U.S. patent application number 17/064823 was filed with the patent office on 2021-04-08 for anti-galectin antibody biomarkers predictive of anti-immune checkpoint and anti-angiogenesis responses.
The applicant listed for this patent is Dana-Farber Cancer Institute, Inc.. Invention is credited to F. Stephen Hodi, Jingjing Li, Xinqi Wu.
Application Number | 20210102948 17/064823 |
Document ID | / |
Family ID | 1000005279510 |
Filed Date | 2021-04-08 |
United States Patent
Application |
20210102948 |
Kind Code |
A1 |
Hodi; F. Stephen ; et
al. |
April 8, 2021 |
ANTI-GALECTIN ANTIBODY BIOMARKERS PREDICTIVE OF ANTI-IMMUNE
CHECKPOINT AND ANTI-ANGIOGENESIS RESPONSES
Abstract
The present invention is based on the identification of novel
biomarkers predictive of responsiveness to a combination of
anti-immune checkpoint and anti-angiogenesis therapies.
Inventors: |
Hodi; F. Stephen;
(Framingham, MA) ; Wu; Xinqi; (Chestnut Hill,
MA) ; Li; Jingjing; (Lexington, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Dana-Farber Cancer Institute, Inc. |
Boston |
MA |
US |
|
|
Family ID: |
1000005279510 |
Appl. No.: |
17/064823 |
Filed: |
October 7, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15523519 |
May 1, 2017 |
10837966 |
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PCT/US15/58276 |
Oct 30, 2015 |
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17064823 |
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62074779 |
Nov 4, 2014 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 16/06 20130101;
A61P 35/00 20180101; C07K 16/2818 20130101; A61K 2039/507 20130101;
C07K 2317/76 20130101; C07K 16/22 20130101; G01N 33/57488 20130101;
C07K 16/30 20130101; C07K 16/2851 20130101 |
International
Class: |
G01N 33/574 20060101
G01N033/574; C07K 16/22 20060101 C07K016/22; C07K 16/28 20060101
C07K016/28; A61P 35/00 20060101 A61P035/00; C07K 16/06 20060101
C07K016/06; C07K 16/30 20060101 C07K016/30 |
Claims
1-8. (canceled)
9. A method of assessing the efficacy of an agent for treating a
cancer in a subject that is unlikely to be responsive to
anti-immune checkpoint and anti-angiogenesis combination therapy,
comprising: a) detecting the amount or activity of at least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof, from a subject in which the agent
has not been administered; b) detecting the amount or activity of
at least one antibody that specifically binds the biomarker listed
in Table 1, or antigen-binding fragment thereof, in the subject in
which the agent has been administered; and c) comparing the amount
or activity of the at least one antibody that specifically binds
the biomarker listed in Table 1, or antigen-binding fragment
thereof, from steps a) and b), wherein a significantly increased
amount or activity of the at least one antibody that specifically
binds the biomarker listed in Table 1, or antigen-binding fragment
thereof, in step b) relative to step a), indicates that the agent
treats the cancer in the subject.
10. (canceled)
11. The method of claim 9, wherein between the first point in time
and the subsequent point in time, the subject has undergone
treatment, completed treatment, and/or is in remission for the
cancer.
12. The method of claim 9, wherein the first and/or at least one
subsequent sample is selected from the group consisting of ex vivo
and in vivo samples.
13. The method of claim 9, wherein the first and/or at least one
subsequent sample is obtained from an animal model of the
cancer.
14. The method of claim 9, wherein the first and/or at least one
subsequent sample is a portion of a single sample or pooled samples
obtained from the subject.
15-16. (canceled)
17. The method or assay of claim 9, wherein the subject sample
and/or the control sample has not been contacted with either a) any
anti-cancer treatment, b) any anti-immune checkpoint agent, or c)
any anti-angiogenesis agent.
18. The method or assay of claim 9, wherein the subject has not
been administered any either a) any anti-cancer treatment, b) any
anti-immune checkpoint agent, or c) any anti-angiogenesis
agent.
19. The method or assay of claim 9, further comprising
recommending, prescribing, or administering at least one additional
anti-cancer therapeutic agent, optionally wherein the at least one
additional anti-cancer therapeutic agent is an anti-immune
checkpoint agent, ipilimumab, an anti-angiogenesis agent, an
anti-VEGF agent, bevacizumab, a neutralizing anti-Gal-1 antibody or
antigen-binding fragment thereof, a neutralizing anti-Gal-3
antibody or antigen-binding fragment thereof, a neutralizing
anti-Gal-9 antibody or antigen-binding fragment thereof, or
combinations thereof.
20. The method or assay of claim 9, wherein the subject sample is
selected from the group consisting of serum, whole blood, plasma,
urine, cells, cell lines, and biopsies.
21. The method or assay of claim 9, wherein the amount of the least
one antibody that specifically binds a biomarker listed in Table 1,
or antigen-binding fragment thereof.
22. The method or assay of claim 21, wherein the reagent is
selected from the group consisting of a Gal-1 polypeptide or
fragment thereof, Gal-3 polypeptide or fragment thereof, Gal-9
polypeptide or fragment thereof, or any combination thereof.
23. The method or assay of claim 9, wherein the at least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof, is assessed by enzyme-linked
immunosorbent assay (ELISA), radioimmune assay (RIA),
immunochemically, Western blot, or flow cytometry.
24. The method or assay of claim 23, wherein the biomarker listed
in Table 1 is immobilized onto a solid support.
25. The method or assay of claim 24, wherein the solid support is
an array, bead, or plate.
26. The method or assay of claim 9, wherein the at least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof, is detected by detecting binding
of an anti-IgG antibody against the antibody or antigen-binding
fragment thereof.
27. The method or assay of claim 9, wherein the at least one
antibody that specifically binds the biomarker listed in Table 1,
or antigen-binding fragment thereof, is an anti-human Gal-1, an
anti-human Gal-3, or an anti-human Gal-9 antibody, or an
antigen-binding fragment thereof, optionally wherein the antibody
or antigen-binding fragment thereof is a neutralizing antibody or
neutralizing antigen-binding fragment thereof.
28. The method or assay of claim 9, wherein the anti-immune
checkpoint and anti-angiogenesis combination therapy comprises at
least one antibody selected from the group consisting of
anti-CTLA-4 antibodies, anti-PD-1 antibodies, anti-PD-L1
antibodies, anti-PD-L2 antibodies, anti-VEGF antibodies, and
combinations thereof.
29. The method or assay of claim 28, wherein the anti-immune
checkpoint therapy comprises ipilimumab and/or anti-angiogenesis
therapy comprises bevacizumab.
30. The method or assay of claim 9, wherein the likelihood of the
cancer in the subject to be responsive to anti-immune checkpoint
and anti-angiogenesis combination therapy is the likelihood of at
least one criteria selected from the group consisting of cellular
proliferation, tumor burden, m-stage, metastasis, progressive
disease, clinical benefit rate, survival until mortality,
pathological complete response, semi-quantitative measures of
pathologic response, clinical complete remission, clinical partial
remission, clinical stable disease, recurrence-free survival,
metastasis free survival, disease free survival, circulating tumor
cell decrease, circulating marker response, and RECIST
criteria.
31. The method or assay of claim 9, wherein the cancer is a solid
tumor.
32. The method or assay of claim 9, wherein the cancer is melanoma,
non-small cell lung cancer (NSCLC), small cell lung cancer (SCLC),
bladder cancer, prostate cancer, metastatic hormone-refractory
prostate cancer, renal cell cancer, colon cancer, ovarian cancer,
or brain glioblastoma multiforme.
33. The method or assay of claim 32, wherein the melanoma is
metastatic melanoma.
34. The method or assay of claim 9, wherein the subject is a
mammal.
35. The method or assay of claim 34, wherein the mammal is an
animal model of cancer.
36. The method or assay of claim 34, wherein the mammal is a human.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Application No. 62/074,779, filed on 4 Nov. 2014; the entire
contents of said application are incorporated herein in their
entirety by this reference.
BACKGROUND OF THE INVENTION
[0002] Cancer immune therapy is a rapidly developing field that has
yielded impressive and promising breakthroughs. For example, CTLA-4
is an immune checkpoint molecule with immunosuppressive function
(Korman et al. (2006) Adv. Immunol. 90:297-339). CTLA-4 ligation on
activated T cells downregulates T cell responses, acting as the
brakes on T cell activation. Clinical studies have shown that
ipilimumab (Ipi), a fully humanized monoclonal antibody that blocks
CTLA-4 activity, improves overall survival in a subset of patients
with metastatic melanoma (Hodi et al. (2010) N. Engl. J. Med.
363:711-723; Robert et al. (2010) N. Engl. J. Med. 364:2517-2526).
These studies have led FDA to approve Ipi for use in advanced
melanoma patients. The limitation of Ipi is that only a relatively
small proportion of patients achieve clinical responses.
Combination of Ipi with other therapeutics is therefore needed to
improve the efficacy of anti-CTLA4 therapy.
[0003] Recent studies have found that higher pre-treatment levels
of pro-angiogenic growth factor VEGF-A, also known as VEGF, was
associated with decreased survival in Ipi treated patients with
metastatic melanoma (Yuan et al. (2014) Cancer Immunol. Res.
2:127-132), indicating that VEGF influences clinical outcomes to
Ipi therapy. Indeed, it has been increasingly appreciated that
angiogenesis has overlapping mechanisms with immune response (Terme
et al. (2012) Clin. Develop. Immunol., Article ID 492920). VEGF has
profound effects on immune regulatory cell function. VEGF inhibits
dendritic cell maturation and antigen presentation and promotes
Treg and MDSC expansion in the tumor microenvironments (Ohm et al.
(2001) Immunol. Res. 23:263-272; Oyama et al. (1998) J. Immunol.
160:1224-1232; Vanneman and Dranoff (2012) Nat Rev. Cancer
12:237-251). Increasing evidence also indicate a role for
angiogenic factors in influencing lymphocyte trafficking across
endothelia into tumor deposits (Kandalaft et al. (2011) Curr. Top.
Microbiol. Immunol. 344:129-148). These findings support
combination of Ipi with anti-VEGF for melanoma treatment. Indeed, a
recent phase I study with metastatic melanoma has shown a
synergistic clinical effect by addition of bevacizumab (Bev), a
fully humanized monoclonal antibody that neutralizes VEGF, to Ipi
(Hodi et al. (2014) Cancer Immunol. Res. 2:632-642). Pathological
studies have shown that Ipi plus Bev (Ipi-Bev) enhanced
infiltration of lymphocytes in tumors (Hodi et al. (2014) Cancer
Immuno. Res. 2:632-642). Furthermore, Ipi-Bev increased memory
effector T cells and levels of antibodies to galectin (Gal)-1, -3
and -9 in the peripheral blood of the patients (Hodi et al. (2014)
Cancer Immunol. Res. 2:632-642).
[0004] While the combination of ipilimumab with anti-VEGF (e.g.,
bevacizumab) or PD-1 blockade increases clinical efficacy and
response rate of ipilimumab, the best response rate thus far
observed has been approximately 50% using ipilimumab in combination
with PD-1 blockade. Reliable biomarkers that can predict response
or resistance to anti-immune checkpoint and anti-angiogenesis
combination therapies (e.g., immune checkpoint blockade, such as
CTLA-4 inhibition, in combination with anti-angiogenesis blockade,
such as VEGF inhibition) are therefore critical for stratifying
patient populations and selecting patients who will or will not
benefit from such immune therapies. However, such biomarkers are
not currently known. Accordingly, there is a great need to identify
such biomarkers useful for diagnostic, prognostic, and therapeutic
purposes.
SUMMARY OF THE INVENTION
[0005] The present invention is based, at least in part, on the
discovery that circulating anti-galectin antibodies (i.e.,
anti-Gal-1, anti-Gal-3, and/or anti-Gal-9 antibodies) are a highly
specific early biomarker for prediction of clinical outcomes (e.g.,
poor clinical outcomes such as progressive disease and shortened
survival) in cancer patients treated with a combination of
anti-immune checkpoint and anti-angiogenesis therapies, such as
those comprising an anti-CTLA-4 and anti-VEGF therapeutic (e.g.,
ipilimumab in combination with bevacizumab, and the like).
Increased circulating anti-galectin antibodies (i.e., anti-Gal-1,
anti-Gal-3, and/or anti-Gal-9 antibodies) is a mechanism for
increased responsiveness to anti-cancer immunotherapy and adding or
promoting anti-galectin antibodies (i.e., anti-Gal-1, anti-Gal-3,
and/or anti-Gal-9 antibodies) is believed to improve the efficacy
of anti-cancer therapies (e.g., immunotherapies) combining
anti-immune checkpoint and anti-angiogenesis agents.
[0006] In one aspect, a method of identifying the likelihood of a
cancer in a subject to be responsive to an anti-immune checkpoint
and anti-angiogenesis combination therapy, the method comprising:
a) obtaining or providing a patient sample from a patient having
cancer; b) measuring the amount or activity of at least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof, in the subject sample; and c)
comparing said amount or activity of the at least one antibody that
specifically binds the biomarker listed in Table 1, or
antigen-binding fragment thereof, in a control sample, wherein a
significantly increased amount or activity of the at least one
antibody that specifically binds the biomarker listed in Table 1,
or antigen-binding fragment thereof, in the subject sample relative
to the control sample identifies the cancer as being more likely to
be responsive to the anti-immune checkpoint and anti-angiogenesis
combination therapy and wherein a significantly decreased amount or
activity of the at least one antibody that specifically binds the
biomarker listed in Table 1, or antigen-binding fragment thereof,
in the subject sample relative to the control sample identifies the
cancer as being less likely to be responsive to the anti-immune
checkpoint and anti-angiogenesis combination therapy, is
provided.
[0007] In another aspect, a method of identifying a subject
afflicted with a cancer as likely to be responsive to anti-immune
checkpoint and anti-angiogenesis combination therapy, the method
comprising: a) obtaining or providing a patient sample from a
patient having cancer; b) measuring the amount or activity of at
least one antibody that specifically binds a biomarker listed in
Table 1, or antigen-binding fragment thereof, in the subject
sample; and c) comparing said amount or activity of the at least
one antibody that specifically binds the biomarker listed in Table
1, or antigen-binding fragment thereof, in a control sample,
wherein a significantly increased amount or activity of the at
least one antibody that specifically binds the biomarker listed in
Table 1, or antigen-binding fragment thereof, in the subject sample
relative to the control sample identifies the subject afflicted
with the cancer as being more likely to be responsive to the
anti-immune checkpoint and anti-angiogenesis combination therapy
and wherein a significantly decreased amount or activity of the at
least one antibody that specifically binds the biomarker listed in
Table 1, or antigen-binding fragment thereof, in the subject sample
relative to the control sample identifies the subject afflicted
with the cancer as being less likely to be responsive to the
anti-immune checkpoint and anti-angiogenesis combination
therapy.
[0008] Numerous embodiments are further provided that can be
applied to any aspect of the present invention described herein.
For example, in one embodiment, the method further comprises
recommending, prescribing, or administering anti-immune checkpoint
and anti-angiogenesis combination therapy if the cancer or subject
is determined likely to be responsive to anti-immune checkpoint and
anti-angiogenesis combination therapy or administering anti-cancer
therapy other than anti-immune checkpoint and anti-angiogenesis
combination therapy if the cancer or subject is determined be less
likely to be responsive to anti-immune checkpoint and
anti-angiogenesis combination therapy. In another embodiment, the
anti-cancer therapy is selected from the group consisting of
targeted therapy, chemotherapy, radiation therapy, and/or hormonal
therapy. In still another embodiment, the control sample is
determined from a cancerous or non-cancerous sample from either the
patient or a member of the same species to which the patient
belongs. In yet another embodiment, the control sample is a
cancerous or non-cancerous sample from the patient obtained from an
earlier point in time than the patient sample, optionally wherein
the control sample is obtained before the patient has received
anti-immune checkpoint and anti-angiogenesis combination therapy
and the patient sample is obtained after the patient has received
anti-immune checkpoint and anti-angiogenesis combination therapy.
In another embodiment, the control sample comprises cells or does
not comprise cells. In still another embodiment, the control sample
comprises cancer cells known to be responsive or non-responsive to
the anti-immune checkpoint and anti-angiogenesis combination
therapy.
[0009] In still another aspect, a method of assessing the efficacy
of an agent for treating a cancer in a subject that is unlikely to
be responsive to anti-immune checkpoint and anti-angiogenesis
combination therapy, comprising: a) detecting the amount or
activity of at least one antibody that specifically binds a
biomarker listed in Table 1, or antigen-binding fragment thereof,
from a subject in which the agent has not been administered; b)
detecting the amount or activity of at least one antibody that
specifically binds the biomarker listed in Table 1, or
antigen-binding fragment thereof, in the subject in which the agent
has been administered; and c) comparing the amount or activity of
the at least one antibody that specifically binds the biomarker
listed in Table 1, or antigen-binding fragment thereof, from steps
a) and b), wherein a significantly increased amount or activity of
the at least one antibody that specifically binds the biomarker
listed in Table 1, or antigen-binding fragment thereof, in step b)
relative to step a), indicates that the agent treats the cancer in
the subject, is provided.
[0010] In yet another aspect, a method of assessing the efficacy of
an anti-immune checkpoint and anti-angiogenesis combination therapy
for treating a cancer in a subject or prognosing progression of a
cancer treated with an anti-immune checkpoint and anti-angiogenesis
combination therapy in a subject, comprising: a) detecting in a
subject sample at a first point in time the amount or activity of
at least one antibody that specifically binds a biomarker listed in
Table 1, or antigen-binding fragment thereof; b) repeating step a)
during at least one subsequent point in time after administration
of the anti-immune checkpoint and anti-angiogenesis combination
therapy; and c) comparing the expression and/or activity detected
in steps a) and b), wherein a significantly increased amount or
activity of the at least one antibody that specifically binds the
biomarker listed in Table 1, or antigen-binding fragment thereof,
in the at least one subsequent subject sample relative to the first
subject sample, indicates that the cancer treated with an
anti-immune checkpoint and anti-angiogenesis combination therapy is
unlikely to progress or that the anti-immune checkpoint and
anti-angiogenesis combination treats the cancer in the subject, is
provided.
[0011] As described above, certain embodiments are applicable to
any method described herein. For example, in one embodiment, the
subject has undergone treatment, completed treatment, and/or is in
remission for the cancer between the first point in time and the
subsequent point in time. In another embodiment, the first and/or
at least one subsequent sample is selected from the group
consisting of ex vivo and in vivo samples. In still another
embodiment, the first and/or at least one subsequent sample is
obtained from an animal model of the cancer. In yet another
embodiment, the first and/or at least one subsequent sample is a
portion of a single sample or pooled samples obtained from the
subject.
[0012] In another aspect, a cell-based assay for screening for
agents that have a cytotoxic or cytostatic effect on a cancer cell
that is unresponsive to anti-immune checkpoint and
anti-angiogenesis combination therapy comprising, contacting the
cancer cell with a test agent, wherein the cancer cell is comprised
within a B cell population, and determining the ability of the test
agent to increase the amount or activity of at least one antibody
that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof, is provided. In one embodiment,
the step of contacting occurs in vivo, ex vivo, or in vitro.
[0013] As described above, certain embodiments are applicable to
any method described herein. For example, in one embodiment, the
subject sample and/or the control sample has not been contacted
with either a) any anti-cancer treatment, b) any anti-immune
checkpoint agent, or c) any anti-angiogenesis agent. In another
embodiment, the subject has not been administered any either a) any
anti-cancer treatment, b) any anti-immune checkpoint agent, or c)
any anti-angiogenesis agent. In still another embodiment, the
method or assay further comprises recommending, prescribing, or
administering at least one additional anti-cancer therapeutic
agent, optionally wherein the at least one additional anti-cancer
therapeutic agent is an anti-immune checkpoint agent, ipilimumab,
an anti-angiogenesis agent, an anti-VEGF agent, bevacizunab, a
neutralizing anti-Gal-1 antibody or antigen-binding fragment
thereof, a neutralizing anti-Gal-3 antibody or antigen-binding
fragment thereof, a neutralizing anti-Gal-9 antibody or
antigen-binding fragment thereof, or combinations thereof. In yet
another embodiment, the subject sample is selected from the group
consisting of serum, whole blood, plasma, urine, cells, cell lines,
and biopsies. In another embodiment, the amount of the least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof. In still another embodiment, the
reagent is selected from the group consisting of a Gal-1
polypeptide or fragment thereof, Gal-3 polypeptid or fragment
thereof, Gal-9 polypeptide or fragment thereof, or any combination
thereof. In yet another embodiment, the at least one antibody that
specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof, is assessed by enzyme-linked
immunosorbent assay (ELISA), radioimmune assay (RIA),
immunochemically, Western blot, or flow cytometry. In another
embodiment, the biomarker listed in Table 1 is immobilized onto a
solid support. In still another embodiment, the solid support is an
array, bead, or plate. In yet another embodiment, the at least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof is detected by detecting binding
of an anti-IgG antibody against the antibody or antigen-binding
fragment thereof. In another embodiment, the at least one antibody
that specifically binds the biomarker listed in Table 1, or
antigen-binding fragment thereof, is an anti-human Gal-1, an
anti-human Gal-3, or an anti-human Gal-9 antibody, or an
antigen-binding fragment thereof, optionally wherein the antibody
or antigen-binding fragment thereof is a neutralizing antibody or
neutralizing antigen-binding fragment thereof. In still another
embodiment, the anti-immune checkpoint and anti-angiogenesis
combination therapy comprises at least one antibody selected from
the group consisting of anti-CTLA-4 antibodies, anti-PD-1
antibodies, anti-PD-L1 antibodies, anti-PD-L2 antibodies, anti-VEGF
antibodies, and combinations thereof. In yet another embodiment,
the anti-immune checkpoint therapy comprises ipilimumab and/or
anti-angiogenesis therapy comprises bevacizumab. In another
embodiment, the likelihood of the cancer in the subject to be
responsive to anti-immune checkpoint and anti-angiogenesis
combination therapy is the likelihood of at least one criteria
selected from the group consisting of cellular proliferation, tumor
burden, m-stage, metastasis, progressive disease, clinical benefit
rate, survival until mortality, pathological complete response,
semi-quantitative measures of pathologic response, clinical
complete remission, clinical partial remission, clinical stable
disease, recurrence-free survival, metastasis free survival,
disease free survival, circulating tumor cell decrease, circulating
marker response, and RECIST criteria. In still another embodiment,
the cancer is a solid tumor. In yet another embodiment, the cancer
is melanoma, non-small cell lung cancer (NSCLC), small cell lung
cancer (SCLC), bladder cancer, prostate cancer, metastatic
hormone-refractory prostate cancer, renal cell cancer, colon
cancer, ovarian cancer, or brain glioblastoma multiforme. In
another embodiment, the melanoma is metastatic melanoma. In still
another embodiment, the subject is a mammal (e.g., an animal model
of cancer or a human).
BRIEF DESCRIPTION OF FIGURES
[0014] FIG. 1 includes 4 panels, identified as panels A, B, C. and
D, which show that ipilimumab plus bevacizumab (Ipi-Bev)
potentiates humoral immune response to Gal-1, -3 and -9 in
metastatic melanoma patients. Panels A-C show anti-Gal-1,
anti-Gal-3, and anti-Gal-9 antibody levels in pre- and
post-treatment plasma samples of Ipi-Bev patients as determined by
Western blot analysis (upper panels) and ELISA (lower panels),
respectively. Results from representative patients (P1, P6, P9,
P12, P13, and P17) are shown. Panel D shows the portions of Ipi-Bev
and Ipi alone patients with increased humoral immune response to
Gal-1 and Gal-3. Pre- and post-treatment plasma Gal-1 and Gal-3 Ig
levels were evaluated using ELISA. Antibody levels were considered
as increased when post-/pre-ratio.gtoreq.1.45.
[0015] FIG. 2 includes 3 panels, identified as panels A, B, and C,
which show that anti-Gal-1, anti-Gal-3, and anti-Gal-9 antibody
increased more frequently in patients with CR, PR or SD than those
with PD as a function of ipilimumab plus bevacizumab treatment
based on a comparison of anti-Gal-1, anti-Gal-3, and anti-Gal-9 Ig
fold changes and clinical response, respectively. For panels A-C,
patients were ordered based on their antibody fold change
(post-/pre-ratio). Clinical responses of each patient are indicated
by bar identification. Antibody levels were considered as increased
when fold change was .gtoreq.1.3 (for Gal-9 Ig) or 1.5 (for Gal-1
and Gal-3 Ig). Dashed lines indicated a fold change of 1.3 (for
Gal-9 Ig) or 1.5 (for Gal-1 and Gal-3 Ig).
[0016] FIG. 3 includes 3 panels, identified as panels A, B, and C,
which show that anti-Gal-1, anti-Gal-3, and anti-Gal-9 antibody
increase is associated with better survival in metastatic melanoma
patients receiving ipilimumab plus bevacizumab. For panels A-C,
patients were grouped based on fold changes (post-/pre-ratio) of
Gal-1 Ig (panel A; post-/pre-ratio.gtoreq.0.1.5), Gal-3 Ig (panel
B; post-/pre-ratio.gtoreq.1.5), and Gal-9 Ig (panel C;
post-pre-ratio.gtoreq.1.3).
[0017] FIG. 4 shows that the increase in Gal-1, Gal-3, and Gal-9
antibodies is associated with higher response rate in metastatic
melanoma patients receiving ipilimumab plus bevacizumab.
[0018] FIG. 5 shows that endogenous anti-Gal-1 antibody abrogates
Gal-1 binding to CD45. Anti-galectin-1 antibody was affinity
purified from the plasma of a responder. HAS-Gal-1 (25 ng) was
incubated with a commercial anti-Gal-1 polyclonal antibody or
control antibody (10 .mu.g/ml), purified serum Gal-1 Ig or normal
human IgG (1.98 .mu.g/ml) prior to incubation with coated CD45. The
binding of HAS-Gal-1 to CD45 was detected with streptavidin-HRP.
Sucrose and lactose were added to the reaction at 5 mM. Results are
presented as mean standard deviation (SD) of 3 experiments.
[0019] FIG. 6 includes 2 panels, identified as panels A and B,
which show that endogenous anti-Gal-3 antibody is functional in
neutralizing Gal-3 binding to CD45. Panel A shows that anti-Gal-3
Ig was depleted from the post-plasma of a responder. Panel B shows
depletion of anti-Gal-3 Ig from the plasma increased Gal-3 binding
to CD45. Binding of Gal-3 to CD45 was detected using recombinant
HAS-Gal-3 and CD45. HAS-Gal-3 was incubated with the plasma or
plasma depleted of Gal-3 Ig prior to incubation with coated CD45.
The mean.+-.SD of 4 independent experiments are shown.
[0020] FIG. 7 includes 2 panels, identified as panels A and B,
which show that endogenous anti-Gal-9 antibody is functional in
neutralizing Gal-9 induced T cell apoptosis. Panel A shows that
anti-Gal-9 Ig was depleted from the post plasma of a responder.
Panel B shows that depletion of anti-Gal-9 Ig from the plasma
increased Gal-9-induced T cell apoptosis. Gal-9 was incubated with
the plasma or plasma depleted of anti-Gal-9 Ig prior to addition to
T cells. The mean SD of 5 independent experiments are shown.
[0021] For any figure showing a bar histogram, curve, or other data
associated with a legend, the bars, curve, or other data presented
from left to right for each indication correspond directly and in
order to the boxes from top to bottom of the legend. Similarly, for
any figure showing survival curves based on percentage survival
from 100% to 0%, the curves showing a higher percentage survival at
the end of the measured time points correspond directly and in
order to the labels from top to bottom of the legend.
DETAILED DESCRIPTION OF THE INVENTION
[0022] It has been determined herein that a humoral anti-Gal-1,
Gal-3, and/or Gal-9 response is a specific biomarker for predicted
clinical outcome in cancer patients (e.g., metastatic melanoma
patients) receiving a combination of anti-immune checkpoint and
anti-angiogenesis therapies (e.g., anti-CTLA-4 and anti-VEGF
therapeutics, ipilimumab in combination with bevacizumab, and the
like). Accordingly, the present invention relates, in part, to
methods for stratifying patients and predicting response of a
cancer in a subject to a combination of anti-immune checkpoint and
anti-angiogenesis therapies based upon a determination and analysis
of biomarkers described herein according to amount (e.g., copy
number or level of expression) and/or activity, relative to a
control. In addition, such analyses can be used in order to provide
useful treatment regimens comprising a combination of anti-immune
checkpoint and anti-angiogenesis therapies (e.g., based on
predictions of clinical response, subject survival or relapse,
timing of adjuvant or neoadjuvant treatment, etc.).
I. Definitions
[0023] The articles "a" and "an" are used herein to refer to one or
to more than one (i.e. to at least one) of the grammatical object
of the article. By way of example, "an element" means one element
or more than one element.
[0024] The term "altered amount" or "altered level" refers to
increased or decreased copy number (e.g., germline and/or somatic)
of a biomarker nucleic acid, e.g., increased or decreased
expression level in a cancer sample, as compared to the expression
level or copy number of the biomarker nucleic acid in a control
sample. The term "altered amount" of a biomarker also includes an
increased or decreased protein level of a biomarker protein in a
sample, e.g., a cancer sample, as compared to the corresponding
protein level in a normal, control sample. Furthermore, an altered
amount of a biomarker protein may be determined by detecting
posttranslational modification such as methylation status of the
marker, which may affect the expression or activity of the
biomarker protein.
[0025] The amount of a biomarker in a subject is "significantly"
higher or lower than the normal amount of the biomarker, if the
amount of the biomarker is greater or less, respectively, than the
normal level by an amount greater than the standard error of the
assay employed to assess amount, and preferably at least 20%, 30%,
40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 300%, 350%, 400%,
500%, 600%, 700%, 800%, 900%, 1000% or than that amount.
Alternately, the amount of the biomarker in the subject can be
considered "significantly" higher or lower than the normal amount
if the amount is at least about two, and preferably at least about
three, four, or five times, higher or lower, respectively, than the
normal amount of the biomarker. Such "significance" can also be
applied to any other measured parameter described herein, such as
for expression, inhibition, cytotoxicity, cell growth, and the
like.
[0026] The term "altered level of expression" of a biomarker refers
to an expression level or copy number of the biomarker in a test
sample, e.g., a sample derived from a patient suffering from
cancer, that is greater or less than the standard error of the
assay employed to assess expression or copy number, and is
preferably at least twice, and more preferably three, four, five or
ten or more times the expression level or copy number of the
biomarker in a control sample (e.g., sample from a healthy subjects
not having the associated disease) and preferably, the average
expression level or copy number of the biomarker in several control
samples. The altered level of expression is greater or less than
the standard error of the assay employed to assess expression or
copy number, and is preferably at least 20%, 30%, 40%, 50%, 60%,
70%, 80%, 90%, 100%, 150%, 200%, 300%, 350%, 400%, 500%, 600%,
700%, 800%, 900%, 1000% or more times the expression level or copy
number of the biomarker in a control sample (e.g., sample from a
healthy subjects not having the associated disease) and preferably,
the average expression level or copy number of the biomarker in
several control samples.
[0027] The term "altered activity" of a biomarker refers to an
activity of the biomarker which is increased or decreased in a
disease state, e.g., in a cancer sample, as compared to the
activity of the biomarker in a normal, control sample. Altered
activity of the biomarker may be the result of, for example,
altered expression of the biomarker, altered protein level of the
biomarker, altered structure of the biomarker, or, e.g., an altered
interaction with other proteins involved in the same or different
pathway as the biomarker or altered interaction with
transcriptional activators or inhibitors.
[0028] The term "altered structure" of a biomarker refers to the
presence of mutations or allelic variants within a biomarker
nucleic acid or protein. e.g., mutations which affect expression or
activity of the biomarker nucleic acid or protein, as compared to
the normal or wild-type gene or protein. For example, mutations
include, but are not limited to substitutions, deletions, or
addition mutations. Mutations may be present in the coding or
non-coding region of the biomarker nucleic acid.
[0029] The term "angiogenesis" or "neovascularization" refers to
the process by which new blood vessels develop from pre-existing
vessels (Varner et al. (1999) Angiogen. 3:53-60); Mousa et al.
(2000) Angiogen. Stim. Inhib. 35:42-44; Kim et al. (2000) Amer. J.
Path. 156:1345-1362; Kim et al. (2000) J. Biol. Chem.
275:33920-33928; Kumar et al. (2000) Angiogenesis: From Molecular
to Integrative Pharm. 169-180). Endothelial cells from pre-existing
blood vessels or from circulating endothelial stem cells (Takahashi
et al. (1995) Nat. Med. 5:434-438; Isner et al. (1999) J. Clin.
Invest. 103:1231-1236) become activated to migrate, proliferate,
and differentiate into structures with lumens, forming new blood
vessels, in response to growth factor or hormonal cues, or hypoxic
or ischemic conditions. During ischemia, such as occurs in cancer,
the need to increase oxygenation and delivery of nutrients
apparently induces the secretion of angiogenic factors by the
affected tissue; these factors stimulate new blood vessel
formation. Several additional terms are related to
angiogenesis.
[0030] For example, the term "tissue exhibiting angiogenesis"
refers to a tissue in which new blood vessels are developing from
pre-existing blood vessels.
[0031] As used herein, the term "inhibiting angiognesis,"
"diminishing angiogenesis," "reducing angiogenesis," and
grammatical equivalents thereof refer to reducing the level of
angiogenesis in a tissue to a quantity which is at least 10%, 15%,
20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,
85%, 90%, 95%, 99% or less than the quantity in a corresponding
control tissue, and most preferably is at the same level which is
observed in a control tissue. A reduced level of angiogenesis need
not, although it may, mean an absolute absence of angiogenesis. The
invention does not require, and is not limited to, methods that
wholly eliminate angiogenesis. The level of angiogenesis may be
determined using methods well known in the art, including, without
limitation, counting the number of blood vessels and/or the number
of blood vessel branch points, as discussed herein and in the
examples. An alternative in vitro assay contemplated includes the
tubular cord formation assay that shows growth of new blood vessels
at the cellular level [D. S. Grant et al., Cell, 58: 933-943
(1989)]. Art-accepted in vivo assays are also known, and involve
the use of various test animals such as chickens, rats, mice,
rabbits and the like. These in vivo assays include the chicken
chorioallantoic membrane (CAM) assay, which is suitable for showing
anti-angiogenic activity in both normal and neoplastic tissues
(Ausprunk (1975) Amer. J. Path. 79:597-610 and Ossonowski and Reich
(1980) Cancer Res. 30:2300-2309). Other in vivo assays include the
mouse metastasis assay, which shows the ability of a compound to
reduce the rate of growth of transplanted tumors in certain mice,
or to inhibit the formation of tumors or preneoplastic cells in
mice which are predisposed to cancer or which express
chemically-induced cancer (Humphries et al. (1986) Science
233:467-470 and Humphries et al. (1988) J. Clin. Invest.
81:782-790). Moreover, in some embodiments, angiogenesis can be
measured according to such attributes as pericyte maturation and
vascular remodeling as described further herein.
[0032] Many anti-angiogenesis inhibitors are known in the art.
Generally, such agents are disrupt angiogenesis to thereby be
useful for treating cancer by either being (1) monoclonal
antibodies directed against specific pro-angiogenic factors and/or
their receptors (e.g., Avastin.TM., Erbitux.TM., Vectibix.TM.,
Herceptin.TM., and the like) or (2) small molecule tyrosine kinase
inhibitors (TKIs) of multiple pro-angiogenic growth factor
receptors (e.g., Tarveca.TM., Nexavar.TM., Sutent.TM., and the
like) or inhibitors of mTOR (mammalian target of rapamycin) (e.g.,
Torisel) or indirect anti-angiogenic agents such as Velcade.TM. and
Celgene.TM.. The first FDA-approved angiogenesis inhibitor,
Bevacizumab (Abastin.TM., Genentech), a monoclonal antibody to
vascular endothelial growth factor (VEGF), is approved as an
anticancer agent, such as to treat metastatic colon cancer
treatment in conjunction with standard conventional chemotherapy
(see, for example U.S. Pat. No. 6,054,297). In one embodiment, the
anti-angiogenesis agent is a VEF inhibitor. The largest class of
drugs that block angiogenesis are the multi-targeted tyrosine
kinase inhibitors (TKIs) that target the VEGF receptor (VEGFR).
These drugs such as sunitinib (Sutent.TM., Pfizer), sorafenib
(Nexavar.TM., Bayer/Onyx Pharmaceuticals), and erlotinib
(Tarvecar.TM., Gennentech/OSI/Roche) have the advantages of hitting
multiple targets, convenient oral administration, and cost
effectiveness.
[0033] Unless otherwise specified here within, the terms "antibody"
and "antibodies" broadly encompass naturally-occurring forms of
antibodies (e.g. IgG, IgA, IgM, IgE) and recombinant antibodies
such as single-chain antibodies, chimeric and humanized antibodies
and multi-specific antibodies, as well as fragments and derivatives
of all of the foregoing, which fragments and derivatives have at
least an antigenic binding site. Antibody derivatives may comprise
a protein or chemical moiety conjugated to an antibody.
[0034] The term "antibody" as used herein also includes an
"antigen-binding portion" of an antibody (or simply "antibody
portion"). The term "antigen-binding portion", as used herein,
refers to one or more fragments of an antibody that retain the
ability to specifically bind to an antigen (e.g., a biomarker
polypeptide or fragment thereof). It has been shown that the
antigen-binding function of an antibody can be performed by
fragments of a full-length antibody. Examples of binding fragments
encompassed within the term "antigen-binding portion" of an
antibody include (i) a Fab fragment, a monovalent fragment
consisting of the VL, VH, CL and CH1 domains; (ii) a F(ab').sub.2
fragment, a bivalent fragment comprising two Fab fragments linked
by a disulfide bridge at the hinge region; (iii) a Fd fragment
consisting of the VH and CH1 domains; (iv) a Fv fragment consisting
of the VL and VH domains of a single arm of an antibody, (v) a dAb
fragment (Ward et al., (1989) Nature 341:544-546), which consists
of a VH domain; and (vi) an isolated complementarity determining
region (CDR). Furthermore, although the two domains of the Fv
fragment, VL and VH, are coded for by separate genes, they can be
joined, using recombinant methods, by a synthetic linker that
enables them to be made as a single protein chain in which the VL
and VH regions pair to form monovalent polypeptides (known as
single chain Fv (scFv); see e.g., Bird et al. (1988) Science
242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA
85:5879-5883; and Osbourn et al. 1998, Nature Biotechnology 16:
778). Such single chain antibodies are also intended to be
encompassed within the term "antigen-binding portion" of an
antibody. Any VH and VL sequences of specific scFv can be linked to
human immunoglobulin constant region cDNA or genomic sequences, in
order to generate expression vectors encoding complete IgG
polypeptides or other isotypes. VH and VL can also be used in the
generation of Fab, Fv or other fragments of immunoglobulins using
either protein chemistry or recombinant DNA technology. Other forms
of single chain antibodies, such as diabodies are also encompassed.
Diabodies are bivalent, bispecific antibodies in which VH and VL
domains are expressed on a single polypeptide chain, but using a
linker that is too short to allow for pairing between the two
domains on the same chain, thereby forcing the domains to pair with
complementary domains of another chain and creating two antigen
binding sites (see e.g., Holliger, P., et al. (1993) Proc. Natl.
Acad. Sci. USA 90:6444-6448; Poljak, R. J., et al. (I994) Structure
2:1121-1123).
[0035] Still further, an antibody or antigen-binding portion
thereof may be part of larger immunoadhesion polypeptides, formed
by covalent or noncovalent association of the antibody or antibody
portion with one or more other proteins or peptides. Examples of
such immunoadhesion polypeptides include use of the streptavidin
core region to make a tetrameric scFv polypeptide (Kipriyanov, S.
M., et al. (1995) Human Antibodies and Hybridomas 6:93-101) and use
of a cysteine residue, biomarker peptide and a C-terminal
polyhistidine tag to make bivalent and biotinylated scFv
polypeptides (Kipriyanov, S. M., et al. (1994) Mol. Immunol.
31:1047-1058). Antibody portions, such as Fab and F(ab').sub.2
fragments, can be prepared from whole antibodies using conventional
techniques, such as papain or pepsin digestion, respectively, of
whole antibodies. Moreover, antibodies, antibody portions and
immunoadhesion polypeptides can be obtained using standard
recombinant DNA techniques, as described herein.
[0036] Antibodies may be polyclonal or monoclonal; xenogeneic,
allogeneic, or syngeneic; or modified forms thereof (e.g.
humanized, chimeric, etc.). Antibodies may also be fully human.
Preferably, antibodies of the present invention bind specifically
or substantially specifically to a biomarker polypeptide or
fragment thereof. The terms "monoclonal antibodies" and "monoclonal
antibody composition", as used herein, refer to a population of
antibody polypeptides that contain only one species of an antigen
binding site capable of immunoreacting with a particular epitope of
an antigen, whereas the term "polyclonal antibodies" and
"polyclonal antibody composition" refer to a population of antibody
polypeptides that contain multiple species of antigen binding sites
capable of interacting with a particular antigen. A monoclonal
antibody composition typically displays a single binding affinity
for a particular antigen with which it immunoreacts.
[0037] Antibodies may also be "humanized", which is intended to
include antibodies made by a non-human cell having variable and
constant regions which have been altered to more closely resemble
antibodies that would be made by a human cell. For example, by
altering the non-human antibody amino acid sequence to incorporate
amino acids found in human germline immunoglobulin sequences. The
humanized antibodies of the present invention may include amino
acid residues not encoded by human germline immunoglobulin
sequences (e.g., mutations introduced by random or site-specific
mutagenesis in vitro or by somatic mutation in vivo), for example
in the CDRs. The term "humanized antibody", as used herein, also
includes antibodies in which CDR sequences derived from the
germline of another mammalian species, such as a mouse, have been
grafted onto human framework sequences.
[0038] The term "assigned score" refers to the numerical value
designated for each of the biomarkers after being measured in a
patient sample. The assigned score correlates to the absence,
presence, or inferred amount of the biomarker in the sample. The
assigned score can be generated manually (e.g., by visual
inspection) or with the aid of instrumentation for image
acquisition and analysis. In certain embodiments, the assigned
score is determined by a qualitative assessment, for example,
detection of a fluorescent readout on a graded scale, or
quantitative assessment. In one embodiment, an "aggregate score,"
which refers to the combination of assigned scores from a plurality
of measured biomarkers, is determined. In one embodiment the
aggregate score is a summation of assigned scores. In another
embodiment, combination of assigned scores involves performing
mathematical operations on the assigned scores before combining
them into an aggregate score. In certain, embodiments, the
aggregate score is also referred to herein as the "predictive
score."
[0039] The term "biomarker" refers to a measurable entity of the
present invention that has been determined to be predictive of
anti-immune checkpoint and anti-angiogenesis combination therapy
effects on a cancer. Biomarkers can include, without limitation,
antibodies to proteins described herein, including those shown in
Table 1, the Examples, and the Figures, as well as antigen-binding
fragments thereof. Nucleic acids encoding same are also included
within the term.
[0040] A "blocking" antibody or an antibody "antagonist" is one
which inhibits or reduces at least one biological activity of the
antigen(s) it binds. In certain embodiments, the blocking
antibodies or antagonist antibodies or fragments thereof described
herein substantially or completely inhibit a given biological
activity of the antigen(s).
[0041] The term "body fluid" refers to fluids that are excreted or
secreted from the body as well as fluids that are normally not
(e.g. amniotic fluid, aqueous humor, bile, blood and blood plasma,
cerebrospinal fluid, cerumen and earwax, cowper's fluid or
pre-ejaculatory fluid, chyle, chyme, stool, female ejaculate,
interstitial fluid, intracellular fluid, lymph, menses, breast
milk, mucus, pleural fluid, pus, saliva, sebum, semen, serum,
sweat, synovial fluid, tears, urine, vaginal lubrication, vitreous
humor, vomit).
