Elevated NDUFAF2 expression correlates with poor prognosis and drives metabolic dependency in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, with limited therapeutic options for advanced and immunotherapy-resistant cases. Mitochondrial oxidative phosphorylation (OXPHOS) has emerged as a key metabolic dependency in a subset of HCCs, yet the molecular regulators of this vulnerability remain poorly understood. Here, we report that NDUFAF2, a core assembly chaperone for mitochondrial Complex I, is significantly overexpressed across multiple human cancers, particularly in HCC, where elevated expression correlates with poor overall survival, progression-free interval, and disease-specific survival in large-scale TCGA and CPTAC cohorts. At the transcriptomic and proteomic levels, NDUFAF2 upregulation was consistently observed in primary HCC tissues compared with paired normal liver samples, and correlated with advanced histological grade, pathological stage, high AFP levels, and vascular invasion. Bioinformatic pathway analyses identified OXPHOS as the dominant biological process associated with NDUFAF2 expression. Mechanistically, stable NDUFAF2 knockdown in two independent HCC cell lines (HCC-LM3 and SNU-449) resulted in profound mitochondrial dysfunction, including reduced oxygen consumption rate, impaired ATP production, increased reactive oxygen species (ROS) accumulation, and compensatory upregulation of glycolytic genes. These metabolic defects ultimately led to suppressed cell proliferation in vitro. Preliminary correlative analyses further suggested weak associations between NDUFAF2 expression and immunosuppressive features in the tumor microenvironment, although these trends remain hypothesis-generating and require experimental validation. Collectively, our findings establish NDUFAF2 as a pivotal regulator of mitochondrial bioenergetics and malignant progression in HCC, identifying it as a promising prognostic biomarker and a potential target for metabolic therapy in OXPHOS-dependent liver cancers.