Accurate detection and quantification of epigenetic and genetic second hits in BRCA1 and BRCA2-associated hereditary breast and ovarian cancer reveals multiple co-acting second hits

Mattias Van Heetvelde; Mieke Van Bockstal; Bruce Poppe; Kathleen Lambein; Toon Rosseel; Lilit Atanesyan; Dieter Deforce; Ivo Van Den Berghe; Kim De Leeneer; Jo Van Dorpe; Anne Vral; Kathleen B M Claes

doi:10.1016/j.canlet.2018.03.026

Accurate detection and quantification of epigenetic and genetic second hits in BRCA1 and BRCA2-associated hereditary breast and ovarian cancer reveals multiple co-acting second hits

Cancer Lett. 2018 Jul 1:425:125-133. doi: 10.1016/j.canlet.2018.03.026. Epub 2018 Mar 23.

Authors

Affiliations

¹ Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Department of Basic Medical Sciences, Ghent University, Entrance 46, De Pintelaan 185, B-9000, Ghent, Belgium. Electronic address: [email protected].
² Department of Pathology, Ghent University Hospital, Entrance 23, Corneel Heymanslaan 10, B-9000, Ghent, Belgium. Electronic address: [email protected].
³ Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium. Electronic address: [email protected].
⁴ Department of Pathology, AZ St Lucas Hospital, Groenebriel 1, B-9000, Ghent, Belgium; Department of Oncology, KU Leuven, Surgical Oncology, University Hospital Leuven Gasthuisberg, Herestraat 49, O&N1 Box 818, B-3000, Leuven, Belgium. Electronic address: [email protected].
⁵ Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium. Electronic address: [email protected].
⁶ MRC-Holland, Willem Schoutenstraat 1, 1057 DL, Amsterdam, The Netherlands. Electronic address: [email protected].
⁷ Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium. Electronic address: [email protected].
⁸ Department of Pathology, AZ Sint Jan Hospital Brugge-Oostend, Ruddershove 10, B-8000, Brugge, Belgium. Electronic address: [email protected].
⁹ Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium. Electronic address: [email protected].
¹⁰ Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Department of Pathology, Ghent University Hospital, Entrance 23, Corneel Heymanslaan 10, B-9000, Ghent, Belgium. Electronic address: [email protected].
¹¹ Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium; Department of Basic Medical Sciences, Ghent University, Entrance 46, De Pintelaan 185, B-9000, Ghent, Belgium. Electronic address: [email protected].
¹² Center for Medical Genetics Ghent, Ghent University Hospital, Medical Research Building 1, Corneel Heymanslaan 10, B-9000, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), B-9000, Ghent, Belgium. Electronic address: [email protected].

PMID: 29580810
DOI: 10.1016/j.canlet.2018.03.026

Abstract

Background: This study characterizes the second hit spectrum in BRCA1 and BRCA2-associated breast and ovarian cancers at both gene loci to investigate if second hit mechanisms are mutually exclusive or able to coincide within the same tumor.

Methods: Loss of heterozygosity, somatic point mutations and copy number alterations along with promoter methylation were studied in 56 breast and 15 ovarian cancers from BRCA1 and BRCA2 germline mutation carriers. A mathematical methodology was introduced to quantify the tumor cell population carrying a second hit.

Results: Copy neutral LOH was the most prevalent LOH mechanism in this cohort (BC 69%, OC 67%). However, only 36% of BC and 47% of OC showed LOH in all cancerous cells. Somatic intragenic deletions and methylated subclones were also found in combination with (partial) loss of heterozygosity. Unequivocal deleterious somatic point mutations were not identified in this cohort.

Conclusion: Different mechanisms inactivating the wild type allele are present within the same tumor sample at various extents. Results indicate that BRCA1/2-linked breast and ovarian cancer cells are predominantly characterized by LOH, but harbor a complex combination of second hits at various frequencies.

Keywords: BRCA1; BRCA2; Loss of heterozygosity; Methylation; Tumor cell percentage.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

BRCA1 Protein / genetics*
BRCA2 Protein / genetics*
Cohort Studies
DNA Copy Number Variations
DNA Methylation
Epigenesis, Genetic
Female
Germ-Line Mutation
Hereditary Breast and Ovarian Cancer Syndrome / genetics*
Humans
Loss of Heterozygosity
Models, Theoretical
Point Mutation
Promoter Regions, Genetic
Sequence Analysis, DNA / methods*

Substances

BRCA1 Protein
BRCA1 protein, human
BRCA2 Protein
BRCA2 protein, human