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Marumo T, Yoshida N, Inoue N, Yamanouchi M, Ubara Y, Urakami S, Fujii T, Takazawa Y, Ohashi K, Kawarazaki W, Nishimoto M, Ayuzawa N, Hirohama D, Nagae G, Fujimoto M, Arai E, Kanai Y, Hoshino J, Fujita T. Aberrant proximal tubule DNA methylation underlies phenotypic changes related to kidney dysfunction in patients with diabetes. Am J Physiol Renal Physiol 2024; 327:F397-F411. [PMID: 38961842 DOI: 10.1152/ajprenal.00124.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Epigenetic mechanisms are considered to contribute to diabetic nephropathy by maintaining memory of poor glycemic control during the early stages of diabetes. However, DNA methylation changes in the human kidney are poorly characterized, because of the lack of cell type-specific analysis. We examined DNA methylation in proximal tubules (PTs) purified from patients with diabetic nephropathy and identified differentially methylated CpG sites, given the critical role of proximal tubules in the kidney injury. Hypermethylation was observed at CpG sites annotated to genes responsible for proximal tubule functions, including gluconeogenesis, nicotinamide adenine dinucleotide synthesis, transporters of glucose, water, phosphate, and drugs, in diabetic kidneys, whereas genes involved in oxidative stress and the cytoskeleton exhibited demethylation. Methylation levels of CpG sites annotated to ACTN1, BCAR1, MYH9, UBE4B, AFMID, TRAF2, TXNIP, FOXO3, and HNF4A were correlated with the estimated glomerular filtration rate, whereas methylation of the CpG site in RUNX1 was associated with interstitial fibrosis and tubular atrophy. Hypermethylation of G6PC and HNF4A was accompanied by decreased expression in diabetic kidneys. Proximal tubule-specific hypomethylation of metabolic genes related to HNF4A observed in control kidneys was compromised in diabetic kidneys, suggesting a role for aberrant DNA methylation in the dedifferentiation process. Multiple genes with aberrant DNA methylation in diabetes overlapped genes with altered expressions in maladaptive proximal tubule cells, including transcription factors PPARA and RREB1. In conclusion, DNA methylation derangement in the proximal tubules of patients with diabetes may drive phenotypic changes, characterized by inflammatory and fibrotic features, along with impaired function in metabolism and transport.NEW & NOTEWORTHY Cell type-specific DNA methylation patterns in the human kidney are not known. We examined DNA methylation in proximal tubules of patients with diabetic nephropathy and revealed that oxidative stress, cytoskeleton, and metabolism genes were aberrantly methylated. The results indicate that aberrant DNA methylation in proximal tubules underlies kidney dysfunction in diabetic nephropathy. Aberrant methylation could be a target for reversing memory of poor glycemic control.
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Affiliation(s)
- Takeshi Marumo
- Department of Pharmacology, School of Medicine, International University of Health and Welfare, Chiba, Japan
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Naoto Yoshida
- Department of Pharmacology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Noriko Inoue
- Nephrology Center, Toranomon Hospital, Tokyo, Japan
| | | | | | | | - Takeshi Fujii
- Department of Pathology, Toranomon Hospital, Tokyo, Japan
| | | | - Kenichi Ohashi
- Department of Human Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Wakako Kawarazaki
- Department of Pharmacology, School of Medicine, International University of Health and Welfare, Chiba, Japan
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Nishimoto
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Nobuhiro Ayuzawa
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Daigoro Hirohama
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Junichi Hoshino
- Nephrology Center, Toranomon Hospital, Tokyo, Japan
- Deparment of Nephrology, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiro Fujita
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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Yan W, Rao D, Fan F, Liang H, Zhang Z, Dong H. Hepatitis B virus X protein and TGF-β: partners in the carcinogenic journey of hepatocellular carcinoma. Front Oncol 2024; 14:1407434. [PMID: 38962270 PMCID: PMC11220127 DOI: 10.3389/fonc.2024.1407434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/21/2024] [Indexed: 07/05/2024] Open
Abstract
Hepatitis B infection is substantially associated with the development of liver cancer globally, with the prevalence of hepatocellular carcinoma (HCC) cases exceeding 50%. Hepatitis B virus (HBV) encodes the Hepatitis B virus X (HBx) protein, a pleiotropic regulatory protein necessary for the transcription of the HBV covalently closed circular DNA (cccDNA) microchromosome. In previous studies, HBV-associated HCC was revealed to be affected by HBx in multiple signaling pathways, resulting in genetic mutations and epigenetic modifications in proto-oncogenes and tumor suppressor genes. In addition, transforming growth factor-β (TGF-β) has dichotomous potentials at various phases of malignancy as it is a crucial signaling pathway that regulates multiple cellular and physiological processes. In early HCC, TGF-β has a significant antitumor effect, whereas in advanced HCC, it promotes malignant progression. TGF-β interacts with the HBx protein in HCC, regulating the pathogenesis of HCC. This review summarizes the respective and combined functions of HBx and TGB-β in HCC occurrence and development.
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Affiliation(s)
- Wei Yan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Dean Rao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Feimu Fan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC), Chinese Academy of Medical Sciences, Wuhan, China
| | - Zunyi Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Hanhua Dong
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
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Kanai Y. Molecular pathological approach to cancer epigenomics and its clinical application. Pathol Int 2024; 74:167-186. [PMID: 38482965 DOI: 10.1111/pin.13418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Careful microscopic observation of histopathological specimens, accumulation of large numbers of high-quality tissue specimens, and analysis of molecular pathology in relation to morphological features are considered to yield realistic data on the nature of multistage carcinogenesis. Since the morphological hallmark of cancer is disruption of the normal histological structure maintained through cell-cell adhesiveness and cellular polarity, attempts have been made to investigate abnormalities of the cadherin-catenin cell adhesion system in human cancer cells. It has been shown that the CDH1 tumor suppressor gene encoding E-cadherin is silenced by DNA methylation, suggesting that a "double hit" involving DNA methylation and loss of heterozygosity leads to carcinogenesis. Therefore, in the 1990s, we focused on epigenomic mechanisms, which until then had not received much attention. In chronic hepatitis and liver cirrhosis associated with hepatitis virus infection, DNA methylation abnormalities were found to occur frequently, being one of the earliest indications that such abnormalities are present even in precancerous tissue. Aberrant expression and splicing of DNA methyltransferases, such as DNMT1 and DNMT3B, was found to underlie the mechanism of DNA methylation alterations in various organs. The CpG island methylator phenotype in renal cell carcinoma was identified for the first time, and its therapeutic targets were identified by multilayer omics analysis. Furthermore, the DNA methylation profile of nonalcoholic steatohepatitis (NASH)-related hepatocellular carcinoma was clarified in groundbreaking studies. Since then, we have developed diagnostic markers for carcinogenesis risk in NASH patients and noninvasive diagnostic markers for upper urinary tract cancer, as well as developing a new high-performance liquid chromatography-based diagnostic system for DNA methylation diagnosis. Research on the cancer epigenome has revealed that DNA methylation alterations occur from the precancerous stage as a result of exposure to carcinogenic factors such as inflammation, smoking, and viral infections, and continuously contribute to multistage carcinogenesis through aberrant expression of cancer-related genes and genomic instability. DNA methylation alterations at the precancerous stages are inherited by or strengthened in cancers themselves and determine the clinicopathological aggressiveness of cancers as well as patient outcome. DNA methylation alterations have applications as biomarkers, and are expected to contribute to diagnosis, as well as preventive and preemptive medicine.
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Affiliation(s)
- Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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Mezzacappa C, Wang Z, Lu L, Risch H, Taddei T, Yu H. Detection of hepatocellular carcinoma methylation markers in salivary DNA. Biosci Rep 2024; 44:BSR20232063. [PMID: 38457142 PMCID: PMC10958141 DOI: 10.1042/bsr20232063] [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: 12/06/2023] [Revised: 02/21/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Alterations to DNA methylation have been identified in both hepatocellular carcinoma (HCC) tumor and circulating DNA from affected individuals. These markers have potential utility in HCC screening. Adherence to HCC screening is poor and acceptable HCC screening tests are needed. METHODS A feasibility study was performed on a subset of case patients and control subjects from a prior study of risk factors for HCC. Case patients (n=12) included adults aged 47-85 years with a first diagnosis of HCC between 2011 and 2016 and without viral hepatitis. Control subjects (n=12) were matched on age, sex, and state of residence. Participants provided saliva samples for DNA genotyping. Log fold change in salivary DNA methylation at 1359 CpG sites representing 25 candidate genes previously associated with HCC was compared across case patients and control subjects. RESULTS The quantity of DNA ranged from 9.65 to 257.79 μg. The purity of DNA isolates was good, with mean OD260/280 ratio of 1.78 (SD: 0.14). Of 25 candidate genes, 16 had at ≥1 CpG site with detectable differences in methylation across HCC case patients and control subjects. Sites differentially methylated in HCC case patients included genes encoding tumor suppressors (PRDM2, RUNX3, p15/16, and RASSF1/5), regulators of cell cycle progression (DAPK1 and TP73), and DNA repair (MGMT and GSTP1). No associations met the significance threshold 3.7 × 10-5 required for multiple comparisons. CONCLUSIONS Salivary DNA may be a feasible alternative to blood samples in the era of novel DNA-based screening tests for HCC. The ease of saliva-based testing supports further investigation of its potential.
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Affiliation(s)
- Catherine Mezzacappa
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Zhanwei Wang
- University of Hawai’i Cancer Consortium, Honolulu, HI, United States
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
| | - Harvey Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
| | - Tamar Taddei
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
| | - Herbert Yu
- University of Hawai’i Cancer Consortium, Honolulu, HI, United States
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
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Makiuchi S, Tian Y, Fujimoto M, Kuramoto J, Tsuda N, Ojima H, Gotoh M, Hiraoka N, Yoshida T, Kanai Y, Arai E. DNA methylation alterations of ADCY5, MICAL2, and PLEKHG2 during the developmental stage of cryptogenic hepatocellular carcinoma. Hepatol Res 2024; 54:284-299. [PMID: 37906571 DOI: 10.1111/hepr.13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
AIM The aim of this study was to clarify the significance of DNA methylation alterations of cryptogenic hepatocellular carcinomas (HCCs). METHODS Using the Infinium assay, we performed genome-wide DNA methylation analysis of 250 liver tissue samples, including noncancerous liver tissue (U-N) and corresponding cancerous tissue (U-T) from patients with cryptogenic HCC without a history of excessive alcohol use and hepatitis virus infection, and whose U-N samples showed no remarkable histological features (no microscopic evidence of simple steatosis, any form of hepatitis including nonalcoholic steatohepatitis, or liver cirrhosis). RESULTS We identified 3272 probes that showed significant differences of DNA methylation levels between U-N and normal liver tissue samples from patients without HCC, indicating that a distinct DNA methylation profile had already been established at the precancerous U-N stage. U-Ns have a DNA methylation profile differing from that of noncancerous liver tissue of patients with nonalcoholic steatohepatitis-related, viral hepatitis-related, and alcoholic liver disease-related HCCs. Such DNA methylation alterations in U-Ns were inherited by U-Ts. The U-Ns showed DNA methylation alteration of ADCY5, resulting in alteration of its mRNA expression, whereas noncancerous liver tissue of patients with nonalcoholic steatohepatitis-, viral hepatitis-, or alcoholic liver disease-related HCCs did not. DNA methylation levels of MICAL2 and PLEKHG2 in U-Ts were correlated with larger tumor diameter and portal vein involvement, respectively. CONCLUSIONS U-N-specific DNA hypermethylation of ADCY5 may have significance, even from the precancerous stage in liver showing no remarkable histological features. DNA hypomethylation of MICAL2 and PLEKHG2 may determine the clinicopathological features of cryptogenic HCC.
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Affiliation(s)
- Satomi Makiuchi
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Junko Kuramoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Noboru Tsuda
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Hidenori Ojima
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Masahiro Gotoh
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Nobuyoshi Hiraoka
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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Wang X, Zhang L, Dong B. Molecular mechanisms in MASLD/MASH-related HCC. Hepatology 2024:01515467-990000000-00739. [PMID: 38349726 PMCID: PMC11323288 DOI: 10.1097/hep.0000000000000786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/16/2024] [Indexed: 03/23/2024]
Abstract
Liver cancer is the third leading cause of cancer-related deaths and ranks as the sixth most prevalent cancer type globally. NAFLD or metabolic dysfunction-associated steatotic liver disease, and its more severe manifestation, NASH or metabolic dysfunction-associated steatohepatitis (MASH), pose a significant global health concern, affecting approximately 20%-25% of the population. The increased prevalence of metabolic dysfunction-associated steatotic liver disease and MASH is parallel to the increasing rates of obesity-associated metabolic diseases, including type 2 diabetes, insulin resistance, and fatty liver diseases. MASH can progress to MASH-related HCC (MASH-HCC) in about 2% of cases each year, influenced by various factors such as genetic mutations, carcinogen exposure, immune microenvironment, and microbiome. MASH-HCC exhibits distinct molecular and immune characteristics compared to other causes of HCC and affects both men and women equally. The management of early to intermediate-stage MASH-HCC typically involves surgery and locoregional therapies, while advanced HCC is treated with systemic therapies, including anti-angiogenic therapies and immune checkpoint inhibitors. In this comprehensive review, we consolidate previous research findings while also providing the most current insights into the intricate molecular processes underlying MASH-HCC development. We delve into MASH-HCC-associated genetic variations and somatic mutations, disease progression and research models, multiomics analysis, immunological and microenvironmental impacts, and discuss targeted/combined therapies to overcome immune evasion and the biomarkers to recognize treatment responders. By furthering our comprehension of the molecular mechanisms underlying MASH-HCC, our goal is to catalyze the advancement of more potent treatment strategies, ultimately leading to enhanced patient outcomes.
