Integrated network pharmacology, transcriptomic analysis, and preliminary cellular validation of Shenqi Dihuang decoction in clear cell renal cell carcinoma

Background Shenqi Dihuang Decoction (SQD), a classical multi-component formula, may exert systems-level antitumor effects; however, its mechanisms in clear cell renal cell carcinoma (ccRCC) remain unclear. Methods Network pharmacology, transcriptomic analysis, immune-infiltration assessment, gene set enrichment analysis, and molecular docking were integrated to identify potential SQD-related targets in ccRCC. Candidate hub genes were further evaluated by quantitative real-time PCR (qRT-PCR), and epidermal growth factor (EGF) was functionally assessed using small interfering RNA-based assays. Results Ninety-three compounds mapped to 206 putative targets, among which 178 overlapped with ccRCC-associated genes. Fifty-seven genes met the differential-expression criteria of adjusted P < 0.05 and | log2 fold change| > log2(2). The protein–protein interaction network identified 10 candidate hub genes, with enrichment in hypoxia-inducible factor 1 (HIF-1) signaling, extracellular matrix–receptor interaction, and renal cell carcinoma-related pathways. Molecular docking predicted favorable interactions of diosgenin with HIF1A (−7.0 kcal/mol) and stigmasterol with PTGS2 (−9.1 kcal/mol). Quantitative real-time PCR showed increased HIF1A expression in 786-O cells ( P < 0.05) and increased PTGS2 expression in Caki-1 ( P < 0.05) and 786-O cells ( P < 0.001) compared with HK-2 cells. EGF was independently selected as a representative hub gene for functional assessment, and its knockdown reduced cell viability at 24–72 h ( P < 0.01 to P < 0.0001), invasion ( P < 0.01), and wound closure ( P < 0.05) in the examined ccRCC cells. Conclusion The integrated analyses identified multiple candidate hub genes and pathways potentially associated with SQD in ccRCC. HIF1A and PTGS2 showed computational and expression-level support, whereas EGF demonstrated biological relevance in preliminary functional assays. These findings are hypothesis-generating and require further direct target-specific validation.