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Chen J, Zhang CH, Tao T, Zhang X, Lin Y, Wang FB, Liu HF, Liu J. A-to-I RNA co-editing predicts clinical outcomes and is associated with immune cells infiltration in hepatocellular carcinoma. Commun Biol 2024; 7:838. [PMID: 38982182 PMCID: PMC11233613 DOI: 10.1038/s42003-024-06520-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Aberrant RNA editing has emerged as a pivotal factor in the pathogenesis of hepatocellular carcinoma (HCC), but the impact of RNA co-editing within HCC remains underexplored. We used a multi-step algorithm to construct an RNA co-editing network in HCC, and found that HCC-related RNA editings are predominantly centralized within the network. Furthermore, five pairs of risk RNA co-editing events were significantly correlated with the overall survival in HCC. Based on presence of risk RNA co-editings resulted in the categorization of HCC patients into high-risk and low-risk groups. Disparities in immune cell infiltrations were observed between the two groups, with the high-risk group exhibiting a greater abundance of exhausted T cells. Additionally, seven genes associated with risk RNA co-editing pairs were identified, whose expression effectively differentiates HCC tumor samples from normal ones. Our research offers an innovative perspective on the etiology and potential therapeutics for HCC.
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Affiliation(s)
- Juan Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Cheng-Hui Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Tao Tao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xian Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yan Lin
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Fang-Bin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hui-Fang Liu
- Department of Endocrinology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China.
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China.
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2
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Funato K, Miyake N, Sekiba K, Miyakawa Y, Seimiya T, Shibata C, Kishikawa T, Otsuka M. Cabozantinib inhibits HBV-RNA transcription by decreasing STAT3 binding to the enhancer region of cccDNA. Hepatol Commun 2023; 7:e0313. [PMID: 37938099 PMCID: PMC10635605 DOI: 10.1097/hc9.0000000000000313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/18/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Precision medicine and customized therapeutics based on the features of each patient are important for maximizing therapeutic effects. Because most cases of HCC occur in the damaged liver through various etiologies, such as hepatitis virus infection, steatohepatitis, and autoimmune hepatitis, there should be a rationale for the choice of therapeutic options based on these etiologies. Although cabozantinib, an oral multikinase inhibitor, has demonstrated clinical effectiveness in advanced HCC, subgroup analyses showed a lower HR for death in HBV-related HCC. This study aimed to determine the therapeutic effects of cabozantinib in HBV-related HCC. METHODS Using HBV infection models and gene knockout cells, we determined the crucial signaling axis responsible for the effects of cabozantinib on HBV. A chromatin immunoprecipitation assay was performed to determine the interaction between the signaling molecules and HBV DNA. Agonists and inhibitors were used for confirmation. RESULTS Cabozantinib inhibited HBV replication through the HGF-mesenchymal-epithelial transition factor-signal transducer and activator of transcription 3 (MET-STAT3) signaling axis. The importance of STAT3 in viral replication has been confirmed using gene-edited STAT3 knockout cells. The chromatin immunoprecipitation assay revealed that the binding levels of phosphorylated STAT3 to enhancer region 1 of HBV covalently closed circular DNA were significantly increased by HGF stimulation. CONCLUSIONS Cabozantinib has favorable therapeutic effects on HBV-related HCC because it inhibits HCC not only directly but also indirectly by means of inhibitory effects on HBV.
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Affiliation(s)
- Kazuyoshi Funato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nozomi Miyake
- Department of Gastroenterology, Graduate School of Medicine, Okayama University, Okayama, Japan
| | - Kazuma Sekiba
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yu Miyakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Seimiya
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chikako Shibata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Takahiro Kishikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Gastroenterology, Graduate School of Medicine, Okayama University, Okayama, Japan
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3
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López-Pérez A, Remeseiro S, Hörnblad A. Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice. Sci Rep 2023; 13:18666. [PMID: 37907668 PMCID: PMC10618177 DOI: 10.1038/s41598-023-45614-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023] Open
Abstract
Several preclinical models have been recently developed for metabolic associated fatty liver disease (MAFLD) and associated hepatocellular carcinoma (HCC) but comprehensive analysis of the regulatory and transcriptional landscapes underlying disease in these models are still missing. We investigated the regulatory and transcriptional landscape in fatty livers and liver tumours from DIAMOND mice that faithfully mimic human HCC development in the context of MAFLD. RNA-sequencing and ChIP-sequencing revealed rewiring of the Wnt/β-catenin regulatory network in DIAMOND tumours, as manifested by chromatin remodelling and associated switching in the expression of the canonical TCF/LEF downstream effectors. We identified splicing as a major mechanism leading to constitutive oncogenic activation of β-catenin in a large subset of DIAMOND tumours, a mechanism that is independent on somatic mutations in the locus and that has not been previously shown. Similar splicing events were found in a fraction of human HCC and hepatoblastoma samples.
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Affiliation(s)
- Ana López-Pérez
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 90187, Umeå, Sweden
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 90187, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 90187, Umeå, Sweden
| | - Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 90187, Umeå, Sweden.
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4
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Wang Y, Deng B. Hepatocellular carcinoma: molecular mechanism, targeted therapy, and biomarkers. Cancer Metastasis Rev 2023; 42:629-652. [PMID: 36729264 DOI: 10.1007/s10555-023-10084-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy and one of the leading causes of cancer-related death. The biological process of HCC is complex, with multiple factors leading to the broken of the balance of inactivation and activation of tumor suppressor genes and oncogenes, the abnormal activation of molecular signaling pathways, the differentiation of HCC cells, and the regulation of angiogenesis. Due to the insidious onset of HCC, at the time of first diagnosis, less than 30% of HCC patients are candidates for radical treatment. Systematic antitumor therapy is the hope for the treatment of patients with middle-advanced HCC. Despite the emergence of new systemic therapies, survival rates for advanced HCC patients remain low. The complex pathogenesis of HCC has inspired researchers to explore a variety of biomolecular targeted therapeutics targeting specific targets. Correct understanding of the molecular mechanism of HCC occurrence is key to seeking effective targeted therapy. Research on biomarkers for HCC treatment is also advancing. Here, we explore the molecular mechanism that are associated with HCC development, summarize targeted therapies for HCC, and discuss potential biomarkers that may drive therapies.
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Affiliation(s)
- Yu Wang
- Department of Infectious Diseases, The First Hospital of China Medical University, 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China
| | - Baocheng Deng
- Department of Infectious Diseases, The First Hospital of China Medical University, 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China.
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LncRNA CARMN Affects Hepatocellular Carcinoma Prognosis by Regulating the miR-192-5p/LOXL2 Axis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9277360. [PMID: 36254230 PMCID: PMC9569233 DOI: 10.1155/2022/9277360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022]
Abstract
Background. Hepatocellular carcinoma (HCC) is aggressive cancer with a poor prognosis. It has been suggested that the aberrant expression of LOXL2 is associated with the development of HCC, but the exact mechanism remains unclear. This research is aimed at examining the expression level and prognostic value of LOXL2 in hepatocellular carcinoma and its relationship with immune infiltration and at predicting its upstream noncoding RNAs (ncRNAs). Method. The transcriptome data of HCC was first downloaded from The Cancer Genome Atlas (TCGA) database to investigate the expression and prognosis of LOXL2. Then, the starBase database was used to find the upstream ncRNAs of LOXL2, and correlation analysis and expression analysis were performed. Finally, the Tumor Immune Estimation Resource (TIMER) was used to explore the association between LOXL2 and immune cell infiltration. Result. CARMN was considered to be the potential upstream lncRNA for the hsa-miR-192-5p/LOXL2 axis in HCC. Furthermore, the level LOXL2 was markedly positively associated with tumor immune cell infiltration and immune checkpoint expression in HCC. Conclusion. Higher expression of LOXL2 mediated by microRNA (miRNA) and long noncoding RNAs (lncRNA) is associated with poor overall survival (OS), immune infiltration, and immune checkpoint expression in HCC.
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Privitera GF, Alaimo S, Ferro A, Pulvirenti A. Virus finding tools: current solutions and limitations. Brief Bioinform 2022; 23:6618234. [PMID: 35753694 DOI: 10.1093/bib/bbac235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/02/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The study of the Human Virome remains challenging nowadays. Viral metagenomics, through high-throughput sequencing data, is the best choice for virus discovery. The metagenomics approach is culture-independent and sequence-independent, helping search for either known or novel viruses. Though it is estimated that more than 40% of the viruses found in metagenomics analysis are not recognizable, we decided to analyze several tools to identify and discover viruses in RNA-seq samples. RESULTS We have analyzed eight Virus Tools for the identification of viruses in RNA-seq data. These tools were compared using a synthetic dataset of 30 viruses and a real one. Our analysis shows that no tool succeeds in recognizing all the viruses in the datasets. So we can conclude that each of these tools has pros and cons, and their choice depends on the application domain. AVAILABILITY Synthetic data used through the review and raw results of their analysis can be found at https://zenodo.org/record/6426147. FASTQ files of real data can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) or ENA (https://www.ebi.ac.uk/ena/browser/home). Raw results of their analysis can be downloaded from https://zenodo.org/record/6425917.
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Affiliation(s)
- Grete Francesca Privitera
- Department of Physics and Astronomy, University of Catania, Viale A. Doria, 6, 95125, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
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Li CL, Yeh SH, Chen PJ. Circulating Virus–Host Chimera DNAs in the Clinical Monitoring of Virus-Related Cancers. Cancers (Basel) 2022; 14:cancers14102531. [PMID: 35626135 PMCID: PMC9139492 DOI: 10.3390/cancers14102531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cell-free tumor DNA (ctDNA), the DNA released into circulation from tumors, is a promising tumor marker with versatile applications. The associations of the amount, somatic mutation frequency, and epigenetic modifications of ctDNA with the tumor burden, tumor behavior, and prognosis have been widely investigated in different types of tumors. However, there are still some challenging issues to be resolved before ctDNA can complement or even replace current serum tumor markers. We propose employing exogenous viral DNA integration that produces unique virus–host chimera DNA (vh-DNA) at junction sites. Cell-free vh-DNA may become a new biomarker because it overcomes background interference detection problems, takes advantage of virus tropism to localize the tumor, and acts as a universal marker for monitoring clonal expansion or tumor loads in tumors related to oncogenic viruses. Abstract The idea of using tumor-specific cell-free DNA (ctDNA) as a tumor biomarker has been widely tested and validated in various types of human cancers and different clinical settings. ctDNA can reflect the presence or size of tumors in a real-time manner and can enable longitudinal monitoring with minimal invasiveness, allowing it to be applied in treatment response assessment and recurrence monitoring for cancer therapies. However, tumor detection by ctDNA remains a great challenge due to the difficulty in enriching ctDNA from a large amount of homologous non-tumor cell-free DNA (cfDNA). Only ctDNA with nonhuman sequences (or rearrangements) can be selected from the background of cfDNA from nontumor DNAs. This is possible for several virus-related cancers, such as hepatitis B virus (HBV)-related HCC or human papillomavirus (HPV)-related cervical or head and neck cancers, which frequently harbor randomly integrated viral DNA. The junction fragments of the integrations, namely virus–host chimera DNA (vh-DNA), can represent the signatures of individual tumors and are released into the blood. Such ctDNA can be enriched by capture with virus-specific probes and therefore exploited as a circulating biomarker to track virus-related cancers in clinical settings. Here, we review virus integrations in virus-related cancers to evaluate the feasibility of vh-DNA as a cell-free tumor marker and update studies on the development of detection and applications. vh-DNA may be a solution to the development of specific markers to manage virus-related cancers in the future.
