Chromosomal mutational signatures of DNA damaging agents at single cell resolution

The chromosomal scale mutational spectrum of small molecules that interact with DNA has been hard to study at scale, as mutational events are distributed in location and occur in parallel in different cells. Here, we present a framework that pairs phylogenetic ancestry reconstruction with mutational signature decomposition to characterise recent, cell-private CNA mutational processes at single-cell resolution. We used this framework to characterize the cell-wise “foreground” of contemporaneous CNAs induced by strand-break inducing chemotherapeutic drugs of different mechanisms. We demonstrate that platinum salts, G-quadruplex stabilizers and topoisomerase II inhibitors, although mechanistically distinct, converge on a mutational signature dominated by telomere-bounded copy-number gain and losses. This signature is observed in different genetic backgrounds and in vivo, in drug treated patient derived-xenograft tumours. We also observe a high rate of endogenous telomere-bounded mutational foreground in BRCA1 deficient cells. We show that the single cell genome derived signature exposures are drug dose-dependent, and use this to identify the decay of mutational load after drug withdrawal. We observe that both cisplatin and a G4 binder molecule (CX5461) exhibit foreground mutational signature persistence up to 3 weeks after drug withdrawal, suggesting that residual effects of exposure may last longer than anticipated. Finally, extending the framework to serially drug-treated patient-derived xenograft (PDX) models, we show that telomere-bounded CNA signature exposure is associated with tumour response across and resistance states exhibit only background levels of mutational signatures. This is consistent with loss of mutational activity on the genome, as opposed to acquired tolerance to chromosomal mutations as a mechanism for some forms of chemotherapeutic drug resistance. Together our results show that scWGS can identify contemporaneous chromosomal mutation patterns induced by small molecules in human tissues.

• Type: Whole Genome Sequencing
• Archive: European Genome-phenome Archive (EGA)