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

Dominik Glodzik,Christel Reuterswärd,Jari Häkkinen,Emma Niméus,Åke Borg,Lisa Rydén,Lao H Saal,Ana Bosch,Mattias Aine,Karolina Holm,Niklas Loman,Anna Ehinger,Serena Nik-Zainal,Martin Malmberg,Shamik Mitra,Hans Ehrencrona,Christer Larsson,Cecilia Hegardt,Johan Hartman,Johan Vallon‐Christersson ,Anders Kvist,Anna Karlsson,Johan Staaf

doi:10.1038/s41467-020-17537-2

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.

Highlights

Homologous recombination deficiency (HRD) is a defining characteristic in BRCA-deficient breast tumors caused by genetic or epigenetic alterations in key pathway genes
We demonstrate that BRCA1 hypermethylation is twice as frequent as BRCA1-null tumors in early-stage unselected triple-negative breast cancers (TNBCs) and that elevated BRCA1 promoter methylation is detectable in peripheral blood DNA of patients with hypermethylation in the tumor
Pyrosequencing classifications were corroborated by Illumina DNA methylation profiling data for BRCA1 gene associated CpGs (Fig. 2a), and markedly reduced BRCA1 mRNA expression from RNA sequencing for hypermethylated cases (Fig. 2b), similar to previous reports[25], that were in line with expression levels for cases with BRCA1 frame shift, nonsense and indel variants (Supplementary Fig. 2)

Summary

Introduction

Homologous recombination deficiency (HRD) is a defining characteristic in BRCA-deficient breast tumors caused by genetic or epigenetic alterations in key pathway genes. We pursued the hypothesis that BRCA1 promoter hypermethylation confers an omics phenotype identical to that of BRCA1-mutated TNBCs, and that the two entities have equivalent patient outcomes in response to standard of care chemotherapy To this end, we analyzed a recently reported unselected population-based cohort of 237 early stage TNBC tumors profiled by comprehensive whole-genome sequencing (WGS), RNA sequencing, global DNA methylation analysis[22], further complemented with 54 additional BRCA1-mutated tumors from previous studies[23,24]. We sought the frequency of BRCA1 promoter hypermethylation, its tumor phenotype compared to tumors with BRCA1 inactivating genetic variants (somatic or germline, BRCA1-null), and its association with clinicopathological variables, molecular subtypes, and patient outcomes in early-stage TNBC. BRCA1 hypermethylation and BRCA1 mutation are associated with better outcome after adjuvant chemotherapy when compared to TNBC patients without BRCA1 inactivation, BRCA1 hypermethylation represents a promising DNAbased prognostic marker

Methods

Results

Conclusion