Single-cell RNA sequencing combined with single-cell genome-wide association study identifies SF3B4 as a hub gene in hepatocellular carcinoma progression

High heterogeneity and poor therapeutic response are major challenges in hepatocellular carcinoma (HCC). This study aimed to identify core hepatocyte subsets and key genes driving HCC progression via a multi-omics approach to inform precise diagnosis and treatment. We analyzed public data from GEO (GSE282701), TCGA-LIHC, and IEU-Open-GWAS (bbj-a-158). scRNA-seq, scPagwas, BayesPrism, and WGCNA were used to identify core HCC cell subsets and genes. SF3B4 expression was validated by Western blot and RT-qPCR in HCC tissues and cell lines. Functional impacts on proliferation and migration were assessed using colony formation, Transwell, and wound healing assays in HepG2 and Huh7 cells. Integrated scRNA-seq and scPagwas analysis identified PKHD1⁺ hepatocytes as a core HCC subset, showing significantly higher trait relevance scores versus other subtypes and a positive correlation with HCC (P < 0.05). BayesPrism quantification in the TCGA-LIHC cohort confirmed that high abundance of PKHD1⁺ hepatocytes correlated with poor prognosis (P < 0.05), immune microenvironment remodeling (increased CAFs and MDSCs), and distinct somatic mutation profiles (elevated CTNNB1 and reduced TP53 mutation rates). SF3B4 was identified as the key gene associated with this subset via WGCNA and differential expression analysis. SF3B4 was upregulated in HCC tissues and cells, and its knockdown suppressed proliferation and migration in HepG2 and Huh7 cells. The PKHD1⁺ hepatocyte subset and SF3B4 represent key regulators of HCC malignancy, offering novel potential targets for prognostic assessment and targeted therapy.