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Affiliation(s)
- Chiao-Ling Li
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
| | - Shiou-Hwei Yeh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
| | - Pei-Jer Chen
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
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8
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Hepatitis B Virus-Associated Hepatocellular Carcinoma. Viruses 2022; 14:v14050986. [PMID: 35632728 PMCID: PMC9146458 DOI: 10.3390/v14050986] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is DNA-based virus, member of the Hepadnaviridae family, which can cause liver disease and increased risk of hepatocellular carcinoma (HCC) in infected individuals, replicating within the hepatocytes and interacting with several cellular proteins. Chronic hepatitis B can progressively lead to liver cirrhosis, which is an independent risk factor for HCC. Complications as liver decompensation or HCC impact the survival of HBV patients and concurrent HDV infection worsens the disease. The available data provide evidence that HBV infection is associated with the risk of developing HCC with or without an underlying liver cirrhosis, due to various direct and indirect mechanisms promoting hepatocarcinogenesis. The molecular profile of HBV-HCC is extensively and continuously under study, and it is the result of altered molecular pathways, which modify the microenvironment and lead to DNA damage. HBV produces the protein HBx, which has a central role in the oncogenetic process. Furthermore, the molecular profile of HBV-HCC was recently discerned from that of HDV-HCC, despite the obligatory dependence of HDV on HBV. Proper management of the underlying HBV-related liver disease is fundamental, including HCC surveillance, viral suppression, and application of adequate predictive models. When HBV-HCC occurs, liver function and HCC characteristics guide the physician among treatment strategies but always considering the viral etiology in the treatment choice.
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9
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Péneau C, Imbeaud S, La Bella T, Hirsch TZ, Caruso S, Calderaro J, Paradis V, Blanc JF, Letouzé E, Nault JC, Amaddeo G, Zucman-Rossi J. Hepatitis B virus integrations promote local and distant oncogenic driver alterations in hepatocellular carcinoma. Gut 2022; 71:616-626. [PMID: 33563643 PMCID: PMC8862055 DOI: 10.1136/gutjnl-2020-323153] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Infection by HBV is the main risk factor for hepatocellular carcinoma (HCC) worldwide. HBV directly drives carcinogenesis through integrations in the human genome. This study aimed to precisely characterise HBV integrations, in relation with viral and host genomics and clinical features. DESIGN A novel pipeline was set up to perform viral capture on tumours and non-tumour liver tissues from a French cohort of 177 patients mainly of European and African origins. Clonality of each integration event was determined with the localisation, orientation and content of the integrated sequence. In three selected tumours, complex integrations were reconstructed using long-read sequencing or Bionano whole genome mapping. RESULTS Replicating HBV DNA was more frequently detected in non-tumour tissues and associated with a higher number of non-clonal integrations. In HCC, clonal selection of HBV integrations was related to two different mechanisms involved in carcinogenesis. First, integration of viral enhancer nearby a cancer-driver gene may lead to a strong overexpression of oncogenes. Second, we identified frequent chromosome rearrangements at HBV integration sites leading to cancer-driver genes (TERT, TP53, MYC) alterations at distance. Moreover, HBV integrations have direct clinical implications as HCC with a high number of insertions develop in young patients and have a poor prognosis. CONCLUSION Deep characterisation of HBV integrations in liver tissues highlights new HBV-associated driver mechanisms involved in hepatocarcinogenesis. HBV integrations have multiple direct oncogenic consequences that remain an important challenge for the follow-up of HBV-infected patients.
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Affiliation(s)
- Camille Péneau
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Sandrine Imbeaud
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Tiziana La Bella
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Theo Z Hirsch
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Julien Calderaro
- Service d’Anatomopathologie, Hôpital Henri Mondor, APHP, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Valerie Paradis
- Service de Pathologie, Hôpital Beaujon, APHP, Clichy, France,Université Paris Diderot, CNRS, Centre de Recherche 27 sur l'Inflammation (CRI), Paris, France
| | - Jean-Frederic Blanc
- Service Hépato-Gastroentérologie et Oncologie Digestive, Hôpital Haut-Lévêque, CHU de Bordeaux, Bordeaux, France,Service de Pathologie, CHU Bordeaux GH Pellegrin, Bordeaux, France,Université Bordeaux, Inserm, Research in Translational Oncology, BaRITOn, Bordeaux, France
| | - Eric Letouzé
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France,Service d’Hépatologie, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, APHP, Bobigny, France
| | - Giuliana Amaddeo
- Service d’Hépato-Gastro-Entérologie, Hôpital Henri Mondor, APHP, Université Paris Est Créteil, Inserm U955, Institut Mondor de recherche biomedicale, Creteil, Île-de-France, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France .,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France.,Hôpital Européen Georges Pompidou, AP-HP, Paris, France
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10
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Bousali M, Karamitros T. Hepatitis B Virus Integration into Transcriptionally Active Loci and HBV-Associated Hepatocellular Carcinoma. Microorganisms 2022; 10:microorganisms10020253. [PMID: 35208708 PMCID: PMC8879149 DOI: 10.3390/microorganisms10020253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B Virus (HBV) DNA integrations into the human genome are considered major causative factors to HBV-associated hepatocellular carcinoma development. In the present study, we investigated whether HBV preferentially integrates parts of its genome in specific genes and evaluated the contribution of the integrations in HCC development per gene. We applied dedicated in-house developed pipelines on all of the available HBV DNA integration data and performed a statistical analysis to identify genes that could be characterized as hotspots of integrations, along with the evaluation of their association with HBV-HCC. Our results suggest that 15 genes are recurrently affected by HBV integrations and they are significantly associated with HBV-HCC. Further studies that focus on HBV integrations disrupting these genes are mandatory in order to understand the role of HBV integrations in clonal advantage gain and oncogenesis promotion, as well as to determine whether inhibition of the HBV-disrupted genes can provide a therapy strategy for HBV-HCC.
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Affiliation(s)
- Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
- Correspondence: ; Tel.: +30-210-6478871
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11
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Cui D, Li W, Jiang D, Wu J, Xie J, Wu Y. Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma. Front Med (Lausanne) 2021; 8:754709. [PMID: 34660653 PMCID: PMC8514776 DOI: 10.3389/fmed.2021.754709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) specifically infects liver cells, leading to progressive liver cirrhosis and significantly increasing the risk of hepatocellular carcinoma (HCC). The maturity of sequencing technology, improvement in bioinformatics data analysis and progress of omics technologies had improved research efficiency. The occurrence and progression of HCC are affected by multisystem and multilevel pathological changes. With the application of single-omics technologies, including genomics, transcriptomics, metabolomics and proteomics in tissue and body fluid samples, and even the novel development of multi-omics analysis on a single-cell platform, HBV-associated HCC changes can be better analyzed. The review summarizes the application of single omics and combined analysis of multi-omics data in HBV-associated HCC and proposes the importance of multi-omics analysis in the type of HCC, which provide the possibility for the precise diagnosis and therapy of HBV-associated HCC.
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Affiliation(s)
- Dawei Cui
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Li
- Center of Research Laboratory, The First People's Hospital of Lianyungang, Lianyungang, China
| | - Daixi Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianguo Wu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Jue Xie
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingping Wu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
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12
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Zhuo Z, Rong W, Li H, Li Y, Luo X, Liu Y, Tang X, Zhang L, Su F, Cui H, Xiao F. Long-read sequencing reveals the structural complexity of genomic integration of HBV DNA in hepatocellular carcinoma. NPJ Genom Med 2021; 6:84. [PMID: 34642322 PMCID: PMC8511263 DOI: 10.1038/s41525-021-00245-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/03/2021] [Indexed: 02/01/2023] Open
Abstract
The integration of HBV DNA into the human genome can disrupt its structure in hepatocellular carcinoma (HCC), but the complexity of HBV genomic integration remains elusive. Here we applied long-read sequencing to precisely elucidate the HBV integration pattern in the human hepatocellular genome. The DNA library was sequenced using the long-read sequencing on GridION and PacBio Sequel II, respectively. The DNA and mRNA were sequenced using next-generation sequencing on Illumina NextSeq. BLAST (Basic Local Alignment Search Tool) and local scripts were used to analyze HBV integration patterns. We established an analytical strategy based on the long-read sequences, and analyzed the complexity of HBV DNA integration into the hepatocellular genome. A total of 88 integrated breakpoints were identified. HBV DNA integration into human genomic DNA was mainly fragmented with different orientations, rarely with a complete genome. The same HBV integration breakpoints were identified among the three platforms. Most breakpoints were observed at P, X, and S genes in the HBV genome, and observed at introns, intergenic sequences, and exons in the human genome. Tumor tissue harbored a much higher integrated number than the adjacent tissue, and the distribution of HBV integrated into human chromosomes was more concentrated. HBV integration shows different patterns between cancer cells and adjacent normal cells. We for the first time obtained the entire HBV integration pattern through long-read sequencing and demonstrated the value of long-read sequencing in detecting the genomic integration structures of viruses in host cells.
