Comprehensive multi-omics analysis reveals RUNX1's prognostic value, immune associations, and MUC13-Mediated mechanistic role in hepatocellular carcinoma pathogenesis

Hepatocellular carcinoma (HCC) is a biologically and clinically heterogeneous malignancy, posing major challenges for early diagnosis, prognostic prediction, and therapeutic intervention. The Runt-related transcription factor (RUNX) family, comprising RUNX1, RUNX2, and RUNX3, plays essential roles in cellular processes and contribute to the pathogenesis of numerous malignancies. This study aims to elucidate their role in tumor progression and its clinical implications. We performed an integrative pan-cancer multi-omics analysis across 33 cancer types to characterize RUNX family expression patterns, prognostic associations, and immune correlations using publicly available datasets. Expression and functional roles were experimentally validated in HCC through <i>in vitro</i> and <i>in vivo</i> assays. Relationships between <i>RUNX1</i> expression and clinical stage, immune subtypes, checkpoint gene expression, immunotherapy sensitivity, and immune-related co-expression networks were assessed. The prognostic significance of <i>RUNX1</i> was determined using Kaplan-Meier survival analysis, Cox regression, and ROC curve evaluation. Transcriptional regulation was investigated via bioinformatic tools, database interrogation, and chromatin immunoprecipitation (ChIP) assays. Functional studies were conducted to determine the effects of <i>RUNX1</i> knockdown on HCC cell proliferation, migration, and invasion. <i>RUNX1</i> was upregulated in multiple tumor types, including breast, lung, liver, and brain cancers, and its elevated expression correlated with poorer overall (OS) and disease-specific survival (DSS). In HCC, RUNX1 expression was significantly associated with advanced clinical stage, distinct immune subtypes, and altered checkpoint expression profiles, indicating a role in shaping the tumor immune microenvironment. Mechanistically, <i>MUC13</i> was identified as a direct transcriptional target of <i>RUNX1</i>, as confirmed by promoter-binding prediction, ChIP validation, and dual-luciferase assays. <i>RUNX1</i> knockdown suppressed HCC cell proliferation, migration, and invasion by attenuating Wnt/β-catenin/EMT signaling activity. These findings highlight RUNX1 as a potential prognostic biomarker and therapeutic target, offering mechanistic insight into HCC pathogenesis and avenues for improved precision oncology.