[0042] The terms "cancer" or"tumor" or "hyperproliferative" refer
to the presence of cells possessing characteristics typical of
cancer-causing cells, such as uncontrolled proliferation,
immortality, metastatic potential, rapid growth and proliferation
rate, and certain characteristic morphological features. In some
embodiments, such cells exhibit such characteristics in part or in
full due to the expression and activity of immune checkpoint
proteins, such as PD-1, PD-L, and/or CTLA-4. Cancer cells are often
in the form of a tumor, but such cells may exist alone within an
animal, or may be a non-tumorigenic cancer cell, such as a leukemia
cell. As used herein, the term "cancer" includes premalignant as
well as malignant cancers. Cancers include, but are not limited to,
B cell cancer, e.g., multiple myeloma, Waldenstrom's
macroglobulinemia, the heavy chain diseases, such as, for example,
alpha chain disease, gamma chain disease, and mu chain disease,
benign monoclonal gammopathy, and immunocytic amyloidosis,
melanomas, breast cancer, lung cancer, bronchus cancer, colorectal
cancer, prostate cancer, pancreatic cancer, stomach cancer, ovarian
cancer, urinary bladder cancer, brain or central nervous system
cancer, peripheral nervous system cancer, esophageal cancer,
cervical cancer, uterine or endometrial cancer, cancer of the oral
cavity or pharynx, liver cancer, kidney cancer, testicular cancer,
biliary tract cancer, small bowel or appendix cancer, salivary
gland cancer, thyroid gland cancer, adrenal gland cancer,
osteosarcoma, chondrosarcoma, cancer of hematologic tissues, and
the like. Other non-limiting examples of types of cancers
applicable to the methods encompassed by the present invention
include 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. In some embodiments,
cancers are epithelial in nature and include but are 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.
[0043] In certain embodiments, the cancer encompasses melanoma. The
term "melanoma" generally refers to cancers derived from
melanocytes. Although melanocytes are predominantly located in
skin, they are also found in other parts of the body, including the
eye and bowel. Although cutaneous melanoma is most common, melanoma
can originate from any melanocyte in the body. Though melanoma is
less than five percent of the skin cancers, it is the seventh most
common malignancy in the U.S. and is responsible for most of the
skin cancer related deaths. The incidence has increased
dramatically in the last several decades due to altered sun
exposure habits of the population. several hereditary risk factors
are also known. Other important risk factors are the number of
pigment nevi, the number dysplastic nevi, and skin type. An
increased risk is coupled to many nevi, both benign and dysplastic,
and fair skin. Familial history of malignant melanomas is a risk
factor, and approximately 8-12% of malignant melanoma cases are
familial. Additional details are well known, such as described in
US Pat. Publs. 2012-0269764 and 2013-0237445.
[0044] Malignant melanomas are clinically recognized based on the
ABCD(E) system, where A stands for asymmetry, B for border
irregularity, C for color variation, D for diameter>5 mm, and E
for evolving. Further, an excision biopsy can be performed in order
to corroborate a diagnosis using microscopic evaluation.
Infiltrative malignant melanoma is traditionally divided into four
principal histopathological subgroups: superficial spreading
melanoma (SSM), nodular malignant melanoma (NMM), lentigo maligna
melanoma (LMM), and acral lentiginous melanoma (ALM). Other rare
types also exists, such as desmoplastic malignant melanoma. A
substantial subset of malignant melanomas appear to arise from
melanocytic nevi and features of dysplastic nevi are often found in
the vicinity of infiltrative melanomas. Melanoma is thought to
arise through stages of progression from normal melanocytes or
nevus cells through a dysplastic nevus stage and further to an in
situ stage before becoming invasive. Some of the subtypes evolve
through different phases of tumor progression, which are called
radial growth phase (RGP) and vertical growth phase (VGP).
[0045] In a preferred embodiment, a melanoma subtype is melanoma
resistant to treatment with inhibitors of BRAF and/or MEK. For
example, the methods described herein are useful for diagnosing
and/or prognosing melanoma subtypes that are resistant to treatment
with inhibitors of BRAF and/or MEK. Inhibitors of BRAF and/or MEK,
especially of mutant versions implicated in cancer (e.g.,
BRAF.sup.V600E) are well-known in the art.
[0046] BRAF is a member of the Raf kinase family of
serine/threonine-specific protein kinases. This protein plays a
role in regulating the MAP kinase/ERKs signaling pathway, which
affects cell division, differentiation, and secretion. BRAF
transduces cellular regulatory signals from Ras to MEK In vivo.
BRAF is also referred to as v-raf murine sarcoma viral oncogene
homolog B1. BRAF mutants are a mutated form of BRAF that has
increased basal kinase activity relative to the basal kinase
activity of wild type BRAF is also an activated form of BRAF. More
than 30 mutations of the BRAF gene that are associated with human
cancers have been identified. The frequency of BRAF mutations in
melanomas and nevi are 80%. In 90% of the cases, a Glu for Val
substitution at position 600 (referred to as V600E) in the
activation segment has been found in human cancers. This mutation
is observed in papillary thyroid cancer, colorectal cancer and
melanoma. Other mutations which have been found are R462I, I463S,
G464E, G464V, G466A, G466E, C466V, G469A, G469E, N591S, E585K,
D594V, F595L, G596R, L597V, T599I, V600D, V600K, V600R, K600E or
A728V. Most of these mutations are clustered to two regions: the
glycine-rich P loop of the N lobe and the activation segment and
flanking regions. A mutated form of BRAF that induces focus
formation more efficiently than wild type BRAF is also an activated
form of BRAF. As used herein, the term "inhibitor of BRAF" refers
to a compound or agent, such as a small molecule, that inhibits,
decreases, lowers, or reduces the activity of BRAF or a mutant
version thereof. Examples of inhibitors of BRAF include, but are
not limited to, vemurafenib (PLX-4032; also known as RG7204,
RO5185426, and vemurafenib, C23H18ClF2N3O3S), PLX 4720
(C17H14ClF2N3O3S), sorafenib (C21H16ClF3N4O3), GSK2118436, and the
like. These and other inhibitors of BRAF, as well as non-limited
examples of their methods of manufacture, are described in, for
example, PCT Publication Nos. WO 2007/002325, WO 2007/002433, WO
2009/047505, WO 03/086467; WO 2009/143024, WO 2010/104945, WO
2010/104973, WO 2010/111527 and WO 2009/152087; U.S. Pat. Nos.
6,187,799 and 7,329,670; and U.S. Patent Application Publication
Nos. 2005/0176740 and 2009/0286783, each of which is herein
incorporated by reference in its entirety).
[0047] MEK1 is a known as dual specificity mitogen-activated
protein kinase 1, which is an enzyme that in human is encoded by
the MAP2K1 gene. Mutations of MEK1 involved in cancer are known and
include, for example, mutation selected from 59delK and P387S or
Q56P or C121S or P124L or F129L, and a MAP2K1 gene having a 175-177
AAG deletion or C1159T. As used herein, the term "inhibitor of MEK"
refers to a compound or agent, such as a small molecule, that
inhibits, decreases, lowers, or reduces the activity of MEK or a
mutant version thereof. Examples of inhibitors of MEK include, but
are not limited to, AZD6244
(6-(4-Bromo-2-chloro-phenylamino)-7-fluoro-3-methyl-3H-benzoimidazole-5-c-
arboxylic acid (2-hydroxy-ethoxy)-amide; selumetinib; Structure
IV), and U0126 (1,4-diamino-2,3-dicyano-1,4-bis
[2-aminophenylthio]butadiene; ARRY-142886; Structure V). Further
non-limiting examples of MEK inhibitors include PD0325901, AZD2171,
GDC-0973/XL-518, PD98059, PD184352, OSK1120212, RDEA436,
RDEA119/BAY869766, AS703026, BX 02188, BIX 02189, CI-1040
(PD184352), PD0325901, and PD98059. These and other inhibitors of
MEK, as well as non-limiting examples of their methods of
manufacture, are described in, for example, U.S. Pat. Nos.
5,525,625; 6,251,943; 7,820,664; 6,809,106; 7,759,518; 7,485,643;
7,576,072; 7,923.456; 7,732,616; 7,271,178; 7,429,667; 6,649,640;
6,495,582; 7,001,905; US Patent Publication No. US20100/331334,
US2009/0143389, US2008/0280957, US2007/0049591, US2011/0118298,
International Patent Application Publication No. WO98/43960,
WO99/01421, WO99/01426, WO00/41505, WO00/42002, WO00/42003,
WO00/41994, WO00/42022, WO00/42029, WO00/68201, WO01/68619,
WO02/06213 and WO03/077914, each of which is herein incorporated by
reference in their entirety.
[0048] Malignant melanomas are staged according to the American
Joint Committee on Cancer (AJCC) TNM-classification system, where
Clark level is considered in T-classification. The T stage
describes the local extent of the primary tumor, i.e., how far the
tumor has invaded and imposed growth into surrounding tissues,
whereas the N stage and M stage describe how the tumor has
developed metastases, with the N stage describing spread of tumor
to lymph nodes and the M stage describing growth of tumor in other
distant organs. Early stages include: T0-1, N0, M0, representing
localized tumors with negative lymph nodes. More advanced stages
include: T2-4, N0, M0, localized tumors with more widespread growth
and T1-4, N1-3, M0, tumors that have metastasized to lymph nodes
and T1-4, N1-3, M1, tumors with a metastasis detected in a distant
organ.
[0049] Stages I and II represent no metastatic disease and for
stage I (T1a/b-2a,N0,M0) prognosis is very good. The 5-year
survival for stage I disease is 90-95%, for stage II
(T2b-4-b,N0,M0) the corresponding survival rate ranges from 80 to
45%. Stages III (T1a-4-b,N1a-3,M0) and IV (T(aII),N(aII),M1a-c)
represent spread disease, and for these stages 5-year survival
rates range from 70 to 24%, and from 19 to 7%, respectively.
"Clark's level" is a measure of the layers of skin involved in a
melanoma and is a melanoma prognostic factor. For example, level I
involves the epidermis. Level II involves the epidermis and upper
dermis. Level III involves the epidermis, upper dermis, and lower
dermis. Level IV involves the epidermis, upper dermis, lower
dermis, and subcutis. When the primary tumor has a thickness of
>1 mm, ulceration, or Clark level IV-V, sentinel node biopsy
(SNB) is typically performed. SNB is performed by identifying the
first draining lymph node/s (i.e., the SN) from the tumor. This is
normally done by injection of radiolabelled colloid particles in
the area around the tumor, followed by injection of Vital Blue dye.
Rather than dissection of all regional lymph nodes, which was the
earlier standard procedure, only the sentinel nodes are generally
removed and carefully examined. Following complete lymph node
dissection is only performed in confirmed positive cases.
[0050] In addition to staging and diagnosis, factors like T-stage,
Clark level, SNB status, Breslow's depth, ulceration, and the like
can be used as endpoints and/or surrogates for analyses according
to the present invention. For example, patients who are diagnosed
at an advanced stage with metastases generally have a poor
prognosis. For patients diagnosed with a localized disease, the
thickness of the tumor measured in mm (Breslow) and ulceration can
be endpoints for prognosis. Breslow's depth is determined by using
an ocular micrometer at a right angle to the skin. The depth from
the granular layer of the epidermis to the deepest point of
invasion to which tumor cells have invaded the skin is directly
measured. Clark level is important for thin lesions (<1 mm).
Other prognostic factors include age, anatomic site of the primary
tumor and gender. The sentinel node (SN) status can also be a
prognostic factor, especially since the 5-year survival of
SN-negative patients has been shown to be as high as 90%.
Similarly, overall survival (OS) can be used as a standard primary
endpoint. OS takes in to account time to death, irrespective of
cause. e.g. if the death is due to cancer or not. Loss to follow-up
is censored and regional recurrence, distant metastases, second
primary malignant melanomas and second other primary cancers are
ignored. Other surrogate endpoints for survival can be used, as
described further herein, such as disease-free survival (DFS),
which includes time to any event related to the same cancer, i.e.
all cancer recurrences and deaths from the same cancer are
events.
[0051] In addition to endpoints, certain diagnostic and prognostic
markers can be analyzed in conjunction with the methods described
herein. For example, lactate dehydrogenase (LDH) can be measured as
a marker for disease progression. Patients with distant metastases
and elevated LDH levels belong to stage IV M1c. Another serum
biomarker of interest is S100B. High S100B levels are associated
with disease progression, and a decrease in the S100B level is an
indicator of treatment response. Melanoma-inhibiting activity (MIA)
is yet another scrum biomarker that has been evaluated regarding
its prognostic value. Studies have shown that elevated MIA levels
are rare in stage I and II disease, whereas in stage III or IV,
elevation in MIA levels can be seen in 60-100% of cases. Addition
useful biomarkers include RGSI (associated with reduced
relapse-free survival (RFS)), osteopontin (associated with both
reduced RFS and disease-specific survival (DSS), and predictive of
SLN metastases), HER3 (associated with reduced survival), and NCOA3
(associated with poor RFS and DSS, and predictive of SLN
metastases). In addition, HMB-45, Ki-67 (MIB1), MITF and
MART-1/Melan-A or combinations of any described marker may be used
for staining (Ivan & Prieto, 2010, Future Oncol. 6(7),
1163-1175; Linos et al., 2011, Biomarkers Med. 5(3) 333-360). In a
literature review Rothberg et al. report that melanoma cell
adhesion molecule (MCAM)/MUC18, matrix metalloproteinase-2, Ki-67,
proliferating cell nuclear antigen (PCNA) and p16/INK4A are
predictive of either all-cause mortality or melanoma specific
mortality (Rothberg et al., 2009 J. Nat. Canc. Inst. 101(7)
452-474).
[0052] Currently, the typical primary treatment of malignant
melanoma is radical surgery. Even though survival rates are high
after excision of the primary tumor, melanomas tend to metastasize
relatively early, and for patients with metastatic melanoma the
prognosis is poor, with a 5-year survival rate of less than 10%.
Radical removal of distant metastases with surgery can be an option
and systemic chemotherapy can be applied, but response rates are
normally low (in most cases less than 20%), and most treatment
regiments fail to prolong overall survival. The first FDA-approved
chemotherapeutic agent for treatment of metastatic melanoma was
dacarbazine (DTIC), which can give response rates of approximately
20%, but where less than 5% may be complete responses. Temozolamid
is an analog of DTIC that has the advantage of oral administration,
and which have been shown to give a similar response as DTIC. Other
chemotherapeutic agents, for example different nitrosureas,
cisplatin, carboplatin, and vinca alkaloids, have been used, but
without any increase in response rates. Since chemotherapy is an
inefficient treatment method, immunotherapy agents have also been
proposed. Most studied are interferon-alpha and interleukin-2. As
single agents they have not been shown to give a better response
than conventional treatment, but in combination with
chemotherapeutic agents higher response rates have been reported.
For patients with resected stage IIB or III melanoma, some studies
have shown that adjuvant interferon alfa has led to longer disease
free survival. For first- or second-line stage III and IV melanoma
systemic treatments include: carboplatin, cisplatin, dacarbazine,
interferon alfa, high-dose interleukin-2, paclitaxcel,
temozolomide, vinblastine or combinations thereof (NCCN Guidelines,
ME-D, MS-9-13). Recently, the FDA approved Zelboraf.TM.
(vemurafenib, also known as INN, PLX4032, RG7204 or R05185426) for
unresectable or metastatic melanoma with the BRAF V600E mutation
(Bollag et al. (2010) Nature 467:596-599 and Chapman et al. (2011)
New Eng. J. Med. 364:2507-2516). Another recently approved drug for
unresectable or metastatic melanoma is Yervoy.RTM. (ipilimumab) an
antibody which binds to cytotoxic T-lymphocyte-associated antigen 4
(CTLA-4) (Hodi et al. (2010) New Eng. J. Med. 363:711-723). Others
recently reported that patients with KIT receptor activating
mutations or over-expression responded to Gleevac.RTM. (imatinib
mesylate) (Carvajal et al. (2011) JAMA 305:2327-2334). In addition,
radiation treatment may be given as an adjuvant after removal of
lymphatic metastases, but malignant melanomas are relatively
radioresistant. Radiation treatment might also be used as
palliative treatment. Melanoma oncologists have also noted that
BRAF mutations are common in both primary and metastatic melanomas
and that these mutations are reported to be present in 50-70% of
all melanomas. This has led to an interest in B-raf inhibitors,
such as Sorafenib, as therapeutic agents.
[0053] The term "coding region" refers to regions of a nucleotide
sequence comprising codons which are translated into amino acid
residues, whereas the term "noncoding region" refers to regions of
a nucleotide sequence that are not translated into amino acids
(e.g., 5' and 3' untranslated regions).
[0054] The term "complementary" refers to the broad concept of
sequence complementarity between regions of two nucleic acid
strands or between two regions of the same nucleic acid strand. It
is known that an adenine residue of a first nucleic acid region is
capable of forming specific hydrogen bonds ("base pairing") with a
residue of a second nucleic acid region which is antiparallel to
the first region if the residue is thymine or uracil. Similarly, it
is known that a cytosine residue of a first nucleic acid strand is
capable of base pairing with a residue of a second nucleic acid
strand which is antiparallel to the first strand if the residue is
guanine. A first region of a nucleic acid is complementary to a
second region of the same or a different nucleic acid if, when the
two regions are arranged in an antiparallel fashion, at least one
nucleotide residue of the first region is capable of base pairing
with a residue of the second region. Preferably, the first region
comprises a first portion and the second region comprises a second
portion, whereby, when the first and second portions are arranged
in an antiparallel fashion, at least about 50%, and preferably at
least about 75%, at least about 90%, or at least about 95% of the
nucleotide residues of the first portion are capable of base
pairing with nucleotide residues in the second portion. More
preferably, all nucleotide residues of the first portion are
capable of base pairing with nucleotide residues in the second
portion.
[0055] The term "control" refers to any reference standard suitable
to provide a comparison to the expression products in the test
sample. In one embodiment, the control comprises obtaining a
"control sample" from which expression product levels are detected
and compared to the expression product levels from the test sample.
Such a control sample may comprise any suitable sample, including
but not limited to a sample from a control cancer patient (can be
stored sample or previous sample measurement) with a known outcome;
normal tissue or cells isolated from a subject, such as a normal
patient or the cancer patient, cultured primary cells/tissues
isolated from a subject such as a normal subject or the cancer
patient, adjacent normal cells/tissues obtained from the same organ
or body location of the cancer patient, a tissue or cell sample
isolated from a normal subject, or a primary cells/tissues obtained
from a depository. In another preferred embodiment, the control may
comprise a reference standard expression product level from any
suitable source, including but not limited to housekeeping genes,
an expression product level range from normal tissue (or other
previously analyzed control sample), a previously determined
expression product level range within a test sample from a group of
patients, or a set of patients with a certain outcome (for example,
survival for one, two, three, four years, etc.) or receiving a
certain treatment (for example, standard of care cancer therapy).
It will be understood by those of skill in the art that such
control samples and reference standard expression product levels
can be used in combination as controls in the methods of the
present invention. In one embodiment, the control may comprise
normal or non-cancerous cell/tissue sample. In another preferred
embodiment, the control may comprise an expression level for a set
of patients, such as a set of cancer patients, or for a set of
cancer patients receiving a certain treatment, or for a set of
patients with one outcome versus another outcome. In the former
case, the specific expression product level of each patient can be
assigned to a percentile level of expression, or expressed as
either higher or lower than the mean or average of the reference
standard expression level. In another preferred embodiment, the
control may comprise normal cells, cells from patients treated with
combination chemotherapy, and cells from patients having benign
cancer. In another embodiment, the control may also comprise a
measured value for example, average level of expression of a
particular gene in a population compared to the level of expression
of a housekeeping gene in the same population. Such a population
may comprise normal subjects, cancer patients who have not
undergone any treatment (i.e., treatment naive), cancer patients
undergoing standard of care therapy, or patients having benign
cancer. In another preferred embodiment, the control comprises a
ratio transformation of expression product levels, including but
not limited to determining a ratio or expression product levels of
two genes in the test sample and comparing it to any suitable ratio
of the same two genes in a reference standard; determining
expression product levels of the two or more genes in the test
sample and determining a difference in expression product levels in
any suitable control; and determining expression product levels of
the two or more genes in the test sample, normalizing their
expression to expression of housekeeping genes in the test sample,
and comparing to any suitable control. In particularly preferred
embodiments, the control comprises a control sample which is of the
same lineage and/or type as the test sample. In another embodiment,
the control may comprise expression product levels grouped as
percentiles within or based on a set of patient samples, such as
all patients with cancer. In one embodiment a control expression
product level is established wherein higher or lower levels of
expression product relative to, for instance, a particular
percentile, are used as the basis for predicting outcome. In
another preferred embodiment, a control expression product level is
established using expression product levels from cancer control
patients with a known outcome, and the expression product levels
from the test sample are compared to the control expression product
level as the basis for predicting outcome. As demonstrated by the
data below, the methods of the present invention are not limited to
use of a specific cut-point in comparing the level of expression
product in the test sample to the control.
[0056] The "copy number" of a biomarker nucleic acid refers to the
number of DNA sequences in a cell (e.g., germline and/or somatic)
encoding a particular gene product. Generally, for a given gene, a
manual has two copies of each gene. The copy number can be
increased, however, by gene amplification or duplication, or
reduced by deletion. For example, germline copy number changes
include changes at one or more genomic loci, wherein said one or
more genomic loci are not accounted for by the number of copies in
the normal complement of germline copies in a control (e.g., the
normal copy number in germline DNA for the same species as that
from which the specific germline DNA and corresponding copy number
were determined). Somatic copy number changes include changes at
one or more genomic loci, wherein said one or more genomic loci are
not accounted for by the number of copies in germline DNA of a
control (e.g., copy number in germline DNA for the same subject as
that from which the somatic DNA and corresponding copy number were
determined).
[0057] The "normal" copy number (e.g., germline and/or somatic) of
a biomarker nucleic acid or "normal" level of expression of a
biomarker nucleic acid or protein is the activity/level of
expression or copy number in a biological sample, e.g., a sample
containing tissue, whole blood, serum, plasma, buccal scrape,
saliva, cerebrospinal fluid, urine, stool, and bone marrow, from a
subject, e.g., a human, not afflicted with cancer, or from a
corresponding non-cancerous tissue in the same subject who has
cancer.
[0058] As used herein, the term "costimulate" with reference to
activated immune cells includes the ability of a costimulatory
molecule to provide a second, non-activating receptor mediated
signal (a "costimulatory signal") that induces proliferation or
effector function. For example, a costimulatory signal can result
in cytokine secretion, e.g., in a T cell that has received a T
cell-receptor-mediated signal. Immune cells that have received a
cell-receptor mediated signal, e.g., via an activating receptor are
referred to herein as "activated immune cells."
[0059] The term "determining a suitable treatment regimen for the
subject" is taken to mean the determination of a treatment regimen
(i.e., a single therapy or a combination of different therapies
that are used for the prevention and/or treatment of the cancer in
the subject) for a subject that is started, modified and/or ended
based or essentially based or at least partially based on the
results of the analysis according to the present invention. One
example is determining whether to provide targeted therapy against
a cancer to provide immunotherapy that generally increases immune
responses against the cancer (e.g., anti-immune checkpoint
therapy). Another example is starting an adjuvant therapy after
surgery whose purpose is to decrease the risk of recurrence,
another would be to modify the dosage of a particular chemotherapy.
The determination can, in addition to the results of the analysis
according to the present invention, be based on personal
characteristics of the subject to be treated. In most cases, the
actual determination of the suitable treatment regimen for the
subject will be performed by the attending physician or doctor.
[0060] The term "diagnosing cancer" includes the use of the
methods, systems, and code of the present invention to determine
the presence or absence of a cancer or subtype thereof in an
individual. The term also includes methods, systems, and code for
assessing the level of disease activity in an individual.
[0061] A molecule is "fixed" or "affixed" to a substrate if it is
covalently or non-covalently associated with the substrate such
that the substrate can be rinsed with a fluid (e.g. standard saline
citrate, pH 7.4) without a substantial fraction of the molecule
dissociating from the substrate.
[0062] The term "expression signature" or "signature" refers to a
group of two or more coordinately expressed biomarkers. For
example, the genes, proteins, metabolites, and the like making up
this signature may be expressed in a specific cell lineage, stage
of differentiation, or during a particular biological response. The
biomarkers can reflect biological aspects of the tumors in which
they are expressed, such as the cell of origin of the cancer, the
nature of the non-malignant cells in the biopsy, and the oncogenic
mechanisms responsible for the cancer. Expression data and gene
expression levels can be stored on computer readable media, e.g.,
the computer readable medium used in conjunction with a microarray
or chip reading device. Such expression data can be manipulated to
generate expression signatures.
[0063] The term "galectins" refers to family of carbohydrate
binding proteins with affinity for f-galactosides, such as
N-acetyllactosamine (Gal.beta.1-3GlcNAc or Gal.beta.1-4GlcNAc)
(Rabinovich el al (2007) Scand. J. Immunol. 66:143). In mammals,
the galectin family includes 15 members, divided in 3 different
groups according to the number of carbohydrate recognition domains
(CRD). The CRD is a beta-sheet represented by approximately 135
amino acids, wherein 6 strands from a concave face and 5 strands
form a convex face such that the concave face forms a groove for a
.beta.-galactoside, up to approximately a linear tetrasaccharide,
to bind (Lobsanov et al. (1993) J. Biol. Chem. 268:27034-27038).
Galectin-1, -2, -5, -7, -10, -11, -13, -14, and -15 are dimeric
galectins that have two identical galectin subunits resulting from
homodimerization. By contrast, galectin-4, -5, -8, -9, and -12 are
tandem galectins because they maintain at least two distinct CRDs
in the same polypeptide linked by a peptide domain. Finally,
galectin-3 has a single CRD and a long, non-lectin domain that can
form various structures, such as a pentamer or a monomer (Liu et al
(2010) Annal. N.Y. Acad. Sci. 1183:158-182). Most galectins exist
in monomeric and non-covalent multimeric forms, secreted by a
non-classical pathway that resembles the Na+/K+-ATPase pump (Hughes
(2001) Biochimie. 83:667); Nickel (2005) Traffic 6:607). Only
Gal-1, 2, 3, 4, 7, 9, 9, 10, 12, and 13 are known in humans.
[0064] Galectin-1, -3, and -9 are specific galectin family members
that are well known to promote tumor growth and progression through
various mechanisms, including promoting tumor growth,
invasion/metastasis, and immune inhibition. Gal-1 and Gal-3 induce
T cell apoptosis by binding to CD45 and inhibit T cell
proliferation by blocking clustering of CD4/CD8 with CD45. Gal-9
inhibits immunity by inducing T cell apoptosis and inhibiting T
cell proliferation and cytokine production via binding to Tim-3 on
T cells. Emerging findings support Gal-1, -3 and -9 as key targets
for cancer therapy.
[0065] Sequences, structures, domains, biophysical characteristics,
and functions of Gal-1 gene and gene products have been described
in the art. See, for example, Rabinovich et al. (2002) Trends
Immunol. 23:313-320; Liu and Rabinovich (2005) Nat. Rev. Cancer
5:29-41; Rubinstein et al. (2004) Cancer Cell 5:241-251; Le et al.
(2005) J. Clin. Oncol 23:8932-8941; Vasta el al. (2004) Curr. Opin.
Struct. Biol. 14:617-630; Toscano et al (2007) Cyt. Growth Fact.
Rev. 18:57-71; Camby et al. (2006) Glycobiol. 16:137R-157R; U.S.
Pat. Publs. 2003-0004132, 2003-0109464, 2006-0189514, 2009-0176223,
2009-0191182, 2012-0028825, and 2013-0011409, each of which is
incorporated herein, by reference, in its entirety. Human Gal-1 in
its monomeric form is a 14.3 kDa protein, encoded by the LSGALS1
gene located on chromosome 22q12. The full-length gene product is
comprised of the splicing of four exons and encodes a 135 amino
acid protein with a single carbohydrate recognition domain (CRD)
specific for binding to glycoconjugates bearing N-acetyllactosamine
(LacNAc) Type 1 (Gal.beta.1-3GlcNAc) or Type 2 (Gal.beta.1-4GlcNAc)
disaccharides, with increased avidity for poly-LacNAc chains
(Schwarz et al. (1998) Biochem. 37:5867). The nucleic acid and
amino acid sequences of a representative human Gal-1 biomarker is
available to the public at the GenBank database under NM_002305.3
and NP_002296.1. Nucleic acid and polypeptide sequences of Gal-1
orthologs in organisms other than humans are well known and
include, for example, monkey Gal-1 (NM_001168627.1 and
NP_001162098.1), chimpanzee Gal-1 (XM_003953882.1 and
XP_003953931.1; XM_003953883.1 and XP_003953932.1; XM_001162104.3
and XP_001162104.1), mouse Gal-1 (NM_008495.1 and NP_032521.1), rat
Gal-1 (NM_019904.1 and NP_063969.1), dog Gal-1 (NM_001201488.1 and
NP_001188417.1), chicken Gal-1 (NM_206905.1 and NP_996788.1), and
cow Gal-1 (NM_175782.1 and NP_786976.1), all of which are
incorporated by reference into Table 1. For example, relevant Gall
sequences useful for detection include those listed below in Table
1. Anti-Gal-1 antibodies suitable for detecting Gal-1 protein are
well-known in the art and include, for example, BML-GA1161 (Enzo
Life Sciences), 10871-05011 and 10871-0521 (AssayPro), PAS-25649
and PA5-19206 (Thermo Fischer Scientific, Inc.), LS-C125647 and
LS-C23787) (Lifespan Biosciences), orb29058, orb20373, and orb10685
(Biorbyt), OAAB07343, OAEB01591, and OAAB03153 (Aviva Systems
Biology), MAB5854 and AF5854 (R&D Systems), HPA049864 (Atlas
Antibodies), and 11858-1-AP (Proteintech Group). It is to be noted
that the term can further be used to refer to any combination of
features described herein regarding Gal-1 molecules. For example,
any combination of sequence composition, percentage identify,
sequence length, domain structure, functional activity, etc. can be
used to describe a Gal-1 molecule of the present invention.
[0066] Sequences, structures, domains, biophysical characteristics,
and functions of Gal-3 gene and gene products have been described
in the art (see, for example, Cherayil et al. (1990) Proc. Natl.
Acad. Sci. U.S.A. 87:7324-7328; Gitt and Barondes (1991) Biochem.
30:82-89; Raz et al. (1991) Cancer Rev. 51:2173-2178; Raimond et
al. (1997) Mamm. Genome 8:706-707; Berbis et al. (2014) Biochem.
Biophys. Res. Commun. 443:126-131). At least two transcript
variants and isoforms of human Gal-3 are known. Transcript variant
1 (NM_002306.3) encodes long isoform 1 (NP_002297.2), whereas
transcript variant 2 (NM_001177388.1) uses an alternative splie
site in the 3' coding region, which causes a frameshift and encodes
an isoform 2 (NP_001170859.1), which has a shorter and distinct
C-terminus relative to isoform 1. Nucleic acid and polypeptide
sequences of Gal-3 orthologs in organisms other than humans are
well known and include, for example, monkey Gal-3 (NM_001266363.1
and NP_001253292.1), chimpanzee Gal-3 (XM_001148424.3 and
XP_001148424.2), mouse Gal-3 (NM_001145953.1, NP_001139425.1,
NM_010705.3, and NP_034835.1), rat Gal-3 (NM_031832.1 and
NP_114020.1), dog Gal-3 (NM_001197043.1 and NP_001183972.1),
chicken Gal-3 (NM_214591.1 and NP_999756.1), and cow Gal-3
(NM_001102341.2 and NP_001095811.1), all of which are incorporated
by reference into Table 1. For example, relevant Gal-3 sequences
useful for detection include those listed below in Table 1.
Anti-Gal-3 antibodies suitable for detecting Gal-3 protein are
well-known in the art and include, for example, orb128279,
orb29909, orb48075, and orb27797 (Biorbyt), ALX-804-284 (Enzo Life
Sciences), 130-101-312, and 130-101-315 (Miltenyi Biotec),
14979-1-AP and 60207-1-Ig (Proteintech Group), AHP2071, MCA4063Z,
and AHP1481B (AbD Serotec), EB10775 (Everest Biotech), MA1-940,
MA5-12367, PA5-34912, and PA5-34819 (Thermo Fisher Scientific), and
HPA003162 (Atlas Antibodies). It is to be noted that the term can
further be used to refer to any combination of features described
herein regarding Gal-3 molecules. For example, any combination of
sequence composition, percentage identify, sequence length, domain
structure, functional activity, etc. can be used to describe a
Gal-3 molecule of the present invention.
[0067] Sequences, structures, domains, biophysical characteristics,
and functions of Gal-9 gene and gene products have been described
in the art (see, for example, Tureci et al. (1997) J. Biol. Chem.
272:6416-6422; Matsumoto et al. (1998) J. Biol. Chem.
273:16976-16984; Matsumoto et al. (2002) J. Immunol. 168:1961-1967;
Kageshita et at (2002) Int. J. Cancer 99:809-816; Heusschen et al.
(2014) Biochem. Biophys. Acta 1842:284-292; Sato et al. (2002)
Glycobiol. 12:191-197; Park et at (2002) Genome Res. 12:729-738;).
Several loci on human chromosome 17p encode variants of human
Gal-9. For example, at least two transcript variants and isoforms
of human Gal-9A are known. Transcript variant 1 (NM_009587.2)
encodes the long isoform 1 of Gal-9A (NP_033665.1). By contrast,
transcript variant 2 (NM_002308.3) lacks an internal, in-frame
coding exon relative to transcript variant 1 resulting a shorter
isoform 2 of Gal-9A (NP_002299.2) missing a 32 amino acid protein
segment. Human Gal-9B was initially thought to represent a
pseudogene, but is protein-encoding and is more centromeric than
the similar Gal-9A locus on human chromosome 17p. Human Gal-9B
sequences are publicly available as NM_001042685.1 and
NP_001036150.1. Similarly, human Gal-9C sequences are publicly
available as NM_001040078.2 and NP_001035167.2. Nucleic acid and
polypeptide sequences of Gal-9 orthologs in organisms other than
humans are well known and include, for example, mouse Gal-9
(NM_010708.2, NP_034838.2, NM_001159301.1, and NP_001152773.1), rat
Gal-9 (NM_12977.1 and NP_037109.1), dog Gal-9 (NM_001003345.1 and
NP_001003345.1), and cow Gal-9 (NM_001039177.2, NP_001034266.1,
NM_001015570.3, and NP_001015570.1), all of which are incorporated
by reference into Table 1. For example, relevant Gal-9 sequences
useful for detection include those listed below in Table 1.
Anti-Gal-9 antibodies suitable for detecting Gal-9 protein are
well-known in the art and include, for example, 130-102-236,
120-102-217, and 130-105-160 (Miltenyi Biotec), PA5-29823 and
PAS-32252 (Thermo Fisher Scientific), orb11543, orb95172,
orb161114, and orb16471 (Biorbyt), LS-B6275, LS-C146970. LS-C81943,
and LS-C300127 (Lifespan Biosciences), 50-9116-41 (eBioscience),
HPA047218 (Atlas Antibodies), AF3535 and MAB3535 (R&D Systems).
OAAF03042, OAAB11184, and ARP54821_P050 (Aviva Systems Biology),
and 17938-1-AP (Proteintech Group). Anti-Gal-9B antibodies for
detection Gal-9B protein are also well-known in the art and
include, for example, PA5-23573 (Thermo Fisher Scientific),
LS-C305017 and LS-C261850 (Lifespan Biosciences), OAAB00068 (Aviva
Systems Biology), orb27913, orb189220, and orb184906 (Biorbyt),
STJ40607 (St. John's Laboratory), AP52471PU-N (Acris Antibodies),
HPA-46876 (Atlas Antibodies), MBS2003379 (MyBioSource), and
AP10065c (Abgent). Similarly, anti-Gal-9C antibodies suitable for
detecting Gal-9C protein are well-known in the art and include, for
example, LS-C294015, LS-C301358, LS-C294014, and LS-C304031
(Lifespan Biosciences), sc-292682 (Santa Cruz Biotechnology),
PAV236Hu02, PA V236Hu01, and PAV236Hu71 (Cloud-Clone Corporation),
orb189221 and orb184907 (Biorbyt). ARP70764_P050 (Aviva Systems
Biology), 140398 and 140399 (United States Biological), and
ab178351 (Abeam). It is to be noted that the term can further be
used to refer to any combination of features described herein
regarding Gal-9 molecules. For example, any combination of sequence
composition, percentage identify, sequence length, domain
structure, functional activity, etc. can be used to describe a
Gal-9 molecule of the present invention.
[0068] "Homologous" as used herein, refers to nucleotide sequence
similarity between two regions of the same nucleic acid strand or
between regions of two different nucleic acid strands. When a
nucleotide residue position in both regions is occupied by the same
nucleotide residue, then the regions are homologous at that
position. A first region is homologous to a second region if at
least one nucleotide residue position of each region is occupied by
the same residue. Homology between two regions is expressed in
terms of the proportion of nucleotide residue positions of the two
regions that are occupied by the same nucleotide residue. By way of
example, a region having the nucleotide sequence 5'-ATTGCC-3' and a
region having the nucleotide sequence 5'-TATGGC-3' share
50.degree.,% homology. Preferably, the first region comprises a
first portion and the second region comprises a second portion,
whereby, at least about 50%, and preferably at least about 75%, at
least about 90%, or at least about 95% of the nucleotide residue
positions of each of the portions are occupied by the same
nucleotide residue. More preferably, all nucleotide residue
positions of each of the portions are occupied by the same
nucleotide residue.
[0069] The term "immune cell" refers to cells that play a role in
the immune response. Immune cells are of hematopoietic origin, and
include lymphocytes, such as B cells and T cells; natural killer
cells; myeloid cells, such as monocytes, macrophages, eosinophils,
mast cells, basophils, and granulocytes.
[0070] The term "immune checkpoint" refers to a group of molecules
on the cell surface of CD4+ and/or CD8+ T cells that fine-tune
immune responses by down-modulating or inhibiting an anti-tumor
immune response. Immune checkpoint proteins are well known in the
art and include, without limitation, CTLA-4, PD-1, VISTA, B7-H2,
B7-H3, PD-11, B7-H4, B7-H6, 2B4, ICOS, HVEM, PD-L2, CD160, gp49B,
PIR-B, KIR family receptors, TIM-1, TIM-3, TIM-4, LAG-3, BTLA,
SIRPalpha (CD47), CD48, 2B4 (CD244), B7.1, B7.2, ILT-2, ILT-4,
TIGIT, 1HHLA2, butyrophilins, and A2aR (see, for example, WO
2012/177624). The term further encompasses biologically active
protein fragment, as well as nucleic acids encoding full-length
immune checkpoint proteins and biologically active protein
fragments thereof. In some embodiment, the term further encompasses
any fragment according to homology descriptions provided
herein.
[0071] "Anti-immune checkpoint therapy" refers to the use of agents
that inhibit immune checkpoint nucleic acids and/or proteins.
Inhibition of one or more immune checkpoints can block or otherwise
neutralize inhibitory signaling to thereby upregulate an immune
response in order to more efficaciously treat cancer. Exemplary
agents useful for inhibiting immune checkpoints include antibodies,
small molecules, peptides, peptidomimetics, natural ligands, and
derivatives of natural ligands, that can either bind and/or
inactivate or inhibit immune checkpoint proteins, or fragments
thereof; as well as RNA interference, antisense, nucleic acid
aptamers, etc. that can downregulate the expression and/or activity
of immune checkpoint nucleic acids, or fragments thereof. Exemplary
agents for upregulating an immune response include antibodies
against one or more immune checkpoint proteins block the
interaction between the proteins and its natural receptor(s); a
non-activating form or one or more immune checkpoint proteins
(e.g., a dominant negative polypeptide); small molecules or
peptides that block the interaction between one or more immune
checkpoint proteins and its natural receptor(s); fusion proteins
(e.g. the extracellular portion of an immune checkpoint inhibition
protein fused to the Pc portion of an antibody or immunoglobulin)
that bind to its natural receptor(s); nucleic acid molecules that
block immune checkpoint nucleic acid transcription or translation;
and the like. Such agents can directly block the interaction
between the one or more immune checkpoints and its natural
receptor(s) (e.g., antibodies) to prevent inhibitory signaling and
upregulate an immune response. Alternatively, agents can indirectly
block the interaction between one or more immune checkpoint
proteins and its natural receptor(s) to prevent inhibitory
signaling and upregulate an immune response. For example, a soluble
version of an immune checkpoint protein ligand such as a stabilized
extracellular domain can binding to its receptor to indirectly
reduce the effective concentration of the receptor to bind to an
appropriate ligand. In one embodiment, anti-PD-1 antibodies,
anti-PD-L1 antibodies, and anti-CTLA-4 antibodies, either alone or
in combination, are used to inhibit immune checkpoints.
[0072] "Ipilimumab" is a representative example of an anti-immune
checkpoint therapy. Ipilimumab (previously MDX-010; Medarex Inc.,
marketed by Bristol-Myers Squibb as YERVOY.TM.) is a fully human
anti-human CTLA-4 monoclonal antibody that blocks the binding of
CTLA-4 to CD80 and CD86 expressed on antigen presenting cells,
thereby, blocking the negative down-regulation of the immune
responses elicited by the interaction of these molecules (see, for
example, WO 2013/169971, U.S. Pat. Publ. 2002/0086014, and U.S.
Pat. Publ. 2003/0086930.
[0073] The term "immune response" includes T cell mediated and/or B
cell mediated immune responses. Exemplary immune responses include
T cell responses, e.g., cytokine production and cellular
cytotoxicity. In addition, the term immune response includes immune
responses that are indirectly effected by T cell activation, e.g.,
antibody production (humoral responses) and activation of cytokine
responsive cells, e.g., macrophages.
[0074] The term "immunotherapeutic agent" can include any molecule,
peptide, antibody or other agent which can stimulate a host immune
system to generate an immune response to a tumor or cancer in the
subject. Various immunotherapeutic agents are useful in the
compositions and methods described herein.
[0075] The term "inhibit" includes the decrease, limitation, or
blockage, of, for example a particular action, function, or
interaction. In some embodiments, cancer is "inhibited" if at least
one symptom of the cancer is alleviated, terminated, slowed, or
prevented. As used herein, cancer is also "inhibited" if recurrence
or metastasis of the cancer is reduced, slowed, delayed, or
prevented.
[0076] The term "interaction", when referring to an interaction
between two molecules, refers to the physical contact (e.g.,
binding) of the molecules with one another. Generally, such an
interaction results in an activity (which produces a biological
effect) of one or both of said molecules.
[0077] An "isolated protein" refers to a protein that is
substantially free of other proteins, cellular material, separation
medium, and culture medium when isolated from cells or produced by
recombinant DNA techniques, or chemical precursors or other
chemicals when chemically synthesized. An "isolated" or "purified"
protein or biologically active portion thereof is substantially
free of cellular material or other contaminating proteins from the
cell or tissue source from which the antibody, polypeptide, peptide
or fusion protein is derived, or substantially free from chemical
precursors or other chemicals when chemically synthesized. The
language "substantially free of cellular material" includes
preparations of a biomarker polypeptide or fragment thereof, in
which the protein is separated from cellular components of the
cells from which it is isolated or recombinantly produced. In one
embodiment, the language "substantially free of cellular material"
includes preparations of a biomarker protein or fragment thereof,
having less than about 30% (by dry weight) of non-biomarker protein
(also referred to herein as a "contaminating protein"), more
preferably less than about 20% of non-biomarker protein, still more
preferably less than about 10% of non-biomarker protein, and most
preferably less than about 5% non-biomarker protein. When antibody,
polypeptide, peptide or fusion protein or fragment thereof, e.g., a
biologically active fragment thereof, is recombinantly produced, it
is also preferably substantially free of culture medium, i.e.,
culture medium represents less than about 20%, more preferably less
than about 10%, and most preferably less than about 5% of the
volume of the protein preparation.