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Affiliation(s)
- Xiaobo Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Liang Zhang
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bingning Dong
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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Kurokawa S, Kobori T, Yoneda M, Ogawa Y, Honda Y, Kessoku T, Imajo K, Saito S, Nakajima A, Hotta K. Identification of differentially methylated regions associated with both liver fibrosis and hepatocellular carcinoma. BMC Gastroenterol 2024; 24:57. [PMID: 38302914 PMCID: PMC10832174 DOI: 10.1186/s12876-024-03149-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Liver fibrosis is a major risk factor for hepatocellular carcinoma (HCC). We have previously reported that differentially methylated regions (DMRs) are correlated with the fibrosis stages of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, the methylation levels of those DMRs in liver fibrosis and subsequent HCC were examined. METHODS The methylation levels of DMRs were investigated using alcoholic cirrhosis and HCC (GSE60753). The data of hepatitis C virus-infected cirrhosis and HCC (GSE60753), and two datasets (GSE56588 and GSE89852) were used for replication analyses. The transcriptional analyses were performed using GSE114564, GSE94660, and GSE142530. RESULTS Hypomethylated DMR and increased transcriptional level of zinc finger and BTB domain containing 38 (ZBTB38) were observed in HCC. Hypermethylated DMRs, and increased transcriptional levels of forkhead box K1 (FOXK1) and zinc finger CCCH-type containing 3 (ZC3H3) were observed in HCC. The methylation levels of DMR of kazrin, periplakin interacting protein (KAZN) and its expression levels were gradually decreased as cirrhosis progressed to HCC. CONCLUSIONS Changes in the methylation and transcriptional levels of ZBTB38, ZC3H3, FOXK1, and KAZN are important for the development of fibrosis and HCC; and are therefore potential therapeutic targets and diagnostic tools for cirrhosis and HCC.
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Affiliation(s)
- Suguru Kurokawa
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Takuro Kobori
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Masato Yoneda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuji Ogawa
- Department of Gastroenterology, National Hospital Organization Yokohama Medical Center, 3-60-2 Harajyuku, Totsuka, Yokohama, 245-8675, Japan
| | - Yasushi Honda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Takaomi Kessoku
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
- Department of Palliative Medicine, International University of Health and Welfare Narita Hospital, 852, Hatakeda, Narita, 286-8520, Japan
| | - Kento Imajo
- Department of Gastroenterology, Shin-yurigaoka General Hospital, 255 Furusawatsuko, Asao, Kawasaki, 2150-0026, Japan
| | - Satoru Saito
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Atsushi Nakajima
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kikuko Hotta
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan.
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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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Zhang Y, Wang JW, Su X, Li JE, Wei XF, Yang JR, Gao S, Fan YC, Wang K. F-box protein 43 promoter methylation as a novel biomarker for hepatitis B virus-associated hepatocellular carcinoma. Front Microbiol 2023; 14:1267844. [PMID: 38029156 PMCID: PMC10652413 DOI: 10.3389/fmicb.2023.1267844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) has a high prevalence and poor prognosis worldwide. Therefore, it is urgent to find effective and timely diagnostic markers. The objective of this study was to evaluate the diagnostic value of F-box protein 43 promoter methylation in peripheral blood mononuclear cells (PBMCs) for HCC. Method A total of 247 participants were included in this study, comprising individuals with 123 hepatitis B virus-associated HCC, 79 chronic hepatitis B, and 45 healthy controls. F-box protein 43 methylation and mRNA levels in PBMCs were detected by MethyLight and quantitative real-time PCR. Result F-box protein 43 promoter methylation levels were significantly lower in HCC PBMCs than the chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Relative mRNA expression levels of F-box protein 43 in HCC PBMCs were significantly higher than those in chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Receiver operating characteristic analysis of F-box protein 43 promoter methylation levels yielded an area under curve (AUC) of 0.793 with 76.42% sensitivity and 68.35% specificity when differentiating HCC from chronic hepatitis. These values for the F-box protein 43 promoter methylation level were superior to those of the alpha-fetoprotein serum (AFP) level (AUC: 0.780, sensitivity: 47.97%, and specificity: 96.20%), with increments in values for the combination of F-box protein 43 promoter methylation AFP levels (AUC: 0.888, sensitivity: 76.42%, and specificity: 86.08%). Conclusion Hypomethylation of the F-box protein 43 promoter in PBMCs is a promising biochemical marker for HBV-associated HCC.
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Affiliation(s)
- Ying Zhang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing-Wei Wang
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xing Su
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jin-E Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Fei Wei
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jie-Ru Yang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
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10
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Fu S, Debes JD, Boonstra A. DNA methylation markers in the detection of hepatocellular carcinoma. Eur J Cancer 2023; 191:112960. [PMID: 37473464 DOI: 10.1016/j.ejca.2023.112960] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and has a poor prognosis. Epigenetic modification has been shown to be deregulated during HCC development by dramatically impacting the differentiation, proliferation, and function of cells. One important epigenetic modification is DNA methylation during which methyl groups are added to cytosines without changing the DNA sequence itself. Studies found that methylated DNA markers can be specific for detection of HCC. On the basis of these findings, the utility of methylated DNA markers as novel biomarkers for early-stage HCC has been measured in blood, and indeed superior sensitivity and specificity have been found in several studies when compared to current surveillance methods. However, a variety of factors currently limit the immediate application of these exciting biomarkers. In this review, we provide a detailed rationalisation of the approach and basis for the use of methylation biomarkers for HCC detection and summarise recent studies on methylated DNA markers in HCC focusing on the importance of the aetiological cause of liver disease in the mechanisms leading to cancer.
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Affiliation(s)
- Siyu Fu
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands
| | - José D Debes
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - André Boonstra
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands.
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11
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Asari Y, Yamazaki J, Thandar O, Suzuki T, Aoshima K, Takeuchi K, Kinoshita R, Kim S, Hosoya K, Ishizaki T, Kagawa Y, Jelinek J, Yokoyama S, Sasaki N, Ohta H, Nakamura K, Takiguchi M. Diverse genome-wide DNA methylation alterations in canine hepatocellular tumours. Vet Med Sci 2023; 9:2006-2014. [PMID: 37483163 PMCID: PMC10508506 DOI: 10.1002/vms3.1204] [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: 07/24/2022] [Revised: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Canine hepatocellular tumours (HCTs) are common primary liver tumours. However, the exact mechanisms of tumourigenesis remain unclear. Although some genetic mutations have been reported, DNA methylation alterations in canine HCT have not been well studied. OBJECTIVES In this study, we aimed to analyse the DNA methylation status of canine HCT. METHODS Tissues from 33 hepatocellular carcinomas, 3 hepatocellular adenomas, 1 nodular hyperplasia, 21 non-tumour livers from the patients and normal livers from 5 healthy dogs were used. We analysed the DNA methylation levels of 72,367 cytosine-guanine dinucleotides (CpG sites) in all 63 samples. RESULTS AND CONCLUSIONS Although a large fraction of CpG sites that were highly methylated in the normal liver became hypomethylated in tumours from most patients, we also found some patients with less remarkable change or no change in DNA methylation. Hierarchical clustering analysis revealed that 32 of 37 tumour samples differed from normal livers, although the remaining 5 tumour livers fell into the same cluster as normal livers. In addition, the number of hypermethylated genes in tumour livers varied among tumour cases, suggesting various DNA methylation patterns in different tumour groups. However, patient and clinical parameters, such as age, were not associated with DNA methylation status. In conclusion, we found that HCTs undergo aberrant and diverse patterns of genome-wide DNA methylation compared with normal liver tissue, suggesting a complex epigenetic mechanism in canine HCT.
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Affiliation(s)
- Yu Asari
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Jumpei Yamazaki
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Oo Thandar
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Tamami Suzuki
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Keisuke Aoshima
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kyosuke Takeuchi
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Ryohei Kinoshita
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Sangho Kim
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Veterinary Surgery, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kenji Hosoya
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Veterinary Surgery, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Teita Ishizaki
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- North LabSapporoJapan
| | | | | | - Shoko Yokoyama
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Noboru Sasaki
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Hiroshi Ohta
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kensuke Nakamura
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Mitsuyoshi Takiguchi
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
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12
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Kouroumalis E, Tsomidis I, Voumvouraki A. Pathogenesis of Hepatocellular Carcinoma: The Interplay of Apoptosis and Autophagy. Biomedicines 2023; 11:1166. [PMID: 37189787 PMCID: PMC10135776 DOI: 10.3390/biomedicines11041166] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
The pathogenesis of hepatocellular carcinoma (HCC) is a multifactorial process that has not yet been fully investigated. Autophagy and apoptosis are two important cellular pathways that are critical for cell survival or death. The balance between apoptosis and autophagy regulates liver cell turnover and maintains intracellular homeostasis. However, the balance is often dysregulated in many cancers, including HCC. Autophagy and apoptosis pathways may be either independent or parallel or one may influence the other. Autophagy may either inhibit or promote apoptosis, thus regulating the fate of the liver cancer cells. In this review, a concise overview of the pathogenesis of HCC is presented, with emphasis on new developments, including the role of endoplasmic reticulum stress, the implication of microRNAs and the role of gut microbiota. The characteristics of HCC associated with a specific liver disease are also described and a brief description of autophagy and apoptosis is provided. The role of autophagy and apoptosis in the initiation, progress and metastatic potential is reviewed and the experimental evidence indicating an interplay between the two is extensively analyzed. The role of ferroptosis, a recently described specific pathway of regulated cell death, is presented. Finally, the potential therapeutic implications of autophagy and apoptosis in drug resistance are examined.
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Affiliation(s)
- Elias Kouroumalis
- Department of Gastroenterology, PAGNI University Hospital, University of Crete School of Medicine, 71500 Heraklion, Crete, Greece
- Laboratory of Gastroenterology and Hepatology, University of Crete Medical School, 71500 Heraklion, Crete, Greece
| | - Ioannis Tsomidis
- Laboratory of Gastroenterology and Hepatology, University of Crete Medical School, 71500 Heraklion, Crete, Greece
- 1st Department of Internal Medicine, AHEPA University Hospital, 54621 Thessaloniki, Central Macedonia, Greece
| | - Argyro Voumvouraki
- 1st Department of Internal Medicine, AHEPA University Hospital, 54621 Thessaloniki, Central Macedonia, Greece
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13
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Kim M, Delgado E, Ko S. DNA methylation in cell plasticity and malignant transformation in liver diseases. Pharmacol Ther 2023; 241:108334. [PMID: 36535346 PMCID: PMC9841769 DOI: 10.1016/j.pharmthera.2022.108334] [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: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The liver possesses extraordinary regenerative capacity mainly attributable to the ability of hepatocytes (HCs) and biliary epithelial cells (BECs) to self-replicate. This ability is left over from their bipotent parent cell, the hepatoblast, during development. When this innate regeneration is compromised due to the absence of proliferative parenchymal cells, such as during cirrhosis, HCs and BEC can transdifferentiate; thus, adding another layer of complexity to the process of liver repair. In addition, dysregulated lineage maintenance in these two cell populations has been shown to promote malignant growth in experimental conditions. Here, malignant transformation, driven in part by insufficient maintenance of lineage reprogramming, contributes to end-stage liver disease. Epigenetic changes are key drivers for cell fate decisions as well as transformation by finetuning overall transcription and gene expression. In this review, we address how altered DNA methylation contributes to the initiation and progression of hepatic cell fate conversion and cancer formation. We also discussed the diagnostic and therapeutic potential of targeting DNA methylation in liver cancer, its current limitations, and what future research is necessary to facilitate its contribution to clinical translation.
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Affiliation(s)
- Minwook Kim
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Evan Delgado
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Sungjin Ko
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America.
