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Wang M, Yan X, Dong Y, Li X, Gao B. From driver genes to gene families: A computational analysis of oncogenic mutations and ubiquitination anomalies in hepatocellular carcinoma. Comput Biol Chem 2024; 112:108119. [PMID: 38852361 DOI: 10.1016/j.compbiolchem.2024.108119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is a widespread primary liver cancer with a high fatality rate. Despite several genes with oncogenic effects in HCC have been identified, many remain undiscovered. In this study, we conducted a comprehensive computational analysis to explore the involvement of genes within the same families as known driver genes in HCC. Specifically, we expanded the concept beyond single-gene mutations to encompass gene families sharing homologous structures, integrating various omics data to comprehensively understand gene abnormalities in cancer. Our analysis identified 74 domains with an enriched mutation burden, 404 domain mutation hotspots, and 233 dysregulated driver genes. We observed that specific low-frequency somatic mutations may contribute to HCC occurrence, potentially overlooked by single-gene algorithms. Furthermore, we systematically analyzed how abnormalities in the ubiquitinated proteasome system (UPS) impact HCC, finding that abnormal genes in E3, E2, DUB families, and Degron genes often result in HCC by affecting the stability of oncogenic or tumor suppressor proteins. In conclusion, expanding the exploration of driver genes to include gene families with homologous structures emerges as a promising strategy for uncovering additional oncogenic alterations in HCC.
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Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China.
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
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Du Y, Xu Y, Guo X, Tan C, Zhu X, Liu G, Lyu X, Bei C. Methylation-regulated tumor suppressor gene PDE7B promotes HCC invasion and metastasis through the PI3K/AKT signaling pathway. BMC Cancer 2024; 24:624. [PMID: 38778317 PMCID: PMC11112795 DOI: 10.1186/s12885-024-12364-w] [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: 10/04/2023] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) has a high mortality rate, and the mechanisms underlying tumor development and progression remain unclear. However, inactivated tumor suppressor genes might play key roles. DNA methylation is a critical regulatory mechanism for inactivating tumor suppressor genes in HCC. Therefore, this study investigated methylation-related tumor suppressors in HCC to identify potential biomarkers and therapeutic targets. METHODS We assessed genome-wide DNA methylation in HCC using whole genome bisulfite sequencing (WGBS) and RNA sequencing, respectively, and identified the differential expression of methylation-related genes, and finally screened phosphodiesterase 7B (PDE7B) for the study. The correlation between PDE7B expression and clinical features was then assessed. We then analyzed the changes of PDE7B expression in HCC cells before and after DNA methyltransferase inhibitor treatment by MassArray nucleic acid mass spectrometry. Furthermore, HCC cell lines overexpressing PDE7B were constructed to investigate its effect on HCC cell function. Finally, GO and KEGG were applied for the enrichment analysis of PDE7B-related pathways, and their effects on the expression of pathway proteins and EMT-related factors in HCC cells were preliminarily explored. RESULTS HCC exhibited a genome-wide hypomethylation pattern. We screened 713 hypomethylated and 362 hypermethylated mCG regions in HCC and adjacent normal tissues. GO analysis showed that the main molecular functions of hypermethylation and hypomethylation were "DNA-binding transcriptional activator activity" and "structural component of ribosomes", respectively, whereas KEGG analysis showed that they were enriched in "bile secretion" and "Ras-associated protein-1 (Rap1) signaling pathway", respectively. PDE7B expression was significantly down-regulated in HCC tissues, and this low expression was negatively correlated with recurrence and prognosis of HCC. In addition, DNA methylation regulates PDE7B expression in HCC. On the contrary, overexpression of PDE7B inhibited tumor proliferation and metastasis in vitro. In addition, PDE7B-related genes were mainly enriched in the PI3K/ATK signaling pathway, and PDE7B overexpression inhibited the progression of PI3K/ATK signaling pathway-related proteins and EMT. CONCLUSION PDE7B expression in HCC may be regulated by promoter methylation. PDE7B can regulate the EMT process in HCC cells through the PI3K/AKT pathway, which in turn affects HCC metastasis and invasion.
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Affiliation(s)
- Yuanxiao Du
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Yuqiu Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Xuefeng Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Chao Tan
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiaonian Zhu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Guoyu Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Xiao Lyu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Chunhua Bei
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China.
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China.
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Wang M, Yan X, Dong Y, Li X, Gao B. Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment. PLoS Comput Biol 2024; 20:e1012113. [PMID: 38728362 DOI: 10.1371/journal.pcbi.1012113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
The heterogeneity of Hepatocellular Carcinoma (HCC) poses a barrier to effective treatment. Stratifying highly heterogeneous HCC into molecular subtypes with similar features is crucial for personalized anti-tumor therapies. Although driver genes play pivotal roles in cancer progression, their potential in HCC subtyping has been largely overlooked. This study aims to utilize driver genes to construct HCC subtype models and unravel their molecular mechanisms. Utilizing a novel computational framework, we expanded the initially identified 96 driver genes to 1192 based on mutational aspects and an additional 233 considering driver dysregulation. These genes were subsequently employed as stratification markers for further analyses. A novel multi-omics subtype classification algorithm was developed, leveraging mutation and expression data of the identified stratification genes. This algorithm successfully categorized HCC into two distinct subtypes, CLASS A and CLASS B, demonstrating significant differences in survival outcomes. Integrating multi-omics and single-cell data unveiled substantial distinctions between these subtypes regarding transcriptomics, mutations, copy number variations, and epigenomics. Moreover, our prognostic model exhibited excellent predictive performance in training and external validation cohorts. Finally, a 10-gene classification model for these subtypes identified TTK as a promising therapeutic target with robust classification capabilities. This comprehensive study provides a novel perspective on HCC stratification, offering crucial insights for a deeper understanding of its pathogenesis and the development of promising treatment strategies.
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Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
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Sgro A, Cursons J, Waryah C, Woodward EA, Foroutan M, Lyu R, Yeoh GCT, Leedman PJ, Blancafort P. Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma. Clin Epigenetics 2023; 15:73. [PMID: 37120619 PMCID: PMC10149030 DOI: 10.1186/s13148-023-01482-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/09/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Epigenetic silencing of tumor suppressor genes (TSGs) is a key feature of oncogenesis in hepatocellular carcinoma (HCC). Liver-targeted delivery of CRISPR-activation (CRISPRa) systems makes it possible to exploit chromatin plasticity, by reprogramming transcriptional dysregulation. RESULTS Using The Cancer Genome Atlas HCC data, we identify 12 putative TSGs with negative associations between promoter DNA methylation and transcript abundance, with limited genetic alterations. All HCC samples harbor at least one silenced TSG, suggesting that combining a specific panel of genomic targets could maximize efficacy, and potentially improve outcomes as a personalized treatment strategy for HCC patients. Unlike epigenetic modifying drugs lacking locus selectivity, CRISPRa systems enable potent and precise reactivation of at least 4 TSGs tailored to representative HCC lines. Concerted reactivation of HHIP, MT1M, PZP, and TTC36 in Hep3B cells inhibits multiple facets of HCC pathogenesis, such as cell viability, proliferation, and migration. CONCLUSIONS By combining multiple effector domains, we demonstrate the utility of a CRISPRa toolbox of epigenetic effectors and gRNAs for patient-specific treatment of aggressive HCC.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Joseph Cursons
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Charlene Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Eleanor A Woodward
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Momeneh Foroutan
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Melbourne, VIC, 3065, Australia
- Melbourne Integrative Genomics/School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Royal Parade, Parkville, VIC, 3010, Australia
| | - George C T Yeoh
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Molecular Sciences, University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Peter J Leedman
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, Perth, WA, 6009, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia.
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Vesting AJ, Jais A, Klemm P, Steuernagel L, Wienand P, Fog-Tonnesen M, Hvid H, Schumacher AL, Kukat C, Nolte H, Georgomanolis T, Altmüller J, Pasparakis M, Schmidt A, Krüger M, Supprian MS, Waisman A, Straub BK, Raschzok N, Bernier M, Birkenfeld AL, Hövelmeyer N, Brüning JC, Wunderlich FT. NIK/MAP3K14 in hepatocytes orchestrates NASH to hepatocellular carcinoma progression via JAK2/STAT5 inhibition. Mol Metab 2022; 66:101626. [PMID: 36356831 PMCID: PMC9676392 DOI: 10.1016/j.molmet.2022.101626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Nonalcoholic fatty liver disease (NAFLD) ranges from steatosis to nonalcoholic steatohepatitis (NASH), which often progresses to hepatocellular carcinoma (HCC) through a largely undefined mechanism. NASH and HCC depend on inflammatory signaling, whose master regulator is the NFκB transcription factor family, activated by canonical and non-canonical pathways. METHODS Here, we investigated non-canonical NFκB-inducing kinase (NIK/MAP3K14) in metabolic NASH, NASH to HCC transition, and DEN-induced HCC. To this end, we performed dietary and chemical interventions in mice that were analyzed via single nucleus sequencing, gene expression and histochemical methods. Ultimately, we verified our mouse results in human patient samples. RESULTS We revealed that hepatocyte-specific NIK deficiency (NIKLKO) ameliorated metabolic NASH complications and reduced hepatocarcinogenesis, independent of its role in the NFκB pathway. Instead, hepatic NIK attenuated hepatoprotective JAK2/STAT5 signaling that is a prerequisite for NASH and NASH to HCC progression in mice and humans. CONCLUSIONS Our data suggest NIK-mediated inhibitory JAK2 phosphorylation at serine 633 that might be amenable for future therapeutic interventions in patients.
