Abstract PR02: A mutational signature in human colorectal cancer induced by genotoxic <i>pks+</i> E. coli

Abstract Various species of intestinal microbiota have been associated with the development of colorectal cancer (CRC), yet a direct role of bacteria in the occurrence of oncogenic mutations has not been established. Escherichia coli can carry the pathogenicity island pks within their genomes, which encodes a set of enzymes that synthesize colibactin. This compound can alkylate nascent DNA on adenine residues, and it has been shown to induce double-strand breaks in cultured cells. We hypothesized that pks+ E. coli are carcinogenic through the mutagenic action of colibactin. To test this, we exposed human intestinal organoids for 5 months to genotoxic pks+ Escherichia coli by repeated luminal injection. Whole-genome sequencing (WGS) of clonal organoids before and after exposure revealed a distinct and reproducible mutational signature, which was completely absent in organoids that were injected with isogenic pks-deficient bacteria. This signature encompasses a single base substitution trinucleotide signature (SBS-pks) with a marked transcriptional strand bias in line with damage on adenine residues, which was accompanied by a specific indel signature (ID-pks). Moreover, a distinct preference for the wider sequence context was detected, fitting a structural model of colibactin bound to DNA. This mutational signature was detected in three cohorts containing more than 6,000 human cancer genomes, and contribution of this signature could be detected in a subset of CRC genomes and more rarely in other cancer types. Finally, we identified driver genes harboring the colibactin target motif and could attribute driver mutations from CRC genomes to the signature. Our study describes a highly specific mutational cancer signature that reflects mutagenic activity of pks+ bacteria in the intestinal lumen, which can induce oncogenic mutations and could contribute to cancer initiation. This abstract is also being presented as Poster A02. Citation Format: Jens Puschhof, Cayetano Pleguezuelos-Manzano, Axel Rosendahl Huber, Ruben van Bostel, Hans Clevers. A mutational signature in human colorectal cancer induced by genotoxic pks+ E. coli [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr PR02.