A meta-analysis of reversion mutations in BRCA genes identifies signatures of DNA end-joining repair mechanisms driving therapy resistance

Abstract

Background: Germline mutations in the BRCA1 or BRCA2 (BRCA) genes predispose to hereditary breast and ovarian cancer and, mostly in the case of BRCA2, are also prevalent in cases of pancreatic and prostate malignancies. Tumours from these patients tend to lose both copies of the wild-type BRCA gene, which makes them exquisitely sensitive to platinum drugs and poly(ADP-ribose) polymerase inhibitors (PARPi), treatments of choice in these disease settings. Reversion secondary mutations with the capacity of restoring BRCA protein expression have been documented in the literature as bona fide mechanisms of resistance to these treatments. Patients and methods: We analysed published sequencing data of BRCA genes (from tumour or circulating tumour DNA) in 327 patients with tumours harbouring mutations in BRCA1 or BRCA2 (234 patients with ovarian cancer, 27 with breast cancer, 13 with pancreatic cancer, 11 with prostate cancer and 42 with a cancer of unknown origin) that progressed on platinum or PARPi treatment. Results: We describe 269 cases of reversion mutations in 86 patients in this cohort (26.0%). Detailed analyses of the reversion events highlight that most amino acid sequences encoded by exon 11 in BRCA1 and BRCA2 are dispensable to generate resistance to platinum or PARPi, whereas other regions are more refractory to sizeable amino acid losses. They also underline the key role of mutagenic end-joining DNA repair pathways in generating reversions, especially in those affecting BRCA2, as indicated by the significant accumulation of DNA sequence microhomologies surrounding deletions leading to reversion events. Conclusions: Our analyses suggest that pharmacological inhibition of DNA end-joining repair pathways could improve durability of drug treatments by preventing the acquisition of reversion mutations in BRCA genes. They also highlight potential new therapeutic opportunities when reversions result in expression of hypomorphic versions of BRCA proteins, especially with agents targeting the response to DNA replication stress.

Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell

“…We observe a slight but significantly increased TINS signature in mBRCA2 compared to mBRCA1 tumors, suggesting mBRCA2 tumors might have a greater reliance on Pol θ mediated Alt-EJ pathway compared to mBRCA1 tumors. On studying reversion mutations in BRCA mutant tumors resistant to PARP inhibitors, two groups have independently shown BRCA2 mutant tumors to have increased Alt-EJ based reversion deletions compared to BRCA1 mutant tumors ( 51 , 52 ). These genomic scar observations support a model in which BRCA2 and BRCA1 have differing influences on Alt-EJ in the context of two-ended DSBs.…”

Relevance of Platinum-free Interval and BRCA Reversion Mutations for Veliparib Monotherapy after Progression on Carboplatin/Paclitaxel for gBRCA Advanced Breast Cancer (BROCADE3 Crossover)

“…This is similar to observations in high-grade serous ovarian carcinoma (HGSOC) where 8 of 97 (8.2%) patients with HGSOC had either germline or somatic BRCA reversion mutations detected in plasma prior to rucaparib treatment; an additional 8 of 78 (10.3%) patients had BRCA reversion mutations identified in plasma samples collected at disease progression (15). Interestingly, the majority of unique reversion mutations (8/9) were detected in BRCA2 as opposed to BRCA1, an observation made previously (26,27). We speculate that differences in the chromatin landscape and length of protein-coding domains are influential in this difference.…”

Long-term survival of an ovarian cancer patient harboring a RAD51C missense mutation

“…Similarly, a RAD51D truncation in a therapy-resistant ovarian cancer has been reported to revert through frame restoration with only a three amino acid scar (one residue insertion/two residue deletion) (Kondrashova et al 2017). However, even with BRCA1/2 truncations, scarring is less pronounced in more conserved domains (Pettitt et al 2020;Tobalina et al 2021), indicating more constraint in protein sequence changes.…”