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Affiliation(s)
- Anna Juliane Vesting
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany, Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany, Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Alexander Jais
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany, Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany, Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), 04103 Leipzig, Germany
| | - Paul Klemm
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany, Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany, Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Lukas Steuernagel
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany, Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany, Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Peter Wienand
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany, Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany, Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Morten Fog-Tonnesen
- Global Drug Discovery, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Maaloev, Denmark
| | - Henning Hvid
- Pathology & Imaging, Novo Nordisk A/S, Novo Nordisk Park 1, DK-2760 Maaloev, Denmark
| | - Anna-Lena Schumacher
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Christian Kukat
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | | | - Janine Altmüller
- University of Cologne, Cologne Center for Genomics, Cologne, Germany
| | - Manolis Pasparakis
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Andreas Schmidt
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Marcus Krüger
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Marc Schmidt Supprian
- Institute of Experimental Hematology, TranslaTUM, Klinikum rechts der Isar der Technischen Universität München, 81675 Munich, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) 69120 Heidelberg, Germany
| | - Ari Waisman
- Institute for Molecular Medicine, Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Beate Katharina Straub
- Institute of Pathology, University Medical Centre of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Nathanael Raschzok
- General, Visceral, and Transplantation Surgery, Charité-University School of Medicine, 13353 Berlin, Germany- Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Surgery, Experimental Surgery, Campus Charité Mitte | Campus Virchow-Klinikum, Berlin, Germany and Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Academy, Clinician Scientist Program, Berlin, Germany
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Andreas L Birkenfeld
- Internal Medicine IV, Clinic of Diabetology, Endocrinology, Nephrology, Internal medicine IV, University Hospital and Faculty of Medicine of the Eberhard Karls University Tübingen, 72016 Tübingen, Germany and Institute of Diabetes Research and Metabolic Diseases, Helmholtz Zentrum München an der Uniklinik Tübingen, Deutsches Zentrum für Diabetesforschung (DZD), Germany
| | - Nadine Hövelmeyer
- Institute for Molecular Medicine, Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Jens C Brüning
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany, Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany, Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - F Thomas Wunderlich
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany, Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany, Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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Autoantibody against Tumor-Associated Antigens as Diagnostic Biomarkers in Hispanic Patients with Hepatocellular Carcinoma. Cells 2022; 11:cells11203227. [PMID: 36291095 PMCID: PMC9600682 DOI: 10.3390/cells11203227] [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: 09/01/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Tumor-associated antigens (TAAs) have been investigated for many years as potential early diagnosis tools, especially for hepatocellular carcinoma (HCC). Nonetheless, very few studies have focused on the Hispanic HCC group that may be associated with distinct etiological risk factors. In the present study, we investigated novel anti-TAA autoantibodies as diagnostic biomarkers for Hispanic HCC patients. Methods: Novel TAA targets were identified by the serological proteome analysis (SERPA) and from differentially expressed HCC driver genes via bioinformatics. The autoantibody levels were validated by enzyme-linked immunosorbent assay (ELISA). Results: Among 19 potential TAA targets, 4 anti-TAA autoantibodies were investigated as potential diagnostic biomarkers with significantly high levels in Hispanic HCC sera, including DNA methyltransferase 3A (DNMT3A), p16, Hear shock protein 60 (Hsp60), and Heat shock protein A5 (HSPA5). The area under the ROC curve (AUC) value of the single autoantibodies varies from 0.7505 to 0.8885. After combining all 4 autoantibodies, the sensitivity of the autoantibody panel increased to 75% compared to the single one with the highest value of 45.8%. In a separate analysis of the Asian cohort, autoantibodies against HSPA5 and p16 showed significantly elevated levels in HCC compared to normal healthy controls, but not for DNMT3A or HSP60. Conclusion: Anti-DNMT3A, p16, HSPA5, and HSP60 autoantibodies have the potential to be diagnostic biomarkers for Hispanic HCC patients, of which DNMT3A and HSP60 might be exclusive for Hispanic HCC diagnosis.
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Diagnostic performance of RASSF1A and CDKN2A gene methylation versus α-fetoprotein in hepatocellular carcinoma. Clin Exp Hepatol 2022; 8:243-252. [PMID: 36685264 PMCID: PMC9850312 DOI: 10.5114/ceh.2022.119315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/07/2022] [Indexed: 01/25/2023] Open
Abstract
Aim of the study This study aimed to evaluate the methylation status of two genes in the peripheral blood as possible non-invasive biomarkers for hepatocellular carcinoma (HCC) development in Egyptian patients with hepatitis C virus (HCV)-related liver cirrhosis, compare them with α-fetoprotein (AFP), and assess their relationship with the clinicopathological characteristics of the tumor. Material and methods Thirty healthy volunteers, forty patients with HCC on top of HCV-associated liver cirrhosis, and forty patients with HCV-associated liver cirrhosis participated in this study. Using methylation-specific polymerase chain reaction (MSP), the methylation status of RASSF1A and CDKN2A was assessed. Results The tumor group was significantly more methylated in both genes than the cirrhosis and the control groups. The RASSF1A gene was highly methylated in advanced tumor characteristics. There was no association between AFP levels in the blood and the methylation state of both genes. The combined diagnostic performance of the methylation status of both genes in predicting HCC in cirrhotic patients was high but not to the degree of that of AFP. Conclusions Methylated RASSF1A and CDKN2A levels in the blood may be employed as a non-invasive biomarker for the detection of HCC, especially in high-risk individuals.
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Kanıt N, Yalçın P, Erbayraktar S, Ozer E. Methylation Profiling of Specific Genes in Ependymomas. Turk Patoloji Derg 2022; 38:213-218. [PMID: 34854470 PMCID: PMC10508420 DOI: 10.5146/tjpath.2021.01565] [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: 10/07/2021] [Accepted: 11/07/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Ependymomas are neuroepithelial tumors of the central nervous system with heterogeneous biology and clinical course. The aim of the present study is to investigate the relationship between the methylation status and clinicopathological parameters in ependymomas. MATERIAL AND METHOD DNA methylation status of CDKN2A, RASSF1A, KLF4 and ZIC2 genes were quantitatively analyzed with pyrosequencing in 44 ependymoma tumor tissues. The relationship of methylation profiles with tumor subtype, histological grade and patient age was statistically analyzed. RESULTS DNA methylation analyses for CDKN2A revealed no difference in methylation levels. Of the 31 included samples for optimal ZIC2 methylation analysis, 10 were hypermethylated (32.3%) and this change was significantly found in the adult spinal ependymomas (p=0.01). KLF4 hypermethylation was observed in 6 of the overall included 35 samples (17.1%); however, there was no statistically significant relation of the methylation status with tumor subtype, histological grade or age group. RASSF1A hypermethylation was observed in overall 40 included samples with varying methylation levels. Higher levels of hypermethylation were significantly related to the grade 3 histology (p=0.01) and spinal ependymomas (p=0.006). The pediatric cases with grade 3 ependymomas and ependymomas of adulthood showed significantly increased RASSF1A hypermethylation levels (p < 0.001 and p=0.001, respectively). CONCLUSION DNA methylation changes are likely to have biological importance in ependymomas. Both ZIC2 and RASSF1A methylation status may be useful parameters in the subclassification of these tumors.