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14
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Hymel E, Fisher KW, Farazi PA. Differential methylation patterns in lean and obese non-alcoholic steatohepatitis-associated hepatocellular carcinoma. BMC Cancer 2022; 22:1276. [PMID: 36474183 PMCID: PMC9727966 DOI: 10.1186/s12885-022-10389-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease affects about 24% of the world's population and may progress to nonalcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma (HCC). While more common in those that are obese, NASH-HCC can develop in lean individuals. The mechanisms by which HCC develops and the role of epigenetic changes in the context of obesity and normal weight are not well understood. METHODS In this study, we used previously generated mouse models of lean and obese HCC using a choline deficient/high trans-fat/fructose/cholesterol diet and a choline supplemented/high trans-fat/fructose/cholesterol diet, respectively, to evaluate methylation differences in HCC progression in lean versus obese mice. Differentially methylated regions were determined using reduced representation bisulfite sequencing. RESULTS A larger number of differentially methylated regions (DMRs) were seen in NASH-HCC progression in the obese mice compared to the non-obese mice. No overlap existed in the DMRs with the largest methylation differences between the two models. In lean NASH-HCC, methylation differences were seen in genes involved with cancer progression and prognosis (including HCC), such as CHCHD2, FSCN1, and ZDHHC12, and lipid metabolism, including PNPLA6 and LDLRAP1. In obese NASH- HCC, methylation differences were seen in genes known to be associated with HCC, including RNF217, GJA8, PTPRE, PSAPL1, and LRRC8D. Genes involved in Wnt-signaling pathways were enriched in hypomethylated DMRs in the obese NASH-HCC. CONCLUSIONS These data suggest that differential methylation may play a role in hepatocarcinogenesis in lean versus obese NASH. Hypomethylation of Wnt signaling pathway-related genes in obese mice may drive progression of HCC, while progression of HCC in lean mice may be driven through other signaling pathways, including lipid metabolism.
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Affiliation(s)
- Emma Hymel
- grid.266813.80000 0001 0666 4105Department of Epidemiology, University of Nebraska Medical Center, 984395 Nebraska Medical Center, Omaha, NE 68198-4395 USA
| | - Kurt W. Fisher
- grid.266813.80000 0001 0666 4105Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Paraskevi A. Farazi
- grid.266813.80000 0001 0666 4105Department of Epidemiology, University of Nebraska Medical Center, 984395 Nebraska Medical Center, Omaha, NE 68198-4395 USA
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15
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Kuramoto J, Arai E, Fujimoto M, Tian Y, Yamada Y, Yotani T, Makiuchi S, Tsuda N, Ojima H, Fukai M, Seki Y, Kasama K, Funahashi N, Udagawa H, Nammo T, Yasuda K, Taketomi A, Kanto T, Kanai Y. Quantification of DNA methylation for carcinogenic risk estimation in patients with non-alcoholic steatohepatitis. Clin Epigenetics 2022; 14:168. [PMID: 36471401 PMCID: PMC9724255 DOI: 10.1186/s13148-022-01379-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In recent years, non-alcoholic steatohepatitis (NASH) has become the main cause of hepatocellular carcinoma (HCC). As a means of improving the treatment of NASH-related HCCs based on early detection, this study investigated the feasibility of carcinogenic risk estimation in patients with NASH. RESULTS Normal liver tissue (NLT), non-cancerous liver tissue showing histological findings compatible with non-alcoholic fatty liver from patients without HCC (NAFL-O), non-cancerous liver tissue showing NASH from patients without HCC (NASH-O), non-cancerous liver tissue showing non-alcoholic fatty liver from patients with HCC (NAFL-W), non-cancerous liver tissue showing NASH from patients with HCC (NASH-W) and NASH-related HCC were analyzed. An initial cohort of 171 tissue samples and a validation cohort of 55 tissue samples were used. Genome-wide DNA methylation screening using the Infinium HumanMethylation450 BeadChip and DNA methylation quantification using high-performance liquid chromatography (HPLC) with a newly developed anion-exchange column were performed. Based on the Infinium assay, 4050 CpG sites showed alterations of DNA methylation in NASH-W samples relative to NLT samples. Such alterations at the precancerous NASH stage were inherited by or strengthened in HCC samples. Receiver operating characteristic curve analysis identified 415 CpG sites discriminating NASH-W from NLT samples with area under the curve values of more than 0.95. Among them, we focused on 21 CpG sites showing more than 85% specificity, even for discrimination of NASH-W from NASH-O samples. The DNA methylation status of these 21 CpG sites was able to predict the coincidence of HCC independently from histopathological findings such as ballooning and fibrosis stage. The methylation status of 5 candidate marker CpG sites was assessed using a HPLC-based system, and for 3 of them sufficient sensitivity and specificity were successfully validated in the validation cohort. By combining these 3 CpG sites including the ZC3H3 gene, NAFL-W and NASH-W samples from which HCCs had already arisen were confirmed to show carcinogenic risk with 95% sensitivity in the validation cohort. CONCLUSIONS After a further prospective validation study using a larger cohort, carcinogenic risk estimation in liver biopsy specimens of patients with NASH may become clinically applicable using this HPLC-based system for quantification of DNA methylation.
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Affiliation(s)
- Junko Kuramoto
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Eri Arai
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Mao Fujimoto
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Ying Tian
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Yuriko Yamada
- grid.471315.50000 0004 1770 184XTsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd., Ryugasaki, 301-0852 Japan
| | - Takuya Yotani
- grid.471315.50000 0004 1770 184XTsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd., Ryugasaki, 301-0852 Japan
| | - Satomi Makiuchi
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Noboru Tsuda
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Hidenori Ojima
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Moto Fukai
- grid.39158.360000 0001 2173 7691Department of Gastroenterological Surgery I, Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638 Japan
| | - Yosuke Seki
- grid.505804.c0000 0004 1775 1986Weight Loss and Metabolic Surgery Center, Yotsuya Medical Cube, Tokyo, 102-0084 Japan
| | - Kazunori Kasama
- grid.505804.c0000 0004 1775 1986Weight Loss and Metabolic Surgery Center, Yotsuya Medical Cube, Tokyo, 102-0084 Japan
| | - Nobuaki Funahashi
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Haruhide Udagawa
- grid.411205.30000 0000 9340 2869Department of Biochemistry, Kyorin University School of Medicine, Tokyo, 181-8611 Japan
| | - Takao Nammo
- grid.136593.b0000 0004 0373 3971Department of Metabolic Medicine and Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University, Suita, 565-0871 Japan
| | - Kazuki Yasuda
- grid.411205.30000 0000 9340 2869Department of Diabetes, Endocrinology and Metabolism, Kyorin University School of Medicine, Tokyo, 181-8611 Japan ,grid.45203.300000 0004 0489 0290Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, 162-8655 Japan
| | - Akinobu Taketomi
- grid.39158.360000 0001 2173 7691Department of Gastroenterological Surgery I, Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638 Japan
| | - Tatsuya Kanto
- grid.45203.300000 0004 0489 0290The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, 272-8516 Japan
| | - Yae Kanai
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
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16
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DNA methylation status of the SPHK1 and LTB genes underlies the clinicopathological diversity of non-alcoholic steatohepatitis-related hepatocellular carcinomas. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04445-9. [DOI: 10.1007/s00432-022-04445-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022]
Abstract
Abstract
Purpose
This study was performed to identify the DNA methylation profiles underlying the clinicopathological diversity of non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinomas (HCCs).
Methods
Genome-wide DNA methylation analysis of 88 liver tissue samples was performed using the Infinium assay.
Results
Principal component analysis revealed that distinct DNA methylation profiles differing from such profiles in normal control liver tissue had already been established in non-cancerous liver tissue showing NASH, which is considered to be a precancerous condition. Hierarchical clustering separated 26 NASH-related HCCs into Cluster I (n = 8) and Cluster II (n = 18). Such epigenetic clustering was significantly correlated with histopathological diversity, i.e. poorer tumor differentiation, tumor steatosis and development of a scirrhous HCC component. Significant differences in DNA methylation levels between the two clusters were accumulated in molecular pathways participating in cell adhesion and cytoskeletal remodeling, as well as cell proliferation and apoptosis. Among tumor-related genes characterizing Clusters I and II, differences in the levels of DNA methylation and mRNA expression for the SPHK1, INHBA, LTB and PDE3B genes were correlated with poorer tumor differentiation. 5-Aza-2′-deoxycytidine treatment of HCC cells revealed epigenetic regulation of the SPHK1 and LTB genes. Knockdown experiments showed that SPHK1 promotes cell proliferation, represses apoptosis and enhances migration, whereas LTB enhances migration of HCC cells. DNA hypomethylation resulting in increased expression of SPHK1 and LTB in poorly differentiated HCCs may underlie the aggressive phenotype of such HCCs.
Conclusion
These data indicate that DNA methylation profiles may determine the clinicopathological heterogeneity of NASH-related HCCs via alterations of tumor-related gene expression.
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17
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Tian Z, Xu C, Yang P, Lin Z, Wu W, Zhang W, Ding J, Ding R, Zhang X, Dou K. Molecular pathogenesis: Connections between viral hepatitis-induced and non-alcoholic steatohepatitis-induced hepatocellular carcinoma. Front Immunol 2022; 13:984728. [PMID: 36189208 PMCID: PMC9520190 DOI: 10.3389/fimmu.2022.984728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Hepatocellular carcinoma(HCC) is the sixth most common cancer in the world and is usually caused by viral hepatitis (HBV and HCV), alcoholic, and non-alcoholic fatty liver disease(NAFLD). Viral hepatitis accounts for 80% of HCC cases worldwide. In addition, With the increasing incidence of metabolic diseases, NAFLD is now the most common liver disease and a major risk factor for HCC in most developed countries. This review mainly described the specificity and similarity between the pathogenesis of viral hepatitis(HBV and HCV)-induced HCC and NAFLD-induced HCC. In general, viral hepatitis promotes HCC development mainly through specific encoded viral proteins. HBV can also exert its tumor-promoting mechanism by integrating into the host chromosome, while HCV cannot. Viral hepatitis-related HCC and NASH-related HCC differ in terms of genetic factors, and epigenetic modifications (DNA methylation, histone modifications, and microRNA effects). In addition, both of them can lead to HCC progression through abnormal lipid metabolism, persistent inflammatory response, immune and intestinal microbiome dysregulation.
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Affiliation(s)
- Zelin Tian
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Chen Xu
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Peijun Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Zhibin Lin
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Wenlong Wu
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Wenjie Zhang
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- Chinese Education Ministry’s Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi’an, China
| | - Jian Ding
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Rui Ding
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Xuan Zhang
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Xuan Zhang, ; Kefeng Dou,
| | - Kefeng Dou
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Xuan Zhang, ; Kefeng Dou,
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18
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Gonçalves E, Gonçalves-Reis M, Pereira-Leal JB, Cardoso J. DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies. Sci Rep 2022; 12:11512. [PMID: 35798798 PMCID: PMC9262906 DOI: 10.1038/s41598-022-15058-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is amongst the cancers with highest mortality rates and is the most common malignancy of the liver. Early detection is vital to provide the best treatment possible and liquid biopsies combined with analysis of circulating tumour DNA methylation show great promise as a non-invasive approach for early cancer diagnosis and monitoring with low false negative rates. To identify reliable diagnostic biomarkers of early HCC, we performed a systematic analysis of multiple hepatocellular studies and datasets comprising > 1500 genome-wide DNA methylation arrays, to define a methylation signature predictive of HCC in both tissue and cell-free DNA liquid biopsy samples. Our machine learning pipeline identified differentially methylated regions in HCC, some associated with transcriptional repression of genes related with cancer progression, that benchmarked positively against independent methylation signatures. Combining our signature of 38 DNA methylation regions, we derived a HCC detection score which confirmed the utility of our approach by identifying in an independent dataset 96% of HCC tissue samples with a precision of 98%, and most importantly successfully separated cfDNA of tumour samples from healthy controls. Notably, our risk score could identify cell-free DNA samples from patients with other tumours, including colorectal cancer. Taken together, we propose a comprehensive HCC DNA methylation fingerprint and an associated risk score for detection of HCC from tissue and liquid biopsies.
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Affiliation(s)
- Emanuel Gonçalves
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal.,INESC-ID, 1000-029, Lisbon, Portugal
| | - Maria Gonçalves-Reis
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal
| | - José B Pereira-Leal
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal
| | - Joana Cardoso
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal.
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19
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Kurokawa S, Yoneda M, Ogawa Y, Honda Y, Kessoku T, Imajo K, Saito S, Nakajima A, Hotta K. Two differentially methylated region networks in nonalcoholic fatty liver disease, viral hepatitis, and hepatocellular carcinoma. BMC Gastroenterol 2022; 22:278. [PMID: 35655171 PMCID: PMC9164838 DOI: 10.1186/s12876-022-02360-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background We previously reported that two differentially methylated region (DMR) networks identified by DMR and co-methylation analyses are strongly correlated with the fibrosis stages of nonalcoholic fatty liver disease (NAFLD). In the current study, we examined these DMR networks in viral hepatitis and hepatocellular carcinoma (HCC). Methods We performed co-methylation analysis of DMRs using a normal dataset (GSE48325), two NAFLD datasets (JGAS000059 and GSE31803), and two HCC datasets (GSE89852 and GSE56588). The dataset GSE60753 was used for validation. Results One DMR network was clearly observed in viral hepatitis and two HCC populations. Methylation levels of genes in this network were higher in viral hepatitis and cirrhosis, and lower in HCC. Fatty acid binding protein 1 (FABP1), serum/glucocorticoid regulated kinase 2 (SGK2), and hepatocyte nuclear factor 4 α (HNF4A) were potential hub genes in this network. Increased methylation levels of the FABP1 gene may be correlated with reduced protection of hepatocytes from oxidative metabolites in NAFLD and viral hepatitis. The decreased methylation levels of SGK2 may facilitate the growth and proliferation of HCC cells. Decreased methylation levels of HNF4A in HCC may be associated with tumorigenesis. The other DMR network was observed in NAFLD, but not in viral hepatitis or HCC. This second network included genes involved in transcriptional regulation, cytoskeleton organization, and cellular proliferation, which are specifically related to fibrosis and/or tumorigenesis in NAFLD. Conclusions Our results suggest that one DMR network was associated with fibrosis and tumorigenesis in both NAFLD and viral hepatitis, while the other network was specifically associated with NAFLD progression. Furthermore, FABP1, SGK2, and HNF4A are potential candidate targets for the prevention and treatment of HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-022-02360-4.
