Metabolic mRNA insufficiency of single cells: Implications for drug targeting and resistance.

With the aim of identifying vulnerabilities of subpopulation-specific metabolic networks, we used single-cell transcriptomics to build mRNA-based metabolic maps for 5512 cells from four proliferating cell populations (three liver cancer-related and a control). Paradoxically, flux balance analysis (FBA) predicted no growth for any cell. Further analysis confirmed that this conclusion was not due to shared metabolites or insufficient mRNA sequencing depth. Instead, using our enzyme-based Vmax-constrained model, FBA showed that each cell population should support biomass production for division, suggesting an enzyme-stability based explanation of growth of individual cells, notwithstanding their apparent mRNA insufficiency. Comparing liver cancer cells and noncancerous liver cells via cell-population-average mRNA data, we identified cholesterol synthesis (SQLEr) and arginine synthesis as potential drug targets. Therefore, we suggest that identifying subclusters and their vulnerabilities reveals new drug targets for subpopulations, which should enable the reduction of drug resistance.