1421 NM_016457 Homo sapiens protein kinase D2 (PKD2),
mRNA 662 NM_006442 Homo sapiens DR1-associated protein 1 (negative
cofactor 2 alpha) (DRAP1), mRNA 561 NM_021019 Homo sapiens myosin,
light polypeptide 6, alkali, smooth muscle and non-muscle (MYL6),
transcript variant 1, mRNA 5933 NM_005112 Homo sapiens WD repeat
domain 1 (WDR1), transcript variant 2, mRNA 809 NM_005370 Homo
sapiens mel transforming oncogene (derived from cell line
NK14)-RAB8 homolog (MEL), mRNA 682 NM_006289 Homo sapiens talin 1
(TLN1), mRNA 1811 NM_005698 Homo sapiens secretory carrier membrane
protein 3 (SCAMP3), transcript variant 1, mRNA 602 NM_ 024011 Homo
sapiens cell division cycle 2-like 2 (CDC2L2), transcript variant
1, mRNA 430 NM_005105 Homo sapiens RNA binding motif protein 8A
(RBM8A), mRNA 785 NM_ 006013 Homo sapiens ribosomal protein L10
(RPL10), mRNA 10721 NM_005786 Homo sapiens serologically defined
colon cancer antigen 33 (SDCCAG33), mRNA 1435 NM_007104 Homo
sapiens ribosomal protein L10a (RPL10A), mRNA 3006 NM_005762 Homo
sapiens tripartite motif-containing 28 (TRIM28), mRNA 1473
NM_012138 Homo sapiens apoptosis antagonizing transcription factor
(AATF), mRNA 504 NM_015318 Homo sapiens Rho-specific guanine
nucleotide exchange factor p114 (P114-RHO-GEF), mRNA 405 NM_012423
Homo sapiens ribosomal protein L13a (RPL13A), mRNA 9545 NM_021128
Homo sapiens polymerase (RNA) II (DNA directed) polypeptide L, 7.6
kDa (POLR2L), mRNA 1524 NM_032635 Homo sapiens seven transmembrane
domain protein (NIFIE14), mRNA 1121 NM_005080 Homo sapiens X-box
binding protein 1 (XBP1), mRNA 1772 NM_006389 Homo sapiens hypoxia
up-regulated 1 (HYOU1), mRNA 1076 NM_024112 Homo sapiens chromosome
9 open reading frame 16 (C9orf16), mRNA 598 NM_006817 Homo sapiens
chromosome 12 open reading frame 8 (C12orf8), mRNA 910 NM_022830
Homo sapiens hypothetical protein FLJ22347 (FLJ22347), mRNA 6021
NM_019884 Homo sapiens glycogen synthase kinase 3 alpha (GSK3A),
mRNA 963 NM_021107 Homo sapiens mitochondrial ribosomal protein S12
(MRPS12), nuclear gene encoding mitochondrial protein, transcript
variant 1, mRNA 828 NM_021074 Homo sapiens NADH dehydrogenase
(ubiquinone) flavoprotein 2, 24 kDa (NDUFV2), mRNA 539 NM_014944
Homo sapiens calsyntenin 1 (CLSTN1), mRNA 1620 NM_014764 Homo
sapiens DAZ associated protein 2 (DAZAP2), mRNA 1802 NM_ 015343
Homo sapiens likely ortholog of Xenopus dullard (HSA011916), mRNA
933 NM_014420 Homo sapiens dickkopf homolog 4 (Xenopus laevis)
(DKK4), mRNA 426 NM_005884 Homo sapiens p21(CDKN1A)-activated
kinase 4 (PAK4), mRNA 375 NM_012407 Homo sapiens protein kinase C,
alpha binding protein (PRKCABP), mRNA 553 NM_012111 Homo sapiens
chromosome 14 open reading frame 3 (C14orf3), mRNA 717 NM_007144
Homo sapiens zinc finger protein 144 (Mel-18) (ZNF144), mRNA 798
NM_007108 Homo sapiens transcription elongation factor B (SIII),
polypeptide 2 (18 kDa, elongin B) (TCEB2), mRNA 1192 NM_007278 Homo
sapiens GABA(A) receptor-associated protein (GABARAP), mRNA 2335
NM_007100 Homo sapiens ATP synthase, H+ transporting, mitochondrial
F0 complex, subunit e (ATP5I), mRNA 2623 NM_006936 Homo sapiens
SMT3 suppressor of mif two 3 homolog 1 (yeast) (SMT3H1), mRNA 1187
NM_006899 Homo sapiens isocitrate dehydrogenase 3 (NAD+) beta
(IDH3B), mRNA 565 NM_006801 Homo sapiens KDEL (Lys-Asp-Glu-Leu)
(SEQ ID NO: 1) endoplasmic reticulum protein retention receptor 1
(KDELR1), mRNA 1270 NM_006612 Homo sapiens kinesin family member 1C
(KIF1C), mRNA 600 NM_006659 Homo sapiens tubulin, gamma complex
associated protein 2 (TUBGCP2), mRNA 701 NM_006595 Homo sapiens
apoptosis inhibitor 5 (API5), mRNA 1173 NM_006401 Homo sapiens
acidic (leucine-rich) nuclear phosphoprotein 32 family, member B
(ANP32B), mRNA 2354 NM_006423 Homo sapiens Rab acceptor 1
(prenylated) (RABAC1), mRNA 1706 NM_006460 Homo sapiens
HMBA-inducible (HIS1), mRNA 369 NM_006356 Homo sapiens ATP
synthase, H+ transporting, mitochondrial F0 complex, subunit d
(ATP5H), mRNA 1047 NM_005891 Homo sapiens acetyl-Coenzyme A
acetyltransferase 2 (acetoacetyl Coenzyme A thiolase) (ACAT2), mRNA
911 NM_005839 Homo sapiens serine/arginine repetitive matrix 1
(SRRM1), mRNA 745 NM_005594 Homo sapiens
nascent-polypeptide-associated complex alpha polypeptide (NACA),
mRNA 3678 NM_005340 Homo sapiens histidine triad nucleotide binding
protein 1 (HINT1), mRNA 2270 NM_005175 Homo sapiens ATP synthase,
H+ transporting, mitochondrial F0 complex, subunit c (subunit 9),
isoform 1 (ATP5G1), mRNA 1266 NM_005165 Homo sapiens aldolase C,
fructose-bisphosphate (ALDOC), mRNA 1052 NM_005001 Homo sapiens
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5 kDa
(NDUFA7), mRNA 806 NM_001402 NM_001958 NM_001961 NM_002714
NM_002808 NM_002809 NM_004898 NM_007182 NM_032378
[0252] In various embodiments of the present invention, the
reference value is chromosome 15 centromere copy number. In various
embodiments, the reference value for chromosome 15q26 copy number
is chromosome 15 centromere copy number.
[0253] The chromosome 15q26 copy number and chromosome 15
centromere copy number can be ascertained by various methods. For
example, they can be ascertained through chip based measurements
with or without a normal reference, or by using centromeric FISH
probes, which is an assay for testing for copy number changes using
microscopy.
[0254] In various embodiments, the number of chromosome 15
centromere probes is compared to the number of 15q26.1 probes, in
each cell using a microscope. If the numbers match, there is no
relative gain of 15q26. Increase in this context can be a numerical
increase, e.g., 2-3 copies. In various embodiments, copy gain can
be defined by the absolute copy number determined in an interphase
FISH assay averaged by counting a minimum of 20 tumor cells. In
various embodiments, copy gain can be defined as the ratio of
15q26/centromere 15 determined in an interphase FISH assay counting
both spots (15q26 and cent15) in the same cells and averaging over
a minimum of 20 cells. In various embodiments, copy gain can be
determined using a normalized genome wide assay such as SNP array,
genome sequencing and the like, wherein the normalization is done
using the ASCAT algorithm or other appropriate algorithms. In
various embodiments, the cutpoints can be anything above normal,
which is 2 absolute copies of 15q26, or ratio >1 for
15q26/cent15. Due to the typical noise in these assays, in certain
embodiments, the cutoff is defined by adding a standard error.
Accordingly, copy >2.6 or ratio >1.3 signify copy number
gain.
[0255] Thus, in various embodiments, a copy number gain of over 2.6
or a ratio of over 1.3 indicates a copy number gain in the
sample.
[0256] In other embodiments, the reference value for chromosome
15q26 is determined from a non-cancer cell sample from the subject
or a member of the same species to which the subject belongs. In
certain embodiments, the reference value is determined from a
non-cancerous cell or tissue sample that is the same type of cell
or tissue as the cancer cell from the subject. In certain
embodiments, the reference value is determined from a non-cancerous
cell or tissue sample that is not the same type of cell or tissue
as the cancer cell from the subject. In various embodiments,
array-based or sequencing-based technologies can be used wherein
the reference can be from patients' normal cells (e.g., blood), or
it can be a collection of blood samples.
[0257] Copy number abnormalities can be detected using methods,
such as, for example, array CGH using BAC, cDNA and/or
oligonucleotide arrays; microsatellite markers; STRs, RFLPS;
etc.
[0258] Additional methods for evaluating copy number of nucleic
acid in a sample include, but are not limited to,
hybridization-based assays. One method for evaluating the copy
number of encoding nucleic acid in a sample involves a Southern
Blot. In a Southern Blot, the genomic DNA (typically fragmented and
separated on an electrophoretic gel) is hybridized to a probe
specific for the target region. Comparison of the intensity of the
hybridization signal from the probe for the target region with
control probe signal from analysis of normal genomic DNA (e.g., a
non-amplified portion of the same or related cell, tissue, organ,
etc.) provides an estimate of the relative copy number of the
target nucleic acid. Alternatively, a Northern blot may be utilized
for evaluating the copy number of encoding nucleic acid in a
sample. In a Northern blot, mRNA is hybridized to a probe specific
for the target region. Comparison of the intensity of the
hybridization signal from the probe for the target region with
control probe signal from analysis of normal mRNA (e.g., a
non-amplified portion of the same or related cell, tissue, organ,
etc.) provides an estimate of the relative copy number of the
target nucleic acid. Similar methods for determining copy number
can be performed using transcriptional arrays, which are well-known
in the art.
[0259] An alternative means for determining the copy number is in
situ hybridization (e.g., Angerer (1987) Meth. Enzymol 152: 649).
Generally, in situ hybridization comprises the following steps: (1)
fixation of tissue or biological structure to be analyzed; (2)
prehybridization treatment of the biological structure to increase
accessibility of target DNA, and to reduce nonspecific binding; (3)
hybridization of the mixture of nucleic acids to the nucleic acid
in the biological structure or tissue; (4) post-hybridization
washes to remove nucleic acid fragments not bound in the
hybridization and (5) detection of the hybridized nucleic acid
fragments. The reagent used in each of these steps and the
conditions for use vary depending on the particular
application.
[0260] Preferred hybridization-based assays include, but are not
limited to, traditional "direct probe" methods such as Southern
blots or in situ hybridization (e.g., FISH and FISH plus SKY), and
"comparative probe" methods such as comparative genomic
hybridization (CGH), e.g., cDNA-based or oligonucleotide-based CGH.
The methods can be used in a wide variety of formats including, but
not limited to, substrate (e.g. membrane or glass) bound methods or
array-based approaches.
[0261] In a typical in situ hybridization assay, cells are fixed to
a solid support, typically a glass slide. If a nucleic acid is to
be probed, the cells are typically denatured with heat or alkali.
The cells are then contacted with a hybridization solution at a
moderate temperature to permit annealing of labeled probes specific
to the nucleic acid sequence encoding the protein. The targets
(e.g., cells) are then typically washed at a predetermined
stringency or at an increasing stringency until an appropriate
signal to noise ratio is obtained.
[0262] The probes are typically labeled, e.g., with radioisotopes
or fluorescent reporters. Preferred probes are sufficiently long so
as to specifically hybridize with the target nucleic acid(s) under
stringent conditions. The preferred size range is from about 200
bases to about 1000 bases.
[0263] In some applications it is necessary to block the
hybridization capacity of repetitive sequences. Thus, in some
embodiments, tRNA, human genomic DNA, or Cot-I DNA is used to block
non-specific hybridization.
[0264] In CGH methods, a first collection of nucleic acids (e.g.,
from a sample, e.g., a possible tumor) is labeled with a first
label, while a second collection of nucleic acids (e.g., a control,
e.g., from a healthy cell/tissue) is labeled with a second label.
The ratio of hybridization of the nucleic acids is determined by
the ratio of the two (first and second) labels binding to each
fiber in the array. Where there are chromosomal deletions or
multiplications, differences in the ratio of the signals from the
two labels will be detected and the ratio will provide a measure of
the copy number. Array-based CGH may also be performed with
single-color labeling (as opposed to labeling the control and the
possible tumor sample with two different dyes and mixing them prior
to hybridization, which will yield a ratio due to competitive
hybridization of probes on the arrays). In single color CGH, the
control is labeled and hybridized to one array and absolute signals
are read, and the possible tumor sample is labeled and hybridized
to a second array (with identical content) and absolute signals are
read. Copy number difference is calculated based on absolute
signals from the two arrays. Hybridization protocols suitable for
use with the methods of the invention are described, e.g., in
Albertson (1984) EMBO J. 3: 1227-1234; Pinkel (1988) Proc. Natl.
Acad. Sci. USA 85: 9138-9142; EPO Pub. No. 430,402; Methods in
Molecular Biology, Vol. 33: In situ Hybridization Protocols, Choo,
ed., Humana Press, Totowa, N.J. (1994), etc. In one embodiment, the
hybridization protocol of Pinkel, et al. (1998) Nature Genetics 20:
207-211, or of Kallioniemi (1992) Proc. Natl Acad Sci USA
89:5321-5325 (1992) is used.
[0265] The methods of the invention are particularly well suited to
array-based hybridization formats. Array-based CGH is described in
U.S. Pat. No. 6,455,258, the contents of which are incorporated
herein by reference. In still another embodiment,
amplification-based assays can be used to measure copy number. In
such amplification-based assays, the nucleic acid sequences act as
a template in an amplification reaction (e.g., Polymerase Chain
Reaction (PCR). In a quantitative amplification, the amount of
amplification product will be proportional to the amount of
template in the original sample. Comparison to appropriate
controls, e.g. healthy tissue, provides a measure of the copy
number.
[0266] Methods of "quantitative" amplification are well known to
those of skill in the art. For example, quantitative PCR involves
simultaneously co-amplifying a known quantity of a control sequence
using the same primers. This provides an internal standard that may
be used to calibrate the PCR reaction. Detailed protocols for
quantitative PCR are provided in Innis, et al. (1990) PCR
Protocols, A Guide to Methods and Applications, Academic Press,
Inc. N.Y.). Measurement of DNA copy number at microsatellite loci
using quantitative PCR anlaysis is described in Ginzonger, et al.
