miR-98-5p, miR-130a-3p, and miR-1246 Profiling in Tissue and Liquid Biopsies of Patients with Hepatocellular Carcinoma

Background/Objectives: Hepatocellular carcinoma (HCC) is the most common primary liver malignancy, often arising in cirrhosis. Its early non-invasive diagnosis and prognostic assessment remain challenging due to the limited availability of reliable circulating biomarkers, creating the need to establish non-invasive biomarkers that distinguish malignant transformation. This preliminary study aimed to: discover EV-associated miRNAs that differ among healthy subjects, patients with liver cirrhosis, and patients with HCC; validate selected candidates by ddPCR in an independent cohort; compare their abundance in plasma-derived EVs, whole plasma, and paired tumoral/peritumoral tissues; and explore their diagnostic performance for HCC versus cirrhosis and their associations with clinical outcomes. Methods: miRNA sequencing was performed on plasma-derived EVs from an exploratory cohort of 10 healthy subjects, 10 cirrhotic patients, and 10 HCC patients. Three candidate miRNAs, miR-98-5p, miR-130a-3p, and miR-1246, were subsequently quantified by droplet digital PCR (ddPCR) in an independent cohort of 29 HCC patients, 30 cirrhotic patients, and 20 healthy subjects using plasma-derived EVs, plasma, and paired tumoral/peritumoral liver tissues. Results: In plasma EVs, miR-98-5p and miR-130a-3p were reduced in HCC and cirrhotic patients compared with healthy subjects, whereas miR-1246 was increased in HCC compared with cirrhosis. In plasma, all three miRNAs were elevated in HCC compared with cirrhosis and healthy controls. Plasma miR-1246 showed the highest diagnostic performance to discriminate HCC from cirrhosis (AUC = 0.87). In tissue, miR-98-5p was upregulated and miR-130a-3p downregulated in tumoral versus peritumoral samples, whereas miR-1246 showed no significant difference. Higher plasma miR-130a-3p and miR-1246 levels were associated with improved overall survival, while increased miR-98-5p levels were associated with lower relapse rates. Conclusions: Among the three miRNAs, plasma miR-1246 showed the strongest diagnostic performance for distinguishing HCC from liver cirrhosis. Combination with miR-98-5p and/or miR-130a-3p did not improve discrimination. Thus, plasma miR-1246 emerged as the leading candidate diagnostic indicator in the HCC cohort, whereas the three miRNAs showed distinct potential associations with prognosis.