RNA sequencing for 31 ccRCC samples which had undergone m6A abundance evaluation via immunohistochemistry (IHC)

In this study, a total of 35 clear cell renal cell carcinoma (ccRCC) specimens were collected from Sir Run Run Shaw Hospital, with 31 cases passing RNA quality control for downstream analysis (SRR-cohort). All patients underwent radical nephrectomy and provided informed consent, with full ethical approval and long-term follow-up. Each tumor was subjected to RNA sequencing and immunohistochemical (IHC) staining for m6A modification using a monoclonal anti-m6A antibody. Based on the derived expression profiles, an in-house risk indicator, the "W system", was applied to quantify m6A dysregulation risk and classify tumors into m6A-hyperdysregulated (W1) and m6A-hypodysregulated (W0) groups. Comparative analysis of m6A abundance validated the predictive value of W system. Furthermore, gene expression data were input into the m6ADEinfer causal inference model to infer m6A heterogeneity-driven effects and assess their correlations with tumor stage and resistance to therapy.