Abstract

   Mutational signatures represent a genomic footprint of endogenous and
   exogenous mutational processes through tumor evolution. However, their
   functional impact on the proteome remains incompletely understood. We
   analyzed the protein-coding impact of single-base substitution (SBS)
   signatures in 12,341 cancer genomes from 18 cancer types. Stop-gain
   mutations (SGMs) (i.e., nonsense mutations) were strongly enriched in
   SBS signatures of tobacco smoking, APOBEC cytidine deaminases, and
   reactive oxygen species. These mutational processes alter specific
   trinucleotide contexts and thereby substitute serines and glutamic
   acids with stop codons. SGMs frequently affect cancer hallmark pathways
   and tumor suppressors such as TP53, FAT1, and APC. Tobacco-driven SGMs
   in lung cancer correlate with smoking history and highlight a
   preventable determinant of these harmful mutations. APOBEC-driven SGMs
   are enriched in YTCA motifs and associate with APOBEC3A expression. Our
   study exposes SGM expansion as a genetic mechanism by which endogenous
   and carcinogenic mutational processes directly contribute to protein
   loss of function, oncogenesis, and tumor heterogeneity.
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   Mutational processes of tobacco smoking and APOBEC disrupt gene
   function in cancer by adding premature stop codons.

INTRODUCTION

   Cancer is driven by a few somatic mutations that enable oncogenic
   properties of cells; however, most mutations in cancer genomes are
   functionally neutral passengers ([38]1, [39]2). Somatic mutations are
   caused by endogenous and exogenous mutational processes with complex
   context- and sequence-specific activities that collectively mark tumor
   evolution and exposures over time ([40]3). Single-base substitution
   (SBS) signatures are the indicators of mutational processes in cancer
   genomes that can be inferred through a computational decomposition of
   somatic single-nucleotide variants (SNVs) and their trinucleotide
   sequence context in large cancer genomics datasets ([41]4, [42]5). SBS
   signatures have been linked to clock-like mutational processes of aging
   ([43]6), deficiencies in DNA repair pathways ([44]7), endogenous
   mutational processes such as the activity of APOBEC cytidine deaminases
   ([45]8), environmental carcinogens such as ultraviolet (UV) light
   ([46]9), lifestyle exposures such as tobacco smoking ([47]10), dietary
   components such as aristolochic acid ([48]11), as well as the effects
   of cancer therapies ([49]12, [50]13). The causes of other signatures
   remain uncharacterized. Mutational signatures are increasingly found in
   healthy tissues, indicating that the mutational processes are active in
   normal and precancerous cells ([51]14, [52]15). Specific driver
   mutations in cancer genomes have been attributed to certain mutational
   processes ([53]16, [54]17). While some mutational signatures identified
   in cancer genomes can be reproduced in experimental systems ([55]9,
   [56]18, [57]19), their mechanistic and etiological characterization is
   an ongoing challenge. As mutational processes are thought to
   predominantly generate passenger mutations, their broad functional
   implications on protein function and cellular pathways remain
   incompletely understood.

   Here, we hypothesized that the mutational processes of SNVs
   specifically affect protein-coding sequence because of their
   trinucleotide sequence preferences encoded in SBS signatures. By