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Affiliation(s)
- Zhongling Zhuo
- Peking University Fifth School of Clinical Medicine, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Li
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuanmei Luo
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaokun Tang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongyuan Cui
- Department of Surgery, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
| | - Fei Xiao
- Peking University Fifth School of Clinical Medicine, Beijing, China. .,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China. .,Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
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13
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Bousali M, Papatheodoridis G, Paraskevis D, Karamitros T. Hepatitis B Virus DNA Integration, Chronic Infections and Hepatocellular Carcinoma. Microorganisms 2021; 9:1787. [PMID: 34442866 PMCID: PMC8398950 DOI: 10.3390/microorganisms9081787] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022] Open
Abstract
Hepatitis B Virus (HBV) is an Old World virus with a high mutation rate, which puts its origins in Africa alongside the origins of Homo sapiens, and is a member of the Hepadnaviridae family that is characterized by a unique viral replication cycle. It targets human hepatocytes and can lead to chronic HBV infection either after acute infection via horizontal transmission usually during infancy or childhood or via maternal-fetal transmission. HBV has been found in ~85% of HBV-related Hepatocellular Carcinomas (HCC), and it can integrate the whole or part of its genome into the host genomic DNA. The molecular mechanisms involved in the HBV DNA integration is not yet clear; thus, multiple models have been described with respect to either the relaxed-circular DNA (rcDNA) or the double-stranded linear DNA (dslDNA) of HBV. Various genes have been found to be affected by HBV DNA integration, including cell-proliferation-related genes, oncogenes and long non-coding RNA genes (lincRNAs). The present review summarizes the advances in the research of HBV DNA integration, focusing on the evolutionary and molecular side of the integration events along with the arising clinical aspects in the light of WHO's commitment to eliminate HBV and viral hepatitis by 2030.
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Affiliation(s)
- Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - George Papatheodoridis
- Department of Gastroenterology, “Laiko” General Hospital of Athens, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
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14
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Zhang D, Zhang K, Protzer U, Zeng C. HBV Integration Induces Complex Interactions between Host and Viral Genomic Functions at the Insertion Site. J Clin Transl Hepatol 2021; 9:399-408. [PMID: 34221926 PMCID: PMC8237140 DOI: 10.14218/jcth.2021.00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV), one of the well-known DNA oncogenic viruses, is the leading cause of hepatocellular carcinoma (HCC). In infected hepatocytes, HBV DNA can be integrated into the host genome through an insertional mutagenesis process inducing tumorigenesis. Dissection of the genomic features surrounding integration sites will deepen our understanding of mechanisms underlying integration. Moreover, the quantity and biological activity of integration sites may reflect the DNA damage within affected cells or the potential survival benefits they may confer. The well-known human genomic features include repeat elements, particular regions (such as telomeres), and frequently interrupted genes (e.g., telomerase reverse transcriptase [i.e. TERT], lysine methyltransferase 2B [i.e. KMT2B], cyclin E1 [CCNE1], and cyclin A2 [CCNA2]). Consequently, distinct genomic features within diverse integrations differentiate their biological functions. Meanwhile, accumulating evidence has shown that viral proteins produced by integrants may cause cell damage even after the suppression of HBV replication. The integration-derived gene products can also serve as tumor markers, promoting the development of novel therapeutic strategies for HCC. Viral integrants can be single copy or multiple copies of different fragments with complicated rearrangement, which warrants elucidation of the whole viral integrant arrangement in future studies. All of these considerations underlie an urgent need to develop novel methodology and technology for sequence characterization and function evaluation of integration events in chronic hepatitis B-associated disease progression by monitoring both host genomic features and viral integrants. This endeavor may also serve as a promising solution for evaluating the risk of tumorigenesis and as a companion diagnostic for designing therapeutic strategies targeting integration-related disease complications.
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Affiliation(s)
- Dake Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Ke Zhang
- SCG Cell Therapy Pte. Ltd, Singapore
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Urlike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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15
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Perisetti A, Goyal H, Yendala R, Thandassery RB, Giorgakis E. Non-cirrhotic hepatocellular carcinoma in chronic viral hepatitis: Current insights and advancements. World J Gastroenterol 2021; 27:3466-3482. [PMID: 34239263 PMCID: PMC8240056 DOI: 10.3748/wjg.v27.i24.3466] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/13/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Primary liver cancers carry significant morbidity and mortality. Hepatocellular carcinoma (HCC) develops within the hepatic parenchyma and is the most common malignancy originating from the liver. Although 80% of HCCs develop within background cirrhosis, 20% may arise in a non-cirrhotic milieu and are referred to non-cirrhotic-HCC (NCHCC). NCHCC is often diagnosed late due to lack of surveillance. In addition, the rising prevalence of non-alcoholic fatty liver disease and diabetes mellitus have increased the risk of developing HCC on non-cirrhotic patients. Viral infections such as chronic Hepatitis B and less often chronic hepatitis C with advance fibrosis are associated with NCHCC. NCHCC individuals may have Hepatitis B core antibodies and occult HBV infection, signifying the role of Hepatitis B infection in NCHCC. Given the effectiveness of current antiviral therapies, surgical techniques and locoregional treatment options, nowadays such patients have more options and potential for cure. However, these lesions need early identification with diagnostic models and multiple surveillance strategies to improve overall outcomes. Better understanding of the NCHCC risk factors, tumorigenesis, diagnostic tools and treatment options are critical to improving prognosis and overall outcomes on these patients. In this review, we aim to discuss NCHCC epidemiology, risk factors, and pathogenesis, and elaborate on NCHCC diagnosis and treatment strategies.
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Affiliation(s)
- Abhilash Perisetti
- Department of Internal Medicine, Division of Gastroenterology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Hemant Goyal
- Department of Internal Medicine, Macon University School of Medicine, Macon, GA 31207, United States
| | - Rachana Yendala
- Department of Hematology and Oncology, Conway Regional Health System (CRHS), Conway, AR 72034, United States
| | - Ragesh B Thandassery
- Department of Gastroenterology and Hepatology, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, United States
| | - Emmanouil Giorgakis
- Department of Transplant, University of Arkansas for Medical Sciences Little Rock, AR 72205, United States
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16
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Yin J, Chen X, Li N, Han X, Liu W, Pu R, Wu T, Ding Y, Zhang H, Zhao J, Han X, Wang H, Cheng S, Cao G. Compartmentalized evolution of hepatitis B virus contributes differently to the prognosis of hepatocellular carcinoma. Carcinogenesis 2021; 42:461-470. [PMID: 33247709 DOI: 10.1093/carcin/bgaa127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/26/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Serum hepatitis B virus (HBV) mutations can predict hepatocellular carcinoma (HCC) occurrence. We aimed to clarify if HBV evolves synchronously in the sera, adjacent liver and tumors and predict HCC prognosis equally. A total of 203 HBV-positive HCC patients with radical hepatectomy in Shanghai, China, during 2011-15 were enrolled in this prospective study. Quasispecies complexity (QC) in HBV core promoter region was assessed using clone-based sequencing. We performed RNA sequencing on tumors and paired adjacent tissues of another 15 HCC patients and analyzed it with three public data sets containing 127 samples. HBV QC was positively correlated to APOBEC3s' expression level (r = 0.28, P < 0.001), higher in the adjacent tissues than in the tumors (P = 6.50e-3), and higher in early tumors than in advanced tumors (P = 0.039). The evolutionary distance between the sera-derived HBV strains and the tumor-derived ones was significantly longer than that between the sera-derived ones and the adjacent tissue-derived ones (P < 0.001). Multivariate Cox regression analyses indicated that high HBV QC in the sera predicted an unfavorable overall survival (P = 0.002) and recurrence-free survival (RFS; P = 0.004) in HCC, whereas, in the tumors, it predicted a favorable RFS (P < 0.001). APOBECs-related HBV mutations, including G1764A, were more frequent in the sera than in the adjacent tissues. High-frequent A1762T/G1764A in the sera predicted an unfavorable RFS (P < 0.001), whereas, in the tumors, it predicted a favorable RFS (P = 0.035). In conclusion, HBV evolves more advanced in the sera than in the tumors. HBV QC and A1762T/G1764A in the sera and tumors have contrary prognostic effects in HCC.
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Affiliation(s)
- Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xi Chen
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Nan Li
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xuewen Han
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Wenbin Liu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Rui Pu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Ting Wu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Yibo Ding
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Hongwei Zhang
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Jun Zhao
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China
| | - Xue Han
- Division of Chronic Diseases, Center for Disease Control and Prevention of Yangpu District, Shanghai, China
| | - Hongyang Wang
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
| | - Shuqun Cheng
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, 8 Panshan Rd, Yangpu District, Shanghai 200433, China.,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, China
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17
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Lin SY, Zhang A, Lian J, Wang J, Chang TT, Lin YJ, Song W, Su YH. Recurrent HBV Integration Targets as Potential Drivers in Hepatocellular Carcinoma. Cells 2021; 10:cells10061294. [PMID: 34071075 PMCID: PMC8224658 DOI: 10.3390/cells10061294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/15/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is the major etiology of hepatocellular carcinoma (HCC), frequently with HBV integrating into the host genome. HBV integration, found in 85% of HBV-associated HCC (HBV–HCC) tissue samples, has been suggested to be oncogenic. Here, we investigated the potential of HBV–HCC driver identification via the characterization of recurrently targeted genes (RTGs). A total of 18,596 HBV integration sites from our in-house study and others were analyzed. RTGs were identified by applying three criteria: at least two HCC subjects, reported by at least two studies, and the number of reporting studies. A total of 396 RTGs were identified. Among the 28 most frequent RTGs, defined as affected in at least 10 HCC patients, 23 (82%) were associated with carcinogenesis and 5 (18%) had no known function. Available breakpoint positions from the three most frequent RTGs, TERT, MLL4/KMT2B, and PLEKHG4B, were analyzed. Mutual exclusivity of TERT promoter mutation and HBV integration into TERT was observed. We present an RTG consensus through comprehensive analysis to enable the potential identification and discovery of HCC drivers for drug development and disease management.
