The role of cancer stem cells in the progression of colorectal cancer and the tumor microenvironment: new perspectives from single-cell RNA sequencing and spatial transcriptomics analyses.

[BACKGROUND] Colorectal cancer (CRC) progression and treatment resistance are closely linked to cancer stem cells (CSCs), yet their spatial dynamics and regulatory mechanisms remain poorly characterized. This study integrates single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to define CRC stem cell subtypes (Co-CSS), map their interactions within the tumor microenvironment, and identify novel prognostic markers driving clinical outcomes.

[METHODS] scRNA-seq was used to analyze cellular heterogeneity in CRC, identifying key Co-CSS. CytoTRACE was applied to assess stemness. ST further mapped the distribution and interactions of Co-CSS with the tumor microenvironment. Gene intersection analysis identified and , whose high expression correlated with poor prognosis. Patient classification based on and expression highlighted treatment response variability, suggesting targets for precision medicine.

[RESULTS] The findings indicate that Co-CSS in CRC can modulate the tumor microenvironment and influence the progression of the disease through various ligand-receptor interactions. It is possible that Co-CSS is regulated by fibroblasts through the WNT signaling pathway. The expression levels of and are significantly correlated with the overall survival of CRC patients, suggesting their potential value as independent prognostic markers.

[CONCLUSIONS] This study offers insights into the role of Co-CSS in CRC through ST and gene expression profiling, uncovering novel markers and pathways. It redefines the interplay between Co-CSS and the tumor microenvironment, offering a foundation for future mechanistic studies and therapeutic interventions aimed at targeting Co-CSS to improve CRC treatment.