(2000) Cancer Research 60:5405-5409. The known nucleic acid
sequence for the genes is sufficient to enable one of skill in the
art to routinely select primers to amplify any portion of the gene.
Fluorogenic quantitative PCR may also be used in the methods of the
invention. In fluorogenic quantitative PCR, quantitation is based
on amount of fluorescence signals, e.g., TaqMan and sybr green.
[0267] Other suitable amplification methods include, but are not
limited to, ligase chain reaction (LCR) (see Wu and Wallace (1989)
Genomics 4: 560, Landegren, et al. (1988) Science 241:1077, and
Barringer et al. (1990) Gene 89: 117), transcription amplification
(Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173),
self-sustained sequence replication (Guatelli, et al. (1990) Proc.
Nat. Acad. Sci. USA 87: 1874), dot PCR, and linker adapter PCR,
etc.
[0268] In still other embodiments of the methods provided herein,
sequencing of individual nucleic molecules (or their amplification
products) is performed, as an alternative to hybridization-based
assays, using nucleic acid sequencing techniques. In one
embodiment, a high throughput parallel sequencing technique that
isolates single nucleic acid molecules of a population of nucleic
acid molecules prior to sequencing may be used. Such strategies may
use so-called "next generation sequencing systems" including,
without limitation, sequencing machines and/or strategies well
known in the art, such as those developed by Illumina/Solexa (the
Genome Analyzer; Bennett et al. (2005) Pharmacogenomics, 6:373-20
382), by Applied Biosystems, Inc. (the SOLiD Sequencer;
solid.appliedbiosystems.com), by Roche (e.g., the 454 GS FLX
sequencer; Margulies et al. (2005) Nature, 437:376-380; U.S. Pat.
Nos. 6,274,320; 6,258,568; 6,210,891), by Heliscope.TM. system from
Helicos Biosciences (see, e.g., U.S. Patent App. Pub. No.
2007/0070349), and by others. Other sequencing strategies such as
stochastic sequencing (e.g., as developed by Oxford Nanopore) may
also be used, e.g., as described in International Application No.
PCT/GB2009/001690 (pub. no. WO/2010/004273). All of the copy number
determining strategies described herein can similarly be applied to
any of other nucleic acid-based analysis described herein, such as
for BLM, FANCI, or 15q26 the like described further below.
Therapies
[0269] These therapies can be selected, used, administered, etc.,
in accordance with various embodiment of the present invention.
[0270] Platinum-comprising therapy, include but are not limited
platinum chemotherapeutic agents, such as cisplatin, carboplatin,
oxaliplatin, nedaplatin, and iproplatin. Other antineoplastic
platinum coordination compounds are well known in the art, can be
modified according to well-known methods in the art, and include
the compounds disclosed in U.S. Pat. Nos. 4,996,337, 4,946,954,
5,091,521, 5,434,256, 5,527,905, and 5,633,243, all of which are
incorporated herein by reference. In various embodiments described
herein, the platinum comprising cancer therapy comprises
cisplatinum or cis-diamminedichloroplatinum, phenanthriplatin,
carboplatin, oxaliplatin, or a platinum complex that is activated
by ultraviolet A light.
[0271] In various embodiments, non-platinum comprising therapies
include, non-platinum chemotherapy. Non-platinum chemotherapy may
be, but is not limited to, those selected from among the following
groups of compounds: cytotoxic antibiotics, antimetabolities,
anti-mitotic agents, alkylating agents, arsenic compounds, DNA
topoisomerase inhibitors, taxanes, nucleoside analogues, plant
alkaloids, and toxins; and synthetic derivatives thereof. Exemplary
compounds include, but are not limited to, alkylating agents:
treosulfan, and trofosfamide; plant alkaloids: vinblastine,
paclitaxel, docetaxol; DNA topoisomerase inhibitors: doxorubicin,
epirubicin, etoposide, camptothecin, topotecan, irinotecan,
teniposide, crisnatol, and mitomycin; anti-folates: methotrexate,
mycophenolic acid, and hydroxyurea; pyrimidine analogs:
5-fluorouracil, doxifluridine, and cytosine arabinoside; purine
analogs: mercaptopurine and thioguanine; DNA antimetabolites:
2'-deoxy-5-fluorouridine, aphidicolin glycinate, and
pyrazoloimidazole; and antimitotic agents: halichondrin,
colchicine, and rhizoxin. Compositions comprising one or more
chemotherapeutic agents (e.g., FLAG, CHOP) may also be used. FLAG
comprises fludarabine, cytosine arabinoside (Ara-C) and G-CSF. CHOP
comprises cyclophosphamide, vincristine, doxorubicin, and
prednisone. In another embodiments, PARP (e.g., PARP-1 and/or
PARP-2) inhibitors are used and such inhibitors are well known in
the art (e.g., Olaparib, ABT-888, BSI-201, BGP-15 (N-Gene Research
Laboratories, Inc.); INO-1001 (Inotek Pharmaceuticals Inc.); PJ34
(Soriano et al., 2001; Pacher et al., 2002b); 3-aminobenzamide
(Trevigen); 4-amino-1,8-naphthalimide; (Trevigen);
6(5H)-phenanthridinone (Trevigen); benzamide (U.S. Pat. Re.
36,397); and NU1025 (Bowman et al.). The foregoing examples of
non-platinum chemotherapeutic agents are illustrative, and are not
intended to be limiting.
[0272] In various embodiments, non-platinum comprising therapies
include, for example, radiation therapy. The radiation used in
radiation therapy can be ionizing radiation. Radiation therapy can
also be gamma rays, X-rays, or proton beams. Examples of radiation
therapy include, but are not limited to, external-beam radiation
therapy, interstitial implantation of radioisotopes (I-125,
palladium, iridium), radioisotopes such as strontium-89, thoracic
radiation therapy, intraperitoneal P-32 radiation therapy, and/or
total abdominal and pelvic radiation therapy. For a general
overview of radiation therapy, see Hellman, Chapter 16: Principles
of Cancer Management: Radiation Therapy, 6th edition, 2001, DeVita
et al., eds., J. B. Lippencott Company, Philadelphia. The radiation
therapy can be administered as external beam radiation or
teletherapy wherein the radiation is directed from a remote source.
The radiation treatment can also be administered as internal
therapy or brachytherapy wherein a radioactive source is placed
inside the body close to cancer cells or a tumor mass. Also
encompassed is the use of photodynamic therapy comprising the
administration of photosensitizers, such as hematoporphyrin and its
derivatives, Vertoporfin (BPD-MA), phthalocyanine, photosensitizer
Pc4, demethoxy-hypocrellin A; and 2BA-2-DMHA.
[0273] In various embodiments, non-platinum comprising therapies
include, for example, immunotherapy. Immunotherapy may comprise,
for example, use of cancer vaccines and/or sensitized antigen
presenting cells. The immunotherapy can involve passive immunity
for short-term protection of a host, achieved by the administration
of pre-formed antibody directed against a cancer antigen or disease
antigen (e.g., administration of a monoclonal antibody, optionally
linked to a chemotherapeutic agent or toxin, to a tumor antigen).
Immunotherapy can also focus on using the cytotoxic
lymphocyte-recognized epitopes of cancer cell lines.
[0274] In various embodiments, non-platinum comprising therapies
include, for example, hormonal therapy, Hormonal therapeutic
treatments can comprise, for example, hormonal agonists, hormonal
antagonists (e.g., flutamide, bicalutamide, tamoxifen, raloxifene,
leuprolide acetate (LUPRON), LH-RH antagonists), inhibitors of
hormone biosynthesis and processing, and steroids (e.g.,
dexamethasone, retinoids, deltoids, betamethasone, cortisol,
cortisone, prednisone, dehydrotestosterone, glucocorticoids,
mineralocorticoids, estrogen, testosterone, progestins), vitamin A
derivatives (e.g., all-trans retinoic acid (ATRA)); vitamin D3
analogs; antigestagens (e.g., mifepristone, onapristone), or
antiandrogens (e.g., cyproterone acetate).
[0275] In various embodiments described herein, the anthracycline
is epirubincin or doxorubicin.
[0276] The duration and/or dose of treatment with anti-cancer
therapies may vary according to the particular anti-cancer agent or
combination thereof. An appropriate treatment time for a particular
cancer therapeutic agent will be appreciated by the skilled
artisan. The invention contemplates the continued assessment of
optimal treatment schedules for each cancer therapeutic agent,
where the genetic signature of the cancer of the subject as
determined by the methods of the invention is a factor in
determining optimal treatment doses and schedules.
Cancers for which the Genetic Signature can be Determined
[0277] The methods of the invention can be used to determine the
genetic signature of many different cancers. Specific examples of
types of cancers for which the genetic signature can be determined
by the methods encompassed by the invention include, but are not
limited to, human sarcomas and carcinomas, e.g., fibrosarcoma,
myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma,
chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma,
lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's
tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma,
colorectal cancer, pancreatic cancer, breast cancer, ovarian
cancer, prostate cancer, squamous cell carcinoma, basal cell
carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland
carcinoma, papillary carcinoma, papillary adenocarcinomas,
cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma,
renal cell carcinoma, hepatoma, bile duct carcinoma, liver cancer,
choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor,
cervical cancer, bone cancer, brain tumor, testicular cancer, lung
carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial
carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma,
ependymoma, pinealoma, hemangioblastoma, acoustic neuroma,
oligodendroglioma, meningioma, melanoma, neuroblastoma,
retinoblastoma; leukemias, e.g., acute lymphocytic leukemia and
acute myelocytic leukemia (myeloblastic, promyelocytic,
myelomonocytic, monocytic and erythroleukemia); chronic leukemia
(chronic myelocytic (granulocytic) leukemia and chronic lymphocytic
leukemia); and polycythemia vera, lymphoma (Hodgkin's disease and
non-Hodgkin's disease), multiple myeloma, Waldenstrom's
macroglobulinemia, and heavy chain disease.
[0278] In some embodiments, the cancer whose genetic signature is
determined by the method of the invention is an epithelial cancer
such as, but not limited to, bladder cancer, breast cancer,
cervical cancer, colon cancer, gynecologic cancers, renal cancer,
laryngeal cancer, lung cancer, oral cancer, head and neck cancer,
ovarian cancer, pancreatic cancer, prostate cancer, or skin cancer.
In other embodiments, the cancer is breast cancer, prostate cancer,
lung cancer, or colon cancer. In still other embodiments, the
epithelial cancer is non-small-cell lung cancer, nonpapillary renal
cell carcinoma, cervical carcinoma, ovarian carcinoma (e.g., serous
ovarian carcinoma), or breast carcinoma. The epithelial cancers may
be characterized in various other ways including, but not limited
to, serous, endometrioid, mucinous, clear cell, brenner, or
undifferentiated. In still other embodiments, the cancer is breast
cancer, ovarian cancer or lung cancer. In particular embodiments,
the cancer is triple negative breast cancer.
Subjects
[0279] In various embodiments, the subject for whom predicted
efficacy of an anti-cancer therapy is determined, is a mammal
(e.g., mouse, rat, primate, non-human mammal, domestic animal such
as dog, cat, cow, horse), and is preferably a human. In another
embodiment of the methods of the invention, the subject has not
undergone chemotherapy or radiation therapy. In alternative
embodiments, the subject has undergone chemotherapy or radiation
therapy (e.g., such as with cisplatin, carboplatin, and/or taxane).
In related embodiments, the subject has not been exposed to levels
of radiation or chemotoxic agents above those encountered generally
or on average by the subjects of a species. In certain embodiments,
the subject has had surgery to remove cancerous or precancerous
tissue. In other embodiments, the cancerous tissue has not been
removed, e.g., the cancerous tissue may be located in an inoperable
region of the body, such as in a tissue that is essential for life,
or in a region where a surgical procedure would cause considerable
risk of harm to the patient, or e.g., the subject is given the
anti-cancer therapy prior to removal of the cancerous tissue.
Nucleic Acid Sample Preparation
[0280] A. Nucleic Acid Isolation
[0281] Nucleic acid samples derived from cancerous and
non-cancerous cells of a subject that can be used in the methods of
the invention to determine the genetic signature of a cancer can be
prepared by means well known in the art. For example, surgical
procedures or needle biopsy aspiration can be used to collect
cancerous samples from a subject. In some embodiments, it is
important to enrich and/or purify the cancerous tissue and/or cell
samples from the non-cancerous tissue and/or cell samples. In other
embodiments, the cancerous tissue and/or cell samples can then be
microdissected to reduce the amount of normal tissue contamination
prior to extraction of genomic nucleic acid or pre-RNA for use in
the methods of the invention. In still another embodiment, the
cancerous tissue and/or cell samples are enriched for cancer cells
by at least 50%, 55%, 60%, 65%, 70%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or more or any range in between, in
cancer cell content. Such enrichment can be accomplished according
to methods well-known in the art, such as needle microdissection,
laser microdissection, fluorescence activated cell sorting, and
immunological cell sorting. In one embodiment, an automated machine
performs the hyperproliferative cell enrichment to thereby
transform the biological sample into a purified form enriched for
the presence of hyperproliferative cells.
[0282] Collecting nucleic acid samples from non-cancerous cells of
a subject can also be accomplished with surgery or aspiration. In
surgical procedures where cancerous tissue is removed, surgeons
often remove non-cancerous tissue and/or cell samples of the same
tissue type of the cancer patient for comparison. Nucleic acid
samples can be isolated from such non-cancerous tissue of the
subject for use in the methods of the invention. In certain
embodiments of the methods of the invention, nucleic acid samples
from non-cancerous tissues are not derived from the same tissue
type as the cancerous tissue and/or cells sampled, and/or are not
derived from the cancer patient. The nucleic acid samples from
non-cancerous tissues may be derived from any non-cancerous and/or
disease-free tissue and/or cells. Such non-cancerous samples can be
collected by surgical or non-surgical procedures. In certain
embodiments, non-cancerous nucleic acid samples are derived from
tumor-free tissues. For example, non-cancerous samples may be
collected from lymph nodes, peripheral blood lymphocytes, and/or
mononuclear blood cells, or any subpopulation thereof. In a
preferred embodiment, the non-cancerous tissue is not pre-cancerous
tissue, e.g., it does not exhibit any indicia of a pre-neoplastic
condition such as hyperplasia, metaplasia, or dysplasia.
