U.S. patent application number 15/345634 was filed with the patent office on 2017-02-23 for biomarkers for prostate cancer and methods for their detection.
This patent application is currently assigned to The United States of America, as represented by the Secretary, Department of Health and Human Serv. The applicant listed for this patent is The United States of America, as represented by the Secretary, Department of Health and Human Serv, The United States of America, as represented by the Secretary, Department of Health and Human Serv. Invention is credited to Christopher Campbell, Jeffrey Gildersleeve, James Gulley, Oyindasola Oyelaran, Jeffrey Schlom.
Application Number | 20170052185 15/345634 |
Document ID | / |
Family ID | 45560097 |
Filed Date | 2017-02-23 |
United States Patent
Application |
20170052185 |
Kind Code |
A1 |
Gildersleeve; Jeffrey ; et
al. |
February 23, 2017 |
BIOMARKERS FOR PROSTATE CANCER AND METHODS FOR THEIR DETECTION
Abstract
The invention provides a method for predicting the clinical
response to a cancer vaccine in a patient having cancer, a method
for determining the immune response to a cancer vaccine in a
patient having cancer who has been administered a cancer vaccine, a
method for determining the long-term survival in a patient having
cancer, corresponding kits therefor, as well as methods of for
improving the efficacy of a virus-based vaccine.
Inventors: |
Gildersleeve; Jeffrey;
(Frederick, MD) ; Campbell; Christopher;
(Baltimore, MD) ; Oyelaran; Oyindasola; (Boston,
MA) ; Gulley; James; (Takoma Park, MD) ;
Schlom; Jeffrey; (Potomac, MD) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The United States of America, as represented by the Secretary,
Department of Health and Human Serv |
Bethesda |
MD |
US |
|
|
Assignee: |
The United States of America, as
represented by the Secretary, Department of Health and Human
Serv
Bethesda
MD
|
Family ID: |
45560097 |
Appl. No.: |
15/345634 |
Filed: |
November 8, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13814337 |
Mar 5, 2013 |
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PCT/US2011/046799 |
Aug 5, 2011 |
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15345634 |
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61443955 |
Feb 17, 2011 |
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61371537 |
Aug 6, 2010 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 33/57469 20130101;
C12N 2710/24143 20130101; A61K 2039/55583 20130101; G01N 2800/52
20130101; A61K 2039/545 20130101; A61K 2039/884 20180801; A61K
2039/575 20130101; A61K 39/001129 20180801; A61K 2039/585 20130101;
A61K 39/001194 20180801; G01N 33/57434 20130101; G01N 2400/02
20130101; A61K 2039/5252 20130101; A61K 39/0011 20130101; A61K
2039/5256 20130101; C12N 2710/24043 20130101 |
International
Class: |
G01N 33/574 20060101
G01N033/574; A61K 39/00 20060101 A61K039/00 |
Claims
1.-42. (canceled)
43. A method for predicting the clinical response to a
poxvirus-based vaccine in a patient and treating cancer in the
patient, the method comprising: obtaining a serum sample from a
patient having cancer who has not been previously administered the
poxvirus-based vaccine; assaying the serum sample to determine the
levels of antibodies in the patient to at least one glycan and/or
glycoprotein antigen selected from the group consisting of
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Sialyl.alpha.2-3Gal.beta.1-4Glc-(GM3),
Fuc.alpha.1-2Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4Glc.beta.-(BG-H1),
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Gal.alpha.1-3Gal-(B.sub.di),
Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-(Ac-S-Tn(Thr)-G-G), BSM, Lactose,
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.-(LNT), Fuc-b, Fuc-a,
Gal.beta.1-6Man-.alpha.-(Galb1-6Man-a),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1),
Gal.alpha.1-4Gal.beta.-(Gala1-4Galb),
Man.alpha.1-6[Man.alpha.1-3]Man.beta.-(ManT),
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-(pLNH),
Rha-a-, GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-(Ac-S-Tn(Ser)-S-G); comparing the
determined levels of antibodies to the at least one glycan and/or
glycoprotein antigen to a control, so as to predict the clinical
response to the poxvirus-based vaccine in the patient; and treating
the cancer by administering the poxvirus-based vaccine to the
patient.
44. The method of claim 43, wherein the serum sample is assayed to
determine the levels of antibodies to at least two glycan and/or
glycoprotein antigens selected from the group consisting of 6'SLac,
SLeX, GM3, BG-H1, GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G,
BSM, Lactose, LNT, Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb,
ManT, pLNH, Rha-.alpha., GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.- (BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-S-Tn(Ser)-S-G.
45. The method of claim 44, wherein the serum sample is assayed to
determine the levels of antibodies to at least three glycan and/or
glycoprotein antigens selected from the group consisting of 6'SLac,
SLeX, GM3, BG-H1, GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G,
BSM, Lactose, LNT, Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb,
ManT, pLNH, Rha-.alpha., GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), and
Ac-S-Tn(Ser)-S-G.
46. The method of claim 45, wherein the serum sample is assayed to
determine the levels of antibodies to at least four glycan and/or
glycoprotein antigens selected from the group consisting of 6'SLac,
SLeX, GM3, BG-H1, GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G,
BSM, Lactose, LNT, Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb,
ManT, pLNH, Rha-.alpha., GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-S-Tn(Ser)-S-G.
47. The method of claim 46, wherein the serum sample is assayed to
determine the levels of antibodies to at least five glycan and/or
glycoprotein antigens selected from the group consisting of 6'SLac,
SLeX, GM3, BG-H1, GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G,
BSM, Lactose, LNT, Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb,
ManT, pLNH, Rha-.alpha., GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-S-Tn(Ser)-S-G.
48. The method of claim 43, wherein the antibodies are selected
from the group consisting of IgG, IgM, IgA, IgD, IgE, and
combinations thereof.
49. The method of claim 43, wherein the serum sample is assayed to
determine the levels of IgM antibodies to BG-A.
50. The method of claim 43, wherein the serum sample is assayed to
determine one or more of the following: the levels of IgG
antibodies to GA1, the levels of IgG antibodies to Rha-a, the
levels of IgA antibodies to Fuc-a, the levels of Ig antibodies to
LNnH, the levels of IgG antibodies to 6'SLac, and the levels of IgG
antibodies to GM3.
51. The method of claim 43, wherein levels of antibodies in the
patient to GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A) is
determined.
52. The method of claim 43, wherein the cancer is selected from the
group consisting of prostate, breast, pancreatic, ovarian, gastric,
head and neck, liver, lung, kidney, bone, brain, colorectal,
uterine, skin, endometrial, esophageal, anal, oral, nasal, and
rectal cancer.
53. The method of claim 43, wherein the cancer is prostate
cancer.
54. The method of claim 43, wherein the poxvirus-based vaccine is
selected from the group consisting of avipox-based vaccine,
orthopox-based vaccine, cowpox-based vaccine, and camelpox-based
vaccine.
55. The method of claim 43, wherein the poxvirus-based vaccine is
an avipox-based vaccine.
56. The method of claim 54, wherein the avipox-based vaccine is a
fowlpox-based vaccine.
57. A method for determining the immune response to a
poxvirus-based vaccine in a patient and treating cancer in the
patient, the method comprising: obtaining a first serum sample from
a patient having cancer who has not been previously administered
the poxvirus-based vaccine; treating the cancer in the patient by
administering the poxvirus-based vaccine to the patient; obtaining
a second serum sample from the patient after administration of the
poxvirus-based vaccine, assaying the first and second serum samples
to determine the first and second levels of antibodies,
respectively, to at least one glycan and/or glycoprotein antigen
selected from the group consisting of the Forssman antigen,
GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A), the Tn antigen,
the TF antigen,
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Sia.alpha.2-3 Gal.beta.1-3[Fuc.alpha.1-4]GlcNAc.beta.1-(SLeA),
Fuc.alpha.1-2Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(LeY),
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4Glc-(GM3),
Fuc.alpha.1-2Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4Glc.beta.-(BG-H1),
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Gal.alpha.1-3Gal-(B.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3
Gal.beta.1-(A-LeB), and fetuin; and comparing the determined first
and second levels of antibodies to the at least one glycan and/or
glycoprotein antigen, so as to determine the immune response to the
poxvirus-based vaccine in the patient.
58. The method of claim 57, wherein the first or second serum
sample is assayed to determine the levels of antibodies to at least
two glycan and/or glycoprotein antigens selected from the group
consisting of Forssman antigen, 6'SLac, SLeX, GM3, BG-H1,
GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G, BSM, Lactose, LNT,
Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb, ManT, pLNH,
Rha-.alpha., GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-S-Tn(Ser)-S-G.
59. The method of claim 58, wherein the first or second serum
sample is assayed to determine the levels of antibodies to at least
three glycan and/or glycoprotein antigens selected from the group
consisting of Forssman antigen, 6'SLac, SLeX, GM3, BG-H1,
GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G, BSM, Lactose, LNT,
Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb, ManT, pLNH,
Rha-.alpha., GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), and
Ac-S-Tn(Ser)-S-G.
60. The method of claim 59, wherein the first or second serum
sample is assayed to determine the levels of antibodies to at least
four glycan and/or glycoprotein antigens selected from the group
consisting of Forssman antigen, 6'SLac, SLeX, GM3, BG-H1,
GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G, BSM, Lactose, LNT,
Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb, ManT, pLNH,
Rha-.alpha., GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-S-Tn(Ser)-S-G.
61. The method of claim 60, wherein the first and second serum
sample is assayed to determine the levels of antibodies to at least
five glycan and/or glycoprotein antigens selected from the group
consisting of Forssman antigen, 6'SLac, SLeX, GM3, BG-H1,
GA2.sub.di, LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G, BSM, Lactose, LNT,
Fuc-b, Fuc-a, Galb1-6Man-a, GA1, Gala1-4Galb, ManT, pLNH,
Rha-.alpha., GalNAc.alpha.1-3 Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-S-Tn(Ser)-S-G.
62. The method of claim 57, wherein the antibodies are selected
from the group consisting of IgG, IgM, IgA, IgD, IgE, and
combinations thereof.
