Colibactin Causes Colorectal Cancer–Associated Mutational Signature

Colibactin, an Escherichia coli metabolite that has been linked with colorectal cancer development, putatively exerts mutagenic effects via DNA alkylation and induction of double-strand breaks (DSB). E. coli harboring the pathogenicity island pks (also called clb), encoding the enzymes that produce colibactin, are found in approximately 20% of healthy individuals, 40% of people with inflammatory bowel disease, and 60% of people with familial adenomatous polyposis or colorectal cancer. To identify the mutational consequences of pks⁺ E. coli exposure, Pleguezuelos-Manzano, Puschhof, Huber, and colleagues microinjected a pks⁺ E. coli strain obtained from a colorectal cancer biopsy into the lumens of clonal human intestinal organoids. Compared with organoids injected with an isogenic negative-control strain incapable of producing colibactin, organoids exposed to pks⁺ E. coli exhibited DSBs and interstrand cross-links, verifying that pks⁺ E. coli caused DNA damage in this model. Organoids were then grown from single cells, enabling five-month exposure to pks⁺ or control E. coli, and subclones from these organoids were used to establish new organoids, which were subjected to whole-genome sequencing. Organoids grown from those exposed to pks⁺ E. coli had higher levels of single-base substitutions, predominantly T-to-N substitutions, which were preferentially found in the middle of ATA, ATT, and TTT nucleotide triplets. pks⁺ E. coli–exposed organoids also had a unique indel signature defined by single-T deletions at T homopolymers, defining—together with the single-base substitutions—a pks⁺ E. coli–induced mutational signature. The mutations caused by the pks⁺ E. coli showed a transcriptional-strand bias, which indicated the repair of damaged adenosines by transcription-coupled nucleotide-excision repair and confirmed that colibactin damages DNA by binding this base. Importantly, the pks⁺ E. coli–induced mutational signature was enriched in samples from colorectal cancer metastases compared with metastases of other origins, a finding validated in an additional genomic dataset derived mostly from primary tumors. Together, these results not only elucidate the pks⁺ E. coli–induced mutational signature, but also build a stronger mechanistic link between exposure to these colibactin-producing bacteria and colorectal cancer.

Pleguezuelos-Manzano C, Puschhof J, Huber AR, van Hoeck A, Wood HM, Nomburg J, et al. Mutational signature in colorectal cancer caused by genotoxic pks⁺ E. coli. Nature 2020;580:269–73.

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