[0283] In one embodiment, the nucleic acid samples used to compute
a reference value are taken from at least 1, 2, 5, 10, 20, 30, 40,
50, 100, or 200 different organisms of that species. According to
certain aspects of the invention, nucleic acid "derived from"
genomic DNA, as used in the methods of the invention, e.g., in
hybridization experiments to determine BLM expression, FANCI
expression, or 15q26 copy number, chromosome 15 centromere copy
number can be fragments of genomic nucleic acid generated by
restriction enzyme digestion and/or ligation to other nucleic acid,
and/or amplification products of genomic nucleic acids, or
pre-messenger RNA (pre-mRNA), amplification products of pre-mRNA,
or genomic DNA fragments grown up in cloning vectors generated,
e.g., by "shotgun" cloning methods. In certain embodiments, genomic
nucleic acid samples are digested with restriction enzymes.
[0284] B. Amplification of Nucleic Acids
[0285] Though the nucleic acid sample need not comprise amplified
nucleic acid, in some embodiments, the isolated nucleic acids can
be processed in manners requiring and/or taking advantage of
amplification. The genomic DNA samples of a subject optionally can
be fragmented using restriction endonucleases and/or amplified
prior to determining analysis. In one embodiment, the DNA fragments
are amplified using polymerase chain reaction (PCR). Methods for
practicing PCR are well known to those of skill in the art. One
advantage of PCR is that small quantities of DNA can be used. For
example, genomic DNA from a subject may be about 150 ng, 175, ng,
200 ng, 225 ng, 250 ng, 275 ng, or 300 ng of DNA.
[0286] In certain embodiments of the methods of the invention, the
nucleic acid from a subject is amplified using a single primer
pair. For example, genomic DNA samples can be digested with
restriction endonucleases to generate fragments of genomic DNA that
are then ligated to an adaptor DNA sequence which the primer pair
recognizes. In other embodiments of the methods of the invention,
the nucleic acid of a subject is amplified using sets of primer
pairs specific to BLM, FANCI, 15q26, or chromosome 15 centromere
copy and in instances wherein BRCA1, BRCA2, ER, PgR and/or HER2
receptor expression is also to be assessed, sets of primer pairs
specific to BRCA1, BRCA2, ER, PgR and/or HER2 receptor. Such sets
of primer pairs each recognize genomic DNA sequences flanking BLM,
FANCI, 15q26, or chromosome 15 centromere and BRCA1, BRCA2, ER, PgR
and/or HER2 receptor wherein the expression is also to be assessed.
A DNA sample suitable for hybridization can be obtained, e.g., by
polymerase chain reaction (PCR) amplification of genomic DNA,
fragments of genomic DNA, fragments of genomic DNA ligated to
adaptor sequences or cloned sequences. Computer programs that are
well known in the art can be used in the design of primers with the
desired specificity and optimal amplification properties, such as
Oligo version 5.0 (National Biosciences). PCR methods are well
known in the art, and are described, for example, in Innis et al.,
eds., 1990, PCR Protocols: A Guide to Methods And Applications,
Academic Press Inc., San Diego, Calif. It will be apparent to one
skilled in the art that controlled robotic systems are useful for
isolating and amplifying nucleic acids and can be used.
[0287] In other embodiments, where genomic DNA of a subject is
fragmented using restriction endonucleases and amplified prior to
analysis, the amplification can comprise cloning regions of genomic
DNA of the subject. In such methods, amplification of the DNA
regions is achieved through the cloning process. For example,
expression vectors can be engineered to express large quantities of
particular fragments of genomic DNA of the subject (Sambrook, J. et
al., eds., 1989, Molecular Cloning: A Laboratory Manual, 2nd Ed.,
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., at
pp. 9.47-9.51).
[0288] In yet other embodiments, where the DNA of a subject is
fragmented using restriction endonucleases and amplified prior to
analysis, the amplification comprises expressing a nucleic acid
encoding a gene, or a gene and flanking genomic regions of nucleic
acids, from the subject. RNA (pre-messenger RNA) that comprises the
entire transcript including introns is then isolated and used in
the methods of the invention to analyze and provide a genetic
signature of a cancer. In certain embodiments, no amplification is
required. In such embodiments, the genomic DNA, or pre-RNA, of a
subject may be fragmented using restriction endonucleases or other
methods. The resulting fragments may be hybridized to SNP probes.
Typically, greater quantities of DNA are needed to be isolated in
comparison to the quantity of DNA or pre-mRNA needed where
fragments are amplified. For example, where the nucleic acid of a
subject is not amplified, a DNA sample of a subject for use in
hybridization may be about 400 ng, 500 ng, 600 ng, 700 ng, 800 ng,
900 ng, or 1000 ng of DNA or greater. Alternatively, in other
embodiments, methods are used that require very small amounts of
nucleic acids for analysis, such as less than 400 ng, 300 ng, 200
ng, 100 ng, 90 ng, 85 ng, 80 ng, 75 ng, 70 ng, 65 ng, 60 ng, 55 ng,
50 ng, or less, such as is used for molecular inversion probe (MIP)
assays. These techniques are particularly useful for analyzing
clinical samples, such as paraffin embedded formalin-fixed material
or small core needle biopsies, characterized as being readily
available but generally having reduced DNA quality (e.g., small,
fragmented DNA) and/or not providing large amounts of nucleic
acids.
[0289] C. Hybridization
[0290] The nucleic acid samples derived from a subject used in the
methods of the invention can be hybridized to arrays comprising
probes (e.g., oligonucleotide probes) in order to identify BLM,
FANCI, 15q26, or chromosome 15 centromere and in instances wherein
BRCA1, BRCA2, ER, PgR and/or HER2 receptor expression is also to be
assessed, comprising probes in order to identify BRCA1, BRCA2, ER,
PgR and/or HER2 receptor. Hybridization can also be used to
determine whether the BLM, FANCI, 15q26, or chromosome 15
centromere identified exhibit total copy number change, copy number
gain, and copy number loss in nucleic acid samples from cancerous
tissues and/or cells of the subject. In preferred embodiments, the
probes used in the methods of the invention comprise an array of
probes that can be tiled on a DNA chip (e.g., SNP oligonucleotide
probes). In some embodiments, BLM expression, FANCI expression,
15q26 copy number, or chromosome 15 centromere copy number is
determined by a method that does not comprise detecting a change in
size of restriction enzyme-digested nucleic acid fragments. In
other embodiments, SNPs are analyzed to identify BLM expression or
FANCI expression, 15q26 copy number or chromosome 15 centromere
copy number. Hybridization and wash conditions used in the methods
of the invention are chosen so that the nucleic acid samples to be
analyzed by the invention specifically bind or specifically
hybridize to the complementary oligonucleotide sequences of the
array, preferably to a specific array site, wherein its
complementary DNA is located. In some embodiments, the
complementary DNA can be completely matched or mismatched to some
degree as used, for example, in Affymetrix oligonucleotide arrays
such as those used to analyze SNPs in MIP assays. The
single-stranded synthetic oligodeoxyribonucleic acid DNA probes of
an array may need to be denatured prior to contact with the nucleic
acid samples from a subject, e.g., to remove hairpins or dimers
which form due to self-complementary sequences.
[0291] Optimal hybridization conditions will depend on the length
of the probes and type of nucleic acid samples from a subject.
General parameters for specific (i.e., stringent) hybridization
conditions for nucleic acids are described in Sambrook, J. et al.,
eds., 1989, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., at pp.
9.47-9.51 and 11.55-11.61; Ausubel et al., eds., 1989, Current
Protocols in Molecules Biology, Vol. 1, Green Publishing
Associates, Inc., John Wiley & Sons, Inc., New York, at pp.
2.10.1-2.10.16. Exemplary useful hybridization conditions are
provided in, e.g., Tijessen, 1993, Hybridization with Nucleic Acid
Probes, Elsevier Science Publishers B. V. and Kricka, 1992,
Nonisotopic DNA Probe Techniques, Academic Press, San Diego,
Calif.
[0292] D. Oligonucleotide Nucleic Acid Arrays
[0293] In some embodiments of the methods of the present invention,
DNA arrays can be used to determine total copy number change, copy
number gain, and copy number loss by measuring the level of
hybridization of the nucleic acid sequence to oligonucleotide
probes that comprise complementary sequences. Hybridization can be
used to determine the presence or absence of heterozygosity.
Various formats of DNA arrays that employ oligonucleotide "probes,"
(i.e., nucleic acid molecules having defined sequences) are well
known to those of skill in the art. Typically, a set of nucleic
acid probes, each of which has a defined sequence, is immobilized
on a solid support in such a manner that each different probe is
immobilized to a predetermined region. In certain embodiments, the
set of probes forms an array of positionally-addressable binding
(e.g., hybridization) sites on a support. Each of such binding
sites comprises a plurality of oligonucleotide molecules of a probe
bound to the predetermined region on the support. More
specifically, each probe of the array is preferably located at a
known, predetermined position on the solid support such that the
identity (i.e., the sequence) of each probe can be determined from
its position on the array (i.e., on the support or surface).
Microarrays can be made in a number of ways, of which several are
described herein. However produced, microarrays share certain
characteristics, they are reproducible, allowing multiple copies of
a given array to be produced and easily compared with each
other.
[0294] Preferably, the microarrays are made from materials that are
stable under binding (e.g., nucleic acid hybridization) conditions.
The microarrays are preferably small, e.g., between about 1
cm.sup.2 and 25 cm.sup.2, preferably about 1 to 3 cm.sup.2.
However, both larger and smaller arrays are also contemplated and
may be preferable, e.g., for simultaneously evaluating a very large
number of different probes. Oligonucleotide probes can be
synthesized directly on a support to form the array. The probes can
be attached to a solid support or surface, which may be made, e.g.,
from glass, plastic (e.g., polypropylene, nylon), polyacrylamide,
nitrocellulose, gel, or other porous or nonporous material. The set
of immobilized probes or the array of immobilized probes is
contacted with a sample containing labeled nucleic acid species so
that nucleic acids having sequences complementary to an immobilized
probe hybridize or bind to the probe. After separation of, e.g., by
washing off, any unbound material, the bound, labeled sequences are
detected and measured. The measurement is typically conducted with
computer assistance. Using DNA array assays, complex mixtures of
labeled nucleic acids, e.g., nucleic acid fragments derived a
restriction digestion of genomic DNA from non-cancerous tissue, can
be analyzed. DNA array technologies have made it possible to
determine the expression level or copy number BLM, FANCI, 15q26, or
chromosome 15 centromere, or BRCA1, BRCA2, ER, PgR and/or HER2
receptor expression in instances where BRCA1, BRCA2, ER, PgR and/or
HER2 receptor expression is also assessed.
[0295] In certain embodiments, high-density oligonucleotide arrays
are used in the methods of the invention. These arrays containing
thousands of oligonucleotides complementary to defined sequences,
at defined locations on a surface can be synthesized in situ on the
surface by, for example, photolithographic techniques (see, e.g.,
Fodor et al., 1991, Science 251:767-773; Pease et al., 1994, Proc.
Natl. Acad. Sci. U.S.A. 91:5022-5026; Lockhart et al., 1996, Nature
Biotechnology 14:1675; U.S. Pat. Nos. 5,578,832; 5,556,752;
5,510,270; 5,445,934; 5,744,305; and 6,040,138). Methods for
generating arrays using inkjet technology for in situ
oligonucleotide synthesis are also known in the art (see, e.g.,
Blanchard, International Patent Publication WO 98/41531, published
Sep. 24, 1998; Blanchard et al., 1996, Biosensors And
Bioelectronics 11:687-690; Blanchard, 1998, in Synthetic DNA Arrays
in Genetic Engineering, Vol. 20, J. K. Setlow, Ed., Plenum Press,
New York at pages 111-123). Another method for attaching the
nucleic acids to a surface is by printing on glass plates, as is
described generally by Schena et al. (1995, Science 270:467-470).
Other methods for making microarrays, e.g., by masking (Maskos and
Southern, 1992, Nucl. Acids. Res. 20:1679-1684), may also be used.
When these methods are used, oligonucleotides (e.g., 15 to 60-mers)
of known sequence are synthesized directly on a surface such as a
derivatized glass slide. The array produced can be redundant, with
several oligonucleotide molecules corresponding to each informative
locus of interest (e.g., SNPs, RFLPs, STRs, etc.).
[0296] One exemplary means for generating the oligonucleotide
probes of the DNA array is by synthesis of synthetic
polynucleotides or oligonucleotides, e.g., using N-phosphonate or
phosphoramidite chemistries (Froehler et al., 1986, Nucleic Acid
Res. 14:5399-5407; McBride et al., 1983, Tetrahedron Lett.
24:246-248). Synthetic sequences are typically between about 15 and
about 600 bases in length, more typically between about 20 and
about 100 bases, most preferably between about 40 and about 70
bases in length. In some embodiments, synthetic nucleic acids
include non-natural bases, such as, but by no means limited to,
inosine. As noted above, nucleic acid analogues may be used as
binding sites for hybridization. An example of a suitable nucleic
acid analogue is peptide nucleic acid (see, e.g., Egholm et al.,
1993, Nature 363:566-568; U.S. Pat. No. 5,539,083). In alternative
embodiments, the hybridization sites (i.e., the probes) are made
from plasmid or phage clones of regions of genomic DNA
corresponding to SNPs or the complement thereof. The size of the
oligonucleotide probes used in the methods of the invention can be
at least 10, 20, 25, 30, 35, 40, 45, or 50 nucleotides in length.
It is well known in the art that although hybridization is
selective for complementary sequences, other sequences which are
not perfectly complementary may also hybridize to a given probe at
some level. Thus, multiple oligonucleotide probes with slight
variations can be used, to optimize hybridization of samples. To
further optimize hybridization, hybridization stringency condition,
e.g., the hybridization temperature and the salt concentrations,
may be altered by methods that are well known in the art.
[0297] In preferred embodiments, the high-density oligonucleotide
arrays used in the methods of the invention comprise
oligonucleotides corresponding to BLM, FANCI, 15q26, or chromosome
15 centromere or in instances wherein BRCA1, BRCA2, ER, PgR and/or
HER2 receptor expression is also assessed, the arrays also comprise
oligonucleotides corresponding to BRCA1, BRCA2, ER, PgR and/or HER2
receptor. The oligonucleotide probes may comprise DNA or DNA
"mimics" (e.g., derivatives and analogues) corresponding to a
portion of each informative locus of interest (e.g., SNPs, RFLPs,
STRs, etc.) in a subject's genome. The oligonucleotide probes can
be modified at the base moiety, at the sugar moiety, or at the
phosphate backbone. Exemplary DNA mimics include, e.g.,
phosphorothioates. For each SNP locus, a plurality of different
oligonucleotides may be used that are complementary to the
sequences of sample nucleic acids. For example, for a single
informative locus of interest (e.g., SNPs, RFLPs, STRs, etc.) about
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more
different oligonucleotides can be used. Each of the
oligonucleotides for a particular informative locus of interest may
have a slight variation in perfect matches, mismatches, and
flanking sequence around the SNP. In certain embodiments, the
probes are generated such that the probes for a particular
informative locus of interest comprise overlapping and/or
successive overlapping sequences which span or are tiled across a
genomic region containing the target site, where all the probes
contain the target site. By way of example, overlapping probe
sequences can be tiled at steps of a predetermined base interval,
e. g. at steps of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 bases intervals.