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Yang L, Zou T, Chen Y, Zhao Y, Wu X, Li M, Du F, Chen Y, Xiao Z, Shen J. Hepatitis B virus X protein mediated epigenetic alterations in the pathogenesis of hepatocellular carcinoma. Hepatol Int 2022; 16:741-754. [PMID: 35648301 DOI: 10.1007/s12072-022-10351-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022]
Abstract
Chronic hepatitis B virus (HBV) infection is a worldwide health problem. Hepatitis B virus X protein (HBx), a pleiotropic regulatory protein encoded by HBV, is necessary for the transcription of HBV covalently closed circular DNA (cccDNA) minichromosomes, and affects the epigenetic regulation of host cells. The epigenetic reprogramming of HBx on host cell genome is strongly involved in HBV-related HCC carcinogenesis. Here, we review the latest findings of the epigenetic regulation induced by HBx protein in hepatocellular carcinoma (HCC), including DNA methylation, histone modification and non-coding RNA expression. The influence of HBx on the epigenetic regulation of cccDNA is also summarized. In addition, preliminary studies of targeted drugs for epigenetic changes induced by HBx are also discussed. The exploration of epigenetic markers as potential targets will help to develop new prevention and/or treatment methods for HBx-related HCC.
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Affiliation(s)
- Liqiong Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Tao Zou
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Yao Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
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21
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Sun D, Gan X, Liu L, Yang Y, Ding D, Li W, Jiang J, Ding W, Zhao L, Hou G, Yu J, Wang J, Yang F, Yuan S, Zhou W. DNA hypermethylation modification promotes the development of hepatocellular carcinoma by depressing the tumor suppressor gene ZNF334. Cell Death Dis 2022; 13:446. [PMID: 35534462 PMCID: PMC9085879 DOI: 10.1038/s41419-022-04895-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
Abstract
DNA methylation plays a pivotal role in the development and progression of tumors. However, studies focused on the dynamic changes of DNA methylation in the development of hepatocellular carcinoma (HCC) are rare. To systematically illustrate the dynamic DNA methylation alternation from premalignant to early-stage liver cancer with the same genetic background, this study enrolled 5 HBV-related patients preceded with liver cirrhosis, pathologically identified as early-stage HCC with dysplastic nodules. Liver fibrosis tissues, dysplastic nodules and early HCC tissues from these patients were used to measure DNA methylation. Here, we report significant differences in the DNA methylation spectrum among the three types of tissues. In the early stage of HCC, DNA hypermethylation of tumor suppressor genes is predominant. Additionally, DNA hypermethylation in the early stage of HCC changes the binding ability of transcription factor TP53 to the promoter of tumor suppressor gene ZNF334, and inhibits the expression of ZNF334 at the transcription level. Furthermore, through a series of in vivo and in vitro experiments, we have clarified the exacerbation effect of tumor suppressor gene ZNF334 deletion in the occurrence of HCC. Combined with clinical data, we found that the overall survival and relapse-free survival of patients with high ZNF334 expression are significantly longer. Thus, we partly elucidated a sequential alternation of DNA methylation modification during the occurrence of HCC, and clarified the biological function and regulatory mechanism of the tumor suppressor gene ZNF334, which is regulated by related DNA methylation sites. Our study provides a new target and clinical evidence for the early diagnosis and sheds light on the precise treatment of liver cancer.
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Affiliation(s)
- Dapeng Sun
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Xiaojie Gan
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Lei Liu
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Yuan Yang
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Dongyang Ding
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Wen Li
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Junyao Jiang
- grid.428926.30000 0004 1798 2725Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou, 510530 China
| | - Wenbin Ding
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Linghao Zhao
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Guojun Hou
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Jian Yu
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Jie Wang
- grid.428926.30000 0004 1798 2725Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou, 510530 China
| | - Fu Yang
- grid.73113.370000 0004 0369 1660The department of Medical Genetics, Naval Medical University, Shanghai, 200438 China
| | - Shengxian Yuan
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Weiping Zhou
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
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22
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Hagiwara S, Nishida N, Ueshima K, Minami Y, Komeda Y, Aoki T, Takita M, Morita M, Chishina H, Yoshida A, Ida H, Kudo M. Accumulation of Genetic and Epigenetic Alterations in the Background Liver and Emergence of Hepatocellular Carcinoma in Patients with Non-Alcoholic Fatty Liver Disease. Cells 2021; 10:cells10113257. [PMID: 34831479 PMCID: PMC8619206 DOI: 10.3390/cells10113257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/28/2022] Open
Abstract
The incidence of hepatocellular carcinoma (HCC) related to non-alcoholic fatty liver disease (NAFLD) is increasing worldwide. We analyzed 16 surgically resected HCC cases in which the background liver was pathologically diagnosed as NAFLD. Specimens with Brunt classification grade 3 or higher were assigned as the fibrotic progression group (n = 8), and those with grade 1 or lower were classified as the non-fibrosis progression group (n = 8). Comprehensive mutational and methylome analysis was performed in cancerous and noncancerous tissues. The target gene mutation analysis with deep sequencing revealed that CTNNB1 and TP53 mutation was observed in 37.5% and TERT promoter mutation was detected in 50% of cancerous samples. Furthermore, somatic mutations in non-cancerous samples were less frequent, but were observed regardless of the progression of fibrosis. Similarly, on cluster analysis of methylome data, status for methylation events involving non-cancerous liver was similar regardless of the progression of fibrosis. It was found that, even in cases of non-progressive fibrosis, accumulation of gene mutations and abnormal methylation within non-cancerous areas were observed. Patients with NAFLD require a rigorous liver cancer surveillance due to the high risk of HCC emergence based on the accumulation of genetic and epigenetic abnormalities, even when fibrosis is not advanced.
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23
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Dongiovanni P, Meroni M, Longo M, Fargion S, Fracanzani AL. Genetics, Immunity and Nutrition Boost the Switching from NASH to HCC. Biomedicines 2021; 9:1524. [PMID: 34829753 PMCID: PMC8614742 DOI: 10.3390/biomedicines9111524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the leading contributor to the global burden of chronic liver diseases. The phenotypic umbrella of NAFLD spans from simple and reversible steatosis to nonalcoholic steatohepatitis (NASH), which may worsen into cirrhosis and hepatocellular carcinoma (HCC). Notwithstanding, HCC may develop also in the absence of advanced fibrosis, causing a delayed time in diagnosis as a consequence of the lack of HCC screening in these patients. The precise event cascade that may precipitate NASH into HCC is intricate and it entails diverse triggers, encompassing exaggerated immune response, endoplasmic reticulum (ER) and oxidative stress, organelle derangement and DNA aberrancies. All these events may be accelerated by both genetic and environmental factors. On one side, common and rare inherited variations that affect hepatic lipid remodeling, immune microenvironment and cell survival may boost the switching from steatohepatitis to liver cancer, on the other, diet-induced dysbiosis as well as nutritional and behavioral habits may furtherly precipitate tumor onset. Therefore, dietary and lifestyle interventions aimed to restore patients' health contribute to counteract NASH progression towards HCC. Even more, the combination of therapeutic strategies with dietary advice may maximize benefits, with the pursuit to improve liver function and prolong survival.
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Affiliation(s)
- Paola Dongiovanni
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Pad. Granelli, 20122 Milan, Italy; (M.M.); (M.L.); (S.F.); (A.L.F.)
| | - Marica Meroni
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Pad. Granelli, 20122 Milan, Italy; (M.M.); (M.L.); (S.F.); (A.L.F.)
| | - Miriam Longo
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Pad. Granelli, 20122 Milan, Italy; (M.M.); (M.L.); (S.F.); (A.L.F.)
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20122 Milan, Italy
| | - Silvia Fargion
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Pad. Granelli, 20122 Milan, Italy; (M.M.); (M.L.); (S.F.); (A.L.F.)
| | - Anna Ludovica Fracanzani
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Pad. Granelli, 20122 Milan, Italy; (M.M.); (M.L.); (S.F.); (A.L.F.)
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy
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24
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Zhang D, Guo S, Schrodi SJ. Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties. Int J Mol Sci 2021; 22:9858. [PMID: 34576022 PMCID: PMC8466338 DOI: 10.3390/ijms22189858] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV), the well-studied oncovirus that contributes to the majority of hepatocellular carcinomas (HCC) worldwide, can cause a severe inflammatory microenvironment leading to genetic and epigenetic changes in hepatocyte clones. HBV replication contributes to the regulation of DNA methyltransferase gene expression, particularly by X protein (HBx), and subsequent methylation changes may lead to abnormal transcription activation of adjacent genes and genomic instability. Undoubtedly, the altered expression of these genes has been known to cause diverse aspects of infected hepatocytes, including apoptosis, proliferation, reactive oxygen species (ROS) accumulation, and immune responses. Additionally, pollutant-induced DNA methylation changes and aberrant methylation of imprinted genes in hepatocytes also complicate the process of tumorigenesis. Meanwhile, hepatocytes also contribute to epigenetic modification of the viral genome to affect HBV replication or viral protein production. Meanwhile, methylation levels of HBV integrants and surrounding host regions also play crucial roles in their ability to produce viral proteins in affected hepatocytes. Both host and viral changes can provide novel insights into tumorigenesis, individualized responses to therapeutic intervention, disease progress, and early diagnosis. As such, DNA methylation-mediated epigenetic silencing of cancer-related genes and viral replication is a compelling therapeutic goal to reduce morbidity and mortality from liver cancer caused by chronic HBV infection. In this review, we summarize the most recent research on aberrant DNA methylation associated with HBV infection, which is involved in HCC development, and provide an outlook on the future direction of the research.
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Affiliation(s)
- Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Steven J. Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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25
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Bai Y, Tong W, Xie F, Zhu L, Wu H, Shi R, Wang L, Yang L, Liu Z, Miao F, Zhao Q, Zhang Y. DNA methylation biomarkers for diagnosis of primary liver cancer and distinguishing hepatocellular carcinoma from intrahepatic cholangiocarcinoma. Aging (Albany NY) 2021; 13:17592-17606. [PMID: 34237708 PMCID: PMC8312421 DOI: 10.18632/aging.203249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are the two most common pathology subtypes of primary liver cancer (PLC). Identifying DNA methylation biomarkers for diagnosis of PLC and further distinguishing HCC from ICC plays a vital role in subsequent treatment options selection. To obtain potential diagnostic DNA methylation sites for PLC, differentially methylated CpG (DMC) sites were first screened by comparing the methylation data between normal liver samples and PLC samples (ICC samples and HCC samples). A random forest algorithm was then used to select specific DMC sites with top Gini value. To avoid overfitting, another cohort was taken as an external validation for evaluating the area under curves (AUCs) of different DMC sites combination. A similar model construction strategy was applied to distinguish HCC from ICC. In addition, we identified DNA Methylation-Driven Genes in HCC and ICC via MethylMix method and performed pathway analysis by utilizing MetaCore. Finally, we not only performed methylator phenotype based on independent prognostic sites but also analyzed the correlations between methylator phenotype and clinical factors in HCC and ICC, respectively. To diagnose PLC, we developed a model based on three PLC-specific methylation sites (cg24035245, cg21072795, and cg00261162), whose sensitivity and specificity achieved 98.8%,94.8% in training set and 97.3%,81% in validation set. Then, to further divide the PLC samples into HCC and ICC, we established another mode through three methylation sites (cg17769836, cg17591574, and cg07823562), HCC accuracy and ICC accuracy achieved 95.8%, 89.8% in the training set and 96.8%,85.4% in the validation set. In HCC, the enrichment pathways were mainly related to protein folding, oxidative stress, and glutathione metabolism. While in ICC, immune response, embryonic hepatocyte maturation were the top pathways. Both in HCC and ICC, methylator phenotype correlated well with overall survival time and clinical factors involved in tumor progression. In summary, our study provides the biomarkers based on methylation sites not only for the diagnosis of PLC but also for distinguishing HCC from ICC.
