The microRNA (miRNA) signatures in different phases of the natural history of chronic hepatitis B virus infection

Chronic hepatitis B virus (HBV) infection (CHB) progresses through distinct clinical phases characterized by dynamic immune responses and changes in intrahepatic gene expression. While hepatic transcriptomes have been studied, hepatic microRNA (miRNA) profiles across the natural history of CHB remain poorly defined. In this study, we aimed to characterize hepatic miRNA expression and its association with liver cell composition across CHB phases. Liver biopsies from 43 treatment-naïve CHB patients across four clinical phases, immune tolerance (IT), immune active (IA), inactive carrier (IC), and HBeAg-negative hepatitis (ENH), were analyzed using miRNA microarrays and mRNA sequencing. Hepatic cell composition was inferred using CIBERSORT and expression of 92 cell-type marker genes. Differentially expressed miRNAs were identified by Mann-Whitney U test, and clustering and correlation analyses were performed to assess associations with immune and liver cell markers. Consistent with previous studies, immune cell infiltration varied by phase, peaking in IA and ENH phases. Sixty-five miRNAs were significantly differentially expressed (|log₂FC| > 0.585), including immune-associated miRNAs such as miR-155-5p, miR-150-5p, and miR-142-5p. Twenty-two miRNAs elevated in IA phase were associated with macrophage and T cell markers. Hepatocyte-enriched miRNAs (e.g., miR-122-5p, miR-192-5p) remained highly expressed across all phases. Clustering analysis identified five miRNA expression patterns, with immune-associated clusters upregulated in IA and ENH phases. Correlation analysis confirmed strong associations between immune-phase miRNAs and αβ T cell markers. Overall, these findings indicate that hepatic miRNA profiles are largely stable across CHB phases, with immune cell infiltration associated with selective miRNA changes, particularly in IA and ENH phases.