In certain embodiments, the assays can be performed using arrays
suitable for use with molecular inversion probe protocols such as
described by Wang et al. (2007) Genome Biol. 8, R246. For
oligonucleotide probes targeted at nucleic acid species of closely
resembled (i.e., homologous) sequences, "cross-hybridization" among
similar probes can significantly contaminate and confuse the
results of hybridization measurements. Cross-hybridization is a
particularly significant concern in the detection of SNPs since the
sequence to be detected (i.e., the particular SNP) must be
distinguished from other sequences that differ by only a single
nucleotide. Cross-hybridization can be minimized by regulating
either the hybridization stringency condition and/or during
post-hybridization washings. Highly stringent conditions allow
detection of allelic variants of a nucleotide sequence, e.g., about
1 mismatch per 10-30 nucleotides. There is no single hybridization
or washing condition which is optimal for all different nucleic
acid sequences. For particular arrays of BLM, FANCI, 15q26, or
chromosome 15 centromere, or of BRCA1, BRCA2, ER, PgR and/or HER2
receptor these conditions can be identical to those suggested by
the manufacturer or can be adjusted by one of skill in the art. In
preferred embodiments, the probes used in the methods of the
invention are immobilized (i.e., tiled) on a glass slide called a
chip. For example, a DNA microarray can comprises a chip on which
oligonucleotides (purified single-stranded DNA sequences in
solution) have been robotically printed in an (approximately)
rectangular array with each spot on the array corresponds to a
single DNA sample which encodes an oligonucleotide. In summary the
process comprises, flooding the DNA microarray chip with a labeled
sample under conditions suitable for hybridization to occur between
the slide sequences and the labeled sample, then the array is
washed and dried, and the array is scanned with a laser microscope
to detect hybridization. In certain embodiments there are at least
250, 500, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000,
9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000,
17,000, 18,000, 19,000, 20,000, 21,000, 22,000, 23,000, 24,000,
25,000, 26,000, 27,000, 28,000, 29,000, 30,000, 31,000, 32,000,
33,000, 34,000, 35,000, 36,000, 37,000, 38,000, 39,000, 40,000,
41,000, 42,000, 43,000, 44,000, 45,000, 50,000, 60,000, 70,000,
80,000, 90,000, 100,000 or more or any range in between, of BLM,
FANCI, 15q26, or chromosome 15 centromere, or of BRCA1, BRCA2, ER,
PgR and/or HER2 receptor for which probes appear on the array (with
match/mismatch probes for a single locus of interest or probes
tiled across a single locus of interest counting as one locus of
interest). The maximum number of BLM, FANCI, 15q26, or chromosome
15 centromere, or of BRCA1, BRCA2, ER, PgR and/or HER2 receptor
being probed per array is determined by the size of the genome and
genetic diversity of the subjects species. DNA chips are well known
in the art and can be purchased in pre-5 fabricated form with
sequences specific to particular species. In some embodiments, the
Genome-Wide Human SNP Array 6.0.TM. and/or the 50K XbaI arrays
(Affymetrix, Santa Clara, Calif.) are used in the methods of the
invention. In other embodiments, SNPs and/or DNA copy number can be
detected and quantitated using sequencing methods, such as
"next-generation sequencing methods" as described further
above.
[0298] E. Signal Detection
[0299] In some embodiments, nucleic acid samples derived from a
subject are hybridized to the binding sites of an array described
herein. In certain embodiments, nucleic acid samples derived from
each of the two sample types of a subject (i.e., cancerous and
non-cancerous) are hybridized to separate, though identical,
arrays. In certain embodiments, nucleic acid samples derived from
one of the two sample types of a subject (i.e., cancerous and
non-cancerous) is hybridized to such an array, then following
signal detection the chip is washed to remove the first labeled
sample and reused to hybridize the remaining sample. In other
embodiments, the array is not reused more than once. In certain
embodiments, the nucleic acid samples derived from each of the two
sample types of a subject (i.e., cancerous and non-cancerous) are
differently labeled so that they can be distinguished. When the two
samples are mixed and hybridized to the same array, the relative
intensity of signal from each sample is determined for each site on
the array, and any relative difference in abundance of an allele of
BLM, FANCI, 15q26, or chromosome 15 centromere, or of BRCA1, BRCA2,
ER, PgR and/or HER2 receptor. Signals can be recorded and, in some
embodiments, analyzed by computer. In one embodiment, the scanned
image is despeckled using a graphics program (e.g., Hij aak
Graphics Suite) and then analyzed using an image gridding program
that creates a spreadsheet of the average hybridization at each
wavelength at each site. If necessary, an experimentally determined
correction for "cross talk" (or overlap) between the channels for
the two fluors may be made. For any particular hybridization site
on the array, a ratio of the emission of the two fluorophores can
be calculated, which may help in eliminating cross hybridization
signals to more accurately determining whether a particular SNP
locus is heterozygous or homozygous.
[0300] F. Labeling
[0301] In some embodiments, the nucleic acids samples, fragments
thereof, or fragments thereof ligated to adaptor regions used in
the methods of the invention are detectably labeled. For example,
the detectable label can be a fluorescent label, e.g., by
incorporation of nucleotide analogues. Other labels suitable for
use in the present invention include, but are not limited to,
biotin, iminobiotin, antigens, cofactors, dinitrophenol, lipoic
acid, olefinic compounds, detectable polypeptides, electron rich
molecules, enzymes capable of generating a detectable signal by
action upon a substrate, and radioactive isotopes.
[0302] Radioactive isotopes include that can be used in conjunction
with the methods of the invention, but are not limited to, 32P and
14C. Fluorescent molecules suitable for the present invention
include, but are not limited to, fluorescein and its derivatives,
rhodamine and its derivatives, texas red, 5'carboxy-fluorescein
("FAM"), 2',7'-dimethoxy-4',5'-dichloro-6-carboxy-fluorescein
("JOE"), N, N, N',N'-tetramethyl-6-carboxy-rhodamine ("TAMRA"),
6-carboxy-X-rhodamine ("ROX"), HEX, TET, IRD40, and IRD41.
[0303] Fluorescent molecules which are suitable for use according
to the invention further include: cyamine dyes, including but not
limited to Cy2, Cy3, Cy3.5, CY5, Cy5.5, Cy7 and FLUORX; BODIPY dyes
including but not limited to BODIPY-FL, BODIPY-TR, BODIPY-TMR,
BODIPY-630/650, and BODIPY-650/670; and ALEXA dyes, including but
not limited to ALEXA-488, ALEXA-532, ALEXA-546, ALEXA-568, and
ALEXA-594; as well as other fluorescent dyes which will be known to
those who are skilled in the art. Electron rich indicator molecules
suitable for the present invention include, but are not limited to,
ferritin, hemocyanin, and colloidal gold.
[0304] Two-color fluorescence labeling and detection schemes may
also be used (Shena et al., 1995, Science 270:467-470). Use of two
or more labels can be useful in detecting variations due to minor
differences in experimental conditions (e.g., hybridization
conditions). In some embodiments of the invention, at least 5, 10,
20, or 100 dyes of different colors can be used for labeling. Such
labeling would also permit analysis of multiple samples
simultaneously which is encompassed by the invention.
[0305] The labeled nucleic acid samples, fragments thereof, or
fragments thereof ligated to adaptor regions that can be used in
the methods of the invention are contacted to a plurality of
oligonucleotide probes under conditions that allow sample nucleic
acids having sequences complementary to the probes to hybridize
thereto. Depending on the type of label used, the hybridization
signals can be detected using methods well known to those of skill
in the art including, but not limited to, X-Ray film, phosphor
imager, or CCD camera. When fluorescently labeled probes are used,
the fluorescence emissions at each site of a transcript array can
be, preferably, detected by scanning confocal laser microscopy. In
one embodiment, a separate scan, using the appropriate excitation
line, is carried out for each of the two fluorophores used.
Alternatively, a laser can be used that allows simultaneous
specimen illumination at wavelengths specific to the two
fluorophores and emissions from the two fluorophores can be
analyzed simultaneously (see Shalon et al. (1996) Genome Res. 6,
639-645). In a preferred embodiment, the arrays are scanned with a
laser fluorescence scanner with a computer controlled X-Y stage and
a microscope objective. Sequential excitation of the two
fluorophores is achieved with a multi-line, mixed gas laser, and
the emitted light is split by wavelength and detected with two
photomultiplier tubes. Such fluorescence laser scanning devices are
described, e.g., in Schena et al. (1996) Genome Res. 6, 639-645.
Alternatively, a fiber-optic bundle can be used such as that
described by Ferguson et al. (1996) Nat. Biotech. 14, 1681-1684.
The resulting signals can then be analyzed to determine the BLM
expression, FANCI expression, 15q26 copy number, or chromosome 15
centromere copy number, using computer software.
[0306] G. Algorithms for Analyzing BLM, FANCI, 15q26, or Chromosome
15 Centromere
[0307] Once the hybridization signal has been detected the
resulting data can be analyzed using algorithms. In certain
embodiments, the algorithm for determining the expression of BLM or
FANCI, or copy number 15q26 or chromosome 15 centromere is based on
well-known methods. Additional representative illustrations of such
well known algorithms are provided in the Examples section
below.
[0308] H. Computer Implementation Systems and Methods
[0309] In certain embodiments, the methods of the invention
implement a computer program to calculate a copy number, copy
number gain, copy number loss, and expression levels. For example,
a computer program can be used to perform the algorithms described
herein. A computer system can also store and manipulate data
generated by the methods of the present invention which comprises a
plurality of hybridization signal changes/profiles during approach
to equilibrium in different hybridization measurements and which
can be used by a computer system in implementing the methods of
this invention. In certain embodiments, a computer system receives
probe hybridization data; (ii) stores probe hybridization data; and
(iii) compares probe hybridization data to determine the state of
BLM, FANCI, 15q26, or, chromosome 15 centromere, and/or of BRCA1,
BRCA2, ER, PgR and/or HER2 receptor in said nucleic acid sample
from cancerous or pre-cancerous tissue. The copy number, copy
number gain, copy number loss, or expression levels is then
calculated. In some embodiments, a computer system (i) compares the
determined copy number, copy number gain, copy number loss, and
expression levels to a threshold value or reference value; and (ii)
outputs an indication of whether said copy number, copy number
gain, copy number loss, and expression levels is above or below a
threshold value, or a genetic signature based on said indication.
In certain embodiments, such computer systems are also considered
part of the present invention.
[0310] Numerous types of computer systems can be used to implement
the analytic methods of this invention according to knowledge
possessed by a skilled artisan in the bioinformatics and/or
computer arts.
[0311] Several software components can be loaded into memory during
operation of such a computer system. The software components can
comprise both software components that are standard in the art and
components that are special to the present invention (e.g., dCHIP
software described in Lin et al. (2004) Bioinformatics 20,
1233-1240; CRLMM software described in Silver et al. (2007) Cell
128, 991-1002; Aroma Affymetrix software described in Richardson et
al. (2006) Cancer Cell 9, 121-132. The methods of the invention can
also be programmed or modeled in mathematical software packages
that allow symbolic entry of equations and high-level specification
of processing, including specific algorithms to be used, thereby
freeing a user of the need to procedurally program individual
equations and algorithms. Such packages include, e.g., Matlab from
Mathworks (Natick, Mass.), Mathematica from Wolfram Research
(Champaign, Ill.) or S-Plus from MathSoft (Seattle, Wash.). In
certain embodiments, the computer comprises a database for storage
of hybridization signal profiles. Such stored profiles can be
accessed and used to calculate a copy number, copy number gain,
copy number loss, or expression level. For example, of the
hybridization signal profile of a sample derived from the
non-cancerous tissue of a subject and/or profiles generated from
population-based distributions of BLM, FANCI, 15q26, or chromosome
15 centromere, and/or of BRCA1, BRCA2, ER, PgR and/or HER2 receptor
in relevant populations of the same species were stored, it could
then be compared to the hybridization signal profile of a sample
derived from the cancerous tissue of the subject.
[0312] In addition to the exemplary program structures and computer
systems described herein, other, alternative program structures and
computer systems will be readily apparent to the skilled artisan.
Such alternative systems, which do not depart from the above
described computer system and programs structures either in spirit
or in scope, are therefore intended to be comprehended within the
accompanying claims.
[0313] Once a laboratory technician or laboratory professional or
group of laboratory technicians or laboratory professionals
determines whether a sample has a copy number, copy number gain,
copy number loss, or expression level as described above (e.g.,
step (1) in many of the methods above), the same or a different
laboratory technician or laboratory professional (or group) can
analyze a plurality of test BLM, FANCI, 15q26, or chromosome 15
centromere to determine whether there is a copy number, copy number
gain, copy number loss, or expression level (e.g., step (2) in many
of the methods above). Next, the same or a different laboratory
technician or laboratory professional (or group) can combine the a
copy number, copy number gain, copy number loss, or expression
level data from the test BLM, FANCI, 15q26, or chromosome 15
centromere to derive a copy number, copy number gain, copy number
loss, or expression level (e.g., step (3) in many of the methods
above). Optionally, the same or a different laboratory technician
or laboratory professional (or group) can correlate the copy
number, copy number gain, copy number loss, or expression level to
an increased or decreased likelihood of response to a particular
therapy (e.g., those mentioned above).
[0314] In various embodiments, provided herein is a computer
readable storage medium comprising: a storing data module
containing data from a sample comprising a cancer cell obtained
from a subject that represents an expression level from an assay
for BLM and/or FANCI, or copy number of 15q26; a comparison module
that compares the data stored on the storing data module with a
reference data and/or control data, and to provide a comparison
content, and an output module displaying the comparison content for
the user, wherein the increased expression of BLM and/or FANCI, or
copy number gain of 15q26 indicates that the subject is susceptible
to platinum-comprising, or anthracycline-comprising cancer
therapy.
[0315] In various embodiments, the control data comprises data from
a population of non-cancerous healthy individuals. In various
embodiments, the control data comprises data BRAC1 expression,
and/or a housekeeping gene expression.
[0316] Embodiments of the invention can be described through
functional modules, which are defined by computer executable
instructions recorded on computer readable media and which cause a
computer to perform method steps when executed. The modules are
segregated by function, for the sake of clarity. However, it should
be understood that the modules/systems need not correspond to
discreet blocks of code and the described functions can be carried
out by the execution of various code portions stored on various
media and executed at various times. Furthermore, it should be
appreciated that the modules may perform other functions, thus the
modules are not limited to having any particular functions or set
of functions.
