1
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Yao S, Prates K, Freydenzon A, Assante G, McRae AF, Morris MJ, Youngson NA. Liver-specific deletion of de novo DNA methyltransferases protects against glucose intolerance in high-fat diet-fed male mice. FASEB J 2024; 38:e23690. [PMID: 38795327 DOI: 10.1096/fj.202301546rr] [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: 08/03/2023] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/27/2024]
Abstract
Alterations to gene transcription and DNA methylation are a feature of many liver diseases including fatty liver disease and liver cancer. However, it is unclear whether the DNA methylation changes are a cause or a consequence of the transcriptional changes. It is even possible that the methylation changes are not required for the transcriptional changes. If DNA methylation is just a minor player in, or a consequence of liver transcriptional change, then future studies in this area should focus on other systems such as histone tail modifications. To interrogate the importance of de novo DNA methylation, we generated mice that are homozygous mutants for both Dnmt3a and Dnmt3b in post-natal liver. These mice are viable and fertile with normal sized livers. Males, but not females, showed increased adipose depots, yet paradoxically, improved glucose tolerance on both control diet and high-fat diets (HFD). Comparison of the transcriptome and methylome with RNA sequencing and whole-genome bisulfite sequencing in adult hepatocytes revealed that widespread loss of methylation in CpG-rich regions in the mutant did not induce loss of homeostatic transcriptional regulation. Similarly, extensive transcriptional changes induced by HFD did not require de novo DNA methylation. The improved metabolic phenotype of the Dnmt3a/3b mutant mice may be mediated through the dysregulation of a subset of glucose and fat metabolism genes which increase both glucose uptake and lipid export by the liver. However, further work is needed to confirm this.
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Affiliation(s)
- S Yao
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - K Prates
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Department of Biotechnology, Genetics, and Cellular Biology, State University of Maringá, Maringá, Brazil
| | - A Freydenzon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - G Assante
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - A F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - M J Morris
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - N A Youngson
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
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2
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Xu L, Fan YH, Zhang XJ, Bai L. Unraveling the relationship between histone methylation and nonalcoholic fatty liver disease. World J Hepatol 2024; 16:703-715. [PMID: 38818286 PMCID: PMC11135277 DOI: 10.4254/wjh.v16.i5.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/09/2024] [Accepted: 04/07/2024] [Indexed: 05/22/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) poses a significant health challenge in modern societies due to shifts in lifestyle and dietary habits. Its complexity stems from genetic predisposition, environmental influences, and metabolic factors. Epigenetic processes govern various cellular functions such as transcription, chromatin structure, and cell division. In NAFLD, these epigenetic tendencies, especially the process of histone methylation, are intricately intertwined with fat accumulation in the liver. Histone methylation is regulated by different enzymes like methyltransferases and demethylases and influences the expression of genes related to adipogenesis. While early-stage NAFLD is reversible, its progression to severe stages becomes almost irreversible. Therefore, early detection and intervention in NAFLD are crucial, and understanding the precise role of histone methylation in the early stages of NAFLD could be vital in halting or potentially reversing the progression of this disease.
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Affiliation(s)
- Li Xu
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Yu-Hong Fan
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Xiao-Jing Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430060, China; State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Lan Bai
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China.
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3
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Leclerc D, Christensen KE, Reagan AM, Keser V, Luan Y, Malysheva OV, Wasek B, Bottiglieri T, Caudill MA, Howell GR, Rozen R. Folate Deficiency and/or the Genetic Variant Mthfr 677C >T Can Drive Hepatic Fibrosis or Steatosis in Mice, in a Sex-Specific Manner. Mol Nutr Food Res 2024; 68:e2300355. [PMID: 38327171 DOI: 10.1002/mnfr.202300355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/24/2023] [Indexed: 02/09/2024]
Abstract
SCOPE Disturbances in one-carbon metabolism contribute to nonalcoholic fatty liver disease (NAFLD) which encompasses steatosis, steatohepatitis, fibrosis, and cirrhosis. The goal is to examine impact of folate deficiency and the Mthfr677C >T variant on NAFLD. METHODS AND RESULTS This study uses the new Mthfr677C >T mouse model for the human MTHFR677C >T variant. Mthfr677CC and Mthfr677TT mice were fed control diet (CD) or folate-deficient (FD) diets for 4 months. FD and Mthfr677TT alter choline/methyl metabolites in liver and/or plasma (decreased S-adenosylmethionine (SAM):S-adenosylhomocysteine (SAH) ratio, methyltetrahydrofolate, and betaine; increased homocysteine [Hcy]). FD, with contribution from Mthfr677TT, provokes fibrosis in males. Studies of normal livers reveal alterations in plasma markers and gene expression that suggest an underlying predisposition to fibrosis induced by FD and/or Mthfr677TT in males. These changes are absent or reverse in females, consistent with the sex disparity of fibrosis. Sex-based differences in methylation potential, betaine, sphingomyelin, and trimethylamine-N-oxide (TMAO) levels may prevent fibrogenesis in females. In contrast, Mthfr677TT alters choline metabolism, dysregulates expression of lipid metabolism genes, and promotes steatosis in females. CONCLUSION This study suggests that folate deficiency predisposes males to fibrosis, which is exacerbated by Mthfr677TT, whereas Mthfr677TT predisposes females to steatosis, and reveal novel contributory mechanisms for these NAFLD-related disorders.
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Affiliation(s)
- Daniel Leclerc
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Karen E Christensen
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | | | - Vafa Keser
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Yan Luan
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Olga V Malysheva
- Division of Nutritional Sciences and Genomics, Cornell University, Ithaca, NY, USA
| | - Brandi Wasek
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Marie A Caudill
- Division of Nutritional Sciences and Genomics, Cornell University, Ithaca, NY, USA
| | | | - Rima Rozen
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
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4
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Hassan A, Rijo P, Abuamara TMM, Ali Lashin LS, Kamar SA, Bangay G, Al-Sawahli MM, Fouad MK, Zoair MA, Abdalrhman TI, Elebeedy D, Ibrahim IA, Mohamed AF, Abd El Maksoud AI. Synergistic Differential DNA Demethylation Activity of Danshensu ( Salvia miltiorrhiza) Associated with Different Probiotics in Nonalcoholic Fatty Liver Disease. Biomedicines 2024; 12:279. [PMID: 38397881 PMCID: PMC10886676 DOI: 10.3390/biomedicines12020279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a major hepatic disorder occurring in non-alcohol-drinking individuals. Salvianic acid A or Danshensu (DSS, 3-(3, 4-dihydroxyphenyl)-(2R)-lactic acid), derived from the root of Danshen (Salvia miltiorrhiza), has demonstrated heart and liver protective properties. In this work, we investigated the antioxidant activity and hepatoprotective activity of Danshensu alone and in combination with different agents, such as probiotic bacteria (Lactobacillus casei and Lactobacillus acidophilus), against several assays. The inhibition mechanism of the methylation gene biomarkers, such as DNMT-1, MS, STAT-3, and TET-1, against DSS was evaluated by molecular docking and RT-PCR techniques. The physicochemical and pharmacokinetic ADMET properties of DSS were determined by SwissADME and pkCSM. The results indicated that all lipid blood test profiles, including cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C), were reduced after the oral administration of Danshensu combined with probiotics (L. casei and L. acidophilus) that demonstrated good, efficient free radical scavenging activity, measured using anti-oxidant assays. ADMET and drug-likeness properties certify that the DSS could be utilized as a feasible drug since DSS showed satisfactory physicochemical and pharmacokinetic ADMET properties.
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Affiliation(s)
- Amr Hassan
- Department of Bioinformatics, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt
| | - Patrícia Rijo
- CBIOS—Lusófona University’s Research Center for Biosciences and Health Technologies, 1749-024 Lisbon, Portugal;
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Tamer M. M. Abuamara
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Histology, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Lashin Saad Ali Lashin
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Medical Physiology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Sherif A. Kamar
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Anatomy and Embryology, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Gabrielle Bangay
- CBIOS—Lusófona University’s Research Center for Biosciences and Health Technologies, 1749-024 Lisbon, Portugal;
- Universidad de Alcalá de Henares. Facultad de Farmacia, Departamento de Ciencias Biomédicas (Área de Farmacología; Nuevos agentes antitumorales, Acción tóxica sobre células leucémicas), Ctra. Madrid-Barcelona km. 33,600, 28805 Alcalá de Henares, Madrid, España
| | - Majid Mohammed Al-Sawahli
- Department of Pharmaceutics, College of Pharmacy, The Islamic University, Najaf 54001, Iraq;
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Kafr Elsheikh University, Kafr Elsheikh 33516, Egypt
| | - Marina K. Fouad
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
| | - Mohammad A. Zoair
- Department of Physiology, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt;
| | - Tamer I. Abdalrhman
- Department of Histology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt;
| | - Dalia Elebeedy
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
| | - Ibrahim A. Ibrahim
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt;
| | - Aly F. Mohamed
- Holding Company for Vaccine and Sera Production (VACSERA), Giza 22311, Egypt;
| | - Ahmed I. Abd El Maksoud
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt
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5
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Stols-Gonçalves D, Mak AL, Madsen MS, van der Vossen EWJ, Bruinstroop E, Henneman P, Mol F, Scheithauer TPM, Smits L, Witjes J, Meijnikman AS, Verheij J, Nieuwdorp M, Holleboom AG, Levin E. Faecal Microbiota transplantation affects liver DNA methylation in Non-alcoholic fatty liver disease: a multi-omics approach. Gut Microbes 2023; 15:2223330. [PMID: 37317027 DOI: 10.1080/19490976.2023.2223330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023] Open
Abstract
Individuals with nonalcoholic fatty liver disease (NAFLD) have an altered gut microbiota composition. Moreover, hepatic DNA methylation may be altered in the state of NAFLD. Using a fecal microbiota transplantation (FMT) intervention, we aimed to investigate whether a change in gut microbiota composition relates to altered liver DNA methylation in NAFLD. Moreover, we assessed whether plasma metabolite profiles altered by FMT relate to changes in liver DNA methylation. Twenty-one individuals with NAFLD underwent three 8-weekly vegan allogenic donor (n = 10) or autologous (n = 11) FMTs. We obtained hepatic DNA methylation profiles from paired liver biopsies of study participants before and after FMTs. We applied a multi-omics machine learning approach to identify changes in the gut microbiome, peripheral blood metabolome and liver DNA methylome, and analyzed cross-omics correlations. Vegan allogenic donor FMT compared to autologous FMT induced distinct differential changes in I) gut microbiota profiles, including increased abundance of Eubacterium siraeum and potential probiotic Blautia wexlerae; II) plasma metabolites, including altered levels of phenylacetylcarnitine (PAC) and phenylacetylglutamine (PAG) both from gut-derived phenylacetic acid, and of several choline-derived long-chain acylcholines; and III) hepatic DNA methylation profiles, most importantly in Threonyl-TRNA Synthetase 1 (TARS) and Zinc finger protein 57 (ZFP57). Multi-omics analysis showed that Gemmiger formicillis and Firmicutes bacterium_CAG_170 positively correlated with both PAC and PAG. E siraeum negatively correlated with DNA methylation of cg16885113 in ZFP57. Alterations in gut microbiota composition by FMT caused widespread changes in plasma metabolites (e.g. PAC, PAG, and choline-derived metabolites) and liver DNA methylation profiles in individuals with NAFLD. These results indicate that FMTs might induce metaorganismal pathway changes, from the gut bacteria to the liver.
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Affiliation(s)
- Daniela Stols-Gonçalves
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Anne Linde Mak
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mette S Madsen
- Gubra, Hørsholm, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Eveline Bruinstroop
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Endocrinology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Peter Henneman
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Human Genetics, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Femke Mol
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Torsten P M Scheithauer
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Internal Medicine, Amsterdam University Medical Centre (UMC), Vrije Universiteit (VU) University Medical Centre, Amsterdam, Netherlands
| | - Loek Smits
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Julia Witjes
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Abraham Stijn Meijnikman
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Joanne Verheij
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Adriaan G Holleboom
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Horaizon BV, Delft, The Netherlands
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6
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Abrahams Y, Willmer T, Patel O, Samodien E, Muller CJF, Windvogel S, Johnson R, Pheiffer C. A high fat, high sugar diet induces hepatic Peroxisome proliferator-activated receptor gamma coactivator 1-alpha promoter hypermethylation in male Wistar rats. Biochem Biophys Res Commun 2023; 680:25-33. [PMID: 37713959 DOI: 10.1016/j.bbrc.2023.09.004] [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: 06/21/2023] [Revised: 07/31/2023] [Accepted: 09/02/2023] [Indexed: 09/17/2023]
Abstract
Previously we reported that a high fat, high sugar (HFHS) diet induced adiposity, hyperinsulinaemia, hyperleptinaemia, hypertriglyceridaemia and increased liver mass in male Wistar rats. In the present study, the mechanisms underlying the increased liver mass were further elucidated by assessing hepatic lipid accumulation and the expression and methylation status of key metabolic genes using histology, quantitative real-time PCR and pyrosequencing, respectively. The HFHS diet induced hepatic steatosis, increased hepatic triglycerides (1.8-fold, p < 0.001), and increased the expression of sterol regulatory element-binding transcription factor 1 (Srebf1) (2.0-fold, p < 0.001) and peroxisome proliferator-activated receptor gamma (Pparg) (1.7-fold, p = 0.017) in the liver. The expression of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (Pgc1a) was decreased (2.6-fold, p < 0.010), which was accompanied by hypermethylation (p = 0.018) of a conserved CpG site in the promoter of Pgc1a in HFHS fed rats compared to controls. In silico analysis identified putative binding sites for CCAAT/enhancer-binding protein beta (C/EBPß) and hepatocyte nuclear factor 1 (HNF1) within proximity to the hypermethylated CpG. As Pgc1a is a co-activator of several transcription factors regulating multiple metabolic pathways, hypermethylation of this conserved CpG site in the promoter of Pgc1a may be one possible mechanism contributing to the development of hepatic steatosis in response to a HFHS diet. However, further work is required to confirm the role of Pgc1a in steatosis.