Description
BACKGROUND OF THE INVENTION
[0001] Vaccine therapies, such as cancer vaccine therapies, have
been shown to only produce a clinical response in a subset of
patients. At present, there is no good method to select the subset
of patients that will respond best to vaccine treatment. Therefore,
methods to predict which patients will benefit from a vaccine
(e.g., cancer vaccine) and strategies to determine which patients
are having a favorable immune response are desired. Such methods
will enable better clinical trial design, more personalized
treatment decisions, and a better use of time and resources.
BRIEF SUMMARY OF THE INVENTION
[0002] The invention provides a method for predicting the clinical
response to a cancer vaccine in a patient having cancer comprising
obtaining a serum sample from a patient who has not been previously
administered the cancer vaccine; assaying the serum sample to
determine the levels of antibodies in the patient to at least one
glycan and/or glycoprotein antigen selected from the group
consisting of Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Sialyl.alpha.2-3Gal.beta.1-4Gc-(GM3),
Fuc.alpha.1l-2Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4Glc.beta.-(BG-H1),
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Gal.alpha.1-3Gal-(B.sub.di),
Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-(Ac-S-Tn(Thr)-G-G), BSM, Lactose,
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.-(LNT), Fuc-b, Fuc-a,
Gal.beta.1-6Man-.alpha.-(Galb1-6Man-a),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1),
Gal.alpha.1-4Gal.beta.-(Gala1-4Galb),
Man.alpha.1-6[Man.alpha.1-3]Man.beta.-(ManT),
Gal.beta.(1-3GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-(pLNH),
Rha-.alpha.-, GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-(Ac-S-Tn(Ser)-S-G); and comparing
the determined levels of antibodies to the at least one glycan
and/or glycoprotein antigen to a control, so as to predict the
clinical response to the cancer vaccine in the patient.
[0003] The invention provides a method for determining the immune
response to a cancer vaccine in a patient having cancer comprising
obtaining a first serum sample from a patient who has not been
previously administered the cancer vaccine; obtaining a second
serum sample from the patient after administration of the cancer
vaccine, assaying the first and second serum samples to determine
the first and second levels of antibodies, respectively, to at
least one glycan and/or glycoprotein antigen selected from the
group consisting of the Forssman antigen (e.g., the Forssman
disaccharide), GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A), the Tn antigen,
the TF antigen,
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Sia.alpha.2-3 Gal.beta.1-3[Fuc.alpha.1-4]GlcNAc.beta.1-(SLeA),
Fuc.alpha.1-2Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(LeY),
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4Glc-(GM3),
Fuc.alpha.1-2Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4Glc.beta.-(BG-H1),
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.sym.1-3)Gal.beta.-(LNnH),
Gal.alpha.1-3Gal-(B.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3-
Gal.beta.1-(A-LeB), and fetuin; and comparing the determined first
and second levels of antibodies to the at least one glycan and/or
glycoprotein antigen, so as to determine the immune response to the
cancer vaccine in the patient.
[0004] The invention provides a method for predicting the clinical
response to a cancer vaccine in a patient having cancer comprising
obtaining a serum sample from a patient who has been previously
administered the cancer vaccine; assaying the serum sample to
determine the levels of antibodies in the patient to at least one
glycan and/or glycoprotein antigen selected from the group
consisting of the Forssman antigen (e.g., the Forssman
disaccharide), GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A), fetuin,
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-,
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4Glc-(GM3), Fuc-a, and
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3-
Gal.beta.1-(A-LeB); and comparing the determined levels of
antibodies to the at least one glycan and/or glycoprotein antigen
to a control, so as to predict the clinical response to the cancer
vaccine in the patient.
[0005] The invention also provides a method for predicting
long-term survival in a patient having cancer comprising obtaining
a serum sample from a patient which has not been previously
administered cancer treatment; assaying the serum sample to
determine the levels of antibodies in the patient to at least one
glycan and/or glycoprotein antigen selected from the group
consisting of GalNAc.beta.1-4Gal.beta.-(GA2.sub.di-),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-(Ac-S-Tn(Thr)-G-G), Fuc-a, Fuc-b,
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1),
Gal.beta.1-6Man-.alpha.-(Galb1-6Man-a),
Gal.alpha.1-4Gal.beta.-(Gal.alpha.1-4Galb),
Man.alpha.1-6[Man.alpha.1-3]Man.beta.-(ManT), Man-.alpha. (Man-a),
Glc.alpha.1-6Glc.beta.-(isomaltose),
Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-(Ara5),
Man.alpha.1-2Man.alpha.1-6(Man.alpha.1-2Man.alpha.1-3)Man.alpha.1-6(Man.a-
lpha.1-2Man.alpha.1-2Man.alpha.1-3)Man.beta.1-4GlcNAc-(Man9),
GalNAc-.beta. (GalNAc-b),
Fuc.alpha.1-2Gal.beta.1-4GlcNAc.beta.-(BG-H2),
Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.-
beta.-(LacNAc (trimeric)), Gal.alpha.1-4Gal.beta.1-4Glc-(Pk or
Gb3), Glc.beta.1-4Glc.beta.-(cellobiose),
Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1 (LNnT),
Man.alpha.1-6Man-.alpha. (Mana1-6Man-a)
Gal.alpha.1-3Gal.beta.1-4Gal.alpha.-(Gal3),
Gal.beta.1-3(Sia.alpha.2-6)GlcNAc.beta.1-3Gal.beta.1- (LSTb),
GalNAc-.alpha.-(GalNAc-a),
Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3Gal.beta.1-4(Fuc.alpha.1-3)GlcN-
Ac.beta.1-3Gal.beta.1-(LeA-LeX), Forssman antigen, and
Ac(Gal.beta.1-3GalNAc.alpha.)Ser-Gly-(Ac-TF(Ser)-G); and comparing
the determined levels of antibodies to the at least one glycan
and/or glycoprotein antigen to a control, so as to predict the
long-term survival in the patient.
[0006] Additionally, the invention provides a kit for predicting
the clinical response to a cancer vaccine in a patient sample from
a patient having prostate cancer comprising a composition including
at least one glycan and/or glycoprotein antigen selected from the
group consisting of Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Sialyl.alpha.2-3Gal.beta.1-4Glc-(GM3),
Fuc.alpha.1-2Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4Glc.beta.-(BG-H1),
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Gal.alpha.1-3Gal-(B.sub.di),
Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-(Ac-S-Tn(Thr)-G-G), BSM, Lactose,
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.-(LNT), Fuc-b, Fuc-a,
Gal.beta.1-6Man-.alpha.-(Galb1-6Man-a),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1),
Gal.alpha.1-4Gal.beta.-(Gal.alpha.1-4Galb),
Man.alpha.1-6[Man.alpha.1-3]Man.beta.-(ManT),
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-(pLNH),
Rha-.alpha.-, GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1), fetuin, and
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-(Ac-S-Tn(Ser)-S-G).
[0007] The invention provides kit for determining the immune
response to a cancer vaccine in a patient sample from a patient
having prostate cancer comprising a composition including at least
one glycan and/or glycoprotein antigen selected from the group
consisting of the Forssman antigen (e.g., the Forssman
disaccharide), GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A), the Tn antigen,
the TF antigen,
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Sia.alpha.2-3 Gal.beta.1-3[Fuc.alpha.1-4]GlcNAc.beta.1-(SLeA),
Fuc.alpha.1-2Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(LeY),
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac), Sialyl.alpha.2-3
Gal.beta.1-4Glc-(GM3), Fuc.alpha.1-2Gal.beta.1-3GlcNAc.beta.1-3
Gal.beta.1-4Glc.beta.-(BG-H1),
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Gal.alpha.1-3Gal-(B.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3-
Gal.beta.1-(A-LeB), and fetuin.
[0008] Additionally, the invention provides a kit for predicting
the clinical response to a cancer vaccine in a patient sample from
a patient having prostate cancer comprising a composition including
at least one glycan and/or glycoprotein antigen selected from the
group consisting of the Forssman antigen (e.g., the Forssman
disaccharide), GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A), fetuin,
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-,
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4Glc- (GM3), Fuc-a, and
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-3
(Fuc.alpha.1-4)GlcNAc.beta.1-3Gal.beta.1-(A-LeB).
[0009] The invention also provides kit for predicting the long-term
survival in a patient sample from a patient having prostate cancer
comprising a composition including at least one glycan and/or
glycoprotein antigen selected from the group consisting of
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di-),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-(Ac-S-Tn(Thr)-G-G), Fuc-a, Fuc-b,
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1),
Gal.beta.1-6Man-.alpha.-(Galb1-6Man-a),
Gal.alpha.1-4Gal.beta.-(Gala1-4Galb),
Man.alpha.1-6[Man.alpha.1-3]Man.beta.-(ManT), Man-.alpha. (Man-a),
Glc.alpha.1-6Glc.beta.-(isomaltose),
Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-(Ara5),
Man.alpha.1-2Man.alpha.1-6(Man.alpha.1-2Man.alpha.1-3)Man.alpha.1-6(Man.a-
lpha.1-2Man.alpha.1-2Man.alpha.1-3)Man.beta.1-4GlcNAc-(Man9),
GalNAc-.beta.(GalNAc-b),
Fuc.alpha.1-2Gal.beta.1-4GlcNAc.beta.-(BG-H2),
Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.-
beta.-(LacNAc(trimeric)), Gal.alpha.1-4Gal.beta.1-4Glc-(Pk or Gb3),
Glc.beta.1-4Glc.beta.-(cellobiose),
Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1 (LNnT),
Man.alpha.1-6Man-.alpha. (Man.alpha.1-6Man-a)
Gal.alpha.1-3Gal.beta.1-4Gal.alpha.-(Gal3),
Gal.beta.1-3(Sia.alpha.2-6)GlcNAc.beta.1-3Gal.beta.1-(LSTb),
GalNAc-.alpha.-(GalNAc-a),
Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3Gal.beta.1-4(Fuc.alpha.1-3)GlcN-
Ac.beta.1-3 Gal.beta.1-(LeA-LeX), Forssman antigen, and
Ac(Gal.beta.1-3GalNAc.alpha.)Ser-Gly-(Ac-TF(Ser)-G).
[0010] The invention provides a method for improving the efficacy
of a virus-based vaccine in a patient comprising enhancing antibody
responses to one or more glycans or glycoprotein antigens.
