Integrated bulk and single-cell transcriptomics reveals TREH as a novel protective biomarker and prognostic predictor in clear cell renal cell carcinoma.

Background: Clear cell renal cell carcinoma (ccRCC) is marked by substantial intratumoral heterogeneity and highly variable clinical outcomes. The identification of robust biomarkers that drive tumor progression is essential for improving prognostic accuracy and guiding therapeutic strategies. Methods: We employed an integrated transcriptomic data analysis strategy, combining Weighted Gene Co-expression Network Analysis (WGCNA) with machine learning algorithms (LASSO and GBM). To screen for prognostic candidates, the TCGA-KIRC cohort was allocated into a 70% training set for model development and a 30% testing set for internal validation. The clinical relevance, immunological landscape, and biological functions of the top candidate were systematically characterized using scRNA-seq analysis and validated through extensive Results: Trehalase (TREH) was identified as a novel, independent protective factor for ccRCC. Low TREH expression correlated significantly with advanced pathologic stages, Fuhrman histological grade, distant metastasis, and poor survival outcomes (OS, DSS, and PFI). A prognostic nomogram integrating TREH expression with clinical parameters demonstrated superior predictive accuracy. At the single-cell level, TREH was predominantly and specifically expressed in epithelial cells. Notably, computational analysis predicted that TREH-deficient epithelial cells may engage in more intensive pro-tumorigenic and angiogenic crosstalk with the microenvironment, particularly through the VEGF, PLG, and APP signaling pathways. Mechanistically, our data suggest that TREH acts as a tumor suppressor. Downregulation of TREH is associated with EMT promotion and an immunosuppressive microenvironment. The causal link between TREH enzymatic activity and these phenotypes remains to be further defined. In addition, TREH overexpression significantly inhibited cell proliferation, migration, and invasion Conclusion: Our study establishes TREH as a robust prognostic biomarker and a functional tumor suppressor in ccRCC. The loss of TREH is associated with tumor progression and correlates with EMT activation and a pro-angiogenic microenvironment, suggesting its potential as a therapeutic target for improving patient outcomes.