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Affiliation(s)
- Yi Bai
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Wen Tong
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Fucun Xie
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), Beijing, China
| | - Liuyang Zhu
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Hao Wu
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Rui Shi
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Lianjiang Wang
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Long Yang
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Zhisong Liu
- Department of Statistics, Tianjin University of Finance and Economics Pearl River College, Tianjin, China
| | - Fei Miao
- Department of Statistics, Tianjin University of Finance and Economics Pearl River College, Tianjin, China
| | - Qiang Zhao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, and College of Life Science, Nankai University, Tianjin, China
| | - Yaming Zhang
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
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Hamada K, Tian Y, Fujimoto M, Takahashi Y, Kohno T, Tsuta K, Watanabe SI, Yoshida T, Asamura H, Kanai Y, Arai E. DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of 'pan-negative'-type lung adenocarcinomas. Carcinogenesis 2021; 42:169-179. [PMID: 33152763 PMCID: PMC7905838 DOI: 10.1093/carcin/bgaa115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/12/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022] Open
Abstract
Although some previous studies have examined epigenomic alterations in lung adenocarcinomas, correlations between epigenomic events and genomic driver mutations have not been fully elucidated. Single-CpG resolution genome-wide DNA methylation analysis with the Infinium HumanMethylation27 BeadChip was performed using 162 paired samples of adjacent normal lung tissue (N) and the corresponding tumorous tissue (T) from patients with lung adenocarcinomas. Correlations between DNA methylation data on the one hand and clinicopathological parameters and genomic driver mutations, i.e. mutations of EGFR, KRAS, BRAF and HER2 and fusions involving ALK, RET and ROS1, were examined. DNA methylation levels in 12 629 probes from N samples were significantly correlated with recurrence-free survival. Principal component analysis revealed that distinct DNA methylation profiles at the precancerous N stage tended not to induce specific genomic driver aberrations. Most of the genes showing significant DNA methylation alterations during transition from N to T were shared by two or more driver aberration groups. After small interfering RNA knockdown of ZNF132, which showed DNA hypermethylation only in the pan-negative group and was correlated with vascular invasion, the proliferation, apoptosis and migration of cancer cell lines were examined. ZNF132 knockdown led to increased cell migration ability, rather than increased cell growth or reduced apoptosis. We concluded that DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of ‘pan-negative’ lung adenocarcinomas. In addition, DNA methylation alterations at the precancerous stage may determine tumor aggressiveness, and such alterations that accumulate after driver mutation may additionally modify clinicopathological features through alterations of gene expression.
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Affiliation(s)
- Kenichi Hamada
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology & Laboratory Medicine, Kansai Medical University, Osaka, Japan
| | - Shun-ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Hisao Asamura
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
- To whom correspondence should be addressed. Tel: +81 3 3353 1211; Fax: +81 3 3353 3290;
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27
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Yang M, Arai E, Takahashi Y, Totsuka H, Chiku S, Taniguchi H, Katai H, Sakamoto H, Yoshida T, Kanai Y. Cooperative participation of epigenomic and genomic alterations in the clinicopathological diversity of gastric adenocarcinomas: significance of cell adhesion and epithelial-mesenchymal transition-related signaling pathways. Carcinogenesis 2021; 41:1473-1484. [PMID: 32710740 PMCID: PMC7665242 DOI: 10.1093/carcin/bgaa079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/27/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
The present study was conducted to clarify the cooperative significance of epigenomic and genomic abnormalities during gastric carcinogenesis. Using 21 samples of normal control gastric mucosa (C), 109 samples of non-cancerous gastric mucosa (N) and 105 samples of cancerous tissue (T) from 109 patients with primary gastric adenocarcinomas, genome-wide DNA methylation analysis was performed using Infinium assay. Among these samples, 66 paired N and corresponding T samples were subjected to whole-exome and single nucleotide polymorphism array analyses. As had been shown in our previous study, 109 patients were clustered clinicopathologically into least aggressive Cluster A (n = 20), most aggressive Cluster B1 (n = 20) and Cluster B2 (n = 69). Most DNA methylation alterations in each cluster had already occurred even in N samples compared with C samples, and DNA methylation alterations at the precancerous N stage were inherited by the established cancers themselves. Recurrent single nucleotide variants and insertions/deletions resulting in functional disruption of the proteins encoded by the ABCA10, BNC2, CDH1, CTNNB1, SMAD4 and VAV2 genes were specific to Cluster B1, whereas those of the APC, EGFR, ERBB2, ERBB3, MLH1 and MUC6 genes were specific to Cluster A. MetaCore pathway analysis revealed that the epigenomically affected TWIST1 gene and genomically affected CDH1, CTNNB1, MMP9, TLN2, ROCK1 and SMAD4 genes were accumulated in signaling pathways related to cell adhesion, cytoskeleton remodeling and epithelial–mesenchymal transition in Cluster B1. These data indicate that epigenomic alterations at the precancerous stage are important in gastric carcinogenesis and that epigenomic and genomic alterations cooperatively underlie the aggressiveness of gastric adenocarcinomas.
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Affiliation(s)
- Menghan Yang
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yoriko Takahashi
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Hirohiko Totsuka
- Bioinformatics Group, Research and Development Center, Solution Division 4, Hitachi Government and Public Corporation System Engineering Ltd., Tokyo, Japan
| | - Suenori Chiku
- Information and Communication Research Division, Mizuho Information and Research Institute, Inc., Tokyo, Japan
| | - Hirokazu Taniguchi
- Department of Clinical Laboratories, JR Tokyo General Hospital, Tokyo, Japan
| | - Hitoshi Katai
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hiromi Sakamoto
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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Endo Y, Fujimoto M, Ito N, Takahashi Y, Kitago M, Gotoh M, Hiraoka N, Yoshida T, Kitagawa Y, Kanai Y, Arai E. Clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma: prediction of early recurrence based on genome-wide DNA methylation profiling. J Cancer Res Clin Oncol 2021; 147:1341-1354. [PMID: 33635431 PMCID: PMC8021514 DOI: 10.1007/s00432-021-03541-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
PURPOSE The present study was conducted to clarify the clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma (PDAC). METHODS Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip, and DNA methylation quantification was verified using pyrosequencing. We analyzed fresh-frozen tissues from an initial cohort (17 samples of normal control pancreatic tissue [C] from 17 patients without PDAC, and 34 samples of non-cancerous pancreatic tissue [N] and 82 samples of cancerous tissue [T] both obtained from 82 PDAC patients) and formalin-fixed paraffin-embedded T samples from 34 patients in a validation cohort. RESULTS The DNA methylation profiles of N samples tended to differ from those of C samples, and 91,907 probes showed significant differences in DNA methylation levels between C and T samples. Epigenetic clustering of T samples was significantly correlated with a larger tumor diameter and early recurrence (ER), defined as relapse within 6 months after surgery. Three marker CpG sites, applicable to formalin-fixed paraffin-embedded surgically resected materials regardless of their tumor cell content, were identified for prediction of ER. The sensitivity and specificity for detection of patients belonging to the ER group using a panel combining these three marker CpG sites, including a CpG site in the CDK14 gene, were 81.8% and 71.7% and 88.9% and 70.4% in the initial and validation cohorts, respectively. CONCLUSION These findings indicate that DNA methylation alterations may have a clinicopathological impact on PDAC. Application of our criteria will ultimately allow prediction of ER after surgery to improve the outcome of PDAC patients.
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Affiliation(s)
- Yutaka Endo
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Department of Surgery, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Nanako Ito
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd., Tokyo, 105-6215, Japan
| | - Minoru Kitago
- Department of Surgery, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Masahiro Gotoh
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Nobuyoshi Hiraoka
- Department of Pathology and Clinical Laboratory, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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Arechederra M, Recalde M, Gárate-Rascón M, Fernández-Barrena MG, Ávila MA, Berasain C. Epigenetic Biomarkers for the Diagnosis and Treatment of Liver Disease. Cancers (Basel) 2021; 13:1265. [PMID: 33809263 PMCID: PMC7998165 DOI: 10.3390/cancers13061265] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Research in the last decades has demonstrated the relevance of epigenetics in controlling gene expression to maintain cell homeostasis, and the important role played by epigenome alterations in disease development. Moreover, the reversibility of epigenetic marks can be harnessed as a therapeutic strategy, and epigenetic marks can be used as diagnosis biomarkers. Epigenetic alterations in DNA methylation, histone post-translational modifications (PTMs), and non-coding RNA (ncRNA) expression have been associated with the process of hepatocarcinogenesis. Here, we summarize epigenetic alterations involved in the pathogenesis of chronic liver disease (CLD), particularly focusing on DNA methylation. We also discuss their utility as epigenetic biomarkers in liquid biopsy for the diagnosis and prognosis of hepatocellular carcinoma (HCC). Finally, we discuss the potential of epigenetic therapeutic strategies for HCC treatment.
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Affiliation(s)
- María Arechederra
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Miriam Recalde
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
| | - María Gárate-Rascón
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Matías A. Ávila
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Carmen Berasain
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
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Zheng Y, Tang L, Chen G, Liu Z. Comprehensive Bioinformatics Analysis of Key Methyltransferases and Demethylases for Histone Lysines in Hepatocellular Carcinoma. Technol Cancer Res Treat 2020; 19:1533033820983284. [PMID: 33355042 PMCID: PMC7871294 DOI: 10.1177/1533033820983284] [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] [Indexed: 12/21/2022] Open
Abstract
Background & Aims: Methylation of lysines on histones, controlled by various methyltransferases and demethylases, is an important component of epigenetic modifications, and abnormal regulation of such enzymes serves as common events in hepatocellular carcinoma. We determined to identify important methyltransferases and demethylases that might regulate the development of hepatocellular carcinoma by bioinformatics. Methods: The Oncomine and UALCAN databases were used to retrieve mRNA expression levels of histone lysine methyltransferases and demethylases in hepatocellular carcinoma. Data analyses of genetic alterations, mainly mutations and copy number alterations, were performed on the cBioportal platform. Protein-protein interactions were established in the STRING database. Results: mRNA expression of 8 genes correlated with clinical staging and grading, whereas 4 genes indicated a role in the prognosis, all co-expressed with SEDB1 and WHSC1. Genetically, 12 genes showing an alteration rate higher than 5% were identified, and only 3 were indicative of prognosis. Copy number gains in ASH1L, SETDB1, and KDM5B might partially contribute to the upregulation of their mRNA expression. The close relationship of mutations in MLL2/MLL3 with driver gene mutations in hepatocellular carcinoma provided a rationale for further investigation. Conclusions: We identified 11 methyltransferases and demethylases for major histone lysines that might be promising research targets in the pathogenesis, development, and prediction of prognosis in hepatocellular carcinoma using bioinformatics.
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Affiliation(s)
- Yang Zheng
- Department of Oncology, First Hospital, 117971Jilin University, Jilin, People's Republic of China
| | - Lili Tang
- Institute of Military Cognition and Brain Sciences, 71040Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Guojiang Chen
- Institute of Pharmacology and Toxicology, 71040Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Ziling Liu
- Department of Oncology, First Hospital, 117971Jilin University, Jilin, People's Republic of China
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Iguchi E, Takai A, Takeda H, Kumagai K, Arasawa S, Eso Y, Shimizu T, Ueda Y, Marusawa H, Seno H. DNA methyltransferase 3B plays a protective role against hepatocarcinogenesis caused by chronic inflammation via maintaining mitochondrial homeostasis. Sci Rep 2020; 10:21268. [PMID: 33277576 PMCID: PMC7719166 DOI: 10.1038/s41598-020-78151-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/20/2020] [Indexed: 12/24/2022] Open
Abstract
Most hepatocellular carcinomas (HCCs) develop on the basis of chronic hepatitis, but the mechanism of epigenetic regulation in inflammatory hepatocarcinogenesis has yet to be elucidated. Among de novo DNA methyltransferases (DNMTs), DNMT3B has lately been reported to act specifically on actively transcribed genes, suggesting the possibility that it plays a role in the pathogenesis of cancer. We confirmed that DNMT3B isoforms lacking its catalytic domain were highly expressed in HCCs compared with non-tumorous liver tissue. To elucidate the role of DNMT3B in hepatocarcinogenesis, we generated a genetically engineered mouse model with hepatocyte-specific Dnmt3b deletion. The liver of the Dnmt3b-deficient mice exhibited an exacerbation of thioacetamide-induced hepatitis, progression of liver fibrosis and a higher incidence of HCC compared with the liver of the control mice. Whole-genome bisulfite sequencing verified a lower CG methylation level in the Dnmt3b-deficient liver, demonstrating differentially methylated regions throughout the genome. Transcriptome analysis revealed decreased expression of genes related to oxidative phosphorylation in the Dnmt3b-deficient liver. Moreover, primary hepatocytes isolated from the Dnmt3b-deficient mice showed reduced mitochondrial respiratory capacity, leading to the enhancement of oxidative stress in the liver tissue. Our findings suggest the protective role of DNMT3B against chronic inflammation and HCC development via maintaining mitochondrial homeostasis.
