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Lyu X, Sze KMF, Lee JMF, Husain A, Tian L, Imbeaud S, Zucman-Rossi J, Ng IOL, Ho DWH. Disparity landscapes of viral-induced structural variations in HCC: Mechanistic characterization and functional implications. Hepatology 2025; 81:1805-1821. [PMID: 39270063 PMCID: PMC12077337 DOI: 10.1097/hep.0000000000001087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND AND AIMS HCC is the most common type of primary liver cancer and is a common malignancy worldwide. About half of all new liver cancers worldwide each year occur in China, including Hong Kong, due to a high prevalence of HBV infection. HBV DNA integrates into the human genome, disrupting the endogenous tumor suppressors/regulatory genes or enhancing the activity of proto-oncogenes. It would be useful to examine the different NGS-based databases to provide a more unbiased and comprehensive survey of HBV integration. APPROACH AND RESULTS We aimed to take advantage of publicly available data sets of different regional cohorts to determine the disparity landscapes of integration events among sample cohorts, tissue types, chromosomal positions, individual host, and viral genes, as well as genic locations. By comparing HCC tumors with non tumorous livers, the landscape of HBV integration was delineated in gene-independent and gene-dependent manners. Moreover, we performed mechanistic investigations on how HBV-TERT integration led to TERT activation and derived a score to predict patients' prognostication according to their clonal disparity landscape of HBV integration. CONCLUSIONS Our study uncovered the different levels of clonal enrichment of HBV integration and identified mechanistic insights and prognostic biomarkers. This strengthens our understanding of HBV-associated hepatocarcinogenesis.
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Affiliation(s)
- Xueying Lyu
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Karen Man-Fong Sze
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Joyce Man-Fong Lee
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Abdullah Husain
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Lu Tian
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Sandrine Imbeaud
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, Inserm, Paris, France
- FunGeST lab, Equipe Labellisée Ligue Nationale Contre le Cancer, Labex Onco-Immunology, Institute du Cancer Paris CARPEM, AP-HP, Paris, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, Inserm, Paris, France
- FunGeST lab, Equipe Labellisée Ligue Nationale Contre le Cancer, Labex Onco-Immunology, Institute du Cancer Paris CARPEM, AP-HP, Paris, France
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
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Lyu X, Mok RWY, Chan HY, Suoangbaji T, Li Q, Zeng F, Long R, Ng IOL, Mak LLY, Ho DWH. AVID enables sensitive and accurate viral integration detection across human cancers. CELL REPORTS METHODS 2025; 5:101007. [PMID: 40132539 PMCID: PMC12049714 DOI: 10.1016/j.crmeth.2025.101007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 11/25/2024] [Accepted: 02/25/2025] [Indexed: 03/27/2025]
Abstract
Oncovirus infection is a key etiological risk factor of human cancers, which triggers virus integration in the host genome. Viral integration can lead to structural variation, gene dysfunction, and genome instability, promoting tumorigenesis. To support the investigation of virus-associated cancer and improve the detection of virus infection, we developed an algorithm called AVID (accurate viral integration detector) for viral integration detection. AVID was built by overcoming the existing detection limitations, enhancing sensitivity and accuracy, and expanding additional functions of viral integration detection. The performance of AVID was estimated in simulated datasets and experimentally validated datasets compared with other tools. To demonstrate its wide applicability, we also tested AVID on viral integration detection in multiple oncovirus-associated human cancers, including hepatocellular carcinoma (HCC), cervical cancer, and nasopharyngeal carcinoma. Taken together, our study developed an improved and applicable tool for viral integration detection and visualization to facilitate further exploration of virus-infected diseases.
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Affiliation(s)
- Xueying Lyu
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Russell Wing-Yeung Mok
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Hoi-Ying Chan
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tina Suoangbaji
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Qian Li
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Fanhong Zeng
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Renwen Long
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Loey Lung-Yi Mak
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Daniel Wai-Hung Ho
- State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
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Long R, Suoangbaji, Ng IOL, Ho DWH. LiverSCA: A comprehensive and user-friendly cell atlas in human hepatocellular carcinoma. Comput Struct Biotechnol J 2024; 23:2740-2745. [PMID: 39050786 PMCID: PMC11266871 DOI: 10.1016/j.csbj.2024.06.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 07/27/2024] Open
Abstract
We developed a cell atlas named LiverSCA on human liver cancer single-cell RNA sequencing data. It has a user-friendly web interface and comprehensive functionalities aiming to help researchers to make easy access to cellular and molecular landscapes of the tumor microenvironment in liver cancer. LiverSCA includes a complete analytical pipeline that allow mechanistic exploration on a wide variety of functionalities, such as cell clustering, cell annotation, identification of differentially expressed genes, functional enrichment analysis, analysis of cellular crosstalk, and pseudo-time trajectory analysis. Notably, our intuitive web interface allows users, particularly wet-lab researchers, to easily explore and undertake data discovery, without the need to handle any of the raw data.