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Affiliation(s)
- Selena Y. Lin
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Adam Zhang
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
| | - Jessica Lian
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
| | - Jeremy Wang
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Medical College, Tainan 704, Taiwan;
| | - Yih-Jyh Lin
- Department of Surgery, National Cheng Kung University Medical College, Tainan 704, Taiwan;
| | - Wei Song
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Ying-Hsiu Su
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
- Correspondence: ; Tel.: +215-489-4907
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18
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Péneau C, Zucman-Rossi J, Nault JC. Genomics of Viral Hepatitis-Associated Liver Tumors. J Clin Med 2021; 10:1827. [PMID: 33922394 PMCID: PMC8122827 DOI: 10.3390/jcm10091827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 12/25/2022] Open
Abstract
Virus-related liver carcinogenesis is one of the main contributors of cancer-related death worldwide mainly due to the impact of chronic hepatitis B and C infections. Three mechanisms have been proposed to explain the oncogenic properties of hepatitis B virus (HBV) infection: induction of chronic inflammation and cirrhosis, expression of HBV oncogenic proteins, and insertional mutagenesis into the genome of infected hepatocytes. Hepatitis B insertional mutagenesis modifies the function of cancer driver genes and could promote chromosomal instability. In contrast, hepatitis C virus promotes hepatocellular carcinoma (HCC) occurrence mainly through cirrhosis development whereas the direct oncogenic role of the virus in human remains debated. Finally, adeno associated virus type 2 (AAV2), a defective DNA virus, has been associated with occurrence of HCC harboring insertional mutagenesis of the virus. Since these tumors developed in a non-cirrhotic context and in the absence of a known etiological factor, AAV2 appears to be the direct cause of tumor development in these patients via a mechanism of insertional mutagenesis altering similar oncogenes and tumor suppressor genes targeted by HBV. A better understanding of virus-related oncogenesis will be helpful to develop new preventive strategies and therapies directed against specific alterations observed in virus-related HCC.
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Affiliation(s)
- Camille Péneau
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
- Hôpital Européen Georges Pompidou, APHP, F-75015 Paris, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
- Service d’hépatologie, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, F-93000 Bobigny, France
- Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris Nord, F-93000 Bobigny, France
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19
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Bubie A, Zoulim F, Testoni B, Miles B, Posner M, Villanueva A, Losic B. Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling. iScience 2021; 24:102368. [PMID: 33889830 PMCID: PMC8050859 DOI: 10.1016/j.isci.2021.102368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/07/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
The role of oncoviral genotype and co-infection driving oncogenesis remains unclear. We have developed a scalable, high throughput tool for sensitive and precise oncoviral genotype deconvolution. Using tumor RNA sequencing data, we applied it to 537 virally infected liver, cervical, and head and neck tumors, providing the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor oncoviral genotype. We find that HBV and HPV genotype and co-infection serve as significant predictors of patient survival and immune activation. Finally, we demonstrate that HPV genotype is more associated with viral oncogene expression than cancer type, implying that expression may be similar across episomal and stochastic integration-based infections. While oncoviral infections are known risk factors for oncogenesis, viral genotype and co-infection are shown to strongly associate with disease progression, patient survival, mutational signatures, and putative tumor neoantigen immunogenicity, facilitating novel clinical associations with infections.
ViralMine parses oncoviral genotypes and co-infection from in situ tumor data Oncoviral genotyping of TCGA CESC, HNSC, and LIHC cohorts Tumor fitness, immunogenicity, and mutational signatures associate with oncoviral genotype
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Affiliation(s)
- Adrian Bubie
- Departments of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Fabien Zoulim
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France
| | - Barbara Testoni
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France
| | - Brett Miles
- Department of Otolaryngology Head and Neck Surgery, New York, NY 10029, USA
| | - Marshall Posner
- Division of Hematology Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Augusto Villanueva
- Departments of Genetics and Genomic Sciences, New York, NY 10029, USA.,Division of Liver Diseases, Division of Hematology/Oncology, Department of Medicine, Graduate School of Biomedical Sciences, Tisch Cancer Institute, Diabetes, Obesity, and Metabolism Institute, New York, NY 10029, USA
| | - Bojan Losic
- Departments of Genetics and Genomic Sciences, New York, NY 10029, USA.,Division of Liver Diseases, Division of Hematology/Oncology, Department of Medicine, Graduate School of Biomedical Sciences, Tisch Cancer Institute, Diabetes, Obesity, and Metabolism Institute, New York, NY 10029, USA
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20
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Chidambaranathan-Reghupaty S, Fisher PB, Sarkar D. Hepatocellular carcinoma (HCC): Epidemiology, etiology and molecular classification. Adv Cancer Res 2020; 149:1-61. [PMID: 33579421 PMCID: PMC8796122 DOI: 10.1016/bs.acr.2020.10.001] [Citation(s) in RCA: 490] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC), the primary malignancy of hepatocytes, is a diagnosis with bleak outcome. According to National Cancer Institute's SEER database, the average five-year survival rate of HCC patients in the US is 19.6% but can be as low as 2.5% for advanced, metastatic disease. When diagnosed at early stages, it is treatable with locoregional treatments including surgical resection, Radio-Frequency Ablation, Trans-Arterial Chemoembolization or liver transplantation. However, HCC is usually diagnosed at advanced stages when the tumor is unresectable, making these treatments ineffective. In such instances, systemic therapy with tyrosine kinase inhibitors (TKIs) becomes the only viable option, even though it benefits only 30% of patients, provides only a modest (~3months) increase in overall survival and causes drug resistance within 6months. HCC, like many other cancers, is highly heterogeneous making a one-size fits all option problematic. The selection of liver transplantation, locoregional treatment, TKIs or immune checkpoint inhibitors as a treatment strategy depends on the disease stage and underlying condition(s). Additionally, patients with similar disease phenotype can have different molecular etiology making treatment responses different. Stratification of patients at the molecular level would facilitate development of the most effective treatment option. With the increase in efficiency and affordability of "omics"-level analysis, considerable effort has been expended in classifying HCC at the molecular, metabolic and immunologic levels. This review examines the results of these efforts and the ways they can be leveraged to develop targeted treatment options for HCC.
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Affiliation(s)
- Saranya Chidambaranathan-Reghupaty
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, United States
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States.
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21
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D'souza S, Lau KCK, Coffin CS, Patel TR. Molecular mechanisms of viral hepatitis induced hepatocellular carcinoma. World J Gastroenterol 2020; 26:5759-5783. [PMID: 33132633 PMCID: PMC7579760 DOI: 10.3748/wjg.v26.i38.5759] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/03/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with viral hepatitis affects half a billion individuals worldwide and can lead to cirrhosis, cancer, and liver failure. Liver cancer is the third leading cause of cancer-associated mortality, of which hepatocellular carcinoma (HCC) represents 90% of all primary liver cancers. Solid tumors like HCC are complex and have heterogeneous tumor genomic profiles contributing to complexity in diagnosis and management. Chronic infection with hepatitis B virus (HBV), hepatitis delta virus (HDV), and hepatitis C virus (HCV) are the greatest etiological risk factors for HCC. Due to the significant role of chronic viral infection in HCC development, it is important to investigate direct (viral associated) and indirect (immune-associated) mechanisms involved in the pathogenesis of HCC. Common mechanisms used by HBV, HCV, and HDV that drive hepatocarcinogenesis include persistent liver inflammation with an impaired antiviral immune response, immune and viral protein-mediated oxidative stress, and deregulation of cellular signaling pathways by viral proteins. DNA integration to promote genome instability is a feature of HBV infection, and metabolic reprogramming leading to steatosis is driven by HCV infection. The current review aims to provide a brief overview of HBV, HCV and HDV molecular biology, and highlight specific viral-associated oncogenic mechanisms and common molecular pathways deregulated in HCC, and current as well as emerging treatments for HCC.
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Affiliation(s)
- Simmone D'souza
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary T2N 1N4, AB, Canada
| | - Keith CK Lau
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary T2N 1N4, AB, Canada
| | - Carla S Coffin
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary T2N 1N4, AB, Canada
| | - Trushar R Patel
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary T2N 1N4, AB, Canada
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge T1K3M4, AB, Canada
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22
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Lau KC, Burak KW, Coffin CS. Impact of Hepatitis B Virus Genetic Variation, Integration, and Lymphotropism in Antiviral Treatment and Oncogenesis. Microorganisms 2020; 8:E1470. [PMID: 32987867 PMCID: PMC7599633 DOI: 10.3390/microorganisms8101470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic Hepatitis B Virus (HBV) infection poses a significant global health burden. Although, effective treatment and vaccinations against HBV are available, challenges still exist, particularly in the development of curative therapies. The dynamic nature and unique features of HBV such as viral variants, integration of HBV DNA into host chromosomes, and extrahepatic reservoirs are considerations towards understanding the virus biology and developing improved anti-HBV treatments. In this review, we highlight the importance of these viral characteristics in the context of treatment and oncogenesis. Viral genotype and genetic variants can serve as important predictive factors for therapeutic response and outcomes in addition to oncogenic risk. HBV integration, particularly in coding genes, is implicated in the development of hepatocellular carcinoma. Furthermore, we will discuss emerging research that has identified various HBV nucleic acids and infection markers within extrahepatic sites (lymphoid cells). Intriguingly, the presence of hepatocellular carcinoma (HCC)-associated HBV variants and viral integration within the lymphoid cells may contribute towards the development of extrahepatic malignancies. Improved understanding of these HBV characteristics will enhance the development of a cure for chronic HBV infection.
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Affiliation(s)
- Keith C.K. Lau
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Calgary Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Kelly W. Burak
- Calgary Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Carla S. Coffin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Calgary Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
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23
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Chen X, Kost J, Li D. Comprehensive comparative analysis of methods and software for identifying viral integrations. Brief Bioinform 2020; 20:2088-2097. [PMID: 30102374 DOI: 10.1093/bib/bby070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Many viruses are capable of integrating in the human genome, particularly viruses involved in tumorigenesis. Viral integrations can be considered genetic markers for discovering virus-caused cancers and inferring cancer cell development. Next-generation sequencing (NGS) technologies have been widely used to screen for viral integrations in cancer genomes, and a number of bioinformatics tools have been developed to detect viral integrations using NGS data. However, there has been no systematic comparison of the methods or software. In this study, we performed a comprehensive comparative analysis of the designs, performance, functionality and limitations among the existing methods and software for detecting viral integrations. We further compared the sensitivity, precision and runtime of integration detection of four representative tools. Our analyses showed that each of the existing software had its own merits; however, none of them were sufficient for parallel or accurate virome-wide detection. After carefully evaluating the limitations shared by the existing methods, we proposed strategies and directions for developing virome-wide integration detection.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Jason Kost
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.,Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, Vermont 05405, USA.,Cancer Center, University of Vermont, Burlington, Vermont 05405, USA
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24
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Eller C, Heydmann L, Colpitts CC, El Saghire H, Piccioni F, Jühling F, Majzoub K, Pons C, Bach C, Lucifora J, Lupberger J, Nassal M, Cowley GS, Fujiwara N, Hsieh SY, Hoshida Y, Felli E, Pessaux P, Sureau C, Schuster C, Root DE, Verrier ER, Baumert TF. A genome-wide gain-of-function screen identifies CDKN2C as a HBV host factor. Nat Commun 2020; 11:2707. [PMID: 32483149 PMCID: PMC7264273 DOI: 10.1038/s41467-020-16517-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 05/03/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic HBV infection is a major cause of liver disease and cancer worldwide. Approaches for cure are lacking, and the knowledge of virus-host interactions is still limited. Here, we perform a genome-wide gain-of-function screen using a poorly permissive hepatoma cell line to uncover host factors enhancing HBV infection. Validation studies in primary human hepatocytes identified CDKN2C as an important host factor for HBV replication. CDKN2C is overexpressed in highly permissive cells and HBV-infected patients. Mechanistic studies show a role for CDKN2C in inducing cell cycle G1 arrest through inhibition of CDK4/6 associated with the upregulation of HBV transcription enhancers. A correlation between CDKN2C expression and disease progression in HBV-infected patients suggests a role in HBV-induced liver disease. Taken together, we identify a previously undiscovered clinically relevant HBV host factor, allowing the development of improved infectious model systems for drug discovery and the study of the HBV life cycle.
