Abstract
Immune checkpoint inhibitors (ICIs) are utilized to treat hepatocellular carcinomas (HCC) without validated biomarkers. We sought to identify genomic signatures and immune patterns predicting treatment efficacy in 1,306 HCC patients to evaluate for potential predictive biomarkers associated with immunotherapy outcome. Programmed death ligand 1 (PD-L1) expression was high in 6.1% and low in 11.6%; deficient mismatch repair/microsatellite instability-high (dMMR/MSI-H) was detected in only 0.2%, and high tumor mutational burden (TMB-H) in 5.1% of the patients. Immuno-oncologic (IO) markers (CD80, HAVCR2, PDCD1, IFNG, CTLA4, IDO1, CD86, LAG3, PDCD1LG2) correlated with PD-L1 expression (q < 0.05). Infiltration of B cells, M1 macrophages, CD8 + T cells, and Tregs also increased with PD-L1 expression (q < 0.05). CTNNB1 mutations occurred more in PD-L1 negative (35%) than in PD-L1 high (21%) patients (p = 0.03). PD-L1 expression did not affect ICI treatment duration, but CTNNB1-high levels were associated with a shorter duration of treatment in PD-L1 negative tumors (p = 0.04). However, in IO non-exposed tumors, CTNNB1-high expression was associated with improved overall survival (HR = 0.97, 95% CI 0.96-0.98, p < 0.00001). In conclusion, our analysis indicates that expression of PD-L1, CTNNB1, and other molecular markers most associated with IO response in other gastrointestinal malignancies are not directly indicative of such responses in HCC.
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Caris Life Sciences owns the deidentified sequencing data, which cannot be publicly shared due to the data usage agreement in place. These data will be made available to researchers for replication and verification purposes through our letter of intent process, which is generally fulfilled within 6 months. For more information on how to access this data, please contact Dr. Joanne Xiu at [jxiu@carisls.com](mailto:jxiu@carisls.com).
References
Vogel, A., Meyer, T., Sapisochin, G., Salem, R. & Saborowski, A. Hepatocellular carcinoma. Lancet 400, 1345–1362 (2022).
Chen, C., Wang, Z., Ding, Y. & Qin, Y. Tumor microenvironment-mediated immune evasion in hepatocellular carcinoma. Front. Immunol. 14, https://doi.org/10.3389/fimmu.2023.1133308 (2023).
Llovet, J. M. et al. Sorafenib in advanced hepatocellular carcinoma. N. Engl. J. Med. 359, 378–390 (2008).
Kudo, M. et al. Lenvatinib versus sorafenib in first-line treatment of patients with unresectable hepatocellular carcinoma: a randomised phase 3 non-inferiority trial. Lancet 391, 1163–1173 (2018).
Bruix, J. et al. Regorafenib for patients with hepatocellular carcinoma who progressed on sorafenib treatment (RESORCE): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet 389, 56–66 (2017).
Abou-Alfa, G. K. et al. Cabozantinib in patients with advanced and progressing hepatocellular carcinoma. N. Engl. J. Med 379, 54–63 (2018).
Zhu, A. X. et al. Ramucirumab after sorafenib in patients with advanced hepatocellular carcinoma and increased alpha-fetoprotein concentrations (REACH-2): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol. 20, 282–296 (2019).
Sangro, B., Sarobe, P., Hervas-Stubbs, S. & Melero, I. Advances in immunotherapy for hepatocellular carcinoma. Nat. Rev. Gastroenterol. Hepatol. 18, 525–543 (2021).
Yau, T. et al. Nivolumab versus sorafenib in advanced hepatocellular carcinoma (CheckMate 459): a randomised, multicentre, open-label, phase 3 trial. Lancet Oncol. 23, 77–90 (2022).
Reig, M. & Sanduzzi-Zamparelli, M. Nivolumab and sorafenib in hepatocellular carcinoma: lessons from the CheckMate 459 study. Lancet Oncol. 23, 4–6 (2022).
Yau, T. et al. Efficacy and safety of nivolumab plus ipilimumab in patients with advanced hepatocellular carcinoma previously treated with sorafenib: the CheckMate 040 randomized clinical trial. JAMA Oncol. 6, e204564 (2020).
Melero, I. et al. Nivolumab plus ipilimumab combination therapy in patients with advanced hepatocellular carcinoma previously treated with sorafenib: 5-year results from CheckMate 040☆. Ann. Oncol. 35, 537–548 (2024).