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Affiliation(s)
- Renwen Long
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Suoangbaji
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
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Zhang CS, Zeng ZM, Zhuo MY, Luo JR, Zhuang XH, Xu JN, Zeng J, Ma J, Lin HF. Anlotinib Combined With Toripalimab as First-Line Therapy for Unresectable Hepatocellular Carcinoma: A Prospective, Multicenter, Phase II Study. Oncologist 2023; 28:e1239-e1247. [PMID: 37329569 PMCID: PMC10712726 DOI: 10.1093/oncolo/oyad169] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/01/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND For patients with unresectable hepatocellular carcinoma (HCC), the first-line therapeutic options are still relatively limited, and treatment outcomes remain poor. We aimed to assess the efficacy and safety of anlotinib combined with toripalimab as first-line therapy for unresectable HCC. METHODS In this single-arm, multicenter, phase II study (ALTER-H-003), patients with advanced HCC without previous systemic anticancer therapy were recruited. Eligible patients were given anlotinib (12 mg on days 1-14) combined with toripalimab (240 mg on day 1) in a 3-week cycle. The primary endpoint was the objective response rate (ORR) by immune-related Response Evaluation Criteria in Solid Tumours (irRECIST)/RECIST v1.1 and modified RECIST (mRECIST). Secondary endpoints included disease control rate (DCR), duration of response (DoR), progression-free survival (PFS), overall survival (OS), and safety. RESULTS Between January 2020 and Jul 2021, 31 eligible patients were treated and included in the full analysis set. At data cutoff (January 10, 2023), the ORR was 29.0% (95% CI: 12.1%-46.0%) by irRECIST/RECIST v1.1, and 32.3% (95% CI: 14.8%-49.7%) by mRECIST criteria, respectively. Confirmed DCR and median DoR by irRECIST/RECIST v1.1 and mRECIST criteria were 77.4 % (95% CI: 61.8%-93.0%) and not reached (range: 3.0-22.5+ months), respectively. Median PFS was 11.0 months (95% CI: 3.4-18.5 months) and median OS was 18.2 months (95% CI: 15.8-20.5 months). Of the 31 patients assessed for adverse events (AEs), the most common grade ≥ 3 treatment-related AEs were hand-foot syndrome (9.7%, 3/31), hypertension (9.7%, 3/31), arthralgia (9.7%, 3/31), abnormal liver function (6.5%, 2/31), and decreased neutrophil counts (6.5%, 2/31). CONCLUSIONS Anlotinib combined with toripalimab showed promising efficacy and manageable safety in Chinese patients with unresectable HCC in the first-line setting. This combination therapy may offer a potential new therapeutic approach for patients with unresectable HCC.
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Affiliation(s)
- Cheng-Sheng Zhang
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, People’s Republic of China
| | - Zhi-Ming Zeng
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Man-Yun Zhuo
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, People’s Republic of China
| | - Jing-Ru Luo
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, People’s Republic of China
| | - Xiao-Hong Zhuang
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, People’s Republic of China
| | - Jun-Nv Xu
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, People’s Republic of China
| | - Jie Zeng
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Hai-Feng Lin
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, People’s Republic of China
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Bicer F, Kure C, Ozluk AA, El-Rayes BF, Akce M. Advances in Immunotherapy for Hepatocellular Carcinoma (HCC). Curr Oncol 2023; 30:9789-9812. [PMID: 37999131 PMCID: PMC10670350 DOI: 10.3390/curroncol30110711] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related deaths in the world. More than half of patients with HCC present with advanced stage, and highly active systemic therapies are crucial for improving outcomes. Immune checkpoint inhibitor (ICI)-based therapies have emerged as novel therapy options for advanced HCC. Only one third of patients achieve an objective response with ICI-based therapies due to primary resistance or acquired resistance. The liver tumor microenvironment is naturally immunosuppressive, and specific mutations in cell signaling pathways allow the tumor to evade the immune response. Next, gene sequencing of the tumor tissue or circulating tumor DNA may delineate resistance mechanisms to ICI-based therapy and provide a rationale for novel combination therapies. In this review, we discuss the results of key clinical trials that have led to approval of ICI-based therapy options in advanced HCC and summarize the ongoing clinical trials. We review resistance mechanisms to ICIs and discuss how immunotherapies may be optimized based on the emerging research of tumor biomarkers and genomic alterations.
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Affiliation(s)
- Fuat Bicer
- Division of Hematology Oncology, Department of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267, USA;
| | - Catrina Kure
- Department of Medicine, Northside Hospital-Gwinnett, Lawrenceville, GA 30046, USA;
| | - Anil A. Ozluk
- Division of Hematology Oncology, Department of Medicine, O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA; (A.A.O.); (B.F.E.-R.)
| | - Bassel F. El-Rayes
- Division of Hematology Oncology, Department of Medicine, O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA; (A.A.O.); (B.F.E.-R.)
| | - Mehmet Akce
- Division of Hematology Oncology, Department of Medicine, O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA; (A.A.O.); (B.F.E.-R.)
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