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 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 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.