A-to-I RNA editing across consensus molecular subtypes of colon cancer: biological insights and prognostic model

Background: Colorectal cancer (CRC) is the second most frequently diagnosed cancer worldwide and represents a major challenge for public health. Despite advances in molecular profiling, important gaps remain in our understanding of tumorigenesis and the regulatory mechanisms underlying CRC progression. The most widely adopted classification system is the Consensus Molecular Subtypes (CMS), which stratifies CRC into four biologically distinct subtypes. Methods: Methods: We investigated the role of A-to-I RNA editing across CMS subtypes in a cohort of 100 CRC patients at various disease stages. Bulk RNA-seq data were analyzed using REDItools to detect editing events, focusing on both recoding sites and edits within repetitive elements, such as Alu sequences. Furthermore, expression levels of the ADAR enzyme family were assessed, and deconvolution analyses were performed on single-cell RNA-seq data from an independent cohort of stage II CRC patients to characterize editing activity within the tumor microenvironment (TME). Competitive endogenous RNA (ceRNA) networks, specific to each CMS subtype, were constructed based on editing events in repetitive elements. A multivariate Cox proportional hazards model was applied to evaluate associations with overall survival (OS). Results: We observed statistically significant differences in ADARB1 expression across CMS subtypes. Single-cell RNA-seq data revealed subtype-specific distribution patterns of ADAR enzymes within the TME. Analysis of editing events showed subtype-specific signatures in both known cancer-related genes (e.g., COPA , CADPS , IGFBP7 ) and novel candidates ( ZNF552 , RALGPS1 ). Editing in repetitive elements informed the construction of distinct ceRNA networks for each CMS subtype, suggesting different post-transcriptional regulatory mechanisms. Survival analysis identified three variables significantly associated with OS, independent of CMS classification and clinical stage: ADARB1 expression, and editing events in NOP14-AS1 (chr4:2960236; p = 0.036; HR = 0.0069), previously linked to 5-FU sensitivity, and ST7-AS2 (chr4:117120557). Conclusion: This study underscores the biological relevance of RNA editing in CRC, highlighting its impact on chemoresistance, the tumor microenvironment, and subtype-specific gene regulation. Our findings suggest that RNA editing represents a critical post-transcriptional regulatory layer in CRC and holds potential as a biomarker and therapeutic target.