Cheng, A. L. et al. Updated efficacy and safety data from IMbrave150: atezolizumab plus bevacizumab vs. sorafenib for unresectable hepatocellular carcinoma. J. Hepatol. 76, 862–873 (2022).
Abou-Alfa, G. K. et al. Tremelimumab plus durvalumab in unresectable hepatocellular carcinoma. NEJM Evid. 1, EVIDoa2100070 (2022).
Galle, P. R. et al. Nivolumab (NIVO) plus ipilimumab (IPI) vs lenvatinib (LEN) or sorafenib (SOR) as first-line treatment for unresectable hepatocellular carcinoma (uHCC): frst results from CheckMate 9DW. J. Clin. Oncol. 42, LBA4008–LBA4008 (2024).
Fashoyin et al. FDA approval summary: pembrolizumab for recurrent locally advanced or metastatic gastric or gastroesophageal junction adenocarcinoma expressing PD-L1. Oncologist 24, 103–109 (2018).
Bodor, J. N., Boumber, Y. & Borghaei, H. Biomarkers for immune checkpoint inhibition in non–small cell lung cancer (NSCLC). Cancer 126, 260–270 (2020).
Thein, K. Z., Lemery, S. J. & Kummar, S. Tissue-agnostic drug development: a new path to drug approval. Cancer Discov. 11, 2139–2144 (2021).
Xu, C. et al. β-catenin signaling in hepatocellular carcinoma. J. Clin. Investig 132, e154515 https://www.jci.org/articles/view/154515(2022).
Wang, B., Tian, T., Kalland, K.-H., Ke, X. & Qu, Y. Targeting Wnt/β-Catenin Signaling for Cancer Immunotherapy. Trends Pharmacol. Sci. 39, 648–658 (2018).
Spranger, S., Bao, R. & Gajewski, T. F. Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity. Nature 523, 231–235 (2015).
Xiao, X., Mo, H. & Tu, K. CTNNB1 mutation suppresses infiltration of immune cells in hepatocellular carcinoma through miRNA-mediated regulation of chemokine expression. Int. Immunopharmacol. 89, 107043 (2020).
Wong, M. et al. Evaluation of tumor mutational burden in small early hepatocellular carcinoma and progressed hepatocellular carcinoma. Hepatic Oncol. 8, HEP39 (2021).
Ang, C. et al. Prevalence of established and emerging biomarkers of immune checkpoint inhibitor response in advanced hepatocellular carcinoma. Oncotarget 10, 4018–4025 (2019).
Sun, J.-M. et al. Pembrolizumab plus chemotherapy versus chemotherapy alone for first-line treatment of advanced oesophageal cancer (KEYNOTE-590): a randomised, placebo-controlled, phase 3 study. Lancet 398, 759–771 (2021).
Doki, Y. et al. Nivolumab combination therapy in advanced esophageal squamous-cell carcinoma. N. Engl. J. Med. 386, 449–462 (2022).
Dienstmann, R. et al. Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer. Nat. Rev. Cancer 17, 79–92 (2017).
Diaz, L. A. Jr et al. Pembrolizumab versus chemotherapy for microsatellite instability-high or mismatch repair-deficient metastatic colorectal cancer (KEYNOTE-177): final analysis of a randomised, open-label, phase 3 study. Lancet Oncol. 23, 659–670 (2022).
Ho, H.-L. et al. PD-L1 is a double-edged sword in colorectal cancer: the prognostic value of PD-L1 depends on the cell type expressing PD-L1. J. Cancer Res. Clin. Oncol. 145, 1785–1794 (2019).
Finn, R. S. et al. Atezolizumab plus bevacizumab in unresectable hepatocellular carcinoma. N. Engl. J. Med. 382, 1894–1905 (2020).
El-Khoueiry, A. B. et al. Nivolumab in patients with advanced hepatocellular carcinoma (CheckMate 040): an open-label, non-comparative, phase 1/2 dose escalation and expansion trial. Lancet 389, 2492–2502 (2017).
Zhu, A. X. et al. Pembrolizumab in patients with advanced hepatocellular carcinoma previously treated with sorafenib (KEYNOTE-224): a non-randomised, open-label phase 2 trial. Lancet Oncol. 19, 940–952 (2018).
Reck, M. et al. Pembrolizumab versus chemotherapy for PD-L1-positive non-small-cell lung cancer. N. Engl. J. Med. 375, 1823–1833 (2016).