[0078] As used herein, the term "isotype" refers to the antibody
class (e.g., IgM or IgG1) that is encoded by heavy chain constant
region genes.
[0079] As used herein, the term "K.sub.D" is intended to refer to
the dissociation equilibrium constant of a particular
antibody-antigen interaction. The binding affinity of antibodies of
the disclosed invention may be measured or determined by standard
antibody-antigen assays, for example, competitive assays,
saturation assays, or standard immunoassays such as ELISA or
RIA.
[0080] A "kit" is any manufacture (e.g. a package or container)
comprising at least one reagent, e.g. a probe or small molecule,
for specifically detecting and/or affecting the expression of a
marker of the present invention. The kit may be promoted,
distributed, or sold as a unit for performing the methods of the
present invention. The kit may comprise one or more reagents
necessary to express a composition useful in the methods of the
present invention. In certain embodiments, the kit may further
comprise a reference standard, e.g., a nucleic acid encoding a
protein that does not affect or regulate signaling pathways
controlling cell growth, division, migration, survival or
apoptosis. One skilled in the art can envision many such control
proteins, including, but not limited to, common molecular tags
(e.g., green fluorescent protein and beta-galactosidase), proteins
not classified in any of pathway encompassing cell growth,
division, migration, survival or apoptosis by GeneOntology
reference, or ubiquitous housekeeping proteins. Reagents in the kit
may be provided in individual containers or as mixtures of two or
more reagents in a single container. In addition, instructional
materials which describe the use of the compositions within the kit
can be included.
[0081] The term "neoadjuvant therapy" refers to a treatment given
before the primary treatment. Examples of neoadjuvant therapy can
include chemotherapy, radiation therapy, and hormone therapy. For
example, in treating breast cancer, neoadjuvant therapy can allows
patients with large breast cancer to undergo breast-conserving
surgery.
[0082] The "normal" level of expression of a biomarker is the level
of expression of the biomarker in cells of a subject, e.g., a human
patient, not afflicted with a cancer. An "over-expression" or
"significantly higher level of expression" of a biomarker refers to
an expression level in a test sample that is greater than the
standard error of the assay employed to assess expression, and is
preferably at least 10%, and more preferably 1.2, 1.3, 1.4, 1.5,
1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7,
2.8, 2.9, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 9, 8.5, 9, 9.5,
10, 10.5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 times or more
higher than the expression activity or level of the biomarker in a
control sample (e.g., sample from a healthy subject not having the
biomarker associated disease) and preferably, the average
expression level of the biomarker in several control samples. A
"significantly lower level of expression" of a biomarker refers to
an expression level in a test sample that is at least 10%, and more
preferably 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.1,
2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.5, 4, 4.5, 5, 5.5, 6,
6.5, 7, 7.5, 8, 9.5, 9, 9.5, 10, 10.5, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20 times or more lower than the expression level of the
biomarker in a control sample (e.g., sample from a healthy subject
not having the biomarker associated disease) and preferably, the
average expression level of the biomarker in several control
samples.
[0083] An "over-expression" or "significantly higher level of
expression" of a biomarker refers to an expression level in a test
sample that is greater than the standard error of the assay
employed to assess expression, and is preferably at least 10%, and
more preferably 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1,
2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.5, 4, 4.5, 5,
5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20 times or more higher than the expression
activity or level of the biomarker in a control sample (e.g.,
sample from a healthy subject not having the biomarker associated
disease) and preferably, the average expression level of the
biomarker in several control samples. A "significantly lower level
of expression" of a biomarker refers to an expression level in a
test sample that is at least 10%, and more preferably 1.2, 1.3,
1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.1, 2.2, 2.3, 2.4, 2.5,
2.6, 2.7, 2.8, 2.9, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5,
9, 9.5, 10, 10.5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 times or
more lower than the expression level of the biomarker in a control
sample (e.g., sample from a healthy subject not having the
biomarker associated disease) and preferably, the average
expression level of the biomarker in several control samples.
[0084] The term "pre-determined" biomarker amount and/or activity
measurement(s) may be a biomarker amount and/or activity
measurement(s) used to, by way of example only, evaluate a subject
that may be selected for a particular treatment, evaluate a
response to a treatment such as anti-immune checkpoint inhibitor
and anti-angiogenesis combination therapy, and/or evaluate the
disease state. A pre-determined biomarker amount and/or activity
measurement(s) may be determined in populations of patients with or
without cancer. The pre-determined biomarker amount and/or activity
measurement(s) can be a single number, equally applicable to every
patient, or the pre-determined biomarker amount and/or activity
measurement(s) can vary according to specific subpopulations of
patients. Age, weight, height, and other factors of a subject may
affect the pre-determined biomarker amount and/or activity
measurement(s) of the individual. Furthermore, the pre-determined
biomarker amount and/or activity can be determined for each subject
individually. In one embodiment, the amounts determined and/or
compared in a method described herein are based on absolute
measurements. In another embodiment, the amounts determined and/or
compared in a method described herein are based on relative
measurements, such as ratios (e.g., serum biomarker normalized to
the expression of a housekeeping or otherwise generally constant
biomarker). The pre-determined biomarker amount and/or activity
measurement(s) can be any suitable standard. For example, the
pre-determined biomarker amount and/or activity measurement(s) can
be obtained from the same or a different human for whom a patient
selection is being assessed. In one embodiment, the pre-determined
biomarker amount and/or activity measurement(s) can be obtained
from a previous assessment of the same patient. In such a manner,
the progress of the selection of the patient can be monitored over
time. In addition, the control can be obtained from an assessment
of another human or multiple humans, e.g., selected groups of
humans, if the subject is a human. In such a manner, the extent of
the selection of the human for whom selection is being assessed can
be compared to suitable other humans, e.g., other humans who are in
a similar situation to the human of interest, such as those
suffering from similar or the same condition(s) and/or of the same
ethnic group.
[0085] The term "predictive" includes the use of a biomarker
nucleic acid and/or protein status, e.g., over- or under-activity,
emergence, expression, growth, remission, recurrence or resistance
of tumors before, during or after therapy, for determining the
likelihood of response of a cancer to anti-immune checkpoint and
anti-angiogenesis combination treatment (e.g., therapeutic
antibodies against CTLA-4, PD-1, PD-L1, VEGF, and the like). Such
predictive use of the biomarker may be confirmed by, e.g., (1)
increased or decreased copy number (e.g., by FISH, FISH plus SKY,
single-molecule sequencing, e.g., as described in the art at least
at J. Biotechnol., 86:289-301, or qPCR), overexpression or
underexpression of a biomarker nucleic acid (e.g., by ISH, Northern
Blot, or qPCR) increased or decreased biomarker protein (e.g., by
IHC), or increased or decreased activity, e.g., in more than about
5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 20%, 25%, 30%,
40%, 50%, 60%, 70%, 80%, 90%, 95%, 100%, or more of assayed human
cancers types or cancer samples; (2) its absolute or relatively
modulated presence or absence in a biological sample, e.g., a
sample containing tissue, whole blood, scrum, plasma, buccal
scrape, saliva, cerebrospinal fluid, urine, stool, or bone marrow,
from a subject, e.g. a human, afflicted with cancer; (3) its
absolute or relatively modulated presence or absence in clinical
subset of patients with cancer (e.g., those responding to a
particular anti-immune checkpoint and anti-angiogenesis combination
therapy or those developing resistance thereto).
[0086] The term "pre-malignant lesions" as described herein refers
to a lesion that, while not cancerous, has potential for becoming
cancerous. It also includes the term "pre-malignant disorders" or
"potentially malignant disorders." In particular this refers to a
benign, morphologically and/or histologically altered tissue that
has a greater than normal risk of malignant transformation, and a
disease or a patient's habit that does not necessarily alter the
clinical appearance of local tissue but is associated with a
greater than normal risk of precancerous lesion or cancer
development in that tissue (leukoplakia, erythroplakia,
erytroleukoplakia lichen planus (lichenoid reaction) and any lesion
or an area which histological examination showed atypia of cells or
dysplasia.
[0087] The terms "prevent," "preventing," "prevention,"
"prophylactic treatment," and the like refer to reducing the
probability of developing a disease, disorder, or condition in a
subject, who does not have, but is at risk of or susceptible to
developing a disease, disorder, or condition.
[0088] The term "probe" refers to any molecule which is capable of
selectively binding to a specifically intended target molecule, for
example, a nucleotide transcript or protein encoded by or
corresponding to a biomarker nucleic acid. Probes can be either
synthesized by one skilled in the art, or derived from appropriate
biological preparations. For purposes of detection of the target
molecule, probes may be specifically designed to be labeled, as
described herein. Examples of molecules that can be utilized as
probes include, but are not limited to, RNA, DNA, proteins,
antibodies, and organic molecules.
[0089] The term "prognosis" includes a prediction of the probable
course and outcome of cancer or the likelihood of recovery from the
disease. In some embodiments, the use of statistical algorithms
provides a prognosis of cancer in an individual. For example, the
prognosis can be surgery, development of a clinical subtype of
cancer (e.g., solid tumors, such as lung cancer, melanoma, and
renal cell carcinoma), development of one or more clinical factors,
development of intestinal cancer, or recovery from the disease.
[0090] The term "response to anti-immune checkpoint and
anti-angiogenesis combination therapy" relates to any response of
the hyperproliferative disorder (e.g., cancer) to an anti-immune
checkpoint and anti-angiogenesis combination therapy, such as
anti-CTLA4 and anti-VEGF therapy, preferably to a change in tumor
mass and/or volume after initiation of neoadjuvant or adjuvant
chemotherapy. Hyperproliferative disorder response may be assessed,
for example for efficacy or in a neoadjuvant or adjuvant situation,
where the size of a tumor after systemic intervention can be
compared to the initial size and dimensions as measured by CT, PET,
mammogram, ultrasound or palpation. Responses may also be assessed
by caliper measurement or pathological examination of the tumor
after biopsy or surgical resection. Response may be recorded in a
quantitative fashion like percentage change in tumor volume or in a
qualitative fashion like "pathological complete response" (pCR),
"clinical complete remission" (cCR), "clinical partial remission"
(cPR), "clinical stable disease" (cSD), "clinical progressive
disease" (cPD) or other qualitative criteria. Assessment of
hyperproliferative disorder response may be done early after the
onset of neoadjuvant or adjuvant therapy, e.g., after a few hours,
days, weeks or preferably after a few months. A typical endpoint
for response assessment is upon termination of neoadjuvant
chemotherapy or upon surgical removal of residual tumor cells
and/or the tumor bed. This is typically three months after
initiation of neoadjuvant therapy. In some embodiments, clinical
efficacy of the therapeutic treatments described herein may be
determined by measuring the clinical benefit rate (CBR). The
clinical benefit rate is measured by determining the sum or the
percentage of patients who are in complete remission (CR), the
number of patients who are in partial remission (PR) and the number
of patients having stable disease (SD) at a time point at least 6
months out from the end of therapy. The shorthand for this formula
is CBR=CR+PR+SD over 6 months. In some embodiments, the CBR for a
particular cancer therapeutic regimen is at least 25%, 30%, 35%,
40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or more.
Additional criteria for evaluating the response to cancer therapies
are related to "survival" which includes all of the following:
survival until mortality, also known as overall survival (wherein
said mortality may be either irrespective of cause or tumor
related); "recurrence-free survival" (wherein the term recurrence
shall include both localized and distant recurrence); metastasis
free survival; disease free survival (wherein the term disease
shall include cancer and diseases associated therewith). The length
of said survival may be calculated by reference to a defined start
point (e.g., time of diagnosis or start of treatment) and end point
(e.g., death, recurrence or metastasis). In addition, criteria for
efficacy of treatment can be expanded to include response to
chemotherapy, probability of survival, probability of metastasis
within a given time period, and probability of tumor recurrence.
For example, in order to determine appropriate threshold values, a
particular cancer therapeutic regimen can be administered to a
population of subjects and the outcome can be correlated to
biomarker measurements that were determined prior to administration
of any cancer therapy. The outcome measurement may be pathologic
response to therapy given in the neoadjuvant setting.
Alternatively, outcome measures, such as overall survival and
disease-free survival can be monitored over a period of time for
subjects following cancer therapy for whom biomarker measurement
values are known. In certain embodiments, the doses administered
are standard doses known in the art for cancer therapeutic agents.
The period of time for which subjects are monitored can vary. For
example, subjects may be monitored for at least 2, 4, 6, 8, 10, 12,
14, 16, 18, 20, 25, 30, 35, 40, 45, 50, 55, or 60 months. Biomarker
measurement threshold values that correlate to outcome of a cancer
therapy can be determined using well-known methods in the art, such
as those described in the Examples section.
[0091] The term "resistance" refers to an acquired or natural
resistance of a cancer sample or a mammal to a cancer therapy
(i.e., being nonresponsive to or having reduced or limited response
to the therapeutic treatment), such as having a reduced response to
a therapeutic treatment by 25% or more, for example, 30%, 40%, 50%,
60%, 70%, 80%, or more, to 2-fold, 3-fold, 4-fold, 5-fold, 10-fold,
15-fold, 20-fold or more. The reduction in response can be measured
by comparing with the same cancer sample or mammal before the
resistance is acquired, or by comparing with a different cancer
sample or a mammal who is known to have no resistance to the
therapeutic treatment. A typical acquired resistance to
chemotherapy is called "multidrug resistance." The multidrug
resistance can be mediated by P-glycoprotein or can be mediated by
other mechanisms, or it can occur when a mammal is infected with a
multi-drug-resistant microorganism or a combination of
microorganisms. The determination of resistance to a therapeutic
treatment is routine in the art and within the skill of an
ordinarily skilled clinician, for example, can be measured by cell
proliferative assays and cell death assays as described herein as
"sensitizing." In some embodiments, the term "reverses resistance"
means that the use of a second agent in combination with a primary
cancer therapy (e.g., chemotherapeutic or radiation therapy) is
able to produce a significant decrease in tumor volume at a level
of statistical significance (e.g., p<0.05) when compared to
tumor volume of untreated tumor in the circumstance where the
primary cancer therapy (e.g., chemotherapeutic or radiation
therapy) alone is unable to produce a statistically significant
decrease in tumor volume compared to tumor volume of untreated
tumor. This generally applies to tumor volume measurements made at
a time when the untreated tumor is growing log rhythmically.
[0092] The terms "response" or "responsiveness" refers to an
anti-cancer response, e.g. in the sense of reduction of tumor size
or inhibiting tumor growth. The terms can also refer to an improved
prognosis, for example, as reflected by an increased time to
recurrence, which is the period to first recurrence censoring for
second primary cancer as a first event or death without evidence of
recurrence, or an increased overall survival, which is the period
from treatment to death from any cause. To respond or to have a
response means there is a beneficial endpoint attained when exposed
to a stimulus. Alternatively, a negative or detrimental symptom is
minimized, mitigated or attenuated on exposure to a stimulus. It
will be appreciated that evaluating the likelihood that a tumor or
subject will exhibit a favorable response is equivalent to
evaluating the likelihood that the tumor or subject will not
exhibit favorable response (I.e., will exhibit a lack of response
or be non-responsive).
[0093] An "RNA interfering agent" as used herein, is defined as any
agent which interferes with or inhibits expression of a target
biomarker gene by RNA interference (RNAi). Such RNA interfering
agents include, but are not limited to, nucleic acid molecules
including RNA molecules which are homologous to the target
biomarker gene of the present invention, or a fragment thereof,
short interfering RNA (siRNA), and small molecules which interfere
with or inhibit expression of a target biomarker nucleic acid by
RNA interference (RNAi).
[0094] "RNA interference (RNAi)" is an evolutionally conserved
process whereby the expression or introduction of RNA of a sequence
that is identical or highly similar to a target biomarker nucleic
acid results in the sequence specific degradation or specific
post-transcriptional gene silencing (PTGS) of messenger RNA (mRNA)
transcribed from that targeted gene (see Coburn, G. and Cullen, B.
(2002) J. of Virology 76(18):9225), thereby inhibiting expression
of the target biomarker nucleic acid. In one embodiment, the RNA is
double stranded RNA (dsRNA). This process has been described in
plants, invertebrates, and mammalian cells. In nature, RNAi is
initiated by the dsRNA-specific endonuclease Dicer, which promotes
processive cleavage of long dsRNA into double-stranded fragments
termed siRNAs. siRNAs are incorporated into a protein complex that
recognizes and cleaves target mRNAs. RNAi can also be initiated by
introducing nucleic acid molecules, e.g., synthetic siRNAs or RNA
interfering agents, to inhibit or silence the expression of target
biomarker nucleic acids. As used herein, "inhibition of target
biomarker nucleic acid expression" or "inhibition of marker gene
expression" includes any decrease in expression or protein activity
or level of the target biomarker nucleic acid or protein encoded by
the target biomarker nucleic acid. The decrease may be of at least
30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 99% or more as compared
to the expression of a target biomarker nucleic acid or the
activity or level of the protein encoded by a target biomarker
nucleic acid which has not been targeted by an RNA interfering
agent.
[0095] The term "sample" used for detecting or determining the
presence or level of at least one biomarker is typically whole
blood, plasma, serum, saliva, urine, stool (e.g., feces), tears,
and any other bodily fluid (e.g., as described above under the
definition of "body fluids"), or a tissue sample (e.g., biopsy)
such as a small intestine, colon sample, or surgical resection
tissue. In certain instances, the method of the present invention
further comprises obtaining the sample from the individual prior to
detecting or determining the presence or level of at least one
marker in the sample.
[0096] The term "sensitize" means to alter cancer cells or tumor
cells in a way that allows for more effective treatment of the
associated cancer with a cancer therapy (e.g., anti-immune
checkpoint, anti-angiogenesis, chemotherapeutic, and/or radiation
therapy). In some embodiments, normal cells are not affected to an
extent that causes the normal cells to be unduly injured by the
anti-immune checkpoint and anti-angiogenesis combination therapy.
An increased sensitivity or a reduced sensitivity to a therapeutic
treatment is measured according to a known method in the art for
the particular treatment and methods described herein below,
including, but not limited to, cell proliferative assays (Tanigawa
N Kern D H, Kikasa Y, Morton D L, Cancer Res 192; 42: 2159-2164),
cell death assays (Weisenthal L M, Shoemaker R H, Marsden J A, Dill
P L, Baker J A, Moran E M, Cancer Res 1984; 94: 161-173; Weisenthal
L M, Lippman M E, Cancer Treat Rep 1985; 69: 615-632; Weisenthal L
M, In: Kaspers G J L, Pieters R, Twentyman P R, Weisenthal L M,
Veerman A J P. eds. Drug Resistance in Leukemia and Lymphoma.
Langhorne, P A: Harwood Academic Publishers, 1993: 415-432;
Weisenthal L M, Contrib Gynecol Obstet 1994; 19: 82-90). The
sensitivity or resistance may also be measured in animal by
measuring the tumor size reduction over a period of time, for
example, 6 month for human and 4-6 weeks for mouse. A composition
or a method sensitizes response to a therapeutic treatment if the
increase in treatment sensitivity or the reduction in resistance is
25% or more, for example, 30%, 40%, 50%, 60%, 70%, 80%, or more, to
2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold or more,
compared to treatment sensitivity or resistance in the absence of
such composition or method. The determination of sensitivity or
resistance to a therapeutic treatment is routine in the art and
within the skill of an ordinarily skilled clinician. It is to be
understood that any method described herein for enhancing the
efficacy of a cancer therapy can be equally applied to methods for
sensitizing hyperproliferative or otherwise cancerous cells (e.g.,
resistant cells) to the cancer therapy.
[0097] The term "specific binding" refers to antibody binding to a
predetermined antigen. Typically, the antibody binds with an
affinity (K.sub.D) of approximately less than 10.sup.-7 M, such as
approximately less than 10.sup.-8 M, 10.sup.-9 M or 10.sup.-10 M or
even lower when determined by surface plasmon resonance (SPR)
technology in a BIACORE.RTM. assay instrument using human Gal-1,
Gal-3, and/or Gal-9 as the analyte and the antibody as the ligand,
and binds to the predetermined antigen with an affinity that is at
least 1.1-, 1.2-, 1.3-, 1.4-, 1.5-, 1.6-, 1.7-, 1.8-, 1.9-, 2.0-,
2.5-, 3.0-, 3.5-, 4.0-, 4.5-, 5.0-, 6.0-, 7.0-, 8.0-, 9.0-, or
10.0-fold or greater than its affinity for binding to a
non-specific antigen (e.g., BSA, casein) other than the
predetermined antigen or a closely-related antigen. The phrases "an
antibody recognizing an antigen" and "an antibody specific for an
antigen" are used interchangeably herein with the term "an antibody
which binds specifically to an antigen."
[0098] The term "synergistic effect" refers to the combined effect
of two or more anti-immune checkpoint and/or anti-angiogenesis
agents can be greater than the sum of the separate effects of the
anticancer agents alone.
[0099] "Short interfering RNA" (siRNA), also referred to herein as
"small interfering RNA" is defined as an agent which functions to
inhibit expression of a target biomarker nucleic acid, e.g., by
RNAi. An siRNA may be chemically synthesized, may be produced by in
vitro transcription, or may be produced within a host cell. In one
embodiment, siRNA is a double stranded RNA (dsRNA) molecule of
about 15 to about 40 nucleotides in length, preferably about 15 to
about 28 nucleotides, more preferably about 19 to about 25
nucleotides in length, and more preferably about 19, 20, 21, or 22
nucleotides in length, and may contain a 3' and/or 5' overhang on
each strand having a length of about 0, 1, 2, 3, 4, or 5
nucleotides. The length of the overhang is independent between the
two strands, i.e., the length of the overhang on one strand is not
dependent on the length of the overhang on the second strand.
Preferably the siRNA is capable of promoting RN A interference
through degradation or specific post-transcriptional gene silencing
(PTGS) of the target messenger RNA (mRNA).
[0100] In another embodiment, an siRNA is a small hairpin (also
called stem loop) RNA (shRNA). In one embodiment, these shRNAs are
composed of a short (e.g., 19-25 nucleotide) antisense strand,
followed by a 5-9 nucleotide loop, and the analogous sense strand.
Alternatively, the sense strand may precede the nucleotide loop
structure and the antisense strand may follow. These shRNAs may be
contained in plasmids, retroviruses, and lentiviruses and expressed
from, for example, the pol Ill U6 promoter, or another promoter
(see, e.g., Stewart, et al. (2003) RNA April; 9(4):493-501
incorporated by reference herein).
[0101] RNA interfering agents, e.g., siRNA molecules, may be
administered to a patient having or at risk for having cancer, to
inhibit expression of a biomarker gene which is overexpressed in
cancer and thereby treat, prevent, or inhibit cancer in the
subject.
[0102] The term "subject" refers to any healthy animal, mammal or
human, or any animal, mammal or human afflicted with a cancer,
e.g., lung, ovarian, pancreatic, liver, breast, prostate, and colon
carcinomas, as well as melanoma and multiple myeloma. The term
"subject" is interchangeable with "patient."
[0103] The term "survival" includes all of the following: survival
until mortality, also known as overall survival (wherein said
mortality may be either irrespective of cause or tumor related);
"recurrence-free survival" (wherein the term recurrence shall
include both localized and distant recurrence); metastasis free
survival; disease free survival (wherein the term disease shall
include cancer and diseases associated therewith). The length of
said survival may be calculated by reference to a defined start
point (e.g. time of diagnosis or start of treatment) and end point
(e.g. death, recurrence or metastasis). In addition, criteria for
efficacy of treatment can be expanded to include response to
chemotherapy, probability of survival, probability of metastasis
within a given time period, and probability of tumor
recurrence.
[0104] The term "therapeutic effect" refers to a local or systemic
effect in animals, particularly mammals, and more particularly
humans, caused by a pharmacologically active substance. The term
thus means any substance intended for use in the diagnosis, cure,
mitigation, treatment or prevention of disease or in the
enhancement of desirable physical or mental development and
conditions in an animal or human. The phrase
"therapeutically-effective amount" means that amount of such a
substance that produces some desired local or systemic effect at a
reasonable benefit/risk ratio applicable to any treatment. In
certain embodiments, a therapeutically effective amount of a
compound will depend on its therapeutic index, solubility, and the
like. For example, certain compounds discovered by the methods of
the present invention may be administered in a sufficient amount to
produce a reasonable benefit/risk ratio applicable to such
treatment.
[0105] The terms "therapeutically-effective amount" and "effective
amount" as used herein means that amount of a compound, material,
or composition comprising a compound of the present invention which
is effective for producing some desired therapeutic effect in at
least a sub-population of cells in an animal at a reasonable
benefit/risk ratio applicable to any medical treatment. Toxicity
and therapeutic efficacy of subject compounds may be determined by
standard pharmaceutical procedures in cell cultures or experimental
animals, e.g., for determining the LD.sub.50 and the ED.sub.50.
Compositions that exhibit large therapeutic indices are preferred.
In some embodiments, the LD.sub.50 (lethal dosage) can be measured
and can be, for example, at least 10%, 20%, 30%, 40%, 50%, 60%,
70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, 600%, 700%, 800%,
900%, 1000% or more reduced for the agent relative to no
administration of the agent. Similarly, the ED.sub.50 (i.e., the
concentration which achieves a half-maximal inhibition of symptoms)
can be measured and can be, for example, at least 10%, 20%, 30%,
40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, 600%,
700%, 800%, 900%, 1000% or more increased for the agent relative to
no administration of the agent. Also, Similarly, the IC.sub.50
(i.e., the concentration which achieves half-maximal cytotoxic or
cytostatic effect on cancer cells) can be measured and can be, for
example, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%,
100%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, 1000% or more
increased for the agent relative to no administration of the agent.
In some embodiments, cancer cell growth in an assay can be
inhibited by at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,
50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or even 100%. In
another embodiment, at least about a 10%, 15%, 20%, 25%, 30%, 35%,
40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or even
100% decrease in a solid malignancy can be achieved.
[0106] A "transcribed polynucleotide" or "nucleotide transcript" is
a polynucleotide (e.g. an mRNA, hnRNA, a cDNA, or an analog of such
RNA or cDNA) which is complementary to or homologous with all or a
portion of a mature mRNA made by transcription of a biomarker
nucleic acid and normal post-transcriptional processing (e.g.
splicing), if any, of the RNA transcript, and reverse transcription
of the RNA transcript.
[0107] As used herein, the term "unresponsiveness" includes
refractivity of immune cells to stimulation, e.g., stimulation via
an activating receptor or a cytokine. Unresponsiveness can occur,
e.g., because of exposure to immunosuppressants or exposure to high
doses of antigen. As used herein, the term "anergy" or "tolerance"
includes refractivity to activating receptor-mediated stimulation.
Such refractivity is generally antigen-specific and persists after
exposure to the tolerizing antigen has ceased. For example, anergy
in T cells (as opposed to unresponsiveness) is characterized by
lack of cytokine production, e.g., IL-2. T cell anergy occurs when
T cells are exposed to antigen and receive a first signal (a T cell
receptor or CD-3 mediated signal) in the absence of a second signal
(a costimulatory signal). Under these conditions, reexposure of the
cells to the same antigen (even if reexposure occurs in the
presence of a costimulatory polypeptide) results in failure to
produce cytokines and, thus, failure to proliferate. Anergic T
cells can, however, proliferate if cultured with cytokines (e.g.,
IL-2). For example, T cell anergy can also be observed by the lack
of IL-2 production by T lymphocytes as measured by ELISA or by a
proliferation assay using an indicator cell line. Alternatively, a
reporter gene construct can be used. For example, anergic T cells
fail to initiate IL-2 gene transcription induced by a heterologous
promoter under the control of the 5' IL-2 gene enhancer or by a
multimer of the AP1 sequence that can be found within the enhancer
(Kang el al. (1992) Science 257:1134).
[0108] There is a known and definite correspondence between the
amino acid sequence or a particular protein and the nucleotide
sequences that can code for the protein, as defined by the genetic
code (shown below). Likewise, there is a known and definite
correspondence between the nucleotide sequence of a particular
nucleic acid and the amino acid sequence encoded by that nucleic
acid, as defined by the genetic code.
Genetic Code
TABLE-US-00001 [0109] Alanine (Ala, A) GCA, GCC, GCG, GCT Arginine
(Arg, R) AGA, ACG, CGA, CGC, CGG, CGT Asparagine (Asn, N) AAC, AAT
Aspartic acid (Asp, D) GAC, GAT Cysteine (Cys, C) TGC, TGT Glutamic
acid (Glu, E) GAA, GAG Glutamine (Gln, Q) CAA, CAG Glycine (Gly, G)
GGA, GGC, GGG, GGT Histidine (His, H) CAC, CAT Isoleucine (Ile, I)
ATA, ATC, ATT Leucine (Leu, L) CTA, CTC, CTG, CTT, TTA, TTG Lysine
(Lys, K) AAA, AAG Methionine (Met, M) ATG Phenylalanine (Phe, F)
TTC, TTT Proline (Pro, P) CCA, CCC, CCG, CCT Serine (Ser, S) AGC,
AGT, TCA, TCC, TCG, TCT Threonine (Thr, T) ACA, ACC, ACG, ACT
Tryptophan (Trp, W) TGG Tyrosine (Tyr, Y) TAC, TAT Valine (Val, V)
GTA, GTC, GTG, GTT Termination signal (end) TAA, TAG, TGA
[0110] An important and well known feature of the genetic code is
its redundancy, whereby, for most of the amino acids used to make
proteins, more than one coding nucleotide triplet may be employed
(illustrated above). Therefore, a number of different nuceotide
sequences may code for a given amino acid sequence. Such nucleotide
sequences are considered functionally equivalent since they result
in the production of the same amino acid sequence in all organisms
(although certain organisms may translate some sequences more
efficiently than they do others). Moreover, occasionally, a
methylated variant of a purine or pyrimidine may be found in a
given nucleotide sequence. Such methylations do not affect the
coding relationship between the trinucleotide codon and the
corresponding amino acid.
[0111] In view of the foregoing, the nucleotide sequence of a DNA
or RNA encoding a biomarker nucleic acid (or any portion thereof)
can be used to derive the polypeptide amino acid sequence, using
the genetic code to translate the DNA or RNA into an amino acid
sequence. Likewise, for polypeptide amino acid sequence,
corresponding nucleotide sequences that can encode the polypeptide
can be deduced from the genetic code (which, because of its
redundancy, will produce multiple nucleic acid sequences for any
given amino acid sequence). Thus, description and/or disclosure
herein of a nucleotide sequence which encodes a polypeptide should
be considered to also include description and/or disclosure of the
amino acid sequence encoded by the nucleotide sequence. Similarly,
description and/or disclosure of a polypeptide amino acid sequence
herein should be considered to also include description and/or
disclosure of all possible nucleotide sequences that can encode the
amino acid sequence.
[0112] Finally, nucleic acid and amino acid sequence information
for the loci and biomarkers of the present invention (e.g.,
biomarkers listed in Table 1) are well known in the art and readily
available on publicly available databases, such as the National
Center for Biotechnology Information (NCBI). For example, exemplary
nucleic acid and amino acid sequences derived from publicly
available sequence databases are provided below.