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Affiliation(s)
- Carla Eller
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Laura Heydmann
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Che C Colpitts
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Houssein El Saghire
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Federica Piccioni
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Frank Jühling
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Karim Majzoub
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Caroline Pons
- Inserm, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard, Lyon, France
| | - Charlotte Bach
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Julie Lucifora
- Inserm, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard, Lyon, France
| | - Joachim Lupberger
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emanuele Felli
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France
| | - Patrick Pessaux
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France
| | - Camille Sureau
- Laboratoire de Virologie Moléculaire, INTS, Paris, France
| | - Catherine Schuster
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Eloi R Verrier
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France.
| | - Thomas F Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France.
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France.
- Institut Universitaire de France (IUF), Paris, France.
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25
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Brown AL, Conrad K, Allende DS, Gromovsky AD, Zhang R, Neumann CK, Owens AP, Tranter M, Helsley RN. Dietary Choline Supplementation Attenuates High-Fat-Diet-Induced Hepatocellular Carcinoma in Mice. J Nutr 2020; 150:775-783. [PMID: 31851339 DOI: 10.1093/jn/nxz315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death in the world. Choline deficiency has been well studied in the context of liver disease; however, less is known about the effects of choline supplementation in HCC. OBJECTIVE The objective of this study was to test whether choline supplementation could influence the progression of HCC in a high-fat-diet (HFD)-driven mouse model. METHODS Four-day-old male C57BL/6J mice were treated with the chemical carcinogen, 7,12-dimethylbenz[a]anthracene, and were randomly assigned at weaning to a cohort fed an HFD (60% kcal fat) or an HFD with supplemental choline (60% kcal fat, 1.2% choline; HFD+C) for 30 wk. Blood was isolated at 15 and 30 wk to measure immune cells by flow cytometry, and glucose-tolerance tests were performed 2 wk prior to killing. Overall tumor burden was quantified, hepatic lipids were measured enzymatically, and phosphatidylcholine species were measured by targeted MS methods. Gene expression and mitochondrial DNA were quantified by quantitative PCR. RESULTS HFD+C mice exhibited a 50-90% increase in both circulating choline and betaine concentrations in the fed state (P ≤ 0.05). Choline supplementation resulted in a 55% decrease in total tumor numbers, a 67% decrease in tumor surface area, and a 50% decrease in hepatic steatosis after 30 wk of diet (P ≤ 0.05). Choline supplementation increased the abundance of mitochondria and the relative expression of β-oxidation genes by 21% and ∼75-100%, respectively, in the liver. HFD+C attenuated circulating myeloid-derived suppressor cells at 15 wk of feeding (P ≤ 0.05). CONCLUSIONS Choline supplementation attenuated HFD-induced HCC and hepatic steatosis in male C57BL/6J mice. These results suggest a therapeutic benefit of choline supplementation in blunting HCC progression.
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Affiliation(s)
- Amanda L Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kelsey Conrad
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Daniela S Allende
- Department of Pathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Anthony D Gromovsky
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Renliang Zhang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chase K Neumann
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - A Phillip Owens
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael Tranter
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Robert N Helsley
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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26
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Kaur H, Dhall A, Kumar R, Raghava GPS. Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. Front Genet 2020; 10:1306. [PMID: 31998366 PMCID: PMC6967266 DOI: 10.3389/fgene.2019.01306] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
The high mortality rate of hepatocellular carcinoma (HCC) is primarily due to its late diagnosis. In the past, numerous attempts have been made to design genetic biomarkers for the identification of HCC; unfortunately, most of the studies are based on small datasets obtained from a specific platform or lack reasonable validation performance on the external datasets. In order to identify a universal expression-based diagnostic biomarker panel for HCC that can be applicable across multiple platforms, we have employed large-scale transcriptomic profiling datasets containing a total of 2,316 HCC and 1,665 non-tumorous tissue samples. These samples were obtained from 30 studies generated by mainly four types of profiling techniques (Affymetrix, Illumina, Agilent, and High-throughput sequencing), which are implemented in a wide range of platforms. Firstly, we scrutinized overlapping 26 genes that are differentially expressed in numerous datasets. Subsequently, we identified a panel of three genes (FCN3, CLEC1B, and PRC1) as HCC biomarker using different feature selection techniques. Three-genes-based HCC biomarker identified HCC samples in training/validation datasets with an accuracy between 93 and 98%, Area Under Receiver Operating Characteristic curve (AUROC) in a range of 0.97 to 1.0. A reasonable performance, i.e., AUROC 0.91–0.96 achieved on validation dataset containing peripheral blood mononuclear cells, concurred their non-invasive utility. Furthermore, the prognostic potential of these genes was evaluated on TCGA-LIHC and GSE14520 cohorts using univariate survival analysis. This analysis revealed that these genes are prognostic indicators for various types of the survivals of HCC patients (e.g., Overall Survival, Progression-Free Survival, Disease-Free Survival). These genes significantly stratified high-risk and low-risk HCC patients (p-value <0.05). In conclusion, we identified a universal platform-independent three-genes-based biomarker that can predict HCC patients with high precision and also possess significant prognostic potential. Eventually, we developed a web server HCCpred based on the above study to facilitate scientific community (http://webs.iiitd.edu.in/raghava/hccpred/).
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Affiliation(s)
- Harpreet Kaur
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Rajesh Kumar
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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27
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Tatsuno K, Midorikawa Y, Takayama T, Yamamoto S, Nagae G, Moriyama M, Nakagawa H, Koike K, Moriya K, Aburatani H. Impact of AAV2 and Hepatitis B Virus Integration Into Genome on Development of Hepatocellular Carcinoma in Patients with Prior Hepatitis B Virus Infection. Clin Cancer Res 2019; 25:6217-6227. [PMID: 31320595 DOI: 10.1158/1078-0432.ccr-18-4041] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/29/2019] [Accepted: 07/11/2019] [Indexed: 12/31/2022]
Abstract
PURPOSE Hepatitis B viral (HBV) DNA is frequently integrated into the genomes of hepatocellular carcinoma (HCC) in patients with chronic HBV infection (chronic HBV, hereafter), whereas the frequency of HBV integration in patients after the disappearance of HBV (prior HBV, hereafter) has yet to be determined. This study aimed to detect integration of HBV and adeno-associated virus type 2 (AAV2) into the human genome as a possible oncogenic event. EXPERIMENTAL DESIGN Virome capture sequencing was performed, using HCC and liver samples obtained from 243 patients, including 73 with prior HBV without hepatitis C viral (HCV) infection and 81 with chronic HBV. RESULTS Clonal HBV integration events were identified in 11 (15.0%) cases of prior HBV without HCV and 61 (75.3%) cases of chronic HBV (P < 0.001). Several driver genes were commonly targeted by HBV, leading to transcriptional activation of these genes; TERT [four (5.4%) vs. 15 (18.5%)], KMT2B [two (2.7%) vs. five (6.1%)], CCNE1 [zero vs. one (1.2%)], CCNA2 [zero vs. one (1.2%)]. Conversely, CCNE1 and CCNA2 were, respectively, targeted by AAV2 only in prior HBV. In liver samples, HBV genome recurrently integrated into fibrosis-related genes FN1, HS6ST3, KNG1, and ROCK1 in chronic HBV. There was not history of alcohol abuse and 3 patients with a history of nucleoside analogue treatment for HBV in 8 prior HBV with driver gene integration. CONCLUSIONS Despite the seroclearance of hepatitis B surface antigen, HBV or AAV2 integration in prior HBV was not rare; therefore, such patients are at risk of developing HCC.
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Affiliation(s)
- Kenji Tatsuno
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Yutaka Midorikawa
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan. .,Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Tadatoshi Takayama
- Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Genta Nagae
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Moriyama
- Department of Gastroenterology and Hepatology, Nihon University School of Medicine, Tokyo, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology, University of Tokyo, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, University of Tokyo, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Diseases, University of Tokyo, Tokyo, Japan
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28
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Jin Y, Lee WY, Toh ST, Tennakoon C, Toh HC, Chow PKH, Chung AYF, Chong SS, Ooi LLPJ, Sung WK, Lee CGL. Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma. J Transl Med 2019; 17:273. [PMID: 31429776 PMCID: PMC6701074 DOI: 10.1186/s12967-019-2025-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
Background Hepatocellular carcinoma is the second most deadly cancer with late presentation and limited treatment options, highlighting an urgent need to better understand HCC to facilitate the identification of early-stage biomarkers and uncover therapeutic targets for the development of novel therapies for HCC. Methods Deep transcriptome sequencing of tumor and paired non-tumor liver tissues was performed to comprehensively evaluate the profiles of both the host and HBV transcripts in HCC patients. Differential gene expression patterns and the dys-regulated genes associated with clinical outcomes were analyzed. Somatic mutations were identified from the sequencing data and the deleterious mutations were predicted. Lastly, human-HBV chimeric transcripts were identified, and their distribution, potential function and expression association were analyzed. Results Expression profiling identified the significantly upregulated TP73 as a nodal molecule modulating expression of apoptotic genes. Approximately 2.5% of dysregulated genes significantly correlated with HCC clinical characteristics. Of the 110 identified genes, those involved in post-translational modification, cell division and/or transcriptional regulation were upregulated, while those involved in redox reactions were downregulated in tumors of patients with poor prognosis. Mutation signature analysis identified that somatic mutations in HCC tumors were mainly non-synonymous, frequently affecting genes in the micro-environment and cancer pathways. Recurrent mutations occur mainly in ribosomal genes. The most frequently mutated genes were generally associated with a poorer clinical prognosis. Lastly, transcriptome sequencing suggest that HBV replication in the tumors of HCC patients is rare. HBV-human fusion transcripts are a common observation, with favored HBV and host insertion sites being the HBx C-terminus and gene introns (in tumors) and introns/intergenic-regions (in non-tumors), respectively. HBV-fused genes in tumors were mainly involved in RNA binding while those in non-tumors tissues varied widely. These observations suggest that while HBV may integrate randomly during chronic infection, selective expression of functional chimeric transcripts may occur during tumorigenesis. Conclusions Transcriptome sequencing of HCC patients reveals key cancer molecules and clinically relevant pathways deregulated/mutated in HCC patients and suggests that while HBV may integrate randomly during chronic infection, selective expression of functional chimeric transcripts likely occur during the process of tumorigenesis.