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Affiliation(s)
- Eriko Iguchi
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Haruhiko Takeda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Ken Kumagai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Soichi Arasawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yuji Eso
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yoshihide Ueda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kobe University, Hyogo, Japan
| | - Hiroyuki Marusawa
- Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Osaka, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
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Fernández-Barrena MG, Arechederra M, Colyn L, Berasain C, Avila MA. Epigenetics in hepatocellular carcinoma development and therapy: The tip of the iceberg. JHEP Rep 2020; 2:100167. [PMID: 33134907 PMCID: PMC7585149 DOI: 10.1016/j.jhepr.2020.100167] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a deadly tumour whose causative agents are generally well known, but whose pathogenesis remains poorly understood. Nevertheless, key genetic alterations are emerging from a heterogeneous molecular landscape, providing information on the tumorigenic process from initiation to progression. Among these molecular alterations, those that affect epigenetic processes are increasingly recognised as contributing to carcinogenesis from preneoplastic stages. The epigenetic machinery regulates gene expression through intertwined and partially characterised circuits involving chromatin remodelers, covalent DNA and histone modifications, and dedicated proteins reading these modifications. In this review, we summarise recent findings on HCC epigenetics, focusing mainly on changes in DNA and histone modifications and their carcinogenic implications. We also discuss the potential drugs that target epigenetic mechanisms for HCC treatment, either alone or in combination with current therapies, including immunotherapies.
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Key Words
- 5acC, 5-acetylcytosine
- 5fC, 5-formylcytosine
- 5hmC, 5-hydoxymethyl cytosine
- 5mC, 5-methylcytosine
- Acetyl-CoA, acetyl coenzyme A
- BER, base excision repair
- BRD, bromodomain
- CDA, cytidine deaminase
- CGI, CpG island
- CIMP, CGI methylator phenotype
- CTLA-4, cytotoxic T-lymphocyte-associated protein 4
- DNMT, DNA methyltransferase
- DNMTi, DNMT inhibitor
- Epigenetics
- FAD, flavin adenine dinucleotide
- HAT, histone acetyltransferases
- HCC, hepatocellular carcinoma
- HDAC, histone deacetylase
- HDACi, HDAC inhibitor
- HDM, histone demethylase
- HMT, histone methyltransferase
- Hepatocellular carcinoma
- KMT, lysine methyltransferase
- LSD/KDM, lysine specific demethylases
- NAFLD, non-alcoholic fatty liver disease
- NK, natural killer
- NPC, nasopharyngeal carcinoma
- PD-L1, programmed cell death ligand-1
- PD1, programmed cell death protein 1
- PHD, plant homeodomain
- PTM, post-translational modification
- SAM, S-adenosyl-L-methionine
- TDG, thymidine-DNA-glycosylase
- TERT, telomerase reverse transcriptase
- TET, ten-eleven translocation
- TME, tumour microenvironment
- TSG, tumour suppressor gene
- Therapy
- UHRF1, ubiquitin like with PHD and ring finger domains 1
- VEGF, vascular endothelial growth factor
- ncRNAs, non-coding RNAs
- α-KG, α-ketoglutarate
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Affiliation(s)
- Maite G. Fernández-Barrena
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María Arechederra
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Leticia Colyn
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Matias A. Avila
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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Wei T, Zhang XF, Bagante F, Ratti F, Marques HP, Soubrane O, Lam V, Poultsides GA, Popescu I, Alexandrescu S, Martel G, Workneh A, Guglielmi A, Hugh T, Aldrighetti L, Pawlik TM. Long-term outcomes after curative resection of HCV-positive versus non-hepatitis related hepatocellular carcinoma: an international multi-institutional analysis. HPB (Oxford) 2020; 22:1549-1556. [PMID: 31987739 DOI: 10.1016/j.hpb.2020.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/01/2020] [Accepted: 01/04/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND To define the chronological changes of long-term survival among patients with non-hepatitis-related hepatocellular carcinoma (Non-Hep-HCC) versus hepatitis C-related HCC (HCV-HCC) over the last two decades. METHODS Patients who underwent curative-intent resection for HCC between 2000 and 2017 were identified from an international multi-institutional database. Overall (OS) and recurrence-free survival (RFS) were analyzed and compared among Non-Hep-HCC versus HCV-HCC patients. Propensity score matching (PSM) was utilized to mitigate residual bias. RESULTS Among 617 patients, 196 (31.8%) patients had HCV-HCC, whereas 421 (68.2%) patients had Non-Hep-HCC. While patients with HCV-HCC had an improvement in OS over time (5-year OS, 2000-2009 55% vs. 2010-2017 67%, p = 0.034), OS among patients with Non-Hep-HCC remain unchanged (5-year OS, 2000-2009 53% vs. 2010-2017 52%, p = 0.905). In the matched cohort, patients with HCV-HCC had a worse OS versus patients with Non-Hep-HCC during 2000 and 2009 (5-year OS, 12% vs. 63%, p = 0.029), but significantly better OS from 2010 to 2017 than patients with Non-Hep-HCC (5-year OS, 86% vs. 73%, p = 0.035). The recurrence timing, patterns and re-treatments were comparable among Non-Hep-HCC and HCV-HCC patients. CONCLUSION While OS of patients with HCV-HCC improved over time, the long-term survival of patients with Non-Hep-HCC patients remained unchanged and was more unfavorable.
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Affiliation(s)
- Tao Wei
- Department of Hepatobiliary Surgery, Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xu-Feng Zhang
- Department of Hepatobiliary Surgery, Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner, Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Fabio Bagante
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner, Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA; Department of Surgery, University of Verona, Verona, Italy
| | | | - Hugo P Marques
- Department of Surgery, Curry Cabral Hospital, Lisbon, Portugal
| | - Olivier Soubrane
- Department of Hepatobiliopancreatic Surgery, APHP, Beaujon Hospital, Clichy, France
| | - Vincent Lam
- Department of Surgery, Westmead Hospital, Sydney, Australia
| | | | - Irinel Popescu
- Department of Surgery, Fundeni Clinical Institute, Bucharest, Romania
| | | | | | - Aklile Workneh
- Department of Surgery, University of Ottawa, Ottawa, Canada
| | | | - Tom Hugh
- Department of Surgery, The University of Sydney, School of Medicine, Sydney, Australia
| | | | - Timothy M Pawlik
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner, Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA.
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Hyun J, Jung Y. DNA Methylation in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2020; 21:ijms21218138. [PMID: 33143364 PMCID: PMC7662478 DOI: 10.3390/ijms21218138] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a widespread hepatic disorder in the United States and other Westernized countries. Nonalcoholic steatohepatitis (NASH), an advanced stage of NAFLD, can progress to end-stage liver disease, including cirrhosis and liver cancer. Poor understanding of mechanisms underlying NAFLD progression from simple steatosis to NASH has limited the development of effective therapies and biomarkers. An accumulating body of studies has suggested the importance of DNA methylation, which plays pivotal roles in NAFLD pathogenesis. DNA methylation signatures that can affect gene expression are influenced by environmental and lifestyle experiences such as diet, obesity, and physical activity and are reversible. Hence, DNA methylation signatures and modifiers in NAFLD may provide the basis for developing biomarkers indicating the onset and progression of NAFLD and therapeutics for NAFLD. Herein, we review an update on the recent findings in DNA methylation signatures and their roles in the pathogenesis of NAFLD and broaden people’s perspectives on potential DNA methylation-related treatments and biomarkers for NAFLD.
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Affiliation(s)
- Jeongeun Hyun
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea;
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
- Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Korea
- Cell and Matter Institute, Dankook University, Cheonan 31116, Korea
| | - Youngmi Jung
- Department of Integrated Biological Science, Pusan National University, Pusan 46241, Korea
- Department of Biological Sciences, Pusan National University, Pusan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2262
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Tian Y, Arai E, Makiuchi S, Tsuda N, Kuramoto J, Ohara K, Takahashi Y, Ito N, Ojima H, Hiraoka N, Gotoh M, Yoshida T, Kanai Y. Aberrant DNA methylation results in altered gene expression in non-alcoholic steatohepatitis-related hepatocellular carcinomas. J Cancer Res Clin Oncol 2020; 146:2461-2477. [PMID: 32685988 PMCID: PMC7467955 DOI: 10.1007/s00432-020-03298-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/20/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE The aim of this study was to investigate DNA methylation alterations in non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinomas (HCCs). METHODS Genome-wide DNA methylation analysis was performed using the Infinium Human Methylation 450 K BeadChip, and levels of mRNA expression were analyzed by quantitative reverse transcription-PCR. RESULTS Compared to 36 samples of normal control liver tissue (C), DNA methylation alterations were observed on 19,281 probes in 22 samples of cancerous tissue (T) obtained from patients showing histological features compatible with NASH in their non-cancerous liver tissue (N). Among those probes, 1396 were located within CpG islands or their shores and shelves, designed around the transcription start sites of 726 genes. In representative genes, such as DCAF4L2, CKLF, TRIM4, PRC1, UBE2C and TUBA1B, both DNA hypomethylation and mRNA overexpression were observed in T samples relative to C samples, and the levels of DNA methylation and mRNA expression were inversely correlated with each other. DNA hypomethylation occurred even in N samples at the precancerous NASH stage, and this was inherited by or further strengthened in T samples. DNA hypomethylation of DCAF4L2, CKLF and UBE2C was observed in both NASH-related and viral hepatitis-related HCCs, whereas that of TRIM4, PRC1 and TUBA1B occurred in a NASH-related HCC-specific manner. DNA hypomethylation and/or mRNA overexpression of these genes was frequently associated with the necroinflammatory grade of NASH and was correlated with poorer tumor differentiation. CONCLUSION DNA methylation alterations may occur under the necroinflammatory conditions characteristic of NASH and participate in NASH-related hepatocarcinogenesis through aberrant expression of tumor-related genes.
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Affiliation(s)
- Ying Tian
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Satomi Makiuchi
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Noboru Tsuda
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Junko Kuramoto
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kentaro Ohara
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd, Tokyo, 105-6215, Japan
| | - Nanako Ito
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hidenori Ojima
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Nobuyoshi Hiraoka
- Pathology Division, Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Masahiro Gotoh
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
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Marumo T, Hoshino J, Kawarazaki W, Nishimoto M, Ayuzawa N, Hirohama D, Yamanouchi M, Ubara Y, Okaneya T, Fujii T, Yuki K, Atsumi Y, Sato A, Arai E, Kanai Y, Shimosawa T, Fujita T. Methylation pattern of urinary DNA as a marker of kidney function decline in diabetes. BMJ Open Diabetes Res Care 2020; 8:e001501. [PMID: 32883689 PMCID: PMC7473659 DOI: 10.1136/bmjdrc-2020-001501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/07/2020] [Accepted: 07/25/2020] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Renal tubular injury contributes to the decline in kidney function in patients with diabetes. Cell type-specific DNA methylation patterns have been used to calculate proportions of particular cell types. In this study, we developed a method to detect renal tubular injury in patients with diabetes by detecting exfoliated tubular cells shed into the urine based on tubular cell-specific DNA methylation patterns. RESEARCH DESIGN AND METHODS We identified DNA methylation patterns specific for human renal proximal tubular cells through compartment-specific methylome analysis. We next determined the methylation levels of proximal tubule-specific loci in urine sediment of patients with diabetes and analyzed correlation with clinical variables. RESULTS We identified genomic loci in SMTNL2 and G6PC to be selectively unmethylated in human proximal tubular cells. The methylation levels of SMTNL2 and G6PC in urine sediment, deemed to reflect the proportion of exfoliated proximal tubular cells due to injury, correlated well with each other. Methylation levels of SMTNL2 in urine sediment significantly correlated with the annual decline in estimated glomerular filtration rate. Moreover, addition of urinary SMTNL2 methylation to a model containing known risk factors significantly improved discrimination of patients with diabetes with faster estimated glomerular filtration rate decline. CONCLUSIONS This study demonstrates that patients with diabetes with continual loss in kidney function may be stratified by a specific DNA methylation signature through epigenetic urinalysis and provides further evidence at the level of exfoliated cells in the urine that injury of proximal tubular cells may contribute to pathogenesis of diabetic kidney disease.
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Affiliation(s)
- Takeshi Marumo
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Department of Pharmacology, School of Medicine, International University of Health and Welfare, Narita, Chiba, Japan
| | - Junichi Hoshino
- Nephrology Center, Toranomon Hospital, Minato-ku, Tokyo, Japan
| | - Wakako Kawarazaki
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Mitsuhiro Nishimoto
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Nobuhiro Ayuzawa
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Daigoro Hirohama
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | | | - Yoshifumi Ubara
- Nephrology Center, Toranomon Hospital Kajigaya, Kawasaki, Kanagawa, Japan
| | | | - Takeshi Fujii
- Department of Pathology, Toranomon Hospital, Minato-ku, Tokyo, Japan
| | - Kazunari Yuki
- Diabetes Center, Eiju General Hospital, Taito-ku, Tokyo, Japan
| | | | - Atsuhisa Sato
- Department of Internal Medicine, School of Medicine, International University of Health and Welfare, Minata-ku, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Tatsuo Shimosawa
- Department of Clinical Laboratory, School of Medicine, International University of Health and Welfare, Minato-ku, Tokyo, Japan
| | - Toshiro Fujita
- Division of Clinical Epigenetics, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
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Zhang H, Dong P, Guo S, Tao C, Chen W, Zhao W, Wang J, Cheung R, Villanueva A, Fan J, Ding H, Schrodi SJ, Zhang D, Zeng C. Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing. BMC Med 2020; 18:200. [PMID: 32741373 PMCID: PMC7397586 DOI: 10.1186/s12916-020-01667-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) methylation has been demonstrated to be a promising approach for non-invasive cancer diagnosis. However, the high cost of whole genome bisulfite sequencing (WGBS) hinders the clinical implementation of a methylation-based cfDNA early detection biomarker. We proposed a novel strategy in low-pass WGBS (~ 5 million reads) to detect methylation changes in circulating cell-free DNA (cfDNA) from patients with liver diseases and hepatocellular carcinoma (HCC). METHODS The effective small sequencing depth were determined by 5 pilot cfDNA samples with relative high-depth WGBS. CfDNA of 51 patients with hepatitis, cirrhosis, and HCC were conducted using low-pass WGBS. The strategy was validated in an independent WGBS cohort of 32 healthy individuals and 26 early-stage HCC patients. Fifteen paired tumor tissue and buffy coat samples were used to characterize the methylation of hepatitis B virus (HBV) integration regions and genome distribution of cfDNA. RESULTS A significant enrichment of cfDNA in intergenic and repeat regions, especially in previously reported HBV integration sites were observed, as a feature of cfDNA and the bias of cfDNA release. Methylation profiles nearby HBV integration sites were a better indicator for hypomethylation of tumor genome comparing to Alu and LINE (long interspersed nuclear element) repeats, and were able to facilitate the cfDNA-based HCC prediction. Hypomethylation nearby HBV integration sites (5 kb flanking) was detected in HCC patients, but not in patients with hepatitis and cirrhosis (MethylHBV5k, median:0.61 vs 0.72, P = 0.0003). Methylation levels of integration sites certain candidate regions exhibited an area under the receiver operation curve (AUC) value > 0.85 to discriminate HCC from non-HCC samples. The validation cohort achieved the prediction performance with an AUC of 0.954. CONCLUSIONS Hypomethylation around viral integration sites aids low-pass cfDNA WGBS to serve as a non-invasive approach for early HCC detection, and inspire future efforts on tumor surveillance for oncovirus with integration activity.
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Affiliation(s)
- Haikun Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peiling Dong
- Department of Hepatology, Beijing You'an Hospital Affiliated with Capital Medical University, Beijing, 100069, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Chengcheng Tao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Wenmin Zhao
- Department of Hepatology, Beijing You'an Hospital Affiliated with Capital Medical University, Beijing, 100069, China
| | - Jiakang Wang
- Biology Department, Stonybrook University, Stonybrook, NY, USA
| | - Ramsey Cheung
- Department of Gastroenterology and Hepatology, VA Palo Alto Health Care System and Stanford University, Palo Alto, CA, USA
| | - Augusto Villanueva
- Liver Cancer Research Program, Division of Liver Diseases, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Fan
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huiguo Ding
- Department of Hepatology, Beijing You'an Hospital Affiliated with Capital Medical University, Beijing, 100069, China
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA. .,Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| | - Dake Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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Risk Factors Contributing to the Occurrence and Recurrence of Hepatocellular Carcinoma in Hepatitis C Virus Patients Treated with Direct-Acting Antivirals. Biomedicines 2020. [PMID: 32630610 DOI: 10.3390/biomedicines8060175.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Although hepatitis C virus (HCV) RNA may be eliminated from blood circulation by direct-acting antivirals (DAA) therapy as assessed by real-time polymerase chain reaction (PCR), HCV RNA can still be present in liver tissue, and this is known as occult HCV. There has been a lot of controversy surrounding the recurrence of hepatocellular carcinoma (HCC) after DAA treatment of hepatic cells infected with chronic HCV. One of the main risk factors that leads to de novo HCC is the chronicity of HCV in hepatic cells. There are many studies regarding the progression of HCV-infected hepatic cells to HCC. However, there is a lack of research on the different molecular mechanisms that lead to the progression of chronic HCV infection to HCC, as well as on the effect of HCV on the alteration of DNA ploidy, which eventually leads to a recurrence of HCC after DAA treatment. In this review article, we will address some risk factors that could lead to the development/recurrence of HCC after treatment of HCV with DAA therapy, such as the role of liver cirrhosis, the alteration of DNA ploidy, the reactivation of hepatitis B virus (HBV), the role of cytokines and the alteration of the immune system, concomitant non- alcoholic fatty liver disease (NAFLD), obesity, alcohol consumption and also occult HCV infection/co-infection. Clinicians should be cautious considering that full eradication of hepatocarcinogenesis cannot be successfully accomplished by anti-HCV treatment alone.
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Kishta S, Tabll A, Omanovic Kolaric T, Smolic R, Smolic M. Risk Factors Contributing to the Occurrence and Recurrence of Hepatocellular Carcinoma in Hepatitis C Virus Patients Treated with Direct-Acting Antivirals. Biomedicines 2020; 8:biomedicines8060175. [PMID: 32630610 PMCID: PMC7344618 DOI: 10.3390/biomedicines8060175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Although hepatitis C virus (HCV) RNA may be eliminated from blood circulation by direct-acting antivirals (DAA) therapy as assessed by real-time polymerase chain reaction (PCR), HCV RNA can still be present in liver tissue, and this is known as occult HCV. There has been a lot of controversy surrounding the recurrence of hepatocellular carcinoma (HCC) after DAA treatment of hepatic cells infected with chronic HCV. One of the main risk factors that leads to de novo HCC is the chronicity of HCV in hepatic cells. There are many studies regarding the progression of HCV-infected hepatic cells to HCC. However, there is a lack of research on the different molecular mechanisms that lead to the progression of chronic HCV infection to HCC, as well as on the effect of HCV on the alteration of DNA ploidy, which eventually leads to a recurrence of HCC after DAA treatment. In this review article, we will address some risk factors that could lead to the development/recurrence of HCC after treatment of HCV with DAA therapy, such as the role of liver cirrhosis, the alteration of DNA ploidy, the reactivation of hepatitis B virus (HBV), the role of cytokines and the alteration of the immune system, concomitant non- alcoholic fatty liver disease (NAFLD), obesity, alcohol consumption and also occult HCV infection/co-infection. Clinicians should be cautious considering that full eradication of hepatocarcinogenesis cannot be successfully accomplished by anti-HCV treatment alone.
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Affiliation(s)
- Sara Kishta
- Microbial Biotechnology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El Behooth Street, Dokki 12622, Egypt; (S.K.); (A.T.)
- Virology Division, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Institute, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Ashraf Tabll
- Microbial Biotechnology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El Behooth Street, Dokki 12622, Egypt; (S.K.); (A.T.)
- Department of immunology, Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo 11517, Egypt
| | - Tea Omanovic Kolaric
- Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, J. Huttlera 4, HR-31000 Osijek, Croatia; (T.O.K.); (R.S.)
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Crkvena 21, HR-3100 Osijek, Croatia
| | - Robert Smolic
- Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, J. Huttlera 4, HR-31000 Osijek, Croatia; (T.O.K.); (R.S.)
- Division of Gastroenterology/Hepatology, Department of Medicine, University Hospital Osijek, J. Huttlera 4, HR-3100 Osijek, Croatia
| | - Martina Smolic
- Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, J. Huttlera 4, HR-31000 Osijek, Croatia; (T.O.K.); (R.S.)
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Crkvena 21, HR-3100 Osijek, Croatia
- Correspondence: ; Tel.: +385-31-512-800
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Fujimoto M, Arai E, Tsumura K, Yotani T, Yamada Y, Takahashi Y, Maeshima AM, Fujimoto H, Yoshida T, Kanai Y. Establishment of diagnostic criteria for upper urinary tract urothelial carcinoma based on genome-wide DNA methylation analysis. Epigenetics 2020; 15:1289-1301. [PMID: 32498593 PMCID: PMC7678936 DOI: 10.1080/15592294.2020.1767374] [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] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to develop a less invasive and accurate diagnostic system for upper urinary tract urothelial carcinoma (UTUC) based on genome-wide DNA methylation profiling. Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip, and DNA methylation quantification was verified using pyrosequencing. We analysed 26 samples of normal control urothelial tissue (C), an initial cohort of 62 samples (31 samples of non-cancerous urothelium [N] from UTUC patients and 31 samples of the corresponding UTUCs), a validation cohort of 82 samples (41 N and 41 UTUC samples), and 14 samples of urinary bladder urothelial carcinoma (BUC). In the initial cohort, we identified 2,448 CpG sites showing significant differences in DNA methylation levels between both C and UTUC and N and UTUC, but not showing differences between C and N. Among these CpG sites, 10 were located within CpG islands or their shores and shelves included in genomic domains where DNA methylation levels are stably controlled, allowing discrimination of UTUC even from BUC. Receiver operating characteristic curve analysis for discrimination of UTUC from N in these 10 CpG and neighbouring sites (37 diagnostic panels in total) yielded area under the curve values of 0.959-1.000, with a sensitivity and specificity of 86.6-100% and 93.5-100%, respectively. The diagnostic impact was successfully confirmed in the validation cohort. Our criteria were useful for diagnosis of UTUC, regardless of its clinicopathological features. Application of our criteria to voided urine samples will ultimately allow non-invasive DNA methylation diagnosis of UTUC.
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Affiliation(s)
- Mao Fujimoto
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
| | - Koji Tsumura
- Department of Urology, Graduate School of Medicine, the University of Tokyo , Tokyo, Japan
| | - Takuya Yotani
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd ., Ryugasaki, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd ., Ryugasaki, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd ., Tokyo, Japan
| | - Akiko Miyagi Maeshima
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital , Tokyo, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital , Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute , Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
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Tsumura K, Arai E, Tian Y, Shibuya A, Nishihara H, Yotani T, Yamada Y, Takahashi Y, Maeshima AM, Fujimoto H, Nakagawa T, Kume H, Homma Y, Yoshida T, Kanai Y. Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis. Carcinogenesis 2020; 40:1308-1319. [PMID: 31241739 DOI: 10.1093/carcin/bgz112] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 05/25/2019] [Accepted: 06/22/2019] [Indexed: 02/02/2023] Open
Abstract
The aim of this study was to establish permutation for cancer risk estimation in the urothelium. Twenty-six samples of normal control urothelium obtained from patients without urothelial carcinomas (C), 47 samples of non-cancerous urothelium without noticeable morphological changes obtained from patients with urothelial carcinomas (N), and 46 samples of the corresponding cancerous tissue (T) in the learning cohort and 64 N samples in the validation cohort, i.e. 183 tissue samples in total, were analyzed. Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation 450K BeadChip, and DNA methylation levels were verified using pyrosequencing and MassARRAY. Amplicon sequencing was performed using the GeneRead DNAseq Targeted Panels V2. Although N samples rarely showed genetic mutations or copy number alterations, they showed DNA methylation alterations at 2502 CpG sites compared to C samples, and such alterations were inherited by or strengthened in T samples, indicating that DNA methylation alterations may participate in field cancerization in the urothelium. Receiver operating characteristic curve analysis confirmed the feasibility of cancer risk estimation to identify urothelium at the precancerous stage by DNA methylation quantification. Cancer risk estimation permutation was established using a combination of two marker CpG loci on the HOXC4, TENM3 and TLR1 genes (sensitivity and specificity 96-100%). Among them, the diagnostic impact of 10 patterns of permutation was successfully validated in the validation cohort (sensitivity and specificity 94-98%). These data suggest that cancer risk estimation using procedures such as urine tests during health checkups might become applicable for clinical use.
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Affiliation(s)
- Koji Tsumura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Ayako Shibuya
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Takuya Yotani
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd, Ryugasaki, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd, Ryugasaki, Japan
| | - Yoriko Takahashi
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Akiko Miyagi Maeshima
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Tohru Nakagawa
- Department of Urology, Teikyo University School of Medicine, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
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Differential hypermethylation of the VTRNA2-1 promoter in hepatocellular carcinoma as a prognostic factor: Tumor marker prognostic study. Int J Surg 2020; 79:282-289. [PMID: 32417463 DOI: 10.1016/j.ijsu.2020.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/16/2020] [Accepted: 05/04/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Vault RNA 2-1 (VTRNA2-1, also called nc886) is a 108-nucleotide noncoding transcript that is epigenetically controlled via 18 CpG dinucleotide modifications of its promoter, and can exert either tumor suppressor or oncogenic functions depending on cell types of cancers. In hepatocellular carcinoma (HCC), the role of VTRNA2-1 in prognosis of patients remains unexplored. Here, we analysed the methylation status of the VTRNA2-1 promoter and its correlation with clinical parameters in patients with HCC. PATIENTS AND METHODS A total of 92 patients with HCC were enrolled, genomic DNA of tumor versus normal tissues were extracted and bisulfite modified. VTRNA2-1 promoter regions chr5: 135416381 (cg06536614), 135416388, 135416394 (cg26328633), and 135416398 (cg25340688) were PCR amplified and pyrosequenced. The methylation status of VTRNA2-1 in patients was further analysed with other clinical parameters via univariate and multivariate analysis. RESULTS The differential hypermethylation status (tumor- normal) of the VTRNA2-1 promoter in HCC correlated well with the presence of large tumor size (p = 0.001), pathological vascular invasion (p = 0.036), tumor recurrence (p = 0.007) and more advanced tumor stage (stage III AJCC) in patients (p = 0.03). In addition, the methylation of the VTRNA2-1 promoter increased in stage III HCC tumor compared with stage I & II tumor (64.7% versus 36.0%, p = 0.030). Furthermore, the differential hypermethylation status of the VTRNA2-1 promoter was an independent factor for patient outcome after partial hepatectomy using multivariate Cox regression analysis (p = 0.011, HR = 2.305). Using another public dataset (GSE89852), we found that the differential hypermethylation of the VTRNA2-1 promoter was also significantly associated with tumor recurrence. CONCLUSIONS Patients had unfavourable outcomes when the VTRNA2-1 promoter was differentially hypermethylated in tumor tissues compared to its adjacent normal tissues. These findings suggest that such patients should receive intensive follow-up care or possible adjuvant therapy after liver resection.
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Lequoy M, Gigante E, Couty JP, Desbois-Mouthon C. Hepatocellular carcinoma in the context of non-alcoholic steatohepatitis (NASH): recent advances in the pathogenic mechanisms. Horm Mol Biol Clin Investig 2020; 41:/j/hmbci.ahead-of-print/hmbci-2019-0044/hmbci-2019-0044.xml. [PMID: 32112699 DOI: 10.1515/hmbci-2019-0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/16/2020] [Indexed: 12/15/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of liver cancer. HCC is particularly aggressive and is one of the leading causes of cancer mortality. In recent decades, the epidemiological landscape of HCC has undergone significant changes. While chronic viral hepatitis and excessive alcohol consumption have long been identified as the main risk factors for HCC, non-alcoholic steatohepatitis (NASH), paralleling the worldwide epidemic of obesity and type 2 diabetes, has become a growing cause of HCC in the US and Europe. Here, we review the recent advances in epidemiological, genetic, epigenetic and pathogenic mechanisms as well as experimental mouse models that have improved the understanding of NASH progression toward HCC. We also discuss the clinical management of patients with NASH-related HCC and possible therapeutic approaches.
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Affiliation(s)
- Marie Lequoy
- Service d'Hépato-Gastro-Entérologie, AP-HP, F-75012 Paris, France
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, F-75012 Paris, France
| | - Elia Gigante
- Service d'Hépato-Gastro-Entérologie, AP-HP, F-75012 Paris, France
| | - Jean-Pierre Couty
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Christèle Desbois-Mouthon
- Centre de Recherche des Cordeliers, INSERM UMR_S1138, 15 rue de l'école de médecine, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
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Kanda T, Goto T, Hirotsu Y, Masuzaki R, Moriyama M, Omata M. Molecular Mechanisms: Connections between Nonalcoholic Fatty Liver Disease, Steatohepatitis and Hepatocellular Carcinoma. Int J Mol Sci 2020; 21:ijms21041525. [PMID: 32102237 PMCID: PMC7073210 DOI: 10.3390/ijms21041525] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 02/22/2020] [Accepted: 02/22/2020] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), including nonalcoholic steatohepatitis (NASH), causes hepatic fibrosis, cirrhosis and hepatocellular carcinoma (HCC). The patatin-like phospholipase-3 (PNPLA3) I148M sequence variant is one of the strongest genetic determinants of NAFLD/NASH. PNPLA3 is an independent risk factor for HCC among patients with NASH. The obesity epidemic is closely associated with the rising prevalence and severity of NAFLD/NASH. Furthermore, metabolic syndrome exacerbates the course of NAFLD/NASH. These factors are able to induce apoptosis and activate immune and inflammatory pathways, resulting in the development of hepatic fibrosis and NASH, leading to progression toward HCC. Small intestinal bacterial overgrowth (SIBO), destruction of the intestinal mucosa barrier function and a high-fat diet all seem to exacerbate the development of hepatic fibrosis and NASH, leading to HCC in patients with NAFLD/NASH. Thus, the intestinal microbiota may play a role in the development of NAFLD/NASH. In this review, we describe recent advances in our knowledge of the molecular mechanisms contributing to the development of hepatic fibrosis and HCC in patients with NAFLD/NASH.
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Affiliation(s)
- Tatsuo Kanda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.K.); (R.M.); (M.M.)
| | - Taichiro Goto
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi 400-8506, Japan
- Correspondence: ; Tel.: +81-55-253-7111
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi 400-8506, Japan; (Y.H.); (M.O.)
| | - Ryota Masuzaki
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.K.); (R.M.); (M.M.)
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.K.); (R.M.); (M.M.)
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi 400-8506, Japan; (Y.H.); (M.O.)
- The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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Ibrahim J, Op de Beeck K, Fransen E, Peeters M, Van Camp G. The Gasdermin E Gene Has Potential as a Pan-Cancer Biomarker, While Discriminating between Different Tumor Types. Cancers (Basel) 2019; 11:cancers11111810. [PMID: 31752152 PMCID: PMC6896019 DOI: 10.3390/cancers11111810] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 01/08/2023] Open
Abstract
Due to the elevated rates of incidence and mortality of cancer, early and accurate detection is crucial for achieving optimal treatment. Molecular biomarkers remain important screening and detection tools, especially in light of novel blood-based assays. DNA methylation in cancer has been linked to tumorigenesis, but its value as a biomarker has not been fully explored. In this study, we have investigated the methylation patterns of the Gasdermin E gene across 14 different tumor types using The Cancer Genome Atlas (TCGA) methylation data (N = 6502). We were able to identify six CpG sites that could effectively distinguish tumors from normal samples in a pan-cancer setting (AUC = 0.86). This combination of pan-cancer biomarkers was validated in six independent datasets (AUC = 0.84–0.97). Moreover, we tested 74,613 different combinations of six CpG probes, where we identified tumor-specific signatures that could differentiate one tumor type versus all the others (AUC = 0.79–0.98). In all, methylation patterns exhibited great variation between cancer and normal tissues, but were also tumor specific. Our analyses highlight that a Gasdermin E methylation biomarker assay, not only has the potential for being a methylation-specific pan-cancer detection marker, but it also possesses the capacity to discriminate between different types of tumors.
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Affiliation(s)
- Joe Ibrahim
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
| | - Ken Op de Beeck
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
| | - Erik Fransen
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- StatUa Centre for Statistics, University of Antwerp, 2000 Antwerp, Belgium
| | - Marc Peeters
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
- Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Guy Van Camp
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
- Correspondence: ; Tel.: +32-3275-9762
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Inada Y, Mizukoshi E, Seike T, Tamai T, Iida N, Kitahara M, Yamashita T, Arai K, Terashima T, Fushimi K, Yamashita T, Honda M, Kaneko S. Characteristics of Immune Response to Tumor-Associated Antigens and Immune Cell Profile in Patients With Hepatocellular Carcinoma. Hepatology 2019; 69:653-665. [PMID: 30102778 DOI: 10.1002/hep.30212] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 08/03/2018] [Indexed: 01/01/2023]
Abstract
Host antitumor immune responses may be different between hepatocellular carcinoma (HCC) caused by metabolic disorders and HCC associated with hepatitis virus infection. In this study, we examined the immune response of tumor-associated antigen (TAA)-specific T cells and immune cell profile in patients with HCC separated by cause. Thirty-two patients with hepatitis B virus (HBV)-related HCC, 42 patients with hepatitis C virus-related HCC, and 18 patients with nonalcoholic steatohepatitis (NASH)-related HCC were analyzed. The frequencies of TAA-specific T cells, the expression levels of surface markers on each immune cell, and the expression of each TAA in HCC tissue were measured. The immune response to TAA and immune cell profile were markedly different among the three groups. The immune response to TAA in the NASH-related HCC group was weaker than the responses in the other two groups. In patients with NASH-related HCC, the frequencies of effector regulatory T cells (eTregs) and cluster of differentiation 8-positive (CD8+ ) T cells strongly expressing cytotoxic T-lymphocyte antigen (CTLA)-4 were high. The frequency of CD8+ T cells strongly expressing programmed cell death 1 was the highest in patients with HBV-related HCC. Among these immune cell profiles, the frequencies of C-X-C motif chemokine receptor 3+ eTregs and CTLA-4+ CD8+ T cells were inversely correlated with the strength of the TAA-specific T-cell immune response, and the restoration of TAA-specific T-cell responses by anti-CTLA-4 antibody was observed. Conclusion: The immune response to TAA were markedly different among the three groups, and a correlation with the immune cell profile was observed, suggesting that development of immunotherapy based on the etiology of HCC may lead to more effective treatment outcomes.
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Affiliation(s)
- Yuki Inada
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Eishiro Mizukoshi
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takuya Seike
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Toshikatsu Tamai
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Noriho Iida
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masaaki Kitahara
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Tatsuya Yamashita
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kuniaki Arai
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takeshi Terashima
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazumi Fushimi
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Taro Yamashita
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masao Honda
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
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Ding W, Chen G, Shi T. Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis. Epigenetics 2019; 14:67-80. [PMID: 30696380 DOI: 10.1080/15592294.2019.1568178] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC > 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC > 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC > 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (p-value < 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.
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Affiliation(s)
- Wubin Ding
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Geng Chen
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Tieliu Shi
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China.,b National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy , Guangxi Medical University , Nanning , China
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Cheng J, Wei D, Ji Y, Chen L, Yang L, Li G, Wu L, Hou T, Xie L, Ding G, Li H, Li Y. Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers. Genome Med 2018; 10:42. [PMID: 29848370 PMCID: PMC5977535 DOI: 10.1186/s13073-018-0548-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/08/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the one of the most common cancers and lethal diseases in the world. DNA methylation alteration is frequently observed in HCC and may play important roles in carcinogenesis and diagnosis. METHODS Using the TCGA HCC dataset, we classified HCC patients into different methylation subtypes, identified differentially methylated and expressed genes, and analyzed cis- and trans-regulation of DNA methylation and gene expression. To find potential diagnostic biomarkers for HCC, we screened HCC-specific CpGs by comparing the methylation profiles of 375 samples from HCC patients, 50 normal liver samples, 184 normal blood samples, and 3780 samples from patients with other cancers. A logistic regression model was constructed to distinguish HCC patients from normal controls. Model performance was evaluated using three independent datasets (including 327 HCC samples and 122 normal samples) and ten newly collected biopsies. RESULTS We identified a group of patients with a CpG island methylator phenotype (CIMP) and found that the overall survival of CIMP patients was poorer than that of non-CIMP patients. Our analyses showed that the cis-regulation of DNA methylation and gene expression was dominated by the negative correlation, while the trans-regulation was more complex. More importantly, we identified six HCC-specific hypermethylated sites as potential diagnostic biomarkers. The combination of six sites achieved ~ 92% sensitivity in predicting HCC, ~ 98% specificity in excluding normal livers, and ~ 98% specificity in excluding other cancers. Compared with previously published methylation markers, our markers are the only ones that can distinguish HCC from other cancers. CONCLUSIONS Overall, our study systematically describes the DNA methylation characteristics of HCC and provides promising biomarkers for the diagnosis of HCC.
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Affiliation(s)
- Jinming Cheng
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dongkai Wei
- Basepair biotechnology Co. LTD, Suzhou, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Liguang Yang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang Li
- Basepair biotechnology Co. LTD, Suzhou, China
| | - Leilei Wu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ting Hou
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Guohui Ding
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Hong Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Yixue Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. .,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. .,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China.
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Altered DNA methylation in liver and adipose tissues derived from individuals with obesity and type 2 diabetes. BMC MEDICAL GENETICS 2018; 19:28. [PMID: 29466957 PMCID: PMC5822594 DOI: 10.1186/s12881-018-0542-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/15/2018] [Indexed: 12/22/2022]
Abstract
Background Obesity is a well-recognized risk factor for insulin resistance and type 2 diabetes (T2D), although the precise mechanisms underlying the relationship remain unknown. In this study we identified alterations of DNA methylation influencing T2D pathogenesis, in subcutaneous and visceral adipose tissues, liver, and blood from individuals with obesity. Methods The study included individuals with obesity, with and without T2D. From these patients, we obtained samples of liver tissue (n = 16), visceral and subcutaneous adipose tissues (n = 30), and peripheral blood (n = 38). We analyzed DNA methylation using Illumina Infinium Human Methylation arrays, and gene expression profiles using HumanHT-12 Expression BeadChip Arrays. Results Analysis of DNA methylation profiles revealed several loci with differential methylation between individuals with and without T2D, in all tissues. Aberrant DNA methylation was mainly found in the liver and visceral adipose tissue. Gene ontology analysis of genes with altered DNA methylation revealed enriched terms related to glucose metabolism, lipid metabolism, cell cycle regulation, and response to wounding. An inverse correlation between altered methylation and gene expression in the four tissues was found in a subset of genes, which were related to insulin resistance, adipogenesis, fat storage, and inflammation. Conclusions Our present findings provide additional evidence that aberrant DNA methylation may be a relevant mechanism involved in T2D pathogenesis among individuals with obesity. Electronic supplementary material The online version of this article (10.1186/s12881-018-0542-8) contains supplementary material, which is available to authorized users.
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