Dissecting metabolism-driven transcriptional reprogramming in human colon and liver cancer cells

Cellular metabolism is a dynamic process that supports tissue homeostasis, growth, and environmental adaptation. Cancer cells exploit this by rewiring metabolic pathways in response to oncogenic cues and microenvironmental pressures. While oncogene-driven metabolic reprogramming is an established cancer hallmark, the extent to which specific metabolic enzymes shape the chromatin and transcriptional landscape of cancer cells remains incompletely understood. Here, we systematically interrogate how loss of individual metabolic enzymes rewires gene expression programs through chromatin-based mechanisms. We performed a CROP-seq screen targeting key metabolic enzymes across major pathways, including the tricarboxylic acid cycle, glycolysis, nucleotide synthesis, amino acid metabolism, fatty acid biosynthesis, and glutaminolysis, combined with single-cell RNA-seq in HCT116 colon cancer cells. Differential expression analysis relative to non-targeting controls revealed substantial transcriptional changes upon loss of several enzymes, indicating strong metabolic control over gene regulatory states. Interestingly, silencing of ACSS2 (acyl-CoA synthetase short-chain family member 2; acetate-to-acetyl-CoA pathway) elicited one of the most pronounced transcriptional effects, and similarly a broad gene expression shift was observed upon shRNA-mediated ACSS2 silencing followed by bulk RNA-seq in HepG2 liver cancer cells. ACSS2 converts acetate into acetyl-CoA in both the cytosol and nucleus, positioning it as a direct metabolic regulator of histone acetylation and chromatin accessibility. Notably, loss of metabolic enzymes upstream of acetyl-CoA production, including fumarate hydratase (FH; tricarboxylic acid cycle) and pyruvate dehydrogenase beta subunit (PDHB; pyruvate-to-acetyl-CoA conversion), induced compensatory upregulation of ACSS2, suggesting a feedback mechanism that maintains nuclear acetyl-CoA availability. Ongoing work couples these transcriptional profiles with ChIP-seq profiling of histone acetylation and other chromatin marks, enabling direct linkage between metabolic perturbation, chromatin remodeling, and transcriptional outcomes. Together, this study reveals how metabolic dependencies converge on chromatin-mediated transcriptional control and contributes to a broader understanding of how metabolic state influences gene regulation in cancer. Full results and mechanistic insights will be presented at the meeting.