A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer

Abstract Left-sided colorectal cancer (LCRC) and right-sided colorectal cancer (RCRC) show marked differences in prognosis and therapeutic response, yet the underlying molecular mechanisms remain poorly understood. We hypothesize that these clinical differences reflect distinct cell-type-specific transcriptional programs and microenvironmental interactions that can be resolved at single-cell resolution. To test this hypothesis, this study analyzed single-cell transcriptomic data from 16 colorectal cancer (CRC) patients (8 LCRC and 8 RCRC), revealing molecular differences between LCRC and RCRC in tumor cells, T cells, B cells, myeloid cells, fibroblasts, and endothelial cells, and constructing a differential atlas of LCRC versus RCRC. Significant molecular and cellular differences were observed between LCRC and RCRC. MTRNR2L8 was markedly upregulated in RCRC tumor cells and associated with poorer patient survival, potentially regulated by transcription factors STAT3, ELK3, and EP300. RCRC showed an increased proportion of the CD8-EFFECTOR 3 subpopulation, which co-expresses effector and exhaustion markers, suggesting favorable immunotherapy response. In contrast, the CD4-heat shock proteins (CD4-HSP) subpopulation was almost exclusively present in LCRC, suggesting a potential correlation with a weaker response to immune checkpoint inhibitors. Additionally, APP-CD74 ligand-receptor interactions were significantly enhanced in RCRC, potentially contributing to worse prognosis by inhibiting APP protein cleavage and promoting its accumulation. Validation was performed using an independent single-cell transcriptomic dataset, bulk RNA-seq data from TCGA CRC samples, and qPCR on locally collected CRC tissue specimens. In addition, a spatial transcriptomic dataset of CRC and immunohistochemistry data from the Human Protein Atlas (HPA) database were also used to validate part of the findings. This study provides a comprehensive single-cell transcriptomic atlas highlighting the molecular and cellular disparities between LCRC and RCRC, offering novel insights into tumor biology and informing the development of personalized therapeutic strategies.