Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers
Dominik Glodzik, Ana Bosch, Johan Hartman, Mattias Aine, Johan Vallon-Christersson, Christel Reuterswärd, Anna Karlsson, Shamik Mitra, Emma Niméus, Karolina Holm, Jari Häkkinen, Cecilia Hegardt, Lao H Saal, Christer Larsson, Martin Malmberg, Lisa Rydén, Anna Ehinger, Niklas Loman, Anders Kvist, Hans Ehrencrona, Serena Nik-Zainal, Åke Borg, Johan Staaf, Dominik Glodzik, Ana Bosch, Johan Hartman, Mattias Aine, Johan Vallon-Christersson, Christel Reuterswärd, Anna Karlsson, Shamik Mitra, Emma Niméus, Karolina Holm, Jari Häkkinen, Cecilia Hegardt, Lao H Saal, Christer Larsson, Martin Malmberg, Lisa Rydén, Anna Ehinger, Niklas Loman, Anders Kvist, Hans Ehrencrona, Serena Nik-Zainal, Åke Borg, Johan Staaf
Abstract
Homologous recombination deficiency (HRD) is a defining characteristic in BRCA-deficient breast tumors caused by genetic or epigenetic alterations in key pathway genes. We investigated the frequency of BRCA1 promoter hypermethylation in 237 triple-negative breast cancers (TNBCs) from a population-based study using reported whole genome and RNA sequencing data, complemented with analyses of genetic, epigenetic, transcriptomic and immune infiltration phenotypes. We demonstrate that BRCA1 promoter hypermethylation is twice as frequent as BRCA1 pathogenic variants in early-stage TNBC and that hypermethylated and mutated cases have similarly improved prognosis after adjuvant chemotherapy. BRCA1 hypermethylation confers an HRD, immune cell type, genome-wide DNA methylation, and transcriptional phenotype similar to TNBC tumors with BRCA1-inactivating variants, and it can be observed in matched peripheral blood of patients with tumor hypermethylation. Hypermethylation may be an early event in tumor development that progress along a common pathway with BRCA1-mutated disease, representing a promising DNA-based biomarker for early-stage TNBC.
Conflict of interest statement
J.H. has received speakers honoraria and travel support from Roche, advisory board fees from MSD, Novartis and Roche, and institutional research grants from Cepheid and Novartis. Anna Ehinger has received speakers honoraria from Novartis, Amgen, Roche, and advisory board fees from Roche. Ana Bosch has participated in advisory boards for Novartis and Pfizer, and has received travel support from Roche. The remaining authors declare no competing interests.
Figures
References
- Gluz O, et al. Triple-negative breast cancer–current status and future directions. Ann. Oncol. 2009;20:1913–1927.
- Foulkes WD, Smith IE, Reis-Filho JS. Triple-negative breast cancer. N. Engl. J. Med. 2010;363:1938–1948.
- Sharma P. Biology and Management of Patients With Triple-Negative Breast Cancer. Oncologist. 2016;21:1050–1062.
- Winter C, et al. Targeted sequencing of BRCA1 and BRCA2 across a large unselected breast cancer cohort suggests that one-third of mutations are somatic. Ann. Oncol. 2016;27:1532–1538.
- Lord CJ, Ashworth A. The DNA damage response and cancer therapy. Nature. 2012;481:287–294.
- Farmer H, et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature. 2005;434:917–921.
- Brok WDd, et al. Homologous recombination deficiency in breast cancer: a clinical review. JCO Precis. Oncol. 2017;1:1–13.
- Ray-Coquard I, et al. Olaparib plus bevacizumab as first-line maintenance in ovarian cancer. N. Engl. J. Med. 2019;381:2416–2428.
- van Verschuer VM, et al. Tumor-associated inflammation as a potential prognostic tool in BRCA1/2-associated breast cancer. Hum. Pathol. 2015;46:182–190.
- Jiang T, et al. Predictors of chemosensitivity in triple negative breast cancer: an integrated genomic analysis. PLoS Med. 2016;13:e1002193.
