Pan-Cancer Bioinformatics-Guided Evaluation of San-Huang-Xie-Xin-Tang Identifies Kidney Renal Clear Cell Carcinoma as...

Background/Objectives: San-Huang-Xie-Xin-Tang (SHXXT) is a classical traditional Chinese herbal formula composed of Coptis chinensis, Scutellaria baicalensis, and Rheum palmatum, with documented anti-inflammatory and anticancer properties. Despite growing interest in its pharmacological potential, systematic evaluation of its gene regulatory effects across multiple cancer types remains limited. This study aimed to assess the prognostic relevance of SHXXT-regulated genes across pan-cancer contexts using publicly available transcriptomic and clinical datasets. Methods: Fifteen active compounds of SHXXT were identified from traditional Chinese medicine databases (Encyclopaedia of Traditional Chinese Medicine (ETCM) 2.0, Chinese Compound Medicine Database (ccTCM), and Integrated Traditional Chinese Medicine Database (ITCM)). Compound-induced gene expression profiles were obtained from MCF7-based transcriptomic perturbation data in the ITCM database and integrated with The Cancer Genome Atlas (TCGA) across 24 cancer types. Survival-associated genes were evaluated using Cox proportional hazards regression and Kaplan-Meier analysis. A weighted prognostic scoring framework, supported by normalization and sensitivity analyses, was developed to prioritize cancer types according to the concordance between SHXXT-induced gene regulation and favorable prognostic patterns. Functional enrichment analysis was performed using Annotation, Visualization, and Integrated Discovery (DAVID), and cancer-related genes were annotated using the OncoKB database. Complementary in vitro studies, including Annexin V/propidium iodide (PI) and MT-1 staining assays, were conducted in Hep3B cells using a Good Manufacturing Practice (GMP)-certified commercial SHXXT preparation. Results: SHXXT-regulated genes were significantly enriched in cancer-related pathways, particularly the PI3K-Akt and MAPK signaling pathways. Pan-cancer analysis revealed substantial heterogeneity in prognostic alignment across cancer types. Among the 24 cancer cohorts analyzed, kidney renal clear cell carcinoma (KIRC) achieved the highest prognostic alignment score within the proposed framework. In KIRC, several genes, including PIK3CA, PIK3CB, KRAS, and RAF1, remained significantly associated with favorable prognostic alignment after multivariable adjustment. Pathway enrichment analysis further identified PI3K-Akt and MAPK signaling as the most significantly represented pathways among favorably aligned genes. In contrast, hepatocellular carcinoma exhibited a relatively low prognostic alignment score, consistent with in vitro observations indicating predominantly non-selective cytotoxic stress rather than cancer-specific therapeutic activity. Conclusions: SHXXT-regulated genes exhibited marked heterogeneity across cancer types, with KIRC was consistently prioritized as the top-ranked cancer type across multiple analytical scenarios, suggesting a strong concordance between SHXXT-associated gene regulation and favorable prognostic signatures. These findings represent computational predictions derived from transcriptomic and survival associations rather than direct evidence of therapeutic efficacy. The study provides a reproducible pan-cancer strategy for prioritizing candidate cancer types for future mechanistic and experimental validation of traditional Chinese medicine formulations.