Stage-dependent transcriptional regulation of ICOS across metabolic liver disease progression and hepatocellular carcinoma

Background and Aim Metabolic dysfunction–associated steatotic liver disease (MASLD) can progress to metabolic dysfunction–associated steatohepatitis (MASH), cirrhosis, and eventually hepatocellular carcinoma (HCC). About 30% of HCC patients die within five years, highlighting an urgent need for early intervention and understanding of disease mechanisms. Immune dysregulation is a key factor in this progression. This study aimed to characterize the stage-dependent transcriptional regulation of inducible T-cell co-stimulator (ICOS) and its ligand (ICOSLG) across metabolic liver disease and HCC. Methods A staged transcriptomic analysis was performed using two independent human liver microarray datasets. GSE89632 assessed early ICOS and ICOSLG expression in metabolic liver disease (Healthy, MASLD, MASH). GSE164760 served as a discovery cohort for advanced disease stages. As the data was not normally distributed, nonparametric analyses were used throughout. For immune pathway enrichment and immune gene signature evaluation, tumour samples were split into ICOS-high and ICOS-low groups. Result ICOS and ICOSLG expression remained stable during early disease stages (p > 0.05). In advanced liver disease, ICOS expression significantly increased with disease stage (p < 0.05). Median expression rose in cirrhosis, adjacent tissue, and HCC. Stratified ICOS-high tumours showed enrichment of immune checkpoints, T-cell activation, exhaustion, and cytokine signaling pathways (FDR < 0.25). No significant differences in ICOSLG expression were detected across disease stages. Conclusion ICOS becomes dysregulated in advanced liver disease and during malignant transformation, not in early metabolic dysfunction. This change is associated with broad remodeling of the immune microenvironment in HCC.