Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss

Masid, M.; Rota, I. A.; Barras, D.; De Carlo, F.; Ginefra, P.; Desbuisson, M.; Ortiz-Miranda, Y.; Zamarin, D.; Shah, S. P.; Vannini, N.; Coukos, G.; Dangaj-Laniti, D.; Hatzimanikatis, V.

doi:10.1101/2025.11.18.689039

bioRxiv · 10.1101/2025.11.18.689039

Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss

Masid, M.·Rota, I. A.·Barras, D.·De Carlo, F.·Ginefra, P.·Desbuisson, M.·Ortiz-Miranda, Y.·Zamarin, D.·Shah, S. P.·Vannini, N.·Coukos, G.·Dangaj-Laniti, D.·Hatzimanikatis, V.

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Abstract

Metabolic reprogramming is a hallmark of cancer, yet how oncogenic drivers shape tumor metabolism across disease progression remains incompletely understood. In this study, we present iMSEA (in silico Metabolic State and Enrichment Analysis), a computational framework that infers flux-based metabolic states from omics profiles. Applying iMSEA to isogenic BRCA1-mutant and BRCA1-wild-type ovarian cancer cells, we identified a shift toward glycolysis, nucleotide biosynthesis, and redox imbalance, coupled with impaired oxidative phosphorylation. These predictions were validated with metabolomics, Seahorse, and SCENITH assays, demonstrating the accuracy of our approach. Extending the analysis to homologous recombination deficient patient tumors at single-cell resolution, we found that BRCA1-deficient cancers display heightened metabolic activity and site-specific adaptations, including altered central carbon fluxes, mitochondrial function, nucleotide biosynthesis, and lipid metabolism. By linking transcriptional programs to functional metabolic states, iMSEA reveals hidden metabolic liabilities in BRCA1-deficient ovarian cancer and provides a broadly applicable strategy for dissecting metabolic heterogeneity and therapeutic vulnerabilities in cancer.

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Masid, M., Rota, I. A., Barras, D., De Carlo, F., Ginefra, P., Desbuisson, M., Ortiz-Miranda, Y., Zamarin, D., Shah, S. P., Vannini, N., Coukos, G., Dangaj-Laniti, D., Hatzimanikatis, V.. 2025-11-18. Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss. https://doi.org/10.1101/2025.11.18.689039

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