TABLE-US-00002 TABLE 1 Human Gal1 cDNA Sequence SEQ ID NO: 1 1
atggcttgtg gtctggtcgc cagcaacctg aatctcaaac ctggagagtg ccttcgagtg
61 cgaggcgagg tggctcctga cgctaagagc ttcgtgctga acctgggcaa
agacagcaac 121 aacctgtgcc tgcacttcaa ccctcgcttc aacgcccacg
gcgacgccaa caccatcgtg 181 tgcaacagca aggacggcgg ggcctggggg
accgagcagc gggaggctgt ctttcccttc 241 cagcctggaa gtgttgcaga
ggtgtgcatc accttcgacc aggccaacct gaccgtcaag 301 ctgccagatg
gatacgaatt caagttcccc aaccgcctca acctggaggc catcaactac 361
atggcagctg acggtgactt caagatcaaa tgtgtggcct ttgactga Human Gal1
Amino Acid Sequence SEQ ID NO: 2 1 macglvasnl nlkpgeclrv rgevapdaks
fvlnlgkdsn nlclhfnprf nahgdantiv 61 cnskdggawg teqreavfpf
qpgsvaevci tfdqanltvk lpdgyefkfp nrlnleainy 121 maadgdfkik Mouse
Gal1 cDNA Sequence SEQ ID NO: 3 1 atggcctgtg gtctggtcgc cagcaacctg
aatctcaaac ctggggaatg tctcaaagtt 61 cggggagagg tggcctcgga
cgccaagagc tttgtgctga acctgggaaa agacagcaac 121 aacctgtgcc
tacacttcaa tcctcgcttc aatgcccatg gagacgccaa caccattgtg 181
tgtaacacca aggaagatgg gacctgggga accgaacacc gggaacctgc cttccccttc
241 cagcccggga gcatcacaga ggtgtgcatc acctttgacc aggctgacct
gaccatcaag 301 ctgccagacg gacatgaatt caagttcccc aaccgcctca
acatggaggc catcaactac 361 atggcggcgg atggagactt caagattaag
tgcgtggcct ttgagtga Mouse Gal1 Amino Acid Sequence SEQ ID NO: 4 1
macglvasnl nlkpgeclkv rgevasdaks fvlnlgkdsn nlclhfnprf nahgdantiv
61 cntkedgtwg tehrepafpf qpgsitevci tfdqadltik lpdghefkfp nrlnmea
ny 121 maadgdfkik cvafe Human Gal-3 cDNA Sequence (transcript
variant 1) SEQ ID NO: 5 1 atggcagaca atttttcgct ccatgatgcg
ttatctgggt ctggaaaccc aaaccctcaa 61 ggatggcctg gcgcatgggg
gaaccagcct gctggggcag ggggctaccc aggggcttcc 121 tatcctgggg
cctaccccgg gcaggcaccc ccaggggctt atcctggaca ggcacctcca 181
ggcgcctacc ctggagcacc tggagcttat cccggagcac ctgcacctgg agtctaccca
241 gggccaccca gcggccctgg ggcctaccca tcttctggac agccaagtgc
caccggagcc 301 taccctgcca ctggccccta tggcgcccct gctgggccac
tgattgtgcc ttataacctg 361 cctttgcctg ggggagtggc gcctcgcatg
ctgataacaa ttctgggcac ggtgaagccc 421 aatgcaaaca gaattgcttt
agatttccaa agagggaatg atgttgcctt ccactttaac 481 ccacgcttca
atgagaacaa caggagagtc attgtttgca atacaaagct ggataataac 541
tggggaaggg aagaaagaca gtcggttttc ccatttgaaa gtgggaaacc attcaaaata
601 caagtactgg ttgaacctga ccacttcaag gttgcagtga atgatgctca
cttgttgcag 661 tacaatcatc gggttaaaaa actcaatgaa atcagcaaac
tgggaatttc tggtgacata 721 gacctcacca gtgcttcata taccatgata taa
Human Gal-3 Amino Acid Sequence (isoform 1) SEQ ID NO: 6 1
madnfslhda lsgsgnpnpq gwpgawgnqp agaggypgas ypgaypgqap pgaypgqapp
61 gaypgapgay pgapapgvyp gppsgpgayp ssgqpsatga ypatgpygap
agplivpynl 121 plpggvvprm litilgtvkp nanrialdfq rgndvafhfn
prfnennrrv ivcntkldnn 181 wgreerqsvf pfesgkpfki qvlvepdhfk
vavndahllq ynhrvkklne isklgisgdi 241 dltsasytmi Human Gal-3 cDNA
Sequence (transcript variant 2) SEQ ID NO: 7 1 atggcagaca
atttttcgct ccatgatgcg ttatctgggt ctggaaaccc aaaccctcaa 61
ggatggcctg gcgcatgggg gaaccagcct gctggggcag ggggctaccc aggggcttcc
121 tatcctgggg cctaccccgg gcaggcaccc ccaggggctt atcctggaca
ggcacctcca 181 ggcgcctacc ctggagcacc tggagcttat cccggagcac
ctgcacctgg agtctaccca 241 gggccaccca gcggccctgg ggcctaccca
tcttctggac agccaagtgc caccggagcc 301 taccctgcca ctggccccta
tggcgcccct gctgggccac tgattgtgcc ttataacctg 361 cctttgcctg
ggggagtggt gcctcgcatg ctgataacaa ttctgggcac ggtgaagccc 421
aatgcaaaca gaattgcttt agatttccaa agagggaatg atgttgcctt ccactttaac
481 ccacgcttca atgagaacaa caggagagtc attgtttgca cttacatgtg
taaaggtttc 541 atgttcactg tgagtgaaaa tttttacatt catcaatatc
cctcttgtaa gtcatctact 601 taa Human Gal-3 Amino Acid Sequence
(isoform 2) SEQ ID NO: 8 1 madnfslhda lsgsgnpnpq gwpgawgnqp
agaggypgas ypgaypgqap pgaypgqapp 61 gaypgapgay pgapapgvyp
gppsgpgayp ssgqpsatga ypatgpygap agplivpynl 121 plpggvvprm
litilgtvkp nanrialdf rgndvafhfn prfnennrrv ivcntkldnn 181
mftvsenfyi hqypscksst Mouse Gal-3 cDNA Sequence (transcript variant
1) SEQ ID NO: 9 1 atggcagaca gcttttcgct taacgatgcc ttagctggct
ctggaaaccc aaaccctcaa 61 ggatatccgg gtgcatgggg gaaccagcct
ggggcagggg gctacccagg ggctgcttat 121 cctggggcct acccaggaca
agctcctcca ggggcctacc caggacaggc tcctccaggg 181 gcctacccag
gacaggctcc tcctagtgcc taccccggcc caactgcccc tggagcttat 241
cctggcccaa ctgcccctgg agcttatcct ggctcaactg cccctggagc cttcccaggg
301 caacctgggg cacctggggc ctaccccagt gctcctggag gctatcctgc
tgctggccct 361 tatggtgtcc ccgctggacc actgacggtg ccctatgacc
tgcccttgcc tggaggagtc 421 atgccccgca tgctgatcac aatcatgggc
acagtgaaac ccaacgcaaa caggattgtt 481 ctagatttca ggagagggaa
tgatgttgcc ttccacttta acccccgctt caatgagaac 541 aacaggagag
tcattgtgtg taacacgaag caggacaata actggggaaa ggaagaaaga 601
cagtcagcct tcccctttga gagtggcaaa ccattcaaaa tacaagtcct ggttgaagct
661 gaccacttca aggttgcggt caacgatgct cacctactgc agtacaacca
tcggatgaag 721 aacctccggg aaatcagcca actggggatc agtggtgaca
taaccctcac cagcgctaac 781 cacgccatga tctaa Mouse Gal-3 Amino Acid
Sequence (isoform 1) SEQ ID NO: 10 1 madsfslnda lagsgnpnpq
gypgawgnqp gaggypgaay pgaypgqapp gaypgqappg 61 aypgqappsa
ypgptapgay pgptapgayp gstapgafpg qpgapgayps apggypaagp 121
ygvpagpltv pydlplpggv mprmlitimg tvkpnanriv ldfrrgndva fhfnprfnen
181 nrrvivcntk qdnnwgkeer qsafpfesgk pfkiqvlvea dhfkvavnda
hllqynhrmk 241 nlreisqlgi sgditltsan hami Mouse Gal-3 cDNA Sequence
(transcript variant 2) SEQ ID NO: 11 1 atggcagaca gcttttcgct
taacgatgcc ttagctggct ctggaaaccc aaaccctcaa 61 ggatatccgg
gtgcatgggg gaaccagcct ggggcagggg gctacccagg ggctgcttat 121
cctggggcct acccaggaca agctcctcca ggggcctacc caggacaggc tcctccaggg
181 gcctacccag gacaggctcc tcctagtgcc taccccggcc caactgcccc
tggagcttat 241 cctggcccaa ctgcccctgg agcttatcct ggctcaactg
cccctggagc cttcccaggg 301 caacctgggg cacctggggc ctaccccagt
gctcctggag gctatcctgc tgctggccct 361 tatggtgtcc ccgctggacc
actgacggtg ccctatgacc tgcccttgcc tggaggagtc 421 atgccccgca
tgctgatcac aatcatgggc acagtgaaac ccaacgcaaa caggattgtt 481
ctagatttca ggagagggaa tgatgttgcc ttccacttta acccccgctt caatgagaac
541 aacaggagag tcattgtgtg taacacgaag caggacaata actggggaaa
ggaagaaaga 601 cagtcagcct tcccctttga gagtggcaaa ccattcaaaa
tacaagtcct ggttgaagct 661 gaccacttca aggttgcggt caacgatgct
cacctactgc agtacaacca tcggatgaag 721 aacctccggg aaatcagcca
actggggatc agtggtgaca taaccctcac cagcgctaac 781 cacgccatga tctaa
Mouse Gal-3 Amino Acid Sequence (isoform 2) SEQ ID NO: 12 1
madsfslnda lagsgnpnpq gypgawgnqp gaggypgaay pgaypgqapp gaypgqappg
61 aypgqappsa ypgptapgay pgptapgayp gstapgafpg qpgapgayps
apggypaagp 121 ygvpagpltv pydlplpggv mprmlitimg tvkpnanriv
ldfrrgndva fhfnprfnen 181 nrrvivcntk qdnnwgkeer qsafpfesgk
pfkiqvlvea dhfkvavnda hllqynhrmk 241 nlreisqlgi sgditltsan hami
Human Gal-9A cDNA Sequence (transcript variant 1) SEQ ID NO: 13 1
atggccttca gcggttccca ggctccctac ctgagtccag ctgtcccctt ttctgggact
61 attcaaggag gtctccagga cggacttcag atcactgtca atgggaccgt
tctcagctcc 121 agtggaacca ggtttgctgt gaactttcag actggcttca
gtggaaatga cattgccttc 181 cacttcaacc ctcggtttga agatggaggg
tacgtggtgt gcaacacgag gcagaacgga 241 agctgggggc ccgaggagag
gaagacacac atgcctttcc agaaggggat gccctttgac 301 ctctgcttcc
tggtgcagag ctcagatttc aaggtgatgg tgaacgggat cctcttcgtg 361
cagtacttcc accgcgtgcc cttccaccgt gtggacacca tctccgtcaa tggctctgtg
421 cagctgtcct acatcagctt ccagaacccc cgcacagtcc ctgttcagcc
tgccttctcc 481 acggtgccgt tctcccagcc tgtctgtttc ccacccaggc
ccagggggcg cagacaaaaa 541 cctcccggcg tgtggcctgc caacccggct
cccattaccc agacagtcat ccacacagtg 601 cagagcgccc ctggacagat
gttctctact cccgccatcc cacctatgat gtacccccac 661 cccgcctatc
cgatgccttt catcaccacc attctgggag ggctgtaccc atccaagtcc 721
atcctcctgt caggcactgt cctgcccagt gctcagaggt tccacatcaa cctgtgctct
781 gggaaccaca tcgccttcca cctgaacccc cgttttgatg agaatgctgt
ggtccgcaac 841 acccagatcg acaactcctg ggggtctgag gagcgaagtc
tgccccgaaa aatgcccttc 901 gtccgtggcc agagcttctc agtgtggatc
ttgtgtgaag ctcactgcct caaggtggcc 961 gtggatggtc agcacctgtt
tgaatactac catcgcctga ggaacctgcc caccatcaac 1021 agactggaag
tggggggcga catccagctg acccatgtgc agacatag Human Gal-9A Amino Acid
Sequence (isoform 1) SEQ ID NO: 14 1 mafsgsqapy lspavpfsgt
iqgglqdglq itvngtvlss sgtrfavnfq tgfsgndiaf
61 hfnprfedgg yvv ntrqng swgpeerkth mpfqkgmpfd lcflvqssdf
kvmvngilfv 121 qyfhrvpfhr vdtisvngsv qlsyisfqnp rtvpvqpafs
tvpfsqpvcf pprprgrrqk 181 ppgvwpanpa pitqtvihtv qsapgqmfst
paippmmyph paypmpfitt ilgglypsks 241 illsgtvlps aqrfhinlcs
gnhiafhlnp rfdenavvrn tqidnswgse erslprkmpf 301 vrgqsfsvwi
lceahclkva vdgqhlfeyy hrlrnlptin rlevggdiql thvqt Human Gal-9A cDNA
Sequence (transcript variant 2) SEQ ID NO: 15 1 atggccttca
gcggttccca ggctccctac ctgagtccag ctgtcccctt ttctgggact 61
attcaaggag gtctccagga cggacttcag atcactgtca atgggaccgt tctcagctcc
121 agtggaacca ggtttgctgt gaactttcag actggcttca gtggaaatga
cattgccttc 181 cacttcaacc ctcggtttga agatggaggg tacgtggtgt
gcaacacgag gcagaacgga 241 agctgggggc ccgaggagag gaagacacac
atgcctttcc agaaggggat gccctttgac 301 ctctgcttcc tggtgcagag
ctcagatttc aaggtgatgg tgaacgggat cctcttcgtg 361 cagtacttcc
accgcgtgcc cttccaccgt gtggacacca tctccgtcaa tggctctgtg 421
cagctgtcct acatcagctt ccagcctccc ggcgtgtggc ctgccaaccc ggctcccatt
481 acccagacag tcatccacac agtgcagagc gcccctggac agatgttctc
tactcccgcc 541 atcccaccta tgatgtaccc ccaccccgcc tatccgatgc
ctttcatcac caccattctg 601 ggagggctgt acccatccaa gtccatcctc
ctgtcaggca ctgtcctgcc cagtgctcag 661 aggttccaca tcaacctgtg
ctctgggaac cacatcgcct tccacctgaa cccccgtttt 721 gatgagaatg
ctgtggtccg caacacccag atcgacaact cctgggggtc tgaggagcga 781
agtctgcccc gaaaaatgcc cttcgtccgt ggccagagct tctcagtgtg gatcttgtgt
841 gaagctcact gcctcaaggt ggccgtggat ggtcagcacc tgtttgaata
ctaccatcgc 901 ctgaggaacc tgcccaccat caacagactg gaagtggggg
gcgacatcca gctgacccat 961 gtgcagacat ag Human Gal-9A Amino Acid
Sequence (isoform 2) SEQ ID NO: 16 1 mafsgsqapy lspavpfsgt
iqgglqdglq itvngtvlss sgtrfavnfq tgfsgndiaf 61 hfnprfedgg
yvvcntrqng swgpeerkth mpfqkgmpfd lcflvqssdf kvmvngilfv 121
qyfhrvpfhr vdtisvngsv qlsyisfqpp gvwpanpapi tqtvihtvqs apgqmfstpa
181 ippmmyphpa ypmpfittil gglypsksil lsgtvlpsaq rfhinlcsgn
hiafhlnprf 241 denavvrntq idnswgseer slprkmpfvr gqsfsvwilc
eahclkvavd gqhlfeyyhr 301 lrnlptinrl evggdiqlth vqt Human Gal-9B
cDNA Sequence SEQ ID NO: 17 1 atggccttca gcggttccca ggctccctat
ctgagcccag ccgtcccctt ttctgggact 61 atccaagggg gtctccagga
cggatttcag atcactgtca atggggccgt tctcagctcc 121 agtggaacca
ggtttgctgt ggactttcag acgggcttca gtggaaacga cattgccttc 181
cacttcaacc ctcggtttga agacggaggg tatgtggtgt gcaacacgag gcagaaagga
241 agatgggggc ccgaggagag gaagatgcac atgcccttcc agaaggggat
gccctttgac 301 ctctgcttcc tggtgcagag ctcagatttc aaggtgatgg
tgaacgggag cctcttcgtg 361 cagtacttcc accgcgtgcc cttccaccgt
gtggacacca tctccgtcaa tggctctgtg 421 cagctgtcct acatcagctt
ccagaatccc cgcacagtcc ccgttcagcc tgccttctcc 481 acggtgccgt
tctcccagcc tgtctgtttc ccacccaggc ccagggggcg cagacaaaaa 541
cctcccagcg tgcggcctgc caacccagct cccattaccc agacagtcat ccacacggtg
601 cagagcgcct ctggacagat gttctctact cccgccatcc cacctatgat
gtacccccac 661 cctgcctatc cgatgccttt catcaccacc attccgggag
ggctgtaccc atccaagtcc 721 atcatcctgt caggcactgt cctgcccagt
gctcagaggt tccacatcaa cctgtgctct 781 gggagccaca tcgccttcca
catgaacccc cgttttgatg agaatgctgt ggtccgtaac 841 acccagatca
acaactcttg ggggtctgag gagcgaagtc tgccccgaaa aatgcccttc 901
gtccgaggcc agagcttctc ggtgtggatc ttgtgtgaag ctcactgcct caaggtggcc
961 gtggatggtc agcacgtgtt tgaatactac catcgcctga ggaacctgcc
caccatcaac 1021 aaactggaag tgggtggcga catccagctg acccacgtgc
agacatag Human Gal-9B Amino Acid Sequence SEQ ID NO: 18 1
mafsgsqapy lspavpfsgt iqgglqdgfq itvngavlss sgtrfavdfq tgfsgndiaf
61 hfnprfedgg yvvcntrqkg rwgpeerkmh mpfqkgmpfd lcflvqssdf
kvmvngslfv 121 qyfhrvpfhr vdtisvngsv qlsyisfqnp rtvpvqpafs
tvpfsqpvcf pprprgrrqk 181 ppsvrpanpa pitgtvihtv qsasgqmfst
paippmmyph paypmpfitt ipgglypsks 241 iilsgtvlps aqrfhinlcs
gshiafhmnp rfdenavvrn tqinnswgse erslprkmpf 301 vrgqsfsvwi
lceahclkva vdgqhvfeyy hrlrnlptin klevggdiql thvqt Human Gal-9C cDNA
Sequence SEQ ID NO: 19 1 atggccttca gcggttgcca ggctccctat
ctgagcccag ccgtcccctt ttctgggact 61 atccaagggg gtctccagga
cggatttcag atcactgtca atggggccgt tctcagctgc 121 agtggaacca
ggtttgctgt ggactttcag acgggcttca gtggaaacga cattgccttc 181
cacttcaacc ctcggtttga agacggaggg tatgtggtgt gcaacacgag gcagaaagga
241 acatgggggc ccgaggagag gaagatgcac atgcccttcc agaaggggat
gccctttgac 301 ctctgcttcc tggtgcagag ctcagatttc aaggtgatgg
tgaacgggag cctcttcgtg 361 cagtacttcc accgcgtgcc cttccaccgt
gtggacacca tctccgtcaa tggctctgtg 421 cagctgtcct acatcagctt
ccagaatccc cgcgcagtcc ccgttcagcc tgccttctcc 481 acggtgccgt
tctcccagcc tgtctgtttc ccacccaggc ccagggggcg cagacaaaaa 541
cctcccagcg tgcggcctgc caacccagct cccattaccc agacagtcat ccacacggtg
601 cagagtgcct ctggacagat gttctctcag actcccgcca tcccacctat
gatgtacccc 661 caccctgcct atccgatgcc tttcatcacc accattccgg
gagggctgta cccatccaag 721 tccatcatcc tgtcaggcac tgtcctgccc
agtgctcaga ggttccacat caacctgtgc 781 tctgggagcc acatcgcctt
ccacatgaac ccccgttttg atgagaatgc tgtggtccgt 841 aacacccaga
tcaacaactc ttgggggtct gaggagcgaa gtctgccccg aaaaatgccc 901
ttcgtccgag gccagagctt ctcggtgtgg atcttgtgtg aagctcactg cctcaaggtg
961 gccgtggatg gtcagcacgt gtttgaatac taccatcgcc tgaggaacct
gcccaccatc 1021 aacaaactgg aagtgggtgg cgacatccag ctgacccacg
tgcagacata g Human Gal-9C Amino Acid Sequence SEQ ID NO: 20 1
mafsgsqapy lspavpfsgt iqgglqdgfq itvngavlss sgtrfavdfq tgfsgndiaf
61 hfnprfedgg yvvcntrqkg rwgpeerkmh mpfqkgmpfd lcflvqssdf
kvmvngslfv 121 qyfhrvpfhr vdtisvngsv qlsyisfqnp ravpvqpafs
tvpfsqpvcf pprprgrrqk 181 ppsvrpanpa pitqtvihtv qsasgqmfsq
tpaippmmyp hpaypmpfit tipgglypsk 241 siilsgtvlp saqrfhinlc
sgshiafhmn prfdenavvr ntqinnswgs eerslprkmp 301 fvrqqsfsvw
ilceahclkv avdgqhvfey yhrlrnlpti nklevggdiq lthvqt Mouse Gal-9 cDNA
Sequence (transcript variant 1) SEQ ID NO: 21 1 atggctctct
tcagtgccca gtctccatac attaacccga tcatcccctt tactggacca 61
atccaaggag ggctgcagga gggacttcag gtgaccctcc aggggactac caagagtttt
121 gcacaaaggt ttgtggtgaa ctttcagaac agcttcaatg gaaatgacat
tgccttccac 181 ttcaaccccc ggtttgagga aggagggtat gtggtttgca
acacgaagca gaacggacag 241 tggggtcctg aggagagaaa gatgcagatg
cccttccaga aggggatgcc ctttgagctt 301 tgcttcctgg tgcagaggtc
agagttcaag gtgatggtga acaagaaatt ctttgtgcag 361 taccaacacc
gcgtacccta ccacctcgtg gacaccatcg ctgtctccgg ctgcttgaag 421
ctgtccttta tcaccttcca gaactctgca gcccctgtcc agcatgtctt ctccacagtg
481 cagttctctc agccagtcca gttcccacgg acccctaagg ggcgcaaaca
gaaaactcag 541 aactttcgtc ctgcccacca ggcacccatg gctcaaacta
ccatccatat ggttcacagc 601 acccctggac agatgttctc tactcctgga
atccctcctg tggtgtaccc caccccagcc 661 tataccatac ctttctacac
ccccattcca aatgggcttt acccgtccaa gtccatcatg 721 atatcaggca
atgtcttgcc agatgctacg aggttccata tcaaccttcg ctgtggaggt 781
gacattgctt tccacctgaa cccccgtttc aatgagaatg ctgttgtccg aaacactcag
841 atcaacaact cctgggggca ggaagagcga agtctgcttg ggaggatgcc
cttcagtcga 901 ggccagagct tctcggtgtg gatcatatgt gaaggtcact
gcttcaaggt agctgtgaat 961 ggtcaacaca tgtgtgaata ttaccaccgc
ctgaagaact tgcaggatat caacactcta 1021 gaagtggcgg gtgatatcca
gctgacccac gtgcagacat ag Mouse Gal-9 Amino Acid Sequence (isoform
1) SEQ ID NO: 22 1 malfsaqspy inpiipftgp iqgglqeglq vtlqgttksf
aqrfvvnfqn sfngndiafh 61 fnprfeeggy vvcntkqngq wgpeerkmqm
pfqkgmpfel cflvqrsefk vmvnkkffvq 121 yqhrvpyhlv dtlavsgclk
lsfitfqnsa apvqhvfstv qfsqpvqfpr tpkgrkqktq 181 nfrpahqapm
aqttihmvhs tpgqmfstpg ippvvyptpa ytipfytpip nglypsksim 241
isgnvlpdat rfhinlrcgg diafhlnprf nenavvrntq innswgqeer sllgrmpfsr
301 gqsfsvwiic eghcfkvavn gqhmceyyhr lknlqdintl evagdiqlth vqt
Mouse Gal-9 cDNA Sequence (transcript variant 2) SEQ ID NO: 23 1
atggctctct tcagtgccca gtctccatac attaacccga tcatcccctt tactggacca
61 atccaaggag ggctgcagga gggacttcag gtgaccctcc aggggactac
caagagtttt 121 gcacaaaggt ttgtggtgaa ctttcagaac agcttcaatg
gaaatgacat tgccttccac 181 ttcaaccccc ggtttgagga aggagggtat
gtggtttgca acacgaagca gaacggacag 241 tggggtcctg aggagagaaa
gatgcagatg cccttccaga aggggatgcc ctttgagctt 301 tgcttcctgg
tgcagaggtc agagttcaag gtgatggtga acaagaaatt ctttgtgcag 361
taccaacacc gcgtacccta ccacctcgtg gacaccatcg ctgtctccgg ctgcttgaag
421 ctgtccttta tcaccttcca gactcagaac tttcgtcctg cccaccaggc
acccatggct 481 caaactacca tccatatggt tcacagcacc cctggacaga
tgttctctac tcctggaatc 541 cctcctgtgg tgtaccccac cccagcctat
accatacctt tctacacccc cattccaaat 601 gggctttacc cgtccaagtc
catcatgata tcaggcaatg tcttgccaga tgctacgagg 661 ttccatatca
accttcgctg tggaggtgac attgctttcc acctgaaccc ccgtttcaat 721
gagaatgctg ttgtccgaaa cactcagatc aacaactcct gggggcagga agagcgaagt
781 ctgcttggga ggatgccctt cagtcgaggc cagagcttct cggtgtggat
catatgtgaa 841 ggtcactgct tcaaggtagc tgtgaatggt caacacatgt
gtgaatatta ccaccgcctg 901 aagaacttgc aggatatcaa cactctagaa
gtggcgggtg atatccagct gacccacgtg 961 cagacatag
Mouse Gal-9 Amino Acid Sequence (isoform 2) SEQ ID NO: 24 1
malfsaqspy inpiipftgp iqgglqeglq vtlqgttksf aqrfvvnfqn sfngndiafh
61 fnprfeeggy vvcntkqngq wgpeerkmqm pfqkgmpfel cflvqrsefk
vmvnkkffvq 121 yqhrvpyhlv dtiavsgclk lsfitfqtqn frpahqapma
qttihmvhst pgqmfstpgi 181 ppvvyptpay tipfytpipn glypsksimi
sgnvlpdatr fhinlrcggd iafhlnprfn 241 enavvrntqi nnswgqeers
llgrmpfsrg qsfsvwiice ghcfkvavng qhmceyyhrl 301 knlqdintle
vagdiqlthv qt * Included in Table 1 are RNA nucleic acid molecules
(e.g., thymines replaced with uredines), nucleic acid molecules
encoding orthologs of the encoded proteins, as well as DNA or RNA
nucleic acid sequences comprising a nucleic acid sequence having at
least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or more identity
across their full length with the nucleic acid sequence of any SEQ
ID NO listed in Table 1, or a portion thereof. Such nucleic acid
molecules can have a function of the full-length nucleic acid as
described further herein. * Included in Table 1 are orthologs of
the proteins, as well as polypeptide molecules comprising an amino
acid sequence having atleast 80%, 81%, 82%, 83%, 84%, 85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,
99.5%, or more identity across their full length with an amino acid
sequence of any SEQ ID NO listed in Table 1, or a portion thereof.
Such polypeptides can have a function of the full-length
polypeptide as described further herein. * Included in Table 1 is
Gal-1, Gal-3, and Gal-9, including any Gal-1, Gal-3, and/or Gal-9
cDNA or polypeptide from any mammal, such as a human or a mouse.
indicates data missing or illegible when filed
II. Subjects
[0113] in one embodiment, the subject for whom predicted likelihood
of efficacy of an anti-immune checkpoint and anti-angiogenesis
combination therapy is determined, is a manual (e.g., mouse, rat,
primate, non-human mammal, domestic animal, such as a dog, cat,
cow, horse, and the like), and is preferably a human.
[0114] In another embodiment of the methods of the present
invention, the subject has not undergone treatment, such as
chemotherapy, radiation therapy, targeted therapy, anti-immune
checkpoint, and/or anti-angiogenesis therapy. In still another
embodiment, the subject has undergone treatment, such as
chemotherapy, radiation therapy, targeted therapy, anti-immune
checkpoint, and/or anti-angiogenesis therapy.
[0115] 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.
[0116] The methods of the present invention can be used to
determine the responsiveness to anti-immune checkpoint and
anti-angiogenesis combination therapies of many different cancers
in subjects such as those described above. In one embodiment, the
cancers are solid tumors, such as lung cancer, melanoma, and/or
renal cell carcinoma. In another embodiment, the cancer is an
epithelial cancer such as, but not limited to, brain cancer (e.g.,
glioblastomas) 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 still 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.
III. Sample Collection, Preparation and Separation
[0117] In some embodiments, biomarker amount and/or activity
measurement(s) in a sample from a subject is compared to a
predetermined control (standard) sample. The sample from the
subject is typically from a diseased tissue such as cancer cells or
tissues. The control sample can be from the same subject or from a
different subject. The control sample is typically a normal,
non-diseased sample. However, in some embodiments, such as for
staging of disease or for evaluating the efficacy of treatment, the
control sample can be from a diseased tissue. The control sample
can be a combination of samples from several different subjects. In
some embodiments, the biomarker amount and/or activity
measurement(s) from a subject is compared to a pre-determined
level. This pre-determined level is typically obtained from normal
samples. As described herein, a "pre-determined" biomarker amount
and/or activity measurement(s) may be a biomarker amount and/or
activity measurement(s) used to, by way of example only, evaluate a
subject that may be selected for treatment, evaluate a response to
an anti-immune checkpoint and anti-angiogenesis combination
therapy, and/or evaluate a response to a combination anti-immune
checkpoint and anti-angiogenesis combination therapy. A
pre-determined biomarker amount and/or activity measurement(s) may
be determined in populations of patients with or without cancer.
The pre-determined biomarker amount and/or activity measurement(s)
can be a single number, equally applicable to every patient, or the
pre-determined biomarker amount and/or activity measurement(s) can
vary according to specific subpopulations of patients. Age, weight,
height, and other factors of a subject may affect the
pre-determined biomarker amount and/or activity measurement(s) of
the individual. Furthermore, the pre-determined biomarker amount
and/or activity can be determined for each subject individually. In
one embodiment, the amounts determined and/or compared in a method
described herein are based on absolute measurements.
[0118] In another embodiment, the amounts determined and/or
compared in a method described herein are based on relative
measurements, such as ratios (e.g., biomarker copy numbers, level,
and/or activity before a treatment vs. after a treatment, such
biomarker measurements relative to a spiked or man-made control,
such biomarker measurements relative to the expression of a
housekeeping gene, and the like). For example, the relative
analysis can be based on the ratio of pre-treatment biomarker
measurement as compared to post-treatment biomarker measurement.
Pre-treatment biomarker measurement can be made at any time prior
to initiation of anti-cancer therapy. Post-treatment biomarker
measurement can be made at any time after initiation of anti-cancer
therapy. In some embodiments, post-treatment biomarker measurements
are made 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20 weeks or more after initiation of anti-cancer therapy,
and even longer toward indefinitely for continued monitoring.
Treatment can comprise anti-cancer therapy, such as a therapeutic
regimen comprising an anti-immune checkpoint inhibitor and
anti-angiogenesis inhibitor (e.g., ipilimumab and bevacizumab)
alone or in combination with other anti-cancer agents.
[0119] The pre-determined biomarker amount and/or activity
measurement(s) can be any suitable standard. For example, the
pre-determined biomarker amount and/or activity measurement(s) can
be obtained from the same or a different human for whom a patient
selection is being assessed. In one embodiment, the pre-determined
biomarker amount and/or activity measurement(s) can be obtained
from a previous assessment of the same patient. In such a manner,
the progress of the selection of the patient can be monitored over
time. In addition, the control can be obtained from an assessment
of another human or multiple humans, e.g., selected groups of
humans, if the subject is a human. In such a manner, the extent of
the selection of the human for whom selection is being assessed can
be compared to suitable other humans, e.g., other humans who are in
a similar situation to the human of interest, such as those
suffering from similar or the same condition(s) and/or of the same
ethnic group.
[0120] In some embodiments of the present invention the change of
biomarker amount and/or activity measurement(s) from the
pre-determined level is about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,
0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.45, 1.5, 1.55, 1.6, 1.65, 1.7,
1.75, 1.8, 1.85, 1.9, 1.95, 2.0, 2.05, 2.1, 2.15, 2.2, 2.25, 2.3,
2.35, 2.4, 2.45, 2.5, 2.55, 2.6, 2.65, 2.7, 2.75, 2.8, 2.85, 2.9,
2.95, 3.0, 3.5, 4.0, 4.5, or 5.0 fold or greater, or any range in
between, inclusive. In embodiment, the pre-determined level is the
pre-serum or pre-plasma amount or activity of the biomarker and the
fold change is determined relative to a post-scrum or post-plasma
amount or activity of the biomarker. Such cutoff values apply
equally when the measurement is based on relative changes, such as
based on the ratio of pre-treatment biomarker measurement as
compared to post-treatment biomarker measurement.
[0121] Biological samples can be collected from a variety of
sources from a patient including a body fluid sample, cell sample,
or a tissue sample comprising nucleic acids and/or proteins. "Body
fluids" refer to fluids that are excreted or secreted from the body
as well as fluids that are normally not (e.g., amniotic fluid,
aqueous humor, bile, blood and blood plasma, cerebrospinal fluid,
cerumen and earwax, cowper's fluid or pre-ejaculatory fluid, chyle,
chyme, stool, female ejaculate, interstitial fluid, intracellular
fluid, lymph, menses, breast milk, mucus, pleural fluid, pus,
saliva, sebum, semen, scrum, sweat, synovial fluid, tears, urine,
vaginal lubrication, vitreous humor, vomit). In a preferred
embodiment, the subject and/or control sample is selected from the
group consisting of cells, cell lines, histological slides,
paraffin embedded tissues, biopsies, whole blood, nipple aspirate,
serum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine,
stool, and bone marrow. In one embodiment, the sample is serum,
plasma, or urine. In another embodiment, the sample is serum.
[0122] The samples can be collected from individuals repeatedly
over a longitudinal period of time (e.g., once or more on the order
of days, weeks, months, annually, biannually, etc.). Obtaining
numerous samples from an individual over a period of time can be
used to verify results from earlier detections and/or to identify
an alteration in biological pattern as a result of, for example,
disease progression, drug treatment, etc. For example, subject
samples can be taken and monitored every month, every two months,
or combinations of one, two, or three month intervals according to
the present invention. In addition, the biomarker amount and/or
activity measurements of the subject obtained over time can be
conveniently compared with each other, as well as with those of
normal controls during the monitoring period, thereby providing the
subject's own values, as an internal, or personal, control for
long-term monitoring.
[0123] Sample preparation and separation can involve any of the
procedures, depending on the type of sample collected and/or
analysis of biomarker measurement(s). Such procedures include, by
way of example only, concentration, dilution, adjustment of pH,
removal of high abundance polypeptides (e.g., albumin, gamma
globulin, and transferrin, etc.), addition of preservatives and
calibrants, addition of protease inhibitors, addition of
denaturants, desalting of samples, concentration of sample
proteins, extraction and purification of lipids.
[0124] The sample preparation can also isolate molecules that are
bound in non-covalent complexes to other protein (e.g., carrier
proteins). This process may isolate those molecules bound to a
specific carrier protein (e.g., albumin), or use a more general
process, such as the release of bound molecules from all carrier
proteins via protein denaturation, for example using an acid,
followed by removal of the carrier proteins.
[0125] Removal of undesired proteins (e.g., high abundance,
uninformative, or undetectable proteins) from a sample can be
achieved using high affinity reagents, high molecular weight
filters, ultracentrifugation and/or electrodialysis. High affinity
reagents include antibodies or other reagents (e.g. aptamers) that
selectively bind to high abundance proteins. Sample preparation
could also include ion exchange chromatography, metal ion affinity
chromatography, gel filtration, hydrophobic chromatography,
chromatofocusing, adsorption chromatography, isoelectric focusing
and related techniques. Molecular weight filters include membranes
that separate molecules on the basis of size and molecular weight.
Such filters may further employ reverse osmosis, nanofiltration,
ultrafiltration and microfiltration.
[0126] Ultracentrifugation is a method for removing undesired
polypeptides from a sample. Ultracentrifugation is the
centrifugation of a sample at about 15,000-60,000 rpm while
monitoring with an optical system the sedimentation (or lack
thereof) of particles. Electrodialysis is a procedure which uses an
electromembrane or semipermable membrane in a process in which ions
are transported through semi-permeable membranes from one solution
to another under the influence of a potential gradient. Since the
membranes used in electrodialysis may have the ability to
selectively transport ions having positive or negative charge,
reject ions of the opposite charge, or to allow species to migrate
through a semipermable membrane based on size and charge, it
renders electrodialysis useful for concentration, removal, or
separation of electrolytes.
[0127] Separation and purification in the present invention may
include any procedure known in the art, such as capillary
electrophoresis (e.g., in capillary or on-chip) or chromatography
(e.g., in capillary, column or on a chip). Electrophoresis is a
method which can be used to separate ionic molecules under the
influence of an electric field. Electrophoresis can be conducted in
a gel, capillary, or in a microchannel on a chip. Examples of gels
used for electrophoresis include starch, acrylamide, polyethylene
oxides, agarose, or combinations thereof. A gel can be modified by
its cross-linking, addition of detergents, or denaturants,
immobilization of enzymes or antibodies (affinity electrophoresis)
or substrates (zymography) and incorporation of a pH gradient.
Examples of capillaries used for electrophoresis include
capillaries that interface with an electrospray.
[0128] Capillary electrophoresis (CE) is preferred for separating
complex hydrophilic molecules and highly charged solutes. CE
technology can also be implemented on microfluidic chips. Depending
on the types of capillary and buffers used, CE can be further
segmented into separation techniques such as capillary zone
electrophoresis (CZE), capillary isoelectric focusing (CIEF),
capillary isotachophoresis (cITP) and capillary
electrochromatography (CEC). An embodiment to couple CE techniques
to electrospray ionization involves the use of volatile solutions,
for example, aqueous mixtures containing a volatile acid and/or
base and an organic such as an alcohol or acetonitrile.
[0129] Capillary isotachophoresis (cITP) is a technique in which
the analytes move through the capillary at a constant speed but are
nevertheless separated by their respective mobilities. Capillary
zone electrophoresis (CZE), also known as free-solution CE (FSCE),
is based on differences in the electrophoretic mobility of the
species, determined by the charge on the molecule, and the
frictional resistance the molecule encounters during migration
which is often directly proportional to the size of the molecule.
Capillary isoelectric focusing (CIEF) allows weakly-ionizable
amphoteric molecules, to be separated by electrophoresis in a pH
gradient. CEC is a hybrid technique between traditional high
performance liquid chromatography (HPLC) and CE.
[0130] Separation and purification techniques used in the present
invention include any chromatography procedures known in the art.
Chromatography can be based on the differential adsorption and
elution of certain analytes or partitioning of analytes between
mobile and stationary phases. Different examples of chromatography
include, but not limited to, liquid chromatography (LC), gas
chromatography (GC), high performance liquid chromatography (HPLC),
etc.
IV. Biomarker Nucleic Acids and Polypeptides
[0131] One aspect of the present invention pertains to the use of
isolated nucleic acid molecules that correspond to biomarker
nucleic acids that encode a biomarker polypeptide or a portion of
such a polypeptide. For example, sequences that encode anti-Gal-1,
anti-Gal-3, and/or anti-Gal-9 immunoglobulins can be detected as
nucleic acids. As used herein, the term "nucleic acid molecule" is
intended to include DNA molecules (e.g., cDNA or genomic DNA) and
RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated
using nucleotide analogs. The nucleic acid molecule can be
single-stranded or double-stranded, but preferably is
double-stranded DNA.
[0132] An "isolated" nucleic acid molecule is one which is
separated from other nucleic acid molecules which are present in
the natural source of the nucleic acid molecule. Preferably, an
"isolated" nucleic acid molecule is free of sequences (preferably
protein-encoding sequences) which naturally flank the nucleic acid
(i.e., sequences located at the 5' and 3' ends of the nucleic acid)
in the genomic DNA of the organism from which the nucleic acid is
derived. For example, in various embodiments, the isolated nucleic
acid molecule can contain less than about 5 kB, 4 k, 3 kB, 2 kB, 1
kB, 0.5 kB or 0.1 kB of nucleotide sequences which naturally flank
the nucleic acid molecule in genomic DNA of the cell from which the
nucleic acid is derived. Moreover, an "isolated" nucleic acid
molecule, such as a cDNA molecule, can be substantially free of
other cellular material or culture medium when produced by
recombinant techniques, or substantially free of chemical
precursors or other chemicals when chemically synthesized.
[0133] A biomarker nucleic acid molecule of the present invention
can be isolated using standard molecular biology techniques and the
sequence information in the database records described herein.
Using all or a portion of such nucleic acid sequences, nucleic acid
molecules of the present invention can be isolated using standard
hybridization and cloning techniques (e.g., as described in
Sambrook et al., ed., Molecular Cloning: A Laboratory Manual, 2nd
ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,
1989).
[0134] A nucleic acid molecule of the present invention can be
amplified using cDNA, mRNA, or genomic DNA as a template and
appropriate oligonuclotides primers according to standard PCR
amplification techniques. The nucleic acid molecules so amplified
can be cloned into an appropriate vector and characterized by DNA
sequence analysis. Furthermore, oligonucleotides corresponding to
all or a portion or a nucleic acid molecule of the present
invention can be prepared by standard synthetic techniques, e.g.,
using an automated DNA synthesizer.
[0135] Moreover, a nucleic acid molecule of the present invention
can comprise only a portion of a nucleic acid sequence, wherein the
full length nucleic acid sequence comprises a marker of the present
invention or which encodes a polypeptide corresponding to a marker
of the present invention. Such nucleic acid molecules can be used,
for example, as a probe or primer. The probe/primer typically is
used as one or more substantially purified oligonucleotides. The
oligonucleotide typically comprises a region of nucleotide sequence
that hybridizes under stringent conditions to at least about 7,
preferably about 15, more preferably about 25, 50, 75, 100, 125,
150, 175, 200, 250, 300, 350, or 400 or more consecutive
nucleotides of a biomarker nucleic acid sequence. Probes based on
the sequence of a biomarker nucleic acid molecule can be used to
detect transcripts or genomic sequences corresponding to one or
more markers of the present invention. The probe comprises a label
group attached thereto, e.g., a radioisotope, a fluorescent
compound, an enzyme, or an enzyme co-factor.
[0136] A biomarker nucleic acid molecules that differ, due to
degeneracy of the genetic code, from the nucleotide sequence of
nucleic acid molecules encoding a protein which corresponds to the
biomarker, and thus encode the same protein, are also
contemplated.
[0137] In addition, it will be appreciated by those skilled in the
art that DNA sequence polymorphisms that lead to changes in the
amino acid sequence can exist within a population (e.g., the human
population). Such genetic polymorphisms can exist among individuals
within a population due to natural allelic variation. An allele is
one of a group of genes which occur alternatively at a given
genetic locus. In addition, it will be appreciated that DNA
polymorphisms that affect RNA expression levels can also exist that
may affect the overall expression level of that gene (e.g., by
affecting regulation or degradation).
[0138] The term "allele," which is used interchangeably herein with
"allelic variant," refers to alternative forms of a gene or
portions thereof. Alleles occupy the same locus or position on
homologous chromosomes. When a subject has two identical alleles of
a gene, the subject is said to be homozygous for the gene or
allele. When a subject has two different alleles of a gene, the
subject is said to be heterozygous for the gene or allele. For
example, biomarker alleles can differ from each other in a single
nucleotide, or several nucleotides, and can include substitutions,
deletions, and insertions or nucleotides. An allele of a gene can
also be a form of a gene containing one or more mutations.
[0139] The term "allelic variant of a polymorphic region of gene"
or "allelic variant", used interchangeably herein, refers to an
alternative form of a gene having one of several possible
nucleotide sequences found in that region of the gene in the
population. As used herein, allelic variant is meant to encompass
functional allelic variants, non-functional allelic variants, SNPs,
mutations and polymorphisms.
[0140] The term "single nucleotide polymorphism" (SNP) refers to a
polymorphic site occupied by a single nucleotide, which is the site
of variation between allelic sequences. The site is usually
preceded by and followed by highly conserved sequences of the
allele (e.g., sequences that vary in less than 1/10 or 1/1000
members of a population). A SNP usually arises due to substitution
of one nucleotide for another at the polymorphic site. SNPs can
also arise from a deletion of a nucleotide or an insertion of a
nucleotide relative to a reference allele. Typically the
polymorphic site is occupied by a base other than the reference
base. For example, where the reference allele contains the base "T"
(thymidine) at the polymorphic site, the altered allele can contain
a "C" (cytidine), "G" (guanine), or "A" (adenine) at the
polymorphic site. SNP's may occur in protein-coding nucleic acid
sequences, in which case they may give rise to a defective or
otherwise variant protein, or genetic disease. Such a SNP may alter
the coding sequence of the gene and therefore specify another amino
acid (a "missense" SNP) or a SNP may introduce a stop codon (a
"nonsense" SNP). When a SNP does not alter the amino acid sequence
of a protein, the SNP is called "silent." SNP's may also occur in
noncoding regions of the nucleotide sequence. This may result in
defective protein expression. e.g., as a result of alternative
spicing, or it may have no effect on the function of the
protein.
[0141] As used herein, the terms "gene" and "recombinant gene"
refer to nucleic acid molecules comprising an open reading frame
encoding a polypeptide corresponding to a marker of the present
invention. Such natural allelic variations can typically result in
1-5% variance in the nucleotide sequence of a given gene.
Alternative alleles can be identified by sequencing the gene of
interest in a number of different individuals. This can be readily
carried out by using hybridization probes to identify the same
genetic locus in a variety of individuals. Any and all such
nucleotide variations and resulting amino acid polymorphisms or
variations that are the result of natural allelic variation and
that do not alter the functional activity are intended to be within
the scope of the present invention.
[0142] In another embodiment, a biomarker nucleic acid molecule is
at least 7, 15, 20, 25, 30, 40, 60, 80, 100, 150, 200, 250, 300,
350, 400, 450, 550, 650, 700, 800, 900, 1000, 1100, 1200, 1300,
1400, 1500, 1600, 1700, 1800, 1900, 2000, 2200, 2400, 2600, 2800,
3000, 3500, 4000, 4500, or more nucleotides in length and
hybridizes under stringent conditions to a nucleic acid molecule
corresponding to a marker of the present invention or to a nucleic
acid molecule encoding a protein corresponding to a marker of the
present invention. As used herein, the term "hybridizes under
stringent conditions" is intended to describe conditions for
hybridization and washing under which nucleotide sequences at least
60% (65%, 70%, 75%, 80%, preferably 85%) identical to each other
typically remain hybridized to each other. Such stringent
conditions are known to those skilled in the art and can be found
in sections 6.3.1-6.3.6 of Current Protocols in Molecular Biology,
John Wiley & Sons. N.Y. (1989). A preferred, non-limiting
example of stringent hybridization conditions are hybridization in
6.times. sodium chloride/sodium citrate (SSC) at about 45.degree.
C. followed by one or more washes in 0.2.times.SSC, 0.1% SDS at
50-65.degree. C.
[0143] In addition to naturally-occurring allelic variants of a
nucleic acid molecule of the present invention that can exist in
the population, the skilled artisan will further appreciate that
sequence changes can be introduced by mutation thereby leading to
changes in the amino acid sequence of the encoded protein, without
altering the biological activity of the protein encoded thereby.
For example, one can make nucleotide substitutions leading to amino
acid substitutions at "non-essential" amino acid residues. A
"non-essential" amino acid residue is a residue that can be altered
from the wild-type sequence without altering the biological
activity, whereas an "essential" amino acid residue is required for
biological activity. For example, amino acid residues that are not
conserved or only semi-conserved among homologs of various species
may be non-essential for activity and thus would be likely targets
for alteration. Alternatively, amino acid residues that are
conserved among the homologs of various species (e.g., murine and
human) may be essential for activity and thus would not be likely
targets for alteration.
[0144] Accordingly, another aspect of the present invention
pertains to nucleic acid molecules encoding a biomarker polypeptide
of the present invention that contain changes in amino acid
residues that are not essential for activity. Such polypeptides
differ in amino acid sequence from the naturally-occurring proteins
which correspond to the markers of the present invention, yet
retain biological activity. In one embodiment, a biomarker protein
has an amino acid sequence that is at least about 40% identical,
50%, 60%, 70%, 75%, 80%, 83%, 85%, 87.5%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99% or identical to the amino acid sequence of
a biomarker protein described herein.
[0145] An isolated nucleic acid molecule encoding a variant protein
can be created by introducing one or more nucleotide substitutions,
additions or deletions into the nucleotide sequence of nucleic
acids of the present invention, such that one or more amino acid
residue substitutions, additions, or deletions are introduced into
the encoded protein. Mutations can be introduced by standard
techniques, such as site-directed mutagenesis and PCR-mediated
mutagenesis. Preferably, conservative amino acid substitutions are
made at one or more predicted non-essential amino acid residues. A
"conservative amino acid substitution" is one in which the amino
acid residue is replaced with an amino acid residue having a
similar side chain. Families of amino acid residues having similar
side chains have been defined in the art. These families include
amino acids with basic side chains (e.g., lysine, arginine,
histidine), acidic side chains (e.g., aspartic acid, glutamic
acid), uncharged polar side chains (e.g., glycine, asparagine,
glutamine, serine, threonine, tyrosine, cysteine), non-polar side
chains (e.g., alanine, valine, leucine, isoleucine, proline,
phenylalanine, methionine, tryptophan), beta-branched side chains
(e.g., threonine, valine, isoleucine) and aromatic side chains
(e.g., tyrosine, phenylalanine, tryptophan, histidine).
Alternatively, mutations can be introduced randomly along all or
part of the coding sequence, such as by saturation mutagenesis, and
the resultant mutants can be screened for biological activity to
identify mutants that retain activity. Following mutagenesis, the
encoded protein can be expressed recombinantly and the activity of
the protein can be determined.
[0146] In some embodiments, the present invention further
contemplates the use of anti-biomarker antisense nucleic acid
molecules, i.e., molecules which are complementary to a sense
nucleic acid of the present invention, e.g., complementary to the
coding strand of a double-stranded cDNA molecule corresponding to a
marker of the present invention or complementary to an mRNA
sequence corresponding to a marker of the present invention.
Accordingly, an antisense nucleic acid molecule of the present
invention can hydrogen bond to (i.e. anneal with) a sense nucleic
acid of the present invention. The antisense nucleic acid can be
complementary to an entire coding strand, or to only a portion
thereof, e.g., all or part of the protein coding region (or open
reading frame). An antisense nucleic acid molecule can also be
antisense to all or part of a non-coding region of the coding
strand of a nucleotide sequence encoding a polypeptide of the
present invention. The non-coding regions ("5' and 3' untranslated
regions") are the 5' and 3' sequences which flank the coding region
and are not translated into amino acids.
[0147] An antisense oligonucleotide can be, for example, about 5,
10, 15, 20, 25, 30, 35, 40, 45, or 50 or more nucleotides in
length. An antisense nucleic acid can be constructed using chemical
synthesis and enzymatic ligation reactions using procedures known
in the art. For example, an antisense nucleic acid (e.g., an
antisense oligonucleotide) can be chemically synthesized using
naturally occurring nucleotides or variously modified nucleotides
designed to increase the biological stability of the molecules or
to increase the physical stability of the duplex formed between the
antisense and sense nucleic acids, e.g., phosphorothioate
derivatives and acridine substituted nucleotides can be used.
Examples of modified nucleotides which can be used to generate the
antisense nucleic acid include 5-fluorouracil, 5-bromouracil,
5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine,
4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N6-adenine, 7-methylguanine,
5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil,
5-methoxyuracil, 2-methylthio-N6-isopentenyladenine,
uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine,
2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,
5-methyluracil, uracil-5-oxyacetic acid methylester,
uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil,
3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and
2,6-diaminopurine. Alternatively, the antisense nucleic acid can be
produced biologically using an expression vector into which a
nucleic acid has been sub-cloned in an antisense orientation (i.e.,
RNA transcribed from the inserted nucleic acid will be of an
antisense orientation to a target nucleic acid of interest,
described further in the following subsection).
[0148] The antisense nucleic acid molecules of the present
invention are typically administered to a subject or generated in
situ such that they hybridize with or bind to cellular mRNA and/or
genomic DNA encoding a polypeptide corresponding to a selected
marker of the present invention to thereby inhibit expression of
the marker, e.g., by inhibiting transcription and/or translation.
The hybridization can be by conventional nucleotide complementarity
to form a stable duplex, or, for example, in the case of an
antisense nucleic acid molecule which binds to DNA duplexes,
through specific interactions in the major groove of the double
helix. Examples of a route of administration of antisense nucleic
acid molecules of the present invention includes direct injection
at a tissue site or infusion of the antisense nucleic acid into a
blood- or bone marrow-associated body fluid. Alternatively,
antisense nucleic acid molecules can be modified to target selected
cells and then administered systemically. For example, for systemic
administration, antisense molecules can be modified such that they
specifically bind to receptors or antigens expressed on a selected
cell surface, e.g., by linking the antisense nucleic acid molecules
to peptides or antibodies which bind to cell surface receptors or
antigens. The antisense nucleic acid molecules can also be
delivered to cells using the vectors described herein. To achieve
sufficient intracellular concentrations of the antisense molecules,
vector constructs in which the antisense nucleic acid molecule is
placed under the control of a strong pol II or pol III promoter are
preferred.
[0149] An antisense nucleic acid molecule of the present invention
can be an .alpha.-anomeric nucleic acid molecule. An
.alpha.-anomeric nucleic acid molecule forms specific
double-stranded hybrids with complementary RNA in which, contrary
to the usual .alpha.-units, the strands run parallel to each other
(Gaultier el al., 1987, Nucleic Acids Res. 15:6625-6641). The
antisense nucleic acid molecule can also comprise a
2'-o-methylribonucleotide (Inoue et al., 1987, Nucleic Acids Res.
15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al., 1987,
FEBS Lett. 215:327-330).
[0150] The present invention also encompasses ribozymes. Ribozymes
are catalytic RNA molecules with ribonuclease activity which are
capable of cleaving a single-stranded nucleic acid, such as an
mRNA, to which they have a complementary region. Thus, ribozymes
(e.g., hammerhead ribozymes as described in Haselhoff and Gerlach,
1988, Nature 334:585-591) can be used to catalytically cleave mRNA
transcripts to thereby inhibit translation of the protein encoded
by the mRNA. A ribozyme having specificity for a nucleic acid
molecule encoding a polypeptide corresponding to a marker of the
present invention can be designed based upon the nucleotide
sequence of a cDNA corresponding to the marker. For example, a
derivative of a Tetrahymena L-19 IVS RNA can be constructed in
which the nucleotide sequence of the active site is complementary
to the nucleotide sequence to be cleaved (see Cech et al. U.S. Pat.
No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742).
Alternatively, an mRNA encoding a polypeptide of the present
invention can be used to select a catalytic RNA having a specific
ribonuclease activity from a pool of RNA molecules (see, e.g.,
Bartel and Szostak, 1993, Science 261:1411-1418).