- Nolan E, et al. Combined immune checkpoint blockade as a therapeutic strategy for BRCA1-mutated breast cancer. Sci. Transl. Med. 2017;9:eaal4922.
- Akashi-Tanaka S, et al. BRCAness predicts resistance to taxane-containing regimens in triple negative breast cancer during neoadjuvant chemotherapy. Clin. Breast Cancer. 2015;15:80–85.
- Telli ML, et al. Homologous recombination deficiency (HRD) score predicts response to platinum-containing neoadjuvant chemotherapy in patients with triple-negative breast cancer. Clin. Cancer Res. 2016;22:3764–3773.
- Zhu X, et al. Hypermethylation of BRCA1 gene: implication for prognostic biomarker and therapeutic target in sporadic primary triple-negative breast cancer. Breast Cancer Res. Treat. 2015;150:479–486.
- Yamashita N, et al. Epigenetic inactivation of BRCA1 through promoter hypermethylation and its clinical importance in triple-negative breast cancer. Clin. Breast Cancer. 2015;15:498–504.
- Sharma P, et al. The prognostic value of BRCA1 promoter methylation in early stage triple negative breast cancer. J. Cancer Ther. Res. 2014;3:1–11.
- Xu Y, et al. Promoter methylation of BRCA1 in triple-negative breast cancer predicts sensitivity to adjuvant chemotherapy. Ann. Oncol. 2013;24:1498–1505.
- Sharma P, et al. Impact of homologous recombination deficiency biomarkers on outcomes in patients with triple-negative breast cancer treated with doxorubicin-based adjuvant chemotherapy (SWOG S9313) Ann. Oncol. 2017;29:654–660.
- Jacot W, et al. BRCA1 promoter hypermethylation is associated with good prognosis and chemosensitivity in triple-negative breast cancer. Cancers. 2020;12:828.
- Brianese RC, et al. BRCA1 deficiency is a recurrent event in early-onset triple-negative breast cancer: a comprehensive analysis of germline mutations and somatic promoter methylation. Breast Cancer Res. Treat. 2018;167:803–814.
- Xie Y, Gou Q, Wang Q, Zhong X, Zheng H. The role of BRCA status on prognosis in patients with triple-negative breast cancer. Oncotarget. 2017;8:87151–87162.
- Staaf J, et al. Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. Nat. Med. 2019;25:1526–1533.
- Jonsson G, et al. The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer. Cancer Res. 2012;72:4028–4036.
- Nik-Zainal S, et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature. 2016;534:47–54.
- Yang D, et al. Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer. J. Am. Med. Assoc. 2011;306:1557–1565.
- Davies H, et al. HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. Nat. Med. 2017;23:517–525.
- Nik-Zainal S, Morganella S. Mutational signatures in breast cancer: the problem at the DNA level. Clin. Cancer Res. 2017;23:2617–2629.
- Parker JS, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J. Clin. Oncol. 2009;27:1160–1167.
- Guedj M, et al. A refined molecular taxonomy of breast cancer. Oncogene. 2012;31:1196–1206.
- Curtis C, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012;486:346–352.
- Lehmann BD, et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J. Clin. Investig. 2011;121:2750–2767.
- Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA. 2001;98:5116–5121.
- Newman AM, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat. Biotechnol. 2019;37:773–782.
- Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol. 2017;18:220.
- Teschendorff AE, Breeze CE, Zheng SC, Beck S. A comparison of reference-based algorithms for correcting cell-type heterogeneity in epigenome-wide association studies. BMC Bioinform. 2017;18:105.
- Schenck RO, Lakatos E, Gatenbee C, Graham TA, Anderson ARA. NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline. BMC Bioinform. 2019;20:264.
- Shukla SA, et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat. Biotechnol. 2015;33:1152–1158.
- Ryden L, et al. Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative. Br. J. Surg. 2018;105:e158–e168.
- Runowicz CD, et al. American Cancer Society/American Society of Clinical Oncology Breast Cancer Survivorship Care Guideline. J. Clin. Oncol. 2016;34:611–635.
