Motif-Centered Analyses Elucidate Mutagenic Mechanisms Operating in Normal Human Tissues

Somatic mutations are inevitable in human genomes and can lead to tumorigenesis. Large-scale bioinformatic analyses of mutation catalogues have unveiled several mutational processes operating in cancer genomes, however, our understanding of baseline mutagenesis in non-cancerous normal cells is scarce. Here, we analyzed the mutation profiles of 11,949 normal samples across 25 tissue types obtained from whole-genome and whole-exome sequencing datasets. We applied stringent statistical hypothesis for detecting enrichment and enrichment-adjusted Minimal Estimate of Mutation Load (MEML) in trinucleotide motifs preferred by known mutagenic processes. We found that several mutational motifs previously identified in human cancers are readily detected in cancer-free tissues. Samples enriched with C to T mutations in nCg motif associated with clock-like spontaneous deamination of meCpG were detected across all tissues. We revealed another ubiquitous clock-like motif in several tissue types - T to C substitutions in aTn motif previously associated with exposure to small epoxides and other S _N 2 electrophiles. Analyses of UV-associated yCn motif and its sub-motifs, as well as a minor UV-motif nTt revealed UV-mutagenesis only in skin. APOBEC-induced C to T and C to G mutations in tCw motif were enriched in bladder, lung, small intestine, liver, and breast with preference for APOBEC3A-like mutagenesis in most. Non-cancerous diseased samples showed significantly higher, age-independent accumulation of the clock-like motifs aTn and nCg compared to healthy tissues. Together, our analyses elucidated several ongoing mutagenic processes in normal human tissues and provided a robust analytical framework for identifying mutagenic sources from low-burden mutation catalogues.