[0151] The present invention also encompasses nucleic acid
molecules which form triple helical structures. For example,
expression of a biomarker protein can be inhibited by targeting
nucleotide sequences complementary to the regulatory region of the
gene encoding the polypeptide (e.g., the promoter and/or enhancer)
to form triple helical structures that prevent transcription of the
gene in target cells. See generally Helene (1991) Anticancer Drug
Des. 6(6):569-84; Helene (1992) Ann. N.Y. Acad. Sci. 660:27-36; and
Maher (1992) Bioassays 14(12):807-15.
[0152] In various embodiments, the nucleic acid molecules of the
present invention can be modified at the base moiety, sugar moiety
or phosphate backbone to improve, e.g., the stability,
hybridization, or solubility of the molecule. For example, the
deoxyribose phosphate backbone of the nucleic acid molecules can be
modified to generate peptide nucleic acid molecules (see Hyrup et
al., 1996, Bioorganic & Medicinal Chemistry 4(1): 5-23). As
used herein, the terms "peptide nucleic acids" or "PNAs" refer to
nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose
phosphate backbone is replaced by a pseudopeptide backbone and only
the four natural nucleobases are retained. The neutral backbone of
PNAs has been shown to allow for specific hybridization to DNA and
RNA under conditions of low ionic strength. The synthesis of PNA
oligomers can be performed using standard solid phase peptide
synthesis protocols as described in Hyrup et al. (1996), supra;
Perry-O'Keefe et al. (1996) Proc. Natl. Acad. Sci. USA
93:14670-675.
[0153] PNAs can be used in therapeutic and diagnostic applications.
For example, PNAs can be used as antisense or antigene agents for
sequence-specific modulation of gene expression by, e.g., inducing
transcription or translation arrest or inhibiting replication. PNAs
can also be used, e.g., in the analysis of single base pair
mutations in a gene by, e.g., PNA directed PCR clamping; as
artificial restriction enzymes when used in combination with other
enzymes, e.g., S1 nucleases (Hyrup (1996), supra; or as probes or
primers for DNA sequence and hybridization (Hyrup, 1996, supra;
Perry-O'Keefe et al., 1996, Proc. Natl. Acad. Sci. USA
93:14670-675).
[0154] In another embodiment. PNAs can be modified, e.g., to
enhance their stability or cellular uptake, by attaching lipophilic
or other helper groups to PNA, by the formation of PNA-DNA
chimeras, or by the use of liposomes or other techniques of drug
delivery known in the art. For example, PNA-DNA chimeras can be
generated which can combine the advantageous properties of PNA and
DNA. Such chimeras allow DNA recognition enzymes, e.g., RNASE H and
DNA polymerases, to interact with the DNA portion while the PNA
portion would provide high binding affinity and specificity.
PNA-DNA chimeras can be linked using linkers of appropriate lengths
selected in terms of base stacking, number of bonds between the
nucleobases, and orientation (Hyrup, 1996, supra). The synthesis of
PNA-DNA chimeras can be performed as described in Hyrup (1996),
supra, and Finn et al. (1996) Nucleic Acids R. 24(17):3357-63. For
example, a DNA chain can be synthesized on a solid support using
standard phosphoramidite coupling chemistry and modified nucleoside
analogs. Compounds such as
5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite can be
used as a link between the PNA and the 5' end of DNA (Mag el al.,
1989, Nucleic Acids Res. 17:5973-88). PNA monomers are then coupled
in a step-wise manner to produce a chimeric molecule with a 5' PNA
segment and a 3' DNA segment (Finn et al., 1996, Nucleic Acids Res.
24(17):3357-63). Alternatively, chimeric molecules can be
synthesized with a 5' DNA segment and a 3 PNA segment (Peterser et
al., 1975, Bioorganic Med. Chem. Lett. 5:1119-11124).
[0155] In other embodiments, the oligonucleotide can include other
appended groups such as peptides (e.g., for targeting host cell
receptors in vivo), or agents facilitating transport across the
cell membrane (see, e.g., Letsinger et al. 1989, Proc. Natl. Acad.
Sci. USA 86:6553-6556; Lemaitre at al., 1987, Proc. Natl. Acad.
Sci. USA 84:648-652; PCT Publication No. WO 88/09810) or the
blood-brain barrier (see, e.g., PCT Publication No. WO 89/10134).
In addition, oligonucleotides can be modified with
hybridization-triggered cleavage agents (see, e.g., Krol et al.,
1988, Bio/Techniques 6:958-976) or intercalating agents (see, e.g.,
Zon, 1988, Pharm. Res. 5:539-549). To this end, the oligonucleotide
can be conjugated to another molecule, e.g., a peptide,
hybridization triggered cross-linking agent, transport agent,
hybridization-triggered cleavage agent, etc.
[0156] Another aspect of the present invention pertains to the use
of biomarker proteins and biologically active portions thereof. In
one embodiment, the native polypeptide corresponding to a marker
can be isolated from cells or tissue sources by an appropriate
purification scheme using standard protein purification techniques.
In another embodiment, polypeptides corresponding to a marker of
the present invention are produced by recombinant DNA techniques.
Alternative to recombinant expression, a polypeptide corresponding
to a marker of the present invention can be synthesized chemically
using standard peptide synthesis techniques.
[0157] An "isolated" or "purified" protein or biologically active
portion thereof is substantially free of cellular material or other
contaminating proteins from the cell or tissue source from which
the protein is derived, or substantially free of chemical
precursors or other chemicals when chemically synthesized. The
language "substantially free of cellular material" includes
preparations of protein in which the protein is separated from
cellular components of the cells from which it is isolated or
recombinantly produced. Thus, protein that is substantially free of
cellular material includes preparations of protein having less than
about 30%, 20%, 10%, or 5% (by dry weight) of heterologous protein
(also referred to herein as a "contaminating protein"). When the
protein or biologically active portion thereof is recombinantly
produced, it is also preferably substantially free of culture
medium, i.e., culture medium represents less than about 20%, 10%,
or 5% of the volume of the protein preparation. When the protein is
produced by chemical synthesis, it is preferably substantially free
of chemical precursors or other chemicals, i.e., it is separated
from chemical precursors or other chemicals which are involved in
the synthesis of the protein. Accordingly such preparations of the
protein have less than about 30%, 20%, 10%, 5% (by dry weight) of
chemical precursors or compounds other than the polypeptide of
interest.
[0158] Biologically active portions of a biomarker polypeptide
include polypeptides comprising amino acid sequences sufficiently
identical to or derived from a biomarker protein amino acid
sequence described herein, but which includes fewer amino acids
than the full length protein, and exhibit at least one activity of
the corresponding full-length protein. Typically, biologically
active portions comprise a domain or motif with at least one
activity of the corresponding protein. A biologically active
portion of a protein of the present invention can be a polypeptide
which is, for example, 10, 25, 50, 100 or more amino acids in
length. Moreover, other biologically active portions, in which
other regions of the protein are deleted, can be prepared by
recombinant techniques and evaluated for one or more of the
functional activities of the native form of a polypeptide of the
present invention.
[0159] Preferred polypeptides have an amino acid sequence of a
biomarker protein encoded by a nucleic acid molecule described
herein. Other useful proteins are substantially identical (e.g., at
least about 40%, preferably 50%, 60%, 70%, 75%, 80%, 83%, 85%, 88%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) to one of
these sequences and retain the functional activity of the protein
of the corresponding naturally-occurring protein yet differ in
amino acid sequence due to natural allelic variation or
mutagenesis.
[0160] To determine the percent identity of two amino acid
sequences or of two nucleic acids, the sequences are aligned for
optimal comparison purposes (e.g., gaps can be introduced in the
sequence of a first amino acid or nucleic acid sequence for optimal
alignment with a second amino or nucleic acid sequence). The amino
acid residues or nucleotides at corresponding amino acid positions
or nucleotide positions are then compared. When a position in the
first sequence is occupied by the same amino acid residue or
nucleotide as the corresponding position in the second sequence,
then the molecules are identical at that position. The percent
identity between the two sequences is a function of the number of
identical positions shared by the sequences (i.e., % identity=#of
identical positions/total #of positions (e.g., overlapping
positions).times.100). In one embodiment the two sequences are the
same length.
[0161] The determination of percent identity between two sequences
can be accomplished using a mathematical algorithm. A preferred,
non-limiting example of a mathematical algorithm utilized for the
comparison of two sequences is the algorithm of Karlin and Altschul
(1990) Proc. Natl. Acad. Sci. USA 87:2264-2268, modified as in
Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
Such an algorithm is incorporated into the NBLAST and XBLAST
programs of Altschul, et al. (1990) J. Mol. Biol. 215:403-410.
BLAST nucleotide searches can be performed with the NBLAST program,
score=100, wordlength=12 to obtain nucleotide sequences homologous
to a nucleic acid molecules of the present invention. BLAST protein
searches can be performed with the XBLAST program, score=50,
wordlength 3 to obtain amino acid sequences homologous to a protein
molecules of the present invention. To obtain gapped alignments for
comparison purposes, Gapped BLAST can be utilized as described in
Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402.
Alternatively, PSI-Blast can be used to perform an iterated search
which detects distant relationships between molecules. When
utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default
parameters of the respective programs (e.g., XBLAST and NBLAST) can
be used. See http://www.ncbi.nm.nih.gov. Another preferred,
non-limiting example of a mathematical algorithm utilized for the
comparison of sequences is the algorithm of Myers and Miller,
(1988) Comput Appl Biosci. 4:11-7. Such an algorithm is
incorporated into the ALIGN program (version 2.0) which is part of
the GCG sequence alignment software package. When utilizing the
ALIGN program for comparing amino acid sequences, a PAM120 weight
residue table, a gap length penalty of 12, and a gap penalty of 4
can be used. Yet another useful algorithm for identifying regions
of local sequence similarity and alignment is the FASTA algorithm
as described in Pearson and Lipman (1988) Proc. Natl. Acad. Sci.
USA 85:2444-2448. When using the FASTA algorithm for comparing
nucleotide or amino acid sequences, a PAM120 weight residue table
can, for example, be used with a k-tuple value of 2.
[0162] The percent identity between two sequences can be determined
using techniques similar to those described above, with or without
allowing gaps. In calculating percent identity, only exact matches
are counted.
[0163] The present invention also provides chimeric or fusion
proteins corresponding to a biomarker protein. As used herein, a
"chimeric protein" or "fusion protein" comprises all or part
(preferably a biologically active part) of a polypeptide
corresponding to a marker of the present invention operably linked
to a heterologous polypeptide (i.e., a polypeptide other than the
polypeptide corresponding to the marker). Within the fusion
protein, the term "operably linked" is intended to indicate that
the polypeptide of the present invention and the heterologous
polypeptide are fused in-frame to each other. The heterologous
polypeptide can be fused to the amino-terminus or the
carboxyl-terminus of the polypeptide of the present invention.
[0164] One useful fusion protein is a GST fusion protein in which a
polypeptide corresponding to a marker of the present invention is
fused to the carboxyl terminus of GST sequences. Such fusion
proteins can facilitate the purification of a recombinant
polypeptide of the present invention.
[0165] In another embodiment, the fusion protein contains a
heterologous signal sequence, immunoglobulin fusion protein, toxin,
or other useful protein sequence. Chimeric and fusion proteins of
the present invention can be produced by standard recombinant DNA
techniques. In another embodiment, the fusion gene can be
synthesized by conventional techniques including automated DNA
synthesizers. Alternatively, PCR amplification of gene fragments
can be carried out using anchor primers which give rise to
complementary overhangs between two consecutive gene fragments
which can subsequently be annealed and re-amplified to generate a
chimeric gene sequence (see, e.g., Ausubel et al., supra).
Moreover, many expression vectors are commercially available that
already encode a fusion moiety (e.g., a GST polypeptide). A nucleic
acid encoding a polypeptide of the present invention can be cloned
into such an expression vector such that the fusion moiety is
linked in-frame to the polypeptide of the present invention.
[0166] A signal sequence can be used to facilitate secretion and
isolation of the secreted protein or other proteins of interest.
Signal sequences are typically characterized by a core of
hydrophobic amino acids which are generally cleaved from the mature
protein during secretion in one or more cleavage events. Such
signal peptides contain processing sites that allow cleavage of the
signal sequence from the mature proteins as they pass through the
secretory pathway. Thus, the present invention pertains to the
described polypeptides having a signal sequence, as well as to
polypeptides from which the signal sequence has been
proteolytically cleaved (i.e., the cleavage products). In one
embodiment, a nucleic acid sequence encoding a signal sequence can
be operably linked in an expression vector to a protein of
interest, such as a protein which is ordinarily not secreted or is
otherwise difficult to isolate. The signal sequence directs
secretion of the protein, such as from a eukaryotic host into which
the expression vector is transformed, and the signal sequence is
subsequently or concurrently cleaved. The protein can then be
readily purified from the extracellular medium by art recognized
methods. Alternatively, the signal sequence can be linked to the
protein of interest using a sequence which facilitates
purification, such as with a GST domain.
[0167] The present invention also pertains to variants of the
biomarker polypeptides described herein. Such variants have an
altered amino acid sequence which can function as either agonists
(mimetics) or as antagonists. For example, biomarker polypeptides
or variants thereof can be cloned or amplified in order to
therapeutically increase anti-Gal-1, anti-Gal-3, and/or anti-Gal-9
activity to enhance anti-cancer effects. Variants can be generated
by mutagenesis, e.g., discrete point mutation or truncation. An
agonist can retain substantially the same, or a subset, of the
biological activities of the naturally occurring form of the
protein. An antagonist of a protein can inhibit one or more of the
activities of the naturally occurring form of the protein by, for
example, competitively binding to a downstream or upstream member
of a cellular signaling cascade which includes the protein of
interest. Thus, specific biological effects can be elicited by
treatment with a variant of limited function. Treatment of a
subject with a variant having a subset of the biological activities
of the naturally occurring form of the protein can have fewer side
effects in a subject relative to treatment with the naturally
occurring form of the protein.
[0168] Variants of a biomarker protein which function as either
agonists (mimetics) or as antagonists can be identified by
screening combinatorial libraries of mutants, e.g., truncation
mutants, of the protein of the present invention for agonist or
antagonist activity. In one embodiment, a variegated library of
variants is generated by combinatorial mutagenesis at the nucleic
acid level and is encoded by a variegated gene library. A
variegated library of variants can be produced by, for example,
enzymatically ligating a mixture of synthetic oligonucleotides into
gene sequences such that a degenerate set of potential protein
sequences is expressible as individual polypeptides, or
alternatively, as a set of larger fusion proteins (e.g., for phage
display). There are a variety of methods which can be used to
produce libraries of potential variants of the polypeptides of the
present invention from a degenerate oligonucleotide sequence.
Methods for synthesizing degenerate oligonuclotides are known in
the art (see. e.g., Narang, 1983, Tetrahedron 39:3; Itakura et al.,
1984, Annu. Rev. Biochem. 53:323; Itakura et al., 1984, Science
198:1056; Ike et al., 1983 Nucleic Acid Res. 11:477).
[0169] In addition, libraries of fragments of the coding sequence
of a polypeptide corresponding to a marker of the present invention
can be used to generate a variegated population of polypeptides for
screening and subsequent selection of variants. For example, a
library of coding sequence fragments can be generated by treating a
double stranded PCR fragment of the coding sequence of interest
with a nuclease under conditions wherein nicking occurs only about
once per molecule, denaturing the double stranded DNA, renaturing
the DNA to form double stranded DNA which can include
sense/antisense pairs from different nicked products, removing
single stranded portions from reformed duplexes by treatment with
S1 nuclease, and ligating the resulting fragment library into an
expression vector. By this method, an expression library can be
derived which encodes amino terminal and internal fragments of
various sizes of the protein of interest.
[0170] Several techniques are known in the art for screening gene
products of combinatorial libraries made by point mutations or
truncation, and for screening cDNA libraries for gene products
having a selected property. The most widely used techniques, which
are amenable to high throughput analysis, for screening large gene
libraries typically include cloning the gene library into
replicable expression vectors, transforming appropriate cells with
the resulting library of vectors, and expressing the combinatorial
genes under conditions in which detection of a desired activity
facilitates isolation of the vector encoding the gene whose product
was detected. Recursive ensemble mutagenesis (REM), a technique
which enhances the frequency of functional mutants in the
libraries, can be used in combination with the screening assays to
identify variants of a protein of the present invention (Arkin and
Yourvan, 1992, Proc. Natl. Acad. Sci. USA 89:7811-7815; Delgrave et
al., 1993, Protein Engineering 6(3):327-331).
[0171] The production and use of biomarker nucleic acid and/or
biomarker polypeptide molecules described herein can be facilitated
by using standard recombinant techniques. In some embodiments, such
techniques use vectors, preferably expression vectors, containing a
nucleic acid encoding a biomarker polypeptide or a portion of such
a polypeptide. As used herein, the term "vector" refers to a
nucleic acid molecule capable of transporting another nucleic acid
to which it has been linked. One type of vector is a "plasmid"
which refers to a circular double stranded DNA loop into which
additional DNA segments can be ligated. Another type of vector is a
viral vector, wherein additional DNA segments can be ligated into
the viral genome. Certain vectors are capable of autonomous
replication in a host cell into which they are introduced (e.g.,
bacterial vectors having a bacterial origin of replication and
episomal mammalian vectors). Other vectors (e.g., non-episomal
mammalian vectors) are integrated into the genome of a host cell
upon introduction into the host cell, and thereby are replicated
along with the host genome. Moreover, certain vectors, namely
expression vectors, are capable of directing the expression of
genes to which they are operably linked. In general, expression
vectors of utility in recombinant DNA techniques are often in the
form of plasmids (vectors). However, the present invention is
intended to include such other forms of expression vectors, such as
viral vectors (e.g., replication defective retroviruses,
adenoviruses and adeno-associated viruses), which serve equivalent
functions.
[0172] The recombinant expression vectors of the present invention
comprise a nucleic acid of the present invention in a form suitable
for expression of the nucleic acid in a host cell. This means that
the recombinant expression vectors include one or more regulatory
sequences, selected on the basis of the host cells to be used for
expression, which is operably linked to the nucleic acid sequence
to be expressed. Within a recombinant expression vector, "operably
linked" is intended to mean that the nucleotide sequence of
interest is linked to the regulatory sequence(s) in a manner which
allows for expression of the nucleotide sequence (e.g., in an in
vitro transcription/translation system or in a host cell when the
vector is introduced into the host cell). The term "regulatory
sequence" is intended to include promoters, enhancers and other
expression control elements (e.g., polyadenylation signals). Such
regulatory sequences are described, for example, in Goeddel,
Methods in Enzymology: Gene Expression Technology vol. 185,
Academic Press, San Diego, Calif. (1991). Regulatory sequences
include those which direct constitutive expression of a nucleotide
sequence in many types of host cell and those which direct
expression of the nucleotide sequence only in certain host cells
(e.g., tissue-specific regulatory sequences). It will be
appreciated by those skilled in the art that the design of the
expression vector can depend on such factors as the choice of the
host cell to be transformed, the level of expression of protein
desired, and the like. The expression vectors of the present
invention can be introduced into host cells to thereby produce
proteins or peptides, including fusion proteins or peptides,
encoded by nucleic acids as described herein.
[0173] The recombinant expression vectors for use in the present
invention can be designed for expression of a polypeptide
corresponding to a marker of the present invention in prokaryotic
(e.g., E. coli) or eukaryotic cells (e.g., insect cells {using
baculovirus expression vector}, yeast cells or mammalian cells).
Suitable host cells are discussed further in Goeddel, supra.
Alternatively, the recombinant expression vector can be transcribed
and translated in vitro, for example using T7 promoter regulatory
sequences and T7 polymerase.
[0174] Expression of proteins in prokaryotes is most often carried
out in E. coli with vectors containing constitutive or inducible
promoters directing the expression of either fusion or non-fusion
proteins. Fusion vectors add a number of amino acids to a protein
encoded therein, usually to the amino terminus of the recombinant
protein. Such fusion vectors typically serve three purposes: 1) to
increase expression of recombinant protein; 2) to increase the
solubility of the recombinant protein; and 3) to aid in the
purification of the recombinant protein by acting as a ligand in
affinity purification. Often, in fusion expression vectors, a
proteolytic cleavage site is introduced at the junction of the
fusion moiety and the recombinant protein to enable separation of
the recombinant protein from the fusion moiety subsequent to
purification of the fusion protein. Such enzymes, and their cognate
recognition sequences, include Factor Xa, thrombin and
enterokinase. Typical fusion expression vectors include pGEX
(Pharmacia Biotech Inc; Smith and Johnson, 1988, Gene 67:31-40),
pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia,
Piscataway, N.J.) which fuse glutathione S-transferase (GST),
maltose E binding protein, or protein A, respectively, to the
target recombinant protein.
[0175] Examples of suitable inducible non-fusion E. coli expression
vectors include pTrc (Amann et al., 1988, Gene 69:301-315) and pET
11d (Studier et al., p. 60-89, In Gene Expression Technology:
Methods in Enzymology vol. 185, Academic Press, San Diego, Calif.,
1991). Target biomarker nucleic acid expression from the pTrc
vector relies on host RNA polymerase transcription from a hybrid
trp-lac fusion promoter. Target biomarker nucleic acid expression
from the pET 1Id vector relies on transcription from a T7 gn10-lac
fusion promoter mediated by a co-expressed viral RNA polymcrasc (T7
gn1). This viral polymerase is supplied by host strains BL21 (DE3)
or HMS174(DE3) from a resident prophage harboring a T7 gn1 gene
under the transcriptional control of the lacUV 5 promoter.
[0176] One strategy to maximize recombinant protein expression in
E. coli is to express the protein in a host bacterium with an
impaired capacity to proteolytically cleave the recombinant protein
(Gottesman, p. 119-128, In Gene Expression Technology: Methods in
Enzymology vol. 185, Academic Press, San Diego, Calif., 1990.
Another strategy is to alter the nucleic acid sequence of the
nucleic acid to be inserted into an expression vector so that the
individual codons for each amino acid are those preferentially
utilized in E. coli (Wada et al., 1992, Nucleic Acids Res.
20:2111-2118). Such alteration of nucleic acid sequences of the
present invention can be carried out by standard DNA synthesis
techniques.
[0177] In another embodiment, the expression vector is a yeast
expression vector. Examples of vectors for expression in yeast S.
cerevisiae include pYepSec1 (Baldari et al., 1987, EMBO J.
6:229-234), pMFa (Kujan and Herskowitz, 1982, Cell 30:933-943),
pJRY88 (Schultz et al., 1987, Gene 54:113-123), pYES2 (Invitrogen
Corporation, San Diego, Calif.), and pPicZ (Invitrogen Corp. San
Diego, Calif.).
[0178] Alternatively, the expression vector is a baculovirus
expression vector. Baculovirus vectors available for expression of
proteins in cultured insect cells (e.g., Sf 9 cells) include the
pAc series (Smith et al., 1983. Mol. Cell Biol. 3:2156-2165) and
the pVL series (Lucklow and Summers, 1989, Virology 170:31-39).
[0179] In yet another embodiment, a nucleic acid of the present
invention is expressed in mammalian cells using a mammalian
expression vector. Examples of mammalian expression vectors include
pCDM8 (Seed, 1987, Nature 329:840) and pMT2PC (Kaufman et al.,
1987, EMBO J. 6:187-195). When used in mammalian cells, the
expression vector's control functions are often provided by viral
regulatory elements. For example, commonly used promoters are
derived from polyoma, Adenovirus 2, cytomegalovirus and Simian
Virus 40. For other suitable expression systems for both
prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook
et al., supra.
[0180] In another embodiment, the recombinant mammalian expression
vector is capable of directing expression of the nucleic acid
preferentially in a particular cell type (e.g. tissue-specific
regulatory elements are used to express the nucleic acid).
Tissue-specific regulatory elements are known in the art.
Non-limiting examples of suitable tissue-specific promoters include
the albumin promoter (liver-specific; Pinker et al., 1987, Genes
Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton,
1988, Adv. Immunol. 43:235-275), in particular promoters of T cell
receptors (Winoto and Baltimore, 1989, EMBO J. 8:729-733) and
immunoglobulins (Banerji et al., 1983, Cell 33:729-740; Queen and
Baltimore, 1983, Cell 33:741-748), neuron-specific promoters (e.g.,
the neurofilament promoter; Byrne and Ruddle, 1989, Proc. Natl.
Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund
et al., 1985, Science 230:912-916), and mammary gland-specific
promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and
European Application Publication No. 264,166).
Developmentally-regulated promoters are also encompassed, for
example the murine hox promoters (Kessel and Gruss, 1990, Science
249:374-379) and the .alpha.-fetoprotein promoter (Camper and
Tilghman, 1989, Genes Dev. 3:537-546).
[0181] The present invention further provides a recombinant
expression vector comprising a DNA molecule cloned into the
expression vector in an antisense orientation. That is, the DNA
molecule is operably linked to a regulatory sequence in a manner
which allows for expression (by transcription of the DNA molecule)
of an RNA molecule which is antisense to the mRNA encoding a
polypeptide of the present invention. Regulatory sequences operably
linked to a nucleic acid cloned in the antisense orientation can be
chosen which direct the continuous expression of the antisense RNA
molecule in a variety of cell types, for instance viral promoters
and/or enhancers, or regulatory sequences can be chosen which
direct constitutive, tissue-specific or cell type specific
expression of antisense RNA. The antisense expression vector can be
in the form of a recombinant plasmid, phagemid, or attenuated virus
in which antisense nucleic acids are produced under the control of
a high efficiency regulatory region, the activity of which can be
determined by the cell type into which the vector is introduced.
For a discussion of the regulation of gene expression using
antisense genes (see Weintraub et al., 1986, Trends in Genetics,
Vol. 1(1)).
[0182] Another aspect of the present invention pertains to host
cells into which a recombinant expression vector of the present
invention has been introduced. The terms "host cell" and
"recombinant host cell" are used interchangeably herein. It is
understood that such terms refer not only to the particular subject
cell but to the progeny or potential progeny of such a cell.
Because certain modifications may occur in succeeding generations
due to either mutation or environmental influences, such progeny
may not, in fact, be identical to the parent cell, but are still
included within the scope of the term as used herein.
[0183] A host cell can be any prokaryotic (e.g., E. coli) or
eukaryotic cell (e.g., insect cells, yeast or mammalian cells).
[0184] Vector DNA can be introduced into prokaryotic or eukaryotic
cells via conventional transformation or transfection techniques.
As used herein, the terms "transformation" and "transfection" are
intended to refer to a variety of art-recognized techniques for
introducing foreign nucleic acid into a host cell, including
calcium phosphate or calcium chloride co-precipitation.
DEAE-dextran-mediated transfection, lipofection, or
electroporation. Suitable methods for transforming or transfecting
host cells can be found in Sambrook, et al. (supra), and other
laboratory manuals.
[0185] For stable transfection of mammalian cells, it is known
that, depending upon the expression vector and transfection
technique used, only a small fraction of cells may integrate the
foreign DNA into their genome. In order to identify and select
these integrants, a gene that encodes a selectable marker (e.g.,
for resistance to antibiotics) is generally introduced into the
host cells along with the gene of interest. Preferred selectable
markers include those which confer resistance to drugs, such as
G418, hygromycin and methotrexate. Cells stably transfected with
the introduced nucleic acid can be identified by drug selection
(e.g., cells that have incorporated the selectable marker gene will
survive, while the other cells die).
V. Analyzing Biomarker Nucleic Acids and Polypeptides
[0186] Biomarker nucleic acids and/or biomarker polypeptides can be
analyzed according to the methods described herein and techniques
known to the skilled artisan to identify such genetic or expression
alterations useful for the present invention including, but not
limited to, 1) an alteration in the level of a biomarker transcript
or polypeptide, 2) a deletion or addition of one or more
nucleotides from a biomarker gene, 4) a substitution of one or more
nucleotides of a biomarker gene, 5) aberrant modification of a
biomarker gene, such as an expression regulatory region, and the
like.
[0187] a. Methods for Detection of Copy Number
[0188] Methods of evaluating the copy number of a biomarker nucleic
acid are well known to those of skill in the art. The presence or
absence of chromosomal gain or loss can be evaluated simply by a
determination of copy number of the regions or markers identified
herein.
[0189] In one embodiment, a biological sample is tested for the
presence of copy number changes in genomic loci containing the
genomic marker. A copy number of at least 3, 4, 5, 6, 7, 8, 9, or
10 is predictive of poorer outcome of anti-immune checkpoint and
anti-angiogenesis combination treatment.
[0190] Methods of evaluating the copy number of a biomarker locus
include, but are not limited to, hybridization-based assays.
Hybridization-based assays include, but are not limited to,
traditional "direct probe" methods, such as Southern blots, in situ
hybridization (e.g., FISH and FISH plus SKY) methods, 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.
[0191] In one embodiment, evaluating the biomarker gene copy number
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 RNA (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, other
methods well known in the art to detect RNA can be used, such that
higher or lower expression relative to an appropriate control
(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.
[0192] An alternative means for determining genomic 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. 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. The probes are
typically labeled, e.g., with radioisotopes or fluorescent
reporters. In one embodiment, probes are sufficiently long so as to
specifically hybridize with the target nucleic acid(s) under
stringent conditions. Probes generally range in length from about
200 bases to about 1000 bases. 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.
[0193] An alternative means for determining genomic copy number is
comparative genomic hybridization. In general, genomic DNA is
isolated from normal reference cells, as well as from test cells
(e.g., tumor cells) and amplified, if necessary. The two nucleic
acids are differentially labeled and then hybridized in situ to
metaphase chromosomes of a reference cell. The repetitive sequences
in both the reference and test DNAs are either removed or their
hybridization capacity is reduced by some means, for example by
prehybridization with appropriate blocking nucleic acids and/or
including such blocking nucleic acid sequences for said repetitive
sequences during said hybridization. The bound, labeled DNA
sequences are then rendered in a visualizable form, if necessary.
Chromosomal regions in the test cells which are at increased or
decreased copy number can be identified by detecting regions where
the ratio of signal from the two DNAs is altered. For example,
those regions that have decreased in copy number in the test cells
will show relatively lower signal from the test DNA than the
reference compared to other regions of the genome. Regions that
have been increased in copy number in the test cells will show
relatively higher signal from the test DNA. 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. In another embodiment of
CGH, array CGH (aCGH), the immobilized chromosome element is
replaced with a collection of solid support bound target nucleic
acids on an array, allowing for a large or complete percentage of
the genome to be represented in the collection of solid support
bound targets. Target nucleic acids may comprise cDNAs, genomic
DNAs, oligonucleotides (e.g., to detect single nucleotide
polymorphisms) and the like. 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. Methods of preparing immobilized
chromosomes or arrays and performing comparative genomic
hybridization are well known in the art (see, e.g., U.S. Pat. Nos.
6,335,167; 6,197,501; 5,830,645; and 5,665,549 and 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 another 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.
[0194] 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.
[0195] 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 analysis 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
present invention. In fluorogenic quantitative PCR quantitation is
based on amount of fluorescence signals, e.g., TaqMan and SYBR
green.
[0196] Other suitable amplification methods include, but are not
limited to, ligase chain reaction (LCR) (see Wu and Wallace (1989)
Genomics 4: 560. Landegren, el 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.
[0197] Loss of heterozygosity (LOH) and major copy proportion (MCP)
mapping (Wang, Z. C., et al. (2004) Cancer Res 64(1):64-71;
Seymour, A. B., et al. (1994) Cancer Res 54, 2761-4; Hahn, S. A.,
et al. (1995) Cancer Res 55, 4670-5; Kimura, M., et al. (199) Genes
Chromosomes Cancer 17, 88-93; Li et al., (2008) MBC Bioinform. 9,
204-219) may also be used to identify regions of amplification or
deletion.
[0198] b. Methods for Detection of Biomarker Nucleic Acid
Expression
[0199] Biomarker expression may be assessed by any of a wide
variety of well known methods for detecting expression of a
transcribed molecule or protein. Non-limiting examples of such
methods include immunological methods for detection of secreted,
cell-surface, cytoplasmic, or nuclear proteins, protein
purification methods, protein function or activity assays, nucleic
acid hybridization methods, nucleic acid reverse transcription
methods, and nucleic acid amplification methods.
[0200] In preferred embodiments, activity of a particular gene is
characterized by a measure of gene transcript (e.g. mRNA), by a
measure of the quantity of translated protein, or by a measure of
gene product activity. Marker expression can be monitored in a
variety of ways, including by detecting mRNA levels, protein
levels, or protein activity, any of which can be measured using
standard techniques. Detection can involve quantification of the
level of gene expression (e.g., genomic DNA, cDNA, mRNA, protein,
or enzyme activity), or, alternatively, can be a qualitative
assessment of the level of gene expression, in particular in
comparison with a control level. The type of level being detected
will be clear from the context.
[0201] In another embodiment, detecting or determining expression
levels of a biomarker and functionally similar homologs thereof,
including a fragment or genetic alteration thereof (e.g., in
regulatory or promoter regions thereof) comprises detecting or
determining RNA levels for the marker of interest. In one
embodiment, one or more cells from the subject to be tested are
obtained and RNA is isolated from the cells. In a preferred
embodiment, a sample of breast tissue cells is obtained from the
subject.
[0202] In one embodiment, RNA is obtained from a single cell. For
example, a cell can be isolated from a tissue sample by laser
capture microdissection (LCM). Using this technique, a cell can be
isolated from a tissue section, including a stained tissue section,
thereby assuring that the desired cell is isolated (see, e.g.,
Bonner et al. (1997) Science 278: 1481; Emmert-Buck et al. (1996)
Science 274:998; Fend et al. (1999) Am. J. Path. 154: 61 and
Murakami et al. (2000) Kidney Int. 58:1346). For example, Murakami
et al., supra, describe isolation of a cell from a previously
immunostained tissue section.
[0203] It is also be possible to obtain cells from a subject and
culture the cells in vitro, such as to obtain a larger population
of cells from which RNA can be extracted. Methods for establishing
cultures of non-transformed cells, i.e., primary cell cultures, are
known in the art.
[0204] When isolating RNA from tissue samples or cells from
individuals, it may be important to prevent any further changes in
gene expression after the tissue or cells has been removed from the
subject. Changes in expression levels are known to change rapidly
following perturbations. e.g., heat shock or activation with
lipopolysaccharide (LPS) or other reagents. In addition, the RNA in
the tissue and cells may quickly become degraded. Accordingly, in a
preferred embodiment, the tissue or cells obtained from a subject
is snap frozen as soon as possible.
[0205] RNA can be extracted from the tissue sample by a variety of
methods, e.g., the guanidium thiocyanate lysis followed by CsCl
centrifugation (Chirgwin et al., 1979, Biochemistry 18:5294-5299).
RNA from single cells can be obtained as described in methods for
preparing cDNA libraries from single cells, such as those described
in Dulac, C. (1998) Curr. Top. Dev. Biol. 36, 245 and Jena et al.
(1996) J. Immunol. Methods 190:199. Care to avoid RNA degradation
must be taken, e.g., by inclusion of RNAsin.
[0206] The RNA sample can then be enriched in particular species.
In one embodiment, poly(A)+ RNA is isolated from the RNA sample. In
general, such purification takes advantage of the poly-A tails on
mRNA. In particular and as noted above, poly-T oligonucleotides may
be immobilized within on a solid support to serve as affinity
ligands for mRNA. Kits for this purpose are commercially available,
e.g., the MessageMaker kit (Life Technologies, Grand Island,
N.Y.).
[0207] In a preferred embodiment, the RNA population is enriched in
marker sequences. Enrichment can be undertaken, e.g., by
primer-specific cDNA synthesis, or multiple rounds of linear
amplification based on cDNA synthesis and template-directed in
vitro transcription (see, e.g., Wang et al. (1989) PNAS 86, 9717;
Dulac et al., supra, and Jena et al., supra).
[0208] The population of RNA, enriched or not in particular species
or sequences, can further be amplified. As defined herein, an
"amplification process" is designed to strengthen, increase, or
augment a molecule within the RNA. For example, where RNA is mRNA,
an amplification process such as RT-PCR can be utilized to amplify
the mRNA, such that a signal is detectable or detection is
enhanced. Such an amplification process is beneficial particularly
when the biological, tissue, or tumor sample is of a small size or
volume.
[0209] Various amplification and detection methods can be used. For
example, it is within the scope of the present invention to reverse
transcribe mRNA into cDNA followed by polymerase chain reaction
(RT-PCR); or, to use a single enzyme for both steps as described in
U.S. Pat. No. 5,322,770, or reverse transcribe mRNA into cDNA
followed by symmetric gap ligase chain reaction (RT-AGLCR) as
described by R. L. Marshall, et al., PCR Methods and Applications
4: 80-84 (1994). Real time PCR may also be used.
[0210] Other known amplification methods which can be utilized
herein include but are not limited to the so-called "NASBA" or
"3SR" technique described in PNAS USA 87: 1874-1878 (1990) and also
described in Nature 350 (No. 6313): 91-92 (1991); Q-beta
amplification as described in published European Patent Application
(EPA) No. 4544610; strand displacement amplification (as described
in G. T. Walker et al., Clin. Chem. 42: 9-13 (1996) and European
Patent Application No. 684315; target mediated amplification, as
described by PCT Publication WO9322461; PCR; ligase chain reaction
(LCR) (see, e.g., Wu and Wallace, Genomics 4, 560 (1989), Landegren
et al., Science 241, 1077 (1988) self-sustained sequence
replication (SSR) (see, e.g., Guatelli et al., Proc. Nat. Acad.
Sci. USA, 87, 1874 (1990)); and transcription amplification (see,
e.g., Kwoh et al., Proc. Natl. Acad. Sci. USA 86, 1173 (1989)).
[0211] Many techniques are known in the state of the art for
determining absolute and relative levels of gene expression,
commonly used techniques suitable for use in the present invention
include Northern analysis, RNase protection assays (RPA),
microarrays and PCR-based techniques, such as quantitative PCR and
differential display PCR. For example, Northern blotting involves
running a preparation of RNA on a denaturing agarose gel, and
transferring it to a suitable support, such as activated cellulose,
nitrocellulose or glass or nylon membranes. Radiolabeled cDNA or
RNA is then hybridized to the preparation, washed and analyzed by
autoradiography.
[0212] In situ hybridization visualization may also be employed,
wherein a radioactively labeled antisense RNA probe is hybridized
with a thin section of a biopsy sample, washed, cleaved with RNase
and exposed to a sensitive emulsion for autoradiography. The
samples may be stained with hematoxylin to demonstrate the
histological composition of the sample, and dark field imaging with
a suitable light filter shows the developed emulsion.
Non-radioactive labels such as digoxigenin may also be used.
[0213] Alternatively, mRNA expression can be detected on a DNA
array, chip or a microarray. Labeled nucleic acids of a test sample
obtained from a subject may be hybridized to a solid surface
comprising biomarker DNA. Positive hybridization signal is obtained
with the sample containing biomarker transcripts. Methods of
preparing DNA arrays and their use are well known in the art (see,
e.g., U.S. Pat. Nos. 6,618,6796; 6,379,897; 6,664,377; 6,451,536;
548,257; U.S. 20030157485 and Schena et al. (1995) Science 20,
467-470; Gerhold et al. (1999) Trends In Biochem. Sci. 24, 168-173;
and Lennon et al. (2000) Drug Discovery Today 5, 59-65, which are
herein incorporated by reference in their entirety). Serial
Analysis of Gene Expression (SAGE) can also be performed (See for
example U.S. Patent Application 20030215858).
[0214] To monitor mRNA levels, for example, mRNA is extracted from
the biological sample to be tested, reverse transcribed, and
fluorescently-labeled cDNA probes are generated. The microarrays
capable of hybridizing to marker cDNA are then probed with the
labeled cDNA probes, the slides scanned and fluorescence intensity
measured. This intensity correlates with the hybridization
intensity and expression levels.
[0215] Types of probes that can be used in the methods described
herein include cDNA, riboprobes, synthetic oligonucleotides and
genomic probes. The type of probe used will generally be dictated
by the particular situation, such as riboprobes for in situ
hybridization, and cDNA for Northern blotting, for example. In one
embodiment, the probe is directed to nucleotide regions unique to
the RNA. The probes may be as short as is required to
differentially recognize marker mRNA transcripts, and may be as
short as, for example, 15 bases; however, probes of at least 17,
18, 19 or 20 or more bases can be used. In one embodiment, the
primers and probes hybridize specifically under stringent
conditions to a DNA fragment having the nucleotide sequence
corresponding to the marker. As herein used, the term "stringent
conditions" means hybridization will occur only if there is at
least 95% identity in nucleotide sequences. In another embodiment,
hybridization under "stringent conditions" occurs when there is at
least 97% identity between the sequences.
[0216] The form of labeling of the probes may be any that is
appropriate, such as the use of radioisotopes, for example,
.sup.32P and .sup.35S. Labeling with radioisotopes may be achieved,
whether the probe is synthesized chemically or biologically, by the
use of suitably labeled bases.
[0217] In one embodiment, the biological sample contains
polypeptide molecules from the test subject. Alternatively, the
biological sample can contain mRNA molecules from the test subject
or genomic DNA molecules from the test subject.
[0218] In another embodiment, the methods further involve obtaining
a control biological sample from a control subject, contacting the
control sample with a compound or agent capable of detecting marker
polypeptide, mRNA, genomic DNA, or fragments thereof, such that the
presence of the marker polypeptide, mRNA, genomic DNA, or fragments
thereof, is detected in the biological sample, and comparing the
presence of the marker polypeptide, mRNA, genomic DNA, or fragments
thereof, in the control sample with the presence of the marker
polypeptide, mRNA, genomic DNA, or fragments thereof in the test
sample.
[0219] c. Methods for Detection of Biomarker Protein Expression
[0220] The activity or level of a biomarker protein can be detected
and/or quantified by detecting or quantifying the expressed
polypeptide. The polypeptide can be detected and quantified by any
of a number of means well known to those of skill in the art.
Aberrant levels of polypeptide expression of the polypeptides
encoded by a biomarker nucleic acid and functionally similar
homologs thereof, including a fragment or genetic alteration
thereof (e.g., in regulatory or promoter regions thereof) are
associated with the likelihood of response of a cancer to an
anti-immune checkpoint and anti-angiogenesis combination therapy.
Any method known in the art for detecting polypeptides can be used.
Such methods include, but are not limited to, immunodiffusion,
immunoelectrophoresis, radioimmunoassay (RIA), enzyme-linked
immunosorbent assays (ELISAs), immunofluorescent assays, Western
blotting, binder-ligand assays, immunohistochemical techniques,
agglutination, complement assays, high performance liquid
chromatography (HPLC), thin layer chromatography (TLC),
hyperdiffusion chromatography, and the like (e.g., Basic and
Clinical Immunology, Sites and Terr, eds., Appleton and Lange,
Norwalk, Conn. pp 217-262, 1991 which is incorporated by
reference). Preferred are binder-ligand immunoassay methods
including reacting antibodies with an epitope or epitopes and
competitively displacing a labeled polypeptide or derivative
thereof.
[0221] For example, ELISA and RIA procedures may be conducted such
that a biomarker antibody is labeled (with a radioisotope such as
.sup.125I or .sup.35S, or an assayable enzyme, such as horseradish
peroxidase or alkaline phosphatase), and is brought together with
the unlabelled sample, whereon a second antibody is used to bind
the first, and radioactivity or the immobilized enzyme assayed
(competitive assay). Alternatively, the biomarker protein in the
sample is allowed to react with the corresponding immobilized
antibody, radioisotope- or enzyme-labeled anti-biomarker protein
antibody is allowed to react with the system, and radioactivity or
the enzyme assayed (ELISA-sandwich assay). Other conventional
methods may also be employed as suitable.
