NDUFA12 is associated with poor prognosis and promotes malignant phenotypes and mitochondrial metabolic alterations in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, yet effective treatment options remain limited. NDUFA12, a subunit of mitochondrial complex I, plays a crucial role in oxidative phosphorylation and cellular energy metabolism; however, its expression pattern, clinical significance, and biological role in HCC remain unclear. In this study, the expression profile and clinical relevance of NDUFA12 were analyzed using The Cancer Genome Atlas (TCGA) data. Genomic and functional features, including differentially expressed genes (DEGs), tumor mutation burden (TMB), functional enrichment, and immune infiltration, were assessed. An institutional cohort of 25 patients with advanced HCC receiving targeted-immunotherapy at our hospital was enrolled, and baseline tumor samples were subjected to RNA sequencing for validation. MHCC-97H and PLC/PRF/5 cells were transfected with small interfering RNAs (siRNAs) targeting NDUFA12. Functional assays, including CCK-8, EdU, wound healing, Transwell assays, Seahorse XF mitochondrial stress tests, Seahorse XF glycolysis stress tests, ATP production, lactate accumulation, mitochondrial membrane potential, and reactive oxygen species (ROS) detection, were performed to evaluate malignant phenotypes and metabolic alterations. NDUFA12 expression was markedly elevated in HCC and was associated with advanced tumor stage, increased TMB, and poorer overall survival and progression-free survival. DEG analysis suggested enrichment in cell cycle-, mitochondrial-, and metabolism-related pathways. Low NDUFA12 expression was associated with distinct immune infiltration patterns according to the CIBERSORT algorithm, and RNA-sequencing data of our cohort further confirmed longer overall survival in patients with low NDUFA12 expression. Functionally, NDUFA12 knockdown reduced cell proliferation, invasion and migration in HCC cells. Metabolic assays showed that NDUFA12 knockdown decreased oxygen consumption rate, ATP production, mitochondrial membrane potential, and intracellular ROS levels, while increasing extracellular acidification rate and lactate production, suggesting impaired mitochondrial respiration and compensatory glycolytic activation. Collectively, these findings suggest that NDUFA12 is associated with poor prognosis, malignant cellular phenotypes, and mitochondrial metabolic alterations in HCC. NDUFA12 may serve as a prognostic biomarker and a candidate target for further functional and translational investigation in HCC.