BRCA1 and BRCA2 5' Noncoding Region Variants Identified in Breast Cancer Patients Alter Promoter Activity and Protein Binding

Hum Mutat. 2018 Dec;39(12):2025-2039. doi: 10.1002/humu.23652. Epub 2018 Sep 24.

Abstract

The widespread use of next generation sequencing for clinical testing is detecting an escalating number of variants in noncoding regions of the genome. The clinical significance of the majority of these variants is currently unknown, which presents a significant clinical challenge. We have screened over 6,000 early-onset and/or familial breast cancer (BC) cases collected by the ENIGMA consortium for sequence variants in the 5' noncoding regions of BC susceptibility genes BRCA1 and BRCA2, and identified 141 rare variants with global minor allele frequency < 0.01, 76 of which have not been reported previously. Bioinformatic analysis identified a set of 21 variants most likely to impact transcriptional regulation, and luciferase reporter assays detected altered promoter activity for four of these variants. Electrophoretic mobility shift assays demonstrated that three of these altered the binding of proteins to the respective BRCA1 or BRCA2 promoter regions, including NFYA binding to BRCA1:c.-287C>T and PAX5 binding to BRCA2:c.-296C>T. Clinical classification of variants affecting promoter activity, using existing prediction models, found no evidence to suggest that these variants confer a high risk of disease. Further studies are required to determine if such variation may be associated with a moderate or low risk of BC.

Keywords: BRCA1; BRCA2; breast cancer; promoter; transcription; variants of unknown clinical significance (VUS).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Age of Onset
  • BRCA1 Protein / chemistry
  • BRCA1 Protein / genetics*
  • BRCA1 Protein / metabolism
  • BRCA2 Protein / chemistry
  • BRCA2 Protein / genetics*
  • BRCA2 Protein / metabolism
  • Breast Neoplasms / genetics*
  • CCAAT-Binding Factor / metabolism
  • Cell Line, Tumor
  • Female
  • Genetic Predisposition to Disease
  • Germ-Line Mutation*
  • Humans
  • MCF-7 Cells
  • PAX5 Transcription Factor / metabolism
  • Promoter Regions, Genetic*
  • Protein Binding

Substances

  • 5' Untranslated Regions
  • BRCA1 Protein
  • BRCA1 protein, human
  • BRCA2 Protein
  • BRCA2 protein, human
  • CCAAT-Binding Factor
  • NFYA protein, human
  • PAX5 Transcription Factor
  • PAX5 protein, human

Supplementary concepts

  • Breast Cancer, Familial