U.S. patent application number 15/534203 was filed with the patent office on 2017-12-21 for plasma autoantibody biomarkers for basal like breast cancer.
The applicant listed for this patent is ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY, NATIONAL INSTITUTES OF HEALTH. Invention is credited to Karen Anderson, Jonine Figueroa, Joshua LaBaer, Jin Park, Ji Qiu, Garrick Wallstrom, Jie Wang.
Application Number | 20170363631 15/534203 |
Document ID | / |
Family ID | 56108127 |
Filed Date | 2017-12-21 |
United States Patent
Application |
20170363631 |
Kind Code |
A1 |
LaBaer; Joshua ; et
al. |
December 21, 2017 |
PLASMA AUTOANTIBODY BIOMARKERS FOR BASAL LIKE BREAST CANCER
Abstract
Cancer patients make antibodies to tumor-derived proteins that
are potential biomarkers for early detection. Twenty-eight antigens
have been identified as potential biomarkers for the early
detection of basal-like breast cancer (Tables 1, 2). Also, a 13-AAb
classifier has been developed that differentiate patients with BLBC
from healthy controls with 33% sensitivity at 98% specificity
(Table 3).
Inventors: |
LaBaer; Joshua; (Chandler,
AZ) ; Wang; Jie; (Glendale, AZ) ; Qiu; Ji;
(Chandler, AZ) ; Wallstrom; Garrick; (Mesa,
AZ) ; Anderson; Karen; (Scottsdale, AZ) ;
Park; Jin; (Phoenix, AZ) ; Figueroa; Jonine;
(Edinburgh, GB) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY
NATIONAL INSTITUTES OF HEALTH |
Scottsdale
Bethesda |
AZ
MD |
US
US |
|
|
Family ID: |
56108127 |
Appl. No.: |
15/534203 |
Filed: |
December 9, 2015 |
PCT Filed: |
December 9, 2015 |
PCT NO: |
PCT/US15/64792 |
371 Date: |
June 8, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
62089631 |
Dec 9, 2014 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 2600/118 20130101;
G01N 33/564 20130101; C12Q 2600/158 20130101; C12N 15/11 20130101;
G01N 33/57415 20130101; C12Q 2600/112 20130101; C12Q 1/6886
20130101; C07K 16/3015 20130101 |
International
Class: |
G01N 33/574 20060101
G01N033/574; C12Q 1/68 20060101 C12Q001/68; C07K 16/30 20060101
C07K016/30 |
Goverment Interests
STATEMENT OF GOVERNMENT RIGHTS
[0002] This invention was made with government support under U01
CA117374 awarded by the National Institutes of Health. The
government has certain rights in the invention.
Claims
1. A method for detection of basal-like breast cancer in a patient
sample harboring one or more antigens, comprising: detecting a
tumor antigen biomarker in said patient sample, wherein the
biomarker is selected from the antigens: P53 (TP53), NY-ESO-1
(CTAG1B), NY-ESO-2 (CTAG2), RNF216, PPHLN1, PIP4K2C, ZBTB16,
TAS2R8, WBP2NL, DOK2, PSRC1, MN1, TRIM21, POU4F1, SSMEM1, LMO4,
BCL2, KRT8, TSGA13, PVRL4, SNRK, DYRK3, RNF32, JUNB, KCNIP3,
CCDC68, CSN3, TRAIP.
2. The method of claim 1, wherein said detecting comprises
utilizing an enzyme-linked immunosorbant assay (ELISA).
3. The method of claim 1, further comprising detecting at least two
of said tumor antigen biomarkers and comparing a level of detection
to predetermined sensitivity and specificity threshold to determine
if basal-like breast cancer is indicated.
4. A basal-like breast cancer diagnostic test kit, comprising an
antibody against a tumor antigen biomarker selected from the group
consisting of: P53 (TP53), NY-ESO-1 (CTAG1B), NY-ESO-2 (CTAG2),
RNF216, PPHLN1, PIP4K2C, ZBTB16, TAS2R8, WBP2NL, DOK2, PSRC1, MN1,
TRIM21, POU4F1, SSMEM1, LMO4, BCL2, KRT8, TSGA13, PVRL4, SNRK,
DYRK3, RNF32, JUNB, KCNIP3, CCDC68, CSN3, TRAIP, and a suitable
detection agent.