Pinato, D. J. et al. Clinical implications of heterogeneity in PD-L1 immunohistochemical detection in hepatocellular carcinoma: the Blueprint-HCC study. Br. J. Cancer 120, 1033–1036 (2019).
Vilain, R. E. et al. Dynamic changes in PD-L1 expression and immune infiltrates early during treatment predict response to PD-1 blockade in melanoma. Clin. Cancer Res. 23, 5024–5033 (2017).
Lu, L. C. et al. Increased expression of programmed death-ligand 1 in infiltrating immune cells in hepatocellular carcinoma tissues after sorafenib treatment. Liver Cancer 8, 110–120 (2019).
Barzi, A. et al. Phase I/II study of regorafenib (rego) and pembrolizumab (pembro) in refractory microsatellite stable colorectal cancer (MSSCRC). J. Clin. Oncol. 40, 15–15 (2022).
Kim, R. D. et al. A phase I/Ib study of regorafenib and nivolumab in mismatch repair proficient advanced refractory colorectal cancer. Eur. J. Cancer 169, 93–102 (2022).
Martinelli, E. et al. Clinical outcome and molecular characterisation of chemorefractory metastatic colorectal cancer patients with long-term efficacy of regorafenib treatment. ESMO Open 2, e000177 (2017).
Lee, J. C. et al. Regulatory T cell control of systemic immunity and immunotherapy response in liver metastasis. Sci. Immunol. 5, eaba0759 (2020).
Fu, J. et al. Increased regulatory T cells correlate with CD8 T-cell impairment and poor survival in hepatocellular carcinoma patients. Gastroenterology 132, 2328–2339 (2007).
Gao, Q. et al. Intratumoral balance of regulatory and cytotoxic T cells is associated with prognosis of hepatocellular carcinoma after resection. J. Clin. Oncol. 25, 2586–2593 (2007).
Sun, C., Sun, H., Zhang, C. & Tian, Z. NK cell receptor imbalance and NK cell dysfunction in HBV infection and hepatocellular carcinoma. Cell. Mol. Immunol. 12, 292–302 (2015).
Sun, H. et al. Accumulation of tumor-infiltrating CD49a+ NK cells correlates with poor prognosis for human hepatocellular carcinoma. Cancer Immunol. Res. 7, 1535–1546 (2019).
Lachenmayer, A. et al. Wnt-pathway activation in two molecular classes of hepatocellular carcinoma and experimental modulation by sorafenib. Clin. Cancer Res. 18, 4997–5007 (2012).
Kudo, M. et al. Association between beta-catenin (CTNNB1) mutations and clinical outcomes of pembrolizumab in advanced hepatocellularcarcinoma (aHCC): Exploratory analyses from KEYNOTE-240. J Clin Oncol 42, 4109–4109 https://ascopubs.org/doi/10.1200/JCO.2024.42.16_suppl.4109 (American Society of Clinical Oncology, 2024).
Hsu, C.-L. et al. Exploring markers of exhausted CD8 T cells to predict response to immune checkpoint inhibitor therapy for hepatocellular carcinoma. Liver Cancer 10, 346–359 (2021).
Haber, P. K. et al. Molecular markers of response to anti-PD1 therapy in advanced hepatocellular carcinoma. Gastroenterology 164, 72–88.e18 (2023).
Zhu, A. X. et al. Molecular correlates of clinical response and resistance to atezolizumab in combination with bevacizumab in advanced hepatocellular carcinoma. Nat. Med. 28, 1599–1611 (2022).
Cowzer, D. et al. Clinicogenomic predictors of outcomes in patients with hepatocellular carcinoma treated with immunotherapy. Oncologist. https://doi.org/10.1093/oncolo/oyae110 (2024).
Kanzaki, H. et al. The impact of FGF19/FGFR4 signaling inhibition in antitumor activity of multi-kinase inhibitors in hepatocellular carcinoma. Sci. Rep. 11, 5303 (2021).
Kim, R. D. et al. First-in-human phase i study of fisogatinib (BLU-554) validates aberrant FGF19 signaling as a driver event in hepatocellular carcinoma. Cancer Discov. 9, 1696–1707 (2019).
Magen, A. et al. Intratumoral dendritic cell–CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat. Med. 29, 1389–1399 (2023).
Finotello, F. et al. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med. 11, 1–20 (2019).
Ayers, M. et al. IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade. J. Clin. Investig. 127, 2930–2940 (2017).
