Characterization of stem cell landscape and identification of stemness-related gene ENY2 in colorectal cancer by intergrated transcriptomic analysis.

BACKGROUND

Cancer stem cells (CSCs) drive colorectal cancer (CRC) progression, metastasis, and therapy resistance, but their heterogeneity limits targeted treatment efficacy. Clarifying the stemness landscape and underlying mechanisms is crucial for developing effective CRC therapies.

METHODS

By integrating 10 ×single-cell data from GSE201348 and GSE161277, we constructed a single-cell atlas of nine primary CRC samples. CSCs were identified via scRNA-seq analyses. Using integrative bioinformatics tools, we identified ENY2 as a stemness-related marker and explored its potential role in CRC. We further compared genetic variants, immune infiltration, and drug sensitivity between high and low ENY2 expression groups.

RESULTS

Stem cell clusters (M0 and M7) in CRC were identified based on copy number variation, pseudotime trajectory, and CytoTRACE analyses. By integrating marker gene profiles, DEGs from GSE33113, CytoTRACE-based CSC genes, and prognostic genes from GSE17536, we identified two key stemness-related markers: ENY2 and PKM. ENY2 was prioritized for further analysis due to its limited investigation in CRC. Bioinformatic analyses revealed that ENY2 was significantly upregulated and associated with poor prognosis. Enrichment analyses indicated its involvement in MYC and E2F targets, G2M checkpoint, and EMT pathways. Drug sensitivity prediction suggested that high ENY2 expression may confer responsiveness to 5-fluorouracil, capecitabine, oxaliplatin, and 24 other potential agents.

CONCLUSIONS

ENY2 may act as a key CSC-associated biomarker that promotes CRC tumorigenesis and metastasis via the EMT pathway, which enhance our understanding of CRC pathogenesis and highlight ENY2 as a potential target for diagnosis and therapy.