Abstract
BackgroundHomologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutations in further genes of the HR pathway or the DNA damage checkpoint also give rise to somatic mutation patterns that can be used for treatment prediction.ResultsUsing whole genome sequencing of an isogenic knockout cell line panel, we find a universal HR deficiency-specific base substitution signature that is similar to COSMIC signature 3. In contrast, we detect different deletion phenotypes corresponding to specific HR mutants. The inactivation of BRCA2 or PALB2 leads to larger deletions, typically with microhomology, when compared to the disruption of BRCA1, RAD51 paralogs, or RAD54. Comparison with the deletion spectrum of Cas9 cut sites suggests that most spontaneously arising genomic deletions are not the consequence of double-strand breaks. Surprisingly, the inactivation of checkpoint kinases ATM and CHK2 has no mutagenic consequences. Analysis of tumor exomes with biallelic inactivating mutations in the investigated genes confirms the validity of the cell line models. We present a comprehensive analysis of sensitivity of the investigated mutants to 13 therapeutic agents for the purpose of correlating genomic mutagenic phenotypes with drug sensitivity.ConclusionOur results suggest that no single genomic mutational class shows perfect correlation with sensitivity to common treatments, but the contribution of COSMIC signature 3 to base substitutions, or a combined measure of different features, may be reasonably good at predicting platinum and PARP inhibitor sensitivity.
Highlights
Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations
Increased single nucleotide substitution mutagenesis in a range of HR mutant cell lines To investigate the genetic dependence of spontaneous mutagenesis, we assembled a collection of isogenic chicken DT40 cell lines harboring homozygous disruptions of each of eight key HR genes plus ATM and CHK2, which are key components of the DNA damage checkpoint
The mutations detected by IsoMut are unique to one sample, thereby providing an accurate catalog of Compared to wild type cells, we observed an approximately seven to eightfold increase in base substitution (SNV) mutagenesis in BRCA1−/− and BRCA2−/− cells as shown previously [16]
Summary
Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutations in further genes of the HR pathway or the DNA damage checkpoint give rise to somatic mutation patterns that can be used for treatment prediction. There is much interest in using genomic mutation patterns for the selection of treatments targeted at cells with specific DNA repair defects. Tumors with biallelic inactivation of BRCA1 or BRCA2 possess genome-wide somatic single nucleotide variations (SNVs) with a distinct spectrum termed COSMIC signature 3, together with specific but different patterns of short insertions and deletion (indels), and of structural rearrangements [12, 13]. Whereas only about 30% of ovarian cancer cases have BRCA mutations or promoter methylation [18], there exists a cohort of non-BRCA mutant ovarian cancer cases with a similar mutation spectrum and mutation burden to BRCA mutants [19], and PARP inhibitor treatment was found to be effective in a patient cohort without germline BRCA mutation as well [20]
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