Abstract
KRAS-mutant colorectal cancer (CRC) undergoes metabolic reprogramming that promotes tumor progression and drug resistance. Cancer-associated fibroblasts (CAFs), a major component of the tumor microenvironment (TME), play a pivotal role in modulating these metabolic adaptations in CRC. This study applies flux sampling combined with representation learning and hierarchical clustering to a computational model of central carbon metabolism to understand how CAFs influence KRAS-mutant CRC metabolic reprogramming following targeted enzyme knockdowns. Focusing on 12 key enzymes involved in glycolysis and the pentose phosphate pathway, knockdowns were simulated under normal CRC media and CAF-conditioned media (CCM) conditions. Analysis revealed CCM induces greater metabolic heterogeneity, with knockdown models exhibiting more variable and distinct metabolic states compared to those cultured in normal CRC media, indicating CAF-derived factors diversify the metabolic responses of CRC cells to enzyme perturbations. Pathway-level flux analysis demonstrated media-specific shifts in central carbon metabolism. Predicted biomass flux showed enzyme knockdowns reduced growth across both conditions, but CCM models indicated a protective effect against perturbation. Overall, simulations illustrated CCM enhances the metabolic adaptability of KRAS-mutant CRC cells to perturbations, emphasizing the importance of including TME components in metabolic modeling and therapeutic development and suggesting that targeting tumor-CAF metabolic interactions may improve treatment strategies.
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Data availability
All relevant datasets and scripts for analysis are available on GitHub at: https://github.com/FinleyLabUSC/CRC_Flux_Sampling.
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The authors thank the members of the Finley Lab at USC for the deep scientific discussions and critical feedback.
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E.E. conducted all metabolic modeling and computational analyses. N.T. and H.C. contributed to scientific discussions of results. E.E. and S.D.F. contributed to manuscript writing and scientific discussions of results. S.D.F. was responsible for the scientific direction of this work. All authors reviewed and provided feedback on the manuscript.
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Elton, E., Tavakoli, N., Cetin, H. et al. Cancer-associated fibroblasts drive metabolic heterogeneity in colorectal cancer cells: predictions from metabolic modeling. npj Syst Biol Appl (2026). https://doi.org/10.1038/s41540-026-00673-8
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DOI: https://doi.org/10.1038/s41540-026-00673-8
