Single-cell transcriptomic prioritization of SQLE and functional validation of SQLE inhibition in colorectal cancer cells

Objective: To analyze treatment-associated epithelial cell-state changes in colorectal cancer (CRC) and identify candidate genes within lipid/cholesterol metabolic programs. Methods: CNP0004138 and GSE254249 were used as discovery cohorts. Epithelial cells were extracted for re-clustering, subtype annotation and differential expression analysis. Genes with concordant changes across cohorts underwent GO/KEGG enrichment and protein-protein interaction (PPI) network analyses. External datasets were used to assess chemotherapy-related expression direction (GSE200407), SQLE expression in normal and tumor tissues (GSE87211 and GSE44076), and overall survival (GSE17536). HCT116 cells were treated with the SQLE inhibitor terbinafine and evaluated using CCK-8, EdU immunofluorescence and colony formation assays. Results: Both discovery cohorts showed treatment-associated remodeling of epithelial cell states. Shared downregulated genes were mainly enriched in cholesterol/sterol biosynthesis and lipid metabolic processes, and lipid/cholesterol metabolism-related genes occupied central positions in the shared downregulated PPI network. In the external mFOLFOX cohort GSE200407, SQLE expression was higher in the chemotherapy-sensitive group than in the insensitive group and showed the strongest directional support among the five candidate genes. SQLE was also expressed at higher levels in CRC tumor tissues and was associated with poorer overall survival. Terbinafine treatment was accompanied by decreased HCT116 cell viability, fewer EdU-positive cells and reduced colony-forming capacity. Conclusion: Decreased lipid/cholesterol metabolic programs represent a consistent feature of treatment-associated epithelial cell-state changes in CRC. SQLE is a candidate gene within this metabolic program, but its causal role requires genetic and mechanistic validation.