[0011] The invention provides a method for improving the efficacy
of a virus-based vaccine in a patient comprising altering levels of
antibodies in the patient prior to vaccine therapy.
[0012] The invention provides a method for improving the efficacy
of a virus-based vaccine in a patient comprising increasing the
amounts of one or more glycans or glycoprotein antigens in the
patient.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S)
[0013] FIGS. 1A-D are Kaplan-Meier curves comparing survival of
patients with pre-vaccination antibody levels above or below the
cutoff for Sialyl LeX (cutoff=9.6, p=0.0002, FIG. 1A), BG-H1
(cutoff=13.2;p=0.0001; FIG. 1B), B.sub.di (cutoff=14.2;p=0.0005;
FIG. 1C), and BG-A (IgM cutoff=11.4; p=0.0001; FIG. 1D). All are at
a dilution of 1:50. In FIGS. 1A and 1B, the survival of patients
above cutoff is represented by the lower (solid) line and the
survival of patients below cutoff is represented by the upper
(dotted) line. In FIG. 1C and 1D, the survival of patients about
cutoff is represented by the upper (dotted) line and the survival
of patients below cutoff is represented by the lower (solid)
line.
[0014] FIG. 2 contains a list of selected array components and the
structures of selected linkers. The array components allow the
detection of the relevant subpopulations of serum antibodies, which
can serve as biomarkers.
DETAILED DESCRIPTION OF THE INVENTION
[0015] Antibodies are a critical element of the immune response.
Although there is good agreement that antibody responses are vital
for many vaccines targeting pathogens, the role of antibody
responses for cancer vaccines is still a matter of debate. Numerous
studies show that antibodies can affect the outcome, but the
response can either be beneficial or detrimental. The effect is
likely to depend on many factors, such as the antibody isotype and
subclass, target antigen, affinity, and selectivity.
[0016] A number of studies show that induction of antibodies by
cancer vaccines correlates with improved survival. In addition,
there is evidence that these antibodies can directly contribute to
anti-tumor immunity by binding and killing tumor cells, a process
that could be especially important for preventing metastases. Other
studies suggest that antibody responses can be unfavorable. In some
cases, antibodies can enhance growth of tumors and protect cells
from killing by cytotoxic T lymphocytes (CTL). In certain mouse
cancer model studies, removal of B cells has been shown to reduce
tumor burden and enhance effectiveness of cancer vaccines.
[0017] Antibodies to glycans also can influence the response to
vaccines. Using pre-clinical models, Stager et al., Nat. Med., 9:
1287-1292 (2003) showed that natural antibodies help stimulate
favorable immune responses to vaccines. Since anti-glycan
antibodies are a major class of natural antibodies, pre-existing
anti-glycan antibodies could influence immune responses to
vaccines. Moreover, individuals with widely different levels of
some anti-glycan antibodies could mount very different immune
responses to the same vaccine. For these reasons, additional
studies are needed to fully understand the role of antibodies for
cancer vaccines.
[0018] Carbohydrate antigens are directly or indirectly involved in
most types of cancer vaccines, but this class of antigens has been
largely understudied. Some vaccines specifically target
tumor-associated carbohydrate antigens. For example, a number of
vaccines targeting tumor-associated carbohydrate antigens, such as
Tn, TF, sialyl-Tn, and Globo H, have been prepared and evaluated
(see, e.g., Keding et al., Proc. Natl. Acad. Sci. USA, 101(33):
11937-11942 (2004)). For these vaccines, a key question is whether
a given patient expresses the target antigen.
[0019] Glycans also can be involved in other vaccines that do not
specifically target a carbohydrate antigen. For example, cells
display an abundance of glycans on their cell surface, and the
glycan content changes significantly with the onset and progression
of cancer. Therefore, vaccines based on whole tumor cells present a
variety of carbohydrate antigens to the immune system, many of
which are not normally present in healthy tissue.
[0020] Vaccines based on specific proteins also can involve
carbohydrates, since many of them are post-translationally modified
with glycans. Glycans can even play a role in vaccines that do not
directly contain carbohydrate antigens. An immune response to a
specific antigen on a target cell can lead to a process referred to
as "antigen spreading" or "antigen cascade" (see, e.g., Ranieri et
al., Immunol. Invest., 29(2): 121-125 (2000), Disis et al., J.
Clin. Oncol., 20(11): 2624-2632 (2002), Butterfield et al., Clin.
Cancer Res., 9(3): 998-1008(2003), Wierecky et al., Cancer Immunol.
Immunother., 55(1): 63-67 (2006), and Arlen et al., Clin. Cancer
Res., 12(4): 1260-1269 (2006)). As cells are killed, presentation
of other cellular components can lead to a broader immune response
against antigens that were not present in the original vaccine.
Antigen cascade is associated with more potent immune responses and
better clinical outcomes. Carbohydrates are an abundant family of
antigens found on tumor cells, but it is not presently known if
antigen spreading to glycans occurs after vaccination, nor is it
known if antigen spreading to glycans is beneficial for clinical
outcomes.
[0021] Through direct and/or indirect mechanisms, there are
numerous glycans that could be involved in the immune response
induced by a vaccine, such as a cancer vaccine. It is extremely
difficult to predict which glycans will be targeted.
[0022] Accordingly, the invention provides a method for predicting
the clinical (immune) response to a cancer vaccine in a patient
having cancer. The method comprises obtaining a serum sample from
the patient prior to the administration of the vaccine to the
patient, assaying the serum sample to determine the levels of
antibodies in the patient to at least one glycan and/or
glycoprotein antigen, and comparing the determined levels of
antibodies to the at least one glycan and/or glycoprotein antigen
to a control, so as to predict the clinical response to the cancer
vaccine in the patient.
[0023] Additionally, the invention provides a method of predicting
long-term survival in a patient having cancer comprising obtaining
a serum sample from a patient who has not received cancer treatment
(e.g., administration of a cancer vaccine), assaying the serum from
the patient for antibody levels to at least one glycan and/or
glycoprotein antigen, and comparing the determined levels of
antibodies to the at least one glycan and/or glycoprotein antigen
to a control, so as to predict the long-term survival in the
patient (e.g., in response to cancer treatment).
[0024] The methods to determine the immune response to these
antigens can be used to predict which patients will have a clinical
benefit from the vaccine. Once the antibody response to these
antigens is determined and compared to a control, the antibody
response can be used as an early indicator of a beneficial
response, an early indicator of efficacy, or an early indicator of
a favorable (or unfavorable) response.
[0025] The term "antibody" refers to a specific protein binding
partner for an antigen and is any substance, or group of
substances, which has a specific binding affinity for an antigen to
the exclusion of other substances. The generic term antibody
includes polyclonal antibodies, monoclonal antibodies, and antibody
fragments. Specific classes of antibodies include, but are not
limited to, IgG, IgM, IgA, IgD, and IgE. The levels of antibodies
measured can be from only one class of antibody (e.g., IgG, IgM,
IgA, IgD, or IgE) or combinations thereof (e.g., two or more
classes of antibodies, three or more classes of antibodies, four or
more classes of antibodies, or five or more classes of antibodies).
For example, the antibody levels of IgG, IgM, and IgA collectively
(anti-Ig) can be measured. Alternatively, the ratios of antibodies,
such as IgA/IgM or (IgA+IgG)/IgM, can be measured.
[0026] The levels of antibodies can be measured at any serum
dilution. For example, serum dilutions of 1:10, 1:25, 1:30, 1:50,
1:100, 1:200, 1:250, 1:300, 1:400, and 1:500 can be used in the
inventive methods.
[0027] Detection of antibodies from the patient samples can be
accomplished using techniques known in the art, such as
immunoenzymatic techniques, e.g., immunoperoxidase staining
technique, or the avidin-biotin technique, or immunofluorescence
techniques (see, e.g., Ciocca et al., Meth. Enzymol., 121:562-79
(1986), and Introduction to Immunology, (2.sup.nd Ed), 113-117,
Macmillan Publishing Company (1986)). Serologic diagnostic
techniques involve the detection and quantification of other
associated antigens that have been secreted or "shed" into the
serum or other biological fluids of patients. Such antigens can be
detected in the biological fluids using techniques known in the
art, such as radioimmunoassays (RIA) or enzyme-linked
immunoabsorbant assays (ELISA), wherein antibody reactive with the
shed antigen is used to detect the presence of the antigen in a
fluid sample (See, e.g., Uotila et al., J. Immunol. Methods, 42:11
(1981) and Fayed et al., Disease Markers, 14: 155-160 (1998)).
[0028] The patient can be a mammal, such as a mouse, rat, hamster,
guinea pig, rabbit, cat, dog, pig, cow, horse, or primate.
Preferably, the patient is human.
[0029] The cancer of the patient is not particularly limited.
Examples include prostate, breast, pancreatic, ovarian, gastric,
head and neck, liver, lung, kidney, bone, brain, colorectal,
uterine, skin, endometrial, esophageal, anal, oral, nasal, and
rectal cancers. Preferably, the cancer of the patient is prostate
cancer.
[0030] The cancer vaccine can be any potential cancer vaccine.
Examples include, but are not limited to, prostate cancer vaccines,
breast cancer vaccines, pancreatic cancer vaccines, ovarian cancer
vaccines, gastric cancer vaccines, head and neck cancer vaccines,
liver cancer vaccines, lung cancer vaccines, kidney cancer
vaccines, bone cancer vaccines, brain cancer vaccines, colorectal
cancer vaccines, uterine cancer vaccines, skin cancer vaccines,
endometrial cancer vaccines, esophageal cancer vaccines, anal
cancer vaccines, oral cancer vaccines, nasal cancer vaccines, and
rectal cancer vaccines.
[0031] The vaccine can be a peptide-based, plasmid-based, or viral
vector-based vaccine. Viral vector-based vaccines include, but are
not limited to, poxvirus-based, adenovirus-based, and
adeno-associated virus-based vaccines. When the vaccine is a
poxvirus-based vaccine, the poxvirus can be any suitable poxvirus,
such as avipox (e.g., fowlpox, canarypox, and pigeonpox) or
orthopox (vaccinia (e.g., MVA and NYVAC), cowpox, camelpox, and
monkeypox). Preferably, the cancer vaccine is a prostate cancer
poxvirus-based vaccine, such as PROSTVAC-VF.
