US20170363631A1 - Plasma autoantibody biomarkers for basal like breast cancer - Google Patents
Plasma autoantibody biomarkers for basal like breast cancer Download PDFInfo
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- US20170363631A1 US20170363631A1 US15/534,203 US201515534203A US2017363631A1 US 20170363631 A1 US20170363631 A1 US 20170363631A1 US 201515534203 A US201515534203 A US 201515534203A US 2017363631 A1 US2017363631 A1 US 2017363631A1
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Classifications
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- G—PHYSICS
- G01—MEASURING; TESTING
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- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
- G01N33/57407—Specifically defined cancers
- G01N33/57415—Specifically defined cancers of breast
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
- C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
- C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
- C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
- C07K16/3015—Breast
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/564—Immunoassay; Biospecific binding assay; Materials therefor for pre-existing immune complex or autoimmune disease, i.e. systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, rheumatoid factors or complement components C1-C9
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
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- C12Q2600/00—Oligonucleotides characterized by their use
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Definitions
- the disclosure herein related to biomarkers for cancer and more particularly to autoantibody biomarkers for breast cancer.
- breast cancer 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.
- 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.
- 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.
- FIG. 1 depicts dotplots of AAb responses in various breast cancer subtypes.
- 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.
- TNBC triple negative breast cancer
- ER estrogen receptor
- PR progesterone receptor
- HER2 human epidermal growth factor receptor 2
- TNBC is associated with African American ethnicity, younger age, advanced stage at diagnosis and poorer outcomes.
- TNBC itself has been found to be molecularly heterogeneous in two recent studies.
- EGFR epidermal growth factor receptor
- CK5/6 basal cytokeratin 5/6
- ER ⁇ , PR ⁇ , HER2 ⁇ , and either EGFR+ or CK5/6+ is highly correlated with BLBC defined by gene expression profiling.
- 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.
- 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.
- 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.
- the biomarker gets diluted in a large volume of plasma volume and only a fraction of the secreted biomarker gets distributed to the plasma.
- 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.
- NAPPA nucleic acid programmable protein array
- 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%.
- 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.
- Paraffin embedded tissue samples were collected for immunohistochemical (IHC) analysis and disease classification.
- IHC immunohistochemical
- 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.
- ELISA enzyme-linked immunosorbant assay
- 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.
- a classifier to differentiate patients with BLBC from healthy controls with 33% sensitivity at 98% specificity (Table 3).
- Antigen-specific cutoffs were set to achieve 98% classifier specificity by adjusting the specificity at the antigen level to 98.7%.
- a patient's plasma sample is obtained, and then subsequently tested for autoantibody responses against the proposed protein panels.
- 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.
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| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US15/534,203 US20170363631A1 (en) | 2014-12-09 | 2015-12-09 | Plasma autoantibody biomarkers for basal like breast cancer |
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| Application Number | Priority Date | Filing Date | Title |
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| US201462089631P | 2014-12-09 | 2014-12-09 | |
| US15/534,203 US20170363631A1 (en) | 2014-12-09 | 2015-12-09 | Plasma autoantibody biomarkers for basal like breast cancer |
| PCT/US2015/064792 WO2016094558A1 (fr) | 2014-12-09 | 2015-12-09 | Biomarqueurs d'auto-anticorps dans le plasma pour cancer du sein de type basal |
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| PCT/US2015/064792 A-371-Of-International WO2016094558A1 (fr) | 2014-12-09 | 2015-12-09 | Biomarqueurs d'auto-anticorps dans le plasma pour cancer du sein de type basal |
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| US16/743,906 Continuation US11525831B2 (en) | 2014-12-09 | 2020-01-15 | Plasma autoantibody biomarkers for basal like breast cancer |
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| US16/743,906 Active 2036-03-30 US11525831B2 (en) | 2014-12-09 | 2020-01-15 | Plasma autoantibody biomarkers for basal like breast cancer |
