Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants

Abstract

Germline pathogenic variants in BRCA1 confer a high risk of developing breast and ovarian cancer. The BRCA1 exon 11 (formally exon 10) is one of the largest exons and codes for the nuclear localization signals of the corresponding gene product. This exon can be partially or entirely skipped during pre‐mRNA splicing, leading to three major in‐frame isoforms that are detectable in most cell types and tissue, and in normal and cancer settings. However, it is unclear whether the splicing imbalance of this exon is associated with cancer risk. Here we identify a common genetic variant in intron 10, rs5820483 (NC_000017.11:g.43095106_43095108dup), which is associated with exon 11 isoform expression and alternative splicing, and with the risk of breast cancer, but not ovarian cancer, in BRCA1 pathogenic variant carriers. The identification of this genetic effect was confirmed by analogous observations in mouse cells and tissue in which a loxP sequence was inserted in the syntenic intronic region. The prediction that the rs5820483 minor allele variant would create a binding site for the splicing silencer hnRNP A1 was confirmed by pull‐down assays. Our data suggest that perturbation of BRCA1 exon 11 splicing modifies the breast cancer risk conferred by pathogenic variants of this gene.

Case Review: Whole-Exome Sequencing Analyses Identify Carriers of a Known Likely Pathogenic Intronic BRCA1 Variant in Ovarian Cancer Cases Clinically Negative for Pathogenic BRCA1 and BRCA2 Variants

“…BRCA1 c.5407-25T>A is located at base pair 25 of intron 21 upstream from the start of exon 22 based on the transcript NM_007294.4 (Figure 1A), or of intron 22 upstream from the start of exon 23 based on the canonical transcript NM_007300.4, a transcript containing exon 4, which was missed due to a historical misannotation of an additional exon 4 in BRCA1 [44]. In this report, we have annotated our variants using the BRCA1 transcript (NM_007294.4), as it is the commonly used in the clinical genetic setting.…”

BRCA1secondary splice-site mutations drive exon-skipping and PARP inhibitor resistance

“…While PARPi-resistant HGSOC PDX #56PP and HGSOC PDX #049 had secondary splice site mutations that explain the high levels of alternative isoform expression, HGSOC PDX #032 and OCS PDX #264 also had high expression of Δ11q, but without driver SSMs in BRCA1 . Certain single nucleotide polymorphisms (SNPs) have been reported to cause elevated expression of the BRCA1 Δ11q isoform (22,36,37), and we investigated these in whole exome sequencing (WES) data for the other PARPi-resistant models HGSOC PDX #032 and OCS PDX #264. None of the SNPs/variants investigated from the literature were identified in these PDX, suggesting other, unknown mechanisms were responsible for BRCA1 Δ11q expression.…”

“…Certain single nucleotide polymorphisms (SNPs) have been reported to cause elevated expression of the BRCA1 D11q isoform (22,36,37), and we investigated these in whole exome sequencing (WES) data for the other PARPi-resistant models HGSOC PDX #032 and OCS PDX #264. None of the SNPs/variants investigated from the literature were identified in these PDX, suggesting other, unknown mechanisms were responsible for BRCA1 D11q expression.…”

Navigating the genetic landscape of breast cancer in South Africa amidst a developing healthcare system

“…This intronic variant is rarely reported in conventional screening assays that focus on coding variants only, due to its intronic gene location. Ruiz De Garibay et al (2021) used linkage disequilibrium analysis to infer BRCA1 haplotypes of pathogenic variants and confirmed the presence of founder groups. Another controversial variant frequently under review for more than 20 years since the discovery of BRCA2 that requires haplotype analysis, is the C-terminal K3326X variant in exon 27.…”