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Affiliation(s)
- Yoonus Abrahams
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa; Centre for Cardio-Metabolic Research in Africa (CARMA), Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tarryn Willmer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa; Centre for Cardio-Metabolic Research in Africa (CARMA), Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Oelfah Patel
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa; Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, University of Stellenbosch, Tygerberg, South Africa
| | - Ebrahim Samodien
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
| | - Christo J F Muller
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa; Centre for Cardio-Metabolic Research in Africa (CARMA), Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Department of Biochemistry and Microbiology, University of Zululand, Kwadlangezwa, South Africa
| | - Shantal Windvogel
- Centre for Cardio-Metabolic Research in Africa (CARMA), Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa; Centre for Cardio-Metabolic Research in Africa (CARMA), Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa; Centre for Cardio-Metabolic Research in Africa (CARMA), Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Department of Obstetrics and Gynaecology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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7
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Ramezani M, Zobeiry M, Abdolahi S, Hatami B, Zali MR, Baghaei K. A crosstalk between epigenetic modulations and non-alcoholic fatty liver disease progression. Pathol Res Pract 2023; 251:154809. [PMID: 37797383 DOI: 10.1016/j.prp.2023.154809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has recently emerged as a major public health concern worldwide due to its rapidly rising prevalence and its potential to progress into end-stage liver disease. While the precise pathophysiology underlying NAFLD remains incompletely understood, it is strongly associated with various environmental triggers and other metabolic disorders. Epigenetics examines changes in gene expression that are not caused by alterations in the DNA sequence itself. There is accumulating evidence that epigenetics plays a key role in linking environmental cues to the onset and progression of NAFLD. Our understanding of how epigenetic mechanisms contribute to NAFLD pathophysiology has expanded considerably in recent years as research on the epigenetics of NAFLD has developed. This review summarizes recent insights into major epigenetic processes that have been implicated in NAFLD pathogenesis including DNA methylation, histone acetylation, and microRNAs that have emerged as promising targets for further investigation. Elucidating epigenetic mechanisms in NAFLD may uncover novel diagnostic biomarkers and therapeutic targets for this disease. However, many questions have remained unanswered regarding how epigenetics promotes NAFLD onset and progression. Additional studies are needed to further characterize the epigenetic landscape of NAFLD and validate the potential of epigenetic markers as clinical tools. Nevertheless, an enhanced understanding of the epigenetic underpinnings of NAFLD promises to provide key insights into disease mechanisms and pave the way for novel prognostic and therapeutic approaches.
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Affiliation(s)
- Meysam Ramezani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Shahrokh Abdolahi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Behzad Hatami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Gastroenterology and Liver Diseases Research center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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8
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Herranz JM, López-Pascual A, Clavería-Cabello A, Uriarte I, Latasa MU, Irigaray-Miramon A, Adán-Villaescusa E, Castelló-Uribe B, Sangro B, Arechederra M, Berasain C, Avila MA, Fernández-Barrena MG. Comprehensive analysis of epigenetic and epitranscriptomic genes' expression in human NAFLD. J Physiol Biochem 2023; 79:901-924. [PMID: 37620598 PMCID: PMC10636027 DOI: 10.1007/s13105-023-00976-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a multifactorial condition with a complex etiology. Its incidence is increasing globally in parallel with the obesity epidemic, and it is now considered the most common liver disease in Western countries. The precise mechanisms underlying the development and progression of NAFLD are complex and still poorly understood. The dysregulation of epigenetic and epitranscriptomic mechanisms is increasingly recognized to play pathogenic roles in multiple conditions, including chronic liver diseases. Here, we have performed a comprehensive analysis of the expression of epigenetic and epitranscriptomic genes in a total of 903 liver tissue samples corresponding to patients with normal liver, obese patients, and patients with non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH), advancing stages in NAFLD progression. We integrated ten transcriptomic datasets in an unbiased manner, enabling their robust analysis and comparison. We describe the complete landscape of epigenetic and epitranscriptomic genes' expression along the course of the disease. We identify signatures of genes significantly dysregulated in association with disease progression, particularly with liver fibrosis development. Most of these epigenetic and epitranscriptomic effectors have not been previously described in human NAFLD, and their altered expression may have pathogenic implications. We also performed a comprehensive analysis of the expression of enzymes involved in the metabolism of the substrates and cofactors of epigenetic and epitranscriptomic effectors. This study provides novel information on NAFLD pathogenesis and may also guide the identification of drug targets to treat this condition and its progression towards hepatocellular carcinoma.
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Affiliation(s)
- Jose M Herranz
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Amaya López-Pascual
- Hepatology Unit, CCUN, Navarra University Clinic, Pamplona, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Alex Clavería-Cabello
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Iker Uriarte
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - M Ujúe Latasa
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Ainara Irigaray-Miramon
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Elena Adán-Villaescusa
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Borja Castelló-Uribe
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Bruno Sangro
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Hepatology Unit, CCUN, Navarra University Clinic, Pamplona, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - María Arechederra
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Matías A Avila
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Maite G Fernández-Barrena
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain.
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain.
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9
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Gîlcă-Blanariu GE, Budur DS, Mitrică DE, Gologan E, Timofte O, Bălan GG, Olteanu VA, Ștefănescu G. Advances in Noninvasive Biomarkers for Nonalcoholic Fatty Liver Disease. Metabolites 2023; 13:1115. [PMID: 37999211 PMCID: PMC10672868 DOI: 10.3390/metabo13111115] [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: 09/14/2023] [Revised: 10/15/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) currently represents one of the most common liver diseases worldwide. Early diagnosis and disease staging is crucial, since it is mainly asymptomatic, but can progress to nonalcoholic steatohepatitis (NASH) or cirrhosis or even lead to the development of hepatocellular carcinoma. Over time, efforts have been put into developing noninvasive diagnostic and staging methods in order to replace the use of a liver biopsy. The noninvasive methods used include imaging techniques that measure liver stiffness and biological markers, with a focus on serum biomarkers. Due to the impressive complexity of the NAFLD's pathophysiology, biomarkers are able to assay different processes involved, such as apoptosis, fibrogenesis, and inflammation, or even address the genetic background and "omics" technologies. This article reviews not only the currently validated noninvasive methods to investigate NAFLD but also the promising results regarding recently discovered biomarkers, including biomarker panels and the combination of the currently validated evaluation methods and serum markers.
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Affiliation(s)
- Georgiana-Emmanuela Gîlcă-Blanariu
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
- Department of Gastroenterology, “Sf Spiridon” County Clinical Emergency Hospital, 100115 Iași, Romania
| | - Daniela Simona Budur
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
| | - Dana Elena Mitrică
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
- Department of Gastroenterology, “Sf Spiridon” County Clinical Emergency Hospital, 100115 Iași, Romania
| | - Elena Gologan
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
| | - Oana Timofte
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
- Department of Gastroenterology, “Sf Spiridon” County Clinical Emergency Hospital, 100115 Iași, Romania
| | - Gheorghe Gh Bălan
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
- Department of Gastroenterology, “Sf Spiridon” County Clinical Emergency Hospital, 100115 Iași, Romania
| | - Vasile Andrei Olteanu
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
- Department of Gastroenterology, “Sf Spiridon” County Clinical Emergency Hospital, 100115 Iași, Romania
| | - Gabriela Ștefănescu
- Gastroenterology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (G.-E.G.-B.); (D.E.M.); (E.G.); (O.T.); (G.G.B.); (V.A.O.)
- Department of Gastroenterology, “Sf Spiridon” County Clinical Emergency Hospital, 100115 Iași, Romania
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10
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Hatano M, Akiyama Y, Shimada S, Yagi K, Akahoshi K, Itoh M, Tanabe M, Ogawa Y, Tanaka S. Loss of KDM6B epigenetically confers resistance to lipotoxicity in nonalcoholic fatty liver disease-related HCC. Hepatol Commun 2023; 7:e0277. [PMID: 37782459 PMCID: PMC10545410 DOI: 10.1097/hc9.0000000000000277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/09/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND NAFLD caused by abnormalities in hepatic lipid metabolism is associated with an increased risk of developing HCC. The molecular mechanisms underlying the progression of NAFLD-related HCC are not fully understood. We investigated the molecular mechanism and role of KDM6B downregulation in NAFLD-related HCC after the KDM6B gene was identified using microarray analysis as commonly downregulated in mouse NAFLD-related HCC and human nonhepatitis B and nonhepatitis C viral-HCC. METHODS The 5-hydroxymethylcytosine levels of KDM6B in HCC cells were determined using glycosylated hydroxymethyl-sensitive PCR. Microarray and chromatin immunoprecipitation analyses using KDM6B-knockout (KO) cells were used to identify KDM6B target genes. Lipotoxicity was assessed using a palmitate-treated cell proliferation assay. Immunohistochemistry was used to evaluate KDM6B expression in human HCC tissues. RESULTS KDM6B expression levels in HCC cells correlated with the 5-hydroxymethylcytosine levels in the KDM6B gene body region. Gene set enrichment analysis revealed that the lipid metabolism pathway was suppressed in KDM6B-KO cells. KDM6B-KO cells acquired resistance to lipotoxicity (p < 0.01) and downregulated the expression of G0S2, an adipose triglyceride lipase/patatin like phospholipase domain containing 2 (ATGL/PNPLA2) inhibitor, through increased histone H3 lysine-27 trimethylation levels. G0S2 knockdown in KDM6B-expressed HCC cells conferred lipotoxicity resistance, whereas ATGL/PNPLA2 inhibition in the KDM6B-KO cells reduced these effects. Immunohistochemistry revealed that KDM6B expression was decreased in human NAFLD-related HCC tissues (p < 0.001), which was significantly associated with decreased G0S2 expression (p = 0.032). CONCLUSIONS KDM6B-disrupted HCC acquires resistance to lipotoxicity via ATGL/PNPLA2 activation caused by epigenetic downregulation of G0S2 expression. Reduced KDM6B and G0S2 expression levels are common in NAFLD-related HCC. Targeting the KDM6B-G0S2-ATGL/PNPLA2 pathway may be a useful therapeutic strategy for NAFLD-related HCC.
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Affiliation(s)
- Megumi Hatano
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshimitsu Akiyama
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shu Shimada
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohei Yagi
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiichi Akahoshi
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Michiko Itoh
- Kanagawa Institute of Industrial Science and Technology, Kanagawa, Japan
| | - Minoru Tanabe
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shinji Tanaka
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
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11
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Aggeletopoulou I, Kalafateli M, Tsounis EP, Triantos C. Epigenetic Regulation in Lean Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2023; 24:12864. [PMID: 37629043 PMCID: PMC10454848 DOI: 10.3390/ijms241612864] [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: 07/31/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), the most prominent cause of chronic liver disease worldwide, is a rapidly growing epidemic. It consists of a wide range of liver diseases, from steatosis to nonalcoholic steatohepatitis, and predisposes patients to liver fibrosis, cirrhosis, and even hepatocellular carcinoma. NAFLD is strongly correlated with obesity; however, it has been extensively reported among lean/nonobese individuals in recent years. Although lean patients demonstrate a lower prevalence of diabetes mellitus, central obesity, dyslipidemia, hypertension, and metabolic syndrome, a percentage of these patients may develop steatohepatitis, advanced liver fibrosis, and cardiovascular disease, and have increased all-cause mortality. The pathophysiological mechanisms of lean NAFLD remain vague. Studies have reported that lean NAFLD demonstrates a close association with environmental factors, genetic predisposition, and epigenetic modifications. In this review, we aim to discuss and summarize the epigenetic mechanisms involved in lean NAFLD and to introduce the interaction between epigenetic patterns and genetic or non genetic factors. Several epigenetic mechanisms have been implicated in the regulation of lean NAFLD. These include DNA methylation, histone modifications, and noncoding-RNA-mediated gene regulation. Epigenetics is an area of special interest in the setting of lean NAFLD as it could provide new insights into the therapeutic options and noninvasive biomarkers that target this under-recognized and challenging disorder.