[0317] The computer readable storage media 30 can be any available
tangible media that can be accessed by a computer. Computer
readable storage media includes volatile and nonvolatile, removable
and non-removable tangible media implemented in any method or
technology for storage of information such as computer readable
instructions, data structures, program modules or other data.
Computer readable storage media includes, but is not limited to,
RAM (random access memory), ROM (read only memory), EPROM
(eraseable programmable read only memory), EEPROM (electrically
eraseable programmable read only memory), flash memory or other
memory technology, CD-ROM (compact disc read only memory), DVDs
(digital versatile disks) or other optical storage media, magnetic
cassettes, magnetic tape, magnetic disk storage or other magnetic
storage media, other types of volatile and non-volatile memory, and
any other tangible medium which can be used to store the desired
information and which can accessed by a computer including and any
suitable combination of the foregoing.
[0318] Computer-readable data embodied on one or more
computer-readable media may define instructions, for example, as
part of one or more programs that, as a result of being executed by
a computer, instruct the computer to perform one or more of the
functions described herein, and/or various embodiments, variations
and combinations thereof. Such instructions may be written in any
of a plurality of programming languages, for example, Java, J#,
Visual Basic, C, C#, C++, Fortran, Pascal, Eiffel, Basic, COBOL
assembly language, and the like, or any of a variety of
combinations thereof. The computer-readable media on which such
instructions are embodied may reside on one or more of the
components of either of a system, or a computer readable storage
medium described herein, may be distributed across one or more of
such components.
[0319] The computer-readable media may be transportable such that
the instructions stored thereon can be loaded onto any computer
resource to implement the aspects of the present invention
discussed herein. In addition, it should be appreciated that the
instructions stored on the computer-readable medium, described
above, are not limited to instructions embodied as part of an
application program running on a host computer. Rather, the
instructions may be embodied as any type of computer code (e.g.,
software or microcode) that can be employed to program a computer
to implement aspects of the present invention. The computer
executable instructions may be written in a suitable computer
language or combination of several languages. Basic computational
biology methods are known to those of ordinary skill in the art and
are described in, for example, Setubal and Meidanis et al.,
Introduction to Computational Biology Methods (PWS Publishing
Company, Boston, 1997); Salzberg, Searles, Kasif, (Ed.),
Computational Methods in Molecular Biology, (Elsevier, Amsterdam,
1998); Rashidi and Buehler, Bioinformatics Basics: Application in
Biological Science and Medicine (CRC Press, London, 2000) and
Ouelette and Bzevanis Bioinformatics: A Practical Guide for
Analysis of Gene and Proteins (Wiley & Sons, Inc., 2nd ed.,
2001).
[0320] The functional modules of certain embodiments of the
invention; for example, as depicted in FIG. 12, include for
example, at a measuring module 40, a storage module 30, a
comparison module 80, and an output module 110. The functional
modules can be executed on one, or multiple, computers, or by using
one, or multiple, computer networks. The measuring module has
computer executable instructions to provide e.g., expression
information in computer readable form.
[0321] The measuring module 40, can comprise any system for
detecting the expression of BLM and/or FANCI, the 15Q26 copy
number. Such systems can include DNA microarrays, RNA expression
arrays, any ELISA detection system and/or any Western blotting
detection system.
[0322] The information determined in the determination system can
be read by the storage module 30. As used herein the "storage
module" is intended to include any suitable computing or processing
apparatus or other device configured or adapted for storing data or
information. Examples of electronic apparatus suitable for use with
the present invention include stand-alone computing apparatus, data
telecommunications networks, including local area networks (LAN),
wide area networks (WAN), Internet, Intranet, and Extranet, and
local and distributed computer processing systems. Storage modules
also include, but are not limited to: magnetic storage media, such
as floppy discs, hard disc storage media, magnetic tape, optical
storage media such as CD-ROM, DVD, electronic storage media such as
RAM, ROM, EPROM, EEPROM and the like, general hard disks and
hybrids of these categories such as magnetic/optical storage media.
The storage module is adapted or configured for having recorded
thereon expression level or protein level information. Such
information may be provided in digital form that can be transmitted
and read electronically, e.g., via the Internet, on diskette, via
USB (universal serial bus) or via any other suitable mode of
communication.
[0323] As used herein, "stored" refers to a process for encoding
information on the storage module. Those skilled in the art can
readily adopt any of the presently known methods for recording
information on known media to generate manufactures comprising
expression level information.
[0324] In one embodiment the reference data stored in the storage
module to be read by the comparison module is e.g., expression data
obtained from a population of non-cancer subjects, a population of
cancer subjects or expression data obtained from the same subject
at a prior time point using the measuring module 40.
[0325] The "comparison module" 80 can use a variety of available
software programs and formats for the comparison operative to
compare expression data determined in the measuring module to
reference samples and/or stored reference data. In one embodiment,
the comparison module is configured to use pattern recognition
techniques to compare information from one or more entries to one
or more reference data patterns. The comparison module may be
configured using existing commercially-available or
freely-available software for comparing patterns, and may be
optimized for particular data comparisons that are conducted. The
comparison module provides computer readable information related to
normalized expression of BLM and/or FANCI, the 15Q26 copy number in
an individual, efficacy of treatment in an individual, and/or
method for treating an individual.
[0326] The comparison module, or any other module of the invention,
may include an operating system (e.g., UNIX) on which runs a
relational database management system, a World Wide Web
application, and a World Wide Web server. World Wide Web
application includes the executable code necessary for generation
of database language statements (e.g., Structured Query Language
(SQL) statements). Generally, the executables will include embedded
SQL statements. In addition, the World Wide Web application may
include a configuration file which contains pointers and addresses
to the various software entities that comprise the server as well
as the various external and internal databases which must be
accessed to service user requests. The Configuration file also
directs requests for server resources to the appropriate
hardware--as may be necessary should the server be distributed over
two or more separate computers. In one embodiment, the World Wide
Web server supports a TCP/IP protocol. Local networks such as this
are sometimes referred to as "Intranets. An advantage of such
Intranets is that they allow easy communication with public domain
databases residing on the World Wide Web (e.g., the GenBank or
Swiss Pro World Wide Web site). Thus, in a particular preferred
embodiment of the present invention, users can directly access data
(via Hypertext links for example) residing on Internet databases
using a HTML interface provided by Web browsers and Web
servers.
[0327] The comparison module provides a computer readable
comparison result that can be processed in computer readable form
by predefined criteria, or criteria defined by a user, to provide a
content-based in part on the comparison result that may be stored
and output as requested by a user using an output module 110.
[0328] The content based on the comparison result, may be an
expression value compared to a reference showing the susceptibility
or nonsusceptibility of treatment with platinum-comprising therapy
or anthracycline-compri sing therapy.
[0329] In various embodiments of the invention, the content based
on the comparison result is displayed on a computer monitor 120. In
various embodiments of the invention, the content based on the
comparison result is displayed through printable media 130. The
display module can be any suitable device configured to receive
from a computer and display computer readable information to a
user. Non-limiting examples include, for example, general-purpose
computers such as those based on Intel PENTIUM-type processor,
Motorola PowerPC, Sun UltraSPARC, Hewlett-Packard PA-RISC
processors, any of a variety of processors available from Advanced
Micro Devices (AMD) of Sunnyvale, Calif., or any other type of
processor, visual display devices such as flat panel displays,
cathode ray tubes and the like, as well as computer printers of
various types.
[0330] In one embodiment, a World Wide Web browser is used for
providing a user interface for display of the content based on the
comparison result. It should be understood that other modules of
the invention can be adapted to have a web browser interface.
Through the Web browser, a user may construct requests for
retrieving data from the comparison module. Thus, the user will
typically point and click to user interface elements such as
buttons, pull down menus, scroll bars and the like conventionally
employed in graphical user interfaces.
[0331] The present invention therefore provides for systems (and
computer readable media for causing computer systems) to perform
methods for selecting treatment of cancer in an individual.
[0332] Systems and computer readable media described herein are
merely illustrative embodiments of the invention for detecting BLM
and/or FANCI expression, or 15Q26 copy number in an individual, and
are not intended to limit the scope of the invention. Variations of
the systems and computer readable media described herein are
possible and are intended to fall within the scope of the
invention.
[0333] The modules of the machine, or those used in the computer
readable medium, may assume numerous configurations. For example,
function may be provided on a single machine or distributed over
multiple machines.
[0334] In some cases, a computing system provided herein can
include computer-executable instructions or a computer program
(e.g., software) containing computer-executable instructions for
formatting an output providing an indication BLM and/or FANCI
expression, 15q26 copy number, or a likelihood that a cancer
patient will respond to a particular cancer treatment regimen
(e.g., a regimen as described above), or a combination of these
items. In some cases, a computing system provided herein can
include computer-executable instructions or a computer program
(e.g., software) containing computer-executable instructions for
determining a desired cancer treatment regimen for a particular
patient based at least in part on increased expression of BLM
and/or FANCI, or 15q26 copy number gain.
[0335] In some cases, a computing system provided herein can
include a pre-processing device configured to process a sample
(e.g., cancer cells) such that a SNP array-based assay or
sequencing-based assay can be performed. Examples of pre-processing
devices include, without limitation, devices configured to enrich
cell populations for cancer cells as opposed to non-cancer cells,
devices configured to lyse cells and/or extract genomic nucleic
acid, and devices configured to enrich a sample for particular
genomic DNA fragments.
[0336] The following numbered paragraphs provide some embodiments
and aspects of the invention. [0337] 1. An assay for selecting a
therapy for a subject having cancer, and optionally administering
the therapy, the assay comprising: [0338] subjecting a sample
comprising a cancer cell taken from the subject to an analysis for
BLM and FANCI expression; [0339] comparing the BLM and FANCI
expression to a reference value; and [0340] selecting a
platinum-comprising cancer therapy for the subject when the BLM and
FANCI expression is increased compared to the reference value based
on the recognition that platinum-comprising cancer therapy is
effective in subjects whose cancer has increased expression of BLM
and FANCI, or selecting a non-platinum-comprising cancer therapy
for the subject when the BLM and FANCI expression is not increased
compared to the reference value based on the recognition that
platinum-comprising cancer therapy is not effective in subjects
whose cancer does not have increased BLM and FANCI expression
compared to the reference value. [0341] 2. The assay of paragraph
1, further comprising: [0342] assaying the BRCA1 and/or BRCA2
status of the subject; and [0343] selecting the platinum-comprising
cancer therapy for the subject when the subject is negative for
BRCA1 and/or BRCA2 mutations, and the BLM and FANCI expression is
increased compared to the reference value based on the recognition
that platinum-comprising cancer therapy is effective in subjects
whose cancer has increased expression of BLM and FANCI and who are
negative for BRCA1 and/or BRCA2 mutations. [0344] 3. The assay of
paragraph 1, the subject is known to be or is determined to be
negative for BRCA1 and/or BRCA2 mutations. [0345] 4. The assay of
paragraph 1, further comprising: [0346] assaying the estrogen
receptor (ER), progesterone receptor (PgR), and HER2 receptor
status of the subject's cancer; and [0347] selecting the
platinum-comprising cancer therapy for the subject when the
subject's cancer does not express a detectable quantity of ER, PgR,
and HER2 receptor, and when the BLM and FANCI expression is
increased compared to the reference value based on the recognition
that platinum-comprising cancer therapy is effective in subjects
whose cancer has increased expression of BLM and FANCI and whose
cancer does not express a detectable quantity of ER, PgR, and HER2
receptor. [0348] 5. The assay of paragraph 1, wherein the subject's
cancer or cancer cell is known to not or is determined to not
express a detectable quantity of ER, PgR, and HER2 receptor. [0349]
6. The assay of paragraphs 1-5, further comprising administering
the selected therapy to the subject. [0350] 7. The assay of any one
of the paragraphs 1-6, wherein the cancer is selected from breast
cancer, ovarian cancer and lung cancer. [0351] 8. The assay of
paragraphs 1-6, wherein the reference value is BRCA1 expression in
the sample and the BLM and/or FANCI expression is increased by at
least two-fold compared to BRCA1 expression. [0352] 9. The assay of
paragraphs 1-6, wherein the reference value is based on at least
BRCA1 gene expression in the cancer cell. [0353] 10. The assay
paragraphs 1-6, wherein the reference value is based on at least
one housekeeping gene expression in the cancer cell. [0354] 11. A
method for selecting platinum-comprising therapy for a subject
having cancer, and optionally administering the platinum-comprising
therapy, the method comprising: [0355] subjecting a sample
comprising a cancer cell taken from the subject to an analysis for
BLM and FANCI expression; [0356] detecting the BLM and FANCI
expression in the sample compared to a reference value; and [0357]
selecting a platinum-comprising cancer therapy for the subject when
the BLM and FANCI expression compared to a reference value is
increased based on the recognition that platinum-comprising cancer
therapy is effective in patients whose cancer has increased BLM and
FANCI expression compared to the reference value. [0358] 12. The
method of paragraph 11, further comprising administering to the
subject the platinum-comprising cancer therapy when the
platinum-comprising cancer therapy is selected. [0359] 13. The
method of paragraph 11, wherein the subject is known to be or is
determined to be negative for BRCA1 and/or BRCA2 mutations. [0360]
14. The method of paragraph 11, wherein the subject's cancer or
cancer cell is known to not or determined to not express a
detectable quantity of ER, PgR, and HER2 receptor. [0361] 15. The
method of any one of the paragraphs 11-14, wherein the cancer is
selected from breast cancer, ovarian cancer and lung cancer. [0362]
16. The method of paragraph 11-15, wherein the reference value is
BRCA1 expression in the sample, and the BLM and/or FANCI expression
is increased by at least two-fold compared to BRCA1 expression.
