Quantifying the pro- and antimutagenic roles of DNA damage and repair

Genome integrity is essential to the survival of any living organism. The genome is constantly challenged by a multitude of endogenous and exogenous mutagenic factors such as environmental exposures or replication errors. Therefore, evolution has supplied cells with a number of repair mechanisms to protect their genetic information; however, excessive exposures or defects in the repair machinery can lead to the accumulation of deleterious mutations which may cause a range of diseases including cancer. Different mutational processes often leave behind characteristic patterns of mutations, so-called mutational signatures. Mutational signature analysis of tumours has gained a lot of attention recently, because it may reveal carcinogenic exposures and also therapeutic vulnerabilities. So far, over 50 mutational signatures have been identified using pattern recognition in large cancer cohorts, reflecting the action of a range of known mutagenic processes, such as UV light, tobacco smoke or mismatch repair deficiency, but for many mutational signatures an underlying generative process is still unknown. The search for the causes behind a given mutational signature is further complicated by the fact that every alteration in the DNA results from failed or incorrect repair of a DNA lesion, hence there are two factors which jointly shape the mutational spectrum of any mutagenic process. In this thesis, I quantify the variability of mutational signatures in model organisms and in human cancer and explore the diversity of DNA damage-repair interactions. Using data from a large mutagenesis screen in C. elegans, including over 50 DNA repair deficient genetic backgrounds, 12 genotoxins and nearly 200 combinations thereof, I characterise the mutational spectra and genomic features of a range of DNA repair deficiencies, and describe the mutational signatures of genotoxins across multiple genetic backgrounds. Importantly, the mutagenic contributions of genetic and mutagenic factors can vary dev pending on the DNA repair components available: over 35% of genotoxin-knockout combinations demonstrated a measurable effect on the mutation rate compared to expected values, and about 10% also presented a new mutational spectrum. Analysis of mutational signatures in cancer exomes demonstrates the relevance of C. elegans results to cancer investigation. Mismatch repair deficiency patterns extracted from C. elegans are comparable to those in gastrointestinal tumours, and help to dissect convoluted mutational processes. The antagonism between DNA damage and repair drives variability in cancer genomes as well: the observed interaction effects were low in magnitude, but evolutionary considerations suggest that cancer risk may be substantially elevated even by small increases in mutagenicity. In summary, this thesis presents the first comprehensive analysis of mutagenic DNA damage-repair interactions using experimental and cancer data. The results show that mutations result from the opposing pro- and anti-mutagenic forces of DNA damage and repair, which shape mutational signatures in highly variable ways. This variation has to be acknowledged and integrated into mutational signature analysis to ensure reliable interpretation and applicability in clinical oncology. Lastly, the cross-species comparison shows that the fundamental laws of mutagenesis are acting similarly across eukaryotic organisms reminding that many mutational processes fuelling tumorigenesis are not exclusive to cancer, but also drive variation and the evolution of species.My PhD studies were funded by the EMBL International PhD Programme