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Affiliation(s)
- Naz Kanıt
- Department of Molecular Medicine, Dokuz Eylul University Institute of Health Sciences, Izmir, Turkey
| | - Pelin Yalçın
- Department of Medical Biology, Dokuz Eylul University Institute of Health Sciences, Izmir, Turkey
| | - Serhat Erbayraktar
- Department of Neurosurgery, Dokuz Eylul University School of Medicine, Izmir, Turkey
| | - Erdener Ozer
- Department of Pathology, Dokuz Eylul University School of Medicine, Izmir, Turkey
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Xu Y, Gu L, Wang J, Wang Z, Zhang P, Zhang X. Detection of Circulating Antibodies to p16 Protein-Derived Peptides in Hepatocellular Carcinoma. Lab Med 2021; 51:574-578. [PMID: 32195537 DOI: 10.1093/labmed/lmaa006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE This study aimed at confirming the alteration of circulating anti-p16 immunoglobulin G (IgG) levels in hepatocellular carcinoma (HCC). METHODS An in-house-developed enzyme-linked immunosorbent assay was used for determining plasma IgG antibodies against p16-derived antigens in 122 HCC patients and 134 healthy controls. RESULTS Plasma anti-p16 IgG levels were significantly higher in HCC patients than in the controls (Z = 3.51, P = 0.0004), with no difference between males and females. A trend of increasing plasma anti-p16 IgG levels was associated with increasing HCC stage, with group 3 patients having the highest anti-p16 IgG levels (Z = 3.38, P = 0.0008). Group 3 exhibited the best sensitivity (19.6%) and specificity (95%) for plasma anti-p16 IgG detection, with an area under the receiver operating characteristic curve of 0.659 (95% confidence interval, 0.564-0.754). CONCLUSION Circulating IgG antibody to p16 protein might be a useful biomarker for HCC prognosis assessment rather than for early malignancy diagnosis.
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Affiliation(s)
- Yangchun Xu
- Second Hospital of Jilin University, Changchun, China
| | - Litong Gu
- Department of Hepatobiliary & Pancreatic Surgery, Jilin Province People's Hospital, Changchun, China
| | - Jiaxin Wang
- Second Hospital of Jilin University, Changchun, China
| | - Zhenqi Wang
- School of Public Health, Jilin University, Changchun, China
| | - Ping Zhang
- Department of Hepatobiliary & Pancreatic Surgery, First Hospital of Jilin University, Changchun, China
| | - Xuan Zhang
- Second Hospital of Jilin University, Changchun, China
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Genistein inhibited the proliferation of kidney cancer cells via CDKN2a hypomethylation: role of abnormal apoptosis. Int Urol Nephrol 2020; 52:1049-1055. [PMID: 32026308 DOI: 10.1007/s11255-019-02372-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/23/2019] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Genistein is recognized as a potent anti-oxidant in soybean-enriched foods, which is a kind of phytoestrogen involved in anticancer activity in various cancers. OBJECTIVE The objective of this study was to investigate the molecular mechanism of CDKN2a hypomethylation involved in the anti-tumor effect of genistein on kidney cancer. METHODS The CDKN2a expression was measured using qRT-PCR. The level of CDKN2a methylation was detected using methylation-specific PCR. The apoptosis was detected via flow-cytometric analysis. The cell viability was detected using the 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. RESULTS Our results indicated that genistein induced cell apoptosis and inhibited the cell proliferation of kidney cancer cells. Moreover, genistein increased the expression of CDKN2a and decreased CDKN2a methylation. CONCLUSIONS Our results demonstrated that the anti-tumor effect of genistein might induce cell apoptosis and inhibit the proliferation of kidney cancer cells via regulating CDKN2a methylation.
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11
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Wang J, Xu Y, Wang Y, Zhang X, Zhang G. Further Study of Circulating Antibodies to P16, CD25 and FOXP3 in Hepatocellular Carcinoma. Onco Targets Ther 2019; 12:10487-10493. [PMID: 31819529 PMCID: PMC6897059 DOI: 10.2147/ott.s226404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Purpose It has been reported that circulating levels of IgG antibodies against p16, CD25 and FOXP3 proteins were significantly changed in patients with lung cancer, breast cancer and esophageal cancer. However, different peptide fragments appear to trigger different immune responses. This work aimed to analyze the alteration of plasma IgG for p16-derived peptide antigen called p16a, CD25-derived peptide antigen called CD25a and a FOXP3-derived antigen in hepatocellular carcinoma (HCC). Patients and methods An enzyme-linked immunosorbent assay (ELISA) was developed in-house to detect plasma IgG to p16a, CD25a and FOXP3 in 119 patients with HCC and 132 control subjects. Results Circulating levels of IgG antibodies for all three peptide antigens were significantly higher in HCC patients than control subjects (P<0.001 for all 3 assays); male patients mainly contributed to increase (P<0.01 for all 3 assays). Further analysis showed that plasma anti-p16a, anti-CD25a and anti-FOXP3 IgG levels were increased mainly in patients with intermediate and late-stage HCC (P<0.01 for both assays). Receiver operating characteristic (ROC) curve analysis showed that with a specificity of >95%, the area under the ROC curve (AUC) was 0.62 with 11.4% sensitivity for anti-p16a assay, 0.68 with 14.3% sensitivity for anti-CD25a IgG assay and 0.64 with 10.1% sensitivity for anti-FOXP3 assay. Of the three groups of HCC patients, group 3 (BCLC stage C+D) showed the best sensitivity for the detection of plasma anti-p16a and anti-FOXP3 IgG levels with an AUC of 0.66 and 0.65. Conclusion Circulating IgG antibody to p16a, CD25a and FOXP3 proteins may be a useful biomarker for assessment of HCC prognosis of this malignancy, especially in male patients with HCC.
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Affiliation(s)
- Jiaxin Wang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Yangchun Xu
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Yanjun Wang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Xuan Zhang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Guizhen Zhang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, People's Republic of China
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12
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Jin J, Xu H, Wu R, Gao N, Wu N, Li S, Niu J. Identification of key genes and pathways associated with different immune statuses of hepatitis B virus infection. J Cell Mol Med 2019; 23:7474-7489. [PMID: 31565863 PMCID: PMC6815815 DOI: 10.1111/jcmm.14616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/18/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023] Open
Abstract
We aimed to identify key genes and pathways associated with different immune statuses of hepatitis B virus (HBV) infection. The gene expression and DNA methylation profiles were analysed in different immune statuses of HBV infection. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified, followed by their functional and integrative analyses. The differential expression of IgG Fc receptors (FcγRs) in chronic HBV-infected patients and immune cells during different stages of HBV infection was investigated. Toll-like receptor (TLR) signalling pathway (including TLR6) and leucocyte transendothelial migration pathway (including integrin subunit beta 1) were enriched during acute infection. Key DEGs, such as FcγR Ib and FcγR Ia, and interferon-alpha inducible protein 27 showed correlation with alanine aminotransferase levels, and they were differentially expressed between acute and immune-tolerant phases and between immune-tolerant and immune-clearance phases. The integrative analysis of DNA methylation profile showed that lowly methylated and highly expressed genes, including cytotoxic T lymphocyte-associated protein 4 and mitogen-activated protein kinase 3 were enriched in T cell receptor signalling pathway during acute infection. Highly methylated and lowly expressed genes, such as Ras association domain family member 1 and cyclin-dependent kinase inhibitor 2A were identified in chronic infection. Furthermore, differentially expressed FcγR Ia, FcγR IIa and FcγR IIb, CD3- CD56+ CD16+ natural killer cells and CD14high CD16+ monocytes were identified between immune-tolerant and immune-clearance phases by experimental validation. The above genes and pathways may be used to distinguish different immune statuses of HBV infection.
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Affiliation(s)
- Jinglan Jin
- Department of Hepatology, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Hongqin Xu
- Department of Hepatology, The First Hospital of Jilin University, Jilin University, Changchun, China.,Jilin Province Key Laboratory of Infectious Diseases, Laboratory of Molecular Virology, Changchun, China
| | - Ruihong Wu
- Department of Hepatology, The First Hospital of Jilin University, Jilin University, Changchun, China.,Jilin Province Key Laboratory of Infectious Diseases, Laboratory of Molecular Virology, Changchun, China
| | - Na Gao
- Department of Infectious Disease, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Na Wu
- Lanshan People's Hospital, Linyi, China
| | - Shibo Li
- Department of Pediatrics, Genetics Laboratory, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, OK, USA
| | - Junqi Niu
- Department of Hepatology, The First Hospital of Jilin University, Jilin University, Changchun, China.,Jilin Province Key Laboratory of Infectious Diseases, Laboratory of Molecular Virology, Changchun, China
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13
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Rice A, Del Rio Hernandez A. The Mutational Landscape of Pancreatic and Liver Cancers, as Represented by Circulating Tumor DNA. Front Oncol 2019; 9:952. [PMID: 31608239 PMCID: PMC6769086 DOI: 10.3389/fonc.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
The mutational landscapes of pancreatic and liver cancers share many common genetic alterations which drive cancer progression. However, these mutations do not occur in all cases of these diseases, and this tumoral heterogeneity impedes diagnosis, prognosis, and therapeutic development. One minimally invasive method for the evaluation of tumor mutations is the analysis of circulating tumor DNA (ctDNA), released through apoptosis, necrosis, and active secretion by tumor cells into various body fluids. By observing mutations in those genes which promote transformation by controlling the cell cycle and oncogenic signaling pathways, a representation of the mutational profile of the tumor is revealed. The analysis of ctDNA is a promising technique for investigating these two gastrointestinal cancers, as many studies have reported on the accuracy of ctDNA assessment for diagnosis and prognosis using a variety of techniques.