[0222] The above techniques may be conducted essentially as a
"one-step" or "two-step" assay. A "one-step" assay involves
contacting antigen with immobilized antibody and, without washing,
contacting the mixture with labeled antibody. A "two-step" assay
involves washing before contacting, the mixture with labeled
antibody. Other conventional methods may also be employed as
suitable. When determining the presence, amount, and/or activity of
anti-galectin antibodies in a biological sample (e.g., blood,
serum, plasma, and the like), antigen can be immobilized and the
test sample containing such anti-galectin antibodies can be
contacted with the immobilized antigen. The description provided
below can be adapted according to well known methods for
immobilized antigens used to profile antibodies in a test sample
(see, for example, US Pats. Publ. 2009/0075305, 2014/0045199, and
2012/0122723 and U.S. Pat. No. 8,278,057). In some embodiments, a
protein chip, bead, or other solid support system is used whereby,
for example, galectin target proteins of interest are comprised
directly or indirectly on a protein chip array and antibodies that
bind the galectin target proteins of interests are contacted with
the bound target antigen.
[0223] In one embodiment, a method for measuring biomarker protein
levels comprises the steps of: contacting a biological specimen
with an antibody or variant (e.g., fragment) thereof which
selectively binds the biomarker protein, and detecting whether said
antibody or variant thereof is bound to said sample and thereby
measuring the levels of the biomarker protein.
[0224] Enzymatic and radiolabeling of biomarker protein and/or the
antibodies may be effected by conventional means. Such means will
generally include covalent linking of the enzyme to the antigen or
the antibody in question, such as by glutaraldehyde specifically so
as not to adversely affect the activity of the enzyme, by which is
meant that the enzyme must still be capable of interacting with its
substrate, although it is not necessary for all of the enzyme to be
active, provided that enough remains active to permit the assay to
be effected. Indeed, some techniques for binding enzyme are
non-specific (such as using formaldehyde), and will only yield a
proportion of active enzyme.
[0225] It is usually desirable to immobilize one component of the
assay system on a support, thereby allowing other components of the
system to be brought into contact with the component and readily
removed without laborious and time-consuming labor. It is possible
for a second phase to be immobilized away from the first, but one
phase is usually sufficient.
[0226] It is possible to immobilize the enzyme itself on a support,
but if solid-phase enzyme is required, then this is generally best
achieved by binding to antibody and affixing the antibody to a
support, models and systems for which are well-known in the art.
Simple polyethylene may provide a suitable support.
[0227] Enzymes employable for labeling are not particularly
limited, but may be selected from the members of the oxidase group,
for example. These catalyze production of hydrogen peroxide by
reaction with their substrates, and glucose oxidase is often used
for its good stability, case of availability and cheapness, as well
as the ready availability of its substrate (glucose). Activity of
the oxidase may be assayed by measuring the concentration of
hydrogen peroxide formed after reaction of the enzyme-labeled
antibody with the substrate under controlled conditions well-known
in the art.
[0228] Other techniques may be used to detect biomarker protein
according to a practitioner's preference based upon the present
disclosure. One such technique is Western blotting (Towbin et al.,
Proc. Nat. Acad. Sci. 76:4350 (1979)), wherein a suitably treated
sample is run on an SDS-PAGE gel before being transferred to a
solid support, such as a nitrocellulose filter. Anti-biomarker
protein antibodies (unlabeled) are then brought into contact with
the support and assayed by a secondary immunological reagent, such
as labeled protein A or anti-immunoglobulin (suitable labels
including .sup.125I, horseradish peroxidase and alkaline
phosphatase). Chromatographic detection may also be used.
[0229] Immunohistochemistry may be used to detect expression of
biomarker protein, e.g., in a biopsy sample. A suitable antibody is
brought into contact with, for example, a thin layer of cells,
washed, and then contacted with a second, labeled antibody.
Labeling may be by fluorescent markers, enzymes, such as
peroxidase, avidin, or radiolabelling. The assay is scored
visually, using microscopy.
[0230] Anti-biomarker protein antibodies, such as intrabodies, may
also be used for imaging purposes, for example, to detect the
presence of biomarker protein in cells and tissues of a subject.
Suitable labels include radioisotopes, iodine (.sup.125I,
.sup.121I), carbon (.sup.14C), sulphur (.sup.35S), tritium
(.sup.3H), indium (.sup.112In), and technetium (.sup.99mTc),
fluorescent labels, such as fluorescein and rhodamine, and
biotin.
[0231] For in vivo imaging purposes, antibodies are not detectable,
as such, from outside the body, and so must be labeled, or
otherwise modified, to permit detection. Markers for this purpose
may be any that do not substantially interfere with the antibody
binding, but which allow external detection. Suitable markers may
include those that may be detected by X-radiography, NMR or MRI.
For X-radiographic techniques, suitable markers include any
radioisotope that emits detectable radiation but that is not
overtly harmful to the subject, such as barium or cesium, for
example. Suitable markers for NMR and MRI generally include those
with a detectable characteristic spin, such as deuterium, which may
be incorporated into the antibody by suitable labeling of nutrients
for the relevant hybridoma, for example.
[0232] The size of the subject, and the imaging system used, will
determine the quantity of imaging moiety needed to produce
diagnostic images. In the case of a radioisotope moiety, for a
human subject, the quantity of radioactivity injected will normally
range from about 5 to 20 millicuries of technetium-99. The labeled
antibody or antibody fragment will then preferentially accumulate
at the location of cells which contain biomarker protein. The
labeled antibody or antibody fragment can then be detected using
known techniques.
[0233] Antibodies that may be used to detect biomarker protein
include any antibody, whether natural or synthetic, full length or
a fragment thereof, monoclonal or polyclonal, that binds
sufficiently strongly and specifically to the biomarker protein to
be detected. An antibody may have a K.sub.d of at most about
10.sup.-6M, 10.sup.-7M, 10.sup.-8M, 10.sup.-9M, 10.sup.-10M,
10.sup.-11M, 10.sup.-12M. The phrase "specifically binds" refers to
binding of, for example, an antibody to an epitope or antigen or
antigenic determinant in such a manner that binding can be
displaced or competed with a second preparation of identical or
similar epitope, antigen or antigenic determinant. An antibody may
bind preferentially to the biomarker protein relative to other
proteins, such as related proteins.
[0234] Antibodies are commercially available or may be prepared
according to methods known in the art.
[0235] Antibodies and derivatives thereof that may be used
encompass polyclonal or monoclonal antibodies, chimeric, human,
humanized, primatized (CDR-grafted), veneered or single-chain
antibodies as well as functional fragments, i.e., biomarker protein
binding fragments, of antibodies. For example, antibody fragments
capable of binding to a biomarker protein or portions thereof,
including, but not limited to, Fv, Fab, Fab' and F(ab') 2 fragments
can be used. Such fragments can be produced by enzymatic cleavage
or by recombinant techniques. For example, papain or pepsin
cleavage can generate Fab or F(ab') 2 fragments, respectively.
Other proteases with the requisite substrate specificity can also
be used to generate Fab or F(ab') 2 fragments. Antibodies can also
be produced in a variety of truncated forms using antibody genes in
which one or more stop codons have been introduced upstream of the
natural stop site. For example, a chimeric gene encoding a F(ab') 2
heavy chain portion can be designed to include DNA sequences
encoding the CH, domain and hinge region of the heavy chain.
[0236] Synthetic and engineered antibodies are described in, e.g.,
Cabilly et al., U.S. Pat. No. 4,816,567 Cabilly et al., European
Patent No. 0,125,023 B1; Boss et al., U.S. Pat. No. 4,816,397; Boss
et al., European Patent No. 0,120,694 B1; Neuberger, M. S. et al.,
WO 86/01533; Neuberger, M. S. et al., European Patent No. 0,194,276
B1; Winter, U.S. Pat. No. 5,225,539; Winter, European Patent No.
0,239,40 B1; Queen et al., European Patent No. 0451216 B1; and
Padlan, E. A. et al., EP 0519596 A1. See also. Newman, R. et al.,
BioTechnology, 10: 1455-1460 (1992), regarding primatized antibody,
and Ladner et al., U.S. Pat. No. 4,946,778 and Bird, R. E. et al.,
Science, 242: 423-426 (1988)) regarding single-chain antibodies.
Antibodies produced from a library, e.g., phage display library,
may also be used.
[0237] In some embodiments, agents that specifically bind to a
biomarker protein other than antibodies are used, such as peptides.
Peptides that specifically bind to a biomarker protein can be
identified by any means known in the art. For example, specific
peptide binders of a biomarker protein can be screened for using
peptide phage display libraries.
3. Anti-Cancer Therapies
[0238] The efficacy of anti-immune checkpoint and anti-angiogenesis
combination therapy is predicted according to biomarker amount
and/or activity associated with a cancer in a subject according to
the methods described herein. In one embodiment, such anti-immune
checkpoint and anti-angiogenesis combination therapy (e.g.,
anti-CTLA4 and anti-VEGF antibodies) can be administered once a
subject is indicated as being a likely responder to anti-immune
checkpoint and anti-angiogenesis combination therapy. In another
embodiment, such anti-immune checkpoint and anti-angiogenesis
combination therapy can be avoided once a subject is indicated as
not being a likely responder to anti-immune checkpoint and
anti-angiogenesis combination therapy and an alternative treatment
regimen, such as targeted and/or untargeted anti-cancer therapies
can be administered. Combination therapies are also contemplated
and can comprise, for example, one or more chemotherapeutic agents
and radiation, one or more chemotherapeutic agents and
immunotherapy, or one or more chemotherapeutic agents, radiation
and chemotherapy, each combination of which can be with anti-immune
checkpoint and anti-angiogenesis combination therapy.
[0239] The term "targeted therapy" refers to administration of
agents that selectively interact with a chosen biomolecule to
thereby treat cancer. For example, anti-Gal-1, anti-Gal-3, and/or
anti-Gal-9 agents, such as therapeutic monoclonal blocking
antibodies, which are well-known in the art and described above,
can be used to target tumor microenvironments and cells expressing
unwanted Gal-1, Gal-3, and Gal-9 respectively. Similarly,
bevacizumab (Avastin.RTM.) is a humanized monoclonal antibody that
targets vascular endothelial growth factor (see, for example, U.S.
Pat. Publ. 2013/0121999, WO 2013/083499, and Presta et al. (1997)
Cancer Res. 57:4593-4599).
[0240] Immunotherapy is one form of targeted therapy that may
comprise, for example, the use of cancer vaccines and/or sensitized
antigen presenting cells. For example, an oncolytic virus is a
virus that is able to infect and lyse cancer cells, while leaving
normal cells unharmed, making them potentially useful in cancer
therapy. Replication of oncolytic viruses both facilitates tumor
cell destruction and also produces dose amplification at the tumor
site. They may also act as vectors for anticancer genes, allowing
them to be specifically delivered to the tumor site. 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. Alternatively,
antisense polynucleotides, ribozymes, RNA interference molecules,
triple helix polynucleotides and the like, can be used to
selectively modulate biomolecules that are linked to the
initiation, progression, and/or pathology of a tumor or cancer.
[0241] The term "untargeted therapy" refers to administration of
agents that do not selectively interact with a chosen biomolecule
yet treat cancer. Representative examples of untargeted therapies
include, without limitation, chemotherapy, gene therapy, and
radiation therapy.
[0242] In one embodiment, chemotherapy is used. Chemotherapy
includes the administration of a chemotherapeutic agent. Such a
chemotherapeutic agent may be, but is not limited to, those
selected from among the following groups of compounds: platinum
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: cisplatin,
treosulfan, and trofosfamide; plant alkaloids: vinblastine,
paclitaxel, docetaxol; DNA topoisomerase inhibitors: 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 c 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 mechanism of action is
generally related to the ability of PARP inhibitors to bind PARP
and decrease its activity. PARP catalyzes the conversion of
.beta.-nicotinamide adenine dinucleotide (NAD+) into nicotinamide
and poly-ADP-ribose (PAR). Both poly (ADP-ribose) and PARP have
been linked to regulation of transcription, cell proliferation,
genomic stability, and carcinogenesis (Bouchard V. J. et. al.
Experimental Hematology, Volume 31. Number 6, June 2003. pp.
446-454(9); Herceg Z.; Wang Z.-Q. Mutation Research/Fundamental and
Molecular Mechanisms of Mutagenesis, Volume 477, Number 1, 2 Jun.
2001, pp. 97-110(14)). Poly(ADP-ribose) polymerase 1 (PARP1) is a
key molecule in the repair of DNA single-strand breaks (SSBs) (de
Murcia J. et al. 1997. Proc Natl Acad Sci USA 94:7303-7307;
Schreiber V, Dantzer F, Ame J C, de Murcia G (2006) Nat Rev Mol
Cell Biol 7:517-528; Wang Z Q, et al. (1997) Genes Dev
11:2347-2358). Knockout of SSB repair by inhibition of PARP1
function induces DNA double-strand breaks (DSBs) that can trigger
synthetic lethality in cancer cells with defective
homology-directed DSB repair (Bryant H E, et al. (2005) Nature
434:913-917; Farmer H, et al. (2005) Nature 434:917-921). The
foregoing examples of chemotherapeutic agents are illustrative, and
are not intended to be limiting.
[0243] In another embodiment, radiation therapy is used. 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.
[0244] In another embodiment, hormone therapy is used. 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).
[0245] In another embodiment, hyperthermia, a procedure in which
body tissue is exposed to high temperatures (up to 106.degree. F.)
is used. Heat may help shrink tumors by damaging cells or depriving
them of substances they need to live. Hyperthermia therapy can be
local, regional, and whole-body hyperthermia, using external and
internal heating devices. Hyperthermia is almost always used with
other forms of therapy (e.g., radiation therapy, chemotherapy, and
biological therapy) to try to increase their effectiveness. Local
hyperthermia refers to heat that is applied to a very small area,
such as a tumor. The area may be heated externally with
high-frequency waves aimed at a tumor from a device outside the
body. To achieve internal heating, one of several types of sterile
probes may be used, including thin, heated wires or hollow tubes
filled with warm water; implanted microwave antennae; and
radiofrequency electrodes. In regional hyperthermia, an organ or a
limb is heated. Magnets and devices that produce high energy are
placed over the region to be heated. In another approach, called
perfusion, some of the patient's blood is removed, heated, and then
pumped (perfused) into the region that is to be heated internally.
Whole-body heating is used to treat metastatic cancer that has
spread throughout the body. It can be accomplished using warm-water
blankets, hot wax, inductive coils (like those in electric
blankets), or thermal chambers (similar to large incubators).
Hyperthermia does not cause any marked increase in radiation side
effects or complications. Heat applied directly to the skin,
however, can cause discomfort or even significant local pain in
about half the patients treated. It can also cause blisters, which
generally heal rapidly.
[0246] In still another embodiment, photodynamic therapy (also
called PDT, photoradiation therapy, photothrapy, or
photochemotherapy) is used for the treatment of some types of
cancer. It is based on the discovery that certain chemicals known
as photosensitizing agents can kill one-celled organisms when the
organisms are exposed to a particular type of light. PDT destroys
cancer cells through the use of a fixed-frequency laser light in
combination with a photosensitizing agent. In PDT, the
photosensitizing agent is injected into the bloodstream and
absorbed by cells all over the body. The agent remains in cancer
cells for a longer time than it does in normal cells. When the
treated cancer cells are exposed to laser light, the
photosensitizing agent absorbs the light and produces an active
form of oxygen that destroys the treated cancer cells. Light
exposure must be timed carefully so that it occurs when most of the
photosensitizing agent has left healthy cells but is still present
in the cancer cells. The laser light used in PDT can be directed
through a fiber-optic (a very thin glass strand). The fiber-optic
is placed close to the cancer to deliver the proper amount of
light. The fiber-optic can be directed through a bronchoscope into
the lungs for the treatment of lung cancer or through an endoscope
into the esophagus for the treatment of esophageal cancer. An
advantage of PDT is that it causes minimal damage to healthy
tissue. However, because the laser light currently in use cannot
pass through more than about 3 centimeters of tissue (a little more
than one and an eighth inch), PDT is mainly used to treat tumors on
or just under the skin or on the lining of internal organs.
Photodynamic therapy makes the skin and eyes sensitive to light for
6 weeks or more after treatment. Patients are advised to avoid
direct sunlight and bright indoor light for at least 6 weeks. If
patients must go outdoors, they need to wear protective clothing,
including sunglasses. Other temporary side effects of PDT are
related to the treatment of specific areas and can include
coughing, trouble swallowing, abdominal pain, and painful breathing
or shortness of breath. In December 1995, the U.S. Food and Drug
Administration (FDA) approved a photosensitizing agent called
porfimer sodium, or Photofrin.RTM., to relieve symptoms of
esophageal cancer that is causing an obstruction and for esophageal
cancer that cannot be satisfactorily treated with lasers alone. In
January 1998, the FDA approved porfimer sodium for the treatment of
early nonsmall cell lung cancer in patients for whom the usual
treatments for lung cancer are not appropriate. The National Cancer
Institute and other institutions are supporting clinical trials
(research studies) to evaluate the use of photodynamic therapy for
several types of cancer, including cancers of the bladder, brain,
larynx, and oral cavity.
[0247] In yet another embodiment, laser therapy is used to harness
high-intensity light to destroy cancer cells. This technique is
often used to relieve symptoms of cancer such as bleeding or
obstruction, especially when the cancer cannot be cured by other
treatments. It may also be used to treat cancer by shrinking or
destroying tumors. The term "laser" stands for light amplification
by stimulated emission of radiation. Ordinary light, such as that
from a light bulb, has many wavelengths and spreads in all
directions. Laser light, on the other hand, has a specific
wavelength and is focused in a narrow beam. This type of
high-intensity light contains a lot of energy. Lasers are very
powerful and may be used to cut through steel or to shape diamonds.
Lasers also can be used for very precise surgical work, such as
repairing a damaged retina in the eye or cutting through tissue (in
place of a scalpel). Although there are several different kinds of
lasers, only three kinds have gained wide use in medicine: Carbon
dioxide (CO.sub.2) laser--This type of laser can remove thin layers
from the skin's surface without penetrating the deeper layers. This
technique is particularly useful in treating tumors that have not
spread deep into the skin and certain precancerous conditions. As
an alternative to traditional scalpel surgery, the CO laser is also
able to cut the skin. The laser is used in this way to remove skin
cancers. Neodymium: yttrium-aluminum-garnet (Nd:YAG) laser--Light
from this laser can penetrate deeper into tissue than light from
the other types of lasers, and it can cause blood to clot quickly.
It can be carried through optical fibers to less accessible parts
of the body. This type of laser is sometimes used to treat throat
cancers. Argon laser--This laser can pass through only superficial
layers of tissue and is therefore useful in dermatology and in eye
surgery. It also is used with light-sensitive dyes to treat tumors
in a procedure known as photodynamic therapy (PDT). Lasers have
several advantages over standard surgical tools, including: Lasers
are more precise than scalpels. Tissue near an incision is
protected, since there is little contact with surrounding skin or
other tissue. The heat produced by lasers sterilizes the surgery
site, thus reducing the risk of infection. Less operating time may
be needed because the precision of the laser allows for a smaller
incision. Healing time is often shortened; since laser heat seals
blood vessels, there is less bleeding, swelling, or scarring. Laser
surgery may be less complicated. For example, with fiber optics,
laser light can be directed to parts of the body without making a
large incision. More procedures may be done on an outpatient basis.
Lasers can be used in two ways to treat cancer: by shrinking or
destroying a tumor with heat, or by activating a chemical--known as
a photosensitizing agent--that destroys cancer cells. In PDT, a
photosensitizing agent is retained in cancer cells and can be
stimulated by light to cause a reaction that kills cancer cells.
CO.sub.2 and Nd:YAG lasers are used to shrink or destroy tumors.
They may be used with endoscopes, tubes that allow physicians to
see into certain areas of the body, such as the bladder. The light
from some lasers can be transmitted through a flexible endoscope
fitted with fiber optics. This allows physicians to see and work in
parts of the body that could not otherwise be reached except by
surgery and therefore allows very precise aiming of the laser beam.
Lasers also may be used with low-power microscopes, giving the
doctor a clear view of the site being treated. Used with other
instruments, laser systems can produce a cutting area as small as
20 microns in diameter--less than the width of a very fine thread.
Lasers are used to treat many types of cancer. Laser surgery is a
standard treatment for certain stages of glottis (vocal cord),
cervical, skin, lung, vaginal, vulvar, and penile cancers. In
addition to its use to destroy the cancer, laser surgery is also
used to help relieve symptoms caused by cancer (palliative care).
For example, lasers may be used to shrink or destroy a tumor that
is blocking a patient's trachea (windpipe), making it easier to
breathe. It is also sometimes used for palliation in colorectal and
anal cancer. Laser-induced interstitial thermotherapy (LITT) is one
of the most recent developments in laser therapy. LITT uses the
same idea as a cancer treatment called hyperthermia; that heat may
help shrink tumors by damaging cells or depriving them of
substances they need to live. In this treatment, lasers are
directed to interstitial areas (areas between organs) in the body.
The laser light then raises the temperature of the tumor, which
damages or destroys cancer cells.
[0248] The duration and/or dose of treatment with anti-immune
checkpoint and anti-angiogenesis combination therapies may vary
according to the particular anti-immune checkpoint agent and/or
anti-angiogenesis agent. An appropriate treatment time for a
particular cancer therapeutic agent will be appreciated by the
skilled artisan. The present invention contemplates the continued
assessment of optimal treatment schedules for each cancer
therapeutic agent, where the phenotype of the cancer of the subject
as determined by the methods of the present invention is a factor
in determining optimal treatment doses and schedules.
[0249] Any means for the introduction of a polynucleotide into
mammals, human or non-human, or cells thereof may be adapted to the
practice of this invention for the delivery of the various
constructs of the present invention into the intended recipient. In
one embodiment of the present invention, the DNA constructs are
delivered to cells by transfection, i.e., by delivery of "naked"
DNA or in a complex with a colloidal dispersion system. A colloidal
system includes macromolecule complexes, nanocapsules,
microspheres, beads, and lipid-based systems including oil-in-water
emulsions, micelles, mixed micelles, and liposomes. The preferred
colloidal system of this invention is a lipid-complexed or
liposome-formulated DNA. In the former approach, prior to
formulation of DNA, e.g., with lipid, a plasmid containing a
transgene bearing the desired DNA constructs may first be
experimentally optimized for expression (e.g., inclusion of an
intron in the 5' untranslated region and elimination of unnecessary
sequences (Feigner, et al., Ann NY Acad Sci 126-139, 1995).
Formulation of DNA, e.g. with various lipid or liposome materials,
may then be effected using known methods and materials and
delivered to the recipient mammal. See, e.g., Canonico et al, Am J
Respir Cell Mol Biol 10:24-29, 1994; Tsan et al, Am J Physiol 268:
Alton et al., Nat Genet. 5:135-142, 1993 and U.S. Pat. No.
5,679,647 by Carson et al.
[0250] The targeting of liposomes can be classified based on
anatomical and mechanistic factors. Anatomical classification is
based on the level of selectivity, for example, organ-specific,
cell-specific, and organelle-specific. Mechanistic targeting can be
distinguished based upon whether it is passive or active. Passive
targeting utilizes the natural tendency of liposomes to distribute
to cells of the reticulo-endothelial system (RES) in organs, which
contain sinusoidal capillaries. Active targeting, on the other
hand, involves alteration of the liposome by coupling the liposome
to a specific ligand such as a monoclonal antibody, sugar,
glycolipid, or protein, or by changing the composition or size of
the liposome in order to achieve targeting to organs and cell types
other than the naturally occurring sites of localization.
[0251] The surface of the targeted delivery system may be modified
in a variety of ways. In the case of a liposomal targeted delivery
system, lipid groups can be incorporated into the lipid bilayer of
the liposome in order to maintain the targeting ligand in stable
association with the liposomal bilayer. Various linking groups can
be used for joining the lipid chains to the targeting ligand. Naked
DNA or DNA associated with a delivery vehicle. e.g., liposomes, can
be administered to several sites in a subject (see below).
[0252] Nucleic acids can be delivered in any desired vector. These
include viral or non-viral vectors, including adenovirus vectors,
adeno-associated virus vectors, retrovirus vectors, lentivirus
vectors, and plasmid vectors. Exemplary types of viruses include
HSV (herpes simplex virus), AAV (adeno associated virus), HIV
(human immunodeficiency virus), BIV (bovine immunodeficiency
virus), and MLV (murine leukemia virus). Nucleic acids can be
administered in any desired format that provides sufficiently
efficient delivery levels, including in virus particles, in
liposomes, in nanoparticles, and complexed to polymers.
[0253] The nucleic acids encoding a protein or nucleic acid of
interest may be in a plasmid or viral vector, or other vector as is
known in the art. Such vectors are well known and any can be
selected for a particular application. In one embodiment of the
present invention, the gene delivery vehicle comprises a promoter
and a demethylase coding sequence. Preferred promoters are
tissue-specific promoters and promoters which are activated by
cellular proliferation, such as the thymidine kinase and
thymidylate synthase promoters. Other preferred promoters include
promoters which are activatable by infection with a virus, such as
the .alpha.- and .beta.-interferon promoters, and promoters which
are activatable by a hormone, such as estrogen. Other promoters
which can be used include the Moloney virus LTR, the CMV promoter,
and the mouse albumin promoter. A promoter may be constitutive or
inducible.
[0254] In another embodiment, naked polynucleotide molecules are
used as gene delivery vehicles, as described in WO 90/11092 and
U.S. Pat. No. 5,580,859. Such gene delivery vehicles can be either
growth factor DNA or RNA and, in certain embodiments, are linked to
killed adenovirus. Curiel et al., Hum. Gene. Ther. 3:147-154, 1992.
Other vehicles which can optionally be used include DNA-ligand (Wu
et al., J. Biol. Chem. 264:16985-16987, 1989), lipid-DNA
combinations (Felgner et al., Proc. Natl. Acad. Sci. USA 84:7413
7417, 1989), liposomes (Wang et al., Proc. Natl. Acad. Sci.
84:7851-7855, 1987) and microprojectilcs (Williams et al., Proc.
Natl. Acad. Sci. 88:2726-2730, 1991).
[0255] A gene delivery vehicle can optionally comprise viral
sequences such as a viral origin of replication or packaging
signal. These viral sequences can be selected from viruses such as
astrovirus, coronavirus, orthomyxovirus, papovavirus,
paramyxovirus, parvovirus, picornavirus, poxvirus, retrovirus,
togavirus or adenovirus. In a preferred embodiment, the growth
factor gene delivery vehicle is a recombinant retroviral vector.
Recombinant retroviruses and various uses thereof have been
described in numerous references including, for example, Mann et
al., Cell 33:153, 1983, Cane and Mulligan, Proc. Nat'l. Acad. Sci.
USA 81:6349, 1984. Miller et al., Human Gene Therapy 1:5-14, 1990,
U.S. Pat. Nos. 4,405,712, 4,861,719, and 4,980,289, and PCT
Application Nos. WO 89/02,468, WO 89/05,349, and WO 90/02,806.
Numerous retroviral gene delivery vehicles can be utilized in the
present invention, including for example those described in EP
0,415,731; WO 90/07936; WO 94/03622; WO 93/25698; WO 93/25234; U.S.
Pat. No. 5,219,740; WO 9311230; WO 9310218; Vile and Hart, Cancer
Res. 53:360-3864, 1993; Vile and Hart, Cancer Res. 53:962-967,
1993; Rami et al., Cancer Res. 53:83-88, 1993; Takamiya et al., J.
Neurosci. Res. 33:493-503, 1992; Baba et al., J. Neurosurg.
79:729-735, 1993 (U.S. Pat. No. 4,777,127, GB 2,200,651, EP
0,345,242 and WO91/02805).
[0256] Other viral vector systems that can be used to deliver a
polynucleotide of the present invention have been derived from
herpes virus, e.g., Herpes Simplex Virus (U.S. Pat. No. 5,631,236
by Woo et al., issued May 20, 1997 and WO 00/08191 by Neurovex),
vaccinia virus (Ridgeway (1988) Ridgeway, "Mammalian expression
vectors," In: Rodriguez R L, Denhardt D T, ed. Vectors: A survey of
molecular cloning vectors and their uses. Stoneham: Butterworth;
Baichwal and Sugden (1986) "Vectors for gene transfer derived from
animal DNA viruses: Transient and stable expression of transferred
genes," In: Kucherlapati R, ed. Gene transfer. New York: Plenum
Press: Coupar et al. (1988) Gene, 68:1-10), and several RNA
viruses. Preferred viruses include an alphavirus, a poxivirus, an
arena virus, a vaccinia virus, a polio virus, and the like. They
offer several attractive features for various mammalian cells
(Friedmann (1989) Science, 244:1275-1281; Ridgeway, 1988, supra;
Baichwal and Sugden, 1986, supra; Coupar et al., 1988; Horwich et
al. (1990) J. Virol., 64:642-650).
[0257] In other embodiments, target DNA in the genome can be
manipulated using well-known methods in the art. For example, the
target DNA in the genome can be manipulated by deletion, insertion,
and/or mutation are retroviral insertion, artificial chromosome
techniques, gene insertion, random insertion with tissue specific
promoters, gene targeting, transposable elements and/or any other
method for introducing foreign DNA or producing modified
DNA/modified nuclear DNA. Other modification techniques include
deleting DNA sequences from a genome and/or altering nuclear DNA
sequences. Nuclear DNA sequences, for example, may be altered by
site-directed mutagenesis.
[0258] In other embodiments, recombinant biomarker polypeptides,
and fragments thereof, can be administered to subjects. In some
embodiments, fusion proteins can be constructed and administered
which have enhanced biological properties. In addition, the
biomarker polypeptides, and fragment thereof, can be modified
according to well-known pharmacological methods in the art (e.g.,
pegylation, glycosylation, oligomerization, etc.) in order to
further enhance desirable biological activities, such as increased
bioavailability and decreased proteolytic degradation.
4. Clinical Efficacy
[0259] Clinical efficacy can be measured by any method known in the
art. For example, the response to a therapy, such as anti-immune
checkpoint and anti-angiogenesis combination therapies, relates to
any response of the cancer, e.g., a tumor, to the therapy,
preferably to a change in tumor mass and/or volume after initiation
of neoadjuvant or adjuvant chemotherapy. Tumor response may be
assessed in a neoadjuvant or adjuvant situation where the size of a
tumor after systemic intervention can be compared to the initial
size and dimensions as measured by CT, PET, mammogram, ultrasound
or palpation and the cellularity of a tumor can be estimated
histologically and compared to the cellularity of a tumor biopsy
taken before initiation of treatment. Response may also be assessed
by caliper measurement or pathological examination of the tumor
after biopsy or surgical resection. Response may be recorded in a
quantitative fashion like percentage change in tumor volume or
cellularity or using a semi-quantitative scoring system such as
residual cancer burden (Symmans et al., J Clin. Oncol. (2007)
25:4414-4422) or Miller-Payne score (Ogston et al., (2003) Breast
(Edinburgh, Scotland) 12:320-327) in a qualitative fashion like
"pathological complete response" (pCR), "clinical complete
remission" (cCR), "clinical partial remission" (cPR), "clinical
stable disease" (cSD), "clinical progressive disease" (cPD) or
other qualitative criteria. Assessment of tumor response may be
performed early after the onset of neoadjuvant or adjuvant therapy,
e.g., after a few hours, days, weeks or preferably ater a few
months. A typical endpoint for response assessment is upon
termination of neoadjuvant chemotherapy or upon surgical removal of
residual tumor cells and/or the tumor bed.
[0260] In some embodiments, clinical efficacy of the therapeutic
treatments described herein may be determined by measuring the
clinical benefit rate (CBR). The clinical benefit rate is measured
by determining the sum of the percentage of patients who are in
complete remission (CR), the number of patients who are in partial
remission (PR) and the number of patients having stable disease
(SD) at a time point at least 6 months out from the end of therapy.
The shorthand for this formula is CBR=CR+PR+SD over 6 months. In
some embodiments, the CBR for a particular anti-immune checkpoint
and anti-angiogenesis combination therapeutic regimen is at least
25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or
more.
[0261] Additional criteria for evaluating the response to
anti-immune checkpoint and anti-angiogenesis combination therapies
are related to "survival," which includes all of the following:
survival until mortality, also known as overall survival (wherein
said mortality may be either irrespective of cause or tumor
related); "recurrence-free survival" (wherein the term recurrence
shall include both localized and distant recurrence) metastasis
free survival; disease free survival (wherein the term disease
shall include cancer and diseases associated therewith). The length
of said survival may be calculated by reference to a defined start
point (e.g., time of diagnosis or start of treatment) and end point
(e.g., death, recurrence or metastasis). In addition, criteria for
efficacy of treatment can be expanded to include response to
chemotherapy, probability of survival, probability of metastasis
within a given time period, and probability of tumor
recurrence.
[0262] For example, in order to determine appropriate threshold
values, a particular anti-immune checkpoint and anti-angiogenesis
combination therapeutic regimen can be administered to a population
of subjects and the outcome can be correlated to biomarker
measurements that were determined prior to administration of any
anti-immune checkpoint and anti-angiogenesis combination therapy.
The outcome measurement may be pathologic response to therapy given
in the neoadjuvant setting. Alternatively, outcome measures, such
as overall survival and disease-free survival can be monitored over
a period of time for subjects following anti-immune checkpoint and
anti-angiogenesis combination therapy for whom biomarker
measurement values are known. In certain embodiments, the same
doses of anti-immune checkpoint and/or anti-angiogenesis
combination agents are administered to each subject. In related
embodiments, the doses administered are standard doses known in the
art for anti-immune checkpoint and/or anti-angiogenesis combination
agents. The period of time for which subjects are monitored can
vary. For example, subjects may be monitored for at least 2, 4, 6,
8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 45, 50, 55, or 60
months. Biomarker measurement threshold values that correlate to
outcome of an anti-immune checkpoint and anti-angiogenesis
combination therapy can be determined using methods such as those
described in the Examples section.
5. Further Uses and Methods of the Present Invention
[0263] The compositions described herein can be used in a variety
of diagnostic, prognostic, and therapeutic applications.
[0264] a. Screening Methods
[0265] One aspect of the present invention relates to screening
assays, including cell based assays. In one embodiment, the assays
provide a method for identifying whether a cancer is likely to
respond to anti-immune checkpoint and anti-angiogenesis combination
therapy and/or whether an agent can inhibit the growth of or kill a
cancer cell that is unlikely to respond to anti-immune checkpoint
and anti-angiogenesis combination therapy.
[0266] In one embodiment, the present invention relates to assays
for screening test agents which bind to, or modulate the biological
activity of, at least one antibody that specifically binds a
biomarker listed in Table 1, or antigen-binding fragment thereof.
In one embodiment, a method for identifying such an agent entails
determining the ability of the agent to modulate, e.g. enhance, the
at least one antibody that specifically binds a biomarker listed in
Table 1, or antigen-binding fragment thereof.
[0267] In one embodiment, an assay is a cell-based assay,
comprising contacting one or more cancer cells comprised within a B
cell population with a test agent and determining of the ability of
the test agent to increase the amount or activity of at least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof. Analyte proteins (or their
respective target polypeptides or molecules) can be coupled with a
radioisotope or enzymatic label such that binding can be determined
by detecting the labeled protein or molecule in a complex. For
example, the proteins can be labeled with .sup.125I, .sup.35S,
.sup.14C, or .sup.3H, either directly or indirectly, and the
radioisotope detected by direct counting of radio emission or by
scintillation counting. Alternatively, the proteins can be
enzymatically labeled with, for example, horseradish peroxidase,
alkaline phosphatase, or luciferase, and the enzymatic label
detected by determination of conversion of an appropriate substrate
to product. Determining interactions between reactants can also be
accomplished using standard binding or enzymatic analysis assays.
In one or more embodiments of the above described assay methods, it
may be desirable to immobilize polypeptides or molecules to
facilitate separation of complexed from uncomplexed forms of one or
both of the proteins or molecules, as well as to accommodate
automation of the assay.
[0268] Binding of a test agent to a target can be accomplished in
any vessel suitable for containing the reactants. Non-limiting
examples of such vessels include microtiter plates, test tubes, and
micro-centrifuge tubes. Immobilized forms of the antibodies of the
present invention can also include antibodies bound to a solid
phase like a porous, microporous (with an average pore diameter
less than about one micron) or macroporous (with an average pore
diameter of more than about 10 microns) material, such as a
membrane, cellulose, nitrocellulose, or glass fibers: a bead, such
as that made of agarose or polyacrylamide or latex; or a surface of
a dish, plate, or well, such as one made of polystyrene.
[0269] The present invention further pertains to novel agents
identified by the above-described screening assays. Accordingly, it
is within the scope of this invention to further use an agent
identified as described herein in an appropriate animal model. For
example, an agent identified as described herein can be used in an
animal model to determine the efficacy, toxicity, or side effects
of treatment with such an agent. Alternatively, an antibody
identified as described herein can be used in an animal model to
determine the mechanism of action of such an agent.
[0270] b. Predictive Medicine
[0271] The present invention also pertains to the field of
predictive medicine in which diagnostic assays, prognostic assays,
and monitoring clinical trials are used for prognostic (predictive)
purposes to thereby treat an individual prophylactically.
Accordingly, one aspect of the present invention relates to
diagnostic assays for determining the amount and/or activity level
of at least one antibody that specifically binds a biomarker listed
in Table 1, or antigen-binding fragment thereof, in the context of
a biological sample (e.g., blood, serum, cells, or tissue) to
thereby determine whether an individual afflicted with a cancer is
likely to respond to anti-immune checkpoint and anti-angiognesis
combination therapy, whether in an original or recurrent cancer.
Such assays can be used for prognostic or predictive purpose to
thereby prophylactically treat an individual prior to the onset or
after recurrence of a disorder characterized by or associated with
biomarker polypeptide, nucleic acid expression or activity. The
skilled artisan will appreciate that any method can determine at
least one antibody that specifically binds to one ore more
biomarkers listed in Table 1, or antigen-binding fragment thereof
(e.g., Gal-1, Gal-3, Gal-9, and combinations thereof).
[0272] Another aspect of the present invention pertains to
monitoring the influence of agents (e.g., drugs, compounds, and
small nucleic acid-based molecules) on the expression or activity
of at least one antibody that specifically binds a biomarker listed
in Table 1, or antigen-binding fragment thereof. These and other
agents are described in further detail in the following
sections.
[0273] The skilled artisan will also appreciated that, in certain
embodiments, the methods of the present invention implement a
computer program and computer system. 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
biomarker signal changes/profiles which can be used by a computer
system in implementing the methods of this invention. In certain
embodiments, a computer system receives biomarker expression data;
(ii) stores the data; and (iii) compares the data in any number of
ways described herein (e.g., analysis relative to appropriate
controls) to determine the state of informative biomarkers from
cancerous or pre-cancerous tissue. In other embodiments, a computer
system (i) compares the determined expression biomarker level to a
threshold value; and (ii) outputs an indication of whether said
biomarker level is significantly modulated (e.g., above or below)
the threshold value, or a phenotype based on said indication.
[0274] In certain embodiments, such computer systems are also
considered part of the present invention. 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. 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 w al. (2004) Bioinformatics 20, 1233-1240; radial
basis machine learning algorithms (RBM) known in the art).
[0275] The methods of the present 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.).
[0276] In certain embodiments, the computer comprises a database
for storage of biomarker data. Such stored profiles can be accessed
and used to perform comparisons of interest at a later point in
time. For example, biomarker expression profiles of a sample
derived from the non-cancerous tissue of a subject and/or profiles
generated from population-based distributions of informative loci
of interest in relevant populations of the same species can be
stored and later compared to that of a sample derived from the
cancerous tissue of the subject or tissue suspected of being
cancerous of the subject.
[0277] 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.
[0278] c. Diagnostic Assays
[0279] The present invention provides, in part, methods, systems,
and code for accurately classifying whether a biological sample is
associated with a cancer that is likely to respond to anti-immune
checkpoint and anti-angiogenesis combination therapy. In some
embodiments, the present invention is useful for classifying a
sample (e.g., from a subject) as associated with or at risk for
responding to or not responding to anti-immune checkpoint and
anti-angiogenesis combination therapy using a statistical algorithm
and/or empirical data (e.g., the amount or activity of at least one
antibody that specifically binds a biomarker listed in Table 1, or
antigen-binding fragment thereof).
[0280] An exemplary method for detecting the amount or activity of
at least one antibody that specifically binds a biomarker listed in
Table 1, or antigen-binding fragment thereof, and thus useful for
classifying whether a sample is likely or unlikely to respond to
anti-immune checkpoint and anti-angiogenesis combination therapy,
involves obtaining a biological sample from a test subject and
contacting the biological sample with an agent, such as a galectin
listed in Table 1, or a nucleic acid-binding agent like an
oligonucleotide, capable of detecting the amount or activity of the
at least one antibody that specifically binds a biomarker listed in
Table 1, or antigen-binding fragment thereof. In some embodiments,
at least one galectin is used, wherein two, three, four, five, six,
seven, eight, nine, ten, or more such galectins be used in
combination (e.g., Gal-1, Gal-3, and Gal-9, as well as other
galectins as negative controls) or in serial. Similarly, at least
one In certain instances, the statistical algorithm is a single
learning statistical classifier system. For example, a single
learning statistical classifier system can be used to classify a
sample as a based upon a prediction or probability value and the
presence or level of the biomarker. The use of a single learning
statistical classifier system typically classifies the sample as,
for example, a likely anti-immune checkpoint and anti-angiogenesis
combination therapy responder or progressor sample with a
sensitivity, specificity, positive predictive value, negative
predictive value, and/or overall accuracy of at least about 75%,
76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%.
[0281] Other suitable statistical algorithms are well known to
those of skill in the art. For example, learning statistical
classifier systems include a machine learning algorithmic technique
capable of adapting to complex data sets (e.g., panel of markers of
interest) and making decisions based upon such data sets. In some
embodiments, a single learning statistical classifier system such
as a classification tree (e.g., random forest) is used. In other
embodiments, a combination of 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
learning statistical classifier systems are used, preferably in
tandem. Examples of learning statistical classifier systems
include, but are not limited to, those using inductive learning
(e.g., decision/classification trees such as random forests,
classification and regression trees (C&RT), boosted trees,
etc.), Probably Approximately Correct (PAC) learning, connectionist
learning (e.g., neural networks (NN), artificial neural networks
(ANN), neuro fuzzy networks (NFN), network structures, perceptrons
such as multi-layer perceptrons, multi-layer feed-forward networks,
applications of neural networks, Bayesian learning in belief
networks, etc.), reinforcement learning (e.g., passive learning in
a known environment such as naive learning, adaptive dynamic
learning, and temporal difference learning, passive learning in an
unknown environment, active learning in an unknown environment,
learning action-value functions, applications of reinforcement
learning, etc.), and genetic algorithms and evolutionary
programming. Other learning statistical classifier systems include
support vector machines (e.g., Kernel methods), multivariate
adaptive regression splines (MARS), Levenberg-Marquardt algorithms,
Gauss-Newton algorithms, mixtures of Gaussians, gradient descent
algorithms, and learning vector quantization (LVQ). In certain
embodiments, the method of the present invention further comprises
sending the sample classification results to a clinician, e.g., an
oncologist.
[0282] In another embodiment, the diagnosis of a subject is
followed by administering to the individual a therapeutically
effective amount of a defined treatment based upon the
diagnosis.
[0283] In one embodiment, the methods further involve obtaining a
control biological sample (e.g., biological sample from a subject
who does not have a cancer or whose cancer is susceptible to
anti-immune checkpoint therapy), a biological sample from the
subject during remission, or a biological sample from the subject
during treatment for developing a cancer progressing despite
anti-immune checkpoint therapy.