[0363] 17. The method of any one of the paragraphs 11-15, wherein
the reference value is based on at least BRCA1 gene expression in
the cancer cell. [0364] 18. The method of any one of the paragraphs
11-15, wherein the reference value is based on at least one
housekeeping gene expression in the cancer cell. [0365] 19. The
method of paragraph 18, wherein the housekeeping gene is selected
from beta-actin, GAPDH, RPLP0, GUS, TFRC and any combination
thereof. [0366] 20. The method of paragraph 19, wherein the
housekeeping gene is RPLP0, and the BLM and/or FANCI expression is
increased by at least six-fold. [0367] 21. A method for selecting a
non-platinum-comprising therapy, and optionally administering the
non-platinum-comprising therapy, for a subject having cancer
comprising: [0368] subjecting a sample comprising a cancer cell
taken from the subject to an analysis for BLM and FANCI expression;
[0369] detecting the BLM and FANCI expression in the sample
compared to a reference value; and [0370] selecting the
non-platinum-comprising cancer therapy for the subject when the BLM
and FANCI expression compared to the reference value is not
increased based on the recognition that non-platinum-comprising
cancer therapy is effective in patients whose cancer does not have
increased gene expression of BLM and FANCI compared to the
reference value. [0371] 22. The method of paragraph 21, further
comprising administering to the subject the non-platinum-comprising
cancer therapy when non-platinum-comprising cancer therapy is
selected. [0372] 23. The method of any one of the paragraphs 21-22,
wherein the cancer is selected from breast cancer, ovarian cancer
and lung cancer. [0373] 24. The method of paragraph 21-23, wherein
the reference value is BRCA1 expression in the sample, and the BLM
and/or FANCI expression is increased by at least two-fold compared
to BRCA1 expression. [0374] 25. The method of any one of the
paragraphs 21-24, wherein the reference value is based on at least
BRCA1 gene expression in the cancer cell. [0375] 26. The method of
any one of the paragraphs 21-22, wherein the reference value is
based on at least one housekeeping gene expression in the cancer
cell. [0376] 27. An assay for selecting a therapy for a subject
having cancer, comprising: [0377] subjecting a sample comprising a
cancer cell taken from the subject to an analysis for BLM and FANCI
expression; [0378] comparing the BLM and FANCI expression to a
reference value; and [0379] selecting an anthracycline-compri sing
cancer therapy for the subject when the BLM and FANCI expression is
increased compared to a reference value based on the recognition
that anthracycline-comprising cancer therapy is effective in
subjects whose cancer has increased expression of BLM and FANCI, or
[0380] selecting a non-anthracycline-comprising cancer therapy for
the subject when the BLM and FANCI expression is not increased
compared to a reference value based on the recognition that
anthracycline-comprising cancer therapy is not effective in
subjects whose cancer does not have increased BLM expression
compared to a reference value. [0381] 28. The assay of paragraph
27, wherein the reference value is BRCA1 expression in the sample,
and the BLM and/or FANCI expression is increased by at least
two-fold compared to BRCA1 expression. [0382] 29. A method for
selecting an anthracycline-comprising cancer therapy for a subject
having cancer and determined to be negative for BRCA1 and/or BRCA2
mutations, comprising: [0383] subjecting a sample comprising a
cancer cell taken from the subject to an analysis for BLM and FANCI
expression; [0384] comparing the BLM and FANCI expression to a
reference value; and [0385] selecting the anthracycline-comprising
cancer therapy for the subject when the BLM and FANCI expression
compared to the reference value is increased based on the
recognition that anthracycline-comprising cancer therapy is
effective in patients whose cancer has increased expression of BLM
and FANCI compared to the reference value. [0386] 30. The method of
paragraph 29, wherein the reference value is BRCA1 expression in
the sample, and the BLM and/or FANCI expression is increased by at
least two-fold compared to BRCA1 expression. [0387] 31. A method of
treating cancer in a human subject, comprising: [0388] detecting
BLM and FANCI expression in a sample comprising a cancer cell taken
from the human subject; and [0389] comparing the BLM and FANCI
expression to a reference value; and [0390] administering a
platinum-comprising cancer therapy to the human subject wherein an
increase of BLM and FANCI expression compared to the reference
value is detected. [0391] 32. The method of paragraph 31, wherein
the human subject's cancer or cancer cell is known to not or is
determined to not express detectable quantities of estrogen
receptor (ER), progesterone receptor (PgR) and HER2 receptor.
[0392] 33. The method of paragraph 31, wherein the cancer is
selected from breast, ovarian, and lung cancers. [0393] 34. The
method of paragraph 31-33, wherein the reference value is BRCA1
expression in the sample, and the BLM and/or FANCI expression is
increased by at least two-fold compared to BRCA1 expression. [0394]
35. The method of any one of the paragraphs 31-33, wherein the
reference value is based on BRCA1 gene expression in the cancer
cell. [0395] 36. The method of any one of the paragraphs 31-33,
wherein the reference value is based on a housekeeping gene
expression in the cancer cell. [0396] 37. A method of treating
cancer in a human subject, comprising: [0397] detecting BLM and
FANCI expression in a sample comprising a cancer cell taken from
the human subject; and [0398] comparing the BLM and FANCI
expression to a reference value; and [0399] administering an
anthracycline-comprising cancer therapy to the human subject
wherein an increase of BLM and FANCI expression compared to the
reference value is detected. [0400] 38. The method of paragraph 37,
wherein the human subject's cancer or cancer cell is known to not
or is determined to not to express detectable quantities of
estrogen receptor (ER), progesterone receptor (PgR) and HER2
receptor. [0401] 39. The method of paragraph 37, wherein the cancer
is selected from breast, ovarian, and lung cancers. [0402] 40. The
method of paragraph 37-39, wherein the reference value is BRCA1
expression in the sample, and the BLM and/or FANCI expression is
increased by at least two-fold compared to BRCA1 expression. [0403]
41. The method of any one of the paragraphs 37-39, wherein the
reference value is based on BRCA1 gene expression in the cancer
cell. [0404] 42. The method of any one of the paragraphs 37-39,
wherein the reference value is based on a housekeeping gene
expression in the cancer cell. [0405] 43. A method for assessing
responsiveness of a cancer cell to cancer therapy, comprising:
[0406] assaying, in a cancer cell or mRNA derived therefrom, BLM
and FANCI expression; and [0407] comparing said BLM and FANCI
expression to a reference value, wherein the cancer cell is
assessed as responsive to a platinum-comprising therapy if the BLM
and FANCI expression is increased compared to the reference value,
or wherein the cancer cell is assessed as poorly or not responsive
to platinum-comprising cancer therapy cancer if the BLM and FANCI
expression is not increased. [0408] 44. The method of paragraph 43,
wherein the step of assaying comprises: [0409] contacting the
cancer cell or mRNA derived therefrom with at least one detectably
labeled probe capable of specifically binding to BLM mRNA, at least
one detectably probe capable of specifically binding to FANCI, at
least one detectably labeled probe capable of specifically binding
to BRCA1 and/or at least one housekeeping gene; and [0410]
measuring the expression of BLM and FANCI compared to the BRCA1
and/or the at least one housekeeping gene. [0411] 45. The method of
paragraph 43-44, wherein the reference value is BRCA1 expression in
the sample, and the BLM and/or FANCI expression is increased by at
least two-fold compared to BRCA1 expression. [0412] 46. A method of
predicting a cancer patient's response to a cancer treatment
regimen comprising platinum or anthracycline, comprising: [0413]
determining, in a cancer cell from the cancer patient, BLM and
FANCI expression; and [0414] correlating the expression to a
reference value, wherein when the expression is increased the
patient is predicted to respond well to a cancer treatment regimen
comprising platinum or anthracycline. [0415] 47. The method of
paragraph 46, wherein the reference value is BRCA1 expression in
the sample, and the BLM and/or FANCI expression is increased by at
least two-fold compared to BRCA1 expression. [0416] 48. A method of
predicting a cancer patient's response to a cancer treatment
regimen comprising platinum or anthracycline, comprising: [0417]
determining, in a cancer cell or mRNA derived therefrom from said
cancer patient, BLM and FANCI expression; and [0418] correlating
the expression to a reference value, wherein when the expression is
not increased the patient is predicted to respond poorly to a
cancer treatment regimen comprising platinum or anthracycline.
[0419] 49. The method of paragraph 48, wherein the reference value
is BRCA1 expression in the sample, and the BLM and/or FANCI
expression is increased by at least two-fold compared to BRCA1
expression. [0420] 50. A method of treating cancer, comprising:
[0421] assaying, in a cancer cell from a cancer patient or mRNA
obtained therefrom, the BLM and FANCI expression compared to a
reference value; and [0422] administering to the cancer patient a
cancer treatment regimen comprising platinum or anthracycline if
the BLM and FANCI expression is increased compared to the reference
value. [0423] 51. The method of paragraph 50, wherein the reference
value is BRCA1 expression in the sample, and the BLM and/or FANCI
expression is increased by at least two-fold compared to BRCA1
expression. [0424] 52. Use of platinum comprising cancer therapy
for treating a cancer patient that has been determined to have a
tumor comprising cancer cells wherein BLM and FANCI expression is
increased compared to a reference value.
[0425] 53. The use of paragraph 52, wherein the cancer patient has
been determined to be negative for BRCA1 and/or BRCA2 mutations.
[0426] 54. The use of paragraph 52, wherein the cancer patient's
cancer or cancer cell is known to not or is determined to not
express detectable quantities of estrogen receptor (ER),
progesterone receptor (PgR) and HER2 receptor. [0427] 55. The use
of paragraph 52-54, wherein the reference value is BRCA1 expression
in the sample, and the BLM and/or FANCI expression is increased by
at least two-fold compared to BRCA1 expression. [0428] 56. A system
for determining responsiveness of a cancer cell to
platinum-comprising therapy from a cancer cell of a cancer patient,
comprising: [0429] a sample analyzer configured to produce a signal
for the mRNA from each one of BLM and FANCI from a cancer cell
sample of a cancer patient; and [0430] a computer sub-system
programmed to calculate, based on the mRNA whether the signal is
greater or not than a reference value. [0431] 57. The system of
paragraph 56, wherein said computer sub-system is programmed to
compare the mRNA to determine [0432] a likelihood of responsiveness
of said cancer cell to platinum-comprising cancer therapy based on
an algorithm that classifies the patient as likely to respond to a
platinum-comprising therapy if the BLM and FANCI expression is
increased and as unlikely to respond to the platinum-comprising
therapy if the BLM and FANCI expression is not increased; or [0433]
a likelihood of responsiveness of said cancer cell to
anthracycline-comprising cancer therapy based on an algorithm that
classifies the patient as likely to respond to a
anthracycline-comprising therapy if the BLM and FANCI expression is
increased and as unlikely to respond to the
anthracycline-comprising therapy if the BLM and FANCI expression is
not increased. [0434] 58. The system of paragraph 56-57, wherein
the reference value is BRCA1 expression, and the BLM and/or FANCI
expression is increased by at least two-fold compared to BRCA1
expression. [0435] 59. A computer program product embodied in a
computer readable medium that, when executing on a computer,
performs steps comprising: [0436] detecting the BLM and FANCI gene
expression in sample comprising a cancer cell from a cancer
patient; and [0437] comparing the BLM and FANCI expression to a
reference value. [0438] 60. The computer program of paragraph 59,
wherein the reference value is BRCA1 expression, and the BLM and/or
FANCI expression is increased by at least two-fold compared to
BRCA1 expression. [0439] 61. A diagnostic kit for detecting a
likelihood of a cancer patient to respond to platinum- or
anthracycline-comprising comprising cancer therapy, comprising:
[0440] no more than 10 probes comprising a combination of
detectably labeled probes or primers for BLM and FANCI, and
optionally for BRCA1 and/or at least one housekeeping gene; and
[0441] the computer program product of Paragraph 59. [0442] 62. Use
of a plurality of oligonucleotides comprising no more than 10
oligonucleotides capable of hybridizing to BLM and FANCI, and
optionally to BRCA1 and/or at least one housekeeping gene, in a
diagnostic kit for determining an increased likelihood that a
cancer patient will respond to cancer treatment regimen comprising
a platinum and/or anthracycline. [0443] 63. The use, method or
assay of any one of the preceding paragraphs, wherein said
anthracycline is epirubincin or doxorubicin. [0444] 64. The use,
method or assay of any one of the preceding paragraphs, wherein
said platinum comprising cancer therapy comprises cisplatinum or
cis-diamminedichloroplatinum, phenanthriplatin, carboplatin,
oxaliplatin, or a platinum complex that is activated by ultraviolet
A light. [0445] 65. An assay for selecting a therapy for a subject
having cancer, and optionally administering the therapy, the assay
comprising: [0446] assaying a sample comprising a cancer cell taken
from the subject for a chromosome 15q26 copy number; [0447]
comparing the chromosome 15q26 copy number to a reference value;
and [0448] selecting a platinum-comprising cancer therapy for the
subject if there is a chromosome 15q26 copy number gain compared to
the reference value, or selecting a non-platinum-comprising cancer
therapy for the subject if there is not a chromosome 15q26 copy
number gain, or if there is a chromosome 15q26 copy number loss.
[0449] 66. The assay of paragraph 65, further comprising: [0450]
assaying the BRCA1 and/or BRCA2 status of the subject; and [0451]
selecting the platinum-comprising cancer therapy for the subject
when the subject is negative for BRCA1 and/or BRCA2 mutations, and
there is a chromosome 15q26 copy number gain based on the
recognition that platinum-comprising cancer therapy is effective in
subjects who have a chromosome 15q26 copy number gain who are
negative for BRCA1 and/or BRCA2 mutations. [0452] 67. The assay of
paragraph 65, the subject is known to be or is determined to be
negative for BRCA1 and/or BRCA2 mutations. [0453] 68. The assay of
paragraph 65, further comprising: [0454] assaying the estrogen
receptor (ER), progesterone receptor (PgR), and HER2 receptor
status of the subject's cancer; and [0455] selecting the
platinum-comprising cancer therapy for the subject when the
subject's cancer does not express a detectable quantity of ER, PgR,
and HER2 receptor, and when there is a chromosome 15q26 copy number
gain based on the recognition that platinum-comprising cancer
therapy is effective in subjects who have a chromosome 15q26 copy
number gain and whose cancer does not express a detectable quantity
of ER, PgR, and HER2 receptor. [0456] 69. The assay of paragraph
65, wherein the subject's cancer or cancer cell is known to not or
is determined to not express a detectable quantity of ER, PgR, and
HER2 receptor. [0457] 70. The assay of paragraphs 65-69, further
comprising administering the selected therapy to the subject.
[0458] 71. The assay of paragraphs 65-71, wherein the cancer is
selected from breast cancer, ovarian cancer and lung cancer. [0459]
72. The assay of paragraphs 65-71, wherein the reference value is
chromosome 15 centromere copy number in the sample. [0460] 73. An
assay for selecting a therapy for a subject having cancer, and
optionally administering the therapy, the assay comprising: [0461]
assaying a sample comprising a cancer cell taken from the subject
for a chromosome 15q26 copy number; [0462] comparing the chromosome
15q26 copy number to a reference value; and [0463] selecting an
anthracycline-comprising cancer therapy for the subject if there is
a chromosome 15q26 copy number gain compared to the reference
value, or selecting a non-anthracycline-comprising cancer therapy
for the subject if there is not a chromosome 15q26 copy number
gain, or if there is a chromosome 15q26 copy number loss. [0464]
74. The assay of paragraph 73, further comprising: [0465] assaying
the BRCA1 and/or BRCA2 status of the subject; and [0466] selecting
the anthracycline-comprising cancer therapy for the subject when
the subject is negative for BRCA1 and/or BRCA2 mutations, and there
is a chromosome 15q26 copy number gain based on the recognition
that anthracycline-comprising cancer therapy is effective in
subjects who have a chromosome 15q26 copy number gain who are
negative for BRCA1 and/or BRCA2 mutations. [0467] 75. The assay of
paragraph 73, the subject is known to be or is determined to be
negative for BRCA1 and/or BRCA2 mutations. [0468] 76. The assay of
paragraph 73, further comprising: [0469] assaying the estrogen
receptor (ER), progesterone receptor (PgR), and HER2 receptor
status of the subject's cancer; and [0470] selecting the
anthracycline-comprising cancer therapy for the subject when the
subject's cancer does not express a detectable quantity of ER, PgR,
and HER2 receptor, and when there is a chromosome 15q26 copy number
gain based on the recognition that anthracycline-comprising cancer
therapy is effective in subjects who have a chromosome 15q26 copy
number gain and whose cancer does not express a detectable quantity
of ER, PgR, and HER2 receptor. [0471] 77. The assay of paragraph
73, wherein the subject's cancer or cancer cell is known to not or
is determined to not express a detectable quantity of ER, PgR, and
HER2 receptor. [0472] 78. The assay of paragraphs 73-77, further
comprising administering the selected therapy to the subject.
