SQLE as a potential diagnostic and prognostic biomarker for LIHC: a multi-cohort and spatial study

Liver hepatocellular carcinoma (LIHC) remains a highly aggressive malignancy, necessitating novel biomarkers for early diagnosis and therapeutic intervention. This study investigates the role of Squalene epoxidase (SQLE), a key enzyme in cholesterol biosynthesis, in LIHC. Integrating multi-cohort analyses of nine GEO datasets and TCGA revealed significant upregulation of SQLE in LIHC tissues. These findings were corroborated at the proteomic level via multiplex immunohistochemistry (mIHC) on a tissue microarray of 48 paired clinical samples, where spatial analysis revealed a strong correlation between SQLE and the epithelial marker Pan Cytokeratin. Clinically, SQLE demonstrated potential diagnostic value and served as an independent prognostic factor for poor overall survival. Functional assays using shRNA knockdown in LIHC cell lines confirmed that SQLE inhibition decreased cellular proliferation, colony formation, and lateral migration. Mechanistically, elevated SQLE expression was associated with lipid metabolism modulation, m6A RNA modification, DNA damage responses, and an immunosuppressive tumor microenvironment. Notably, mIHC analysis of clinical TMAs revealed that high SQLE protein expression in tumor cells was significantly and negatively correlated with the infiltration of CD8 + T cells. Collectively, these results highlight SQLE as a promising diagnostic and prognostic biomarker that is associated with LIHC progression, potentially through metabolic and immunomodulatory pathways.