| US17/940,883 Pending US20230079737A1 (en) | 2014-12-09 | 2022-09-08 | Plasma autoantibody biomarkers for basal like breast cancer |
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| US17/940,883 Pending US20230079737A1 (en) | 2014-12-09 | 2022-09-08 | Plasma autoantibody biomarkers for basal like breast cancer |
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| US (3) | US20170363631A1 (fr) |
| EP (1) | EP3230745B1 (fr) |
| WO (1) | WO2016094558A1 (fr) |
Cited By (11)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US10618932B2 (en) | 2017-02-21 | 2020-04-14 | Arizona Board Of Regents On Behalf Of Arizona State University | Method for targeted protein quantification by bar-coding affinity reagent with unique DNA sequences |
| US10648978B2 (en) | 2017-02-09 | 2020-05-12 | Mayo Foundation For Medical Education And Research | Methods for detecting novel autoantibodies in Crohn's disease |
| US10787710B2 (en) | 2014-08-19 | 2020-09-29 | Arizona Board Of Regents On Behalf Of Arizona State University | Radiation biodosimetry systems |
| US10802026B2 (en) | 2010-08-13 | 2020-10-13 | Arizona Board of Regents, a body corporate acting for and on behalf of Arizona State University | Biomarkers for the early detection of breast cancer |
| US11124791B2 (en) | 2015-09-14 | 2021-09-21 | Arizona Board Of Regents On Behalf Of Arizona State University | Generating recombinant affinity reagents with arrayed targets |
| US11208640B2 (en) | 2017-07-21 | 2021-12-28 | Arizona Board Of Regents On Behalf Of Arizona State University | Modulating human Cas9-specific host immune response |
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| WO2023101359A1 (fr) * | 2021-11-30 | 2023-06-08 | 광주과학기술원 | Composition comprenant un inhibiteur de pip4k2c comme principe actif pour le traitement du cancer |
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| JP2011515666A (ja) * | 2008-03-14 | 2011-05-19 | ドナー， インコーポレイテッド | トリプルネガティブ乳がんに関連するｄｎａ修復タンパク質およびその使用法 |
| WO2009131673A1 (fr) * | 2008-04-25 | 2009-10-29 | Ludwig Institute For Cancer Research Ltd. | Traitement ciblé pour des sujets avec des cancers du sein négatifs au récepteur de l'œstrogène et négatifs au récepteur de la progestérone |
| WO2010065944A1 (fr) * | 2008-12-05 | 2010-06-10 | Serametrix | Systèmes et procédés de détection d’auto-anticorps |
| EP3054299B1 (fr) | 2010-08-13 | 2021-03-24 | Arizona Board of Regents, a body corporate acting on behalf of Arizona State University | Biomarqueurs pour la détection précoce du cancer du sein |
| WO2013019680A1 (fr) | 2011-08-04 | 2013-02-07 | Arizona Board Of Regents, A Body Corporate Of The State Of Arizona Acting For & On Behalf Of Arizona | Matériaux à base de cellules et procédé pour définir des différences pharmacogénétiques dans le métabolisme des médicaments |
| CN103945930B (zh) | 2011-10-25 | 2016-10-05 | 亚利桑那董事会，代表亚利桑那州立大学行事的亚利桑那州法人团体 | 可编程的阵列 |
| US9442111B2 (en) | 2011-12-14 | 2016-09-13 | Arizona Board Of Regents | Method and apparatus for measuring phosphorylation kinetics on large arrays |
| WO2013176774A1 (fr) | 2012-05-25 | 2013-11-28 | Arizona Board Of Regents | Marqueurs de microbiome et thérapies pour troubles du spectre autistique |
| US9535070B2 (en) | 2012-11-09 | 2017-01-03 | Arizona Board Of Regents, A Body Corporate Of The State Of Arizona, Acting For And On Behalf Of Arizona State University | High throughput detection of fusion proteins |
| RU2522231C1 (ru) * | 2012-11-14 | 2014-07-10 | Евгений Иосифович Гоуфман | Способ диагностики онкологических заболеваний и иммуноферментный набор для его осуществления |
| WO2014120902A1 (fr) | 2013-01-31 | 2014-08-07 | Arizona Board Of Regents, A Body Corporate Of The State Of Arizona, Acting For And On Behalf Of Ari | Signature d'auto-anticorps pour la détection précoce du cancer des ovaires |
| EP4036579A1 (fr) | 2013-03-15 | 2022-08-03 | Arizona Board of Regents on behalf of Arizona State University | Compositions et procédés de microréseau de biocapteur |
| US9938523B2 (en) | 2013-03-15 | 2018-04-10 | Arizona Board Of Regents On Behalf Of Arizona State University | Nucleic acid-tagged compositions and methods for multiplexed protein-protein interaction profiling |
| US20170176423A1 (en) | 2014-03-25 | 2017-06-22 | Arizona Board Of Regents On Behalf Of Arizona State University | Magnetic programmable bead enzyme-linked immunosorbent assay |
| EP3137902A4 (fr) | 2014-04-28 | 2017-10-11 | Arizona Board of Regents on behalf of Arizona State University | Nouveaux procédés, tests biologiques, et marqueurs biologiques pour des affections liées au hpv |
| US10435747B2 (en) | 2014-08-19 | 2019-10-08 | Arizona Board Of Regents On Behalf Of Arizona State University | Radiation biodosimetry systems |
| US20160195546A1 (en) | 2015-01-07 | 2016-07-07 | Arizona Board Of Regents On Behalf Of Arizona State University | Type 1 Diabetes Biomarkers |
| WO2016141044A1 (fr) | 2015-03-04 | 2016-09-09 | Arizona Board Of Regents On Behalf Of Arizona State University | Inhibiteurs de erbb4 et leurs procédés d'utilisation |