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Affiliation(s)
- Ioanna Aggeletopoulou
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece; (I.A.); (E.P.T.)
| | - Maria Kalafateli
- Department of Gastroenterology, General Hospital of Patras, 26332 Patras, Greece;
| | - Efthymios P. Tsounis
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece; (I.A.); (E.P.T.)
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece; (I.A.); (E.P.T.)
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12
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Basheer M, Saad E, Jeries H, Assy N. Liver Fat Storage Is a Better Predictor of Coronary Artery Disease than Visceral Fat. Metabolites 2023; 13:896. [PMID: 37623840 PMCID: PMC10456344 DOI: 10.3390/metabo13080896] [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: 06/16/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Fatty liver is one aspect of metabolic syndrome. The roles and contributions of fatty liver and visceral fat storage to coronary artery disease (CAD) are not clear. This study measured associations among visceral fat storage, fatty liver, insulin resistance, atherosclerosis, and CAD. Patients were divided into three groups: excess visceral fat (visceral fat area >330 ± 99 cm2), non-alcoholic fatty liver disease (NAFLD), and a control group. The definition of fatty liver is liver minus spleen density greater than or equal to -10. We defined early atherosclerosis as intima-media thickness of the common carotid artery >7 mm in men and >0.65 mm in women, measured with Doppler ultrasound. Visceral fat area was defined using CT (>330 ± 99 cm2). Insulin-resistance biomarkers (HOMA), CRP, and oxidant-antioxidant status (MDA-Paraoxonase) were also measured. Patients with high liver or visceral fat showed higher coronary plaque prevalence (50% (p < 0.001), 38% (p < 0.01), respectively vs. 25% in the control group), higher prevalence of coronary stenosis (30% (p < 0.001), 22% (p < 0.01) vs. 11% in the control group), higher intimal thickening (0.98 ± 0.3 (p< 0.01), 0.86 ± 0.1 (p < 0.01) vs. 0.83 ± 0.1 in the control group), higher HOMA (4.0 ± 3.0 (p < 0.005), 3.0 ± 1.0 (p < 0.001) vs. 1.5 ± 1.2 in the control group), and higher triglyceride levels (196.8 ± 103 (p < 0.005), 182.6 ± 90.87 (p < 0.005) vs. 145 ± 60 in the control group). Multiple logistic regression analysis showed that fatty liver predicted CAD (OR 2.7, 95% CI 2.3-4.9, p < 0.001) independently of visceral fat storage (OR 2.01, 95% CI 1.2-2.8, p < 0.001). Liver fat storage is a strong independent risk factor for CAD and carotid atherosclerosis and contributes more than visceral fat storage.
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Affiliation(s)
- Maamoun Basheer
- Internal Medicine Department, Galilee Medical Center, Nahariya 221001, Israel; (M.B.); (E.S.); (H.J.)
| | - Elias Saad
- Internal Medicine Department, Galilee Medical Center, Nahariya 221001, Israel; (M.B.); (E.S.); (H.J.)
- Azrieli Faculty of Medicine, Bar-Ilan University, Safad 1311502, Israel
| | - Helena Jeries
- Internal Medicine Department, Galilee Medical Center, Nahariya 221001, Israel; (M.B.); (E.S.); (H.J.)
| | - Nimer Assy
- Internal Medicine Department, Galilee Medical Center, Nahariya 221001, Israel; (M.B.); (E.S.); (H.J.)
- Azrieli Faculty of Medicine, Bar-Ilan University, Safad 1311502, Israel
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13
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Thomsen KL, Eriksen PL, Kerbert AJC, De Chiara F, Jalan R, Vilstrup H. Role of ammonia in NAFLD: An unusual suspect. JHEP Rep 2023; 5:100780. [PMID: 37425212 PMCID: PMC10326708 DOI: 10.1016/j.jhepr.2023.100780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 07/11/2023] Open
Abstract
Mechanistically, the symptomatology and disease progression of non-alcoholic fatty liver disease (NAFLD) remain poorly understood, which makes therapeutic progress difficult. In this review, we focus on the potential importance of decreased urea cycle activity as a pathogenic mechanism. Urea synthesis is an exclusive hepatic function and is the body's only on-demand and definitive pathway to remove toxic ammonia. The compromised urea cycle activity in NAFLD is likely caused by epigenetic damage to urea cycle enzyme genes and increased hepatocyte senescence. When the urea cycle is dysfunctional, ammonia accumulates in liver tissue and blood, as has been demonstrated in both animal models and patients with NAFLD. The problem may be augmented by parallel changes in the glutamine/glutamate system. In the liver, the accumulation of ammonia leads to inflammation, stellate cell activation and fibrogenesis, which is partially reversible. This may be an important mechanism for the transition of bland steatosis to steatohepatitis and further to cirrhosis and hepatocellular carcinoma. Systemic hyperammonaemia has widespread negative effects on other organs. Best known are the cerebral consequences that manifest as cognitive disturbances, which are prevalent in patients with NAFLD. Furthermore, high ammonia levels induce a negative muscle protein balance leading to sarcopenia, compromised immune function and increased risk of liver cancer. There is currently no rational way to reverse reduced urea cycle activity but there are promising animal and human reports of ammonia-lowering strategies correcting several of the mentioned untoward aspects of NAFLD. In conclusion, the ability of ammonia-lowering strategies to control the symptoms and prevent the progression of NAFLD should be explored in clinical trials.
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Affiliation(s)
- Karen Louise Thomsen
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Denmark
- UCL Institute of Liver and Digestive Health, University College London, United Kingdom
| | - Peter Lykke Eriksen
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Denmark
| | - Annarein JC. Kerbert
- UCL Institute of Liver and Digestive Health, University College London, United Kingdom
| | - Francesco De Chiara
- UCL Institute of Liver and Digestive Health, University College London, United Kingdom
| | - Rajiv Jalan
- UCL Institute of Liver and Digestive Health, University College London, United Kingdom
- European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
| | - Hendrik Vilstrup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Denmark
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14
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Chen Y, Wang W, Morgan MP, Robson T, Annett S. Obesity, non-alcoholic fatty liver disease and hepatocellular carcinoma: current status and therapeutic targets. Front Endocrinol (Lausanne) 2023; 14:1148934. [PMID: 37361533 PMCID: PMC10286797 DOI: 10.3389/fendo.2023.1148934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Obesity is a global epidemic and overwhelming evidence indicates that it is a risk factor for numerous cancers, including hepatocellular carcinoma (HCC), the third leading cause of cancer-related deaths worldwide. Obesity-associated hepatic tumorigenesis develops from nonalcoholic fatty liver disease (NAFLD), progressing to nonalcoholic steatohepatitis (NASH), cirrhosis and ultimately to HCC. The rising incidence of obesity is resulting in an increased prevalence of NAFLD and NASH, and subsequently HCC. Obesity represents an increasingly important underlying etiology of HCC, in particular as the other leading causes of HCC such as hepatitis infection, are declining due to effective treatments and vaccines. In this review, we provide a comprehensive overview of the molecular mechanisms and cellular signaling pathways involved in the pathogenesis of obesity-associated HCC. We summarize the preclinical experimental animal models available to study the features of NAFLD/NASH/HCC, and the non-invasive methods to diagnose NAFLD, NASH and early-stage HCC. Finally, since HCC is an aggressive tumor with a 5-year survival of less than 20%, we will also discuss novel therapeutic targets for obesity-associated HCC and ongoing clinical trials.
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Affiliation(s)
- Yinshuang Chen
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Weipeng Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Maria P. Morgan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Tracy Robson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Stephanie Annett
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
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15
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Feng Y, Guo S, Zhao Y, Dong H, Qian J, Hu Y, Wu L, Jia Y, Zhao R. DNA 5mC and RNA m 6A modification successively facilitates the initiation and perpetuation stages of HSC activation in liver fibrosis progression. Cell Death Differ 2023; 30:1211-1220. [PMID: 36841889 PMCID: PMC10154415 DOI: 10.1038/s41418-023-01130-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/27/2023] Open
Abstract
Hepatic stellate cells (HSC) are key effector cells in liver fibrosis. Upon stimulation, the quiescent HSC undergoes complex morphological and functional changes to transdifferentiate into activated collagen-producing myofibroblasts. DNA/RNA methylations (5mC/m6A) are both implicated to participate in hepatic fibrosis, yet their respective roles and specific targets in HSC activation remain elusive. Here, we demonstrate that 5mC is indispensable for the initiation stage of HSC activation (myofibroblast transdifferentiation), whereas m6A is essential for the perpetuation stage of HSC activation (excessive ECM production). Mechanistically, DNA 5mC hypermethylation on the promoter of SOCS3 and PPARγ genes leads to STAT3-mediated metabolic reprogramming and lipid loss in the initiation stage. RNA m6A hypermethylation on the transcripts of major collagen genes enhances the mRNA stability in a YTHDF1-dependent manner, which contributes to massive ECM production. Vitamin A-coupled YTHDF1 siRNA alleviates CCl4-induced liver fibrosis in mice through HSC-specific inhibition of collagen production. HIF-1α, which is transactivated by STAT3, serves as a bridge linking the initiation and the perpetuation stages through transactivating YTHDF1. These findings indicate successive roles of DNA 5mC and RNA m6A modification in the progression of HSC activation, which provides new drug targets for epigenetic therapy of liver fibrosis.
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Affiliation(s)
- Yue Feng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Shihui Guo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yulan Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Haibo Dong
- Center for Translational Biomedical Research, UNCG, Kannapolis, NC, USA
| | - Jiayu Qian
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yun Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Lei Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yimin Jia
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Ruqian Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
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16
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Zaiou M. Peroxisome Proliferator-Activated Receptor-γ as a Target and Regulator of Epigenetic Mechanisms in Nonalcoholic Fatty Liver Disease. Cells 2023; 12:cells12081205. [PMID: 37190114 DOI: 10.3390/cells12081205] [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: 03/11/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Peroxisome proliferator-activated receptor-γ (PPARγ) belongs to the superfamily of nuclear receptors that control the transcription of multiple genes. Although it is found in many cells and tissues, PPARγ is mostly expressed in the liver and adipose tissue. Preclinical and clinical studies show that PPARγ targets several genes implicated in various forms of chronic liver disease, including nonalcoholic fatty liver disease (NAFLD). Clinical trials are currently underway to investigate the beneficial effects of PPARγ agonists on NAFLD/nonalcoholic steatohepatitis. Understanding PPARγ regulators may therefore aid in unraveling the mechanisms governing the development and progression of NAFLD. Recent advances in high-throughput biology and genome sequencing have greatly facilitated the identification of epigenetic modifiers, including DNA methylation, histone modifiers, and non-coding RNAs as key factors that regulate PPARγ in NAFLD. In contrast, little is still known about the particular molecular mechanisms underlying the intricate relationships between these events. The paper that follows outlines our current understanding of the crosstalk between PPARγ and epigenetic regulators in NAFLD. Advances in this field are likely to aid in the development of early noninvasive diagnostics and future NAFLD treatment strategies based on PPARγ epigenetic circuit modification.
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Affiliation(s)
- Mohamed Zaiou
- Institut Jean-Lamour, Université de Lorraine, UMR 7198 CNRS, 54505 Vandoeuvre-les-Nancy, France
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17
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Liu Y, Chen M. Histone Demethylation Profiles in Nonalcoholic Fatty Liver Disease and Prognostic Values in Hepatocellular Carcinoma: A Bioinformatic Analysis. Curr Issues Mol Biol 2023; 45:3640-3657. [PMID: 37185761 PMCID: PMC10136463 DOI: 10.3390/cimb45040237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with multifactorial pathogenesis; histone demethylases (HDMs) are emerging as attractive targets. We identified HDM genes (including KDM5C, KDM6B, KDM8, KDM4A, and JMJD7) that were differentially expressed in NAFLD and normal samples by exploring gene expression profiling datasets. There was no significant difference in the expression of genes related to histone demethylation between mild and advanced NAFLD. In vitro and in vivo studies indicated that KDM6B and JMJD7 were upregulated at the mRNA level in NAFLD. We explored the expression levels and prognostic values of the identified HDM genes in hepatocellular carcinoma (HCC). KDM5C and KDM4A were upregulated in HCC compared to normal tissue, while KDM8 showed downregulation. The abnormal expression levels of these HDMs could provide prognostic values. Furthermore, KDM5C and KDM4A were associated with immune cell infiltration in HCC. HDMs were associated with cellular and metabolic processes and may be involved in the regulation of gene expression. Differentially expressed HDM genes identified in NAFLD may provide value to understanding pathogenesis and in the development of epigenetic therapeutic targets. However, on the basis of the inconsistent results of in vitro studies, future in vivo experiments combined with transcriptomic analysis are needed for further validation.
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Affiliation(s)
- Yuanbin Liu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No. 99 Zhang Zhidong Road, Wuhan 430000, China
| | - Mingkai Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No. 99 Zhang Zhidong Road, Wuhan 430000, China
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Wang J, Zhang F, Yang W, Gao D, Yang L, Yu C, Chen C, Li X, Zhang JS. FGF1 ameliorates obesity-associated hepatic steatosis by reversing IGFBP2 hypermethylation. FASEB J 2023; 37:e22881. [PMID: 36934380 DOI: 10.1096/fj.202201950r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/20/2023]
Abstract
Obesity is a major contributing factor for metabolic-associated fatty liver disease (MAFLD). Fibroblast growth factor (FGF) 1 is the first paracrine FGF family member identified to exhibit promising metabolic regulatory properties capable of conferring glucose-lowering and insulin-sensitizing effect. This study explores the role and molecular underpinnings of FGF1 in obesity-associated hepatic steatosis. In a mouse high-fat diet (HFD)-induced MAFLD model, chronic treatment with recombinant FGF1(rFGF1) was found to effectively reduce the severity of insulin resistance, hyperlipidemia, and inflammation. FGF1 treatment decreased lipid accumulation in the mouse liver and palmitic acid-treated AML12 cells. These effects were associated with decreased mature form SREBF1 expression and its target genes FASN and SCD1. Interestingly, we uncovered that rFGF1 significantly induced IGFBP2 expression at both mRNA and protein levels in HFD-fed mouse livers and cultured hepatocytes treated with palmitic acid. Adeno-associated virus-mediated IGFBP2 suppression significantly diminished the therapeutic benefit of rFGF1 on MAFLD-associated phenotypes, indicating that IGFBP2 plays a crucial role in the FGF1-mediated reduction of hepatic steatosis. Further analysis revealed that rFGF1 treatment reduces the recruitment of DNA methyltransferase 3 alpha to the IGFBP2 genomic locus, leading to decreased IGFBP2 gene methylation and increased mRNA and protein expression. Collectively, our findings reveal FGF1 modulation of lipid metabolism via epigenetic regulation of IGFBP2 expression, and unravel the therapeutic potential of the FGF1-IGFBP2 axis in metabolic diseases associated with obesity.
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Affiliation(s)
- Jie Wang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Feng Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Weiwei Yang
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dandan Gao
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Linglong Yang
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chenhua Yu
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Xiaokun Li
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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19
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Zhu Y, Zhang H, Jiang P, Xie C, Luo Y, Chen J. Transcriptional and Epigenetic Alterations in the Progression of Non-Alcoholic Fatty Liver Disease and Biomarkers Helping to Diagnose Non-Alcoholic Steatohepatitis. Biomedicines 2023; 11:biomedicines11030970. [PMID: 36979950 PMCID: PMC10046227 DOI: 10.3390/biomedicines11030970] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) encompasses a broad spectrum of conditions from simple steatosis (non-alcoholic fatty liver (NAFL)) to non-alcoholic steatohepatitis (NASH), and its global prevalence continues to rise. NASH, the progressive form of NAFLD, has higher risks of liver and non-liver related adverse outcomes compared with those patients with NAFL alone. Therefore, the present study aimed to explore the mechanisms in the progression of NAFLD and to develop a model to diagnose NASH based on the transcriptome and epigenome. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) among the three groups (normal, NAFL, and NASH) were identified, and the functional analysis revealed that the development of NAFLD was primarily related to the oxidoreductase-related activity, PPAR signaling pathway, tight junction, and pathogenic Escherichia coli infection. The logistic regression (LR) model, consisting of ApoF, THOP1, and BICC1, outperformed the other five models. With the highest AUC (0.8819, 95%CI: 0.8128-0.9511) and a sensitivity of 97.87%, as well as a specificity of 64.71%, the LR model was determined as the diagnostic model, which can differentiate NASH from NAFL. In conclusion, several potential mechanisms were screened out based on the transcriptome and epigenome, and a diagnostic model was built to help patient stratification for NAFLD populations.
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Affiliation(s)
- Yalan Zhu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - He Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Pengjun Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengxia Xie
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yao Luo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
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Tryndyak VP, Willett RA, Nagumalli SK, Li D, Avigan MI, Beland FA, Rusyn I, Pogribny IP. Effect of an obesogenic high-fat and high-sucrose diet on hepatic gene expression signatures in male Collaborative Cross mice. Am J Physiol Gastrointest Liver Physiol 2023; 324:G232-G243. [PMID: 36625475 PMCID: PMC10191133 DOI: 10.1152/ajpgi.00225.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 01/01/2023] [Indexed: 01/11/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD), the most prevalent chronic liver disease, is characterized by substantial variations in case-level severity. In this study, we used a genetically diverse Collaborative Cross (CC) mouse population model to analyze the global transcriptome and clarify the molecular mechanisms involved in hepatic fat accumulation that determine the level and severity of NAFLD. Twenty-four strains of male CC mice were maintained on a high-fat/high-sucrose (HF/HS) diet for 12 wk, and their hepatic gene expression profiles were determined by next-generation RNA sequencing. We found that the development of the nonalcoholic fatty liver (NAFL) phenotype in CC mice coincided with significant changes in the expression of hepatic genes at the population level, evidenced by the presence of 724 differentially expressed genes involved in lipid and carbohydrate metabolism, cell morphology, vitamin and mineral metabolism, energy production, and DNA replication, recombination, and repair. Importantly, expression of 68 of these genes strongly correlated with the extent of hepatic lipid accumulation in the overall population of HF/HS diet-fed male CC mice. Results of partial least squares (PLS) modeling showed that these derived hepatic gene expression signatures help to identify the individual mouse strains that are highly susceptible to the development of NAFLD induced by an HF/HS diet. These findings imply that gene expression profiling, combined with a PLS modeling approach, may be a useful tool to predict NAFLD severity in genetically diverse patient populations.NEW & NOTEWORTHY Feeding male Collaborative Cross mice an obesogenic diet allows modeling NAFLD at the population level. The development of NAFLD coincided with significant hepatic transcriptomic changes in this model. Genes (724) were differentially expressed and expression of 68 genes strongly correlated with the extent of hepatic lipid accumulation. Partial least squares modeling showed that derived hepatic gene expression signatures may help to identify individual mouse strains that are highly susceptible to the development of NAFLD.
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Affiliation(s)
- Volodymyr P Tryndyak
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Rose A Willett
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Suresh K Nagumalli
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Dan Li
- Division of Bioinformatics and Biostatistics, Food and Drug Agency-National Center for Toxicological Research, Jefferson, Arkansas
| | - Mark I Avigan
- Office of Pharmacovigilance and Epidemiology, Food and Drug Administration-Center for Drug Evaluation and Research, Silver Spring, Maryland
| | - Frederick A Beland
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Ivan Rusyn
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas
| | - Igor P Pogribny
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
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21
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Wang L, Yi J, Guo J, Ren X. Weigh change across adulthood is related to the presence of NAFLD: results from NHANES III. J Transl Med 2023; 21:142. [PMID: 36823668 PMCID: PMC9951528 DOI: 10.1186/s12967-023-04007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Obesity is a widely recognized driving factor of Non-alcoholic fatty liver disease (NAFLD), it remains unclear whether historical weight status was associated with the presence of NAFLD. The study aimed to explore the relationship between weight change across adulthood and the presence of NAFLD. METHODS Data from the National Health and Nutrition Examination Survey III included 6586 participants. Weight change was assessed according to body mass index (BMI) at baseline, at 25 years old, and 10 years before baseline. Obesity was defined as BMI ≥ 30 kg/m2. NAFLD was assessed by hepatic ultrasonography. RESULTS The prevalence of NAFLD was highest among stable obese participants (48.1%), and the lowest among stable non-obese participants (18.9%). Among non-obese participants, those who get obese in early adulthood had a higher risk for the presence of NAFLD than those who were never obese (odds ratio [OR], 1.82; 95% confidence interval [CI] 1.17-2.92). Among obese participants, those who become obese in middle-late adulthood had a lower risk of NAFLD (OR, 0.79; 95% CI 0.65-0.96) than those with stable obesity. A weight gain of more than 12 kg and 4 kg since early and middle-late adulthood respectively were associated with increased risks of NAFLD. CONCLUSION Among current nonobese individuals, those with a history of obesity in their early adulthood had a higher risk of NAFLD than those never obese. Among the currently obese population, those who became obese after mid-adulthood have a significantly lower risk of NAFLD compared with those who were stable obese.
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Affiliation(s)
- Lili Wang
- grid.506261.60000 0001 0706 7839Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100035 China
| | - Jiayi Yi
- grid.506261.60000 0001 0706 7839Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100035 China
| | - Jiajun Guo
- grid.13291.380000 0001 0807 1581Department of Cardiology, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| | - Xiangpeng Ren
- Department of Biochemistry, Medical College, Jiaxing University, No.899 Guangqiong Road, Jiaxing, 314001, Zhejiang, China.
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22
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Vasconcellos C, Ferreira O, Lopes MF, Ribeiro AF, Vasques J, Guerreiro CS. Nutritional Genomics in Nonalcoholic Fatty Liver Disease. Biomedicines 2023; 11:biomedicines11020319. [PMID: 36830856 PMCID: PMC9953045 DOI: 10.3390/biomedicines11020319] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common chronic condition associated with genetic and environmental factors in which fat abnormally accumulates in the liver. NAFLD is epidemiologically associated with obesity, type 2 diabetes, and dyslipidemia. Environmental factors, such as physical inactivity and an unbalanced diet, interact with genetic factors, such as epigenetic mechanisms and polymorphisms for the genesis and development of the condition. Different genetic polymorphisms seem to be involved in this context, including variants in PNPLA3, TM6SF2, PEMT, and CHDH genes, playing a role in the disease's susceptibility, development, and severity. From carbohydrate intake and weight loss to omega-3 supplementation and caloric restriction, different dietary and nutritional factors appear to be involved in controlling the onset and progression of NAFLD conditions influencing metabolism, gene, and protein expression. The polygenic risk score represents a sum of trait-associated alleles carried by an individual and seems to be associated with NAFLD outcomes depending on the dietary context. Understanding the exact extent to which lifestyle interventions and genetic predispositions can play a role in the prevention and management of NAFLD can be crucial for the establishment of a personalized and integrative approach to patients.
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Affiliation(s)
- Carolina Vasconcellos
- Laboratório de Nutrição, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Oureana Ferreira
- Laboratório de Nutrição, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Marta Filipa Lopes
- Laboratório de Nutrição, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - André Filipe Ribeiro
- Laboratório de Nutrição, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - João Vasques
- Laboratório de Nutrição, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Catarina Sousa Guerreiro
- Laboratório de Nutrição, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Correspondence:
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23
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Dnmt1/Tet2-mediated changes in Cmip methylation regulate the development of nonalcoholic fatty liver disease by controlling the Gbp2-Pparγ-CD36 axis. Exp Mol Med 2023; 55:143-157. [PMID: 36609599 PMCID: PMC9898513 DOI: 10.1038/s12276-022-00919-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/17/2022] [Accepted: 11/13/2022] [Indexed: 01/07/2023] Open
Abstract
Dynamic alteration of DNA methylation leads to various human diseases, including nonalcoholic fatty liver disease (NAFLD). Although C-Maf-inducing protein (Cmip) has been reported to be associated with NAFLD, its exact underlying mechanism remains unclear. Here, we aimed to elucidate this mechanism in NAFLD in vitro and in vivo. We first identified alterations in the methylation status of the Cmip intron 1 region in mouse liver tissues with high-fat high-sucrose diet-induced NAFLD. Knockdown of DNA methyltransferase (Dnmt) 1 significantly increased Cmip expression. Chromatin immunoprecipitation assays of AML12 cells treated with oleic and palmitic acid (OPA) revealed that Dnmt1 was dissociated and that methylation of H3K27me3 was significantly decreased in the Cmip intron 1 region. Conversely, the knockdown of Tet methylcytosine dioxygenase 2 (Tet2) decreased Cmip expression. Following OPA treatment, the CCCTC-binding factor (Ctcf) was recruited, and H3K4me3 was significantly hypermethylated. Intravenous Cmip siRNA injection ameliorated NAFLD pathogenic features in ob/ob mice. Additionally, Pparγ and Cd36 expression levels were dramatically decreased in the livers of ob/ob mice administered siCmip, and RNA sequencing revealed that Gbp2 was involved. Gbp2 knockdown also induced a decrease in Pparγ and Cd36 expression, resulting in the abrogation of fatty acid uptake into cells. Our data demonstrate that Cmip and Gbp2 expression levels are enhanced in human liver tissues bearing NAFLD features. We also show that Dnmt1-Trt2/Ctcf-mediated reversible modulation of Cmip methylation regulates the Gbp2-Pparγ-Cd36 signaling pathway, indicating the potential of Cmip as a novel therapeutic target for NAFLD.
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Zhang N, Tian X, Yan T, Wang H, Zhang D, Lin C, Liu Q, Jiang S. Insights into the role of nucleotide methylation in metabolic-associated fatty liver disease. Front Immunol 2023; 14:1148722. [PMID: 37020540 PMCID: PMC10067741 DOI: 10.3389/fimmu.2023.1148722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/22/2023] [Indexed: 04/07/2023] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) is a chronic liver disease characterized by fatty infiltration of the liver. In recent years, the MAFLD incidence rate has risen and emerged as a serious public health concern. MAFLD typically progresses from the initial hepatocyte steatosis to steatohepatitis and then gradually advances to liver fibrosis, which may ultimately lead to cirrhosis and carcinogenesis. However, the potential evolutionary mechanisms still need to be clarified. Recent studies have shown that nucleotide methylation, which was directly associated with MAFLD's inflammatory grading, lipid synthesis, and oxidative stress, plays a crucial role in the occurrence and progression of MAFLD. In this review, we highlight the regulatory function and associated mechanisms of nucleotide methylation modification in the progress of MAFLD, with a particular emphasis on its regulatory role in the inflammation of MAFLD, including the regulation of inflammation-related immune and metabolic microenvironment. Additionally, we summarize the potential value of nucleotide methylation in the diagnosis and treatment of MAFLD, intending to provide references for the future investigation of MAFLD.
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Affiliation(s)
- Ni Zhang
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xinchen Tian
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Haochen Wang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Jining Medical University, Jining, China
| | - Dengtian Zhang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Jining Medical University, Jining, China
| | - Cong Lin
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Jining Medical University, Jining, China
- *Correspondence: Qingbin Liu, ; Shulong Jiang,
| | - Shulong Jiang
- Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Jining Medical University, Jining, China
- *Correspondence: Qingbin Liu, ; Shulong Jiang,
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25
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Pal SC, Eslam M, Mendez-Sanchez N. Detangling the interrelations between MAFLD, insulin resistance, and key hormones. Hormones (Athens) 2022; 21:573-589. [PMID: 35921046 DOI: 10.1007/s42000-022-00391-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/19/2022] [Indexed: 11/04/2022]
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD) has increasingly become a significant and highly prevalent cause of chronic liver disease, displaying a wide array of risk factors and pathophysiologic mechanisms of which only a few have so far been clearly elucidated. A bidirectional interaction between hormonal discrepancies and metabolic-related disorders, including obesity, type 2 diabetes mellitus (T2DM), and polycystic ovarian syndrome (PCOS) has been described. Since the change in nomenclature from non-alcoholic fatty liver disease (NAFLD) to MAFLD is based on the clear impact of metabolic elements on the disease, the reciprocal interactions of hormones such as insulin, adipokines (leptin and adiponectin), and estrogens have strongly pointed to the intrinsic links that lead to the heterogeneous epidemiology, clinical presentations, and risk factors involved in MAFLD in different populations. The objective of this work is twofold. Firstly, there is a brief discussion regarding the change in nomenclature as well as epidemiology, risk factors, and pathophysiologic mechanisms other than hormonal effects, which include nutrition and the gut microbiome, as well as genetic and epigenetic influences. Secondly, we review the basis of the most important hormonal factors involved in the development and progression of MAFLD that act both independently and in an interrelated manner.
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Affiliation(s)
- Shreya C Pal
- Faculty of Medicine, National Autonomous University of Mexico, Av. Universidad 3000, Coyoacán, 4510, Mexico City, Mexico
- Liver Research Unit, Medica Sur Clinic & Foundation, Puente de Piedra 150. Col. Toriello Guerra, 14050, Tlalpan, Mexico City, Mexico
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital, University of Sydney, Sydney, NSW, Australia
| | - Nahum Mendez-Sanchez
- Faculty of Medicine, National Autonomous University of Mexico, Av. Universidad 3000, Coyoacán, 4510, Mexico City, Mexico.
- Liver Research Unit, Medica Sur Clinic & Foundation, Puente de Piedra 150. Col. Toriello Guerra, 14050, Tlalpan, Mexico City, Mexico.
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PPARα in the Epigenetic Driver Seat of NAFLD: New Therapeutic Opportunities for Epigenetic Drugs? Biomedicines 2022; 10:biomedicines10123041. [PMID: 36551797 PMCID: PMC9775974 DOI: 10.3390/biomedicines10123041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a growing epidemic and the most common cause of chronic liver disease worldwide. It consists of a spectrum of liver disorders ranging from simple steatosis to NASH which predisposes patients to further fibrosis, cirrhosis and even hepatocarcinoma. Despite much research, an approved treatment is still lacking. Finding new therapeutic targets has therefore been a main priority. Known as a main regulator of the lipid metabolism and highly expressed in the liver, the nuclear receptor peroxisome proliferator-activated receptor-α (PPARα) has been identified as an attractive therapeutic target. Since its expression is silenced by DNA hypermethylation in NAFLD patients, many research strategies have aimed to restore the expression of PPARα and its target genes involved in lipid metabolism. Although previously tested PPARα agonists did not ameliorate the disease, current research has shown that PPARα also interacts and regulates epigenetic DNMT1, JMJD3, TET and SIRT1 enzymes. Moreover, there is a growing body of evidence suggesting the orchestrating role of epigenetics in the development and progression of NAFLD. Therefore, current therapeutic strategies are shifting more towards epigenetic drugs. This review provides a concise overview of the epigenetic regulation of NAFLD with a focus on PPARα regulation and highlights recently identified epigenetic interaction partners of PPARα.
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27
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Vachher M, Bansal S, Kumar B, Yadav S, Burman A. Deciphering the role of aberrant DNA methylation in NAFLD and NASH. Heliyon 2022; 8:e11119. [PMID: 36299516 PMCID: PMC9589178 DOI: 10.1016/j.heliyon.2022.e11119] [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: 05/05/2022] [Revised: 07/30/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
The global incidence of nonalcoholic fatty liver disease (NAFLD) is mounting incessantly, and it is emerging as the most frequent cause of chronic and end stage liver disorders. It is the starting point for a range of conditions from simple steatosis to more progressive nonalcoholic steatohepatitis (NASH) and associated hepatocellular carcinoma (HCC). Dysregulation of insulin secretion and dyslipidemia due to obesity and other lifestyle variables are the primary contributors to establishment of NAFLD. Onset and progression of NAFLD is orchestrated by an interplay of metabolic environment with genetic and epigenetic factors. An incompletely understood mechanism of NAFLD progression has greatly hampered the progress in identification of novel prognostic and therapeutic strategies. Emerging evidence suggests altered DNA methylation pattern as a key determinant of NAFLD pathogenesis. Environmental and lifestyle factors can manipulate DNA methylation patterns in a reversible manner, which manifests as changes in gene expression. In this review we attempt to highlight the importance of DNA methylation in establishment and progression of NAFLD. Development of novel diagnostic, prognostic and therapeutic strategies centered around DNA methylation signatures and modifiers has also been explored.
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28
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Ding P, Peng B, Li G, Sun X, Wang G. Glucosamine-phosphate N-acetyltransferase 1 and its DNA methylation can be biomarkers for the diagnosis and prognosis of lung cancer. J Clin Lab Anal 2022; 36:e24628. [PMID: 35929347 PMCID: PMC9459321 DOI: 10.1002/jcla.24628] [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: 04/14/2022] [Revised: 07/04/2022] [Accepted: 07/16/2022] [Indexed: 12/05/2022] Open
Abstract
Objective Lung cancer ranking high in the cancer‐related list has long perplexed patients, in which glucosamine‐phosphate N‐acetyltransferase 1 (GNPNAT1) is found to be highly expressed. Besides, DNA methylation is perceived as a biomarker to assess the prognosis of patients with various cancers. However, the correlation between GNPNAT1 and DNA methylation and the role of GNPNAT1 in lung cancer remain vague. Methods Principal component analysis (PCA), heatmap, volcano map, Venn diagram, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to screen out the candidate genes. The viability, migration, and invasion of lung cancer cells were detected by CCK‐8 and Transwell assays. An xenograft tumor mouse model was established. The relative expressions of GNPNAT1, E‐cadherin, vimentin, Matrix metalloproteinase‐2 (MMP‐2), tissue inhibitor of metalloproteinase‐2 (TIMP‐2), E2F1, and cyclin D1 in cells or xenograft tumor tissues were quantified by Western blot, RT‐qPCR, or immunohistochemistry assay. Results GNPNAT1 was screened as the research object. GNPNAT1 methylation was downregulated, while GNPNAT1 expression was upregulated in lung cancer tissues. The methylation and mRNA levels of GNPNAT1 were correlated with the patient prognosis. GNPNAT1 increased cell viability, migration and invasion, and promoted the xenograft tumor volume and weight, whereas shGNPNAT1 acted oppositely. Moreover, expressions of Vimentin, MMP‐2, E2F1, and cyclin D1 were increased, but E‐cadherin and TIMP‐2 expressions were decreased by overexpressed GNPNAT1, whilst GNPNAT1 knockdown ran conversely. Conclusion GNPNAT1 and methylated GNPNAT1 coverage are biomarkers for the diagnosis and prognosis of lung cancer.
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Affiliation(s)
- Peikun Ding
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Bin Peng
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Guofeng Li
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Xuefeng Sun
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Guangsuo Wang
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
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Advance of Serum Biomarkers and Combined Diagnostic Panels in Nonalcoholic Fatty Liver Disease. DISEASE MARKERS 2022; 2022:1254014. [PMID: 35811662 PMCID: PMC9259243 DOI: 10.1155/2022/1254014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/06/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) affects approximately 25-30% population worldwide, which progresses from simple steatosis to nonalcoholic steatohepatitis (NASH), fibrosis, cirrhosis, and hepatocellular carcinoma, and has complications such as cardiovascular events. Liver biopsy is still the gold standard for the diagnosis of NAFLD, with some limitations, such as invasive, sampling deviation, and empirical judgment. Therefore, it is urgent to develop noninvasive diagnostic biomarkers. Currently, a large number of NAFLD-related serum biomarkers have been identified, including apoptosis, inflammation, fibrosis, adipokines, hepatokines, and omics biomarkers, which could effectively diagnose NASH and exclude patients with progressive fibrosis. We summarized serum biomarkers and combined diagnostic panels of NAFLD, to provide some guidance for the noninvasive diagnosis and further clinical studies.
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Sang H, Lee KN, Jung CH, Han K, Koh EH. Association between organochlorine pesticides and nonalcoholic fatty liver disease in the National Health and Nutrition Examination Survey 2003-2004. Sci Rep 2022; 12:11590. [PMID: 35803990 PMCID: PMC9270488 DOI: 10.1038/s41598-022-15741-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/28/2022] [Indexed: 12/31/2022] Open
Abstract
While endocrine disruptors are emerging as a cause of nonalcoholic fatty liver disease (NAFLD), little is known about the link between NAFLD and organochlorine pesticides (OCPs), one of the endocrine disruptors. We retrospectively analyzed the U.S. National Health and Nutrition Examination Survey 2003-2004 and compared the baseline demographics in individuals according to the presence of NAFLD (fatty liver index [FLI] ≥ 60). Logistic regression analysis was performed to determine whether OCP concentration affected NAFLD prevalence and subgroup analyses regarding NAFLD-related variables and advanced hepatic fibrosis (FIB-4 ≥ 2.67) were performed. Of the 1515 individuals, 579 (38.2%) had NAFLD. Oxychlordane showed concentration-dependent risk for NAFLD (OR 3.471 in fourth quartile [Q4]; 95% CI 1.865-6.458; P = 0.007). p,p'-DDE and trans-nonachlor showed similar trends without statistical significance. Conversely, mirex showed the lowest risk for NAFLD in the highest concentration quartile (OR 0.29 in Q4; 95% CI 0.175-0.483; P < 0.001). Oxychlordane showed the most pronounced association with the levels of each component of FLI and liver enzymes. None of the OCPs were significantly associated with advanced fibrosis. In conclusion, among OCPs, exposure to oxychlordane showed the most prominent impact associated with NAFLD.
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Affiliation(s)
- Hyunji Sang
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kyu-Na Lee
- Department of Biomedicine & Health Science, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chang Hee Jung
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kyungdo Han
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, Republic of Korea
| | - Eun Hee Koh
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Furthner D, Weghuber D, Dalus C, Lukas A, Stundner-Ladenhauf HN, Mangge H, Pixner T. Nonalcoholic Fatty Liver Disease in Children with Obesity: Narrative Review and Research Gaps. Horm Res Paediatr 2022; 95:167-176. [PMID: 34351306 DOI: 10.1159/000518595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/20/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is the leading hepatic disease in children, ranging from steatosis to steatohepatitis and fibrosis. Age, sex, hormonal levels, pubertal stages, genetic risk- and epigenetic factors are among the many influencing factors. Appearing predominantly in children with obesity, but not exclusively, it is the liver's manifestation of the metabolic syndrome but can also exist as an isolated entity. SUMMARY Pediatric NAFLD differs from the adult phenotype. This narrative review on NAFLD in children with obesity provides an overview of the current knowledge on risk factors, screening, and diagnostic methods, as well state-of-the-art treatment. The recent discussion on the proposition of a new nomenclature - Metabolic [Dysfunction-] Associated Liver Disease - is featured, and current gaps of knowledge are discussed. KEY MESSAGES Currently, there is no international consensus on screening and monitoring of pediatric NAFLD. With lifestyle interventions being the cornerstone of treatment, no registered pharmacological treatment for pediatric NAFLD is available. Development and validation of additional noninvasive biomarkers, scores and imaging tools suitable to subcategorize, screen and monitor pediatric patients are necessary. With a variety of upcoming and promising agents, clear recommendations for pediatric nonalcoholic steatohepatitis trials are urgently needed.