5. The kit of claim 4, wherein an antibody against each of said
tumor antigen biomarkers is present in said kit.
6. A method for diagnosing basal-like breast cancer from a patient
sample harboring one or more antigens, comprising: a) detecting a
tumor antigen biomarker in said patient sample, wherein the
biomarker is selected from the antigens: P53 (TP53), NY-ESO-1
(CTAG1B), NY-ESO-2 (CTAG2), RNF216, PPHLN1, PIP4K2C, ZBTB16,
TAS2R8, WBP2NL, DOK2, PSRC1, MN1, TRIM21, POU4F1, SSMEM1, LMO4,
BCL2, KRT8, TSGA13, PVRL4, SNRK, DYRK3, RNF32, JUNB, KCNIP3,
CCDC68, CSN3, TRAIP; and b) comparing a detection result of step a)
with a control.
Description
CROSS REFERENCE
[0001] This application claims priority to U.S. provisional patent
application 62/089,631 filed on Dec. 9, 2014, which is incorporated
by reference herein in its entirety.
TECHNICAL FIELD
[0003] The disclosure herein related to biomarkers for cancer and
more particularly to autoantibody biomarkers for breast cancer.
BACKGROUND
[0004] Despite significant improvement in early detection by
routine mammography, breast cancer remains a global challenge.
Current screening mammography only detects 70% of breast cancers.
Breast tumors associated with high breast density and highly
proliferative cancers are frequently not detected by screening.
Therefore, there is an urgent need for biomarkers that can detect
potentially invasive breast cancer in their early stages.
[0005] Like other cancers, breast cancer is heterogeneous,
comprising multiple molecular subtypes with unique characteristics
of prognosis, response to treatment and risk of recurrence. This
heterogeneity affects the biomarker discovery, requiring both
larger sample sizes and different statistical approaches from
traditional methods of evaluation. A biomarker (or panel) may
perform well for one molecular subtype but not another.
[0006] Current screening mammography also has limitations in
detecting the basal-like subtype cancers. The fraction of BLBC
within all breast cancer cases detected by mammography is less than
its natural frequency in the general population, indicating that
BLBC was under-diagnosed by routine mammography and more frequently
detected as interval breast cancer. Early detection of BLBC by
screening mammography is compromised partly by its high
proliferation rate and lack of suspicious features of regular
breast malignancy, such as microcalcifications, irregular
spiculated masses or pleomorphic microcalcifications. Moreover,
BLBC is often present in women less than 50 years old, who are not
recommended for routine mammogram by US Preventative Service Task
Force mammogram guidelines.
[0007] Considering the high frequency of disease in women younger
than 50 years old, a potentially large population with BLBC does
not benefit from present breast cancer screening and would benefit
from a molecular test for the disease. Therefore, there is an
urgent need for biomarkers that can detect potentially invasive
basal like breast cancer in their early stages.
SUMMARY
[0008] We have identified 28 antigens as potential biomarkers for
the early detection of basal like breast cancer. These biomarkers
were selected out of 10,000 tumor antigens in a sequential
screening study and yielded supporting evidence in a blinded
validation study. These biomarkers should be useful components of
diagnostic tests and personalized therapeutics for breast
cancer.
[0009] All references cited throughout are hereby incorporated by
reference herein.
DESCRIPTION OF DRAWINGS
[0010] FIG. 1 depicts dotplots of AAb responses in various breast
cancer subtypes.
DETAILED DESCRIPTION
[0011] Notably, the sensitivity of a subtype-specific biomarker can
never be higher than the prevalence of that subtype in the
population where it is tested. The ability to find biomarkers for
cancer detection with high sensitivities has likely been impaired
by this effect. This is especially true for disease subtypes that
are less common in the overall population. Basal like breast cancer
is a breast cancer subtype with aggressive disease progression and
poor prognosis. It overlaps significantly with triple negative
breast cancer (TNBC), a clinical pathological subtype characterized
by negative tissue staining of estrogen receptor (ER), progesterone
receptor (PR), and the absence of human epidermal growth factor
receptor 2 (HER2) amplification.
