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Glodzik D, Bosch A, Hartman J, Aine M, Vallon-Christersson J, Reuterswärd C, Karlsson A, Mitra S, Niméus E, Holm K, Häkkinen J, Hegardt C, Saal LH, Larsson C, Malmberg M, Rydén L, Ehinger A, Loman N, Kvist A, Ehrencrona H, Nik-Zainal S, Borg Å, Staaf J. Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers. Nat Commun 2020; 11:3747. [PMID: 32719340 PMCID: PMC7385112 DOI: 10.1038/s41467-020-17537-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
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.
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Affiliation(s)
- Dominik Glodzik
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA, Cambridge, UK
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute, SE-17177, Stockholm, Sweden
| | - Mattias Aine
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, SE-22184, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Anna Karlsson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Shamik Mitra
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Division of Surgery, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Karolina Holm
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, SE-22184, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Anders Kvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Hans Ehrencrona
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, SE-22184, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-22184, Lund, Sweden
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, CB2 0QQ, Cambridge, UK
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.
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