Background: Glypican-3 (GPC3) is overexpressed in most hepatocellular carcinoma (HCC) tissues but is absent in normal adult liver. We evaluated whether tumor GPC3 expression is associated with clinical outcomes in patients with advanced HCC treated with atezolizumab–bevacizumab (AB). Methods: We conducted a single-center retrospective cohort study of 139 patients with Barcelona Clinic Liver Cancer (BCLC) stage C HCC who received AB between January 2022 and August 2025. Tumor GPC3 expression was assessed by immunohistochemistry. The primary endpoints were overall survival (OS) and progression-free survival (PFS), and the secondary endpoint was objective response rate (ORR) according to modified Response Evaluation Criteria in Solid Tumors (mRECIST). Results: Baseline characteristics were largely balanced between GPC3-positive (n = 87) and GPC3-negative (n = 52) groups. Median OS was significantly shorter in patients with GPC3-positive tumors than in those with GPC3-negative tumors (p = 0.006). In multivariable analysis, GPC3 positivity remained independently associated with higher mortality (hazard ratio [HR] 1.77, 95% confidence interval [CI] 1.05–3.00; p = 0.033), along with Child–Pugh class B. PFS did not differ significantly between the groups (p = 0.712). ORR was lower in GPC3-positive tumors than in GPC3-negative tumors (approximately 17–18% vs. ~32%; p = 0.023). Membranous GPC3 localization was associated with inferior OS compared with cytoplasmic or absent expression (p = 0.025). Conclusions: Tumor GPC3 expression was associated with decreased OS and lower ORR among AB-treated patients with advanced HCC, suggesting potential clinical relevance and may help in risk stratification.

To enhance our understanding of the tumor immune microenvironment (TIME) in hepatocellular carcinoma (HCC), we investigated the heterogeneity of T-cell exhaustion and its association with HBV integrations and direct oncogenic potential in HCC. We conducted a multi-omics analysis, including single-cell RNA sequencing, whole-exome sequencing, whole-transcriptome sequencing, and next-generation sequencing (NGS)-based HBV integration analysis, in eight patients with virus-related HCC. For validation, bulk RNA sequencing and NGS-based HBV integration analysis were performed in an independent cohort (n = 106). Based on the expression scores of exhaustion markers in effector CD8⁺ T cells, patients were classified into high (n = 2) and low (n = 6) exhaustion groups (p <0.001). The high-exhaustion group exhibited higher clonal expansion (Gini index: 0.83 vs. 0.48, p = 0.006) and sharing of CD8⁺ T effector memory and cycling T cells with elevated exhaustion markers. This group also showed increased clonal expansion of CD4⁺ regulatory T cells and follicular helper T cells (p <0.001) with higher PDCD1 expression. In addition, the high-exhaustion group had higher TP53 mutation rates and signature scores for proliferation subtypes compared with the low-exhaustion group, who predominantly harbored TERT mutations. Moreover, the high-exhaustion group demonstrated more pronounced HBV integrations with elevated intrahepatic covalently closed circular DNA (cccDNA) and pregenomic (pg)RNA levels. Similarly, in the validation cohort, the high-exhaustion group (n = 28) demonstrated stronger proliferation subtype signatures (p <0.001), along with higher HBV integrations, S-fusion transcripts, and an increased intrahepatic viral reservoir (cccDNA/pgRNA) (p <0.05) compared with the low-exhaustion group (n = 78). Our study revealed the heterogeneity in T-cell exhaustion in the TIME of HCC, along with differences in HBV integrations and molecular subtypes. These findings provide insight into the intricate relationship between high exhaustion, proliferation subtype, increased HBV integrations, and enhanced HBV-induced oncogenic potential in virus-related HCC. This study provides a comprehensive immune landscape of T-cell exhaustion using multi-omics analysis, offering critical insights into T cell heterogeneity in virus-related HCC. It establishes a strong association between higher HBV integration, enhanced oncogenic potential, T-cell exhaustion, and proliferation subtypes in HCC. Our results also establish a basis for personalized therapies tailored to the immune-exhaustion status within the TIME of each patient with HCC.

Background/Objectives: Telomere dysfunction and the shelterin complex are implicated in cancer, yet the specific functions and interactions of telomerase and shelterin genes in hepatocellular carcinoma (HCC) tumorigenesis remain poorly understood. This study aims to investigate the clinico-biological functions and collaborative contributions of telomerase and shelterin components in hepatocarcinogenesis. Methods: We analyzed tumor and matched non-tumor tissues from 274 HCC patients who underwent hepatectomy. Telomere-related parameters, including TERT (telomerase reverse transcriptase) expression and telomere length measured by qRT-PCR, telomerase activity assessed by the Telomerase Repeated Amplification Protocol assay, and six shelterin components analyzed by RNA sequencing, were correlated with clinicopathological features. siRNA-mediated knockdown of TPP1 (POT1–TIN2 organizing protein) was performed to evaluate its regulatory effect on TERT expression. Findings were externally validated. Results: TERT and TPP1 were upregulated in tumors with increased telomerase activity and shortened telomere length. Among the shelterin components, TPP1 showed the strongest correlation with TERT, and its expression increased with tumor multiplicity and advancing stage. TPP1 expression also correlated with proliferation-associated genes, consistent with Gene Set Enrichment Analysis suggesting TPP1 involvement in proliferative activity. TPP1 knockdown suppressed TERT protein expression and inhibited HCC cell proliferation, with the strongest anti-proliferative effect observed after dual TERT–TPP1 knockdown. Clinically, high TPP1 expression was associated with significantly earlier HCC recurrence, and co-high expression of TPP1–TERT was linked to significantly worse survival after hepatectomy. Conclusions: The TERT–TPP1 axis enhances proliferative activity and is associated with aggressive features and poor outcomes in HCC. TPP1 represents a potential therapeutic target and prognostic biomarker for HCC.