[0012] TNBC is associated with African American ethnicity, younger
age, advanced stage at diagnosis and poorer outcomes. However, TNBC
itself has been found to be molecularly heterogeneous in two recent
studies. Among patients with TNBC, a core basal subtype with
expression of epidermal growth factor receptor (EGFR) or basal
cytokeratin 5/6 (CK5/6) characterized a group of patients with
worse prognosis than the rest of the patients with TNBC. This five
marker subtyping (ER-, PR-, HER2-, and either EGFR+ or CK5/6+) is
highly correlated with BLBC defined by gene expression
profiling.
[0013] Current screening mammography has limitations in detecting
the basal-like subtype. The fraction of BLBC within all breast
cancer cases detected by mammography is less than its natural
frequency in the general population, indicating that BLBC was
under-diagnosed by routine mammography and more frequently detected
as interval breast cancer. Early detection of BLBC by screening
mammography is compromised partly by its high proliferation rate
and lack of suspicious features of regular breast malignancy, such
as microcalcifications, irregular spiculated masses or pleomorphic
microcalcifications.
[0014] Moreover, BLBC is often present in women less than 50 years
old, who are not recommended for routine mammogram by US
Preventative Service Task Force mammogram guidelines. Considering
the high frequency of disease in women younger than 50 years old, a
potentially large population with BLBC does not benefit from
present breast cancer screening and would benefit from a molecular
test for the disease.
[0015] In practical terms, molecular diagnostic tests for the early
detection of cancer should be performed on readily accessible
samples, like plasma, because they are likely to be performed on
many individuals. The concentration of many cancer biomarkers in
blood tends to be very low because it relies upon secretion by
cancer cells which are few in number in the pre-clinical stage.
Moreover, the biomarker gets diluted in a large volume of plasma
volume and only a fraction of the secreted biomarker gets
distributed to the plasma.
[0016] An alternative strategy is to exploit the ability of the
immune system to detect the presence of tumor cells through the
generation of autoantibodies. These responses of the adaptive
immune system against target tumor antigens amplify the signals
from the minute amount of tumor proteins released from cancer
tissue.
[0017] We have previously conducted an autoantibody biomarker
discovery for breast cancer on our nucleic acid programmable
protein array (NAPPA) platform. NAPPA allows us to display
thousands of freshly produced full length human proteins on glass
slides without the need of protein purification and has been
applied to the study of disease specific antibodies in diseases
ranging from infectious to autoimmune to cancers. In that study, we
took a three stage study design to identify autoantibody markers
from 4988 human proteins.
[0018] The goal for the discovery stage 1 was to eliminate
non-reactive and uninformative (i.e. no difference between case and
control) antigens and reduce the total number of antigens. The top
761 antigens were selected based on differential reactivity between
cases and controls. The goal for the training stage II was to
identify candidate autoantibody markers. The goal for the blinded
validation stage III was to validate potential biomarkers. This
yielded a panel of 28 markers showing sensitivities in the 10-30%
range with specificities from 80-100%.
[0019] However, the sample cohort used in this study was a mixed
population of predominantly women with ER+PR+ breast cancer.
Therefore, the utility of these markers in subtypes like BLBC or
Her2+ are likely limited, considering their relatively low
percentage among breast cancer patients. Here, we aimed to identify
BLBC specific autoantibodies by profiling humeral immune responses
of BLBC patients against 10,000 human proteins.
[0020] One challenge associated with the use of "omics" technology
to study a homogeneous cancer subtype is the requirement of a large
number of samples to have sufficient power of analysis. To this
end, our study was supported by the Polish Breast Cancer Study, in
which over 2386 breast cancer patients were enrolled.