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Affiliation(s)
- Alistair Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Armando Del Rio Hernandez
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
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14
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Huang B, Ji L, Liang B, Cao Q, Tu T, Ye X. A simple and low-cost screen printed electrode for hepatocellular carcinoma methylation detection. Analyst 2019; 144:3282-3288. [PMID: 30942220 DOI: 10.1039/c9an00191c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is a great demand for robust diagnostic and prognostic approaches for Hepatocellular Carcinoma (HCC). DNA methylation, a common epigenetic modification, has been found in many promoter regions of tumor suppressor genes. Hypermethylation of these gene promoters will repress the gene transcription and lead to the occurrence of cancers. The abnormal methyation level of the p16 gene promoter could be a promising marker for the detection of HCC. The adsorption affinities between different DNA bases and AuNPs are not the same. After bisulfite treatment and asymmetric PCR, methylation and unmethylation sequences can be changed into guanine-enriched and adenine-enriched sequences, respectively. A home-made gold nanoparticle modified screen printed carbon electrode (AuNP-SPCE) was employed to distinguish the adsorption affinities between guanine-enriched and adenine-enriched sequences, which could be used to analyze the level of DNA methylation. Several key experimental factors were investigated and optimized. The results had shown that the optimal AuNP electrodeposition time was 100 s and 15 min of adsorption could distinguish guanine-enriched and adenine-enriched sequences with a concentration of 100 nM at 25 °C. The detection limit of our AuNP-SPCE was 1.1 ng, and the assay had a good sensitivity of 10% methylation change and was able to distinguish only one methylated CpG site. What's more, the RSD over three assays with a disposable AuNP-SPCE was ≤7.2%. The assay was applied to real samples including cell lines and clinical tissues. Compared with normal hepatic cell lines and normal tissues, lower signals of HCC cell lines and cancer tissues were observed, respectively. It had shown a good discrimination of the abnormal methylation level of the p16 gene promoter.
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Affiliation(s)
- Bobo Huang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, PR China.
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15
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Zhou Y, Wang XB, Qiu XP, Shuai Zhang, Wang C, Zheng F. CDKN2A promoter methylation and hepatocellular carcinoma risk: A meta-analysis. Clin Res Hepatol Gastroenterol 2018; 42:529-541. [PMID: 30143452 DOI: 10.1016/j.clinre.2017.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/17/2017] [Accepted: 07/28/2017] [Indexed: 02/04/2023]
Abstract
AIM Lots of studies have explored cyclin-dependent kinase inhibitor 2A (CDKN2A) promoter methylation in hepatocellular carcinoma (HCC), but the established results were controversial. Hence, we conducted the meta-analysis to comprehensively investigate the association between CDKN2A promoter methylation and HCC risk. METHODS A comprehensive search was implemented through searching PubMed, Web of Science and Embase. Associations of CDKN2A promoter methylation with HCC risk, clinicopathological features, and CDKN2A expression were assessed by the pooled odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Subgroup analyses and meta-regression were served for exploring the potential sources of heterogeneity. RESULTS A total of 59 articles including 3067 cases and 2951 controls were incorporated in this meta-analysis. Overall, we observed a high CDKN2A promoter methylation rate (58.18%) in HCC and a significant association between the methylation and HCC risk (OR, 7.07; 95% CI, 5.67-8.80). Furthermore, CDKN2A promoter methylation was robustly associated with decreased mRNA (OR, 13.89; 95% CI, 5.44-35.45) and protein (OR, 48.19; 95% CI, 5.56-417.29). In addition, we found the methylation was related with HBV infection (OR, 3.31; 95% CI, 1.47-7.47), HCV infection (OR, 2.76; 95% CI, 1.80-4.23), cirrhosis status (OR, 1.57; 95% CI, 1.01-2.44) and older age (OR, 1.83; 95% CI, 1.14-2.94). CONCLUSIONS Our results indicated that CDKN2A promoter methylation was associated with an enhancive HCC risk and played a crucial role in the process of HCC with a potential value to being a triage marker for HCC.
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Affiliation(s)
- Ye Zhou
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Xue-Bin Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Xue-Ping Qiu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Shuai Zhang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Chen Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China.
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Abstract
CDKN2A is a tumor suppressor gene and is frequently inactivated in human cancers by hypermethylation of its promoter. However, the role and diagnostic value of CDKN2A methylation in esophageal cancer (EC) remains controversial. Therefore, we performed a meta-analysis, including data from 42 articles (2656 ECs, 612 precancerous lesions, and 2367 controls). A significant increase in the frequency of CDKN2A methylation was identified during EC carcinogenesis: cancer vs. controls, odds ratio (OR) = 12.60 (95 % CI, 8.90–17.85); cancer vs. precancerous lesions, OR = 2.89 (95% CI, 2.20–3.79); and precancerous lesions vs. controls, OR = 7.38, 95% (CI, 4.31–12.66). CDKN2A promoter methylation was associated with EC tumor grade (OR = 1.79; 95% CI, 1.20–2.67) and clinical stage (OR = 2.56; 95% CI, 1.33–4.92). Additionally, the sensitivity, specificity, and area under the summary receiver operating characteristic curve (AUC) for diagnosis of EC based on CDKN2A methylation were 0.52 (95% CI, 0.44–0.59), 0.96 (95% CI, 0.93–0.98), and 0.83 (95% CI, 0.79–0.86), respectively. AUCs for blood and tissue sample subgroups were 0.90 and 0.82, respectively. Our findings indicate that CDKN2A methylation has a vital role in EC tumorigenesis and could be a biomarker for early diagnosis of EC.
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17
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Wang G, Dong F, Xu Z, Sharma S, Hu X, Chen D, Zhang L, Zhang J, Dong Q. MicroRNA profile in HBV-induced infection and hepatocellular carcinoma. BMC Cancer 2017; 17:805. [PMID: 29191172 PMCID: PMC5709924 DOI: 10.1186/s12885-017-3816-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/22/2017] [Indexed: 02/07/2023] Open
Abstract
Background MicroRNAs (miRNAs) exhibit essential regulatory functions related to cell growth, apoptosis, development and differentiation. Dysregulated expression of miRNAs is associated with a wide variety of human diseases. As such miRNA signatures are valuable as biomarkers for disease and for making treatment decisions. Hepatitis B virus (HBV) is a major risk factor for hepatocellular carcinoma (HCC). Here we screened for miRNAs in chronic HBV associated HCC. Methods To determine the miRNAs in HCC occurrence associated with HBV infection, we analyzed global miRNA expression profiles in 12 pairs of HCC and adjacent matched non-HCC tissues from HBV-positive and HBV-negative patients using microarray analyses. The microarray result was validated by real-time PCR in 32 HBV-positive and 24 HBV-negative patient HCC samples. The potential candidate target genes of the miRNAs were predicted by miRWalk software. Genes simultaneously predicted as targets by two or more miRNAs were subjected to GO and KEGG pathway analysis. The miRNA regulatory network analysis was performed using the Ingenuity Pathway Analysis (IPA) software. Results Eight miRNAs (miR-223, miR-98, miR-15b, miR-199a-5p, miR-19b, miR-22, miR-451, and miR-101) were involved in HBV-unrelated HCC, 5 miRNAs (miR-98, miR-375, miR-335, miR-199a-5p, and miR-22) were involved in HBV infection, and 7 miRNAs (miR-150, miR-342-3p, miR-663, miR-20b, miR-92a-3p, miR-376c-3p and miR-92b) were specifically altered in HBV-related HCC. Gene Ontology and KEGG analyses predict that these HBV-related HCC miRNAs are involved in the regulation of: transcription, RNA polymerase II promoter, phosphorylation of proteins through MAPK signaling pathway, focal adhesion, and actin cytoskeleton. IPA analysis also suggest that these miRNAs act on AGO2, TP53, CCND1, and 11 other genes that significantly influence HCC occurrence and HBV infection. Conclusion Our data indicates that the unique 7 miRNAs expression signature could be involved in the development HBV- related HCC. Electronic supplementary material The online version of this article (10.1186/s12885-017-3816-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guanyu Wang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fulu Dong
- Institutes of Biology and Medical Sciences, Soochow University, Soochow, Jiangsu, China
| | - Zhiyao Xu
- Key Lab of Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sherven Sharma
- David Geffen School of Medicine at UCLA, and the Department of Veterans Affairs, Los Angeles, CA, USA
| | - Xiaotong Hu
- Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Dafang Chen
- Key Lab of Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lumin Zhang
- Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jinping Zhang
- Institutes of Biology and Medical Sciences, Soochow University, Soochow, Jiangsu, China.
| | - Qinghua Dong
- Key Lab of Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China. .,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Hangzhou, China.