| WO2017048709A1 (fr) | 2015-09-14 | 2017-03-23 | Arizona Board Of Regents On Behalf Of Arizona State University | Génération de réactifs d'affinité recombinants avec des cibles en réseau |
| WO2017075141A1 (fr) | 2015-10-27 | 2017-05-04 | Arizona Board Of Regents On Behalf Of Arizona State University | Identification à haut rendement d'antigènes et d'épitopes de reconnaissance des lymphocytes t |
| WO2017123648A1 (fr) | 2016-01-12 | 2017-07-20 | Arizona Board Of Regents On Behalf Of Arizona State University | Biomarqueurs de type auto-anticorps plasmatiques pour le diagnostic du cancer du poumon |
| US20200386754A1 (en) | 2016-06-14 | 2020-12-10 | Arizona Board Of Regents On Behalf Of Arizona State University | Identification and medical applications of anti-citrullinated-protein antibodies in rheumatoid arthritis |
| WO2018013531A1 (fr) | 2016-07-11 | 2018-01-18 | Arizona Bopard Of Regents On Behalf Of Arizona State University | Biomarqueurs d'auto-anticorps pour la détection précoce du cancer de l'ovaire |
| US10648978B2 (en) | 2017-02-09 | 2020-05-12 | Mayo Foundation For Medical Education And Research | Methods for detecting novel autoantibodies in Crohn's disease |
| US20190162725A1 (en) | 2017-11-29 | 2019-05-30 | Mitch Magee | Materials and methods relating to antibody targets for tuberculosis serology |
| US20210163926A1 (en) | 2018-01-04 | 2021-06-03 | Arizona Board Of Regents On Behalf Of Arizona State University | Versatile amplicon single-cell droplet sequencing-based shotgun screening platform to accelerate functional genomics |
| US20220042982A1 (en) | 2018-06-12 | 2022-02-10 | Arizona Board Of Regents On Behalf Of Arizona State University | Adaptation of nappa for surface plasmon resonance imaging analyses |
-
2015
- 2015-12-09 US US15/534,203 patent/US20170363631A1/en not_active Abandoned
- 2015-12-09 EP EP15868296.3A patent/EP3230745B1/fr active Active
- 2015-12-09 WO PCT/US2015/064792 patent/WO2016094558A1/fr active Application Filing
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2020
- 2020-01-15 US US16/743,906 patent/US11525831B2/en active Active
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2022
- 2022-09-08 US US17/940,883 patent/US20230079737A1/en active Pending
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| Publication number | Priority date | Publication date | Assignee | Title |
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| US11624747B2 (en) | 2010-08-13 | 2023-04-11 | Arizona Board Of Regents | Biomarkers for the early detection of breast cancer |
| US10802026B2 (en) | 2010-08-13 | 2020-10-13 | Arizona Board of Regents, a body corporate acting for and on behalf of Arizona State University | Biomarkers for the early detection of breast cancer |
| US10787710B2 (en) | 2014-08-19 | 2020-09-29 | Arizona Board Of Regents On Behalf Of Arizona State University | Radiation biodosimetry systems |
| US11124791B2 (en) | 2015-09-14 | 2021-09-21 | Arizona Board Of Regents On Behalf Of Arizona State University | Generating recombinant affinity reagents with arrayed targets |
| US11913138B2 (en) | 2015-09-14 | 2024-02-27 | Arizona Board Of Regents On Behalf Of Arizona State University | Generating recombinant affinity reagents with arrayed targets |
| US11243208B2 (en) | 2016-07-11 | 2022-02-08 | Arizona Board Of Regents On Behalf Of Arizona State University | Autoantibody biomarkers for the early detection of ovarian cancer |
| US11832801B2 (en) | 2016-07-11 | 2023-12-05 | Arizona Board Of Regents On Behalf Of Arizona State University | Sweat as a biofluid for analysis and disease identification |
| US10648978B2 (en) | 2017-02-09 | 2020-05-12 | Mayo Foundation For Medical Education And Research | Methods for detecting novel autoantibodies in Crohn's disease |
| US10618932B2 (en) | 2017-02-21 | 2020-04-14 | Arizona Board Of Regents On Behalf Of Arizona State University | Method for targeted protein quantification by bar-coding affinity reagent with unique DNA sequences |
| US11208640B2 (en) | 2017-07-21 | 2021-12-28 | Arizona Board Of Regents On Behalf Of Arizona State University | Modulating human Cas9-specific host immune response |
| US11524063B2 (en) | 2017-11-15 | 2022-12-13 | Arizona Board Of Regents On Behalf Of Arizona State University | Materials and methods relating to immunogenic epitopes from human papillomavirus |
| US12030909B2 (en) | 2020-03-06 | 2024-07-09 | Arizona Board Of Regents On Behalf Of Arizona State University | Methods for targeted protein quantification by bar-coding affinity reagent with unique DNA sequences |
| CN113897437A (zh) * | 2021-11-30 | 2022-01-07 | 深圳市人民医院 | 检测样本中标志物表达水平的试剂在制备用于诊断乳腺癌的试剂盒中的应用 |
Also Published As
| Publication number | Publication date |
|---|---|
| EP3230745B1 (fr) | 2021-02-17 |
| EP3230745A4 (fr) | 2018-08-22 |
| US11525831B2 (en) | 2022-12-13 |
| US20230079737A1 (en) | 2023-03-16 |
| US20200182874A1 (en) | 2020-06-11 |
| WO2016094558A1 (fr) | 2016-06-16 |
| EP3230745A1 (fr) | 2017-10-18 |
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