ArticleNPJ systems biology and applications2025
Constraint based modeling of drug induced metabolic changes in a cancer cell line.
Article in NPJ systems biology and applications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
2 citing papers in PubMed.
- MechAInistic: A Reviewer-Supervised Multi-Agent LLM System for Auditable Mechanistic Drug-Hypothesis Generation.bioRxiv : the preprint server for biology · 2026Article
- Identification of biomarkers related to amino acid metabolism in nonobstructive azoospermia by bioinformatics.Medicine · 2026Article
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Authors and funding
4 authors.
Funding
Abstract
Cancer cells frequently reprogramme their metabolism to support growth and survival, making metabolic pathways attractive targets for therapy. In this study, we investigated the metabolic effects of three kinase inhibitors and their synergistic combinations in the gastric cancer cell line AGS using genome-scale metabolic models and transcriptomic profiling. We applied the tasks inferred from the differential expression (TIDE) algorithm to infer pathway activity changes in the different conditions. We also explored a variant of TIDE that uses task-essential genes to infer metabolic task changes, providing a complementary perspective to the original algorithm. Our results revealed widespread down-regulation of biosynthetic pathways, particularly in amino acid and nucleotide metabolism. Combinatorial treatments induced condition-specific metabolic alterations, including strong synergistic effects in the PI3Ki-MEKi condition affecting ornithine and polyamine biosynthesis. These metabolic shifts provide insight into drug synergy mechanisms and highlight potential therapeutic vulnerabilities. To support reproducibility, we developed an open-source Python package, MTEApy, implementing both TIDE frameworks.
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Registered trials
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