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Allen JC, Nault JC, Zhu G, Khor AYK, Liu J, Lim TKH, Zucman-Rossi J, Chow PK. The transcriptomic G1-G6 signature of hepatocellular carcinoma in an Asian population: Association of G3 with microvascular invasion. Medicine (Baltimore) 2016; 95:e5263. [PMID: 27893662 PMCID: PMC5134855 DOI: 10.1097/md.0000000000005263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In this study, a transcriptomic group classification based on a European population is tested on a Singapore cohort. The results highlight the genotype/phenotype correlation in a Southeast Asian population. The G1-G6 transcriptomic classification derived from hepatocellular carcinoma (HCC) resected from European patients, robustly reflected group-specific clinical/pathological features. We investigated the application of this molecular classification in Southeast Asian HCC patients.Gene expression analysis was carried out on HCC surgically resected in Singapore patients who were grouped into G1-G6 transcriptomic categories according to expression of 16 predictor genes (illustrated in Supplementary Table 1, http://links.lww.com/MD/B413 and Supplementary Fig. 1, http://links.lww.com/MD/B413) using quantitative reverse transcription polymerase chain reaction (RT-PCR). Univariate and multivariate polytomous logistic regression was used to investigate association between clinical variables and pooled transcriptomic classes G12, G3, and G456.HCC from Singapore (n = 82) were distributed (%) into G1 (13.4), G2 (24.4), G3 (15.9), G4 (24.4), G5 (14.6), and G6 (7.3) subgroups. Compared to the European data, the Singapore samples were relatively enriched in G1-G3 versus G4-G6 tumors (53.7% vs 46.3%) reflecting the higher proportion of hepatitis B virus (HBV) patients in Singapore versus Europe samples (43% vs 30%). Pooled classes were defined as G12, G3, and G456. G12 was associated with higher alpha-fetoprotein (AFP) concentrations (OR = 1.69, 95% CI: 1.30-2.20; P < 0.0001) and G3 with microvascular invasion (OR = 4.91, 95% CI: 1.06-24.8; P = 0.047).The European and Singapore cohorts were generally similar relative to associations between transcriptomic groups and clinical features. This lends credence to the G1-G6 transcriptomic classifications being applicable regardless of the ethnic origin of HCC patients. The G3 group was associated with microvascular invasion and holds potential for investigation into the underlying mechanisms and selection for therapeutic clinical trials.
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Affiliation(s)
- John Carson Allen
- Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jean-Charles Nault
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, IUH
- Université Paris Descartes, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Guili Zhu
- Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Andrew Yu Keat Khor
- Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jin Liu
- Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, Singapore, Singapore
| | | | - Jessica Zucman-Rossi
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, IUH
- Université Paris Descartes, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Pierce K.H. Chow
- Department of Surgical Oncology, National Cancer Centre
- Office of Clinical Sciences, Duke-NUS Medical School, Singapore
- Department of HPB and Transplant Surgery, Singapore General Hospital, Singapore, Singapore
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Li J, Zhou C, Zhou H, Bao T, Gao T, Jiang X, Ye M. The association between methylated CDKN2A and cervical carcinogenesis, and its diagnostic value in cervical cancer: a meta-analysis. Ther Clin Risk Manag 2016; 12:1249-60. [PMID: 27574435 PMCID: PMC4994797 DOI: 10.2147/tcrm.s108094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Cervical cancer is the second deadliest gynecologic malignancy, characterized by apparently precancerous lesions and cervical intraepithelial neoplasia (CIN), and having a long course from the development of CIN to cervical cancer. Cyclin-dependent kinase inhibitor 2A (CDKN2A) is a well-documented tumor suppressor gene and is commonly methylated in cervical cancer. However, the relationship between methylated CDKN2A and carcinogenesis in cervical cancer is inconsistent, and the diagnostic accuracy of methylated CDKN2A is underinvestigated. In this study, we attempted to quantify the association between CDKN2A methylation and the carcinogenesis of cervical cancer, and its diagnostic power. Methods We systematically reviewed four electronic databases and identified 26 studies involving 1,490 cervical cancers, 1,291 CINs, and 964 controls. A pooled odds ratio (OR) with corresponding 95% confidence intervals (95% CI) was calculated to evaluate the association between methylated CDKN2A and the carcinogenesis of cervical cancer. Specificity, sensitivity, the area under the receiver operating characteristic curve, and the diagnostic odds ratio were computed to assess the effect of methylated CDKN2A in the diagnosis of cervical cancer. Results Our results indicated an upward trend in the methylation frequency of CDKN2A in the carcinogenesis of cervical cancer (cancer vs control: OR =23.67, 95% CI =15.54–36.06; cancer vs CIN: OR =2.53, 95% CI =1.79–3.5; CIN vs control: OR =9.68, 95% CI =5.82–16.02). The specificity, sensitivity, area under the receiver operating characteristic curve, and diagnostic odds ratio were 0.99 (95% CI: 0.97–0.99), 0.36 (95% CI: 0.28–0.45), 0.93 (95% CI: 0.91–0.95), and 43 (95% CI: 19–98), respectively. Conclusion Our findings indicate that abnormal CDKN2A methylation may be strongly correlated with the pathogenesis of cervical cancer. Our results also demonstrate that CDKN2A methylation might serve as an early detector of cervical cancer. These findings require further confirmation.
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Affiliation(s)
- Jinyun Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Ningbo University; Department of Medical Oncology, Affiliated Hospital, Ningbo University
| | - Chongchang Zhou
- Department of Biochemistry and Molecular Biology, School of Medicine, Ningbo University
| | - Haojie Zhou
- Department of Molecular Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, Zhejiang, People's Republic of China
| | - Tianlian Bao
- Department of Biochemistry and Molecular Biology, School of Medicine, Ningbo University
| | - Tengjiao Gao
- Department of Biochemistry and Molecular Biology, School of Medicine, Ningbo University
| | - Xiangling Jiang
- Department of Biochemistry and Molecular Biology, School of Medicine, Ningbo University
| | - Meng Ye
- Department of Biochemistry and Molecular Biology, School of Medicine, Ningbo University; Department of Medical Oncology, Affiliated Hospital, Ningbo University
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Hlady RA, Tiedemann RL, Puszyk W, Zendejas I, Roberts LR, Choi JH, Liu C, Robertson KD. Epigenetic signatures of alcohol abuse and hepatitis infection during human hepatocarcinogenesis. Oncotarget 2015; 5:9425-43. [PMID: 25294808 PMCID: PMC4253444 DOI: 10.18632/oncotarget.2444] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the second most common cause of cancer deaths worldwide. Deregulated DNA methylation landscapes are ubiquitous in human cancers. Interpretation of epigenetic aberrations in HCC is confounded by multiple etiologic drivers and underlying cirrhosis. We globally profiled the DNA methylome of 34 normal and 122 liver disease tissues arising in settings of hepatitis B (HBV) or C (HCV) viral infection, alcoholism (EtOH), and other causes to examine how these environmental agents impact DNA methylation in a manner that contributes to liver disease. Our results demonstrate that each 'exposure' leaves unique and overlapping signatures on the methylome. CpGs aberrantly methylated in cirrhosis-HCV and conserved in HCC were enriched for cancer driver genes, suggesting a pathogenic role for HCV-induced methylation changes. Additionally, large genomic regions displaying stepwise hypermethylation or hypomethylation during disease progression were identified. HCC-HCV/EtOH methylomes overlap highly with cryptogenic HCC, suggesting shared epigenetically deregulated pathways for hepatocarcinogenesis. Finally, overlapping methylation abnormalities between primary and cultured tumors unveil conserved epigenetic signatures in HCC. Taken together, this study reveals profound epigenome deregulation in HCC beginning during cirrhosis and influenced by common environmental agents. These results lay the foundation for defining epigenetic drivers and clinically useful methylation markers for HCC.
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Affiliation(s)
- Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Rochelle L Tiedemann
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA. Cancer Center, Georgia Regents University, Augusta, GA, USA
| | - William Puszyk
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Ivan Zendejas
- Department of Surgery, University of Florida, Gainesville, FL, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | | | - Chen Liu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
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Li H, Yang F, Gao B, Yu Z, Liu X, Xie F, Zhang J. Hepatitis B virus infection in hepatocellular carcinoma tissues upregulates expression of DNA methyltransferases. Int J Clin Exp Med 2015; 8:4175-4185. [PMID: 26064328 PMCID: PMC4443162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
PURPOSE Our previous research identified that Hepatitis B virus (HBV) infection results in the increased methylation of p16; however, the mechanism(s) of the methylation changes observed following HBV infection are yet to be deduced. DNA methylation is governed by the interaction of DNA methyltransferases (DNMT). To investigate the expression of DNMT in cancerous tissue, cirrhotic tissues and non-cancerous tissue, we examined the relationship between HBV infection and DNMT expression. METHODS We compared the mRNA expression levels of the four DNMTs in cancerous, cirrhotic and matched non-cancerous tissues of HCC with HBV infection by real-time PCR. RESULTS The results showed that compared with the level in the corresponding non-cancerous liver tissues, the levels of DNMT1, DNMT3A and DNMT3B were elevated in 54.5%, 68.2% and 38.6% of cancerous tissues and 31.4%, 40% and 25.8% of cirrhotic tissues, respectively. The average mRNA expression for DNMT2 in cancerous and cirrhotic tissues of HCC was not significantly different from that in the corresponding non-cancerous liver tissues. In HBV-associated tissue samples, both the average level and the elevated frequency of DNMT1, DNMT3A and DNMT3B mRNA expression were significantly higher than in non-HBV-associated cirrhotic and cancerous tissues; even in non-cancerous tissues, the mRNA levels of DNMT1 and DNMT3A in HBV-associated samples were significantly higher than in the non-HBV-associated samples. Correlations analysis demonstrated a significant association between HBV infection and the overexpression of DNMTs and p16 methylation. CONCLUSIONS The results of our current study suggest that persistent HBV infection can stimulate the overexpression of DNMTs, particularly DNMT1, DNMT3A and DNMT3B, which may result in the hyper-methylation/inactivation of p16, thus indirectly regulating the progression of hepatocellular carcinogenesis.
