Integrated transcriptomic profiling glucosylceramide synthase enriches cancer stem cells

Colorectal cancer (CRC) is a leading cause of cancer-related mortality, with cancer stem cells (CSCs) driving therapy resistance and tumor progression. Ceramide glycosylation, catalyzed by glucosylceramide synthase (GCS) and encoded by UGCG, has been implicated in CSC regulation. Here, we investigated the role of UGCG in CRC using bulk RNA sequencing of CRC cell models and single-nuclei RNA sequencing (snRNA-seq) of xenograft tumors treated with oxaliplatin. A UGCG-knockout CRC cell line (WiDr/UGCG-) was generated using CRISPR/Cas9. RNA-seq analysis revealed that UGCG knockout altered gene expression in key pathways, including type I interferon signaling and extracellular matrix remodeling. SnRNA-seq identified a reduced stem cell-like cluster in UGCG-knockout tumors (p < 0.001), alongside distinct CD44-centered protein interaction networks. These findings suggest that ceramide glycosylation influences CSC maintenance and chemoresistance, highlighting its potential as a therapeutic target in CRC.