Uncovering the role of RNA binding proteins in colorectal cancer through single-cell transcriptomic analysis

Colorectal cancer (CRC) is a globally prevalent malignancy associated with high mortality rates. Despite the existence of various treatment modalities, the prognosis for CRC remains relatively poor. This study aims to explore the role of RNA-binding proteins (RBPs) in CRC progression and their potential as prognostic biomarkers and therapeutic targets. We first identified 166 prognosis-related RBPs, including LIN28B, PPARGC1A, RBM47, and AFF3, by performing univariate Cox regression analysis on bulk transcriptomic and clinical data from The Cancer Genome Atlas (TCGA). Next, single-cell RNA sequencing data from normal, adenoma, and CRC tissues of four patients were analyzed to determine cell type-specific expression patterns of RBPs. Ten upregulated RBPs (HSPB1, RBM47, HMGN2, BRD2, BST2, RBM6, YBX3, CANX, PLEC, and RNASET2) were identified as CRC-associated. Among them, HSPB1, RBM47, HMGN2, BRD2, BST2, and PLEC were predominantly expressed in epithelial cell subsets, whereas RNASET2, RBM6, YBX3, and G3BP2 showed higher expression in T cell subpopulations. Aberrant expression of these RBPs was significantly associated with clinical features such as age, cancer stage, and overall survival (p < 0.05). To validate the above findings, we performed qRT-PCR experiments on 15 paired CRC tumor and adjacent normal tissue samples. The results showed that the expression levels of CANX, RNASET2, YBX3, and BST2 were significantly higher in tumor tissues compared to adjacent normal tissues. Furthermore, we validated the expression levels and prognostic significance of these genes using the TCGA-COAD and READ cohorts, and found that their high expression was significantly associated with poorer overall survival. We suggest that RBPs may influence the occurrence and progression of CRC by affecting epithelial cells and T-cell subtypes, thus serving as promising prognostic biomarkers and potential targets for cancer immunotherapy in CRC.