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Affiliation(s)
- Haiping Li
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of MedicineShiyan 442000, Hubei, China
| | - Fengmei Yang
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of MedicineShiyan 442000, Hubei, China
| | - Bo Gao
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of MedicineShiyan 442000, Hubei, China
| | - Zongtao Yu
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of MedicineShiyan 442000, Hubei, China
| | - Xiaobo Liu
- Department of Gestroenterology, Taihe Hospital, Hubei University of MedicineShiyan 442000, Hubei, China
| | - Fei Xie
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of MedicineShiyan 442000, Hubei, China
| | - Jicai Zhang
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of MedicineShiyan 442000, Hubei, China
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Zhang Y, Wang X, Han L, Zhou Y, Sun S. Green tea polyphenol EGCG reverse cisplatin resistance of A549/DDP cell line through candidate genes demethylation. Biomed Pharmacother 2015; 69:285-90. [DOI: 10.1016/j.biopha.2014.12.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 12/10/2014] [Indexed: 01/29/2023] Open
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He S, Zhang H, Liu H, Zhu H. LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. ACTA ACUST UNITED AC 2014; 31:178-86. [PMID: 25262155 DOI: 10.1093/bioinformatics/btu643] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION In mammalian cells, many genes are silenced by genome methylation. DNA methyltransferases and polycomb repressive complexes, which both lack sequence-specific DNA-binding motifs, are recruited by long non-coding RNA (lncRNA) to specific genomic sites to methylate DNA and chromatin. Increasing evidence indicates that many lncRNAs contain DNA-binding motifs that can bind to DNA by forming RNA:DNA triplexes. The identification of lncRNA DNA-binding motifs and binding sites is essential for deciphering lncRNA functions and correct and erroneous genome methylation; however, such identification is challenging because lncRNAs may contain thousands of nucleotides. No computational analysis of typical lncRNAs has been reported. Here, we report a computational method and program (LongTarget) to predict lncRNA DNA-binding motifs and binding sites. We used this program to analyse multiple antisense lncRNAs, including those that control well-known imprinting clusters, and obtained results agreeing with experimental observations and epigenetic marks. These results suggest that it is feasible to predict many lncRNA DNA-binding motifs and binding sites genome-wide. AVAILABILITY AND IMPLEMENTATION Website of LongTarget: lncrna.smu.edu.cn, or contact: hao.zhu@ymail.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sha He
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
| | - Hai Zhang
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
| | - Haihua Liu
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
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Genome-wide and gene-specific epigenomic platforms for hepatocellular carcinoma biomarker development trials. Gastroenterol Res Pract 2014; 2014:597164. [PMID: 24829571 PMCID: PMC4009191 DOI: 10.1155/2014/597164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 12/31/2022] Open
Abstract
The majority of the epigenomic reports in hepatocellular carcinoma have focused on identifying novel differentially methylated drivers or passengers of the oncogenic process. Few reports have considered the technologies in place for clinical translation of newly identified biomarkers. The aim of this study was to identify epigenomic technologies that need only a small number of samples to discriminate HCC from non-HCC tissue, a basic requirement for biomarker development trials. To assess that potential, we used quantitative Methylation Specific PCR, oligonucleotide tiling arrays, and Methylation BeadChip assays. Concurrent global DNA hypomethylation, gene-specific hypermethylation, and chromatin alterations were observed as a hallmark of HCC. A global loss of promoter methylation was observed in HCC with the Illumina BeadChip assays and the Nimblegen oligonucleotide arrays. HCC samples had lower median methylation peak scores and a reduced number of significant promoter-wide methylated probes. Promoter hypermethylation of RASSF1A, SSBP2, and B4GALT1 quantified by qMSP had a sensitivity ranging from 38% to 52%, a specificity of 100%, and an AUC from 0.58 to 0.75. A panel combining these genes with HCC risk factors had a sensitivity of 87%, a specificity of 100%, and an AUC of 0.91.
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25
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Molecular Signatures of Recurrent Hepatocellular Carcinoma Secondary to Hepatitis C Virus following Liver Transplantation. J Transplant 2013; 2013:878297. [PMID: 24377043 PMCID: PMC3860124 DOI: 10.1155/2013/878297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/25/2013] [Indexed: 01/12/2023] Open
Abstract
Chronic hepatitis C virus (HCV) induced hepatocellular carcinoma (HCC) is a primary indication for liver transplantation (LT). In western countries, the estimated rate of HCC recurrence following LT is between 15% and 20% and is a major cause of mortality. Currently, there is no standard method to treat patients who are at high risk for HCC recurrence. The aim of this study was to investigate the molecular signatures underlying HCC recurrence that may lead to future studies on gene regulation contributing to new therapeutic options. Two groups of patients were selected, one including patients with HCV who developed HCC recurrence (HCC-R) ≤3 years from LT and the second group including patients with HCV who did not have recurrent HCC (HCC-NR). Microarray analysis containing more than 29,000 known genes was performed on formalin-fixed-paraffin-embedded (FFPE) liver tissue from explanted livers. Gene expression profiling revealed 194 differentially regulated genes between the two groups. These genes belonged to cellular networks including cell cycle G1/S checkpoint regulators, RAN signaling, chronic myeloid leukemia signaling, molecular mechanisms of cancer, FXR/RXR activation and hepatic cholestasis. A subset of molecular signatures associated with HCC recurrence was found. The expression levels of these genes were validated by quantitative PCR analysis.
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Zhang JC, Gao B, Yu ZT, Liu XB, Lu J, Xie F, Luo HJ, Li HP. Promoter hypermethylation of p14 (ARF) , RB, and INK4 gene family in hepatocellular carcinoma with hepatitis B virus infection. Tumour Biol 2013; 35:2795-802. [PMID: 24254306 DOI: 10.1007/s13277-013-1372-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/28/2013] [Indexed: 01/14/2023] Open
Abstract
Both hepatitis B virus (HBV) and gene methylation play important roles in hepatocarcinogenesis. However, their association between HBV infection and gene methylation is not fully understood. Cell cycle control involving RB1 gene-related cell inhibitors is one of the main regulatory pathways were reported to be altered in hepatocellular carcinoma (HCC). The purpose of this research is to assess the methylation status of p14 (ARF) and INK4 gene family (p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and p18 (INK4C) ) in HCC with HBV infection and HCC without it, and discuss possible role of HBV-induced hypermethylation in the mechanism of hepatocarcinogenesis. Methylation status of RB, p14 (ARF) , and INK4 gene family in 64 case of HCC with HBV infection and 24 cases without it were detected by methylation-specific polymerase chain reaction, and HBV-DNA of the plasma were detected by quantitative real-time polymerase chain reaction. p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB hypermethylation were observed in 30 (34.1%), 50 (56.8%), 62 (70.5%), and 24(27.3%) of 88 hepatocellular carcinomas, respectively. Methylation frequencies of them between HCC with HBV infection and HCC without it were 43.8% versus 8.3 % (p14 (ARF) ), 68.9% versus 25% (p15 (INK4B) ), 90.6% versus 16.7% ( p16 (INK4A) ), and 28.1 % versus 25% (RB), respectively. In HBV-associated HCC, the numbers of methylated genes were also more than HCC without virus infection, more than two methylated genes were seen in 48 of 64 (75 %) cases; more than three methylated genes were found in 32 of 64 (50%); correspondently, no one case has more than two genes methylated. p18 (INK4C) methylation product was not found in cancerous or non-cancerous tissues of 88 HCC. HBV infection is associated with p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB gene methylation (P = 0.048, 0.035, 0.02); HBV-DNA replication is associated with p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB gene methylation (P = 0.048, 0.035, 0.02); high rate of p14 (ARF) , p15 (INK4B) , and p16 (INK4A) in HCC with HBV infection suggests that HBV-induced hypermethylation may be one of the mechanisms of HBV involved in hepatocellular carcinogenesis.