[0032] PROSTVAC-VF is composed of an initial vaccination with a
recombinant vaccinia virus containing the human genes for prostate
specific antigen (PSA) and three costimulatory molecules (B7.1,
LFA-3, and ICAM-1), followed by booster injections with a fowlpox
virus with the same four transgenes (see, e.g., Garnett et al.,
Curr. Pharm. Des., 12: 351-361 (2006), and Madan et al., Expert
Opin. Biol. Ther., 10: 19-28 (2010)). The vaccine is designed to
stimulate an immune response to prostate tumor cells that express
high levels of PSA. The vaccine has been evaluated in several phase
I and phase II clinical trials with excellent results (see, e.g.,
Gulley et al., Cancer Immunol. Immunother., 2(2): 155-158 (2010),
Lechleider et al., Clin. Cancer Res., 14: 5284-5291 (2008), Madan
et al., Clin. Cancer Res., 14: 4526-4531 (2008), Garnett et al.,
Clin. Cancer Res., 14: 3536-3544 (2008), Arlen et al., J. Urol.,
178: 1515-1520 (2007), Theoret et al., Clin. Genitourin. Cancer, 5:
347-350 (2007), and Arlen et al., Clin. Cancer Res., 12: 1260-1269
(2006)).
[0033] The number of glycan and/or glycoprotein antigens assayed
can be any suitable number (e.g., one, two, three, four, five, six,
seven, eight, nine, ten, or more). Preferably, the number of glycan
and/or glycoprotein antigens assayed is at least two (e.g., at
least three, at least four, at least five, at least six, at least
seven, at least eight, at least nine, or at least ten).
[0034] The glycan and/or glycoprotein antigens for use in the
inventive methods and kits can be presented on an antigen surface,
such as an array (e.g., a glycan array as described in Example 1
and Oyelaran et al., J. Proteome Res., 8: 3529-3538 (2009)).
[0035] It is known in the art that multivalent binding is important
for antibody recognition of glycans. Therefore, the glycans and/or
glycoproteins can be attached (e.g., conjugated) to carrier
molecules (scaffolds), such as proteins, dendrimers, nanoparticles,
liposomes, and certain biocompatible polymers known to those in the
art. Preferably, the glycans are attached to a protein, such as
bovine serum albumin (BSA) or human serum albumin (HSA).
[0036] It is also known in the art that the spacing and orientation
of antigens and their epitopes are important for antibody
recognition and the formation of multivalent interactions.
Therefore, the glycans can be attached to the carrier molecules in
varying amounts to produce conjugates with varying glycan
densities. For example, the number of glycans attached to each
carrier molecule (e.g., albumin, such as BSA) can be modulated to
produce glycan-carrier conjugates (e.g., glycoproteins) with
varying densities. When these conjugates are immobilized on a
surface, the surface will display varying glycan densities.
Conjugation ratios for the carrier molecules, such as albumin, can
be as little as zero (i.e., no addition of carrier molecules) or
fifty or more (i.e., for every carrier molecule, there are fifty
glycan molecules). Exemplary conjugation ratios include 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50.
[0037] Alternatively, the density of glycan-carrier conjugates can
be varied by mixing unmodified carrier molecules with the glycan
and/or glycoprotein antigens and immobilizing the mixture on a
surface. For example, the glycan and/or glycoprotein antigens can
be mixed with differing amounts of albumin (e.g., BSA or HSA) and
added to a surface (e.g., an array surface). As the proportion of
the albumin increases, the glycan and/or glycoprotein antigens
become further spaced apart on the surface. The larger the amount
of albumin, the lower the density of the glycan and/or glycoprotein
antigens on the surface (see, e.g., Zhang et al., Mol. Biosyst., 6:
1-9 (2010)).
[0038] In another embodiment, the glycans (e.g., oligosaccharide
lactols) and/or glycoproteins can be attached directly to an
antigen surface using a hydrazide, hydrazine, amino-, or aminoxy
modified surface, or can incorporate other linkers with an
appropriate functional group for attaching to a surface.
[0039] Linkers for use in the inventive methods and kits include,
but are not limited to Hex, CETE, APE, APD, and MEAG (see FIG. 2);
however, other molecules can be used, including other organic
molecules, polypeptides, or polymers known to those in the art.
[0040] The glycan and/or glycoprotein antigens for use in the
inventive methods and kits include, but are not limited to, those
listed in FIG. 2. In particular, the glycan and/or glycoprotein
antigens can be selected from the group consisting of
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLeX),
Sialyl.alpha.2-3Gal.beta.1-4Glc-(GM3),
Fuc.alpha.1-2Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4Glc.beta.-(BG-H1),
GalNAc.beta.1-4Gal.beta.-(GA2.sub.di),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(LNnH),
Gal.alpha.1-3Gal-(B.sub.di),
Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-(Ac-S-Tn(Thr)-G-G), bovine
submaxillary mucin (BSM), Lactose,
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.-(LNT), Fuc-b, Fuc-a,
Gal.beta.1-6Man-.alpha. (Galb1-6Man-a),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(GA1),
Gal.alpha.1-4Gal.beta.-(Gal.alpha.1-4Galb),
Man.alpha.1-6[Man.alpha.1-3]Man.beta.-(ManT),
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-(pLNH),
the Forssman antigen (e.g., the Forssman disaccharide,
GalNAc.alpha.1-3GalNAc.beta.1-),
GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A), the Tn antigen,
the TF antigen,
Sia.alpha.2-3Gal.beta.1-3[Fuc.alpha.1-4]GlcNAc.beta.1-(SLeA),
Fuc.alpha.1-2Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(LeY), Man-.alpha.
(Man-a), Glc.alpha.1-6Glc.beta.-(isomaltose),
Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1-5Ara.alpha.1
(Ara5),
Man.alpha.1-2Man.alpha.1-6(Man.alpha.1-2Man.alpha.1-3)Man.alpha.1-6(Man.a-
lpha.1-2Man.alpha.1-2Man.alpha.1-3)Man.beta.1-4GlcNAc-(Man9),
GalNAc-.beta.-(GalNAc-b),
Fuc.alpha.1-2Gal.beta.1-4GlcNAc.beta.-(BG-H2),
Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.-
beta.-(LacNAc(trimeric)), Gal.alpha.1-4Gal.beta.1-4Glc-(Pk or Gb3),
Glc.beta.1-4Glc.beta.-(cellobiose),
Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1 (LNnT),
Man.alpha.1-6Man-.alpha. (Mana1-6Man-a)
Gal.alpha.1-3Gal.beta.1-4Gal.alpha.-(Gal3),
Gal.beta.1-3(Sia.alpha.2-6)GlcNAc.beta.1-3Gal.beta.1-(LSTb),
GalNAc-.alpha.-(GalNAc-a),
Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3Gal.beta.1-4(Fuc.alpha.1-3)GlcN-
Ac.beta.1-3Gal.beta.1-(LeA-LeX), Rha-.alpha., fetuin,
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-(Ac-S-Tn(Ser)-S-G), and
Ac(Gal.beta.1-3GalNAc.alpha.)Ser-Gly-(Ac-TF(Ser)-G), and
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-3(Fuc.alpha.1-4)GlcNAc.beta.1-3-
Gal.beta.1-(A-LeB). Additionally, encompassed by the invention are
fragments or substructures of these glycans and/or glycoprotein
antigens, as well larger glycans and/or glycoprotein antigens that
include these structures as fragments. For example, LNnH is a
hexasaccharide; however, fragments of the full hexasaccharide
(e.g., tetrasaccharide and pentasaccharide) also are encompassed by
the invention. Furthermore, Rha-.alpha. is a monosaccharide and
other glycans that comprise this monosaccharide as a terminal
structure are encompassed by the invention.
[0041] A preferred example of the glycan and/or glycoprotein
antigens for use in the inventive methods and kits is the Forssman
antigen. As used herein, the term "Forssman antigen" encompasses
the full pentasaccharide, as well as the trisaccharide,
tetrasaccharide, or the disaccharide discussed above (i.e.,
fragments or substructures of the full pentasaccharide). In
addition, it encompasses longer oligosaccharides or polysaccharides
that contain a Forssman antigen.
[0042] The invention also encompasses glycan and/or glycoprotein
antigens that are similar in structure to the Forssman antigen. An
example is the "core 5" glycan (GalNAc.alpha.1-3GalNAc.alpha.1-)
that is very close in structure to the Forssman disaccharide
(GalNAc.alpha.1-3GalNAc.beta.1-). Core 5 glycan alternatively could
be used to detect anti-Forssman antibodies, since core 5 glycan is
similar in structure and has cross-reactivity.
[0043] Another preferred example of the glycan and/or glycoprotein
antigens for use in the inventive methods and kits is the blood
group A antigen (BG-A). As used herein, the term "BG-A" encompasses
the trisaccharide as well as other oligosaccharides or
polysaccharides that contain the blood group A trisaccharide as a
substructure.
