Long-term cultivation shifts transcriptomic profile of HCT-116 cells

Human cancer cell lines are widely used in artificial culture systems to study cancer biology due to their immortalization, enabling extended culturing compared to primary cells. However, genomic instability can rapidly alter cellular behavior, raising questions about the transcriptome stability for controlled studies. We cultivated HCT-116 cells over 25 passages (~16 weeks), and observed a stable transcriptome up to passage 20, with only minimal differential gene expression. Above passage 20, genes corresponding to cell proliferation and cell death were upregulated suggesting a change in general cellular regulation and underlining defined cell culture time periods for stable and reproducible experimental conditions.