Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells

The bacterial genotoxin colibactin is enriched in a fraction of colorectal cancers (CRCs) and promotes the accumulation of mutations that drive tumorigenesis. However, systematic assessment of its impact on DNA repair function is lacking and the effect of colibactin exposure on response to genotoxic agents in clinical use (such as chemotherapy) is unknown. Exploiting an in vitro bacterial co-culture system, we found that CRC cell lines displayed differential sensitivity to colibactin-induced genotoxic stress, and that homologous recombination (HR) proficiency discriminated colibactin-tolerant from sensitive cells. While inhibition of DNA double-strand break repair by genetic inactivation of ATM significantly sensitized cells to colibactin, restoration of HR activity was sufficient to induce a colibactin-tolerant phenotype in previously colibactin-sensitive cells. Conversely, chronic reinfection of CRC cells with colibactin selected a tolerant phenotype characterized by restoration of HR activity. Notably, we found a significant correlation between sensitivity to colibactin and irinotecan active metabolite SN38, both in cell lines and patient-derived organoids, suggesting that both agents similarly activated a DNA damage response. Of translational relevance, CRC cells that acquire colibactin-tolerance develop cross-resistance to SN38, and a trend towards poorer response to irinotecan was observed in a retrospective cohort of CRCs harboring the pks genomic island. Our results shed novel insight into colibactin genotoxic mechanism and provide preclinical and translational evidence on its role in promoting chemoresistance in CRC.