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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.

Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers