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Zhao J, Liu Z, Yang K, Shen S, Peng J. DNA methylation regulator-based molecular subtyping and tumor microenvironment characterization in hepatocellular carcinoma. Front Immunol 2024; 15:1333923. [PMID: 38736884 PMCID: PMC11082416 DOI: 10.3389/fimmu.2024.1333923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Backgroud Although recent studies have reported the regulation of the immune response in hepatocellular carcinoma (HCC) through DNA methylation, the comprehensive impact methylation modifications on tumor microenvironment characteristics and immunotherapy efficacy has not been fully elucidated. Methods In this research, we conducted a comprehensive assessment of the patterns of DNA methylation regulators and the profiles of the tumor microenvironment (TME) in HCC, focusing on 21 specific DNA methylation regulators. We subsequently developed a unique scoring system, a DNA methylation score (DMscore), to assess the individual DNA methylation modifications among the three distinct methylation patterns for differentially expressed genes (DEGs). Results Three distinct methylation modification patterns were identified with distinct TME infiltration characteristics. We demonstrated that the DMscore could predict patient subtype, TME infiltration, and patient prognosis. A low DMscore, characterized by an elevated tumor mutation burden (TMB), hepatitis B virus (HBV)/hepatitis C virus (HCV) infection, and immune activation, indicates an inflamed tumor microenvironment phenotype with a 5-year survival rate of 7.8%. Moreover, a low DMscore appeared to increase the efficacy of immunotherapy in the anti-CTLA-4/PD-1/PD-L1 cohort. Conclusions In brief, this research has enhanced our understanding of the correlation between modifications in DNA methylation patterns and the profile of the tumor microenvironment in individuals diagnosed with HCC. The DMscore may serve as an alternative biomarker for survival and efficacy of immunotherapy in patients with HCC.
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Affiliation(s)
- Junsheng Zhao
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
| | - Zhengtao Liu
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Keda Yang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Sijia Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan (Hangzhou) Hospital Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jing Peng
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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2
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Liang X, Justice AC, Marconi VC, Aouizerat BE, Xu K. Co-occurrence of injection drug use and hepatitis C increases epigenetic age acceleration that contributes to all-cause mortality among people living with HIV. Epigenetics 2023; 18:2212235. [PMID: 37191953 PMCID: PMC10190198 DOI: 10.1080/15592294.2023.2212235] [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: 11/17/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Co-occurrence of injection drug use (IDU) and hepatitis C virus infection (HCV) is common in people living with HIV (PLWH) and leads to significantly increased mortality. Epigenetic clocks derived from DNA methylation (DNAm) are associated with disease progression and all-cause mortality. In this study, we hypothesized that epigenetic age mediates the relationships between the co-occurrence of IDU and HCV with mortality risk among PLWH. We tested this hypothesis in the Veterans Aging Cohort Study (n = 927) by using four established epigenetic clocks of DNAm age (i.e., Horvath, Hannum, Pheno, Grim). Compared to individuals without IDU and HCV (IDU-HCV-), participants with IDU and HCV (IDU+HCV+) showed a 2.23-fold greater risk of mortality estimated using a Cox proportional hazards model (hazard ratio: 2.23; 95% confidence interval: 1.62-3.09; p = 1.09E-06). IDU+HCV+ was associated with a significantly increased epigenetic age acceleration (EAA) measured by 3 out of 4 epigenetic clocks, adjusting for demographic and clinical variables (Hannum: p = 8.90E-04, Pheno: p = 2.34E-03, Grim: p = 3.33E-11). Furthermore, we found that epigenetic age partially mediated the relationship between IDU+HCV+ and all-cause mortality, up to a 13.67% mediation proportion. Our results suggest that comorbid IDU with HCV increases EAA in PLWH that partially mediates the increased mortality risk.
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Affiliation(s)
- Xiaoyu Liang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Amy C. Justice
- VA Connecticut Healthcare System, West Haven, CT, USA
- New Haven Veterans Affairs Connecticut Healthcare System, Yale University School of Medicine, New Haven, CT, USA
| | - Vincent C. Marconi
- Emory University School of Medicine and Rollins School of Public Health; the Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Bradley E. Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, NY, USA
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, NY, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
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3
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Yıldırım HÇ, Kavgaci G, Chalabiyev E, Dizdar O. Advances in the Early Detection of Hepatobiliary Cancers. Cancers (Basel) 2023; 15:3880. [PMID: 37568696 PMCID: PMC10416925 DOI: 10.3390/cancers15153880] [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: 05/29/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Hepatocellular cancer (HCC) and biliary tract cancers (BTCs) have poor survival rates and a low likelihood of a cure, especially in advanced-stage disease. Early diagnosis is crucial and can significantly improve survival rates through curative treatment approaches. Current guidelines recommend abdominal ultrasonography (USG) and alpha-fetoprotein (AFP) monitoring for HCC screening in high-risk groups, and abdominal USG, magnetic resonance imaging (MRI), and magnetic resonance cholangiopancreatography (MRCP) monitoring for biliary tract cancer. However, despite this screening strategy, many high-risk individuals still develop advanced-stage HCC and BTC. Blood-based biomarkers are being developed for use in HCC or BTC high-risk groups. Studies on AFP, AFP-L3, des-gamma-carboxy prothrombin, glypican-3 (GPC3), osteopontin (OPN), midkine (MK), neopterin, squamous cell carcinoma antigen (SCCA), Mac-2-binding protein (M2BP), cyclic guanosine monophosphate (cGMP), and interleukin-6 biomarkers for HCC screening have shown promising results when evaluated individually or in combination. In the case of BTCs, the potential applications of circulating tumor DNA, circulating microRNA, and circulating tumor cells in diagnosis are also promising. These biomarkers have shown potential in detecting BTCs in early stages, which can significantly improve patient outcomes. Additionally, these biomarkers hold promise for monitoring disease progression and evaluating response to therapy in BTC patients. However, further research is necessary to fully understand the clinical utility of these biomarkers in the diagnosis and management of HCC and BTCs.
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Affiliation(s)
| | | | | | - Omer Dizdar
- Department of Medical Oncology, Faculty of Medicine, Hacettepe University, 06230 Ankara, Turkey; (H.Ç.Y.); (G.K.); (E.C.)
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4
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Gao Q, Zeng Q, Wang Z, Li C, Xu Y, Cui P, Zhu X, Lu H, Wang G, Cai S, Wang J, Fan J. Start of an era: circulating cell-free DNA for early detection of cancers. Innovation (N Y) 2022; 3:100259. [PMID: 35647572 PMCID: PMC9133648 DOI: 10.1016/j.xinn.2022.100259] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/02/2022] [Indexed: 11/29/2022] Open
Abstract
Effective screening modalities are currently available for only a small subset of cancers, and they generally have suboptimal performance with complicated procedures. Therefore, there is an urgent need to develop simple, accurate, and non-invasive methods for early detection of cancers. Genetic and epigenetic alterations in plasma circulating cell-free DNA (cfDNA) have shown the potential to revolutionize methods of early detection of cancers and facilitate subsequent diagnosis to improve survival of patients. The medical interest in cfDNA assays has been inspired by emerging single- and multi-early detection of cancers studies. This review summarizes current technological and clinical advances, in the hopes of providing insights into the development and applications of cfDNA assays in various cancers and clinical scenarios. The key phases of clinical development of biomarkers are highlighted, and the future developments of cfDNA-based liquid biopsies in early detection of cancers are outlined. It is hoped that this study can boost the potential integration of cfDNA-based early detection of cancers into the current clinical workflow. Liquid biopsy, characterized by minimal invasiveness and user friendliness, can identify multiple cancers at the early stage and localize the tissue of origin The state-of-the-art technology facilitates the application of circulating cell-free DNA (cfDNA) assays in the early detection of cancers cfDNA assays are expected to be integrated into the clinical workflow after technological refinement and clinical trial validation The development and application strategies of cfDNA assays in various cancers and clinical scenarios can vary, and the harm-and-benefit should be balanced carefully
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Affiliation(s)
- Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qiang Zeng
- Health Management Institute, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100006, China
| | | | - Yu Xu
- Burning Rock Biotech, Guangzhou 510320, China
| | - Peng Cui
- Burning Rock Biotech, Guangzhou 510320, China
| | - Xin Zhu
- Burning Rock Biotech, Guangzhou 510320, China
| | - Huafei Lu
- Burning Rock Biotech, Guangzhou 510320, China
| | | | - Shangli Cai
- Burning Rock Biotech, Guangzhou 510320, China
- Corresponding author
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100006, China
- Corresponding author
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Corresponding author
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5
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Destoumieux-Garzón D, Matthies-Wiesler F, Bierne N, Binot A, Boissier J, Devouge A, Garric J, Gruetzmacher K, Grunau C, Guégan JF, Hurtrez-Boussès S, Huss A, Morand S, Palmer C, Sarigiannis D, Vermeulen R, Barouki R. Getting out of crises: Environmental, social-ecological and evolutionary research is needed to avoid future risks of pandemics. ENVIRONMENT INTERNATIONAL 2022; 158:106915. [PMID: 34634622 PMCID: PMC8500703 DOI: 10.1016/j.envint.2021.106915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 05/05/2023]
Abstract
The implementation of One Health/EcoHealth/Planetary Health approaches has been identified as key (i) to address the strong interconnections between risk for pandemics, climate change and biodiversity loss and (ii) to develop and implement solutions to these interlinked crises. As a response to the multiple calls from scientists on that subject, we have here proposed seven long-term research questions regarding COVID-19 and emerging infectious diseases (EIDs) that are based on effective integration of environmental, ecological, evolutionary, and social sciences to better anticipate and mitigate EIDs. Research needs cover the social ecology of infectious disease agents, their evolution, the determinants of susceptibility of humans and animals to infections, and the human and ecological factors accelerating infectious disease emergence. For comprehensive investigation, they include the development of nature-based solutions to interlinked global planetary crises, addressing ethical and philosophical questions regarding the relationship of humans to nature and regarding transformative changes to safeguard the environment and human health. In support of this research, we propose the implementation of innovative multidisciplinary facilities embedded in social ecosystems locally: ecological health observatories and living laboratories. This work was carried out in the frame of the European Community project HERA (www.HERAresearchEU.eu), which aims to set priorities for an environment, climate and health research agenda in the European Union by adopting a systemic approach in the face of global environmental change.
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Affiliation(s)
| | - Franziska Matthies-Wiesler
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Germany.
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Aurélie Binot
- Animals, health, Territories, Risks and Ecosystem (ASTRE), University of Montpellier, Agricultural Research for Development (CIRAD), National Research Institute for Agriculture, Food and the Environment (INRAE), Montpellier, France
| | - Jérôme Boissier
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | | | - Jeanne Garric
- Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), UR Riverly, F-69625 Villeurbanne, France
| | - Kim Gruetzmacher
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin Germany
| | - Christoph Grunau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - Jean-François Guégan
- Animals, health, Territories, Risks and Ecosystem (ASTRE), University of Montpellier, Agricultural Research for Development (CIRAD), National Research Institute for Agriculture, Food and the Environment (INRAE), Montpellier, France; MIVEGEC, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Sylvie Hurtrez-Boussès
- MIVEGEC, Univ Montpellier, IRD, CNRS, Montpellier, France; Département de Biologie-Ecologie, Faculté des Sciences, Univ Montpellier, Montpellier, France
| | | | - Serge Morand
- Centre National de la Recherche Scientifique - UMR ASTRE, CIRAD, INRAE - Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Clare Palmer
- Department of Philosophy, YMCA Building, Texas A&M University, College Station, TX 77843, USA
| | - Denis Sarigiannis
- Aristotle University of Thessaloniki, Thessaloniki 54164, Greece; University School for Advanced Study IUSS, Pavia, Italy
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6
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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: 1.3] [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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7
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Merle P. Pragmatic tools for the prediction and potential early diagnosis of hepatitis B virus-related hepatocellular carcinoma? Clin Res Hepatol Gastroenterol 2021; 45:101722. [PMID: 34146725 DOI: 10.1016/j.clinre.2021.101722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/24/2021] [Indexed: 02/04/2023]
Affiliation(s)
- Philippe Merle
- Unité d'Hépatologie et Gastroentérologie, Hôpital de la Croix Rousse, Hospices Civils de Lyon, France; Centre de Recherche en Cancérologie de Lyon, INSERM U1052, Lyon, France; Université Claude Bernard Lyon 1, Lyon, France.
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8
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Abo El-Khair SM, Elalfy H, Diasty M, Ebrahim EE, Elsamanoudy AZ. Methylation degree of metalloproteinase inhibitor RECK gene: Links to RECK protein level and hepatocellular carcinoma in chronic HCV infection patients. J Biochem Mol Toxicol 2021; 35:e22886. [PMID: 34392581 DOI: 10.1002/jbt.22886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 07/21/2021] [Accepted: 08/06/2021] [Indexed: 11/11/2022]
Abstract
The RECK gene, a tumor suppressor gene, inhibits angiogenesis, invasion, and tumor metastasis. Epigenetic regulation of the RECK gene constitutes a potent approach to the molecular basis of liver malignancy. This study aims to evaluate the promoter methylation status of the RECK gene and its serum level in patients with hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) and the potential association of RECK gene methylation with clinical criteria of HCC. One hundred and fifty-five subjects were included (healthy control [55], chronic HCV patients [55], HCV-related HCC patients [45]). The methylation status of the RECK gene promoter and serum RECK level were investigated by methylation-specific PCR and enzyme-linked immunosorbent assay techniques, respectively. RECK gene promoter hypermethylation was recorded in 46.7% of HCC patients, and 10.9% of HCV patients, but not in control subjects (0%). It was related to RECK protein level, varices, edema, ascites, lymph node metastasis, vascular invasion, and the largest diameter of focal lesions. Meanwhile, it was not associated with focal lesion number nor distant metastasis of HCC. In conclusion, RECK gene promoter hypermethylation is linked to HCV genotype-4-related HCC. Moreover, different degrees of RECK gene promoter methylation are associated with serum RECK level, lymph node metastasis, and vascular invasion, which could prove its pathogenic role in hepatocarcinogenesis in chronic HCV-infected patients.
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Affiliation(s)
- Salwa M Abo El-Khair
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Hatem Elalfy
- Tropical Medicine Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Muhammad Diasty
- Tropical Medicine Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Eman E Ebrahim
- Tropical Medicine Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Ayman Z Elsamanoudy
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.,Clinical Biochemistry Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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9
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Jiang Y, Han Q, Zhao H, Zhang J. The Mechanisms of HBV-Induced Hepatocellular Carcinoma. J Hepatocell Carcinoma 2021; 8:435-450. [PMID: 34046368 PMCID: PMC8147889 DOI: 10.2147/jhc.s307962] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy, and the hepatitis B virus (HBV) is its major pathogenic factor. Over the past decades, it has been confirmed that HBV infection could promote disease progression through a variety of mechanisms, ultimately leading to the malignant transformation of liver cells. Many factors have been identified in the pathogenesis of HBV-associated HCC (HBV-HCC), including HBV gene integration, genomic instability caused by mutation, and activation of cancer-promoting signaling pathways. As research in the progression of HBV-HCC progresses, the role of many new mechanisms, such as epigenetics, exosomes, autophagy, metabolic regulation, and immune suppression, is also being continuously explored. The occurrence of HBV-HCC is a complex process caused by interactions across multiple genes and multiple steps, where the synergistic effects of various cancer-promoting mechanisms accelerate the process of disease evolution from inflammation to tumorigenesis. In this review, we aim to provide a brief overview of the mechanisms involved in the occurrence and development of HBV-HCC, which may contribute to a better understanding of the role of HBV in the occurrence and development of HCC.
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Affiliation(s)
- Yu Jiang
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong Province, People's Republic of China
| | - Qiuju Han
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong Province, People's Republic of China
| | - Huajun Zhao
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong Province, People's Republic of China
| | - Jian Zhang
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, Shandong Province, People's Republic of China
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10
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Wang X, Cheng Y, Yan LL, An R, Wang XY, Wang HY. Exploring DNA Methylation Profiles Altered in Cryptogenic Hepatocellular Carcinomas by High-Throughput Targeted DNA Methylation Sequencing: A Preliminary Study for Cryptogenic Hepatocellular Carcinoma. Onco Targets Ther 2020; 13:9901-9916. [PMID: 33116575 PMCID: PMC7547808 DOI: 10.2147/ott.s267812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/19/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) includes cryptogenic hepatocellular carcinomas (CR-HCC) that lack a defined cause. Specific DNA methylation patterns and comparisons of the aberrant alterations in DNA methylation between CR-HCC and adjacent peritumor tissues (APTs) have not yet been reported. Methods The SureSelectXT Methyl-Seq Target Enrichment System was used to sequence targeted DNA methylation in three paired CR-HCC tissues and APTs. Gene Ontology (GO) enrichment and KEGG pathway analysis were performed to investigate the DNA methylation mechanism of CR-HCC. The mRNA expression levels of HOXB-AS3, HOXB6, HOXB3, USP18, MAP3K6, TIRAP, TNNI2, SHC3, CTTN, and TFAP2A, selected from the identified signaling pathways, were evaluated by quantitative real-time PCR (qPCR). Results A total of 1728 differentially methylated regions (DMRs) were identified in tumor tissues compared with non-tumor tissues, of which 868 DMRs were hypermethylated and 860 were hypomethylated. The DMRs were mapped within 2091 DMR-associated genes (DMGs). The mRNA expression of HOXB-AS3, HOXB3, and MAP3K6 was downregulated in CR-HCC tissues compared to the APTs. However, the mRNA expression of TIRAP, SHC3, and CTTN was upregulated in the CR-HCC tissues. Differences between the mRNA expression of HOXB6, USP18, TNNI2, and TFAP2A in the CR-HCC and APTS tissues were not statistically significant. GO analysis showed that the molecular functions of “binding”, “protein binding”, and “cytoskeletal protein binding” were the main categories for the hypermethylated DMGs. The hypomethylated DMGs were mostly enriched in the molecular functions “binding”, “protein binding”, “calcium ion binding”, among others. KEGG pathway analysis showed that the hypermethylated DMGs were enriched in several pathways such as “estrogen signaling pathway”, while hypomethylated DMGs were enriched in several pathways such as “proteoglycans in cancer”, suggesting that epigenetic modifications play important roles in the cryptogenic hepatocarcinogenesis. Conclusion These results provide useful information for future work to characterize the functions of epigenetic mechanisms on CR-HCC.