[0284] d. Prognostic Assays
[0285] The diagnostic methods described herein can furthermore be
utilized to identify subjects having or at risk of developing a
cancer that is likely or unlikely to be responsive to anti-immune
checkpoint and anti-angiogenesis combination therapy. The assays
described herein, such as the preceding diagnostic assays or the
following assays, can be utilized to identify a subject having or
at risk of developing a disorder associated with a misregulation of
the amount or activity of at least one biomarker described in Table
1, such as in cancer. Alternatively, the prognostic assays can be
utilized to identify a subject having or at risk for developing a
disorder associated with a misregulation of the at least one
biomarker described in Table 1, such as in cancer. Furthermore, the
prognostic assays described herein can be used to determine whether
a subject can be administered an agent (e.g., an agonist,
antagonist, peptidomimetic, polypeptide, peptide, nucleic acid,
small molecule, or other drug candidate) to treat a disease or
disorder associated with the aberrant biomarker expression or
activity.
[0286] c. Treatment Methods
[0287] The compositions described herein (including anti-Gal-1,
anti-Gal-3, and/or anti-Gal-9 antibodies and derivatives and
conjugates thereof) can be used in a variety of in vitro and in
vivo therapeutic applications using the formulations and/or
combinations described herein. In one embodiment, anti-immune
checkpoint and anti-angiogenesis combination agents can be used to
tat cancers determined to be responsive thereto. Moreover, such
antibodies can be used in combination with other anti-cancer
agents. For example, antibodies that block the interaction between
VEGF, PD-L1, PD-L2, and/or CTLA-4 and their receptors (e.g., PD-L1
binding to PD-1, PD-L2 binding to PD-1, and the like) can be used
to treat cancer in subjects identified as likely responding
thereto.
6. Pharmaceutical Compositions
[0288] In another aspect, the present invention provides
pharmaceutically acceptable compositions which comprise a
therapeutically-effective amount of an agent that modulates (e.g.,
decreases) biomarker expression and/or activity, formulated
together with one or more pharmaceutically acceptable carriers
(additives) and/or diluents. As described in detail below, the
pharmaceutical compositions of the present invention may be
specially formulated for administration in solid or liquid form,
including those adapted for the following: (1) oral administration,
for example, drenches (aqueous or non-aqueous solutions or
suspensions), tablets, boluses, powders, granules, pastes; (2)
parenteral administration, for example, by subcutaneous,
intramuscular or intravenous injection as, for example, a sterile
solution or suspension; (3) topical application, for example, as a
cream, ointment or spray applied to the skin; (4) intravaginally or
intrarectally, for example, as a pessary, cream or foam; or (5)
aerosol, for example, as an aqueous aerosol, liposomal preparation
or solid particles containing the compound.
[0289] The phrase "therapeutically-effective amount" as used herein
means that amount of an agent that modulates (e.g., inhibits)
biomarker expression and/or activity, or expression and/or activity
of the complex, or composition comprising an agent that modulates
(e.g., inhibits) biomarker expression and/or activity, or
expression and/or activity of the complex, which is effective for
producing some desired therapeutic effect, e.g., cancer treatment,
at a reasonable benefit/risk ratio.
[0290] The phrase "pharmaceutically acceptable" is employed herein
to refer to those agents, materials, compositions, and/or dosage
forms which are, within the scope of sound medical judgment,
suitable for use in contact with the tissues of human beings and
animals without excessive toxicity, irritation, allergic response,
or other problem or complication, commensurate with a reasonable
benefit/risk ratio.
[0291] The phrase "pharmaceutically-acceptable carrier" as used
herein means a pharmaceutically-acceptable material, composition or
vehicle, such as a liquid or solid filler, diluent, excipient,
solvent or encapsulating material, involved in carrying or
transporting the subject chemical from one organ, or portion of the
body, to another organ, or portion of the body. Each carrier must
be "acceptable" in the sense of being compatible with the other
ingredients of the formulation and not injurious to the subject.
Some examples of materials which can serve as
pharmaceutically-acceptable carriers include: (1) sugars, such as
lactose, glucose and sucrose; (2) starches, such as corn starch and
potato starch; (3) cellulose, and its derivatives, such as sodium
carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4)
powdered tragacanth; (5) malt; (6) gelatin (7) talc; (8)
excipients, such as cocoa butter and suppository waxes; (9) oils,
such as peanut oil, cottonseed oil, safflower oil, sesame oil,
olive oil, corn oil and soybean oil; (10) glycols, such as
propylene glycol; (11) polyols, such as glycerin, sorbitol,
mannitol and polyethylene glycol; (12) esters, such as ethyl oleate
and ethyl laurate; (13) agar; (14) buffering agents, such as
magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16)
pyrogen-free water; (17) isotonic saline; (18) Ringer's solution;
(19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other
non-toxic compatible substances employed in pharmaceutical
formulations.
[0292] The term "pharmaceutically-acceptable salts" refers to the
relatively non-toxic, inorganic and organic acid addition salts of
the agents that modulates (e.g., inhibits) biomarker expression
and/or activity, or expression and/or activity of the complex
encompassed by the present invention. These salts can be prepared
in situ during the final isolation and purification of the
respiration uncoupling agents, or by separately reacting a purified
respiration uncoupling agent in its free base form with a suitable
organic or inorganic acid, and isolating the salt thus formed.
Representative salts include the hydrobromide, hydrochloride,
sulfate, bisulfate, phosphate, nitrate, acetate, valerate, oleate,
palmitate, stearate, laurate, benzoate, lactate, phosphate,
tosylate, citrate, maleate, fumarate, succinate, tartrate,
napthylate, mesylate, glucoheptonate, lactobionate, and
laurylsulphonate salts and the like (See, for example, Berge w al.
(1977) "Pharmaceutical Salts", J. Pharm. Sci. 66:1-19).
[0293] In other cases, the agents useful in the methods of the
present invention may contain one or more acidic functional groups
and, thus, are capable of forming pharmaceutically-acceptable salts
with pharmaceutically-acceptable bases. The term
"pharmaceutically-acceptable salts" in these instances refers to
the relatively non-toxic, inorganic and organic base addition salts
of agents that modulates (e.g., inhibits) biomarker expression
and/or activity, or expression and/or activity of the complex.
These salts can likewise be prepared in situ during the final
isolation and purification of the respiration uncoupling agents, or
by separately reacting the purified respiration uncoupling agent in
its free acid form with a suitable base, such as the hydroxide,
carbonate or bicarbonate of a pharmaceutically-acceptable metal
cation, with ammonia, or with a pharmaceutically-acceptable organic
primary, secondary or tertiary amine. Representative alkali or
alkaline earth salts include the lithium, sodium, potassium,
calcium, magnesium, and aluminum salts and the like. Representative
organic amines useful for the formation of base addition salts
include ethylamine, diethylamine, ethylenediamine, ethanolamine,
diethanolamine, piperazine and the like (see, for example, Berge et
al., supra).
[0294] Wetting agents, emulsifiers and lubricants, such as sodium
lauryl sulfate and magnesium stearate, as well as coloring agents,
release agents, coating agents, sweetening, flavoring and perfuming
agents, preservatives and antioxidants can also be present in the
compositions.
[0295] Examples of pharmaceutically-acceptable antioxidants
include: (1) water soluble antioxidants, such as ascorbic acid,
cysteine hydrochloride, sodium bisulfate, sodium metabisulfite,
sodium sulfite and the like; (2) oil-soluble antioxidants, such as
ascorbyl palmitate, butylated hydroxyanisole (BUA), butylated
hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol,
and the like; and (3) metal chelating agents, such as citric acid,
ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid,
phosphoric acid, and the like.
[0296] Formulations useful in the methods of the present invention
include those suitable for oral, nasal, topical (including buccal
and sublingual), rectal, vaginal, aerosol and/or parenteral
administration. The formulations may conveniently be presented in
unit dosage form and may be prepared by any methods well known in
the art of pharmacy. The amount of active ingredient which can be
combined with a carrier material to produce a single dosage form
will vary depending upon the host being treated, the particular
mode of administration. The amount of active ingredient, which can
be combined with a carrier material to produce a single dosage form
will generally be that amount of the compound which produces a
therapeutic effect. Generally, out of one hundred percent, this
amount will range from about 1 percent to about ninety-nine percent
of active ingredient, preferably from about 5 percent to about 70
percent, most preferably from about 10 percent to about 30
percent.
[0297] Methods of preparing these formulations or compositions
include the step of bringing into association an agent that
modulates (e.g., inhibits) biomarker expression and/or activity,
with the carrier and, optionally, one or more accessory
ingredients. In general, the formulations are prepared by uniformly
and intimately bringing into association a respiration uncoupling
agent with liquid carriers, or finely divided solid carriers, or
both, and then, if necessary, shaping the product.
[0298] Formulations suitable for oral administration may be in the
form of capsules, cachets, pills, tablets, lozenges (using a
flavored basis, usually sucrose and acacia or tragacanth), powders,
granules, or as a solution or a suspension in an aqueous or
non-aqueous liquid, or as an oil-in-water or water-in-oil liquid
emulsion, or as an elixir or syrup, or as pastilles (using an inert
base, such as gelatin and glycerin, or sucrose and acacia) and/or
as mouth washes and the like, each containing a predetermined
amount of a respiration uncoupling agent as an active ingredient. A
compound may also be administered as a bolus, electuary or
paste.
[0299] In solid dosage forms for oral administration (capsules,
tablets, pills, dragees, powders, granules and the like), the
active ingredient is mixed with one or more
pharmaceutically-acceptable carriers, such as sodium citrate or
dicalcium phosphate, and/or any of the following: (1) fillers or
extenders, such as starches, lactose, sucrose, glucose, mannitol,
and/or silicic acid; (2) binders, such as, for example,
carboxyethylcellulose, alginates, gelatin, polyvinyl pyrrolidone,
sucrose and/or acacia; (3) humectants, such as glycerol; (4)
disintegrating agents, such as agar-agar, calcium carbonate, potato
or tapioca starch, alginic acid, certain silicates, and sodium
carbonate; (5) solution retarding agents, such as paraffin; (6)
absorption accelerators, such as quaternary ammonium compounds; (7)
wetting agents, such as, for example, acetyl alcohol and glycerol
monostearate; (8) absorbents, such as kaolin and bentonite clay;
(9) lubricants, such a talc, calcium stearate, magnesium stearate,
solid polyethylene glycols, sodium lauryl sulfate, and mixtures
thereof; and (10) coloring agents. In the case of capsules, tablets
and pills, the pharmaceutical compositions may also comprise
buffering agents. Solid compositions of a similar type may also be
employed as fillers in soft and hard-filled gelatin capsules using
such excipients as lactose or milk sugars, as well as high
molecular weight polyethylene glycols and the like.
[0300] A tablet may be made by compression or molding, optionally
with one or more accessory ingredients. Compressed tablets may be
prepared using binder (for example, gelatin or hydroxypropylmethyl
cellulose), lubricant, inert diluent, preservative, disintegrant
(for example, sodium starch glycolate or cross-linked sodium
carboxymethyl cellulose), surface-active or dispersing agent.
Molded tablets may be made by molding in a suitable machine a
mixture of the powdered peptide or peptidomimetic moistened with an
inert liquid diluent.
[0301] Tablets, and other solid dosage forms, such as dragees,
capsules, pills and granules, may optionally be scored or prepared
with coatings and shells, such as enteric coatings and other
coatings well known in the pharmaceutical-formulating art. They may
also be formulated so as to provide slow or controlled release of
the active ingredient therein using, for example,
hydroxypropylmethyl cellulose in varying proportions to provide the
desired release profile, other polymer matrices, liposomes and/or
microspheres. They may be sterilized by, for example, filtration
through a bacteria-retaining filter, or by incorporating
sterilizing agents in the form of sterile solid compositions, which
can be dissolved in sterile water, or some other sterile injectable
medium immediately before use. These compositions may also
optionally contain opacifying agents and may be of a composition
that they release the active ingredient(s) only, or preferentially,
in a certain portion of the gastrointestinal tract, optionally, in
a delayed manner. Examples of embedding compositions, which can be
used include polymeric substances and waxes. The active ingredient
can also be in micro-encapsulated form, if appropriate, with one or
more of the above-described excipients.
[0302] Liquid dosage forms for oral administration include
pharmaceutically acceptable emulsions, microemulsions, solutions,
suspensions, syrups and elixirs. In addition to the active
ingredient, the liquid dosage forms may contain inert diluents
commonly used in the art, such as, for example, water or other
solvents, solubilizing agents and emulsifiers, such as ethyl
alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl
alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol,
oils (in particular, cottonseed, groundnut, corn, germ, olive,
castor and sesame oils), glycerol, tetrahydrofuryl alcohol,
polyethylene glycols and fatty acid esters of sorbitan, and
mixtures thereof.
[0303] Besides inert diluents, the oral compositions can also
include adjuvants such as wetting agents, emulsifying and
suspending agents, sweetening, flavoring, coloring, perfuming and
preservative agents.
[0304] Suspensions, in addition to the active agent may contain
suspending agents as, for example, ethoxylated isostearyl alcohols,
polyoxyethylene sorbitol and sorbitan esters, microcrystalline
cellulose, aluminum metahydroxide, bentonite, agar-agar and
tragacanth, and mixtures thereof.
[0305] Formulations for rectal or vaginal administration may be
presented as a suppository, which may be prepared by mixing one or
more respiration uncoupling agents with one or more suitable
nonirritating excipients or carriers comprising, for example, cocoa
butter, polyethylene glycol, a suppository wax or a salicylate, and
which is solid at room temperature, but liquid at body temperature
and, therefore, will melt in the rectum or vaginal cavity and
release the active agent.
[0306] Formulations which are suitable for vaginal administration
also include pessaries, tampons, creams, gels, pastes, foams or
spray formulations containing such carriers as are known in the art
to be appropriate.
[0307] Dosage forms for the topical or transdermal administration
of an agent that modulates (e.g., inhibits) biomarker expression
and/or activity include powders, sprays, ointments, pastes, creams,
lotions, gets, solutions, patches and inhalants. The active
component may be mixed under sterile conditions with a
pharmaceutically-acceptable carrier, and with any preservatives,
buffers, or propellants which may be required.
[0308] The ointments, pastes, creams and gels may contain, in
addition to a respiration uncoupling agent, excipients, such as
animal and vegetable fats, oils, waxes, paraffins, starch,
tragacanth, cellulose derivatives, polyethylene glycols, silicones,
bentonites, silicic acid, talc and zinc oxide, or mixtures
thereof.
[0309] Powders and sprays can contain, in addition to an agent that
modulates (e.g., inhibits) biomarker expression and/or activity,
excipients such as lactose, talc, silicic acid, aluminum hydroxide,
calcium silicates and polyamide powder, or mixtures of these
substances. Sprays can additionally contain customary propellants,
such as chlorofluorohydrocarbons and volatile unsubstituted
hydrocarbons, such as butane and propane.
[0310] The agent that modulates (e.g., inhibits) biomarker
expression and/or activity, can be alternatively administered by
aerosol. This is accomplished by preparing an aqueous aerosol,
liposomal preparation or solid particles containing the compound. A
nonaqueous (e.g., fluorocarbon propellant) suspension could be
used. Some nebulizers are preferred because they minimize exposing
the agent to shear, which can result in degradation of the
compound.
[0311] Ordinarily, an aqueous aerosol is made by formulating an
aqueous solution or suspension of the agent together with
conventional pharmaceutically acceptable carriers and stabilizers.
The carriers and stabilizers vary with the requirements of the
particular compound, but typically include nonionic surfactants
(Tweens, Pluronics, or polyethylene glycol), innocuous proteins
like serum albumin, sorbitan esters, oleic acid, lecithin, amino
acids such as glycine, buffers, salts, sugars or sugar alcohols.
Aerosols generally are prepared from isotonic solutions.
[0312] Transdermal patches have the added advantage of providing
controlled delivery of a respiration uncoupling agent to the body.
Such dosage forms can be made by dissolving or dispersing the agent
in the proper medium. Absorption enhancers can also be used to
increase the flux of the peptidomimetic across the skin. The rate
of such flux can be controlled by either providing a rate
controlling membrane or dispersing the peptidomimetic in a polymer
matrix or gel.
[0313] Ophthalmic formulations, eye ointments, powders, solutions
and the like, are also contemplated as being within the scope of
this invention.
[0314] Pharmaceutical compositions of this invention suitable for
parenteral administration comprise one or more respiration
uncoupling agents in combination with one or more
pharmaceutically-acceptable sterile isotonic aqueous or nonaqueous
solutions, dispersions, suspensions or emulsions, or sterile
powders which may be reconstituted into sterile injectable
solutions or dispersions just prior to use, which may contain
antioxidants, buffers, bacteriostats, solutes which render the
formulation isotonic with the blood of the intended recipient or
suspending or thickening agents.
[0315] Examples of suitable aqueous and nonaqueous carriers which
may be employed in the pharmaceutical compositions of the present
invention include water, ethanol, polyols (such as glycerol,
propylene glycol, polyethylene glycol, and the like), and suitable
mixtures thereof, vegetable oils, such as olive oil, and injectable
organic esters, such as ethyl oleate. Proper fluidity can be
maintained, for example, by the use of coating materials, such as
lecithin, by the maintenance of the required particle size in the
case of dispersions, and by the use of surfactants.
[0316] These compositions may also contain adjuvants such as
preservatives, wetting agents, emulsifying agents and dispersing
agents. Prevention of the action of microorganisms may be ensured
by the inclusion of various antibacterial and antifungal agents,
for example, paraben, chlorobutanol, phenol sorbic acid, and the
like. It may also be desirable to include isotonic agents, such as
sugars, sodium chloride, and the like into the compositions. In
addition, prolonged absorption of the injectable pharmaceutical
form may be brought about by the inclusion of agents which delay
absorption such as aluminum monostearate and gelatin.
[0317] In some cases, in order to prolong the effect of a drug, it
is desirable to slow the absorption of the drug from subcutaneous
or intramuscular injection. This may be accomplished by the use of
a liquid suspension of crystalline or amorphous material having
poor water solubility. The rate of absorption of the drug then
depends upon its rate of dissolution, which, in turn, may depend
upon crystal size and crystalline form. Alternatively, delayed
absorption of a parenterally-administered drug form is accomplished
by dissolving or suspending the drug in an oil vehicle.
[0318] Injectable depot forms are made by forming microencapsule
matrices of an agent that modulates (e.g., inhibits) biomarker
expression and/or activity, in biodegradable polymers such as
polylactide-polyglycolide. Depending on the ratio of drug to
polymer, and the nature of the particular polymer employed, the
rate of drug release can be controlled. Examples of other
biodegradable polymers include poly(orthoesters) and
poly(anhydrides). Depot injectable formulations are also prepared
by entrapping the drug in liposomes or microemulsions, which are
compatible with body tissue.
[0319] When the respiration uncoupling agents of the present
invention are administered as pharmaceuticals, to humans and
animals, they can be given per se or as a pharmaceutical
composition containing, for example, 0.1 to 99.5% (more preferably,
0.5 to 90%) of active ingredient in combination with a
pharmaceutically acceptable carrier.
[0320] Actual dosage levels of the active ingredients in the
pharmaceutical compositions of this invention may be determined by
the methods of the present invention so as to obtain an amount of
the active ingredient, which is effective to achieve the desired
therapeutic response for a particular subject, composition, and
mode of administration, without being toxic to the subject.
[0321] The nucleic acid molecules of the present invention can be
inserted into vectors and used as gene therapy vectors. Gene
therapy vectors can be delivered to a subject by, for example,
intravenous injection, local administration (see U.S. Pat. No.
5,328,470) or by stereotactic injection (see e.g., Chen et al.
(1994) Proc. Natl. Acad. Sci. USA 91:3054 3057). The pharmaceutical
preparation of the gene therapy vector can include the gene therapy
vector in an acceptable diluent, or can comprise a slow release
matrix in which the gene delivery vehicle is imbedded.
Alternatively, where the complete gene delivery vector can be
produced intact from recombinant cells, e.g., retroviral vectors,
the pharmaceutical preparation can include one or more cells which
produce the gene delivery system.
[0322] The present invention also encompasses kits for detecting
and/or modulating biomarkers described herein. A kit of the present
invention may also include instructional materials disclosing or
describing the use of the kit or an antibody of the disclosed
invention in a method of the disclosed invention as provided
herein. A kit may also include additional components to facilitate
the particular application for which the kit is designed. For
example, a kit may additionally contain means of detecting the
label (e.g., enzyme substrates for enzymatic labels, filter sets to
detect fluorescent labels, appropriate secondary labels such as a
sheep anti-mouse-HRP, etc.) and reagents necessary for controls
(e.g., control biological samples or standards). A kit may
additionally include buffers and other reagents recognized for use
in a method of the disclosed invention. Non-limiting examples
include agents to reduce non-specific binding, such as a carrier
protein or a detergent.
EXEMPLIFICATION
[0323] This invention is further illustrated by the following
examples, which should not be construed as limiting.
Example 1: Materials and Methods for Examples 2-4
[0324] a. Collection of Patient Plasma
[0325] Blood samples were collected from the patients enrolled in
the phase 1 clinical trial of Ipi-Bev (Hodi et al. (2014) Cancer
Immunol. Res. 2:632-642). Blood samples were collected in
Vacutainer.TM. tubes containing heparin. They were diluted with
equal volume of RPMI1640 and subjected to Ficoll density gradient
separation of PBMC. The supernatant above the PBMC layer was
collected and used as plasma. Aliquots of plasma were stored at
.ltoreq.-20.degree. C.
[0326] b. Screening Protein Microarray with Patient Plasma
Samples
[0327] Antibodies presented in the post sera of 4 patients (3
Ipi-Bev patients and 1 Ipi alone patient) were screened using
ProtoArray.RTM. Human Protein Microarray V5 (Life Technologies,
Grand Island, N.Y.) as guided by the manufacturer. Briefly, the
proteins arrays were blocked in the synthetic blocking solutions
(Life Technologies) for 1 hour and then incubated with plasma
samples diluted in the blocking solution (1:500) overnight at
4.degree. C. The arrays were washed and detected with Alexa
Fluor.RTM. 647 goat anti-human IgG (Life Technologies). The arrays
were scanned and image data were acquired using a GenePix.RTM.
scanner (Molecular Devices). Image data were analyzed using the
ProtoArray.RTM. Prospector data analysis software (Life
Technologies). Potential antibody targets were identified using Z
factor cutoff of 0.4 as recommended by the manufacturer.
[0328] c. Detection of Galectin Antibodies in Patient Plasma
Samples by Western Blot Analysis Measurement
[0329] The presence of galectin-1, -3 and -9 antibodies in patient
serum samples were further confirmed by Western blot analysis (Hodi
el a. (2014) Cancer Immunol. Res. 2:632-642). Briefly, recombinant
human galectin-1, -3 and -9 (R&D Systems. Minneapolis, Minn.)
were run in SDS gels and transferred onto PVDF membranes. The
membranes was blocked with 5% fatty acid free, nuclease- and
protease free BAS (Calbiochem, La Jolla, Calif.) in PBS overnight
and then incubated with plasma samples that were diluted by 2,000
fold in PBS with 2% fatty acid free, nuclease- and protease free
BAS overnight. Antibodies bound to galectins were detected with HRP
conjugated goat anti-human IgG antibody (Life Technologies) and
visualized with electrochemiluminescence (ECL). In order to compare
antibody levels in pre- and post-sera, membranes with galectins
were incubated with pre-sera and post-sera samples from the same
patients in parallel.
[0330] d. Quantitative Analysis of Gal-1, -3 and -9 Antibody in
Patient Plasma Samples Using ELISA
[0331] Recombinant human Gal-1, -3 and -9 proteins and a His tag
with 8 His residues (used as background) were coated in TBS onto
96-well plates overnight respectively. The plates were blocked with
a BSA free blocking solution (Thermo Scientific, Tewksbury, Mass.)
for 1 hour at room temperature (RT). Plasma samples were diluted
(1:1,000 to 1:60,000) in the blocking solution containing 0.1%
Tween-20 and incubated with the coated galectins or His tag for 1
hour at 4.degree. C. After wash with PBST (PBS plus 0.05%
Tween-20), the wells were incubated with Rabbit F(ab')2 HPR
anti-human IgG (Southern Biotech, Birmingham. Ala.) diluted at
1:2,000 in the blocking solution containing 0.1% Tween-20 for 1
hour at RT. After washing thoroughly with PBST, the signal was
amplified using the ELAST.RTM. ELISA Amplification System as guided
by the manufacturer (PerkinElmer, Waltham, Mass.). Briefly, the
washed wells were incubated with diluted biotinyl-tyramide for 15
minutes at RT. After thorough washing with PBST, the wells were
incubated with streptavidin-HRP diluted in PBST+1% BSA for 30
minutes at RT. The wells were washed thoroughly with PBST and
developed with TMB (Dako, Carpinteria, Calif.). The reaction was
stopped with 1 N HCl. OD at 450 and 570 nm were recorded using a
microplate reader. Galectin antibody titer (OD.sub.Gal) and
background (OD.sub.His) was calculated by subtracting OD.sub.570
from OD.sub.450. Fold change of galectin antibody titers in
response to treatment were calculated using the following formula:
Fold
change=(OD.sub.Gal-OD.sub.His).sub.Post/(OD.sub.Gal-OD.sub.His).sub.Pre.
An increase was considered as significant when the fold change was
.gtoreq.1.45.
[0332] c. Preparation of Biotinylated his-Avi-SUMO Tagged
Galectin-1 and -3 (HAS-Gal-1 and -Gal-3)
[0333] The Expresso.RTM. Biotin Cloning & Expression System
(Lucigen, Middleton. Wis.) for production of biotinylated proteins
with His, Avi and SUMO tags was used. Primer design and PCR
amplification to incorporate His, Avi and SUMO tags into galectin
cDNA were performed according to instructions provided by the
manufacturer. The primers used for generation of galectin-1 and -3
fusion proteins by PCR include: Gal-1 sense:
5'-CGCGAACAGATTGGAGGTgcttgtggtctggtcgcagcaac; Gal-1 antisense:
5'-GTGGCGGCCGCTCTATTAGtcaaaggccacacatttgatett; Ga-3 sense:
5'-CGCGAACAGATTGGAGGTgcagacaatitttcgctccatgat; and Gal-3 antisense:
5'-GTGGCGGCCGCTCTATTAGTatcatggtatagaagcactggt. The resulting PCR
fragments were mixed with the pAviTag N-His Vector (Lucigen) and
used to transform BIOTIN XCell.TM. F' Chemically Competent Cells
(Lucigen). The insertion of galectin cDNAs with tags were confirmed
by PCR and DNA sequencing. Single colonics were picked up and grown
in LB overnight. Cell pellets were suspended in PBS with 500 mM
NaCl and subjected to sonication. After extraction with 1% Triton
X-100, His-tagged proteins were purified using HisPur Ni-NTA Resin
(Thermo Scientific) following the instructions provided by the
manufacturer. Proteins were eluted using PBS plus 250 mM Imidazole,
dialyzed against PBS and stored in aliquots at -20.degree. C.
Protein identity and biotinylation were confirmed by Western
analysis and ELISA using commercial Gal-1 and -3 antibodies
(R&D Systems) and streptavidin-HRP respectively. HAS-Gal-1 and
-3 were used to show that serum anti-Gal-1 and anti-Gal-3
antibodies are functional and capable of inhibiting binding of
Gal-1 and Gal-3 to CD45.
[0334] f. Affinity Purification of Anti-Gal-1 Antibody from Patient
Plasma
[0335] Recombinant Gal-1 (6 .mu.g) was coupled to the activated NHS
magnet beads (40 .mu.l) as guided by the manufacturer (Thermo
Scientific). Plasma samples (400 .mu.l) were diluted with PBS (800
.mu.l) and incubated with the Gal-1 coupled beads with rotation for
2 hours at RT. The beads were pulled down with a magnet and washed
with PBS 5 times and the antibodies bound were eluted from the
beads with 0.1 M glycine (pH 2.5) and neutralized with 1/10 volume
of 1 M Tris-Cl (pH 9.0). The antibody fractions were concentrated
using an Amicon Ultra filter (Millipore, Billerica, Mass.) and
stored in PBS supplemented with 0.02% BSA at 4.degree. C.
Anti-Gal-1 IgG content was determined by ELISA using normal human
IgG (Life Technologies) as standards.
[0336] g. Absorption of Anti-Gal-3 and -9 Antibodies from Plasma
Samples
[0337] Recombinant Gal-3, Gal-9, or BSA (as control) was coated
onto 96-well plates in the coating buffer by incubation overnight
at 4.degree. C. The coated plates were washed with PBS and blocked
with 2.5% BSA in PBS overnight. Plasma samples were diluted with 3
volumes of PBS and incubated in the control wells or Gal-3 or -9
coated wells overnight at 4.degree. C. This incubation was repeated
two more times in fresh BSA, Gal-3 or Gal-9 coated wells. The
plasma samples were collected and used in Gal-3/CD45 interaction or
Gal-9 induced T cell apoptosis assays.
[0338] h. Binding of Galectin-1 and Galectin-3 to CD45
[0339] CD45 (R&D Systems; 25 ng/well for Gal-1 binding or 50
ng/well for Gal-3 binding) was coated onto 96-well plates at
4.degree. C. overnight. The plates were blocked with 2.5% fatty
acid free, nuclease- and protease free BSA in PBS for 1 hour at RT.
Biotinylated HAS-Gal-1 (25 ng in 50 .mu.l PBS plus 0.05% Tween-20
and 0.1% BSA) or HAS-Gal-3 (50 ng in 50 .mu.l PBS containing 0.1%
BSA) was added to each well coated with CD45 and incubated for 1
hour at RT. The plates were washed with PBS (for Gal-3) or PBST
(for Gal-1) and incubated with streptavidin-HRP diluted in PBS (for
Gal-3) or PBST (for Gal-1) with 1% BSA for 1 hour at RT. After
thorough washing with PBS or PBST, substrate TBM (Sigma, St Louis,
Mo.) was added to each well and incubated for appropriate time. The
reaction was stopped with 0.1 N HCl. OD450 and OD570 were measured
in a microplate reader. In some experiments, HAS-Gal-1 was
pre-incubated with 60 ng of normal human IgG or affinity purified
patient plasma anti-Gal-1 antibody for 1 hour at RT and HAS-Gal-3
was pre-incubated with patient plasma or plasma that had been
depleted of anti-Gal-3 antibody for 1 hour at 4.degree. C. before
addition to CD45 coated plates.
[0340] i. T Cell Preparation and Expansion
[0341] PBMC were isolated from cord blood of normal donors using
Ficoll.TM. density gradient separation. T cells were enriched from
PBMC using the Dynabeads.RTM. Untouched.TM. Human T cells kit
according to the instructions provided by the manufacturer (Life
Technologies). T cells were activated and expanded in RPMI1640
containing 10% FBS and PHA (5 .mu.g/ml).
[0342] j. T Cell Apoptosis Assay
[0343] For functional analysis of anti-Gal-9 antibody in plasma,
galectin-9 (0.1 .mu.g) was preincubated with plasma pre-absorbed
with PBS or Gal-9 in U bottomed 96-well plate for 2 hours at
4.degree. C. PHA-activated T cells (2.times.10.sup.5 cells) were
added to each well and incubated for 16 hours at 37.degree. C. and
5% CO.sub.2. Apoptotic cells were detected by staining with
FITC-Annexin V and PI and FACS analysis.
[0344] k. Statistical Analysis
[0345] GraphPad Prism 6 software was used to determine Log-rank
(Mantel-Cox) test of association of antibody increase with patient
overall survival. The Student t-test was used for statistical
analysis of Gal-1/CD45 and Gal-3/CD45 binding and Gal-9 induced T
cell apoptosis. Differences with P<0.05 were considered as being
significant.
Example 2: Ipilimumab Plus Bevacizumab Treatment Potentiates
Humoral Immune Response to Gal-1, Gal-3, and Gal-9
[0346] Clinical data indicate synergistic effect of Ipi plus Bev on
advanced melanoma (metastatic melanoma) patients (Hodi et al.
(2014) Cancer Immunol. Res. 2:632-642). To understand the acting
mechanism(s) behind this synergy, it was determined whether Ipi-Bev
induced humoral immune response in patients using Western blot
analysis of whole lysates of cultured melanoma cells, tumor
associated endothelial cells (TEC), and mesenchymal stem cells
(TMSC) with pre- and post-plasma samples of the patients. A number
of proteins in the melanoma cells, TEC, and TMSC were recognized by
antibodies in the pre-treatment samples. Importantly, new antibody
recognitions or enhanced antibody recognitions were detected with
the post-treatment samples. These findings indicate that humoral
immune response was indeed triggered as function of Ipi-Bev
therapy.
[0347] To identify the reactive antibodies, protein microarrays
with .about.9,000 distinct proteins were screened with the
post-treatment plasma samples from 3 Ipi-Bev patients and 1 Ipi
alone patient. Thousands of hits were generated based on
Z-Factor.gtoreq.0.4 as recommended by the manufacturer. Because
only functional humoral immune responses are relevant to clinical
outcomes, antibodies that recognize membrane receptors,
extracellular proteins, and/or secreted proteins known to promote
tumor growth, angiogenesis, metastasis, and/or immune suppression
and evasion were of interest. Among the hits generated from these
screenings, antibodies recognizing galectin-1 and -3 were found in
post-sera of 3 and 2 out of 4 patients, respectively.
[0348] Gal-1 and Gal-3 are of particularly interest because they
are well documented to play a key role in tumor growth and
progression, angiogenesis, and immune escape. Therefore, it was
determined whether Gal-1 and Gal-3 Ig titers changed as a function
of Ipi-Bev treatment using Western blot analysis and ELISA. Gal-9
was not included in the protein microarray, but given the biology
of galectin-9 in immune regulation, galectin-9 antibody levels in
sera from the patients was also determined. Varying levels of
Gal-1, -3 and -9 Ig were detected in the pre-treatment plasma
samples and Ipi-Bev induced antibody increases were detected in the
post-treatment samples by both Western blot analysis and ELISA
(FIGS. 1A-1C). An increase in antibody was considered as
significant when the fold change (post-/pre-ratio).gtoreq.1.5.
Based on this cut-off, an increase in Gal-1 antibody level was
detected in 37.2% (16 out of 43) of the Ipi-Bev patients compared
to 15.8% (6 out of 38) of the Ipi patients as function of the
treatment (FIG. 1D). Increased Gal-3 antibody levels were seen in
32.6% (14 out of 43) of the Ipi-Bev patients, while in 26.3% (10
out of 38) of the Ipi patients (FIG. 1D). These findings indicate
that humoral immune responses to Gal-1 and -3 might occur more
frequently in Ipi-Bev patients (synergistic therapeutic effect)
than Ipi alone patients. An increase by 30% or more was considered
a significant change for Gal-9 antibodies. Based on this cut-off
value, 18.4% (7 out of 38) and 23.3% (10 out of 43) of the Ipi
alone and Ipi-Bev patients displayed an increase in Gal-9 antibody
levels, respectively (FIG. 1D).
Example 3: Humoral Immune Response to Gal-1, -3 and -9 is
Associated with Clinical Response and Outcomes to Ipi-Bev
Therapy
[0349] It was next examined whether enhanced humoral immune
response was associated with clinical outcomes to Ipi-Bev therapy.
Among the 16 patients with increased Gal-1 Ig, 5 (31.3%), 8(50%)
and 3 (18.8%) had CR/PR, SD, and PD respectively (FIG. 2A). Gal-1
Ig increase was observed in 62.3% (5 out of 8) of CR and PR
patients, 36.4% (8 out of 22) of SD patients, and 23.1% (3 out of
13) of PD patients as function of Ipi-Bev treatment. The mean fold
change of Gal-1 antibody in the CRPR group was significantly
greater than that of PD patients (2.51.+-.0.38 vs. 1.33.+-.0.29,
p=0.039). The median survival of the patients with the Gal-1 Ig
fold change <1.5 was 70 weeks, while that of patients with Gal-1
Ig fold change .gtoreq.1.5 was undefined because >50% of the
patients were still alive at the time of this analysis (1
months-.infin.) (FIG. 3A). Among the 14 patients with increased
Gal-3 Ig, 7 (50%), 5 (35.7%), and 2 (14.3%) had CR/PR, SD, and PD
respectively (FIG. 2B). Gal-3 Ig increase was observed in 87.5% (7
out of 8) of CR and PR patients, 22.7% (5 out of 22) of SD
patients, and 15.4%(2 out of 13) of PD patients as function of
Ipi-Bev treatment. The median survival of the patients with the
Gal-3 Ig fold change <1.5 was 73 weeks, while that of patients
with Gal-3 Ig fold change .gtoreq.1.5 was undefined (FIG. 3B).
Among the 10 patients with increased Gal-9 Ig, 5 (50%), 5 (50%),
and 0 (0%) had CR/PR, SD, and PD respectively (FIG. 2C). Gal-9 Ig
increase was observed in 71.4% (5 out of 7) of CR and PR patients,
22.7% (5 out of 22) of SD patients, and 0% (0 out of 13) of PD
patients as function of Ipi-Bev treatment. The median survival of
the patients with the Gal-9Ig fold change <1.3 was 70 weeks,
while that of patients with Gal-9Ig fold change .gtoreq.1.3 was
undefined (FIG. 3C). Gal-3 and Gal-9 antibody increase was
significantly associated with higher response rate, respectively
(FIG. 4). A trend of association of Gal-1 antibody increase with
response rate was also noted (FIG. 4). These findings indicate that
enhanced humoral immune response to Gal-1, -3 and -9 was associated
with better clinical response and overall survival of the
patients.
Example 4: Anti-Gal-1. Anti-Gal-3, and Anti-Gal-9 Antibodies are
Functional
[0350] It is well known that Gal-1, -3 and -9 promote angiogenesis,
tumor growth and immunosuppression. In order to determine if
Ipi-Bev induced humeral responses to these galectins are
functionally relevant, it was determined whether circulating Gal-1,
-3 and -9 antibodies could block biological activities of the
galectins. Gal-1, -3 and -9 are well known to induce T cell
apoptosis. As binding of Gal-1 or -3 to CD45 induces T cell
apoptosis, it was examined whether antibodies recognizing Gal-1 or
-3 in the serum of responders could block binding of these
galectins to CD45. In order to assess binding of Gal-1 or Gal-3 to
CD45, Gal-1 and Gal-3 were expressed in a form having
His-SUMO-Biotinylation tags at the N-terminus (HAS-Gal-1 and
HAS-Gal-3) in bacterial cells. These fusion proteins were
biotinylated and recognized by commercial Gal-1 and -3 antibodies
and streptavidin, respectively. Binding of HAS-Gal-1 to CD45 was
confirmed to be Gal-1- and glycan-dependent, as this binding was
blocked by commercial anti-Gal-1 antibody and .beta.-lactose, but
not a control antibody or sucrose (FIG. 5). Similarly, binding of
HAS-Gal-3 to CD45 was confirmed to be Gal-3- and glycan-dependent.
To test functionality of circulating galectin antibodies, Gal-1 Ig
was affinity purified, while Gal-3 and Gal-9 antibody was depleted
from the post-sera of responders with increased humoral immune
response to the galectin. The purified anti-Gal-1 Ig was capable of
inhibiting Gal-1 binding to CD45, while normal human Ig that does
not recognize Gal-1 did not (FIG. 5). Depletion of anti-Gal-3
antibody from patient plasma increased the binding of HAS-Gal-3 to
CD45 (FIG. 6), indicating inhibitory effects of anti-Gal-3 antibody
on binding of Gal-3 to CD45. Gal-9 is known to induce apoptosis of
activated T cells. Treatment of PHA activated T cells with Gal-9
for 20 hours induced apoptosis in 12% of T cells in the presence of
post-serum of a responder with humoral immune response to Gal-9,
but in .about.18% of T cells when anti-Gal-9 antibody was depleted
from the serum (FIG. 7). These findings indicate that anti-Gal-9
antibody in the serum could neutralize apoptosis inducing activity
of Gal-9. Taken together, these results indicate that anti-Gal-1,
Gal-3 and Gal-9 antibodies in patient serum could neutralize the
biological activities of these galectins.
[0351] Treatment of advanced melanoma with Ipi improved the overall
survival (Hodi et al. (2010) N. Eng. J. Med. 363:711-723; Robert et
al. (2010), N. Engl. J. Med. 364:2517-2526). Recent phase 1
clinical studies showed synergic effects by addition of Bev to Ipi
in metastatic melanoma patients (Hodi et al. (2014) Cancer Immunol.
Res. 2:632-642). The results described herein describe Ipi-Bev
potentiated humoral immune responses to pro-tumor,
pro-angiogenesis, and/or immunosuppressive Gal-1, -3 and -9 in
substantial portions of advanced melanoma patients. While enhanced
humoral immune response to Gal-1 and -3 was also seen in melanoma
patients treated with Ipi alone, this occurred in a significantly
smaller portion of patients as compared to Ipi-Bev patients.
Humoral immune responses to Gal-1, -3 and -9 more frequently
occurred in patients with CR, PR or SD than those with PD and
associated with better overall survival, thus associated with
better clinical outcomes to Ipi-Bev therapy. It is believed that
humoral response to these galectins are functionally relevant and
are one of the acting mechanisms for the synergy of combining Bev
with Ipi. This notion is further supported by in vitro findings
that the endogenous galectin antibodies were capable of
neutralizing the CD45 binding activity of Gal-1 and -3 and T cell
apoptosis inducing activity of Gal-9 that are known to be important
for the immune suppressive activity of these galectins. The results
described herein demonstrate a new anti-tumor mechanism for cancer
immunotherapy by enhancing humoral immune response to Gal-1, -3 and
-9 and provide compelling evidence for consideration of addition of
functional anti-Gal-1, -3 and/or -9 antibody to immunotherapy
or/and anti-angiogenesis therapy of cancer.
INCORPORATION BY REFERENCE
[0352] 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.
[0353] 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
[0354] 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 present invention
described herein. Such equivalents are intended to be encompassed
by the following claims.