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Affiliation(s)
- Ji-Cai Zhang
- Department of Laboratory Medicine, Taihe Hospital Affiliated to Hubei University of Medicine, Shiyan, 442000, People's Republic of China
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Yuan D, Ye S, Pan Y, Bao Y, Chen H, Shao C. Long-term cadmium exposure leads to the enhancement of lymphocyte proliferation via down-regulating p16 by DNA hypermethylation. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 757:125-31. [DOI: 10.1016/j.mrgentox.2013.07.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 06/26/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022]
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28
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Ayub A, Ashfaq UA, Haque A. HBV induced HCC: major risk factors from genetic to molecular level. BIOMED RESEARCH INTERNATIONAL 2013; 2013:810461. [PMID: 23991421 PMCID: PMC3749539 DOI: 10.1155/2013/810461] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/09/2013] [Indexed: 12/15/2022]
Abstract
Hepatocellular carcinoma (HCC) is a deadly and emerging disease leading to death in Asian countries. High hepatitis B virus (HBV) load and chronic hepatitis B (CHB) infection increase the risk of developing HCC. HBV is a DNA virus that can integrate DNA into host genome thereby increase the yield of transactivator protein HBxAg that may deregulate many pathways involving in metabolism of cells. Several monogenic and polygenic risk factors are also involved in HCC development. This review summarizes the mechanism involved in HCC development and discusses some promising therapies to make HCC curative.
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Affiliation(s)
- Ambreen Ayub
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Asma Haque
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
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Matsuda Y, Wakai T, Kubota M, Takamura M, Yamagiwa S, Aoyagi Y, Osawa M, Fujimaki S, Sanpei A, Genda T, Ichida T. Clinical significance of cell cycle inhibitors in hepatocellular carcinoma. Med Mol Morphol 2013; 46:185-92. [PMID: 23640750 DOI: 10.1007/s00795-013-0047-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/03/2013] [Indexed: 01/11/2023]
Abstract
It is well accepted that cell cycle regulators are strongly implicated in the progression of cancer development. p16 and p27 are potent cyclin-dependent kinase (CDK) inhibitors involved in G1 phase progression, and are regarded as adverse prognostic biomarkers for various types of cancers. It has been reported that the main mechanism for p16 inactivation is aberrant DNA methylation, while p27 is exclusively inactivated by proteasome-mediated protein degradation. We have found that p27 is decreased in around half of hepatocellular carcinomas (HCCs), and in some cases p27 is inactivated by inappropriate interaction with cyclin D1/CDK4 complexes. In such cases, p16 is concomitantly inactivated through DNA methylation. Taking into consideration the complex interaction between p16 and p27, a comprehensive analysis including p16 and p27 would be useful for predicting the prognosis of HCC patients.
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Affiliation(s)
- Yasunobu Matsuda
- Department of Medical Technology, Niigata University Graduate School of Health Sciences, 2-746 Asahimachi-dori, Niigata, 951-8518, Japan,
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Tsuchiya T, Wang L, Yafune A, Kimura M, Ohishi T, Suzuki K, Mitsumori K, Shibutani M. Disruptive cell cycle regulation involving epigenetic downregulation of Cdkn2a (p16Ink4a) in early-stage liver tumor-promotion facilitating liver cell regeneration in rats. Toxicology 2012; 299:146-54. [DOI: 10.1016/j.tox.2012.05.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/14/2012] [Accepted: 05/21/2012] [Indexed: 11/29/2022]
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Zha TZ, Hu BS, Yu HF, Tan YF, Zhang Y, Zhang K. Overexpression of HOXA1 correlates with poor prognosis in patients with hepatocellular carcinoma. Tumour Biol 2012; 33:2125-34. [PMID: 22864671 DOI: 10.1007/s13277-012-0472-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 07/23/2012] [Indexed: 01/06/2023] Open
Abstract
HOXA1 overexpression is sufficient for malignant transformation of nontumorigenic epithelial cells. It is known that HOXA1, which was upregulated in squamous cell carcinomas, affects both cell growth and death. The forced expression of HOXA1 in human breast cancer cells results in increased cell growth activity. However, it has not been reported in hepatocellular carcinoma (HCC). In this study, we used immunohistochemistry to compare HOXA1 protein expression in HCC and normal liver tissues and further analyzed HOXA1 protein expression in 156 clinicopathologically characterized HCC cases. We stably knocked down the endogenous expression level of HOXA1 in HepG2 cells with specific shRNA-expressing lentiviral vector. Following the successful establishment of stable cells, we examined in vitro cell growth by the MTT assay, anchorage-independent growth through a soft agar colony formation assay and cell migration/invasion by transwell and Boyden chamber assay. In addition, we also investigated in vivo tumor growth by xenograft transplantation of HepG2 cells into nude mice. Our results showed that the protein expression level of HOXA1 was markedly higher in HCC tissues than that in normal liver tissue (P = 0.019). In addition, a high expression level of HOXA1 protein was positively correlated with the T classification (P < 0.001), the N classification (P < 0.001), distant metastasis (P = 0.004), and the clinical stage (P < 0.001) of HCC patients. Patients with higher HOXA1 expression showed a significantly shorter overall survival time compared with patients with low HOXA1 expression. Multivariate analysis suggested that HOXA1 expression might be an independent prognostic indicator (P < 0.001) for the survival of patients with HCC. HOXA1-specific shRNA (shHOXA1) successfully knocked down HOXA1 endogenous expression in HepG2 cells. Compared to the parental and control shRNA-transfected (shCtrl) HepG2 cells, the shHOXA1 cells exhibited significantly reduced in vitro cell growth, anchorage-independent growth, and cell migration and invasion (P < 0.05). In vivo, the xenograft transplants from shHOXA1 cells gave rise to much smaller tumors compared with those from shCtrl cells. Collectively, high HOXA1 expression is associated with poor overall survival in patients with HCC. The downregulation of HOXA1 inhibits growth, anchorage-independent growth, and migration and invasion of HepG2 cells.
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Affiliation(s)
- Tian-Zhou Zha
- Department of General Surgery, Yixing People's Hospital, No 75, Tongzhen Guan Rd, Yixing 214200, China
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Yasaei H, Gilham E, Pickles JC, Roberts TP, O'Donovan M, Newbold RF. Carcinogen-specific mutational and epigenetic alterations in INK4A, INK4B and p53 tumour-suppressor genes drive induced senescence bypass in normal diploid mammalian cells. Oncogene 2012; 32:171-9. [DOI: 10.1038/onc.2012.45] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Koturbash I, Melnyk S, James SJ, Beland FA, Pogribny IP. Role of epigenetic and miR-22 and miR-29b alterations in the downregulation of Mat1a and Mthfr genes in early preneoplastic livers in rats induced by 2-acetylaminofluorene. Mol Carcinog 2011; 52:318-27. [PMID: 22213190 DOI: 10.1002/mc.21861] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 11/22/2011] [Accepted: 11/30/2011] [Indexed: 12/15/2022]
Abstract
Carcinogenesis is a multistep sequential process of clonal expansion of initiated cells associated with the accumulation of multiple cancer-specific heritable phenotypes. The acquisition of these heritable cancer-specific alterations may be triggered by mutational and/or non-mutational changes in the genome that affect the regulation of gene expression. Currently, cancer-specific epigenetically mediated changes in gene expression are regarded as driving events in tumorigenesis. In the present study, we investigated the role of gene-specific expression changes in the mechanism of rat hepatocarcinogenesis induced by the complete hepatocarcinogen 2-acetylaminofluorene (2-AAF). The results of the present study demonstrate significant alterations in gene expression, especially of Mat1a and Mthfr genes, during early stages of rat 2-AAF-induced liver carcinogenesis. Both of these genes were downregulated in the livers of 2-AAF-treated male rats. Inhibition of Mat1a expression was associated with an increase in histone H3 lysine 27 trimethylation and a decrease in histone H3 lysine 18 acetylation at the gene promoter/first exon region. Additionally, we demonstrate for the first time a critical contribution of miR-22 and miR-29b microRNAs in the inhibition of Mat1a and Mthfr gene expression during 2-AAF-induced rat hepatocarcinogenesis. The downregulation of Mat1a and Mthfr genes was accompanied by marked functional alterations in one-carbon metabolism. The results of the present study suggest that downregulation of the Mat1a and Mthfr genes may be one of the main driver events that promote liver carcinogenesis by causing a profound accumulation of subsequent epigenetic abnormalities during progression of the carcinogenic process.