[0473] 79. The assay of paragraphs 73-78, wherein the cancer is
selected from breast cancer, ovarian cancer and lung cancer. [0474]
80. The assay of paragraphs 73-79, wherein the reference value is
chromosome 15 centromere copy number in the sample. [0475] 81. A
method of treating cancer in a human subject, comprising: [0476]
detecting a chromosome 15q26 copy number in a sample comprising a
cancer cell taken from the subject; [0477] comparing the chromosome
15q26 copy number to a reference value; and [0478] administering an
platinum-comprising cancer therapy for the subject if there is a
chromosome 15q26 copy number gain compared to the reference value,
or administering a non-platinum-comprising cancer therapy for the
subject if there is not a chromosome 15q26 copy number gain, or if
there is a chromosome 15q26 copy number loss. [0479] 82. The method
of paragraphs 81, wherein the cancer is selected from breast
cancer, ovarian cancer and lung cancer. [0480] 83. The method of
paragraphs 81-82, wherein the reference value is chromosome 15
centromere copy number in the sample. [0481] 84. The method of
paragraph 81-83, wherein the subject's cancer is known to not
express a detectable quantity of ER, PgR, and HER2 receptor. [0482]
85. A method of treating cancer in a human subject, comprising:
[0483] detecting a chromosome 15q26 copy number in a sample
comprising a cancer cell taken from the subject; [0484] comparing
the chromosome 15q26 copy number to a reference value; and [0485]
administering an anthracycline-comprising cancer therapy for the
subject if there is a chromosome 15q26 copy number gain compared to
the reference value, or administering a
non-anthracycline-comprising cancer therapy for the subject if
there is not a chromosome 15q26 copy number gain, or if there is a
chromosome 15q26 copy number loss. [0486] 86. The method of
paragraphs 85, wherein the cancer is selected from breast cancer,
ovarian cancer and lung cancer. [0487] 87. The method of paragraphs
85-86, wherein the reference value is chromosome 15 centromere copy
number in the sample. [0488] 88. The method of paragraph 85-88,
wherein the subject's cancer or cancer cell is known to not or is
determined to not express a detectable quantity of ER, PgR, and
HER2 receptor. [0489] 89. A method for assessing responsiveness of
a cancer cell to a cancer therapy, and optionally administering the
cancer therapy, comprising: [0490] assaying a sample comprising a
cancer cell taken from the subject for a chromosome 15q26 copy
number; [0491] and comparing the chromosome 15q26 copy number to a
reference value, wherein the cancer cell is assessed as responsive
to a platinum-comprising therapy if there is a chromosome 15q26
copy number gain compared to the reference value, or wherein the
cancer cell is assessed as poorly or not responsive to
platinum-comprising cancer therapy cancer if there is not a
chromosome 15q26 copy number gain or if there is a chromosome 15q26
copy number loss. [0492] 90. The method of paragraph 89, wherein
the reference value is copy number of chromosome 15. 91. The method
of paragraph 89, wherein the cancer is selected from breast cancer,
ovarian cancer and lung cancer. [0493] 92. The method of paragraph
89, further comprising administering the platinum-comprising
therapy if there is a chromosome 15q26 copy number gain. [0494] 93.
A method of predicting a cancer patient's response to a cancer
treatment regimen comprising platinum or anthracycline, comprising:
[0495] determining, in a cancer cell from the cancer patient,
chromosome 15q26 copy number; and [0496] correlating the chromosome
15q26 copy number to a reference value, [0497] wherein when there
is a chromosome 15q26 copy number gain, the patient is predicted to
respond well to a cancer treatment comprising platinum or
anthracycline, or wherein when there is not a chromosome 15q26 copy
number gain or a chromosome 15q26 copy number loss, the patient is
predicted respond poorly to a cancer treatment comprising platinum
or anthracycline. [0498] 94. The method of paragraph 93, wherein
the reference value is chromosome 15 centromere copy number in the
sample. [0499] 95. Use of platinum comprising cancer therapy for
treating a cancer patient that has been determined to have a tumor
comprising cancer cells wherein a chromosome 15q26 copy gain is
detected compared to a reference value. [0500] 96. The use of
paragraph 95, wherein the cancer patient is known to be or is
determined to be negative for BRCA1 and/or BRCA2 mutations. [0501]
97. The use of paragraph 95, wherein the cancer patient's cancer or
cancer cell is known to not or is determined to not express
detectable quantities of estrogen receptor (ER), progesterone
receptor (PgR) and HER2 receptor. [0502] 98. The use of paragraph
95-97, wherein the reference value is chromosome 15 centromere copy
number in the sample. [0503] 99. A system for determining
responsiveness of a cancer cell to platinum-comprising therapy from
a cancer cell of a cancer patient, comprising: [0504] a sample
analyzer configured to produce a signal for chromosome 15q26 copy
number from a cancer cell sample of a cancer patient; and [0505] a
computer sub-system programmed to calculate, based on the mRNA
whether the signal is greater or not than a reference value. [0506]
100. The system of paragraph 99, wherein said computer sub-system
is programmed to compare the mRNA to determine [0507] a likelihood
of responsiveness of said cancer cell to platinum-comprising cancer
therapy and/or or a anthracycline-comprising cancer therapy based
on an algorithm that classifies the patient as likely to respond to
a platinum-comprising therapy if there is a chromosome 15q26 copy
number gain and as unlikely to respond to the platinum-comprising
therapy if there is not a chromosome 15q26 copy number gain or if
there is a chromosome 15q26 copy number loss. [0508] 101. The
system of paragraph 99-100, wherein the reference value is
chromosome 15 centromere copy number in the sample. [0509] 102. A
computer program product embodied in a computer readable medium
that, when executing on a computer, performs steps comprising:
[0510] detecting chromosome 15q26 copy number in sample comprising
a cancer cell from a cancer patient; and [0511] comparing the
chromosome 15q26 copy number to a reference value. [0512] 103. The
computer program of paragraph 102, wherein the reference value is
chromosome 15 centromere copy number in the sample. [0513] 104. A
diagnostic kit for detecting a likelihood of a cancer patient to
respond to platinum- or anthracycline-comprising cancer therapy,
comprising:
[0514] no more than 10 probes comprising a combination of
detectably labeled probes or primers for chromosome 15q26, and
optionally for chromosome 15 centromere; and [0515] the computer
program product of Paragraph 102. [0516] 105. Use of a plurality of
oligonucleotides comprising no more than 10 oligonucleotides
capable of hybridizing to chromosome 15q26, and optionally for
chromosome 15 centromere, in a diagnostic kit for determining an
increased likelihood that a cancer patient will respond to cancer
treatment regimen comprising a platinum and/or anthracycline.
[0517] 106. The use, method or assay of paragraphs 65-105, wherein
said anthracycline is epirubincin or doxorubicin. [0518] 107. The
use, method or assay paragraphs 65-105, wherein said platinum
comprising cancer therapy comprises cisplatinum or
cis-diamminedichloroplatinum, phenanthriplatin, carboplatin,
oxaliplatin, or a platinum complex that is activated by ultraviolet
A light.
[0519] The following examples are provided to better illustrate the
claimed invention and are not to be interpreted as limiting the
scope of the invention. To the extent that specific materials are
mentioned, it is merely for purposes of illustration and is not
intended to limit the invention. One skilled in the art may develop
equivalent means or reactants without the exercise of inventive
capacity and without departing from the scope of the invention.
Example 1
[0520] Two clinical trials with cisplatin given to women with
triple negative breast cancer were evaluated.
[0521] Cisplatin-1 (DFHCC 04-183; Silver et al., JCO 2010): 28 TNBC
patients received neoadjuvant cisplatin as single agent. 10 (36%)
achieved at least 90% reduction in tumor size. Good quality RNA and
DNA were acquired from 21 tumors. Copy number and gene expression
were assayed using AFFYMETRIX arrays.
[0522] Cisplatin-2 (DFHCC 06-202; Ryan et al., JCO 2009): 51 TNBC
patients received neoadjuvant cisplatin in combination with the
angiogenesis inhibitor bevacizumab. [0523] 44 patients completed
therapy. 17 (39%) achieved at least 90% reduction in tumor size.
Frozen DNA samples were acquired from 24 tumors, mRNA from 21. Copy
number and gene expression assayed using AFFYMETRIX arrays.
Example 2
[0524] In order to find regions or genes where gain or loss were
significantly associated with sensitivity of resistance cisplatin,
.about.40,000 SNP probes were used in Cisplatin-1 trial and
.about.330,000 SNP probes were used in Cisplatin-2 trial to
determine sensitivity and resistance. GISTIC identified chromosomal
regions that were significantly enriched in either group. Gene copy
number comparison showed that genes significantly gained or lost
between sensitive and resistant cases, in both cohorts. Comparison
to gene expression showed overlap with genes showing differential
expression between sensitive and resistant cancers. See e.g., FIGS.
1-3.
Example 3
[0525] In a comparison to gene expression data, the inventors found
genes that show both significant gain and higher expression in
sensitive sample. In Cisplatin-1 trial, there were 21 cases;
Cisplatin-2 trial, there were 21 cases. In an ovarian cancer trial
(OV-01 trial; Ahmed et al., Cancer Cell 2007), the two arm
carboplatinum had 15 cases and paclitaxel had 19 cases. A
leave-one-out analysis of the gene expression data was performed
from both platinum breast cancer trials and the carboplatinum arm
of OVO1. See e.g., FIGS. 4-5.
Example 4
[0526] In evaluating Hess et al., JCO 2006; Popovici et al., Breast
Cancer Res 2010; and Andre et al., Clin Cancer Res 2009, expression
of BLM or FANCI is not found to be associated with response to
multi-agent chemotherapy regimens in TNBC. See e.g., FIG. 6.
Example 5
[0527] In evaluating Desmedt et al., JCO 2011, BLM is associated
with response to single agent epirubicin. See e.g., FIG. 7.
Example 6
Chromosome 15q26 Copy Number and Overexpression of BLM and FANCI
Predict for Cisplatin Sensitivity
[0528] To elucidate if particular genomic aberrations may affect
cancer cells sensitivity to cisplatin, we compared the tumor DNA
copy number profiles in sensitive versus resistant TN breast tumors
in the two separate cisplatin clinical trials. We identified
several sites of DNA copy number change in each trial, but only a
short 15 megabase (MB) region on chromosome 15q26 was significantly
different between responders and nonresponders in both trials. In
addition to SNP profiles, we have analyzed the pretreatment tumor
samples for both Cisplatin1 and Cisplatin2 for mRNA expression
profiles on Affymetrix microarrays. In addition, gene expression
array data was publically available from the carboplatin arm of a
previously published two-arm trial of carboplatin and paclitaxel in
serous ovarian cancer[31]. To determine if any specific genes were
consistently differentially expressed in platinum sensitive
compared to resistant tumors, we performed a leave-one-out analysis
in each trial, where we in each round compared the sensitive to the
resistant tumors, and scored how many genes showed a significant
association. We found that only 3 genes were consistently
significantly different in all three platinum-based trials: MCM2,
BLM, and FANCI. Interestingly, FANCI and BLM are both located on
15q26.1 and the proteins have been shown to localize to sites of
DNA damage. This shows that using two different methods measuring
two different biomolecules, high levels of BLM and FANCI DNA and
mRNA is associated with greater sensitivity to platinum-based
chemotherapy.
[0529] To investigate if higher expression of BLM and FANCI were
specifically associated with platinum chemotherapy response, we
analyzed the gene expression in the paclitaxel arm of the ovarian
trial[31], and across the TN breast cancer subset of three
neoadjuvant cohorts that received taxane-containing combination
chemotherapy[32-34].
[0530] In the ovarian paclitaxel trial and in the TN subset of the
taxane-containing multidrug trials there was no association between
either BLM or FANCI and therapy response. These data suggests that
high expression of BLM and FANCI are possibly specifically
associated with sensitivity to DNA damaging agents like the
platinum salts, but not with response to chemotherapeutics that
alter microtubules such as taxanes.
[0531] We combined the mRNA results into a predictive gene
signature: (BRCA1 mRNA)/(average of FANCI and BLM mRNA). ROC
analysis demonstrates that this 3gene mRNA signature is
significantly associated with cisplatin response in both TN
cisplatin trials (FIG. 10A). A prediction model combining NtAI and
the 3 gene signature improved the prediction of cisplatin
sensitivity (FIG. 10B). Based on the combined model, 25% of cases
are "biomarker positive" with predictive accuracy of 0.86, a
positive predictive value of 0.89, a negative predictive value of
0.85, sensitivity of 0.67, and specificity of 0.96 with a p-value
of 0.00016.
Example 7
Optimization of BRCA1-BLM-FANCI mRNA Measurement
[0532] Several different RT-PCR primer pair assays will be designed
to measure mRNA expression for each of the three genes. Data from
the Cisplatin2 trial comparing the BRCA1, BLM, and FANCI mRNA
levels on microarray to mRNA levels as measured by quantitative
real-time PCR and found good correlation. The 3-gene predictive
model of BRCA1/(avg of BLM+FANCI) using the RT-PCR measurements
performed very well for prediction of cisplatin response (FIG.
11).
