Probiotic neoantigen delivery vectors for precision cancer immunotherapy
Microbial systems have been synthetically engineered to deploy therapeutic payloads in vivo. With emerging evidence that bacteria naturally home to tumors and modulate anti-tumor immunity one promising application is the development of bacterial vectors as precision cancer vaccines. In this study, we engineered probiotic E. coli Nissle 1917 (EcN) as an anti-tumor vaccination platform optimized for enhanced production and cytosolic delivery of neoepitope-containing peptide arrays, with increased susceptibility to blood clearance and phagocytosis. These features enhance both safety and immunogenicity, achieving a system which drives potent and specific T cell–mediated anti-cancer immunity that effectively controls or eliminates tumor growth and extends survival in advanced murine primary and metastatic solid tumors. We demonstrate that the elicited anti-tumor immune response involves extensive priming and activation of neoantigen-specific CD4+ and CD8+ T cells, broader activation of both T and NK cells, and a reduction of tumor-infiltrating immunosuppressive myeloid and regulatory T and B cell populations. Taken together, this work leverages the advantages of living medicines to deliver arrays of tumor-specific neoantigen–derived epitopes within the optimal context to induce specific, effective, and durable systemic anti-tumor immunity. Overall design: To predict neoantigens generated by tumor-specific mutations present in the murine CT26 colorectal carcinoma and the murine B16F10 melanoma, we grew each tumor line subcutaneously in the respective MHC-haplotype matched murine host, harvested and homogenized tumors, and extracted total RNA and DNA. We performed RNA-sequencing with gene expression analysis, and whole-exome sequencing with exonic mutation analysis.