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Affiliation(s)
- Dieter Furthner
- Department of Pediatric and Adolescent Medicine, Salzkammergutklinikum Voecklabruck, Voecklabruck, Austria.,Obesity Research Unit, Paracelsus Medical University, Salzburg, Austria
| | - Daniel Weghuber
- Obesity Research Unit, Paracelsus Medical University, Salzburg, Austria.,University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Christopher Dalus
- Obesity Research Unit, Paracelsus Medical University, Salzburg, Austria.,University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Andreas Lukas
- Department of Pediatric and Adolescent Medicine, Salzkammergutklinikum Voecklabruck, Voecklabruck, Austria.,Obesity Research Unit, Paracelsus Medical University, Salzburg, Austria
| | | | - Harald Mangge
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Thomas Pixner
- Department of Pediatric and Adolescent Medicine, Salzkammergutklinikum Voecklabruck, Voecklabruck, Austria.,Obesity Research Unit, Paracelsus Medical University, Salzburg, Austria
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de Oliveira DT, de Paiva NCN, Carneiro CM, Guerra-Sá R. Dynamic changes in hepatic DNA methylation during the development of nonalcoholic fatty liver disease induced by a high-sugar diet. J Physiol Biochem 2022; 78:763-775. [PMID: 35716250 DOI: 10.1007/s13105-022-00900-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/17/2022] [Indexed: 11/28/2022]
Abstract
DNA methylation is an important epigenetic mechanism of gene expression control. The present study aimed to evaluate the temporal effect of isocaloric high-sugar diet (HSD) intake on the development of nonalcoholic fatty liver disease (NAFLD) and the role of DNA methylation in this event. Newly weaned Wistar rats were divided into eight groups and fed a standard chow diet or an HSD ad libitum for 4 weeks, 8 weeks, 15 weeks, and 18 weeks. After the experimental periods, the animals were euthanized and their livers were removed for histological analysis, gene expression of maintenance methylase (Dnmt1), de novo methylases (Dnmt3a and Dnmt3b), demethylases (Tet2 and Tet3) of DNA, and global DNA methylation. HSD intake led to the gradual development of NAFLD. HSD intake for 18 weeks was associated with downregulation of Dnmt1 expression and global DNA hypomethylation; these results were negatively correlated with more severe steatosis scores observed in these animals. The HSD consumption for 18 weeks was also associated with a decrease in Dnmt3a and Tet2 expression. Interestingly, the expression of de novo methyltransferase Dnmt3b was reduced by HSD during all experimental periods. Together, these results indicate that the downregulation of de novo DNA methylation, Dnmt3b, induced by HSD is the primary factor in the development of NAFLD. On the other hand, disease progression is associated with downregulation of maintenance DNA methylation and global DNA hypomethylation. These results suggest a link between the dynamic changes in hepatic DNA methylation and the development of NAFLD induced by an HSD intake.
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Affiliation(s)
- Daiane Teixeira de Oliveira
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Nívia Carolina Nogueira de Paiva
- Laboratório de Imunopatologia, Núcleo de Pesquisas Em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Cláudia Martins Carneiro
- Laboratório de Imunopatologia, Núcleo de Pesquisas Em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Renata Guerra-Sá
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
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Wen L, Li M, Lin X, Li Y, Song H, Chen H. AgNPs Aggravated Hepatic Steatosis, Inflammation, Oxidative Stress, and Epigenetic Changes in Mice With NAFLD Induced by HFD. Front Bioeng Biotechnol 2022; 10:912178. [PMID: 35677306 PMCID: PMC9169095 DOI: 10.3389/fbioe.2022.912178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/29/2022] [Indexed: 12/30/2022] Open
Abstract
The recent development of silver nanoparticles (AgNPs) has sparked increased interest in biomedical and pharmaceutical applications, leading to the possibility of human exposure. The liver is the primary target organ in the metabolism and transport of nanoparticles. Non-alcoholic fatty liver disease (NAFLD) is the most common and leading cause of hepatic metabolic syndrome with approximately 15% of patients will develop into non-alcoholic steatohepatitis, fibrosis, cirrhosis, and eventually hepatocellular carcinoma. Thus, the potential hepatotoxicity of AgNPs on NAFLD development and progression should be of great concern. Herein, we explored the potential hepatic effect of a single intravenously injected dose of 0.5, 2.5, and 12.5 mg/kg BW on the liver function of high-fat-diet (HFD)-fed mice for 7 days. AgNP treatment increased serum levels of alanine aminotransferase, aspartate transaminase, triglycerides and cholesterols, the number of lipid droplets, and the contents of triglycerides and cholesterols in NAFLD mice livers compared to HFD-fed mice. The mechanism of AgNP-induced worsen hepatotoxicity in mice is associated with hyperactivation of SREBP-1c-mediated de novo lipogenesis and liver inflammation. Additionally, HFD-fed mice treated with AgNPs had significantly higher oxidative damage and lower global DNA methylation and DNA hydroxymethylation than NAFLD mice. This study suggests that AgNP treatment exacerbated HFD-induced hepatic steatosis, liver inflammation, oxidative stress, and epigenetic changes in mice, which is relevant to the risk of AgNP exposure on NAFLD development and progression.
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Affiliation(s)
- Ling Wen
- Guangzhou Twelfth People’s Hospital, Guangzhou, China
| | - Minyan Li
- Guangzhou Twelfth People’s Hospital, Guangzhou, China
| | - Xiaojun Lin
- Department of Gastroenterology, Guangzhou Twelfth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yan Li
- Guangzhou Twelfth People’s Hospital, Guangzhou, China
| | - Huidong Song
- Guangzhou Twelfth People’s Hospital, Guangzhou, China
| | - Hanqing Chen
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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Bashir A, Duseja A, De A, Mehta M, Tiwari P. Non-alcoholic fatty liver disease development: A multifactorial pathogenic phenomena. LIVER RESEARCH 2022. [DOI: 10.1016/j.livres.2022.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Wang H, Wu Y, Tang W. Methionine cycle in nonalcoholic fatty liver disease and its potential applications. Biochem Pharmacol 2022; 200:115033. [PMID: 35395242 DOI: 10.1016/j.bcp.2022.115033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
As a chronic metabolic disease affecting epidemic proportions worldwide, the pathogenesis of Nonalcoholic Fatty Liver Disease (NAFLD) is not clear yet. There is also a lack of precise biomarkers and specific medicine for the diagnosis and treatment of NAFLD. Methionine metabolic cycle, which is critical for the maintaining of cellular methylation and redox state, is involved in the pathophysiology of NAFLD. However, the molecular basis and mechanism of methionine metabolism in NAFLD are not completely understood. Here, we mainly focus on specific enzymes that participates in methionine cycle, to reveal their interconnections with NAFLD, in order to recognize the pathogenesis of NAFLD from a new angle and at the same time, explore the clinical characteristics and therapeutic strategies.
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Affiliation(s)
- Haoyu Wang
- University of Chinese Academy of Sciences, Beijing, 100049, PR China; Laboratory of Anti-inflammation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China
| | - Yanwei Wu
- Laboratory of Anti-inflammation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China
| | - Wei Tang
- University of Chinese Academy of Sciences, Beijing, 100049, PR China; Laboratory of Anti-inflammation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China.
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Sun QF, Tang LJ, Wang MJ, Zhu PW, Li YY, Ma HL, Huang OY, Hong L, Li G, Byrne CD, Targher G, Liu WY, Lu Y, Ding JG, Zheng MH. Potential Blood DNA Methylation Biomarker Genes for Diagnosis of Liver Fibrosis in Patients With Biopsy-Proven Non-alcoholic Fatty Liver Disease. Front Med (Lausanne) 2022; 9:864570. [PMID: 35433752 PMCID: PMC9008751 DOI: 10.3389/fmed.2022.864570] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 12/29/2022] Open
Abstract
Background and objectiveThis pilot study aimed to identify potential blood DNA methylation (BDM) biomarker genes for the diagnosis of liver fibrosis in non-alcoholic fatty liver disease (NAFLD).MethodsWe included a total of 16 NAFLD patients with significant (SLF, liver fibrosis stage ≥ 2) and 16 patients with non-significant liver fibrosis (NSLF, fibrosis stages 0–1). The association between BDM and liver fibrosis was analyzed. Genes were selected based on a stepwise-filtering with CpG islands containing significant differentially methylated probes.ResultsThe two groups of patients were distinguishable through both t-distributed stochastic neighbor embedding (t-SNE) analysis and unsupervised hierarchical clustering analysis based on their BDM status. BDM levels were significantly higher in the NSLF group than in the SLF group. The methylation levels in the island and shelf regions were also significantly higher in the NSLF group, as well as the methylation levels in the first exon, 3′-untranslated region, body, ExonBnd, non-intergenic region, transcription start site (TSS)1500, and TSS200 regions (all p < 0.05). BDM status was associated with greater histological liver fibrosis, but not with age, sex, or other histological features of NAFLD (p < 0.05). The methylation levels of the hypomethylated CpG island region of CISTR, IFT140, and RGS14 genes were increased in the NSLF group compared to the SLF group (all p < 0.05).ConclusionBDM may stratify NAFLD patients with significant and non-significant liver fibrosis. The CISTR, IFT140, and RGS14 genes are potential novel candidate BDM biomarkers for liver fibrosis and these pilot data suggest further work on BDM biomarkers is warranted.
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Affiliation(s)
- Qing-Feng Sun
- Department of Infectious Diseases, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liang-Jie Tang
- NAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ming-Jie Wang
- Department of Gastroenterology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pei-Wu Zhu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yang-Yang Li
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hong-Lei Ma
- NAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Practice, Affiliated People’s Hospital, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Ou-Yang Huang
- NAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liang Hong
- Department of Infectious Diseases, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Gang Li
- NAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Christopher D. Byrne
- National Institute for Health Research Southampton Biomedical Research Centre, University Hospital Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Giovanni Targher
- Section of Endocrinology, Diabetes and Metabolism, Department of Medicine, Azienda Ospedaliera Universitaria Integrata Verona, University of Verona, Verona, Italy
| | - Wen-Yue Liu
- Department of Endocrinology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yan Lu
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ji-Guang Ding
- Department of Infectious Diseases, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Ji-Guang Ding,
| | - Ming-Hua Zheng
- NAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Hepatology, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Diagnosis and Treatment for the Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China
- *Correspondence: Ming-Hua Zheng,
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Ko YK, Kim H, Lee Y, Lee YS, Gim JA. DNA Methylation Patterns According to Fatty Liver Index and Longitudinal Changes from the Korean Genome and Epidemiology Study (KoGES). Curr Issues Mol Biol 2022; 44:1149-1168. [PMID: 35723298 PMCID: PMC8947460 DOI: 10.3390/cimb44030075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
The role of differentially methylated regions (DMRs) in nonalcoholic fatty liver disease (NAFLD) is unclear. This study aimed to identify the role of DMR in NAFLD development and progression using the Korean Genome and Epidemiology Study (KoGES) cohort. We used laboratory evaluations and Illumina Methylation 450 k DNA methylation microarray data from KoGES. The correlation between fatty liver index (FLI) and genomic CpG sites was analyzed in 322 subjects. Longitudinal changes over 8 years were confirmed in 33 subjects. To identify CpG sites and genes related to FLI, we obtained enrichment terms for 6765 genes. DMRs were identified for both high (n = 128) and low (n = 194) groups on the basis of FLI 30 in 142 men and 180 women. To confirm longitudinal changes in 33 subjects, the ratio of follow-up and baseline investigation values was obtained. Correlations and group comparisons were performed for the 8 year change values. PITPNM3, RXFP3, and THRB were hypermethylated in the increased FLI groups, whereas SLC9A2 and FOXI3 were hypermethylated in the decreased FLI groups. DMRs describing NAFLD were determined, and functions related to inflammation were identified. Factors related to longitudinal changes are suggested, and blood circulation-related functions appear to be important in the management of NAFLD.