[0021] Paraffin embedded tissue samples were collected for
immunohistochemical (IHC) analysis and disease classification. We
successfully collected plasma samples from 145 patients classified
to be basal-like subtype by either PAM50 gene signature based on
mRNA expression profiling, or tissue IHC staining of ER, PR, HER2,
EGFR and CK5/6. In addition, for each patient, we also collect
plasma sample from an age, gender and location matched healthy
donor. Here, we first profiled sero-reactivity against
.about.10,000 human proteins in 45 BLBC patients and 45 matched
controls.
[0022] Candidate antigens were selected, assayed for their
autoantibodies in BLBC using customized NAPPA and enzyme-linked
immunosorbant assay (ELISA), and validated using an independent
patient cohort in a blind fashion. See, for example, "Tracking
humoral responses using self assembling protein microarrays,"
Proteomics Clin Appl. 2008 Oct. 2 (10-11):1518-27. A biomarker
signature was also developed to discriminate basal-like tumors from
age and location matched healthy individuals. We further evaluated
the specificity of the panel of autoantibodies to basal-like tumors
using a set of patients with other breast cancer subtypes.
[0023] The 28 antigens that we have identified as potential
biomarkers for the early detection of basal like breast cancer are
(Table 1, Table 2): P53 (TP53), NY-ESO-1 (CTAG1B), NY-ESO-2
(CTAG2), RNF216, PPHLN1, PIP4K2C, ZBTB16, TAS2R8, WBP2NL, DOK2,
PSRC1, MN1, TRIM21, POU4F1, SSMEM1, LMO4, BCL2, KRT8, TSGA13,
PVRL4, SNRK, DYRK3, RNF32, JUNB, KCNIP3, CCDC68, CSN3, TRAIP, which
are available at the DNASU Plasmid Repository at the Bio Design
Institute of the Arizona State University, Tempe, Ariz. In
addition, we also developed a classifier to differentiate patients
with BLBC from healthy controls with 33% sensitivity at 98%
specificity (Table 3).
[0024] We designated samples as positive if they exceeded
antigen-specific cutoffs for at least 2 of the 13 antigens.
Antigen-specific cutoffs were set to achieve 98% classifier
specificity by adjusting the specificity at the antigen level to
98.7%.
[0025] A point of novelty is the identification of the 28 antigens
that are potential biomarkers for early detection of basal like
breast cancer (Table 1, 2). Many of these 28 antigens have not been
previously associated with basal like breast cancer. In addition,
we also developed a classifier to differentiate patients with BLBC
from healthy controls with 33% sensitivity at 98% specificity
(Table 3).
TABLE-US-00001 TABLE 1 Training and Validation Statistics for
Potential basal-like breast cancer Biomarkers Training
(Cohort1&2: basal, Validation (Cohort3: basal, n = 95; healthy,
n = 95) n = 50; healthy, n = 50) Antigen sensitivity specificity
cutoffs sensitivity specificity CTAG1B 0.213 0.979 1.606 0.200
1.000 CTAG2 0.191 0.979 1.149 0.180 0.960 TRIM21 0.158 0.979 1.208
0.140 0.860 RNF216 0.110 0.978 1.369 0.043 0.956 MN1 0.105 0.979
1.311 0.060 0.920 PIP4K2C 0.105 0.979 1.200 0.020 1.000 TP53 0.084
0.979 3.171 0.200 1.000 ZBTB16 0.084 0.979 1.393 0.040 0.980 TRAIP
0.074 0.979 2.682 0.040 0.980 DOK2 0.074 0.979 1.164 0.060 1.000
CSN3 0.063 0.979 1.955 0.060 0.980 PPHLN1 0.063 0.979 3.394 0.080
1.000 TAS2R8 0.063 0.979 1.064 0.080 0.940 SSMEM1 0.063 0.979 1.562