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Affiliation(s)
- Yu Jin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Wai Yeow Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Soo Ting Toh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | | | - Han Chong Toh
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Pierce Kah-Hoe Chow
- Duke-NUS Medical School, Singapore, 169547, Singapore.,Department of Surgery, Singapore General Hospital, Singapore, 169608, Singapore
| | - Alexander Y-F Chung
- Department of Surgery, Singapore General Hospital, Singapore, 169608, Singapore
| | - Samuel S Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, 119074, Singapore
| | - London L-P-J Ooi
- Department of Surgery, Singapore General Hospital, Singapore, 169608, Singapore.,Department of Surgical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Wing-Kin Sung
- Genome Institute of Singapore, Singapore, Singapore.,School of Computing, National University of Singapore, Singapore, Singapore
| | - Caroline G-L Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore. .,Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore, 169610, Singapore. .,Duke-NUS Medical School, Singapore, 169547, Singapore.
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29
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Hu X, Jiang J, Ni C, Xu Q, Ye S, Wu J, Ge F, Han Y, Mo Y, Huang D, Yang L. HBV Integration-mediated Cell Apoptosis in HepG2.2.15. J Cancer 2019; 10:4142-4150. [PMID: 31417659 PMCID: PMC6692610 DOI: 10.7150/jca.30493] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/01/2019] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and the second leading cause of cancer deaths in the word. Hepatitis B virus (HBV) infection plays an important role in the development of HCC. However, the mechanisms by which HBV integration affects host cells remain poorly understood. HepG2.2.15 cell line is derived from HCC cell line HepG2 with stable transfection HBV expression. In this study, HepG2.2.15 cells showed decreased proliferation, G1 cell cycle arrest and increased apoptosis, when compared to HepG2 cells. HBV capture sequencing was conducted in both genome and transcriptome level, followed by RNA expression sequencing in HepG2.2.15. Here, CAMSAP2/CCDC12/DPP7/OR4F3 were found to be targets for HBV integration in both genome and transcriptome level, accompanied by alteration in their expression when compared to HepG2. Among these genes, DPP7 was the only one gene with HBV integration into its exon, meanwhile DPP7 expression level was also downregulated in HepG2.2.15 as compared to HepG2. Furthermore, DPP7 knockdown resulted in increased apoptosis through upregulation of the Bax/Bcl2 ratio in HepG2 cells. Our results suggest that HBV integration of DPP7 was involved in cell apoptosis.
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Affiliation(s)
- Xiaoge Hu
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Jiahong Jiang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Chao Ni
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Department of General surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Qiuran Xu
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Song Ye
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The Secondary Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P. R. China
| | - Junjie Wu
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Feimin Ge
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Yong Han
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Yinyuan Mo
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - Dongsheng Huang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Department of General surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
| | - Liu Yang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China.,Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P. R. China
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Zhu C, Wu L, Lv Y, Guan J, Bai X, Lin J, Liu T, Yang X, Robson SC, Sang X, Xue C, Zhao H. The fusion landscape of hepatocellular carcinoma. Mol Oncol 2019; 13:1214-1225. [PMID: 30903738 PMCID: PMC6487730 DOI: 10.1002/1878-0261.12479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 12/30/2022] Open
Abstract
Most cases of hepatocellular carcinoma (HCC) are already advanced at the time of diagnosis, which limits treatment options. Challenges in early‐stage diagnosis may be due to the genetic complexity of HCC. Gene fusion plays a critical function in tumorigenesis and cancer progression in multiple cancers, yet the identities of fusion genes as potential diagnostic markers in HCC have not been investigated. Here, we employed STAR‐Fusion and identified 43 recurrent fusion events in our own and four public RNA‐seq datasets. We identified 2354 different gene fusions in two hepatitis B virus (HBV)‐HCC patients. Validation analysis against the four RNA‐seq datasets revealed that only 1.8% (43/2354) were recurrent fusions. Comparison with the four fusion databases demonstrated that 19 recurrent fusions were not previously annotated to diseases and three were annotated as disease‐related fusion events. Finally, we validated six of the novel fusion events, including RP11‐476K15.1‐CTD‐2015H3.2, by RT‐PCR and Sanger sequencing of 14 pairs of HBV‐related HCC samples. In summary, our study provides new insights into gene fusions in HCC and may contribute to the development of anti‐HCC therapy.
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Affiliation(s)
- Chengpei Zhu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liangcai Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanling Lv
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,My Health Gene Technology Co., Ltd., Service Centre of Tianjin Chentang Science and Technology Commercial District, China
| | - Jinxia Guan
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,My Health Gene Technology Co., Ltd., Service Centre of Tianjin Chentang Science and Technology Commercial District, China
| | - Xue Bai
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianzhen Lin
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tingting Liu
- My Health Gene Technology Co., Ltd., Service Centre of Tianjin Chentang Science and Technology Commercial District, China
| | - Xiaobo Yang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Simon C Robson
- Liver Center and The Transplant Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xinting Sang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenghai Xue
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,My Health Gene Technology Co., Ltd., Service Centre of Tianjin Chentang Science and Technology Commercial District, China.,Joint Laboratory of Large-scale Medical Data Pattern Mining and Application, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Haitao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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31
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Chen X, Kost J, Sulovari A, Wong N, Liang WS, Cao J, Li D. A virome-wide clonal integration analysis platform for discovering cancer viral etiology. Genome Res 2019; 29:819-830. [PMID: 30872350 PMCID: PMC6499315 DOI: 10.1101/gr.242529.118] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/11/2019] [Indexed: 12/31/2022]
Abstract
Oncoviral infection is responsible for 12%–15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contamination and noncausal viruses complicate the process of identifying genuine oncoviruses. Here, we propose a novel strategy to address these challenges by performing virome-wide screening of early-stage clonal viral integrations. To implement this strategy, we developed VIcaller, a novel platform for identifying viral integrations that are derived from any characterized viruses and shared by a large proportion of tumor cells using whole-genome sequencing (WGS) data. The sensitivity and precision were confirmed with simulated and benchmark cancer data sets. By applying this platform to cancer WGS data sets with proven or speculated viral etiology, we newly identified or confirmed clonal integrations of hepatitis B virus (HBV), human papillomavirus (HPV), Epstein-Barr virus (EBV), and BK Virus (BKV), suggesting the involvement of these viruses in early stages of tumorigenesis in affected tumors, such as HBV in TERT and KMT2B (also known as MLL4) gene loci in liver cancer, HPV and BKV in bladder cancer, and EBV in non-Hodgkin's lymphoma. We also showed the capacity of VIcaller to identify integrations from some uncharacterized viruses. This is the first study to systematically investigate the strategy and method of virome-wide screening of clonal integrations to identify oncoviruses. Searching clonal viral integrations with our platform has the capacity to identify virus-caused cancers and discover cancer viral etiologies.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Jason Kost
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Nathalie Wong
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong 999077, P.R. China
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jian Cao
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, Vermont 05405, USA.,Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA
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32
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Huang W, Skanderup AJ, Lee CG. Advances in genomic hepatocellular carcinoma research. Gigascience 2018; 7:5232228. [PMID: 30521023 PMCID: PMC6335342 DOI: 10.1093/gigascience/giy135] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/01/2018] [Indexed: 12/14/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the cancer with the second highest mortality in the world due to its late presentation and limited treatment options. As such, there is an urgent need to identify novel biomarkers for early diagnosis and to develop novel therapies. The availability of next-generation sequencing (NGS) data from tumors of liver cancer patients has provided us with invaluable resources to better understand HCC through the integration of data from different sources to facilitate the identification of promising biomarkers or therapeutic targets. Findings Here, we review key insights gleaned from more than 20 NGS studies of HCC tumor samples, comprising approximately 582 whole genomes and 1,211 whole exomes mainly from the East Asian population. Through consolidation of reported somatic mutations from multiple studies, we identified genes with different types of somatic mutations, including single nucleotide variations, insertion/deletions, structural variations, and copy number alterations as well as genes with multiple frequent viral integration. Pathway analysis showed that this curated list of somatic mutations is critically involved in cancer-related pathways, viral carcinogenesis, and signaling pathways. Lastly, we addressed the future directions of HCC research as more NGS datasets become available. Conclusions Our review is a comprehensive resource for the current NGS research in HCC, consolidating published articles, potential gene candidates, and their related biological pathways.
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Affiliation(s)
- Weitai Huang
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Graduate School of Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Caroline G Lee
- Graduate School of Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.,Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Center Singapore, Singapore 169610, Singapore.,Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
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33
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Schuette D, Moore LM, Robert ME, Taddei TH, Ehrlich BE. Hepatocellular Carcinoma Outcome Is Predicted by Expression of Neuronal Calcium Sensor 1. Cancer Epidemiol Biomarkers Prev 2018; 27:1091-1100. [PMID: 29789326 PMCID: PMC8465775 DOI: 10.1158/1055-9965.epi-18-0167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/06/2018] [Accepted: 05/17/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death worldwide. There is an urgent demand for prognostic biomarkers that facilitate early tumor detection, as the incidence of HCC has tripled in the United States in the last three decades. Biomarkers to identify populations at risk would have significant impact on survival. We recently found that expression of Neuronal Calcium Sensor 1 (NCS1), a Ca2+-dependent signaling molecule, predicted disease outcome in breast cancer, but its predictive value in other cancer types is unknown. This protein is potentially useful because increased NCS1 regulates Ca2+ signaling and increased Ca2+ signaling is a hallmark of metastatic cancers, conferring cellular motility and an increasingly aggressive phenotype to tumors.Methods: We explored the relationship between NCS1 expression levels and patient survival in two publicly available liver cancer cohorts and a tumor microarray using data mining strategies.Results: High NCS1 expression levels are significantly associated with worse disease outcome in Asian patients within these cohorts. In addition, a variety of Ca2+-dependent and tumor growth-promoting genes are transcriptionally coregulated with NCS1 and many of them are involved in cytoskeleton organization, suggesting that NCS1 induced dysregulated Ca2+ signaling facilitates cellular motility and metastasis.Conclusions: We found NCS1 to be a novel biomarker in HCC. Furthermore, our study identified a pharmacologically targetable signaling complex that can influence tumor progression in HCC.Impact: These results lay the foundation for using NCS1 as a prognostic biomarker in prospective cohorts of HCC patients and for further functional assessment of the characterized signaling axis. Cancer Epidemiol Biomarkers Prev; 27(9); 1091-100. ©2018 AACR.