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Affiliation(s)
- Young Kyung Ko
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Korea;
| | - Hayeon Kim
- Department of Pathology, Korea University College of Medicine, Seoul 08308, Korea;
| | - Yoonseok Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Korea;
| | - Young-Sun Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Korea;
- Correspondence: (Y.-S.L.); (J.-A.G.); Tel.: +82-2-2626-3013 (Y.-S.L.); +82-2-2626-2362 (J.-A.G.)
| | - Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea
- Correspondence: (Y.-S.L.); (J.-A.G.); Tel.: +82-2-2626-3013 (Y.-S.L.); +82-2-2626-2362 (J.-A.G.)
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Diagnostic Modalities of Non-Alcoholic Fatty Liver Disease: From Biochemical Biomarkers to Multi-Omics Non-Invasive Approaches. Diagnostics (Basel) 2022; 12:diagnostics12020407. [PMID: 35204498 PMCID: PMC8871470 DOI: 10.3390/diagnostics12020407] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 02/05/2023] Open
Abstract
Non-Alcoholic Fatty Liver Disease (NAFLD) is currently the most common cause of chronic liver disease worldwide, and its prevalence is increasing globally. NAFLD is a multifaceted disorder, and its spectrum includes steatosis to steatohepatitis, which may evolve to advanced fibrosis and cirrhosis. In addition, the presence of NAFLD is independently associated with a higher cardiometabolic risk and increased mortality rates. Considering that the vast majority of individuals with NAFLD are mainly asymptomatic, early diagnosis of non-alcoholic steatohepatitis (NASH) and accurate staging of fibrosis risk is crucial for better stratification, monitoring and targeted management of patients at risk. To date, liver biopsy remains the gold standard procedure for the diagnosis of NASH and staging of NAFLD. However, due to its invasive nature, research on non-invasive tests is rapidly increasing with significant advances having been achieved during the last decades in the diagnostic field. New promising non-invasive biomarkers and techniques have been developed, evaluated and assessed, including biochemical markers, imaging modalities and the most recent multi-omics approaches. Our article provides a comprehensive review of the currently available and emerging non-invasive diagnostic tools used in assessing NAFLD, also highlighting the importance of accurate and validated diagnostic tools.
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Rodríguez-Sanabria JS, Escutia-Gutiérrez R, Rosas-Campos R, Armendáriz-Borunda JS, Sandoval-Rodríguez A. An Update in Epigenetics in Metabolic-Associated Fatty Liver Disease. Front Med (Lausanne) 2022; 8:770504. [PMID: 35087844 PMCID: PMC8787199 DOI: 10.3389/fmed.2021.770504] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) is characterized by hepatic steatosis accompanied by one of three features: overweight or obesity, T2DM, or lean or normal weight with evidence of metabolic dysregulation. It is distinguished by excessive fat accumulation in hepatocytes, and a decrease in the liver's ability to oxidize fats, the accumulation of ectopic fat, and the activation of proinflammatory pathways. Chronic damage will keep this pathophysiologic cycle active causing progression from hepatic steatosis to cirrhosis and eventually, hepatocarcinoma. Epigenetics affecting gene expression without altering DNA sequence allows us to study MAFLD pathophysiology from a different perspective, in which DNA methylation processes, histone modifications, and miRNAs expression have been closely associated with MAFLD progression. However, these considerations also faced us with the circumstance that modifying those epigenetics patterns might lead to MAFLD regression. Currently, epigenetics is an area of great interest because it could provide new insights in therapeutic targets and non-invasive biomarkers. This review comprises an update on the role of epigenetic patterns, as well as innovative therapeutic targets and biomarkers in MAFLD.
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Affiliation(s)
- J Samael Rodríguez-Sanabria
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Rebeca Escutia-Gutiérrez
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Rebeca Rosas-Campos
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Juan S Armendáriz-Borunda
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico.,School of Medicine and Health Sciences, Tecnologico de Monterrey, Campus Guadalajara, Zapopan, Mexico
| | - Ana Sandoval-Rodríguez
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
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DeVito LM, Barzilai N, Cuervo AM, Niedernhofer LJ, Milman S, Levine M, Promislow D, Ferrucci L, Kuchel GA, Mannick J, Justice J, Gonzales MM, Kirkland JL, Cohen P, Campisi J. Extending human healthspan and longevity: a symposium report. Ann N Y Acad Sci 2022; 1507:70-83. [PMID: 34498278 PMCID: PMC10231756 DOI: 10.1111/nyas.14681] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022]
Abstract
For many years, it was believed that the aging process was inevitable and that age-related diseases could not be prevented or reversed. The geroscience hypothesis, however, posits that aging is, in fact, malleable and, by targeting the hallmarks of biological aging, it is indeed possible to alleviate age-related diseases and dysfunction and extend longevity. This field of geroscience thus aims to prevent the development of multiple disorders with age, thereby extending healthspan, with the reduction of morbidity toward the end of life. Experts in the field have made remarkable advancements in understanding the mechanisms underlying biological aging and identified ways to target aging pathways using both novel agents and repurposed therapies. While geroscience researchers currently face significant barriers in bringing therapies through clinical development, proof-of-concept studies, as well as early-stage clinical trials, are underway to assess the feasibility of drug evaluation and lay a regulatory foundation for future FDA approvals in the future.
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Affiliation(s)
| | - Nir Barzilai
- Albert Einstein College of Medicine, Bronx, New York
| | | | | | - Sofiya Milman
- Albert Einstein College of Medicine, Bronx, New York
| | | | | | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - George A Kuchel
- University of Connecticut School of Medicine, Farmington, Connecticut
| | | | - Jamie Justice
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Mitzi M Gonzales
- University of Texas Health Sciences Center San Antonio, San Antonio, Texas
| | | | - Pinchas Cohen
- USC Leonard Davis School of Gerontology, Los Angeles, California
| | - Judith Campisi
- The Buck Institute for Research on Aging, Novato, California
- Lawrence Berkeley National Laboratory, Berkley, California
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41
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Chen X, Luo J, Liu J, Chen T, Sun J, Zhang Y, Xi Q. Exploration of the Effect on Genome-Wide DNA Methylation by miR-143 Knock-Out in Mice Liver. Int J Mol Sci 2021; 22:13075. [PMID: 34884879 PMCID: PMC8658369 DOI: 10.3390/ijms222313075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
MiR-143 play an important role in hepatocellular carcinoma and liver fibrosis via inhibiting hepatoma cell proliferation. DNA methyltransferase 3 alpha (DNMT3a), as a target of miR-143, regulates the development of primary organic solid tumors through DNA methylation mechanisms. However, the effect of miR-143 on DNA methylation profiles in liver is unclear. In this study, we used Whole-Genome Bisulfite Sequencing (WGBS) to detect the differentially methylated regions (DMRs), and investigated DMR-related genes and their enriched pathways by miR-143. We found that methylated cytosines increased 0.19% in the miR-143 knock-out (KO) liver fed with high-fat diet (HFD), compared with the wild type (WT). Furthermore, compared with the WT group, the CG methylation patterns of the KO group showed lower CG methylation levels in CG islands (CGIs), promoters and hypermethylation in CGI shores, 5'UTRs, exons, introns, 3'UTRs, and repeat regions. A total of 984 DMRs were identified between the WT and KO groups consisting of 559 hypermethylation and 425 hypomethylation DMRs. Furthermore, DMR-related genes were enriched in metabolism pathways such as carbon metabolism (serine hydroxymethyltransferase 2 (Shmt2), acyl-Coenzyme A dehydrogenase medium chain (Acadm)), arginine and proline metabolism (spermine synthase (Sms), proline dehydrogenase (Prodh2)) and purine metabolism (phosphoribosyl pyrophosphate synthetase 2 (Prps2)). In summary, we are the first to report the change in whole-genome methylation levels by miR-143-null through WGBS in mice liver, and provide an experimental basis for clinical diagnosis and treatment in liver diseases, indicating that miR-143 may be a potential therapeutic target and biomarker for liver damage-associated diseases and hepatocellular carcinoma.
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Affiliation(s)
| | | | | | | | | | - Yongliang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China; (X.C.); (J.L.); (J.L.); (T.C.); (J.S.)
| | - Qianyun Xi
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China; (X.C.); (J.L.); (J.L.); (T.C.); (J.S.)
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42
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Li K, Song Y, Qin L, Li A, Jiang S, Ren L, Zang C, Sun J, Zhao Y, Zhang Y. A CpG Methylation Signature as a Potential Marker for Early Diagnosis of Hepatocellular Carcinoma From HBV-Related Liver Disease Using Multiplex Bisulfite Sequencing. Front Oncol 2021; 11:756326. [PMID: 34745991 PMCID: PMC8564137 DOI: 10.3389/fonc.2021.756326] [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: 08/11/2021] [Accepted: 09/27/2021] [Indexed: 12/04/2022] Open
Abstract
Background Aberrant methylation of CpG sites served as an epigenetic marker for building diagnostic, prognostic, and recurrence models for hepatocellular carcinoma (HCC). Methods Using Illumina 450K and EPIC Beadchip, we identified 34 CpG sites in peripheral blood mononuclear cell (PBMC) DNA that were differentially methylated in early HCC versus HBV-related liver diseases (HBVLD). We employed multiplex bisulfite sequencing (MBS) based on next-generation sequencing (NGS) to measure methylation of 34 CpG sites in PBMC DNA from 654 patients that were divided into a training set (n = 442) and a test set (n = 212). Using the training set, we selected and built a six-CpG-scorer (namely, cg14171514, cg07721852, cg05166871, cg18087306, cg05213896, and cg18772205), applying least absolute shrinkage and selection operator (LASSO) regression. We performed multivariable analyses of four candidate risk predictors (namely, six-CpG-scorer, age, sex, and AFP level), using 20 times imputation of missing data, non-linearly transformed, and backwards feature selection with logistic regression. The final model’s regression coefficients were calculated according to “Rubin’s Rules”. The diagnostic accuracy of the model was internally validated with a 10,000 bootstrap validation dataset and then applied to the test set for validation. Results The area under the receiver operating characteristic curve (AUROC) of the model was 0.81 (95% CI, 0.77–0.85) and it showed good calibration and decision curve analysis. Using enhanced bootstrap validation, adjusted C-statistics and adjusted Brier score were 0.809 and 0.199, respectively. The model also showed an AUROC value of 0.84 (95% CI 0.79–0.88) of diagnosis for early HCC in the test set. Conclusions Our model based on the six-CpG-scorer was a reliable diagnosis tool for early HCC from HBVLD. The usage of the MBS method can realize large-scale detection of CpG sites in clinical diagnosis of early HCC and benefit the majority of patients.
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Affiliation(s)
- Kang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yi Song
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ling Qin
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Ang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | | | - Lei Ren
- Pharmacology Department, Air Force Medical Center, People's Liberation Army of China (PLA), Beijing, China
| | - Chaoran Zang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Jianping Sun
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Clinical Laboratory Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yonghong Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
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43
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Wu N, Yuan F, Yue S, Jiang F, Ren D, Liu L, Bi Y, Guo Z, Ji L, Han K, Yang X, Feng M, Su K, Yang F, Wu X, Lu Q, Li X, Wang R, Liu B, Le S, Shi Y, He G. Effect of exercise and diet intervention in NAFLD and NASH via GAB2 methylation. Cell Biosci 2021; 11:189. [PMID: 34736535 PMCID: PMC8569968 DOI: 10.1186/s13578-021-00701-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is a disorder that extends from simple hepatic steatosis to nonalcoholic steatohepatitis (NASH), which is effectively alleviated by lifestyle intervention. Nevertheless, DNA methylation mechanism underling the effect of environmental factors on NAFLD and NASH is still obscure. The aim of this study was to investigate the effect of exercise and diet intervention in NAFLD and NASH via DNA methylation of GAB2. METHODS Methylation of genomic DNA in human NAFLD was quantified using Infinium Methylation EPIC BeadChip assay after exercise (Ex), low carbohydrate diet (LCD) and exercise plus low carbohydrate diet (ELCD) intervention. The output Idat files were processed using ChAMP package. False discovery rate on genome-wide analysis of DNA methylation (q < 0.05), and cytosine-guanine dinucleotides (CpGs) which are located in promoters were used for subsequent analysis (|Δβ|≥ 0.1). K-means clustering was used to cluster differentially methylated genes according to 3D genome information from Human embryonic stem cell. To quantify DNA methylation and mRNA expression of GRB2 associated binding protein 2 (GAB2) in NASH mice after Ex, low fat diet (LFD) and exercise plus low fat diet (ELFD), MassARRAY EpiTYPER and quantitative reverse transcription polymerase chain reaction were used. RESULTS Both LCD and ELCD intervention on human NAFLD can induce same DNA methylation alterations at critical genes in blood, e.g., GAB2, which was also validated in liver and adipose of NASH mice after LFD and ELFD intervention. Moreover, methylation of CpG units (i.e., CpG_10.11.12) inversely correlated with mRNA expression GAB2 in adipose tissue of NASH mice after ELFD intervention. CONCLUSIONS We highlighted the susceptibility of DNA methylation in GAB2 to ELFD intervention, through which exercise and diet can protect against the progression of NAFLD and NASH on the genome level, and demonstrated that the DNA methylation variation in blood could mirror epigenetic signatures in target tissues of important biological function, i.e., liver and adipose tissue. Trial registration International Standard Randomized Controlled Trial Number Register (ISRCTN 42622771).
