Modeling Microbiome Modulation of Tumor Metabolic Networks to Predict Synergistic Therapies

Abstract

Differences in microbiome composition profoundly influence drug response, yet methods to model the metabolic interplay between tumors, microbes, and therapeutics remain limited. We present a generalizable framework combining machine-learning and genome-scale metabolic modeling to prioritize combination therapies for colorectal cancer (CRC) in the presence of Fusobacterium nucleatum (Fn) and other pathogenic, probiotic, and commensal microbes. Trained on 6,514 drug combinations in microbe-free CRC cell lines, the model predicted synergistic combinations in both microbe-free and microbe-associated contexts and generalized to immunotherapy-associated conditions. Predictions were validated using an asymmetric co-culture system that mimics the colons normoxic-anaerobic gradient, confirming synergistic combinations in HCT116 cells with Fn, including drugs not typically used in CRC therapy. Mechanistic analysis and targeted pharmacological perturbations revealed phospho-inositol metabolism and cysteine transport as key determinants of Fn-dependent drug synergy. Together, this work introduces a scalable, microbiome-aware framework to enable discovery of context-specific combination therapies.