Example 8
[0533] Platinum salts are effective treatment and standard therapy
for a number of cancer types including serous ovarian carcinoma,
high grade urothelial carcinoma, pancreatic adenocarcinoma,
glioblastoma multiforme, and lung squamous cell carcinoma. Breast
adenocarcinomas arising in women carrying BRCA1 or BRCA2 mutations
are also sensitive to cisplatin chemotherapy (Byrski, 2008). BRCA1
is a tumor suppressor that plays important roles in several aspects
of maintenance of genome integrity. Complete absence of functional
BRCA1, as occurs in tumors of BRCA1 mutation carriers with loss of
the wild-type allele, leads to defective error-free homologous
recombination-type double strand break repair. These BRCA1-/-
tumors are sensitive to inhibitors of PARP1 (ref) whereas, so far,
few or no sporadic BRCA wild-type breast cancers have responded to
these agents. Recent studies have shown that in addition to double
strand break repair, BRCA1 also plays an important role in response
to replication stress and repair of stalled or collapsed
replication forks (Pathania, 2011). Preliminary evidence suggests
the replication repair functions of BRCA1 may be haploinsufficient
in BRCA1 heterozygous cells (Pathania, unpublished data). The
platinum salts generate interstrand and intrastrand crosslinks that
distort DNA and lead to stalled replication forks. If these stalled
forks collapse, double strand breaks will results. It is possible
that several BRCA1-dependent pathways are involved in
platinum-induced DNA damage response including damage recognition
and lesion excision, suppression of translesion synthesis,
checkpoint activation, and repair of DS breaks after fork
collapse.
[0534] The activity of cisplatin has recently been extended to
estrogen, progesterone, and HER2 receptor negative sporadic breast
cancers (triple-negative breast cancers, TNBC)(Silver, 2010;
Birkbak, 2012; Ryan, 2009). When carboplatin was added to
anthracycline and taxane chemotherapy for treatment of TNBC, the
response rate was higher but resulted in notably greater toxicity.
Predictors of tumor response to platinum salts are needed to
determine which patients may derive the greatest benefit from the
addition of platinum. Previous molecular studies have shown the
platinum-sensitive TNBC and serous ovarian cancers carry high
levels of genomic rearrangements and chromosomal allelic imbalance,
suggesting these cancers may share similar defects in DNA repair,
which may make them particularly sensitive to platinum chemotherapy
(Birkbak, 2012). Many of the platinum-sensitive sporadic TNBCs have
promoter methylation and reduction in the expression of BRCA1
(Birkbak, 2012; Silver, 2010). These result suggests that platinum
sensitivity may be related to a functional defect that occurs when
there is insufficient BRCA1 levels, raising the possibility that
defects in a haploinsufficient function of BRCA1, such as
replication-dependent stalled fork repair, may be indicative of
sensitivity to interstrand cross-linkers such as the platinum
salts.
[0535] To further explore and define other specific molecular
alterations that might be associated with cisplatin sensitivity, we
took and integrated genomic approach combining differential
analysis of gene expression and DNA copy number in cisplatin
sensitive compared to cisplatin resistant triple negative breast
cancers. We identify two genes, the Bloom helicase (BLM) and
Fanconi anemia complementation group I (FANCI), that have both
increased DNA copy number at chr 15q26 and concordant mRNA
overexpression in the TNBC with increased sensitivity to cisplatin
therapy. In vitro modulation of BLM and FANCI expression suggest
these two genes play a functional role and promote DNA damage and
sensitivity to platinum salts, but have no effect on taxane
sensitivity.
[0536] Identification of genes critical for tumor response to
specific chemotherapy drugs is a challenge, but important for
tailoring therapy and avoiding unnecessary toxicity in patients.
Integrated genomic approaches that combine DNA copy number analysis
with gene expression profile analysis has successfully indicated
genomic alterations associated with chemotherapy resistance and
tumor response (Li, 2010). We have previously published the results
of two trials of cisplatin chemotherapy in TNBC in which
presurgical treatment with cisplatin resulted in greater than 90%
reduction in tumor volume in 36% and 39% of patients respectively
(Silver, 2010; Ryan, 2009). Molecular inversion probe SNP copy
number profiles of pretreatment tumors from both cisplatin TNBC
trials were reported previously (Birkbak, 2012). Gene expression
profiles from the pretreatment tumor samples from the first
cisplatin TNBC trial were also reported previously (Silver, 2010).
For this study, we generated gene expression profiles from the
pretreatment tumor biopsies from the second cisplatin TNBC
trial.
[0537] To determine genes whose expression is significantly and
robustly associated with response to cisplatin, we performed a
leave-one-out differential gene expression analysis in each trial,
comparing the gene expression of tumors resistant to cisplatin to
tumors that were sensitive to cisplatin. For each leave-one-out
round, one sample was removed and all genes significantly
associated with response were determined. The direction of
association for each gene (higher in sensitive vs. lower in
sensitive) was also noted. Permutation testing of this gene
expression comparison exercise indicated that a gene must be
present in 85% or more rounds to be significant. This analysis
identified only 12 genes whose expression was significantly
associated with platinum response, in the same direction, in at
least 85% of all rounds in both cisplatin TNBC cohorts.
[0538] We performed next a similar leave one out comparison
analysis of the DNA copy numbers of cisplatin sensitive vs.
cisplatin resistant TNBC tumors in the two trials. Permutation
testing of the DNA copy number LOO analysis indicated that a gene
must be present in 50% or more LOO rounds to be significant. This
analysis identified 234 genes from four different chromosomes with
differential copy number associated with cisplatin response in at
least 50% of all rounds in both cisplatin TNBC cohorts.
[0539] Only two genes were identified in both the DNA copy number
and gene expression leave-one-out analyses for association with
platinum sensitivity, Bloom helicase (BLM) and Fanconi anemia
complementation group I (FANCI), both located at chromosome 15q26.
The DNA copy number of the 15q26 region containing these two genes
was significantly higher in the cisplatin-sensitive tumors in both
TNBC cohorts (p=0.00236 and p=0.0107, respectively. Similarly,
cisplatin sensitive tumors had significantly higher BLM expression
in both TNBC cohorts (cisplatin-1, mean log 2 expression, 8.26
versus 7.54, p=0.00278; cisplatin-2, mean log 2 expression, 10.67
versus 9.41, p=0.00745; FIG. 1C-D). FANCI expression was higher in
the cisplatin-sensitive TNBCs in both cohorts (cisplatin-1, mean
log 2 expression 7.87 versus 6.80, p=0.00356; cisplatin-2, mean log
2 expression 10.74 versus 9.77, p=0.0125).
[0540] The gene expression of BLM and FANCI as measured by
Affymetrix U133 array was validated by RT-PCR in the same samples
and the results showed good correlation (BLM, r=0.866; FANCI,
r=0.733). BLM (and FANCI) are reported to have post-translational
mechanisms of protein regulation. To determine if overexpression of
BLM and FANCI mRNA also results in increased expression of the
protein, we measured BLM (and FANCI) protein by western blot
analysis in protein extracts from a series of frozen breast tumor
samples for which mRNA gene array expression levels were known (Lu,
2008). BLM normalized to actin (and FANCI) showed good correlation
between mRNA expression levels and protein expression levels
(r=0.70).
[0541] BRCA1 as measured by RT-PCR was identified in our previous
studies as significantly associated with cisplatin resistance
(Birkbak, 2012; Silver, 2010). In contrast to BLM and FANCI, BRCA1
expression as measured by microarray was poorly correlated with
expression as measured by RT-PCR (r=xxx); the microarray BRCA1
probe performance was especially poor in the data from first
cisplatin TNBC cohort. Therefore, we used the RT-PCR expression
data to test the association of the ratio of BRCA1/average
(BLM+FANCI) expression and cisplatin response. The ratio was
significantly higher in the cisplatin sensitive tumors in both
cohorts (cisplatin-1, median x vs y, p=0.023; cisplatin-2, median
7.69 vs 4.07, p=0.0016).
[0542] To validate these specific gene associations with platinum
response, we tested a publically available gene expression data set
from a serous ovarian cancer trial of either carboplatin
monotherapy or paclitaxel monotherapy and sought associations with
response to the therapy received. The average expression of BLM and
FANCI was significantly higher in the carboplatin-sensitive ovarian
cancers (median 5.46 versus 4.50, p=0.026). The ratio of
BLM+FANCI/BRCA1 was also significantly higher in carboplatin
sensitive ovarian cancers (median 1.29 vs 0.42, p=0.026).
Interestingly, the association of BLM and FANCI with paclitaxel
response was not significant and the trend was in the opposite
direction (median 5.17 versus 4.79, p=0.27).
[0543] We also showed protein abundance of BRCA1, BLM, FANCI, and
Cyclin A was measured by Western blot analysis in protein extracts
from a panel of breast cancer cell lines. The bands were
quantitated by densitometry and displayed in bar plots. We showed
the quantitation of BLM to Actin and BRCA1 to BLM ratio. Three cell
lines (BT549, HCC1143, and HCC38) are normal genotype for BRCA1 and
have high BLMIActin and low ratio of BRCA1/BLM. Two cell lines
(MDA231 and MDA453) are also normal genotype for BRCA1 but have
relatively higher expression of BRCA1/BLM and lower BLM/actin.
HCC1937 and MDA436 have homozygous mutation in BRCA1 and
undetectable BRCA1/BLM, and higher expression of BLM/Actin.
[0544] A panel of cell lines was evaluated for sensitivity to
various treatments as indicated by colony formation assay and
calculation of IC50 values. We showed a pattern of sensitivity to
cisplatin, UV radiation treatment, and Parp inhibitor Olaparib
across the panel of cell lines is associated with the pattern of
relative expression of BRCA1/BLM and BLM/Actin. The two BRCA1
mutated cell lines and the three cell lines with low BRCA1/BLM and
high BLM/actin have greater sensitivity to DNA strand cross-linker
cisplatin, PARP inhibitor Olaparib, and UV irradiation. The two
cell lines with low BLM and high BRCA1/BLM (MDA231, MDA453) are
relatively resistant to these treatments. In contrast, there is no
apparent association between BLM and BRCA1 expression with the
pattern of sensitivity to the microtubule stabilizer
Paclitaxel.
[0545] We also treated U2OS cells treated shRNA to BRCA1. After 1
week, the expression of BRCA1 and BLM were measured by Western blot
analysis. Cells treated with the BRCA1 specific shRNA showed
increased expression of BLM compared to control cells treated with
shRNA to luciferase.
[0546] We further treated BT549 breast cancer cells, with inherent
high levels of BLM and FANCI were treated with gene-specific siRNAs
to BLM or FANCI or with a scramble control. Gene specific siRNA
treatment resulted in reduced mRNA expression as determined by
RT-PCR. Sensitivity to cisplatin and to paclitaxel was determined
by colony formation assay to calculate the IC50. siRNA knockdown of
either BLM or FANCI resulted in increased IC50 (greater resistance)
to cisplatin treatment but no significant effect on sensitivity to
paclitaxel.
[0547] MDA231 cells have low levels of BLM and relative resistance
to cisplatin. These cells were used in experiments to assess the
effect of increasing the expression of BLM. A lentivirus expression
vector for HA-tagged BLM cDNA or a control vector was transfected
into MDA231 cells. BLM expression was assessed by Western blot
analysis for endogenous BLM or for the HA-tag in cells treated with
control vector, BLM cDNA, BLM cDNA and a small molecule inhibitor
of BLM helicase (BLMi), or BLM cDNA and BLM siRNA. We showed that
siRNA for BLM reduced the expression of endogeneous and HA-tagged
BLM whereas the small molecule inhibitor (BLMi) had no effect on
protein expression of BLM.
[0548] IC50 for cisplatin was determined by colony formation assay
in MDA231 breast cancer cells treated with control vector, BLM cDNA
vector, BLM cDNA plus the BLM small molecule inhibitor, and BLM
cDNA plus BLM siRNA. Overexpression of BLM resulted in decrease in
the IC50 (greater sensitivity) to cisplatin. Consistent with the
other findings, this effect was reversed by treatment with the BLM
helicase inhibitor and by siRNA knockdown of BLM.
[0549] We also performed an immunofluorescence assay for markers of
DNA damage (H2Ax-p and 53BP1-p) in MDA231 cells treated with
control vector, BLM cDNA, BLM cDNA+BLM inhibitor, or BLM cDNA+BLM
siRNA. Overexpression of BLM results in increased H2AX and 53BP1
foci in the absence of any cisplatin treatment indicating
spontaneous DNA damage. This effect is even greater in cells
treated with cisplatin after 4 hours. The quantitation of foci is
shown in the lower bar graphs. The addition of a small molecule BLM
helicase inhibitor (Bi) or siRNA to BLM (si) blocks the effect of
BLM overexpression on DNA damage foci.
INCORPORATION BY REFERENCE
[0550] All publications, patents, and patent applications mentioned
herein are hereby incorporated by reference in their entirety as if
each individual publication, patent or patent application was
specifically and individually indicated to be incorporated by
reference. In case of conflict, the present application, including
any definitions herein, will control.
[0551] Also incorporated by reference in their entirety are any
polynucleotide and polypeptide sequences which reference an
accession number correlating to an entry in a public database, such
as those maintained by The Institute for Genomic Research (TIGR) on
the world wide web and/or the National Center for Biotechnology
Information (NCBI) on the world wide web.
EQUIVALENTS
[0552] Those skilled in the art will recognize, or be able to
ascertain using no more than routine experimentation, many
equivalents to the specific embodiments of the invention described
herein. Such equivalents are intended to be encompassed by the
following claims.
[0553] Various embodiments of the invention are described above in
the Detailed Description. While these descriptions directly
describe the above embodiments, it is understood that those skilled
in the art may conceive modifications and/or variations to the
specific embodiments shown and described herein. Any such
modifications or variations that fall within the purview of this
description are intended to be included therein as well. Unless
specifically noted, it is the intention of the inventors that the
words and phrases in the specification and claims be given the
ordinary and accustomed meanings to those of ordinary skill in the
applicable art(s).
[0554] The foregoing description of various embodiments of the
invention known to the applicant at this time of filing the
application has been presented and is intended for the purposes of
illustration and description. The present description is not
intended to be exhaustive nor limit the invention to the precise
form disclosed and many modifications and variations are possible
in the light of the above teachings. The embodiments described
serve to explain the principles of the invention and its practical
application and to enable others skilled in the art to utilize the
invention in various embodiments and with various modifications as
are suited to the particular use contemplated. Therefore, it is
intended that the invention not be limited to the particular
embodiments disclosed for carrying out the invention.
[0555] While particular embodiments of the present invention have
been shown and described, it will be obvious to those skilled in
the art that, based upon the teachings herein, changes and
modifications may be made without departing from this invention and
its broader aspects and, therefore, the appended claims are to
encompass within their scope all such changes and modifications as
are within the true spirit and scope of this invention. It will be
understood by those within the art that, in general, terms used
herein are generally intended as "open" terms (e.g., the term
"including" should be interpreted as "including but not limited
to," the term "having" should be interpreted as "having at least,"
the term "includes" should be interpreted as "includes but is not
limited to," etc.).
Sequence CWU 1
1
114PRTHomo sapiens 1Lys Asp Glu Leu1
* * * * *