Bao, R., Stapor, D. & Luke, J. J. Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types. Genome Med. 12, 1–19 (2020).
Merino, D. M. et al. Establishing guidelines to harmonize tumor mutational burden (TMB): in silico assessment of variation in TMB quantification across diagnostic platforms: phase I of the friends of cancer research TMB harmonization project. J. Immunother. Cancer 8 https://doi.org/10.1136/jitc-2019-000147 (2020).
Vanderwalde, A., Spetzler, D., Xiao, N., Gatalica, Z. & Marshall, J. Microsatellite instability status determined by next-generation sequencing and compared with PD-L1 and tumor mutational burden in 11,348 patients. Cancer Med. 7, 746–756 (2018).
Acknowledgements
EL thanks the following groups for donations in support of cancer research: Friends and family of Gayle Huntington, the Mu Sigma Chapter of the Phi Gamma Delta Fraternity, University of Minnesota (FIJI), the Litman Family Fund for Cancer Research, Dick and Lynnae Koats, Ms. Patricia Johnson, and Love Like Laurie Legacy. This study has no funding support. However, ESA is partially supported by NCI Cancer Center Support Grant P30 CA077598 and DOD Grant W81XWH-22-2-0025. EL reports research grants from the American Cancer Society (RSG-22-022-01-CDP) 2022-2026, and Minnesota Ovarian Cancer Alliance in 2019, 2021, and 2022.
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E.L. conceived the study design. G.S., Y.B., and E.L. performed initial analysis of data. G.S. and E.L. drafted the manuscript. J.H., E.S.A., A.S., S.G., A.P., B.A.W., A.S., and V.K.C. reviewed and edited the study and made major revisions. All authors read the manuscript and provided critical analysis and edits. All authors read and approved the final version for submission.
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EL disclosed the following financial relationships from the past two years: equipment for laboratory-based research 2018-present, Novocure, Ltd; honorarium for panel discussion organized by Antidote Education for a CME module on diagnostics and treatment of HER2+ gastric and colorectal cancers, funded by Daiichi-Sankyo, 2021 (honorarium donated to lab); compensation for scientific review of proposed printed content; Elsevier Publishing and Johns Hopkins Press; consultant, Nomocan Pharmaceuticals (no financial compensation); Institutional Principal Investigator for clinical trials sponsored by Celgene, Novocure, Intima Bioscience, Inc., the National Cancer Institute, and the University of Minnesota membership in the Caris Life Sciences Precision Oncology Alliance (no financial compensation). ESA has served as a paid consultant/advisor for Sanofi, Dendreon, Janssen Biotech, Merck, AstraZeneca, Clovis Oncology, Lilly, Bayer, and has received honoraria from Sanofi, Dendreon, Janssen Biotech, Astellas Pharma, Merck, AstraZeneca, and Clovis Oncology; has received research funding from Janssen Biotech, Johnson & Johnson, Sanofi, Dendreon, Genentech, Novartis, Astellas Pharma, Merck, AstraZeneca, Clovis Oncology, and Constellation Pharmaceuticals, a well as travel accommodations from Sanofi, and Dendreon; He is a co-inventor of a biomarker technology licensed to Qiagen. AS reports a leadership role with Autem therapeutics, Exelixis, KAHR medical and Bristol-Myers Squibb; consulting or advisory board role with AstraZeneca, Bristol-Myers Squibb, Merck, Exelixis, Pfizer, Xilio therapeutics, Taiho, Amgen, Autem therapeutics, KAHR medical, and Daiichi Sankyo; institutional research funding from AstraZeneca, Bristol-Myers Squibb, Merck, Clovis, Exelixis, Actuate therapeutics, Incyte Corporation, Daiichi Sankyo, Five prime therapeutics, Amgen, Innovent biologics, Dragonfly therapeutics, Oxford Biotherapeutics, Arcus therapeutics, and KAHR medical; and participation as a data safety monitoring board chair for Arcus therapeutics. YB, CN, and JX are employees of Caris Life Sciences. The authors declare no other financial or non-financial interests.
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Sharma, G., Baca, Y., Goel, S. et al. Evaluation of immuno-oncologic biomarkers and β-catenin expression in response of hepatocellular carcinomas to immunotherapy. npj Precis. Onc. (2026). https://doi.org/10.1038/s41698-026-01275-7
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DOI: https://doi.org/10.1038/s41698-026-01275-7