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Affiliation(s)
- Daniel Schuette
- Department of Pharmacology, Yale University, New Haven, Connecticut
| | - Lauren M Moore
- Department of Pharmacology, Yale University, New Haven, Connecticut
| | - Marie E Robert
- Department of Pathology, Yale University, New Haven, Connecticut
| | - Tamar H Taddei
- Department of Medicine (Digestive Diseases), Yale University, New Haven, Connecticut
| | - Barbara E Ehrlich
- Department of Pharmacology, Yale University, New Haven, Connecticut.
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Zhang BL, Ji X, Yu LX, Gao Y, Xiao CH, Liu J, Zhao DX, Le Y, Diao GH, Sun JY, Li GH, Lei GL, Yu P, Wang RL, Wu JZ, Yang PH, Yan J, Li JY, Xu JJ, Zhang SG, Tian H. Somatic mutation profiling of liver and biliary cancer by targeted next generation sequencing. Oncol Lett 2018; 16:6003-6012. [PMID: 30344748 DOI: 10.3892/ol.2018.9371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/13/2018] [Indexed: 12/23/2022] Open
Abstract
Liver and biliary cancers are highly lethal cancer types lacking effective treatments. The somatic mutations, particularly those with low mutant allele frequencies, in Chinese patients with liver and biliary cancer have not been profiled, and the frequency of patients benefiting from targeted therapy has not been studied. The present study evaluated the tumor tissues of 45 Chinese patients with hepatocellular carcinoma (HCC) and 12 Chinese patients with biliary tract cancer (BTC) by targeted next generation sequencing, with an average coverage of 639×, to identify alterations in 372 cancer-related genes. A total of 263 variants were identified in 139 genes, with 85.6% of these variants not previously reported in the Catalogue Of Somatic Mutations In Cancer database, and the mutation profile was different from the current datasets, including The Cancer Genome Atlas dataset and the National Cancer Center Japan (NCC_JP) dataset. Patients with hepatitis B virus (HBV) infection harbored more mutations than those without HBV infection, and the mutations in HBV carriers occurred preferentially in genes involved in vascular endothelial growth factor signaling pathways. Mutations in fibroblast growth factor and RAS signaling pathways were enriched in patients with cirrhosis, and alterations in interleukin and transforming growth factor signaling pathways were more frequently identified in individuals with abnormal bilirubin expression. Of all the patients, 7% exhibited variants in the target of sorafenib, and 42% harbored variants in the targets of drugs that have been approved to treat other types of cancer. These findings indicate diverse HCC/BTC variants patterns in different populations, and that the mutation load and patterns are correlated with clinical features. Further clinical studies are now warranted to evaluate the efficacies of other targeted drugs besides sorafenib in the treatment of patients with liver and biliary cancer.
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Affiliation(s)
- Bo-Lun Zhang
- Department of General Surgery, Clinical Medical College of Weifang Medical University, Weifang, Shandong 261042, P.R. China
| | - Xu Ji
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Ling-Xiang Yu
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Yuan Gao
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Chao-Hui Xiao
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Jia Liu
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - De-Xi Zhao
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Yi Le
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Guang-Hao Diao
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Jia-Yi Sun
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Gao-Hua Li
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Guang-Lin Lei
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Peng Yu
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Rui-Lan Wang
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Jian-Zhong Wu
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Peng-Hui Yang
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Jin Yan
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Jing-Yu Li
- Institute of Precision Medicine, 3D Medicines, Inc., Shanghai 201114, P.R. China
| | - Jia-Jia Xu
- Institute of Precision Medicine, 3D Medicines, Inc., Shanghai 201114, P.R. China
| | - Shao-Geng Zhang
- Department of Hepatobiliary Surgery, 302 Military Hospital of China, Beijing 100039, P.R. China
| | - Hu Tian
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
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35
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Budzinska MA, Shackel NA, Urban S, Tu T. Cellular Genomic Sites of Hepatitis B Virus DNA Integration. Genes (Basel) 2018; 9:E365. [PMID: 30037029 PMCID: PMC6071206 DOI: 10.3390/genes9070365] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022] Open
Abstract
Infection with the Hepatitis B Virus (HBV) is one of the strongest risk-factors for liver cancer (hepatocellular carcinoma, HCC). One of the reported drivers of HCC is the integration of HBV DNA into the host cell genome, which may induce pro-carcinogenic pathways. These reported pathways include: induction of chromosomal instability; generation of insertional mutagenesis in key cancer-associated genes; transcription of downstream cancer-associated cellular genes; and/or formation of a persistent source of viral protein expression (particularly HBV surface and X proteins). The contribution of each of these specific mechanisms towards carcinogenesis is currently unclear. Here, we review the current knowledge of specific sites of HBV DNA integration into the host genome, which sheds light on these mechanisms. We give an overview of previously-used methods to detect HBV DNA integration and the enrichment of integration events in specific functional and structural cellular genomic sites. Finally, we posit a theoretical model of HBV DNA integration during disease progression and highlight open questions in the field.
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Affiliation(s)
| | - Nicholas A Shackel
- Centenary Institute, University of Sydney, Sydney NSW 2050, Australia.
- South Western Sydney Clinical School, University of New South Wales, Liverpool NSW 2170, Australia.
- Gastroenterology, Liverpool Hospital, Liverpool NSW 2170, Australia.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
- German Center for Infection Research (DZIF), Partner Site Heidelberg, D-69120 Heidelberg, Germany.
| | - Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
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36
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Hu B, Wang R, Fu J, Su M, Du M, Liu Y, Li H, Wang H, Lu F, Jiang J. Integration of hepatitis B virus S gene impacts on hepatitis B surface antigen levels in patients with antiviral therapy. J Gastroenterol Hepatol 2018; 33:1389-1396. [PMID: 29266382 DOI: 10.1111/jgh.14075] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 11/29/2017] [Accepted: 12/12/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIM The aim of this study is to investigate the impact of hepatitis B virus (HBV) S gene integration on serum hepatitis B surface antigen (HBsAg) levels in chronic hepatitis B with long-term nucleos(t)ide analogue (NUC) therapy. METHODS Chronic hepatitis B patients who performed liver biopsy at baseline and treated with long-term NUC therapy were recruited. The integration of HBV S gene in baseline liver biopsy specimen was detected by Alu polymerase chain reaction method. Serum HBsAg levels were measured at baseline and the second year and the fourth year after NUC therapy by Roche reagent, respectively. Serum HBsAg levels between HBV S gene integrated group and nonintegrated group were compared and analyzed. RESULTS Seventy patients were eligible for this study. Among them, 11 (15.7%) were found to have HBV S gene integration in their baseline liver biopsy specimens. Similar significant decrease of HBsAg levels was found in both integrated and nonintegrated groups (2.63 vs 2.65 log IU/mL, P = 0.478) after the first 2 years of NUC therapy. Thereafter, the decrease of HBsAg level from 2 to 4 years after therapy was largely unchanged in integrated group as compared with that of nonintegrated group (0.1 vs 2.53 log IU/mL, P = 0.002), with statistical difference. CONCLUSIONS Serum HBsAg could be originated from the expression of the integrated HBV S gene in patients with S gene integration, which implicated the limitations when regarding HBsAg as a surrogate biomarker of covalently closed circular DNA activity and as an indicator of safe NUC discontinuation.
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Affiliation(s)
- Bobin Hu
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Rongming Wang
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Jiaxin Fu
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Minghua Su
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Man Du
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Yu Liu
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Huijiao Li
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Huiwen Wang
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianning Jiang
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, China
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37
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Li L, Zheng YC, Kayani MUR, Xu W, Wang GQ, Sun P, Ao N, Zhang LN, Gu ZQ, Wu LC, Zhao HT. Comprehensive analysis of circRNA expression profiles in humans by RAISE. Int J Oncol 2017; 51:1625-1638. [PMID: 29039477 PMCID: PMC5673025 DOI: 10.3892/ijo.2017.4162] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are pervasively expressed circles of non-coding RNAs. Even though many circRNAs have been reported in humans, their expression patterns and functions remain poorly understood. In this study, we employed a pipeline named RAISE to detect circRNAs in RNA-seq data. RAISE can fully characterize circRNA structure and abundance. We evaluated inter-individual variations in circRNA expression in humans by applying this pipeline to numerous non-poly(A)-selected RNA-seq data. We identified 59,128 circRNA candidates in 61 human liver samples, with almost no overlap in the circRNA of the recruited samples. Approximately 89% of the circRNAs were detected in one or two samples. In comparison, 10% of the linear mRNAs and non-coding RNAs were detected in each sample. We estimated the variation in other tissues, especially the circRNA high-abundance tissues, in advance. Only 0.5% of the 50,631 brain circRNA candidates were shared among the 30 recruited brain samples, which is similar to the proportion in liver. Moreover, we found inter- and intra-individual diversity in circRNAs expression in the granulocyte RNA-seq data from seven individuals sampled 3 times at one-month intervals. Our findings suggest that careful consideration of inter-individual diversity is required when extensively identifying human circRNAs or proposing their use as potential biomarkers and therapeutic targets in disease.