[0044] Exemplary embodiments of glycan and/or glycoprotein antigens
for use in the inventive methods and kits, which antigens are
attached to linkers and/or carrier molecules (e.g., BSA), include,
but are not limited to, GalNAc.beta.1-4Gal.beta.-(37/BSA)
(GA2.sub.di-37),
Gal.beta.1-4GlcNAc.beta.1-6(Gal.beta.1-4GlcNAc.beta.1-3)Gal.beta.-(11/BSA-
) (LNnH-11), Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-Hex-(7/BSA)
(Ac-S-Tn(Thr)-G-G-07),
Ac-Ser-(GalNAc.alpha.)Thr-Gly-Gly-Hex-(24/BSA)
(Ac-S-Tn(Thr)-G-G-24), Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.-(5/BSA)
(LNT-05), Fuc-b-(4/BSA) (Fuc-b-04), Fuc-b-(22/B SA) (Fuc-b-22),
Fuc-a-(4/B SA) (Fuc-a-04), Fuc-a-(22/B SA) (Fuc-a-22),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(6/BSA) (GA1-06),
Gal.beta.1-3GalNAc.beta.1-4Gal.beta.1-(20/BSA) (GA1-20),
Gal.beta.1-3GlcNAc.beta.1-3Gal.beta.1-4GlcNAc.beta.1-3Gal.beta.1-(7/BSA)
(pLNH-07), GalNAc.alpha.1-3GalNAc.beta.1-(4/BSA) (Forssman di-04),
GalNAc.alpha.1-3GalNAc.beta.1-21/B SA) (Forssman di-21),
GalNAc.alpha.1-3GalNAc.beta.1-(31/BSA) (Forssman di-31), and
GalNAc-.alpha.-BSA (4/BSA) (GalNAc-a-04), GalNAc-.alpha.-BSA
(22/BSA) (GalNAc-.alpha.-22), Gal.beta.1-4GlcNAc.beta.1-3
Gal.beta.1-BSA (14/BSA) (LNnt-14),
GalNAc.alpha.1-3Gal.beta.-(4/BSA) (A.sub.di-04),
GalNAc.alpha.1-3Gal.beta.-(17/BSA) (A.sub.di-17),
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-Hex-(4/BSA)
(Ac-S-Tn(Ser)-S-G-04),
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-Hex-(22/BSA)
(Ac-S-Tn(Ser)-S-G-22),
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-Hex-(33/BSA)
(Ac-S-Tn(Ser)-S-G-33),
Ac(Gal.beta.1-3GalNAc.alpha.)Ser-Gly-Hex-(4/BSA) (Ac-TF(Ser)-G-04),
Ac(Gal.beta.1-3GalNAc.alpha.)Ser-Gly-Hex-(24/BSA)
(Ac-TF(Ser)-G-24), Rha-1-BSA, ManT-BSA, BG-A, fetuin, and A-LeB.
Carrier molecules, such as proteins (e.g., BSA and HSA),
dendrimers, nanoparticles, liposomes, and biocompatible polymers
can be used.
[0045] In one embodiment, a method is provided for predicting the
clinical (immune) response to a cancer vaccine in a patient having
cancer comprising obtaining a serum sample from a patient who has
not been previously administered the cancer vaccine; assaying the
serum sample to determine the levels of antibodies in the patient
to at least one glycan and/or glycoprotein antigen selected from
the group consisting of 6' SLac, SLeX, GM3, BG-H1, GA2.sub.di,
LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G, BSM, Lactose, LNT, Fuc-b, Fuc-a,
Galb1-6Man-a, GA1, Gala1-4Galb, ManT, pLNH, Rha-.alpha., A.sub.di,
BG-A, GA1, fetuin, and Ac-S-Tn(Ser)-S-G; and comparing the
determined levels of antibodies to the at least one glycan and/or
glycoprotein antigen to a control, so as to predict the immune
response to the cancer vaccine in the patient. Such a method can be
used to predict whether a patient will have a positive response to
treatment with a vaccine (e.g., cancer vaccine).
[0046] Preferably, this method comprises determining the levels of
antibodies in the patient to at least one glycan and/or
glycoprotein antigen selected from the group consisting of 6' SLac,
GM3, LNnH, Fuc-a, Rha-.alpha., A.sub.di, BG-A, GA1, fetuin, and
Ac-S-Tn(Ser)-S-G, as well as fragments or substructures of these
glycans and/or glycoprotein antigens and larger glycans and/or
glycoprotein antigens that include these structures as
fragments.
[0047] Most preferably, the levels of IgM antibodies to blood group
A or a derivative of blood group A (BG-A) are assayed. Additionally
or alternatively, the levels of IgG antibodies to GA1, the levels
of IgG antibodies to Rha-.alpha., the levels of IgA antibodies to
Fuc-a, the levels of Ig antibodies to LNnH, the levels of IgG
antibodies to 6' SLac, and/or the levels of IgG antibodies to GM3
are measured.
[0048] In another embodiment, a method is provided for determining
the immune response to a cancer vaccine in a patient having cancer
comprising obtaining a first serum sample from a patient who has
not been previously administered the cancer vaccine; obtaining a
second serum sample from the patient after administration of the
cancer vaccine, assaying the first and second serum samples to
determine the first and second levels of antibodies, respectively,
to at least one glycan and/or glycoprotein antigen selected from
the group consisting of Forssman antigen (e.g., Forssman
disaccharide or an antigen similar in structure to the Forssman
antigen, such as core 5), A.sub.di, BG-A, the Tn antigen, the TF
antigen, SLeX, SLeA, LeY, 6'SLac, GM3, BG-H1, GA2.sub.di, LNnH,
B.sub.di, A-LeB, and fetuin; and comparing the determined first and
second levels of antibodies to the at least one glycan and/or
glycoprotein antigen, so as to determine the immune response to the
cancer vaccine in the patient. Such a method can be used to
determine whether a patient will clinically benefit from
administration of the vaccine.
[0049] Preferably, this method comprises determining the levels of
antibodies to at least one glycan and/or glycoprotein antigen
selected from the group consisting of Forssman antigen, core 5,
A-LeB, A.sub.di, BG-A, and fetuin, as well as fragments or
substructures of these glycans and/or glycoprotein antigens and
larger glycans and/or glycoprotein antigens that include these
structures as fragments.
[0050] Most preferably, this method comprises determining the
levels of IgA or Ig antibodies to the Forssman antigen (e.g.,
Forssman disaccharide or an antigen similar in structure to the
Forssman antigen, such as core 5).
[0051] In another embodiment, a method is provided for predicting
the clinical response to a cancer vaccine in a patient having
cancer comprising obtaining a serum sample from a patient who has
been previously administered the cancer vaccine (e.g., 2 months, 3
months, or 4 months post-vaccination); assaying the serum sample to
determine the levels of antibodies in the patient to at least one
glycan and/or glycoprotein antigen selected from the group
consisting of the Forssman antigen (e.g., the Forssman
disaccharide), A.sub.di, BG-A, fetuin,
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-, 6'SLac, GM3, Fuc-a, and A-LeB;
and comparing the determined levels of antibodies to the at least
one glycan and/or glycoprotein antigen to a control, so as to
predict the clinical response to the cancer vaccine in the
patient.
[0052] In yet another embodiment, a method is provided for
predicting long-term survival in a patient having cancer comprising
obtaining a serum sample from a patient which has not been
previously administered cancer treatment; assaying the serum sample
to determine the levels of antibodies in the patient to at least
one glycan and/or glycoprotein antigen selected from the group
consisting of GA2.sub.di, LNnH, SLeX, Ac-S-Tn(Thr)-G-G, Fuc-a,
Fuc-b, Galb1-6Man-a, GA1, Gala1-4Galb, ManT, Man-a, isolmaltose,
Ara5, Man9, GalNAc-b, BG-H2, LacNAc (trimeric), Pk or Gb3,
cellobiose, LNnT, Mana1-6Man-a, Gal3, LSTb, GalNAc-a, LeA-LeX,
Forssman antigen (e.g., Forssman disaccharide or an antigen similar
in structure to the Forssman antigen, such as core 5), and
Ac-TF(Ser)-G; and comparing the determined levels of antibodies to
the at least one glycan and/or glycoprotein antigen to a control,
so as to predict the long-term survival in the patient.
[0053] Preferably, this method comprises determining the levels of
antibodies to at least one glycan and/or glycoprotein antigen
selected from the group consisting of Gala1-4Galb, ManT, LSTb,
Forssman antigen, core 5, and Ac-TF(Ser)-G, as well as fragments or
substructures of these glycans and/or glycoprotein antigens and
larger glycans and/or glycoprotein antigens that include these
structures as fragments. Additionally or alternatively, the levels
of antibodies to BS-A can be determined and compared to a
control.
[0054] The control to which the levels of antibodies to a
particular antigen are compared can be any suitable control. The
control can be a positive or negative control. Examples of positive
controls include (i) a value determined to be an average level of
the antibodies to the particular antigen in the serum of patients
that respond positively to the cancer vaccine (i.e., patients who
exemplified a strong immune response to the cancer vaccine), (ii) a
value determined to be the threshold value above or below which the
patient will respond positively to the cancer vaccine, (iii) a
value determined to be an average level of the antibodies to the
particular antigen in the serum of patients who exhibit long-term
survival, and (iv) a threshold value above or below which there is
an increased likelihood that the patient will exhibit long-term
survival.
[0055] Examples of negative controls include (i) a value determined
to be an average level of the antibodies to the particular antigen
in the serum of patients that respond negatively to the cancer
vaccine (i.e., patients who exemplified little (weak) or no immune
response to the cancer vaccine), (ii) a value determined to be the
threshold value above or below which the patient will respond
negatively to the cancer vaccine, (iii) a value determined to be an
average level of the antibodies to the particular antigen in the
serum of patients that do not exhibit long-term survival, and (iv)
a threshold value above or below which there is an increased
likelihood that the patient will not exhibit long-term survival. A
threshold value can be determined by any conventional method.
[0056] A positive response to treatment (e.g., the cancer vaccine)
includes, but is not limited to, an increased immune response to
the cancer, a decrease in tumor size, a decrease in tumor mass, a
decrease in the number of tumor cells, a decrease in metastasis,
and/or increased survival.
[0057] Long-term survival refers to a survival of greater than the
average survival in patients having a particular cancer (e.g., at
least 6 months, at least 1 year, at least 2 years, at least 3
years, at least 4 years, at least five years, at least six years,
at least seven years, at least eight years, at least nine years, at
least ten years, or more when compared to the average survival in
patients having a particular cancer).
[0058] When two values are being compared (e.g., the levels of
antibodies to one or more antigens between a first and second serum
sample), the values preferably are significantly different (e.g.,
statistically significant (p.ltoreq.0.05)).
[0059] Kits comprising at least one (e.g., at least two, at least
three, at least four, at least five, at least six, at least seven,
at least eight, at least nine, at least ten, or more) glycan and/or
glycoprotein antigen also is encompassed by the invention. The
components in the kit can be provided in packaged combination in
the same or in separate containers, depending on their
cross-reactivities and stabilities. The amounts and proportions of
reagents provided in the kit can be selected so as to provide
optimum results for a particular application.
[0060] The kit further can comprise ligands of the analyte and
calibration and control materials, and also can include antibody
standards for the antigens tested. The components of the kit can be
in any suitable form, such as liquid or lyophilized.