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Affiliation(s)
- Na Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yuan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Siran Yue
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fengyan Jiang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Decheng Ren
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Liangjie Liu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Bi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenming Guo
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Mofan Feng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Su
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ruirui Wang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baocheng Liu
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shenglong Le
- Exercise Translational Medicine Center, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China. .,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China. .,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
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44
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Gao W, Liu JL, Lu X, Yang Q. Epigenetic regulation of energy metabolism in obesity. J Mol Cell Biol 2021; 13:480-499. [PMID: 34289049 PMCID: PMC8530523 DOI: 10.1093/jmcb/mjab043] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/24/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Obesity has reached epidemic proportions globally. Although modern adoption of a sedentary lifestyle coupled with energy-dense nutrition is considered to be the main cause of obesity epidemic, genetic preposition contributes significantly to the imbalanced energy metabolism in obesity. However, the variants of genetic loci identified from large-scale genetic studies do not appear to fully explain the rapid increase in obesity epidemic in the last four to five decades. Recent advancements of next-generation sequencing technologies and studies of tissue-specific effects of epigenetic factors in metabolic organs have significantly advanced our understanding of epigenetic regulation of energy metabolism in obesity. The epigenome, including DNA methylation, histone modifications, and RNA-mediated processes, is characterized as mitotically or meiotically heritable changes in gene function without alteration of DNA sequence. Importantly, epigenetic modifications are reversible. Therefore, comprehensively understanding the landscape of epigenetic regulation of energy metabolism could unravel novel molecular targets for obesity treatment. In this review, we summarize the current knowledge on the roles of DNA methylation, histone modifications such as methylation and acetylation, and RNA-mediated processes in regulating energy metabolism. We also discuss the effects of lifestyle modifications and therapeutic agents on epigenetic regulation of energy metabolism in obesity.
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Affiliation(s)
- Wei Gao
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Jia-Li Liu
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Xiang Lu
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Qin Yang
- Department of Medicine, Physiology and Biophysics, UC Irvine Diabetes Center, University of California Irvine, Irvine, CA 92697, USA
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45
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Dong XC, Chowdhury K, Huang M, Kim HG. Signal Transduction and Molecular Regulation in Fatty Liver Disease. Antioxid Redox Signal 2021; 35:689-717. [PMID: 33906425 PMCID: PMC8558079 DOI: 10.1089/ars.2021.0076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significance: Fatty liver disease is a major liver disorder in the modern societies. Comprehensive understanding of the pathophysiology and molecular mechanisms is essential for the prevention and treatment of the disease. Recent Advances: Remarkable progress has been made in the recent years in basic and translational research in the field of fatty liver disease. Multiple signaling pathways have been implicated in the development of fatty liver disease, including AMP-activated protein kinase, mechanistic target of rapamycin kinase, endoplasmic reticulum stress, oxidative stress, inflammation, transforming growth factor β, and yes1-associated transcriptional regulator/transcriptional coactivator with PDZ-binding motif (YAP/TAZ). In addition, critical molecular regulations at the transcriptional and epigenetic levels have been linked to the pathogenesis of fatty liver disease. Critical Issues: Some critical issues remain to be solved so that research findings can be translated into clinical applications. Robust and reliable biomarkers are needed for diagnosis of different stages of the fatty liver disease. Effective and safe molecular targets remain to be identified and validated. Prevention strategies require solid scientific evidence and population-wide feasibility. Future Directions: As more data are generated with time, integrative approaches are needed to comprehensively understand the disease pathophysiology and mechanisms at multiple levels from population, organismal system, organ/tissue, to cell. The interactions between genes and environmental factors require deeper investigation for the purposes of prevention and personalized treatment of fatty liver disease. Antioxid. Redox Signal. 35, 689-717.
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Affiliation(s)
- Xiaocheng Charlie Dong
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Kushan Chowdhury
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Menghao Huang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Hyeong Geug Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Dietary Patterns Influence Target Gene Expression through Emerging Epigenetic Mechanisms in Nonalcoholic Fatty Liver Disease. Biomedicines 2021; 9:biomedicines9091256. [PMID: 34572442 PMCID: PMC8468830 DOI: 10.3390/biomedicines9091256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) refers to the pathologic buildup of extra fat in the form of triglycerides in liver cells without excessive alcohol intake. NAFLD became the most common cause of chronic liver disease that is tightly associated with key aspects of metabolic disorders, including insulin resistance, obesity, diabetes, and metabolic syndrome. It is generally accepted that multiple mechanisms and pathways are involved in the pathogenesis of NAFLD. Heredity, sedentary lifestyle, westernized high sugar saturated fat diet, metabolic derangements, and gut microbiota, all may interact on a on genetically susceptible individual to cause the disease initiation and progression. While there is an unquestionable role for gene-diet interaction in the etiopathogenesis of NAFLD, it is increasingly apparent that epigenetic processes can orchestrate many aspects of this interaction and provide additional mechanistic insight. Exciting research demonstrated that epigenetic alterations in chromatin can influence gene expression chiefly at the transcriptional level in response to unbalanced diet, and therefore predispose an individual to NAFLD. Thus, further discoveries into molecular epigenetic mechanisms underlying the link between nutrition and aberrant hepatic gene expression can yield new insights into the pathogenesis of NAFLD, and allow innovative epigenetic-based strategies for its early prevention and targeted therapies. Herein, we outline the current knowledge of the interactive role of a high-fat high-calories diet and gene expression through DNA methylation and histone modifications on the pathogenesis of NAFLD. We also provide perspectives on the advancement of the epigenomics in the field and possible shortcomings and limitations ahead.
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47
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Peng XF, Huang SF, Chen LJ, Xu L, Ye WC. Targeting epigenetics and lncRNAs in liver disease: From mechanisms to therapeutics. Pharmacol Res 2021; 172:105846. [PMID: 34438063 DOI: 10.1016/j.phrs.2021.105846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/19/2022]
Abstract
Early onset and progression of liver diseases can be driven by aberrant transcriptional regulation. Different transcriptional regulation processes, such as RNA/DNA methylation, histone modification, and ncRNA-mediated targeting, can regulate biological processes in healthy cells, as well also under various pathological conditions, especially liver disease. Numerous studies over the past decades have demonstrated that liver disease has a strong epigenetic component. Therefore, the epigenetic basis of liver disease has challenged our knowledge of epigenetics, and epigenetics field has undergone an important transformation: from a biological phenomenon to an emerging focus of disease research. Furthermore, inhibitors of different epigenetic regulators, such as m6A-related factors, are being explored as potential candidates for preventing and treating liver diseases. In the present review, we summarize and discuss the current knowledge of five distinct but interconnected and interdependent epigenetic processes in the context of hepatic diseases: RNA methylation, DNA methylation, histone methylation, miRNAs, and lncRNAs. Finally, we discuss the potential therapeutic implications and future challenges and ongoing research in the field. Our review also provides a perspective for identifying therapeutic targets and new hepatic biomarkers of liver disease, bringing precision research and disease therapy to the modern era of epigenetics.
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Affiliation(s)
- Xiao-Fei Peng
- Department of General Surgery, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Shi-Feng Huang
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Ling-Juan Chen
- Department of Clinical Laboratory, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Lingqing Xu
- Department of Clinical Laboratory, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Wen-Chu Ye
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China.
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48
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Epigenetic Changes Affecting the Development of Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13164237. [PMID: 34439391 PMCID: PMC8392268 DOI: 10.3390/cancers13164237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/15/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hepatocellular carcinoma is a life-threatening disease. Despite many efforts to understand the exact pathogenesis and the signaling pathways involved in its formation, treatment remains unsatisfactory. Currently, an important function in the development of neoplastic diseases and treatment effects is attributed to changes taking place at the epigenetic level. Epigenetic studies revealed modified methylation patterns in HCC, dysfunction of enzymes engaged in the DNA methylation process, the aberrant function of non-coding RNAs, and a set of histone modifications that influence gene expression. The aim of this review is to summarize the current knowledge on the role of epigenetics in the formation of hepatocellular carcinoma. Abstract Hepatocellular carcinoma (HCC) remains a serious oncologic issue with still a dismal prognosis. So far, no key molecular mechanism that underlies its pathogenesis has been identified. Recently, by specific molecular approaches, many genetic and epigenetic changes arising during HCC pathogenesis were detected. Epigenetic studies revealed modified methylation patterns in HCC tumors, dysfunction of enzymes engaged in the DNA methylation process, and a set of histone modifications that influence gene expression. HCC cells are also influenced by the disrupted function of non-coding RNAs, such as micro RNAs and long non-coding RNAs. Moreover, a role of liver cancer stem cells in HCC development is becoming evident. The reversibility of epigenetic changes offers the possibility of influencing them and regulating their undesirable effects. All these data can be used not only to identify new therapeutic targets but also to predict treatment response. This review focuses on epigenetic changes in hepatocellular carcinoma and their possible implications in HCC therapy.
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49
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Johnson ND, Wu X, Still CD, Chu X, Petrick AT, Gerhard GS, Conneely KN, DiStefano JK. Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD. Clin Epigenetics 2021; 13:152. [PMID: 34353365 PMCID: PMC8340447 DOI: 10.1186/s13148-021-01129-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is characterized by changes in cell composition that occur throughout disease pathogenesis, which includes the development of fibrosis in a subset of patients. DNA methylation (DNAm) is a plausible mechanism underlying these shifts, considering that DNAm profiles differ across tissues and cell types, and DNAm may play a role in cell-type differentiation. Previous work investigating the relationship between DNAm and fibrosis in NAFLD has been limited by sample size and the number of CpG sites interrogated. RESULTS Here, we performed an epigenome-wide analysis using Infinium MethylationEPIC array data from 325 individuals with NAFLD, including 119 with severe fibrosis and 206 with no histological evidence of fibrosis. After adjustment for latent confounders, we identified 7 CpG sites whose DNAm associated with fibrosis (p < 5.96 × 10-8). Analysis of RNA-seq data collected from a subset of individuals (N = 56) revealed that gene expression at 288 genes associated with DNAm at one or more of the 7 fibrosis-related CpGs. DNAm-based estimates of cell-type proportions showed that estimated proportions of natural killer cells increased, while epithelial cell proportions decreased with disease stage. Finally, we used an elastic net regression model to assess DNAm as a biomarker of fibrotic stage and found that our model predicted fibrosis with a sensitivity of 0.93 and provided information beyond a model based solely on cell-type proportions. CONCLUSION These findings are consistent with DNAm as a mechanism underpinning or marking fibrosis-related shifts in cell composition and demonstrate the potential of DNAm as a possible biomarker of NAFLD fibrosis.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Xiumei Wu
- Diabetes and Fibrotic Disease Unit, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Xin Chu
- Geisinger Obesity Institute, Danville, PA, USA
| | | | - Glenn S Gerhard
- Lewis Katz School of Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Johanna K DiStefano
- Diabetes and Fibrotic Disease Unit, Translational Genomics Research Institute, Phoenix, AZ, USA.
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Zhang C, Yang M. Current Options and Future Directions for NAFLD and NASH Treatment. Int J Mol Sci 2021; 22:ijms22147571. [PMID: 34299189 PMCID: PMC8306701 DOI: 10.3390/ijms22147571] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide, with a broad spectrum ranging from simple steatosis to advanced stage of nonalcoholic steatohepatitis (NASH). Although there are many undergoing clinical trials for NAFLD treatment, there is no currently approved treatment. NAFLD accounts as a major causing factor for the development of hepatocellular carcinoma (HCC), and its incidence rises accompanying the prevalence of obesity and diabetes. Reprogramming of antidiabetic and anti-obesity medicine is a major treatment option for NAFLD and NASH. Liver inflammation and cellular death, with or without fibrosis account for the progression of NAFLD to NASH. Therefore, molecules and signaling pathways involved in hepatic inflammation, fibrosis, and cell death are critically important targets for the therapy of NAFLD and NASH. In addition, the avoidance of aberrant infiltration of inflammatory cytokines by treating with CCR antagonists also provides a therapeutic option. Currently, there is an increasing number of pre-clinical and clinical trials undergoing to evaluate the effects of antidiabetic and anti-obesity drugs, antibiotics, pan-caspase inhibitors, CCR2/5 antagonists, and others on NAFLD, NASH, and liver fibrosis. Non-invasive serum diagnostic markers are developed for fulfilling the need of diagnostic testing in a large amount of NAFLD cases. Overall, a better understanding of the underlying mechanism of the pathogenesis of NAFLD is helpful to choose an optimized treatment.
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Affiliation(s)
- Chunye Zhang
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA;
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO 65211, USA
- Correspondence:
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