EP300 promotes hepatocellular carcinoma proliferation, migration and in vivo tumorigenicity revealed by integrated experimental and bioinformatic analyses

Hepatocellular carcinoma (HCC) remains a lethal malignancy with high heterogeneity and limited effective biomarkers for risk stratification. EP300 (p300), a central histone acetyltransferase and transcriptional co-activator, is frequently dysregulated in cancer, yet its integrated multi-omic and functional roles in HCC require further clarification. We integrated transcriptomic and clinical data from TCGA-LIHC, proteomic data from CPTAC, and public survival resources, and validated EP300 expression in ten paired HCC tumors and adjacent tissues by RT-qPCR and western blotting. EP300 was silenced by siRNA in Huh-7 and SK-hep-1 cells followed by CCK-8, colony formation, wound-healing, and Transwell assays. Tumorigenicity was evaluated using a subcutaneous xenograft model. Immune associations were explored using established deconvolution algorithms. EP300 was significantly upregulated in HCC at both the mRNA level (TCGA unpaired: p = 2.3 × 10− 5; paired: p = 2.2 × 10− 5) and the protein level (CPTAC, n = 165 tumors vs 165 normals: p = 6.7006 × 10− 3 6), and was higher in clinically high-risk strata (AFP > 400 ng/mL: p = 0.01; stage III–IV vs I–II: p = 0.04). High EP300 expression was associated with inferior overall survival in Kaplan–Meier analysis (HR = 1.43, 95% p < 0.05), while the association was attenuated after adjustment for key clinical covariates (multivariable Cox: p = 0.511). Functionally, EP300 knockdown reduced proliferation and clonogenicity (p < 0.0001) and impaired migration/invasion, and suppressed xenograft tumor growth. EP300 expression also correlated with an immunosuppressive tumor microenvironment signature in bulk RNA-seq analyses. EP300 is consistently upregulated in HCC and supports malignant phenotypes in vitro and in vivo. Its prognostic signal appears context-dependent after multivariable adjustment, suggesting EP300 is better interpreted as a progression-associated marker and potential therapeutic vulnerability. Immune-microenvironment associations derived from bulk data are hypothesis-generating and warrant orthogonal validation.