[0061] In one embodiment, a kit is provided for predicting the
clinical (immune) response to a cancer vaccine in a patient sample
from a patient having cancer comprising a composition including at
least one or more (e.g., two, three, four, five, six, seven, eight,
nine, ten, or more) glycan and/or glycoprotein antigen selected
from the group consisting of: 6'SLac, SLeX, GM3, BG-H1, GA2.sub.di,
LNnH, B.sub.di, Ac-S-Tn(Thr)-G-G, BSM, Lactose, LNT, Fuc-b, Fuc-a,
Galb1-6Man-a, GA1, Gala1-4Galb, ManT, Rha-.alpha.-, A.sub.di, BG-A,
GA1, Ac-S-Tn(Ser)-S-G, fetuin, and pLNH. Such a kit can be used to
predict whether a patient (from which the sample was obtained) will
benefit from administration of the cancer vaccine.
[0062] In another embodiment, a kit is provided for determining the
immune response to a cancer vaccine in a patient sample from a
patient having cancer (e.g., prostate cancer) comprising
composition including at least one (e.g., two, three, four, five,
six, seven, eight, nine, ten, or more) glycan and/or glycoprotein
antigen selected from the group consisting of the Forssman antigen
(e.g., the Forssman disaccharide), A.sub.di, BG-A, the Tn antigen,
the TF antigen, SLeX, SLeA, LeY, 6'SLac, GM3, BG-H1, GA2.sub.di,
LNnH, B.sub.di, A-LeB, and fetuin.
[0063] In another embodiment, a kit is provided for predicting the
clinical (immune) response to a cancer vaccine in a patient sample
from a patient having cancer (e.g., prostate cancer) comprising a
composition including at least one glycan and/or glycoprotein
antigen selected from the group consisting of the Forssman antigen
(e.g., the Forssman disaccharide),
GalNAc.alpha.1-3Gal.beta.-(A.sub.di),
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.-(BG-A), fetuin,
Ac-Ser-(GalNAc.alpha.)Ser-Ser-Gly-,
Sialyl.alpha.2-6Gal.beta.1-4Glc-(6'SLac),
Sialyl.alpha.2-3Gal.beta.1-4Glc-(GM3), Fuc-a,
GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-3
(Fuc.alpha.1-4)GlcNAc.beta.1-3 Gal.beta.1-(A-LeB).
[0064] In yet another embodiment, a kit is provided for predicting
the long-term survival in a patient sample from a patient having
cancer (e.g., prostate cancer) comprising a composition including
at least one glycan and/or glycoprotein antigen selected from the
group consisting of GA2.sub.di, LNnH, SLeX, Ac-S-Tn(Thr)-G-G,
Fuc-a, Fuc-b, Galb1-6Man-a, GA1, Gala1-4Galb, ManT, Man-a,
isolmaltose, Ara5, Man9, GalNAc-b, BG-H2, LacNAc (trimeric), Pk or
Gb3, cellobiose, LNnT, Man.alpha.1-6Man-a, Gal3, LSTb, GalNAc-a,
LeA-LeX, Forssman antigen (e.g., the Forssman disaccharide), and
Ac-TF(Ser)-G. Additionally or alternatively, the kit can comprise
BS-Al.
[0065] The invention also includes methods for improving the
efficacy of a virus-based vaccine in a patient. The method
comprises enhancing antibody responses to the glycans and/or
glycoprotein antigens described in connection with the inventive
methods and/or stimulating responses to the particular glycans
and/or glycoprotein antigens in patients (e.g., the Forssman
antigen and/or BG-A).
[0066] For example, in order to improve the efficacy of a vaccine
in a patient, responses to the Forssman antigen (or fragments or
substructures of the Forssman antigen and larger glycans and/or
glycoprotein antigens that include these structures as fragments)
can be purposely enhanced and/or stimulated. Enhancing and/or
stimulating response to the Forssman antigen can be done using any
suitable means known in the art. For example, host cells can be
genetically engineered to produce (more) Forssman antigen (e.g.,
Forssman disaccharide), such as by administering a vector
comprising a nucleic acid sequence encoding the enzymes involved in
the biosynthesis of the Forssman antigen. Tissue culture conditions
can be altered to induce higher expression of the Forssman antigen,
such as by supplementing the culture with GalNAc or treating the
culture with a small molecule inducer of GalNAc alpha transferase.
Host cell lines with enhanced production of the Forssman antigen
can be identified, and the virus-based vaccine can be grown using
that cell line. Forssman or Forssman-like oligosaccharides can be
chemically or enzymatically added to the viral surface of the
virus-based vaccine. A Forssman-containing protein, dendrimer,
nanoparticle, liposome, or polymer (or other conjugate suitable for
inducing antibodies) can be added as a second component of the
vaccine or as a secondary injection. Additionally or alternatively,
vaccination can be performed with a Forssman-containing protein,
dendrimer, nanoparticle, liposome, or polymer prior to or after
vaccination with the vaccine (e.g., PROSTVAC-VF or ALVAC-HIV).
[0067] The invention also includes methods for improving the
efficacy of a virus-based vaccine in a patient through altering the
patient's antibody populations prior to starting vaccine therapy.
For example, in order to improve the efficacy of a vaccine in a
patient, antibody levels to IgM in the patient could be increased
by pre-vaccinating with a BG-A-containing protein, dendrimer,
nanoparticle, liposome, or polymer (or other conjugate suitable for
inducing antibodies).
[0068] The invention also includes methods for improving the
efficacy of a virus-based vaccine by increasing the amounts of key
glycans and/or glycoprotein antigens, such as BG-A and the Forssman
antigen, such that pre-existing antibodies more readily recognize
the virus. For example, host cells can be genetically engineered to
produce (more) BG-A antigen (e.g., BG-A trisaccharide), such as by
administering a vector comprising a nucleic acid sequence encoding
the enzymes involved in the biosynthesis of the BG-A antigen.
Tissue culture conditions can be altered to induce higher
expression of the BG-A antigen. Host cell lines with enhanced
production of the BG-A antigen can be identified, and the
virus-based vaccine can be grown using that cell line.
[0069] The virus-based vaccine can be any suitable vaccine,
including, but not limited to, poxvirus-based, adenovirus-based,
and adeno-associated virus-based vaccines. Preferably, the vaccine
is a poxvirus-based vaccine, such as a vaccine based on avipox
(e.g., fowlpox, canarypox, and pigeonpox) or orthopox (vaccinia
(e.g., MVA and NYVAC), cowpox, camelpox, and monkeypox)
viruses.
[0070] The vaccine can be used for any suitable purpose and
preferably is used to prevent or treat cancer or to treat or
prevent infection by a virus. Examples of suitable cancer vaccines
include, but are not limited to, prostate cancer vaccines, breast
cancer vaccines, pancreatic cancer vaccines, ovarian cancer
vaccines, gastric cancer vaccines, head and neck cancer vaccines,
liver cancer vaccines, lung cancer vaccines, kidney cancer
vaccines, bone cancer vaccines, brain cancer vaccines, colorectal
cancer vaccines, uterine cancer vaccines, skin cancer vaccines,
endometrial cancer vaccines, esophageal cancer vaccines, anal
cancer vaccines, oral cancer vaccines, nasal cancer vaccines, and
rectal cancer vaccines. Preferably, the cancer vaccine is a
prostate cancer poxvirus-based vaccine, such as PROSTVAC-VF.
[0071] Examples of suitable vaccines against viral infection
include, but are not limited to, HIV vaccines, hepatitis virus
vaccines, influenza virus vaccines, HPV vaccines, and Ebola virus
vaccines. Preferably, the virus vaccine is a poxvirus-based HIV
vaccine, such as ALVAC-HIV (see, e.g., Kim et al., New England
Journal of Medicine, 361: 2209-2220 (2009): Estaban, Human
Vaccines, 5(12): 867-871 (2009); and Kaufman et al., Expert Opinion
on Biological Therapy, 4: 575-588 (2004)).
[0072] The following examples further illustrate the invention but,
of course, should not be construed as in any way limiting its
scope.
EXAMPLE 1
[0073] This example demonstrates the identification of predictive
markers and markers of efficacy of a clinical vaccine treatment for
prostate cancer.
[0074] Initial studies were conducted on serum samples from 29
patients immunized with the PROSTVAC-VF vaccine (see, e.g., Gulley
et al., Cancer Immunol. Immunother., 2(2): 155-158 (2010)).
Briefly, patients with metastatic castrate-resistant prostate
cancer were vaccinated once with a recombinant vaccinia virus
containing the human genes for prostate specific antigen (PSA) and
three costimulatory molecules (B7.1, LFA-3, and ICAM-1). Patients
received monthly boosters with the recombinant fowlpox virus
containing the same four transgenes. Patients with a rising PSA or
new lesions were taken off study for disease progression, but
survival status was updated periodically. Sera prior to vaccination
and 3 months after vaccination were profiled on a neoglycoprotein
array as described in Zhang et al., Mol. Biosyst., 6: 1-9 (2010).
Exemplary array components are listed in FIG. 2. IgG, IgM, and IgA
collectively (anti-Ig) at dilutions of 1:50 and 1:200 were
measured.
Predictive Biomarkers
[0075] Predictive biomarkers are useful for tailoring treatment to
individual patients. To evaluate relationships between antibody
levels and survival, the Partek Genomics Suite software was used.
With this software, correlations (e.g., Pearson correlation) were
evaluated, hazard ratios (HR) (e.g., Cox regression) were
determined, and Kaplan-Meier curves were generated.
[0076] For the majority of carbohydrate antigens, lower serum
antibody levels were associated with increased survival. Tables 1
and 2 indicate the hazard ratios, Pearson correlations with overall
survival, and associated p-values for the best antigens at serum
dilutions of 1:50 (Table 1) and 1:200 (Table 2).