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Affiliation(s)
- Lin Li
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, P.R. China
| | - Yong-Chang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Masood Ur Rehman Kayani
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, P.R. China
| | - Wen Xu
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, P.R. China
| | - Guan-Qun Wang
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, P.R. China
| | - Pei Sun
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, P.R. China
| | - Ning Ao
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Li-Na Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P.R. China
| | - Zhao-Qi Gu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Liang-Cai Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Hai-Tao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
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38
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Cao J, Hou P, Chen J, Wang P, Wang W, Liu W, Liu C, He X. The overexpression and prognostic role of DCAF13 in hepatocellular carcinoma. Tumour Biol 2017. [PMID: 28631558 DOI: 10.1177/1010428317705753] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DDB1 and CUL4 associated factor 13 (DCAF13) is a protein coding gene located on chromosome 8q22.3, which is a hotspot amplified in various cancers. DCAF13 has been reported to be frequently amplified in breast cancer patients. However, the genetic alteration and potential role of DCAF13 in other cancers, including hepatocellular carcinoma, have not been investigated yet. In this study, we found that DCAF13 was amplified in 14.7% of the cases and its expression was upregulated (p < 0.001) in hepatocellular carcinoma samples in The Cancer Genome Atlas dataset. Increased expression of DCAF13 was also noticed in 40 paired hepatocellular carcinoma and adjacent non-tumor tissues both at messenger RNA and protein levels (p = 0.0002 and 0.0016, respectively). A positive relationship was observed between augmented DCAF13 levels and poorer tumor grade (p = 0.005), and we also found that hepatocellular carcinoma patients with increased DCAF13 expression in their tumors had significantly poorer survival compared with those with decreased DCAF13 expression (median survival time: 45.73 and 70.53 months, respectively). Multivariate Cox regression analysis showed that DCAF13 was an independent prognostic predictor of survival in hepatocellular carcinoma patients. Gene ontology and Kyoto Encyclopedia of Genes and genomes analysis indicated the potential role of DCAF13 as a crucial cell cycle regulator. Collectively, our findings revealed that the overexpression of DCAF13 in hepatocellular carcinoma was significantly associated with poor survival and may participate in the regulation of cell cycle progression.
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Affiliation(s)
- Jianzhong Cao
- 1 Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Pengjiao Hou
- 2 Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, P.R. China
| | - Jiemin Chen
- 1 Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Penghui Wang
- 1 Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Wenqin Wang
- 1 Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Wei Liu
- 1 Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Changzheng Liu
- 2 Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, P.R. China
| | - Xiaodong He
- 1 Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P.R. China
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39
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Feng Y, Xiao F, Yang N, Zhu N, Fu Y, Zhang HB, Yang GS. Overexpression of Sox3 is associated with promoted tumor progression and poor prognosis in hepatocellular carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:7873-7881. [PMID: 31966635 PMCID: PMC6965222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/27/2017] [Indexed: 06/10/2023]
Abstract
Hepatocellular carcinoma (HCC) is a common malignant tumor lacking sensitive biomarkers for prognosis. Sox3, a member of the Sex determining region Y box gene superfamily, has been demonstrated to be an oncogene in many cancers. However, the expression and clinical importance of Sox3 in HCC remains elusive. In this study, fifty pairs of HCC tissues with adjacent non-tumor samples were collected for detecting Sox3 expression by qPCR and immunoblotting analyses. A total of 104 HCC tissues were included for immunohistochemistry assay and analyzed by immunostaining scores. The correlation of Sox3 expression with clinicopathological factors and prognosis of HCC patients were calculated. Sox3 expression in HCC tissues was significantly higher than that in the non-tumor counterparts at the mRNA and protein levels. High staining scores of Sox3 was detected in 75.96% of HCC tissues. Statistical analyses demonstrated that highly expressed Sox3 was significantly correlated with low tumor capsule formation, advanced tumor stage and poor tumor differentiation. Moreover, patients with high Sox3 expression showed worse recurrence-free survival and overall survival than those with low Sox3 expression, and multivariate analyses further indicated that status of Sox3 expression is an independent prognostic factor in HCC patients. Therefore, our results suggested that overexpression of Sox3 in HCC tissues is correlated with increased tumor development and poor prognosis in HCC.
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Affiliation(s)
- Yun Feng
- The Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University Shanghai, P. R. China
| | - Feng Xiao
- The Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University Shanghai, P. R. China
| | - Ning Yang
- The Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University Shanghai, P. R. China
| | - Nan Zhu
- The Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University Shanghai, P. R. China
| | - Yong Fu
- The Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University Shanghai, P. R. China
| | - Hai-Bin Zhang
- The Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University Shanghai, P. R. China
| | - Guang-Shun Yang
- The Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University Shanghai, P. R. China
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40
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Yang X, Wu L, Lin J, Wang A, Wan X, Wu Y, Robson SC, Sang X, Zhao H. Distinct hepatitis B virus integration patterns in hepatocellular carcinoma and adjacent normal liver tissue. Int J Cancer 2017; 140:1324-1330. [PMID: 27943263 DOI: 10.1002/ijc.30547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
Infection by the hepatitis B virus (HBV) is one of the main etiologies of hepatocellular carcinoma (HCC). During chronic infection, HBV DNA can integrate into the human genome, and this has been postulated as a possible mechanism of HBV-induced HCC. In this study we used 2199 HBV integration sites from Dr.VIS v2.0 and mapped them to the human genome (hg19) to obtain viral integration sites (VIS) related to protein-coding and non-protein-coding genes. In total, we found 1,377 and 767 VIS within close proximity to protein coding genes and noncoding genes, respectively. Genes affected more than two times included 23.1% of protein-coding genes and 24.7% of long noncoding RNAs (lncRNA). Only 4.8% of VIS were shared between HCC and non-tumor tissues. HBV integrations were more common in chromosomes 5, 8, 10, and 19 in HCC tissue and chromosomes 1 and 2 in non-tumorous tissue. The number of integration sites on each chromosome correlated with the number of fragile sites in non-tumorous tissue but not in HCC tissue. Functional enrichment analysis of the protein-coding genes containing or in close proximity to HBV integration sites in HCC tissue showed an enrichment of cancer related gene ontology terms. Additionally, the most frequently associated lncRNA genes were related to telomere maintenance, protein modification processes, and chromosome localization. Thus, HBV may have preferred integration sites in the human genome that serve a critical role in HCC development. These results show that HCC treatment may benefit from the development of next generation anti-viral therapies.
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Affiliation(s)
- Xiaobo Yang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Liangcai Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jianzhen Lin
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Anqiang Wang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xueshuai Wan
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yan Wu
- Department of Medicine, Liver Center and The Transplant Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA.,Department of Surgery, Liver Center and The Transplant Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Simon C Robson
- Department of Medicine, Liver Center and The Transplant Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA.,Department of Surgery, Liver Center and The Transplant Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Xinting Sang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Haitao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China.,Center of Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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41
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Tu T, Budzinska MA, Shackel NA, Urban S. HBV DNA Integration: Molecular Mechanisms and Clinical Implications. Viruses 2017; 9:v9040075. [PMID: 28394272 PMCID: PMC5408681 DOI: 10.3390/v9040075] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with the Hepatitis B Virus (HBV) is a major cause of liver-related morbidity and mortality. One peculiar observation in cells infected with HBV (or with closely‑related animal hepadnaviruses) is the presence of viral DNA integration in the host cell genome, despite this form being a replicative dead-end for the virus. The frequent finding of somatic integration of viral DNA suggests an evolutionary benefit for the virus; however, the mechanism of integration, its functions, and the clinical implications remain unknown. Here we review the current body of knowledge of HBV DNA integration, with particular focus on the molecular mechanisms and its clinical implications (including the possible consequences of replication-independent antigen expression and its possible role in hepatocellular carcinoma). HBV DNA integration is likely to influence HBV replication, persistence, and pathogenesis, and so deserves greater attention in future studies.
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Affiliation(s)
- Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
| | - Magdalena A Budzinska
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Nicholas A Shackel
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
- Liverpool Hospital, Gastroenterology, Sydney, NSW 2170, Australia.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
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42
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Zhang F, Cui L, Kuo MD. Diversity of Gene Expression in Hepatocellular Carcinoma Cells. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 13:377-82. [PMID: 26779818 PMCID: PMC4747664 DOI: 10.1016/j.gpb.2015.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 11/19/2022]
Abstract
Understanding tumor diversity has been a long-lasting and challenging question for researchers in the field of cancer heterogeneity or tumor evolution. Studies have reported that compared to normal cells, there is a higher genetic diversity in tumor cells, while higher genetic diversity is associated with higher progression risks of tumor. We thus hypothesized that tumor diversity also holds true at the gene expression level. To test this hypothesis, we used t-test to compare the means of Simpson’s diversity index for gene expression (SDIG) between tumor and non-tumor samples. We found that the mean SDIG in tumor tissues is significantly higher than that in the non-tumor or normal tissues (P < 0.05) for most datasets. We also combined microarrays and next-generation sequencing data for validation. This cross-platform and cross-experimental validation greatly increased the reliability of our results.
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Affiliation(s)
- Fan Zhang
- Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
| | - Li Cui
- Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0949, USA
| | - Michael D Kuo
- Department of Radiological Sciences, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, CA 90095, USA.
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Dong H, Qian Z, Zhang L, Chen Y, Ren Z, Ji Q. Genomic and transcriptome profiling identified both human and HBV genetic variations and their interactions in Chinese hepatocellular carcinoma. GENOMICS DATA 2015; 6:1-3. [PMID: 26697315 PMCID: PMC4664659 DOI: 10.1016/j.gdata.2015.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 02/04/2023]
Abstract
Interaction between HBV and host genome integrations in hepatocellular carcinoma (HCC) development is a complex process and the mechanism is still unclear. Here we described in details the quality controls and data mining of aCGH and transcriptome sequencing data on 50 HCC samples from the Chinese patients, published by Dong et al. (2015) (GEO#: GSE65486). In additional to the HBV-MLL4 integration discovered, we also investigated the genetic aberrations of HBV and host genes as well as their genetic interactions. We reported human genome copy number changes and frequent transcriptome variations (e.g. TP53, CTNNB1 mutation, especially MLL family mutations) in this cohort of the patients. For HBV genotype C, we identified a novel linkage disequilibrium region covering HBV replication regulatory elements, including basal core promoter, DR1, epsilon and poly-A regions, which is associated with HBV core antigen over-expression and almost exclusive to HBV-MLL4 integration.
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Affiliation(s)
- Hua Dong
- AstraZeneca Asian and Emerging Market iMed, Zhangjiang Hi-Tech Park, Shanghai, PR China
| | - Ziliang Qian
- AstraZeneca Asian and Emerging Market iMed, Zhangjiang Hi-Tech Park, Shanghai, PR China
| | - Lan Zhang
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, PR China
| | - Yunqin Chen
- R&D Information, AstraZeneca, Shanghai, PR China
| | - Zhenggang Ren
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, PR China
| | - Qunsheng Ji
- AstraZeneca Asian and Emerging Market iMed, Zhangjiang Hi-Tech Park, Shanghai, PR China
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