0.060 0.960 DYRK3 0.063 0.979 1.462 0.040 0.940 KRT8 0.053 0.979
1.645 0.060 0.960 LMO4 0.053 0.979 1.199 0.020 0.980 WBP2NL 0.053
0.979 1.991 0.060 0.980 JUNB 0.042 0.979 1.165 0.020 0.960 TSGA13
0.042 0.979 1.313 0.020 0.980 PVRL4 0.042 0.979 0.899 0.020 0.920
CCDC68 0.042 0.979 2.438 0.000 0.940 BCL2 0.042 0.979 1.160 0.000
1.000 SNRK 0.032 0.979 4.127 0.020 0.960 PSRC1 0.032 0.979 1.372
0.120 0.960 KCNIP3 0.032 0.979 0.973 0.000 0.960 POU4F1 0.032 0.979
0.992 0.080 0.940 RNF32 0.021 0.979 1.445 0.040 0.980
TABLE-US-00002 TABLE 2 Performance of 28 antigens in all subtypes
of breast cancer. Sensitivity basal- luminal luminal Her2- Antigen
like A B enriched Specificity CTAG1B 0.208 0.033 0.045 0.056 0.979
CTAG2 0.188 0.000 0.000 0.000 0.979 TP53 0.124 0.033 0.000 0.056
0.979 RNF216 0.088 0.133 0.095 0.000 0.978 PPHLN1 0.083 0.100 0.182
0.000 0.979 PIP4K2C 0.076 0.100 0.091 0.111 0.979 ZBTB16 0.069
0.000 0.000 0.000 0.979 TAS2R8 0.069 0.000 0.000 0.056 0.979 WBP2NL
0.069 0.100 0.091 0.000 0.979 DOK2 0.069 0.133 0.091 0.056 0.979
PSRC1 0.063 0.033 0.045 0.056 0.979 MN1 0.062 0.100 0.000 0.056
0.979 TRAIP 0.062 0.067 0.045 0.000 0.979 CSN3 0.062 0.100 0.182
0.000 0.979 TRIM21 0.055 0.033 0.000 0.056 0.979 POU4F1 0.048 0.033
0.000 0.222 0.979 SSMEM1 0.048 0.033 0.136 0.000 0.979 LMO4 0.041
0.033 0.000 0.056 0.979 BCL2 0.041 0.033 0.045 0.000 0.979 KRT8
0.034 0.033 0.000 0.056 0.979 TSGA13 0.034 0.000 0.000 0.056 0.979
PVRL4 0.034 0.000 0.000 0.000 0.979 SNRK 0.028 0.000 0.045 0.000
0.979 DYRK3 0.028 0.033 0.045 0.000 0.979 RNF32 0.028 0.033 0.000
0.056 0.979 JUNB 0.021 0.000 0.000 0.000 0.979 KCNIP3 0.014 0.033
0.000 0.000 0.979 CCDC68 0.007 0.000 0.000 0.000 0.979
TABLE-US-00003 TABLE 3 Cutoffs for 13-AAb classifier Antigen Cutoff
CTAG1B 1.606 CTAG2 1.176 TP53 3.171 RNF216 1.459 PPHLN1 3.448
PIP4K2C 1.201 ZBTB16 1.925 TAS2R8 1.178 WBP2NL 2.120 DOK2 1.164
PSRC1 1.461 MN1 1.687 TRIM21 5.509
[0026] An example of how a patient sample would be handled to
detect and diagnose basal-like breast cancer using one or more of
the discovered biomarkers in a kit with a suitable detection agent
is as follows.
[0027] A patient's plasma sample is obtained, and then subsequently
tested for autoantibody responses against the proposed protein
panels. Briefly, protein targets are produced either freshly in
situ or purified ahead of time, and immobilized on solid surface. A
plasma sample is then incubated with these protein targets. Labeled
secondary antibody that can recognize human immunoglobulins are
used for the signal read out. Accordingly, data such as that shown
in FIG. 1 can be obtained and used to detect and/or diagnose
basal-like breast cancer.
[0028] Various changes in the details and components that have been
described may be made by those skilled in the art within the
principles and scope of the invention herein described in the
specification and defined in the appended claims. Therefore, while
the present invention has been shown and described herein in what
is believed to be the most practical and preferred embodiments, it
is recognized that departures can be made therefrom within the
scope of the invention, which is not to be limited to the details
disclosed herein but is to be accorded the full scope of the claims
so as to embrace any and all equivalent processes and products.
* * * * *