TABLE-US-00001 TABLE 1 Characteristics of the best predictive
biomarkers at a dilution of 1:50. Antigen Cox Regression Pearson
Correlation 6'SLac HR = 1.45 (p = 0.011) r = -0.49 (p = 0.007) SLeX
HR = 1.22 (p = 0.012) r = -0.48 (p = 0.008) GM3 HR = 1.38 (p =
0.015) r = -0.47 (p = 0.009) BG-H1 HR = 1.53 (p = 0.008) r = -0.51
(p = 0.004) GA2.sub.di-37 HR = 2.00 (p = 0.018) r = -0.47 (p =
0.009) LNnH-11 HR = 1.70 (p = 0.004) r = -0.41 (p = 0.028) B.sub.di
HR = 0.68 (p = 0.044) r = 0.30 (p = 0.118) Ac-S-Tn(Thr)-G-G-07 HR =
1.49 (p = 0.027) r = -0.46 (p = 0.0118) Ac-S-Tn(Thr)-G-G-24 HR =
2.00 (p = 0.0213) r = -0.52 (p = 0.0042) BSM HR = 1.36 (p = 0.0428)
r = -0.38 (p = 0.0411) Lactose HR = 1.88 (p = 0.0398) r = -0.41 (p
= 0.0257) LNT-05 HR = 1.19 (p = 0.0393) r = -0.37 (p = 0.0474)
Fuc-b-04 HR = 1.24 (p = 0.047) r = -0.38 (p = 0.0414) Fuc-b-22 HR =
1.58 (p = 0.0247) r = -0.49 (p = 0.0072) Fuc-a-04 HR = 1.37 (p =
0.067) r = -0.45 (p = 0.0145) Fuc-a-22 HR = 1.39 (p = 0.098) r =
-0.42 (p = 0.027) Galb1-6Man-a HR = 1.29 (p = 0.0909) r = -0.45 (p
= 0.0139)
TABLE-US-00002 TABLE 2 Characteristics of the best predictive
biomarkers at a dilution of 1:200. Antigen Cox Regression Pearson
Correlation BG-H1 HR = 1.39 (p = 0.0255) r = -0.39 (p = 0.039)
B.sub.di HR = 1.66 (p = 0.011) r = 0.41 (p = 0.0259) GA1-06 HR =
0.73 (p = 0.0366) r = 0.29 (p = 0.1297) GA1-20 HR = 0.68 (p =
0.0283) r = 0.34 (p = 0.0723) Gala1-4Galb HR = 0.61 (p = 0.0164) r
= -0.37 (p = 0.051) ManT HR = 0.64 (p = 0.0206) r = -0.29 (p =
0.1217) pLNH-07 HR = 4.2 (p = 0.0175) r = -0.34 (p = 0.0742)
[0077] FIGS. 1A-C include several examples of Kaplan-Meier survival
curves that take into consideration the length of survival and
whether or not the patient was still alive at the final time point.
Patients were separated into two groups based on whether their
antibody levels were above or below a cutoff, and the proportion of
surviving patients was plotted over time. For example, patients
with anti-sialyl LeX (anti-SLeX) levels about 9.6 had a 4 year
survival of 8%, while patients with antibody levels below the
cutoff had a 4 year survival of 60% (see FIG. 1A; p=0.0002).
Kaplan-Meier curves were generated at a range of cutoffs for each
array component to give an overall view of the performance of the
biomarker.
[0078] For a small number of antigens, such as B.sub.di, higher
serum antibody levels correlated with improved survival (HR for
B.sub.di=0.68). For example, patients with anti-B.sub.di levels
above a cutoff of 14.2 had a 4 year survival of 63%, while patients
below the cutoff had a 4 year survival of 13% (see FIG. 1C). The
difference in survival was statistically significant.
[0079] Combinations of antigens can provide even better predictive
power. It is notable that many of the antigens identified have no
correlation with the Halabi predicted survival and appear to be
independent markers.
Efficacy Biomarkers
[0080] Changes in antibody levels were evaluated in 28 of the 29
patients. Sera were profiled before and after vaccination at
dilutions of 1:50 and 1:200. A significant change was defined as
greater than 2.6 fold based on previous studies. Significant
antibody increases to a number of carbohydrate antigens were
observed. All patients had at least one measurable change, and one
patient had changes to 154 array components. The median number of
changes per person was 14 at 1:50 and 8.5 at 1:200.
[0081] The most common changes were to the Forssman disaccharide
(Forssman di-04; 18/28 patients at 1:200),
GalNAc.alpha.1-3Gal.beta.-(4/BSA) (A.sub.di-04) (13/28 patients at
1:200), and GalNAc.alpha.1-3(Fuc.alpha.1-2)Gal.beta.1-(BG-A) (11/28
patients at 1:200). Changes ranged from 3 fold to 68 fold. Changes
to tumor antigens also were observed, especially at the higher
serum concentration (dilution of 1:50). Changes to the Tn antigen,
the TF antigen,
Sialyl.alpha.2-3Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(SLex),
SialylGal.beta.1-3 (Fuc.alpha.1-4)GlcNAc.beta.1-3
Gal.beta.1-4Glc.beta.-(SLeA), and
Fuc.alpha.1-2Gal.beta.1-4(Fuc.alpha.1-3)GlcNAc-(LeY) were observed
in 4-8 patients. Changes to other tumor antigens were detected, but
less frequently (1-2 patients).
[0082] Several of the observed changes were to carbohydrate
antigens known to be over-expressed on at least some patients'
prostate tumors and their metastatic lesions, such as Tn, TF, SLeX,
and LeY. Modest levels of expression of A.sub.di were observed on
some prostate tumors.
[0083] Relationships between antibody responses and survival were
also evaluated. Based on the Kaplan-Meier curve, patients with
changes to Forssman di-04 at 1:200 showed a statistically
significant correlation with improved survival (p=0.015; log rank).
Antibody responses to Tn and TF also were associated with longer
survival, while changes to A.sub.di did not show a significant
correlation with improved survival in the subset of patients that
were originally tested. There was no correlation between survival
and the total number of changes for a given person.
EXAMPLE 2
[0084] This example demonstrates the identification of prognostic
markers for prostate cancer.
[0085] There are a number treatment options for prostate cancer
patients, but many of these treatments can cause significant side
effects. In addition, many prostate tumors end up growing slowly
and do not need treatment; however, it is very difficult to
determine which patients should be treated aggressively and which
are better served by a "watch and wait" approach. Better prognostic
markers could be useful for aiding treatment decisions.
[0086] The Halabi nomogram provides a good estimation of life
expectancy on treatment for patients with prostate cancer. It is
most accurate for groups of patients, but also provides a
reasonable projection on an individual basis. The nomogram combines
many different measures of tumor aggressiveness and tumor burden,
such as PSA levels and Gleason scores.
[0087] Antibody subpopulations in serum of patients were identified
that correlate with the Halabi predicted survival. The best
correlations are listed in Tables 3 and 4.
TABLE-US-00003 TABLE 3 Characteristics of the best prognostic
biomarkers at a dilution of 1:50. Antigen Pearson Correlation
GA2.sub.di-37 r = -0.39 (p = 0.036) LNnH-11 r = -0.38 (p = 0.0392)
SLeX r = -0.45 (p = 0.0136) Ac-S-Tn(Thr)-G-G-07 r = -0.39 (p =
0.0353) Ac-S-Tn(Thr)-G-G-24 r = -0.42 (p = 0.022) Fuc-a-04 r =
-0.48 (p = 0.0092) Fuc-a-022 r = -0.43 (p = 0.0187) Fuc-b-04 r =
-0.37 (p = 0.0479) Fuc-b-22 r = -0.42 (p = 0.0233) Galb1-6Man-a r =
-0.38 (p = 0.0412) Man-a r = -0.4529 (p = 0.014) Isomaltose r =
-0.4413 (p = 0.017) Ara5 r = -0.4119 (p = 0.026) Man9 r = -0.406 (p
= 0.029) GalNAc-b r = -0.398 (p = 0.032) BG-H2 r = -0.396 (p =
0.033) LacNAc (trimeric) r = -0.3958 (p = 0.034) Pk or Gb3 r =
-0.3913 (p = 0.036) Cellobiose r = -0.3881 (p = 0.037) LNnT-14 r =
-0.3769 (p = 0.044) Mana1-6Man-a r = -0.3742 (p = 0.046) Gal3 r =
-0.372 (p = 0.047)
TABLE-US-00004 TABLE 4 Characteristics of the best prognostic
biomarkers at a dilution of 1:200. Antigen Pearson Correlation
GA1-20 r = 0.44 (p = 0.0158) Gala1-4Galb r = 0.39 (p = 0.0349) ManT
r = 0.40 (p = 0.0304) LSTb r = 0.51793 (p = 0.004) GalNAc-a-22 r =
0.48366 (p = 0.008) GalNAc-a-04 r = 0.45712 (p = 0.013) Forssman
di-04 r = 0.44945 (p = 0.014) LNT-21 r = 0.43332 (p = 0.019)
LeA-LeX r = 0.43103 (p = 0.020) Forssman di-31 r = 0.37687 (p =
0.044) Forssman di-21 r = 0.36976 (p = 0.048)
[0088] These biomarkers (i.e., antibody levels to the particular
glycan or glycoprotein antigen) can be used as prognostic markers
for prostate cancer. Since they are found in serum, they could be
more readily used than the Halabi nomogram, which requires
measurements of a variety of parameters including samples that are
not easily accessed (biopsy samples).
EXAMPLE 3
[0089] This example describes experiments to validate the
above-described findings with a larger set of patients.
[0090] A multicenter phase II trial was completed on the
PROSTVAC-VF vaccine involving 112 patients. Patients received PRO
STVAC-VF therapy or control vectors. The inclusion criteria,
vaccine construct, and therapeutic protocol for this trial were
essentially the same as the 29 patients described in Example 1.
[0091] Anti-glycan antibody populations in sera before and 3 months
after vaccination at both 1:50 and 1:200 were be profiled using the
array technology described in Example 1. Combined antibody levels
(anti-Ig), as well as IgG and IgM separately, were examined. All
clinical data was blinded until after the profiling was complete.
Once the survival data was unblinded, the relationships between
antibody signals and survival were analyzed. Pearson correlations,
hazard ratios, Kaplan-Meier curves, ROC curves, and each of their
corresponding p-values were evaluated as discussed in Example 1. In
addition, the relationships between changes and survival were
evaluated. Analysis of the relationships between biomarker levels
and survival in the control arm allowed the determination whether
the markers are general prognostic markers or specific markers for
vaccine therapy.
[0092] Tables 5 and 6 indicate the hazard ratios, Pearson
correlations with overall survival, and associated p-values for the
best predictive (Table 5) and efficacy (Table 6) biomarkers
associated with this study.
