Enrichment of colibactin-associated mutational signatures in unexplained colorectal polyposis patients

Abstract

Background: Colibactin, a genotoxin produced by polyketide synthase harboring (pks⁺) bacteria, induces double-strand breaks and chromosome aberrations. Consequently, enrichment of pks⁺Escherichia coli in colorectal cancer and polyposis suggests a possible carcinogenic effect in the large intestine. Additionally, specific colibactin-associated mutational signatures; SBS88 and ID18 in the Catalogue of Somatic Mutations in Cancer database, are detected in colorectal carcinomas. Previous research showed that a recurrent APC splice variant perfectly fits SBS88.

Methods: In this study, we explore the presence of colibactin-associated signatures and fecal pks in an unexplained polyposis cohort. Somatic targeted Next-Generation Sequencing (NGS) was performed for 379 patients. Additionally, for a subset of 29 patients, metagenomics was performed on feces and mutational signature analyses using Whole-Genome Sequencing (WGS) on Formalin-Fixed Paraffin Embedded (FFPE) colorectal tissue blocks.

Results: NGS showed somatic APC variants fitting SBS88 or ID18 in at least one colorectal adenoma or carcinoma in 29% of patients. Fecal metagenomic analyses revealed enriched presence of pks genes in patients with somatic variants fitting colibactin-associated signatures compared to patients without variants fitting colibactin-associated signatures. Also, mutational signature analyses showed enrichment of SBS88 and ID18 in patients with variants fitting these signatures in NGS compared to patients without.

Conclusions: These findings further support colibactins ability to mutagenize colorectal mucosa and contribute to the development of colorectal adenomas and carcinomas explaining a relevant part of patients with unexplained polyposis.

Keywords: Bacterial pathogenesis; Colorectal adenomas; Intestinal microbiology; Polyposis.

Fig. 1

Study design and patient selection. In total, 379 patients were tested using targeted NGS. The case group are patients with at least one APC variant fitting colibactin-associated mutational signature. Twenty cases are selected for additional fecal metagenomics and WGS. Patients without APC variant fitting colibactin-associated signatures serve as controls. Nine controls were selected for fecal metagenomics and WGS. Four patients could not be included for fecal metagenomics since they did not respond to sample request (N = 3) or passed away (N = 1). Two cases were excluded for WGS due to insufficient amount of DNA