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Affiliation(s)
- Xin Wang
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, People's Republic of China
| | - Ya Cheng
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, People's Republic of China
| | - Liang-Liang Yan
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, People's Republic of China
| | - Ran An
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, People's Republic of China
| | - Xing-Yu Wang
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, People's Republic of China
| | - Heng-Yi Wang
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, People's Republic of China
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11
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Zhang C, Ge S, Wang J, Jing X, Li H, Mei S, Zhang J, Liang K, Xu H, Zhang X, Zhang C. Epigenomic profiling of DNA methylation for hepatocellular carcinoma diagnosis and prognosis prediction. J Gastroenterol Hepatol 2019; 34:1869-1877. [PMID: 31038805 DOI: 10.1111/jgh.14694] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/31/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM DNA hypermethylation has emerged as a novel molecular biomarker for the diagnosis and prognosis prediction of many cancers. We aimed to identify clinically useful biomarkers regulated by DNA methylation in hepatocellular carcinoma (HCC). METHODS Genome-wide methylation analysis in HCCs and paired noncancerous tissues was performed using an Illumina Infinium HumanMethylation 450K BeadChip array. Methylation-specific polymerase chain reaction and pyrosequencing were used to validate the methylation status of selected genes in 100 paired HCCs and noncancerous samples. RESULTS A total of 97 027 (20.0%) out of 485 577 CpG sites significantly were differed between HCC and noncancerous tissues. Among all the significant CpG sites, 48.8% are hypermethylated and 51.2% are hypomethylated in HCCs. Multiple signaling pathways (AMP-activated protein kinase, estrogen, and adipocytokine) involved in gene methylation were identified in HCC. FES was selected for further analysis based on its high level of methylation confirmed by polymerase chain reaction and pyrosequencing. The result showed that FES hypermethylation was correlated with tumor size (0.001), serum alpha fetoprotein (0.023), and tumor differentiation (0.006). FES protein was significantly downregulated in 51/100 (51%) HCCs, and 94.12% (48/51) of them were due to promoter hypermethylation. Both FES hypermethylation and protein downregulation were associated with the progression-free survival and overall survival of HCC patients. Overexpressed and knockdown of FES confirmed its inhibitory effect on the proliferation and migration of HCC cells. CONCLUSIONS We identified many new differentially methylated CpGs in HCCs and demonstrate that FES functions as a tumor suppressor gene in HCC and its methylation status could be used as an indicator for prognosis of HCC.
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Affiliation(s)
- Cheng Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Shuang Ge
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Jun Wang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaotong Jing
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | | | - Shuyu Mei
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Juan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Ke Liang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Hui Xu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaoying Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
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Sasaki R, Kanda T, Kato N, Yokosuka O, Moriyama M. Hepatitis C virus-associated hepatocellular carcinoma after sustained virologic response. World J Hepatol 2018; 10:898-906. [PMID: 30631394 PMCID: PMC6323517 DOI: 10.4254/wjh.v10.i12.898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/08/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023] Open
Abstract
The introduction of a direct-acting antiviral (DAA) for patients with hepatitis C virus (HCV) infection, could lead to higher sustained virologic response (SVR) rates with fewer adverse events, and it could shorten the treatment duration relative to the interferon era. Although most recent clinical studies have demonstrated that the occurrence rates of hepatocellular carcinoma (HCC) are decreased by SVR with both interferon-based and interferon-free-regimens, there are several reports about the unexpected observation of high rates of early tumor occurrence and recurrence in patients with HCV-related HCC undergoing interferon-free therapy despite SVR. Several mechanisms of HCC occurrence and rapid immunological changes, including cytokines and chemokines during and after DAA treatment, have also been reported. We focused on the possibilities that HCC occurs or recurs during and after DAA treatment, based on the reported clinical and basic studies. Further studies and observations will be needed to determine the short-term and long-term effects on hepatocarcinogenesis caused by the eradication of HCV with DAAs. New serum biomarkers and a follow-up system for HCV-patients with SVR should be established.
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Affiliation(s)
- Reina Sasaki
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Tatsuo Kanda
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Itabashi-ku 173-8610, Japan
| | - Naoya Kato
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Itabashi-ku 173-8610, Japan
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