TABLE-US-00005 TABLE 5 Characteristics of the best predictive
biomarkers. Pearson Cox correlation regression Best p- Hazard p-
Array component dilution Measurement r value Ratio value LNnH-11
1:200 Pre-vaccination -0.2611 0.023 2.5276 0.003 6'Slac 1:50
Pre-vaccination -0.2398 0.037 1.55682 0.0051 GM3 1:50
Pre-vaccination -0.2315 0.044 1.46536 0.0067 Rha-a 1:50
Pre-vaccination 0.1881 0.104 0.7291 0.029 Ac-S-Tn(Ser)-S-G-33 1:50
Pre-vaccination 0.2719 0.018 0.6705 0.0044 Blood Group A (IgM) 1:50
Pre-vaccination 0.37 0.0009 0.79 0.0009 Ac-S-Tn(Ser)-S-G-22 1:200
Pre-vaccination 0.20899 0.070 0.7808 0.032
TABLE-US-00006 TABLE 6 Characteristics of the best efficacy
biomarkers. Pearson Cox correlation regression Best p- Hazard p-
Array component dilution Measurement r value Ratio value
Forssman-04 1:200 Change 0.2477 0.031 0.8083 0.048 fetuin 1:50
Change 0.2656 0.020 0.7841 0.043 A-LeB-hexa 1:50 Change 0.2940
0.010 0.7952 0.035
[0093] Serum IgM antibody levels to the blood group A trisaccharide
(BG-A) consistently demonstrated positive correlations with overall
survival in a variety of statistical models (see FIG. 1D). Median
survival was more than a year longer in subjects with abundant
pre-existing IgM antibodies for BG-A. The highest quartile of
subjects with anti-BG-A IgM antibodies prior to vaccination
survived nearly twice as long as the lowest quartile.
Post-vaccination survival correlated strongly with pre-vaccination
BG-A IgM (HR=0.79, p=0.00085). ROC analysis showed an AUC of 0.77
for post-vaccination survival of at least 30 months. BG-A IgM
antibodies appear to be an independent prognostic marker without
correlation to Halabi predicted survival, Gleason score, age, or
PSA level.
[0094] As was observed with the initial study described in Example
1, patients frequently showed humoral responses to the Forssman
disaccharide. Changes in binding to Forssman disaccharide were
measured best at a serum dilution of 1:200. Robust changes to
Forssman disaccharide correlated with longer post-vaccination
survival. The median survival of patients with at least a four-fold
increase in anti-Forssman disaccharide antibodies was 8 months
longer than the median survival of patients with little or no
response to Forssman disaccharide (p=0.005). Moreover, among the
patients with responses to Forssman disaccharide, odds-ratio
calculations demonstrated that larger responses to Forssman
disaccharide were associated with greater likelihood of long-term
survival (.gtoreq.3.5 years post-vaccination). Patients with the
highest likelihood of surviving at least 3.5 years had six to
ten-fold increases in antibodies to Forssman disaccharide, which
were associated with eight-fold better probability of living at
least 3.5 years post-vaccination than patients with lower
responses.
[0095] Antibody responses to the Forssman antigen (e.g., Forssman
disachharide) were independent risk factors that did not correlate
with overall titers to viral vectors, T-cell responses, Halabi
predicted survival, age, PSA level, or Gleason score.
[0096] Since patients with antibody responses to the Forssman
antigen (e.g., Forssman disaccharide) and BG-A have longer
survival, the efficacy of the vaccine may be improved by purposely
enhancing responses to Forssman and/or BG-A and/or stimulating
responses to Forssman and/or BG-A in all patients.
[0097] Interestingly, control patients also showed increases in
antibodies for BG-A after inoculation with inactive, wild-type
viral vectors. Similarly, control patients showed increases in
antibodies for the Forssman disaccharide after inoculation with
inactive, wild-type viral vectors. Survival in control patients,
however, was not correlated with responses to Forssman
disaccharide. This indicates that increases in Forssman
disaccharide alone are not general prognostic indicators. Instead,
it shows that these responses are specific markers of efficacy for
the vaccine.
[0098] While not wishing to be bound by any particular theory, the
Forssman antigen, a fragment or substructure of the Forssman
antigen, a larger glycan and/or glycoprotein antigen that includes
the fragment or substructure, or an antigen with a similar
structure (e.g., core 5) and/or BG-A or a derivative thereof may be
located on some poxvirus vector vaccines (e.g., PROSTVAC-VF and
ALVAC-HIV).
[0099] To test this theory, the expression of BG-A and the Forssman
antigen on vaccinia and fowlpox viruses was evaluated using ELISA
and a competition assay. The expression of BG-A and the Forssman
antigen was confirmed on both viral vectors. The BG-A and Forssman
antigen carbohydrates likely are acquired by carry-over from their
host cells (chicken embryo dermal cells) in a manner similar to
that reported for influenza viruses propogated in chicken cells.
Consistent with this, chickens are known to synthesize both
Forssman antigen and BG-A. Based on these results, it appears that
the responses to BG-A and the Forssman antigen induced by
PROSTVAC-VF are a result of the viral vector rather than a response
to PSA or a response derived from antigen-spreading.
[0100] Implications of these results also extends to other
vaccines. Several poxvirus-based cancer vaccines are in clinical
trials, such as PANVAC and rV-NY-ESO-1. Oncolytic poxviruses also
are being developed (see, e.g., Ziauddin et al., Gene Ther., 17:
550-559 (2010); and Kim et al., Nature Reviews Cancer, 9: 64-71
(2009)), and povirus-based vaccines are being investiganted to
prevent infection of many pathogens (e.g., ALVAC-HIV). Many of
these vectors are produced in chicken embryo dermal cells, and
antibodies to BG-A and the Forssman antigen likely are relevant to
their clinical efficacy.
[0101] Since the results indicate that glycan composition and
consistency are a critical feature of vaccine potency, the choice
of host cell may significantly impact clinical outcomes for
pox-virus based vaccines. Additionally, glycan analysis of viral
vectors could serve as a quality control assessment for virus-based
vaccines.
[0102] All references, including publications, patent applications,
and patents, cited herein are hereby incorporated by reference to
the same extent as if each reference were individually and
specifically indicated to be incorporated by reference and were set
forth in its entirety herein.
[0103] The use of the terms "a" and "an" and "the" and similar
referents in the context of describing the invention (especially in
the context of the following claims) are to be construed to cover
both the singular and the plural, unless otherwise indicated herein
or clearly contradicted by context. The terms "comprising,"
"having," "including," and "containing" are to be construed as
open-ended terms (i.e., meaning "including, but not limited to,")
unless otherwise noted. Recitation of ranges of values herein are
merely intended to serve as a shorthand method of referring
individually to each separate value falling within the range,
unless otherwise indicated herein, and each separate value is
incorporated into the specification as if it were individually
recited herein. All methods described herein can be performed in
any suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g., "such as") provided herein, is
intended merely to better illuminate the invention and does not
pose a limitation on the scope of the invention unless otherwise
claimed. No language in the specification should be construed as
indicating any non-claimed element as essential to the practice of
the invention.
[0104] Preferred embodiments of this invention are described
herein, including the best mode known to the inventors for carrying
out the invention. Variations of those preferred embodiments may
become apparent to those of ordinary skill in the art upon reading
the foregoing description. The inventors expect skilled artisans to
employ such variations as appropriate, and the inventors intend for
the invention to be practiced otherwise than as specifically
described herein. Accordingly, this invention includes all
modifications and equivalents of the subject matter recited in the
claims appended hereto as permitted by applicable law. Moreover,
any combination of the above-described elements in all possible
variations thereof is encompassed by the invention unless otherwise
indicated herein or otherwise clearly contradicted by context.
Sequence CWU 1
1
2114PRTArtificial SequenceSynthetic 1Xaa Xaa Ser Gly 1
26PRTArtificial SequenceSynthetic 2Xaa Val Xaa Ser Ala Gly 1 5
34PRTArtificial SequenceSynthetic 3Xaa Xaa Thr Gly 1
44PRTArtificial SequenceSynthetic 4Xaa Ser Ser Gly 1
54PRTArtificial SequenceSynthetic 5Xaa Xaa Ser Gly 1
64PRTArtificial SequenceSynthetic 6Xaa Thr Ser Gly 1
74PRTArtificial SequenceSynthetic 7Xaa Xaa Ser Gly 1
84PRTArtificial SequenceSynthetic 8Xaa Xaa Ala Gly 1
94PRTArtificial SequenceSynthetic 9Xaa Xaa Gly Gly 1
104PRTArtificial SequenceSynthetic 10Xaa Xaa Ser Gly 1
114PRTArtificial SequenceSynthetic 11Xaa Xaa Xaa Gly 1
124PRTArtificial SequenceSynthetic 12Xaa Xaa Val Gly 1
134PRTArtificial SequenceSynthetic 13Xaa Xaa Xaa Gly 1
144PRTArtificial SequenceSynthetic 14Xaa Xaa Pro Gly 1
154PRTArtificial SequenceSynthetic 15Xaa Xaa Xaa Gly 1
164PRTArtificial SequenceSynthetic 16Xaa Xaa Ser Gly 1
1717PRTArtificial SequenceSynthetic 17Asp Thr Val Pro Leu Pro Thr
Ala His Gly Xaa Ser Ala Ser Ser Thr 1 5 10 15 Gly 1817PRTArtificial
SequenceSynthetic 18Asp Thr Val Pro Leu Pro Thr Ala His Gly Xaa Xaa
Ala Ser Ser Thr 1 5 10 15 Gly 1917PRTArtificial SequenceSynthetic
19Asp Thr Val Pro Leu Pro Thr Ala His Gly Thr Ser Ala Ser Ser Thr 1
5 10 15 Gly 2017PRTArtificial SequenceSynthetic 20Asp Thr Val Pro
Leu Pro Thr Ala His Gly Thr Xaa Ala Ser Ser Thr 1 5 10 15 Gly
2117PRTArtificial SequenceSynthetic 21Asp Thr Val Pro Leu Pro Xaa
Ala His Gly Thr Ser Ala Ser Ser Thr 1 5 10 15 Gly
* * * * *