Friday, April 25, 2025
4/25/2025
Targeting a human gut bacterial genotoxin via engineered commensal bacteria - Abstract While microbial therapies have employed toxins and immune agonists as therapeutic payloads against cancer, there remains a gap in knowledge and technology to reduce tumorigenesis caused by oncogenic bacteria and their associated metabolites. In line with PAR-22- 085, this multi-PI R01 application aims to co-opt a bacterial toxin-antitoxin system to address colorectal cancer (CRC) associated with colibactin (hereinafter pks+) bacteria. An increasing number of people are colonized by enteric bacteria that produce colibactin, which can induce DNA damage, genome instability, senescence, and carcinogenesis in the host. Clinical studies have linked pks+ bacteria to the high incidence of CRC. Despite efforts to understand the fundamental mechanisms underlying colibactin-induced CRC, a therapeutic strategy has yet to be developed to target colibactin. Interestingly, pks+ bacteria cope with colibactin-mediated self-DNA damage by synthesizing an enzyme, ClbS, to catalytically inactivate colibactin in the cytoplasm and confer self-protection. Inspired by prior fundamental studies, our team displayed the anti-toxin enzyme ClbS on the surface of various E. coli strains to neutralize colibactin at the interface of microbes and the host. We showed that the surface display of ClbS can prevent colibactin-mediated DNA damage in cell lines and colon organoids. Importantly, an E. coli model strain engineered to display ClbS markedly reduces tumorigenesis in a colitis-associated CRC mouse model (DSS/Apcmin) infected with pks+ bacteria. Motivated by our preliminary data, three complementary aims will be performed to demonstrate translational potential. In Aim 1, the surface display of ClbS will be further optimized to enhance the removal of colibactin via a combination of computational and experimental approaches. In Aim 2, human organoid models will be utilized to evaluate the protection efficacy of engineered strains against pks+ E. coli in the presence of a synthetic polymicrobial community. In addition to quantifying double-stranded DNA breaks, whole genome sequencing will be used to assess the reduction of colibactin-associated mutational DNA motifs matched to those in clinical CRC specimens. In Aim 3, a native E. coli strain will be employed to harness its durable engraftment efficiency in different intestinal compartments in the host. The ability of this strain displaying ClbS to reduce tumorigenesis will be assessed in a clinically relevant early CRC mouse model. Administration frequency, timing, and dose will be comprehensively investigated for future clinical translation. This R01 application will be conducted by an interdisciplinary team with expertise in bacterial engineering (Dr. Li), organoids and mouse CRC models (Dr. Yilmaz), CRC prevention and treatment (Drs. Chan and Drew), bioinformatics (Dr. Levine) and statistics (Dr. Baladandayuthapani). While engineering E. coli is not a novel concept, this proposal departs from the status quo because it targets a bacterial genotoxin with implications for the development of CRC. The long- term goals are to produce (1) a first-of-its-kind intervention against colibactin-induced CRC and (2) a new tool to selectively remove microbial products to understand the causality between microbial products and cancer.
HHS’ Tracking Accountability in Government Grants System (TAGGS) website provides access to detailed descriptions of grants, loans, aggregated direct payments and other types of financial assistance awarded by the HHS Operating Divisions (OPDIVs) and the Office of the Secretary Staff Divisions (STAFFDIVs).