Sequence CWU 1
1
281408DNAHomo sapiens 1atggcttgtg gtctggtcgc cagcaacctg aatctcaaac
ctggagagtg ccttcgagtg 60cgaggcgagg tggctcctga cgctaagagc ttcgtgctga
acctgggcaa agacagcaac 120aacctgtgcc tgcacttcaa ccctcgcttc
aacgcccacg gcgacgccaa caccatcgtg 180tgcaacagca aggacggcgg
ggcctggggg accgagcagc gggaggctgt ctttcccttc 240cagcctggaa
gtgttgcaga ggtgtgcatc accttcgacc aggccaacct gaccgtcaag
300ctgccagatg gatacgaatt caagttcccc aaccgcctca acctggaggc
catcaactac 360atggcagctg acggtgactt caagatcaaa tgtgtggcct ttgactga
4082135PRTHomo sapiens 2Met Ala Cys Gly Leu Val Ala Ser Asn Leu Asn
Leu Lys Pro Gly Glu1 5 10 15Cys Leu Arg Val Arg Gly Glu Val Ala Pro
Asp Ala Lys Ser Phe Val 20 25 30Leu Asn Leu Gly Lys Asp Ser Asn Asn
Leu Cys Leu His Phe Asn Pro 35 40 45Arg Phe Asn Ala His Gly Asp Ala
Asn Thr Ile Val Cys Asn Ser Lys 50 55 60Asp Gly Gly Ala Trp Gly Thr
Glu Gln Arg Glu Ala Val Phe Pro Phe65 70 75 80Gln Pro Gly Ser Val
Ala Glu Val Cys Ile Thr Phe Asp Gln Ala Asn 85 90 95Leu Thr Val Lys
Leu Pro Asp Gly Tyr Glu Phe Lys Phe Pro Asn Arg 100 105 110Leu Asn
Leu Glu Ala Ile Asn Tyr Met Ala Ala Asp Gly Asp Phe Lys 115 120
125Ile Lys Cys Val Ala Phe Asp 130 1353408DNAMus musculus
3atggcctgtg gtctggtcgc cagcaacctg aatctcaaac ctggggaatg tctcaaagtt
60cggggagagg tggcctcgga cgccaagagc tttgtgctga acctgggaaa agacagcaac
120aacctgtgcc tacacttcaa tcctcgcttc aatgcccatg gagacgccaa
caccattgtg 180tgtaacacca aggaagatgg gacctgggga accgaacacc
gggaacctgc cttccccttc 240cagcccggga gcatcacaga ggtgtgcatc
acctttgacc aggctgacct gaccatcaag 300ctgccagacg gacatgaatt
caagttcccc aaccgcctca acatggaggc catcaactac 360atggcggcgg
atggagactt caagattaag tgcgtggcct ttgagtga 4084135PRTMus musculus
4Met Ala Cys Gly Leu Val Ala Ser Asn Leu Asn Leu Lys Pro Gly Glu1 5
10 15Cys Leu Lys Val Arg Gly Glu Val Ala Ser Asp Ala Lys Ser Phe
Val 20 25 30Leu Asn Leu Gly Lys Asp Ser Asn Asn Leu Cys Leu His Phe
Asn Pro 35 40 45Arg Phe Asn Ala His Gly Asp Ala Asn Thr Ile Val Cys
Asn Thr Lys 50 55 60Glu Asp Gly Thr Trp Gly Thr Glu His Arg Glu Pro
Ala Phe Pro Phe65 70 75 80Gln Pro Gly Ser Ile Thr Glu Val Cys Ile
Thr Phe Asp Gln Ala Asp 85 90 95Leu Thr Ile Lys Leu Pro Asp Gly His
Glu Phe Lys Phe Pro Asn Arg 100 105 110Leu Asn Met Glu Ala Ile Asn
Tyr Met Ala Ala Asp Gly Asp Phe Lys 115 120 125Ile Lys Cys Val Ala
Phe Glu 130 1355753DNAHomo sapiens 5atggcagaca atttttcgct
ccatgatgcg ttatctgggt ctggaaaccc aaaccctcaa 60ggatggcctg gcgcatgggg
gaaccagcct gctggggcag ggggctaccc aggggcttcc 120tatcctgggg
cctaccccgg gcaggcaccc ccaggggctt atcctggaca ggcacctcca
180ggcgcctacc ctggagcacc tggagcttat cccggagcac ctgcacctgg
agtctaccca 240gggccaccca gcggccctgg ggcctaccca tcttctggac
agccaagtgc caccggagcc 300taccctgcca ctggccccta tggcgcccct
gctgggccac tgattgtgcc ttataacctg 360cctttgcctg ggggagtggt
gcctcgcatg ctgataacaa ttctgggcac ggtgaagccc 420aatgcaaaca
gaattgcttt agatttccaa agagggaatg atgttgcctt ccactttaac
480ccacgcttca atgagaacaa caggagagtc attgtttgca atacaaagct
ggataataac 540tggggaaggg aagaaagaca gtcggttttc ccatttgaaa
gtgggaaacc attcaaaata 600caagtactgg ttgaacctga ccacttcaag
gttgcagtga atgatgctca cttgttgcag 660tacaatcatc gggttaaaaa
actcaatgaa atcagcaaac tgggaatttc tggtgacata 720gacctcacca
gtgcttcata taccatgata taa 7536250PRTHomo sapiens 6Met Ala Asp Asn
Phe Ser Leu His Asp Ala Leu Ser Gly Ser Gly Asn1 5 10 15Pro Asn Pro
Gln Gly Trp Pro Gly Ala Trp Gly Asn Gln Pro Ala Gly 20 25 30Ala Gly
Gly Tyr Pro Gly Ala Ser Tyr Pro Gly Ala Tyr Pro Gly Gln 35 40 45Ala
Pro Pro Gly Ala Tyr Pro Gly Gln Ala Pro Pro Gly Ala Tyr Pro 50 55
60Gly Ala Pro Gly Ala Tyr Pro Gly Ala Pro Ala Pro Gly Val Tyr Pro65
70 75 80Gly Pro Pro Ser Gly Pro Gly Ala Tyr Pro Ser Ser Gly Gln Pro
Ser 85 90 95Ala Thr Gly Ala Tyr Pro Ala Thr Gly Pro Tyr Gly Ala Pro
Ala Gly 100 105 110Pro Leu Ile Val Pro Tyr Asn Leu Pro Leu Pro Gly
Gly Val Val Pro 115 120 125Arg Met Leu Ile Thr Ile Leu Gly Thr Val
Lys Pro Asn Ala Asn Arg 130 135 140Ile Ala Leu Asp Phe Gln Arg Gly
Asn Asp Val Ala Phe His Phe Asn145 150 155 160Pro Arg Phe Asn Glu
Asn Asn Arg Arg Val Ile Val Cys Asn Thr Lys 165 170 175Leu Asp Asn
Asn Trp Gly Arg Glu Glu Arg Gln Ser Val Phe Pro Phe 180 185 190Glu
Ser Gly Lys Pro Phe Lys Ile Gln Val Leu Val Glu Pro Asp His 195 200
205Phe Lys Val Ala Val Asn Asp Ala His Leu Leu Gln Tyr Asn His Arg
210 215 220Val Lys Lys Leu Asn Glu Ile Ser Lys Leu Gly Ile Ser Gly
Asp Ile225 230 235 240Asp Leu Thr Ser Ala Ser Tyr Thr Met Ile 245
2507603DNAHomo sapiens 7atggcagaca atttttcgct ccatgatgcg ttatctgggt
ctggaaaccc aaaccctcaa 60ggatggcctg gcgcatgggg gaaccagcct gctggggcag
ggggctaccc aggggcttcc 120tatcctgggg cctaccccgg gcaggcaccc
ccaggggctt atcctggaca ggcacctcca 180ggcgcctacc ctggagcacc
tggagcttat cccggagcac ctgcacctgg agtctaccca 240gggccaccca
gcggccctgg ggcctaccca tcttctggac agccaagtgc caccggagcc
300taccctgcca ctggccccta tggcgcccct gctgggccac tgattgtgcc
ttataacctg 360cctttgcctg ggggagtggt gcctcgcatg ctgataacaa
ttctgggcac ggtgaagccc 420aatgcaaaca gaattgcttt agatttccaa
agagggaatg atgttgcctt ccactttaac 480ccacgcttca atgagaacaa
caggagagtc attgtttgca cttacatgtg taaaggtttc 540atgttcactg
tgagtgaaaa tttttacatt catcaatatc cctcttgtaa gtcatctact 600taa
6038200PRTHomo sapiens 8Met Ala Asp Asn Phe Ser Leu His Asp Ala Leu
Ser Gly Ser Gly Asn1 5 10 15Pro Asn Pro Gln Gly Trp Pro Gly Ala Trp
Gly Asn Gln Pro Ala Gly 20 25 30Ala Gly Gly Tyr Pro Gly Ala Ser Tyr
Pro Gly Ala Tyr Pro Gly Gln 35 40 45Ala Pro Pro Gly Ala Tyr Pro Gly
Gln Ala Pro Pro Gly Ala Tyr Pro 50 55 60Gly Ala Pro Gly Ala Tyr Pro
Gly Ala Pro Ala Pro Gly Val Tyr Pro65 70 75 80Gly Pro Pro Ser Gly
Pro Gly Ala Tyr Pro Ser Ser Gly Gln Pro Ser 85 90 95Ala Thr Gly Ala
Tyr Pro Ala Thr Gly Pro Tyr Gly Ala Pro Ala Gly 100 105 110Pro Leu
Ile Val Pro Tyr Asn Leu Pro Leu Pro Gly Gly Val Val Pro 115 120
125Arg Met Leu Ile Thr Ile Leu Gly Thr Val Lys Pro Asn Ala Asn Arg
130 135 140Ile Ala Leu Asp Phe Gln Arg Gly Asn Asp Val Ala Phe His
Phe Asn145 150 155 160Pro Arg Phe Asn Glu Asn Asn Arg Arg Val Ile
Val Cys Thr Tyr Met 165 170 175Cys Lys Gly Phe Met Phe Thr Val Ser
Glu Asn Phe Tyr Ile His Gln 180 185 190Tyr Pro Ser Cys Lys Ser Ser
Thr 195 2009795DNAMus musculus 9atggcagaca gcttttcgct taacgatgcc
ttagctggct ctggaaaccc aaaccctcaa 60ggatatccgg gtgcatgggg gaaccagcct
ggggcagggg gctacccagg ggctgcttat 120cctggggcct acccaggaca
agctcctcca ggggcctacc caggacaggc tcctccaggg 180gcctacccag
gacaggctcc tcctagtgcc taccccggcc caactgcccc tggagcttat
240cctggcccaa ctgcccctgg agcttatcct ggctcaactg cccctggagc
cttcccaggg 300caacctgggg cacctggggc ctaccccagt gctcctggag
gctatcctgc tgctggccct 360tatggtgtcc ccgctggacc actgacggtg
ccctatgacc tgcccttgcc tggaggagtc 420atgccccgca tgctgatcac
aatcatgggc acagtgaaac ccaacgcaaa caggattgtt 480ctagatttca
ggagagggaa tgatgttgcc ttccacttta acccccgctt caatgagaac
540aacaggagag tcattgtgtg taacacgaag caggacaata actggggaaa
ggaagaaaga 600cagtcagcct tcccctttga gagtggcaaa ccattcaaaa
tacaagtcct ggttgaagct 660gaccacttca aggttgcggt caacgatgct
cacctactgc agtacaacca tcggatgaag 720aacctccggg aaatcagcca
actggggatc agtggtgaca taaccctcac cagcgctaac 780cacgccatga tctaa
79510264PRTMus musculus 10Met Ala Asp Ser Phe Ser Leu Asn Asp Ala
Leu Ala Gly Ser Gly Asn1 5 10 15Pro Asn Pro Gln Gly Tyr Pro Gly Ala
Trp Gly Asn Gln Pro Gly Ala 20 25 30Gly Gly Tyr Pro Gly Ala Ala Tyr
Pro Gly Ala Tyr Pro Gly Gln Ala 35 40 45Pro Pro Gly Ala Tyr Pro Gly
Gln Ala Pro Pro Gly Ala Tyr Pro Gly 50 55 60Gln Ala Pro Pro Ser Ala
Tyr Pro Gly Pro Thr Ala Pro Gly Ala Tyr65 70 75 80Pro Gly Pro Thr
Ala Pro Gly Ala Tyr Pro Gly Ser Thr Ala Pro Gly 85 90 95Ala Phe Pro
Gly Gln Pro Gly Ala Pro Gly Ala Tyr Pro Ser Ala Pro 100 105 110Gly
Gly Tyr Pro Ala Ala Gly Pro Tyr Gly Val Pro Ala Gly Pro Leu 115 120
125Thr Val Pro Tyr Asp Leu Pro Leu Pro Gly Gly Val Met Pro Arg Met
130 135 140Leu Ile Thr Ile Met Gly Thr Val Lys Pro Asn Ala Asn Arg
Ile Val145 150 155 160Leu Asp Phe Arg Arg Gly Asn Asp Val Ala Phe
His Phe Asn Pro Arg 165 170 175Phe Asn Glu Asn Asn Arg Arg Val Ile
Val Cys Asn Thr Lys Gln Asp 180 185 190Asn Asn Trp Gly Lys Glu Glu
Arg Gln Ser Ala Phe Pro Phe Glu Ser 195 200 205Gly Lys Pro Phe Lys
Ile Gln Val Leu Val Glu Ala Asp His Phe Lys 210 215 220Val Ala Val
Asn Asp Ala His Leu Leu Gln Tyr Asn His Arg Met Lys225 230 235
240Asn Leu Arg Glu Ile Ser Gln Leu Gly Ile Ser Gly Asp Ile Thr Leu
245 250 255Thr Ser Ala Asn His Ala Met Ile 26011795DNAMus musculus
11atggcagaca gcttttcgct taacgatgcc ttagctggct ctggaaaccc aaaccctcaa
60ggatatccgg gtgcatgggg gaaccagcct ggggcagggg gctacccagg ggctgcttat
120cctggggcct acccaggaca agctcctcca ggggcctacc caggacaggc
tcctccaggg 180gcctacccag gacaggctcc tcctagtgcc taccccggcc
caactgcccc tggagcttat 240cctggcccaa ctgcccctgg agcttatcct
ggctcaactg cccctggagc cttcccaggg 300caacctgggg cacctggggc
ctaccccagt gctcctggag gctatcctgc tgctggccct 360tatggtgtcc
ccgctggacc actgacggtg ccctatgacc tgcccttgcc tggaggagtc
420atgccccgca tgctgatcac aatcatgggc acagtgaaac ccaacgcaaa
caggattgtt 480ctagatttca ggagagggaa tgatgttgcc ttccacttta
acccccgctt caatgagaac 540aacaggagag tcattgtgtg taacacgaag
caggacaata actggggaaa ggaagaaaga 600cagtcagcct tcccctttga
gagtggcaaa ccattcaaaa tacaagtcct ggttgaagct 660gaccacttca
aggttgcggt caacgatgct cacctactgc agtacaacca tcggatgaag
720aacctccggg aaatcagcca actggggatc agtggtgaca taaccctcac
cagcgctaac 780cacgccatga tctaa 79512264PRTMus musculus 12Met Ala
Asp Ser Phe Ser Leu Asn Asp Ala Leu Ala Gly Ser Gly Asn1 5 10 15Pro
Asn Pro Gln Gly Tyr Pro Gly Ala Trp Gly Asn Gln Pro Gly Ala 20 25
30Gly Gly Tyr Pro Gly Ala Ala Tyr Pro Gly Ala Tyr Pro Gly Gln Ala
35 40 45Pro Pro Gly Ala Tyr Pro Gly Gln Ala Pro Pro Gly Ala Tyr Pro
Gly 50 55 60Gln Ala Pro Pro Ser Ala Tyr Pro Gly Pro Thr Ala Pro Gly
Ala Tyr65 70 75 80Pro Gly Pro Thr Ala Pro Gly Ala Tyr Pro Gly Ser
Thr Ala Pro Gly 85 90 95Ala Phe Pro Gly Gln Pro Gly Ala Pro Gly Ala
Tyr Pro Ser Ala Pro 100 105 110Gly Gly Tyr Pro Ala Ala Gly Pro Tyr
Gly Val Pro Ala Gly Pro Leu 115 120 125Thr Val Pro Tyr Asp Leu Pro
Leu Pro Gly Gly Val Met Pro Arg Met 130 135 140Leu Ile Thr Ile Met
Gly Thr Val Lys Pro Asn Ala Asn Arg Ile Val145 150 155 160Leu Asp
Phe Arg Arg Gly Asn Asp Val Ala Phe His Phe Asn Pro Arg 165 170
175Phe Asn Glu Asn Asn Arg Arg Val Ile Val Cys Asn Thr Lys Gln Asp
180 185 190Asn Asn Trp Gly Lys Glu Glu Arg Gln Ser Ala Phe Pro Phe
Glu Ser 195 200 205Gly Lys Pro Phe Lys Ile Gln Val Leu Val Glu Ala
Asp His Phe Lys 210 215 220Val Ala Val Asn Asp Ala His Leu Leu Gln
Tyr Asn His Arg Met Lys225 230 235 240Asn Leu Arg Glu Ile Ser Gln
Leu Gly Ile Ser Gly Asp Ile Thr Leu 245 250 255Thr Ser Ala Asn His
Ala Met Ile 260131068DNAHomo sapiens 13atggccttca gcggttccca
ggctccctac ctgagtccag ctgtcccctt ttctgggact 60attcaaggag gtctccagga
cggacttcag atcactgtca atgggaccgt tctcagctcc 120agtggaacca
ggtttgctgt gaactttcag actggcttca gtggaaatga cattgccttc
180cacttcaacc ctcggtttga agatggaggg tacgtggtgt gcaacacgag
gcagaacgga 240agctgggggc ccgaggagag gaagacacac atgcctttcc
agaaggggat gccctttgac 300ctctgcttcc tggtgcagag ctcagatttc
aaggtgatgg tgaacgggat cctcttcgtg 360cagtacttcc accgcgtgcc
cttccaccgt gtggacacca tctccgtcaa tggctctgtg 420cagctgtcct
acatcagctt ccagaacccc cgcacagtcc ctgttcagcc tgccttctcc
480acggtgccgt tctcccagcc tgtctgtttc ccacccaggc ccagggggcg
cagacaaaaa 540cctcccggcg tgtggcctgc caacccggct cccattaccc
agacagtcat ccacacagtg 600cagagcgccc ctggacagat gttctctact
cccgccatcc cacctatgat gtacccccac 660cccgcctatc cgatgccttt
catcaccacc attctgggag ggctgtaccc atccaagtcc 720atcctcctgt
caggcactgt cctgcccagt gctcagaggt tccacatcaa cctgtgctct
780gggaaccaca tcgccttcca cctgaacccc cgttttgatg agaatgctgt
ggtccgcaac 840acccagatcg acaactcctg ggggtctgag gagcgaagtc
tgccccgaaa aatgcccttc 900gtccgtggcc agagcttctc agtgtggatc
ttgtgtgaag ctcactgcct caaggtggcc 960gtggatggtc agcacctgtt
tgaatactac catcgcctga ggaacctgcc caccatcaac 1020agactggaag
tggggggcga catccagctg acccatgtgc agacatag 106814355PRTHomo sapiens
14Met Ala Phe Ser Gly Ser Gln Ala Pro Tyr Leu Ser Pro Ala Val Pro1
5 10 15Phe Ser Gly Thr Ile Gln Gly Gly Leu Gln Asp Gly Leu Gln Ile
Thr 20 25 30Val Asn Gly Thr Val Leu Ser Ser Ser Gly Thr Arg Phe Ala
Val Asn 35 40 45Phe Gln Thr Gly Phe Ser Gly Asn Asp Ile Ala Phe His
Phe Asn Pro 50 55 60Arg Phe Glu Asp Gly Gly Tyr Val Val Cys Asn Thr
Arg Gln Asn Gly65 70 75 80Ser Trp Gly Pro Glu Glu Arg Lys Thr His
Met Pro Phe Gln Lys Gly 85 90 95Met Pro Phe Asp Leu Cys Phe Leu Val
Gln Ser Ser Asp Phe Lys Val 100 105 110Met Val Asn Gly Ile Leu Phe
Val Gln Tyr Phe His Arg Val Pro Phe 115 120 125His Arg Val Asp Thr
Ile Ser Val Asn Gly Ser Val Gln Leu Ser Tyr 130 135 140Ile Ser Phe
Gln Asn Pro Arg Thr Val Pro Val Gln Pro Ala Phe Ser145 150 155
160Thr Val Pro Phe Ser Gln Pro Val Cys Phe Pro Pro Arg Pro Arg Gly
165 170 175Arg Arg Gln Lys Pro Pro Gly Val Trp Pro Ala Asn Pro Ala
Pro Ile 180 185 190Thr Gln Thr Val Ile His Thr Val Gln Ser Ala Pro
Gly Gln Met Phe 195 200 205Ser Thr Pro Ala Ile Pro Pro Met Met Tyr
Pro His Pro Ala Tyr Pro 210 215 220Met Pro Phe Ile Thr Thr Ile Leu
Gly Gly Leu Tyr Pro Ser Lys Ser225 230 235 240Ile Leu Leu Ser Gly
Thr Val Leu Pro Ser Ala Gln Arg Phe His Ile 245 250 255Asn Leu Cys
Ser Gly Asn His Ile Ala Phe His Leu Asn Pro Arg Phe 260 265 270Asp
Glu Asn Ala Val Val Arg Asn Thr Gln Ile Asp Asn Ser Trp Gly 275 280
285Ser Glu Glu Arg Ser Leu Pro Arg Lys Met Pro Phe Val Arg Gly Gln
290 295 300Ser Phe Ser Val Trp Ile Leu Cys Glu Ala His Cys Leu Lys
Val Ala305 310 315 320Val Asp Gly Gln His Leu Phe Glu Tyr Tyr His
Arg Leu Arg Asn Leu 325 330 335Pro Thr Ile Asn Arg Leu Glu Val Gly
Gly Asp Ile Gln Leu Thr His 340 345 350Val Gln Thr 35515972DNAHomo
sapiens
15atggccttca gcggttccca ggctccctac ctgagtccag ctgtcccctt ttctgggact
60attcaaggag gtctccagga cggacttcag atcactgtca atgggaccgt tctcagctcc
120agtggaacca ggtttgctgt gaactttcag actggcttca gtggaaatga
cattgccttc 180cacttcaacc ctcggtttga agatggaggg tacgtggtgt
gcaacacgag gcagaacgga 240agctgggggc ccgaggagag gaagacacac
atgcctttcc agaaggggat gccctttgac 300ctctgcttcc tggtgcagag
ctcagatttc aaggtgatgg tgaacgggat cctcttcgtg 360cagtacttcc
accgcgtgcc cttccaccgt gtggacacca tctccgtcaa tggctctgtg
420cagctgtcct acatcagctt ccagcctccc ggcgtgtggc ctgccaaccc
ggctcccatt 480acccagacag tcatccacac agtgcagagc gcccctggac
agatgttctc tactcccgcc 540atcccaccta tgatgtaccc ccaccccgcc
tatccgatgc ctttcatcac caccattctg 600ggagggctgt acccatccaa
gtccatcctc ctgtcaggca ctgtcctgcc cagtgctcag 660aggttccaca
tcaacctgtg ctctgggaac cacatcgcct tccacctgaa cccccgtttt
720gatgagaatg ctgtggtccg caacacccag atcgacaact cctgggggtc
tgaggagcga 780agtctgcccc gaaaaatgcc cttcgtccgt ggccagagct
tctcagtgtg gatcttgtgt 840gaagctcact gcctcaaggt ggccgtggat
ggtcagcacc tgtttgaata ctaccatcgc 900ctgaggaacc tgcccaccat
caacagactg gaagtggggg gcgacatcca gctgacccat 960gtgcagacat ag
97216323PRTHomo sapiens 16Met Ala Phe Ser Gly Ser Gln Ala Pro Tyr
Leu Ser Pro Ala Val Pro1 5 10 15Phe Ser Gly Thr Ile Gln Gly Gly Leu
Gln Asp Gly Leu Gln Ile Thr 20 25 30Val Asn Gly Thr Val Leu Ser Ser
Ser Gly Thr Arg Phe Ala Val Asn 35 40 45Phe Gln Thr Gly Phe Ser Gly
Asn Asp Ile Ala Phe His Phe Asn Pro 50 55 60Arg Phe Glu Asp Gly Gly
Tyr Val Val Cys Asn Thr Arg Gln Asn Gly65 70 75 80Ser Trp Gly Pro
Glu Glu Arg Lys Thr His Met Pro Phe Gln Lys Gly 85 90 95Met Pro Phe
Asp Leu Cys Phe Leu Val Gln Ser Ser Asp Phe Lys Val 100 105 110Met
Val Asn Gly Ile Leu Phe Val Gln Tyr Phe His Arg Val Pro Phe 115 120
125His Arg Val Asp Thr Ile Ser Val Asn Gly Ser Val Gln Leu Ser Tyr
130 135 140Ile Ser Phe Gln Pro Pro Gly Val Trp Pro Ala Asn Pro Ala
Pro Ile145 150 155 160Thr Gln Thr Val Ile His Thr Val Gln Ser Ala
Pro Gly Gln Met Phe 165 170 175Ser Thr Pro Ala Ile Pro Pro Met Met
Tyr Pro His Pro Ala Tyr Pro 180 185 190Met Pro Phe Ile Thr Thr Ile
Leu Gly Gly Leu Tyr Pro Ser Lys Ser 195 200 205Ile Leu Leu Ser Gly
Thr Val Leu Pro Ser Ala Gln Arg Phe His Ile 210 215 220Asn Leu Cys
Ser Gly Asn His Ile Ala Phe His Leu Asn Pro Arg Phe225 230 235
240Asp Glu Asn Ala Val Val Arg Asn Thr Gln Ile Asp Asn Ser Trp Gly
245 250 255Ser Glu Glu Arg Ser Leu Pro Arg Lys Met Pro Phe Val Arg
Gly Gln 260 265 270Ser Phe Ser Val Trp Ile Leu Cys Glu Ala His Cys
Leu Lys Val Ala 275 280 285Val Asp Gly Gln His Leu Phe Glu Tyr Tyr
His Arg Leu Arg Asn Leu 290 295 300Pro Thr Ile Asn Arg Leu Glu Val
Gly Gly Asp Ile Gln Leu Thr His305 310 315 320Val Gln
Thr171068DNAHomo sapiens 17atggccttca gcggttccca ggctccctat
ctgagcccag ccgtcccctt ttctgggact 60atccaagggg gtctccagga cggatttcag
atcactgtca atggggccgt tctcagctcc 120agtggaacca ggtttgctgt
ggactttcag acgggcttca gtggaaacga cattgccttc 180cacttcaacc
ctcggtttga agacggaggg tatgtggtgt gcaacacgag gcagaaagga
240agatgggggc ccgaggagag gaagatgcac atgcccttcc agaaggggat
gccctttgac 300ctctgcttcc tggtgcagag ctcagatttc aaggtgatgg
tgaacgggag cctcttcgtg 360cagtacttcc accgcgtgcc cttccaccgt
gtggacacca tctccgtcaa tggctctgtg 420cagctgtcct acatcagctt
ccagaatccc cgcacagtcc ccgttcagcc tgccttctcc 480acggtgccgt
tctcccagcc tgtctgtttc ccacccaggc ccagggggcg cagacaaaaa
540cctcccagcg tgcggcctgc caacccagct cccattaccc agacagtcat
ccacacggtg 600cagagcgcct ctggacagat gttctctact cccgccatcc
cacctatgat gtacccccac 660cctgcctatc cgatgccttt catcaccacc
attccgggag ggctgtaccc atccaagtcc 720atcatcctgt caggcactgt
cctgcccagt gctcagaggt tccacatcaa cctgtgctct 780gggagccaca
tcgccttcca catgaacccc cgttttgatg agaatgctgt ggtccgtaac
840acccagatca acaactcttg ggggtctgag gagcgaagtc tgccccgaaa
aatgcccttc 900gtccgaggcc agagcttctc ggtgtggatc ttgtgtgaag
ctcactgcct caaggtggcc 960gtggatggtc agcacgtgtt tgaatactac
catcgcctga ggaacctgcc caccatcaac 1020aaactggaag tgggtggcga
catccagctg acccacgtgc agacatag 106818355PRTHomo sapiens 18Met Ala
Phe Ser Gly Ser Gln Ala Pro Tyr Leu Ser Pro Ala Val Pro1 5 10 15Phe
Ser Gly Thr Ile Gln Gly Gly Leu Gln Asp Gly Phe Gln Ile Thr 20 25
30Val Asn Gly Ala Val Leu Ser Ser Ser Gly Thr Arg Phe Ala Val Asp
35 40 45Phe Gln Thr Gly Phe Ser Gly Asn Asp Ile Ala Phe His Phe Asn
Pro 50 55 60Arg Phe Glu Asp Gly Gly Tyr Val Val Cys Asn Thr Arg Gln
Lys Gly65 70 75 80Arg Trp Gly Pro Glu Glu Arg Lys Met His Met Pro
Phe Gln Lys Gly 85 90 95Met Pro Phe Asp Leu Cys Phe Leu Val Gln Ser
Ser Asp Phe Lys Val 100 105 110Met Val Asn Gly Ser Leu Phe Val Gln
Tyr Phe His Arg Val Pro Phe 115 120 125His Arg Val Asp Thr Ile Ser
Val Asn Gly Ser Val Gln Leu Ser Tyr 130 135 140Ile Ser Phe Gln Asn
Pro Arg Thr Val Pro Val Gln Pro Ala Phe Ser145 150 155 160Thr Val
Pro Phe Ser Gln Pro Val Cys Phe Pro Pro Arg Pro Arg Gly 165 170
175Arg Arg Gln Lys Pro Pro Ser Val Arg Pro Ala Asn Pro Ala Pro Ile
180 185 190Thr Gln Thr Val Ile His Thr Val Gln Ser Ala Ser Gly Gln
Met Phe 195 200 205Ser Thr Pro Ala Ile Pro Pro Met Met Tyr Pro His
Pro Ala Tyr Pro 210 215 220Met Pro Phe Ile Thr Thr Ile Pro Gly Gly
Leu Tyr Pro Ser Lys Ser225 230 235 240Ile Ile Leu Ser Gly Thr Val
Leu Pro Ser Ala Gln Arg Phe His Ile 245 250 255Asn Leu Cys Ser Gly
Ser His Ile Ala Phe His Met Asn Pro Arg Phe 260 265 270Asp Glu Asn
Ala Val Val Arg Asn Thr Gln Ile Asn Asn Ser Trp Gly 275 280 285Ser
Glu Glu Arg Ser Leu Pro Arg Lys Met Pro Phe Val Arg Gly Gln 290 295
300Ser Phe Ser Val Trp Ile Leu Cys Glu Ala His Cys Leu Lys Val
Ala305 310 315 320Val Asp Gly Gln His Val Phe Glu Tyr Tyr His Arg
Leu Arg Asn Leu 325 330 335Pro Thr Ile Asn Lys Leu Glu Val Gly Gly
Asp Ile Gln Leu Thr His 340 345 350Val Gln Thr 355191071DNAHomo
sapiens 19atggccttca gcggttgcca ggctccctat ctgagcccag ccgtcccctt
ttctgggact 60atccaagggg gtctccagga cggatttcag atcactgtca atggggccgt
tctcagctgc 120agtggaacca ggtttgctgt ggactttcag acgggcttca
gtggaaacga cattgccttc 180cacttcaacc ctcggtttga agacggaggg
tatgtggtgt gcaacacgag gcagaaagga 240acatgggggc ccgaggagag
gaagatgcac atgcccttcc agaaggggat gccctttgac 300ctctgcttcc
tggtgcagag ctcagatttc aaggtgatgg tgaacgggag cctcttcgtg
360cagtacttcc accgcgtgcc cttccaccgt gtggacacca tctccgtcaa
tggctctgtg 420cagctgtcct acatcagctt ccagaatccc cgcgcagtcc
ccgttcagcc tgccttctcc 480acggtgccgt tctcccagcc tgtctgtttc
ccacccaggc ccagggggcg cagacaaaaa 540cctcccagcg tgcggcctgc
caacccagct cccattaccc agacagtcat ccacacggtg 600cagagtgcct
ctggacagat gttctctcag actcccgcca tcccacctat gatgtacccc
660caccctgcct atccgatgcc tttcatcacc accattccgg gagggctgta
cccatccaag 720tccatcatcc tgtcaggcac tgtcctgccc agtgctcaga
ggttccacat caacctgtgc 780tctgggagcc acatcgcctt ccacatgaac
ccccgttttg atgagaatgc tgtggtccgt 840aacacccaga tcaacaactc
ttgggggtct gaggagcgaa gtctgccccg aaaaatgccc 900ttcgtccgag
gccagagctt ctcggtgtgg atcttgtgtg aagctcactg cctcaaggtg
960gccgtggatg gtcagcacgt gtttgaatac taccatcgcc tgaggaacct
gcccaccatc 1020aacaaactgg aagtgggtgg cgacatccag ctgacccacg
tgcagacata g 107120356PRTHomo sapiens 20Met Ala Phe Ser Gly Cys Gln
Ala Pro Tyr Leu Ser Pro Ala Val Pro1 5 10 15Phe Ser Gly Thr Ile Gln
Gly Gly Leu Gln Asp Gly Phe Gln Ile Thr 20 25 30Val Asn Gly Ala Val
Leu Ser Cys Ser Gly Thr Arg Phe Ala Val Asp 35 40 45Phe Gln Thr Gly
Phe Ser Gly Asn Asp Ile Ala Phe His Phe Asn Pro 50 55 60Arg Phe Glu
Asp Gly Gly Tyr Val Val Cys Asn Thr Arg Gln Lys Gly65 70 75 80Thr
Trp Gly Pro Glu Glu Arg Lys Met His Met Pro Phe Gln Lys Gly 85 90
95Met Pro Phe Asp Leu Cys Phe Leu Val Gln Ser Ser Asp Phe Lys Val
100 105 110Met Val Asn Gly Ser Leu Phe Val Gln Tyr Phe His Arg Val
Pro Phe 115 120 125His Arg Val Asp Thr Ile Ser Val Asn Gly Ser Val
Gln Leu Ser Tyr 130 135 140Ile Ser Phe Gln Asn Pro Arg Ala Val Pro
Val Gln Pro Ala Phe Ser145 150 155 160Thr Val Pro Phe Ser Gln Pro
Val Cys Phe Pro Pro Arg Pro Arg Gly 165 170 175Arg Arg Gln Lys Pro
Pro Ser Val Arg Pro Ala Asn Pro Ala Pro Ile 180 185 190Thr Gln Thr
Val Ile His Thr Val Gln Ser Ala Ser Gly Gln Met Phe 195 200 205Ser
Gln Thr Pro Ala Ile Pro Pro Met Met Tyr Pro His Pro Ala Tyr 210 215
220Pro Met Pro Phe Ile Thr Thr Ile Pro Gly Gly Leu Tyr Pro Ser
Lys225 230 235 240Ser Ile Ile Leu Ser Gly Thr Val Leu Pro Ser Ala
Gln Arg Phe His 245 250 255Ile Asn Leu Cys Ser Gly Ser His Ile Ala
Phe His Met Asn Pro Arg 260 265 270Phe Asp Glu Asn Ala Val Val Arg
Asn Thr Gln Ile Asn Asn Ser Trp 275 280 285Gly Ser Glu Glu Arg Ser
Leu Pro Arg Lys Met Pro Phe Val Arg Gly 290 295 300Gln Ser Phe Ser
Val Trp Ile Leu Cys Glu Ala His Cys Leu Lys Val305 310 315 320Ala
Val Asp Gly Gln His Val Phe Glu Tyr Tyr His Arg Leu Arg Asn 325 330
335Leu Pro Thr Ile Asn Lys Leu Glu Val Gly Gly Asp Ile Gln Leu Thr
340 345 350His Val Gln Thr 355211062DNAMus musculus 21atggctctct
tcagtgccca gtctccatac attaacccga tcatcccctt tactggacca 60atccaaggag
ggctgcagga gggacttcag gtgaccctcc aggggactac caagagtttt
120gcacaaaggt ttgtggtgaa ctttcagaac agcttcaatg gaaatgacat
tgccttccac 180ttcaaccccc ggtttgagga aggagggtat gtggtttgca
acacgaagca gaacggacag 240tggggtcctg aggagagaaa gatgcagatg
cccttccaga aggggatgcc ctttgagctt 300tgcttcctgg tgcagaggtc
agagttcaag gtgatggtga acaagaaatt ctttgtgcag 360taccaacacc
gcgtacccta ccacctcgtg gacaccatcg ctgtctccgg ctgcttgaag
420ctgtccttta tcaccttcca gaactctgca gcccctgtcc agcatgtctt
ctccacagtg 480cagttctctc agccagtcca gttcccacgg acccctaagg
ggcgcaaaca gaaaactcag 540aactttcgtc ctgcccacca ggcacccatg
gctcaaacta ccatccatat ggttcacagc 600acccctggac agatgttctc
tactcctgga atccctcctg tggtgtaccc caccccagcc 660tataccatac
ctttctacac ccccattcca aatgggcttt acccgtccaa gtccatcatg
720atatcaggca atgtcttgcc agatgctacg aggttccata tcaaccttcg
ctgtggaggt 780gacattgctt tccacctgaa cccccgtttc aatgagaatg
ctgttgtccg aaacactcag 840atcaacaact cctgggggca ggaagagcga
agtctgcttg ggaggatgcc cttcagtcga 900ggccagagct tctcggtgtg
gatcatatgt gaaggtcact gcttcaaggt agctgtgaat 960ggtcaacaca
tgtgtgaata ttaccaccgc ctgaagaact tgcaggatat caacactcta
1020gaagtggcgg gtgatatcca gctgacccac gtgcagacat ag 106222353PRTMus
musculus 22Met Ala Leu Phe Ser Ala Gln Ser Pro Tyr Ile Asn Pro Ile
Ile Pro1 5 10 15Phe Thr Gly Pro Ile Gln Gly Gly Leu Gln Glu Gly Leu
Gln Val Thr 20 25 30Leu Gln Gly Thr Thr Lys Ser Phe Ala Gln Arg Phe
Val Val Asn Phe 35 40 45Gln Asn Ser Phe Asn Gly Asn Asp Ile Ala Phe
His Phe Asn Pro Arg 50 55 60Phe Glu Glu Gly Gly Tyr Val Val Cys Asn
Thr Lys Gln Asn Gly Gln65 70 75 80Trp Gly Pro Glu Glu Arg Lys Met
Gln Met Pro Phe Gln Lys Gly Met 85 90 95Pro Phe Glu Leu Cys Phe Leu
Val Gln Arg Ser Glu Phe Lys Val Met 100 105 110Val Asn Lys Lys Phe
Phe Val Gln Tyr Gln His Arg Val Pro Tyr His 115 120 125Leu Val Asp
Thr Ile Ala Val Ser Gly Cys Leu Lys Leu Ser Phe Ile 130 135 140Thr
Phe Gln Asn Ser Ala Ala Pro Val Gln His Val Phe Ser Thr Val145 150
155 160Gln Phe Ser Gln Pro Val Gln Phe Pro Arg Thr Pro Lys Gly Arg
Lys 165 170 175Gln Lys Thr Gln Asn Phe Arg Pro Ala His Gln Ala Pro
Met Ala Gln 180 185 190Thr Thr Ile His Met Val His Ser Thr Pro Gly
Gln Met Phe Ser Thr 195 200 205Pro Gly Ile Pro Pro Val Val Tyr Pro
Thr Pro Ala Tyr Thr Ile Pro 210 215 220Phe Tyr Thr Pro Ile Pro Asn
Gly Leu Tyr Pro Ser Lys Ser Ile Met225 230 235 240Ile Ser Gly Asn
Val Leu Pro Asp Ala Thr Arg Phe His Ile Asn Leu 245 250 255Arg Cys
Gly Gly Asp Ile Ala Phe His Leu Asn Pro Arg Phe Asn Glu 260 265
270Asn Ala Val Val Arg Asn Thr Gln Ile Asn Asn Ser Trp Gly Gln Glu
275 280 285Glu Arg Ser Leu Leu Gly Arg Met Pro Phe Ser Arg Gly Gln
Ser Phe 290 295 300Ser Val Trp Ile Ile Cys Glu Gly His Cys Phe Lys
Val Ala Val Asn305 310 315 320Gly Gln His Met Cys Glu Tyr Tyr His
Arg Leu Lys Asn Leu Gln Asp 325 330 335Ile Asn Thr Leu Glu Val Ala
Gly Asp Ile Gln Leu Thr His Val Gln 340 345 350Thr23969DNAMus
musculus 23atggctctct tcagtgccca gtctccatac attaacccga tcatcccctt
tactggacca 60atccaaggag ggctgcagga gggacttcag gtgaccctcc aggggactac
caagagtttt 120gcacaaaggt ttgtggtgaa ctttcagaac agcttcaatg
gaaatgacat tgccttccac 180ttcaaccccc ggtttgagga aggagggtat
gtggtttgca acacgaagca gaacggacag 240tggggtcctg aggagagaaa
gatgcagatg cccttccaga aggggatgcc ctttgagctt 300tgcttcctgg
tgcagaggtc agagttcaag gtgatggtga acaagaaatt ctttgtgcag
360taccaacacc gcgtacccta ccacctcgtg gacaccatcg ctgtctccgg
ctgcttgaag 420ctgtccttta tcaccttcca gactcagaac tttcgtcctg
cccaccaggc acccatggct 480caaactacca tccatatggt tcacagcacc
cctggacaga tgttctctac tcctggaatc 540cctcctgtgg tgtaccccac
cccagcctat accatacctt tctacacccc cattccaaat 600gggctttacc
cgtccaagtc catcatgata tcaggcaatg tcttgccaga tgctacgagg
660ttccatatca accttcgctg tggaggtgac attgctttcc acctgaaccc
ccgtttcaat 720gagaatgctg ttgtccgaaa cactcagatc aacaactcct
gggggcagga agagcgaagt 780ctgcttggga ggatgccctt cagtcgaggc
cagagcttct cggtgtggat catatgtgaa 840ggtcactgct tcaaggtagc
tgtgaatggt caacacatgt gtgaatatta ccaccgcctg 900aagaacttgc
aggatatcaa cactctagaa gtggcgggtg atatccagct gacccacgtg 960cagacatag
96924322PRTMus musculus 24Met Ala Leu Phe Ser Ala Gln Ser Pro Tyr
Ile Asn Pro Ile Ile Pro1 5 10 15Phe Thr Gly Pro Ile Gln Gly Gly Leu
Gln Glu Gly Leu Gln Val Thr 20 25 30Leu Gln Gly Thr Thr Lys Ser Phe
Ala Gln Arg Phe Val Val Asn Phe 35 40 45Gln Asn Ser Phe Asn Gly Asn
Asp Ile Ala Phe His Phe Asn Pro Arg 50 55 60Phe Glu Glu Gly Gly Tyr
Val Val Cys Asn Thr Lys Gln Asn Gly Gln65 70 75 80Trp Gly Pro Glu
Glu Arg Lys Met Gln Met Pro Phe Gln Lys Gly Met 85 90 95Pro Phe Glu
Leu Cys Phe Leu Val Gln Arg Ser Glu Phe Lys Val Met 100 105 110Val
Asn Lys Lys Phe Phe Val Gln Tyr Gln His Arg Val Pro Tyr His 115 120
125Leu Val Asp Thr Ile Ala Val Ser Gly Cys Leu Lys Leu Ser Phe Ile
130 135 140Thr Phe Gln Thr Gln Asn Phe Arg Pro Ala His Gln Ala Pro
Met Ala145 150 155 160Gln Thr Thr Ile His Met Val His Ser Thr Pro
Gly Gln Met Phe Ser 165 170 175Thr Pro Gly Ile Pro Pro Val Val Tyr
Pro Thr Pro Ala Tyr Thr Ile 180 185
190Pro Phe Tyr Thr Pro Ile Pro Asn Gly Leu Tyr Pro Ser Lys Ser Ile
195 200 205Met Ile Ser Gly Asn Val Leu Pro Asp Ala Thr Arg Phe His
Ile Asn 210 215 220Leu Arg Cys Gly Gly Asp Ile Ala Phe His Leu Asn
Pro Arg Phe Asn225 230 235 240Glu Asn Ala Val Val Arg Asn Thr Gln
Ile Asn Asn Ser Trp Gly Gln 245 250 255Glu Glu Arg Ser Leu Leu Gly
Arg Met Pro Phe Ser Arg Gly Gln Ser 260 265 270Phe Ser Val Trp Ile
Ile Cys Glu Gly His Cys Phe Lys Val Ala Val 275 280 285Asn Gly Gln
His Met Cys Glu Tyr Tyr His Arg Leu Lys Asn Leu Gln 290 295 300Asp
Ile Asn Thr Leu Glu Val Ala Gly Asp Ile Gln Leu Thr His Val305 310
315 320Gln Thr2542DNAArtificial Sequence/note="Description of
Artificial Sequence Gal-1 sense synthetic primer" 25cgcgaacaga
ttggaggtgc ttgtggtctg gtcgccagca ac 422642DNAArtificial
Sequence/note="Description of Artificial Sequence Gal-1 antisense
synthetic primer" 26gtggcggccg ctctattagt caaaggccac acatttgatc tt
422742DNAArtificial Sequence/note="Description of Artificial
Sequence Gal-3 sense synthetic primer" 27cgcgaacaga ttggaggtgc
agacaatttt tcgctccatg at 422843DNAArtificial
Sequence/note="Description of Artificial Sequence Gal-3 antisense
synthetic primer" 28gtggcggccg ctctattagt atcatggtat atgaagcact ggt
43
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References