- Lönning P, Eikesdal H, Löes IM, Knappskog S. Consitutional Mosaic Epimutations—a hidden cause of cancer? Cell Stress. 2019;3:118–135.
- Al-Moghrabi N, et al. Methylation of BRCA1 and MGMT genes in white blood cells are transmitted from mothers to daughters. Clin. Epigenet. 2018;10:99.
- Chen J, et al. High-resolution bisulfite-sequencing of peripheral blood DNA methylation in early-onset and familial risk breast cancer patients. Clin. Cancer Res. 2019;25:5301–5314.
- Lonning PE, et al. White blood cell BRCA1 promoter methylation status and ovarian cancer risk. Ann. Intern. Med. 2018;168:326–334.
- Prajzendanc K, et al. BRCA1 promoter methylation in peripheral blood is associated with the risk of triple-negative breast cancer. Int. J. Cancer. 2020;146:1293–1298.
- Azzollini J, et al. Constitutive BRCA1 promoter hypermethylation can be a predisposing event in isolated early-onset breast cancer. Cancers. 2019;11:58.
- Tang Q, Cheng J, Cao X, Surowy H, Burwinkel B. Blood-based DNA methylation as biomarker for breast cancer: a systematic review. Clin. Epigenet. 2016;8:115.
- Polak P, et al. A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. Nat. Genet. 2017;49:1476–1486.
- Tutt A, et al. Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: the TNT Trial. Nat. Med. 2018;24:628–637.
- Isakoff SJ, et al. TBCRC009: a multicenter phase II clinical trial of platinum monotherapy with biomarker assessment in metastatic triple-negative breast cancer. J. Clin. Oncol. 2015;33:1902–1909.
- Zhao EY, et al. Homologous recombination deficiency and platinum-based therapy outcomes in advanced breast cancer. Clin. Cancer Res. 2017;23:7521–7530.
- Telli ML, et al. Homologous recombination deficiency (HRD) status predicts response to standard neoadjuvant chemotherapy in patients with triple-negative or BRCA1/2 mutation-associated breast cancer. Breast Cancer Res. Treat. 2018;168:625–630.
- Sobral-Leite M, et al. Assessment of PD-L1 expression across breast cancer molecular subtypes, in relation to mutation rate, BRCA1-like status, tumor-infiltrating immune cells and survival. Oncoimmunology. 2018;7:e1509820.
- Loi S, et al. Tumor-infiltrating lymphocytes and prognosis: a pooled individual patient analysis of early-stage triple-negative breast cancers. J. Clin. Oncol. 2019;37:559–569.
- Solinas C, et al. BRCA gene mutations do not shape the extent and organization of tumor infiltrating lymphocytes in triple negative breast cancer. Cancer Lett. 2019;450:88–97.
- Saal LH, et al. The Sweden Cancerome Analysis Network—Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine. Genome Med. 2015;7:20.
- SCAN-B. (2020).
- Saal LH, et al. Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair. Nat. Genet. 2008;40:102–107.
- Du P, et al. Comparison of beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinform. 2010;11:587.
- Gene Expression Omnibus. (2020).
- Brueffer C, et al. Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative. JCO Precis. Oncol. 2018;2:1–18.
- Paquet ER, Hallett MT. Absolute assignment of breast cancer intrinsic molecular subtype. J. Natl Cancer Inst. 2015;107:357.
- Ali HR, et al. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biol. 2014;15:431.
- Chen X, et al. TNBCtype: a subtyping tool for triple-negative breast cancer. Cancer Inf. 2012;11:147–156.
- Schmid P, et al. Atezolizumab and nab-paclitaxel in advanced triple-negative breast cancer. N. Engl. J. Med. 2018;379:2108–2121.
- Hudis CA, et al. Proposal for standardized definitions for efficacy end points in adjuvant breast cancer trials: the STEEP system. J. Clin. Oncol. 2007;25:2127–2132.
Source: PubMed