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Affiliation(s)
- Igor Koturbash
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
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Demokan S, Chuang A, Suoğlu Y, Ulusan M, Yalnız Z, Califano JA, Dalay N. Promoter methylation and loss of p16(INK4a) gene expression in head and neck cancer. Head Neck 2011; 34:1470-5. [PMID: 22106032 DOI: 10.1002/hed.21949] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/25/2011] [Accepted: 09/05/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. In this study we aimed to evaluate aberrant p16(INK4a) gene promoter methylation in patients with head and neck cancer. METHODS Methylation of the gene was investigated by bisulfite modification/methylation-specific polymerase chain reaction and gene expression levels were analyzed by quantitative reverse transcription-polymerase chain reaction in tumors and matched normal tissue samples from Turkish patients with head and neck cancer. RESULTS The promoter region of the p16(INK4a) gene was methylated in 67.5% and 28.6% of the primary tumors and the corresponding normal tissue, respectively. This difference was highly significant. In concordance, p16(INK4a) gene expression was downregulated in 67.5% of the tumor samples. Methylation and the absence of expression in the tumors were observed in 48% of the patients. CONCLUSIONS Our data indicate that methylation of the p16(INK4a) gene is a frequent event in primary head and neck cancer and that it plays a major role in the silencing of p16(INK4a) gene expression during tumor development.
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Affiliation(s)
- Semra Demokan
- Department of Basic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkey
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Wang T, Chen M, Liu L, Cheng H, Yan YE, Feng YH, Wang H. Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production. Toxicol Appl Pharmacol 2011; 257:328-37. [PMID: 21971485 DOI: 10.1016/j.taap.2011.09.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/15/2011] [Accepted: 09/16/2011] [Indexed: 12/18/2022]
Abstract
Steroidogenic acute regulatory protein (StAR) mediates the rate-limiting step in the synthesis of steroid hormones, essential to fetal development. We have reported that the StAR expression in fetal adrenal is inhibited in a rat model of nicotine-induced intrauterine growth retardation (IUGR). Here using primary human fetal adrenal cortex (pHFAC) cells and a human fetal adrenal cell line NCI-H295A, we show that nicotine inhibits StAR expression and cortisol production in a dose- and time-dependent manner, and prolongs the inhibitory effect on cells proliferating over 5 passages after termination of nicotine treatment. Methylation detection within the StAR promoter region uncovers a single site CpG methylation at nt -377 that is sensitive to nicotine treatment. Nicotine-induced alterations in frequency of this point methylation correlates well with the levels of StAR expression, suggesting an important role of the single site in regulating StAR expression. Further studies using bioinformatics analysis and siRNA approach reveal that the single CpG site is part of the Pax6 binding motif (CGCCTGA) in the StAR promoter. The luciferase activity assays validate that Pax6 increases StAR gene expression by binding to the glucagon G3-like motif (CGCCTGA) and methylation of this site blocks Pax6 binding and thus suppresses StAR expression. These data identify a nicotine-sensitive CpG site at the Pax6 binding motif in the StAR promoter that may play a central role in regulating StAR expression. The results suggest an epigenetic mechanism that may explain how nicotine contributes to onset of adult diseases or disorders such as metabolic syndrome via fetal programming.
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Affiliation(s)
- Tingting Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China
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Shiraz OB, Galehdari H, Yavarian M, Geramizadeh B. Possible down regulation of the p16 gene promoter in individuals with hepatocellular carcinoma. HEPATITIS MONTHLY 2011; 11:719-23. [PMID: 22235214 PMCID: PMC3234541 DOI: 10.5812/kowsar.1735143x.732] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 06/28/2011] [Accepted: 07/07/2011] [Indexed: 12/11/2022]
Abstract
BACKGROUND The p16 tumor suppressor gene is an important negative regulator of the cell cycle. Inactivation of p16, especially via promoter hypermethylation, has been found in numerous human cancers such as breast, lung, colorectal, and liver. OBJECTIVES To determine the role of epigenetic methylation in p16 regulation in Iranian patients with hepatocellular carcinoma (HCC). PATIENTS AND METHODS The methylation pattern in the p16 gene promoter was analyzed by bisulfite direct sequencing in 43 paraffin-embedded formalin-fixed tissues from patients with HCC. In addition, normal specimens from liver graft donors were used as the control group. RESULTS The bisulfite direct sequencing showed heterozygous hypermethylation in 13.9% of individuals with HCC. Homozygous methylation within the GC-box IV was detected in another 58.1% of the patients. CONCLUSIONS It is proposed that methylation, but not necessarily hypermethylation, may play a role in the down-regulation of the p16 gene promoter at least in some Iranian patients with HCC.
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Koukoura O, Sifakis S, Zaravinos A, Apostolidou S, Jones A, Hajiioannou J, Widschwendter M, Spandidos DA. Hypomethylation along with increased H19 expression in placentas from pregnancies complicated with fetal growth restriction. Placenta 2010; 32:51-7. [PMID: 21129773 DOI: 10.1016/j.placenta.2010.10.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/12/2010] [Accepted: 10/12/2010] [Indexed: 10/18/2022]
Abstract
The expression of imprinted genes is regulated by epigenetic modifications, such as DNA methylation. Many imprinted genes are expressed in the placenta and affect nutrient transfer capacity of the placental exchange barrier. The H19 gene is abundantly expressed by the human placenta and is implicated in the pathogenesis of congenital growth disorders such as Beckwith-Wiedemann (BWS) and Silver-Russell (SRS) syndromes. The aim of this study was to investigate the role of DNA methylation on H19 transcription and imprinting, in the pathophysiology of fetal growth restriction (FGR). Thirty one and 17 placentas from FGR-complicated and normal pregnancies were collected, respectively. We studied gene transcription, genotyping and methylation analysis of the AluI H19 on exon 5 polymorphism. Placental expression levels of H19 were significantly increased in the FGR group. The H19 mRNA levels were similar between normal placental samples that demonstrated loss and maintenance of imprinting. Placentas from growth-restricted pregnancies had lower methylation levels compared to normals, in the H19 promoter region. We have demonstrated an increased H19 transcription in the FGR group of placentas. The hypomethylation of the H19 promoters is compatible with the aberrant expression. The association of these two findings is reported for the first time in placental tissues, however, its significance remains unknown. Whether the results of this study represent an adaptation of the placenta to hypoperfusion, or they are part of FGR pathophysiology has to be further investigated.
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Affiliation(s)
- O Koukoura
- Department of Obstetrics & Gynaecology, University Hospital of Heraklion, Crete Greece
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Zhou Y, Zhou N, Fang W, Huo J. Overexpressed HDGF as an independent prognostic factor is involved in poor prognosis in Chinese patients with liver cancer. Diagn Pathol 2010; 5:58. [PMID: 20846397 PMCID: PMC2949719 DOI: 10.1186/1746-1596-5-58] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/16/2010] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Hepatoma-derived growth factor (HDGF) is involved in the hepatocarcinogenesis. In this study, we investigated the HDGF expression in hepatocellular carcinoma (HCC) and its correlation with clinicopathologic features, including the survival of patients with HCC. Furthermore, we examined the biological processes regulated by HDGF during the development of using HepG2 cell line as a model system. METHODS We used immunohistochemistry to compare HDGF protein expression in HCC and normal liver tissues and further analyze the HDGF protein expression in clinicopathologically characterized 137 HCC cases. We stably knocked down the endogenous expression level of HDGF in HepG2 cells with specific shRNA-expressing lentiviral vector. Following the successful establishment of stable cells, we examined in vitro cell growth by MTT assay, anchorage-independent growth by soft-agar colony formation assay and cell migration/invasion by transwell and boyden chamber assay. And in addition, we also investigated the in vivo tumor growth by xenograft transplantation of HepG2 cells into nude mice. RESULTS Protein expression level of HDGF was markedly higher in HCC tissues than that in the normal liver tissues(P = 0.011). In addition, high expression of HDGF protein was positively correlated with T classification(p < 0.001), N classification (p < 0.001), and clinical stage (p < 0.001) of HCC patients. Patients with higher HDGF expression showed a significantly shorter overall survival time than did patients with low HDGF expression. Multivariate analysis suggested that HDGF expression might be an independent prognostic indicator(p < 0.001) for the survival of patients with HCC. HDGF-specific shRNA (shHDGF) successfully knocked down its endogenous expression in HepG2 cells. Compared to the parental and control shRNA-transfected (shCtrl) HepG2 cells, the shHDGF cells exhibited significantly reduced in vitro cell growth, anchorage-independent growth, cell migration and invasion (p < 0.05). In vivo, the xenograft transplants from shHDGF cells gave rise to much smaller tumors as compared to those from shCtrl cells. CONCLUSION High HDGF expression is associated with poor overall survival in patients with HCC. Down-regulation of HDGF inhibits the growth, anchorage-independent growth, migration and invasion of HepG2 cells.
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Affiliation(s)
- Yanyan Zhou
- Department of Gastroenterology, Second Xiangya Hospital of Central South University, People's Road 139, Changsha, 410011, China
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