A mast cell-associated apoptosis-related transcriptomic signature in clear cell renal cell carcinoma and in vitro characterization of YBX3

Background Clear cell renal cell carcinoma (ccRCC) exhibits substantial molecular and immune heterogeneity. Mast cells participate in tumor-microenvironment remodeling, but the prognostic relevance of mast cell-associated apoptosis-related transcriptional features remains unclear. Methods Single-cell RNA sequencing was used to identify mast cells in ccRCC. Genes associated with the annotated mast-cell cluster were intersected with the HALLMARK_APOPTOSIS gene set to develop a mast cell-associated apoptosis score (MCAS) using machine-learning survival algorithms. MCAS was evaluated in TCGA-KIRC and two external cohorts. Associations with clinicopathological features, mutation profiles and model-derived genes were analyzed. YBX3 was functionally characterized using qRT-PCR, western blotting, CCK-8, colony formation, EdU, Transwell migration and flow cytometry assays. Results A TPSAB1/CPA3-positive mast cell population was identified. The CoxBoost plus random survival forest model showed the best performance for MCAS construction. High MCAS scores predicted poor survival in the training and validation cohorts and were associated with advanced clinicopathological features and tumor mutation burden. SurvSHAP and SurvLIME jointly identified BNIP3, CX3CR1, HMOX1, and YBX3. High YBX3 expression was associated with unfavorable prognosis. Functionally, YBX3 knockdown inhibited proliferation, colony formation, DNA synthesis and migration, and promoted apoptosis with increased BAX and decreased Bcl-2, whereas YBX3 overexpression enhanced proliferative and migratory phenotypes. Conclusions MCAS is a mast cell-associated apoptosis-related transcriptomic signature for prognostic stratification in ccRCC. The in vitro findings suggest that YBX3 may contribute to malignant phenotypes and apoptosis resistance in ccRCC cells.