Validation of Interferon Regulatory Factor 1 and Nicotinamide Phosphoribosyltransferase as Prognostic Biomarkers and Potential Therapeutic Targets in Clear Cell Renal Cell Carcinoma

Background Clear cell renal cell carcinoma (ccRCC) exhibits marked epithelial cell heterogeneity. The aim of this study was to identify an epithelial cell-related regulon in ccRCC. Methods Epithelial cell‑specific gene regulatory networks (GRNs) were inferred using SCENIC to identify key transcription factors (TFs) and their corresponding regulons, and direct transcriptional regulation was validated by chromatin immunoprecipitation followed by quantitative PCR (ChIP‑qPCR). The associations between the risk model and tumor immune infiltration, genomic features, and drug sensitivity were systematically assessed. In vitro experiments, including gene silencing, overexpression, cell viability, migration, invasion, and immune cell co-culture assays, as well as an in vivo xenograft model in nude mice were employed to validate the functional roles of the identified regulatory axis. Finally, immunohistochemical staining was performed on tumor tissues from 64 ccRCC patients. Results ChIP‑qPCR suggested potential binding of interferon regulatory factor 1 ( IRF1 ) to the nicotinamide phosphoribosyltransferase ( NAMPT ) promoter. Silencing IRF1 and NAMPT reduced ccRCC cell viability and suppressed migration and invasion, whereas IRF1 overexpression enhanced these malignant phenotypes. In an independent clinical cohort, elevated protein levels of both IRF1 and NAMPT were significantly associated with adverse outcomes. The NAMPT -related Riskscore model was associated with distinct immune infiltration and different genomic features. However, further experiments, such as dual-luciferase reporter assays, are needed to confirm the transcriptional regulation relationship effect of IRF1 on NAMPT . Conclusion This study identified a novel regulatory axis and its derived prognostic model as valuable tools for risk stratification in ccRCC.