Clinical BRCA1/2 Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance

SJ Pettitt, JR Frankum, M Punta, S Lise, J Alexander… - Cancer discovery, 2020 - AACR
SJ Pettitt, JR Frankum, M Punta, S Lise, J Alexander, Y Chen, TA Yap, S Haider, ANJ Tutt
Cancer discovery, 2020AACR
Reversion mutations in BRCA1 or BRCA2 are associated with resistance to PARP inhibitors
and platinum. To better understand the nature of these mutations, we collated, codified, and
analyzed more than 300 reversions. This identified reversion “hotspots” and “deserts” in
regions encoding the N and C terminus, respectively, of BRCA2, suggesting that pathogenic
mutations in these regions may be at higher or lower risk of reversion. Missense and splice-
site pathogenic mutations in BRCA1/2 also appeared less likely to revert than truncating …
Abstract
Reversion mutations in BRCA1 or BRCA2 are associated with resistance to PARP inhibitors and platinum. To better understand the nature of these mutations, we collated, codified, and analyzed more than 300 reversions. This identified reversion “hotspots” and “deserts” in regions encoding the N and C terminus, respectively, of BRCA2, suggesting that pathogenic mutations in these regions may be at higher or lower risk of reversion. Missense and splice-site pathogenic mutations in BRCA1/2 also appeared less likely to revert than truncating mutations. Most reversions were <100 bp deletions. Although many deletions exhibited microhomology, this was not universal, suggesting that multiple DNA-repair processes cause reversion. Finally, we found that many reversions were predicted to encode immunogenic neopeptides, suggesting a route to the treatment of reverted disease. As well as providing a freely available database for the collation of future reversion cases, these observations have implications for how drug resistance might be managed in BRCA-mutant cancers.
Significance
Reversion mutations in BRCA genes are a major cause of clinical platinum and PARP inhibitor resistance. This analysis of all reported clinical reversions suggests that the position of BRCA2 mutations affects the risk of reversion. Many reversions are also predicted to encode tumor neoantigens, providing a potential route to targeting resistance.
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