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Oh S, Baek YH, Jung S, Yoon S, Kang B, Han SH, Park G, Ko JY, Han SY, Jeong JS, Cho JH, Roh YH, Lee SW, Choi GB, Lee YS, Kim W, Seong RH, Park JH, Lee YS, Yoo KH. Identification of signature gene set as highly accurate determination of metabolic dysfunction-associated steatotic liver disease progression. Clin Mol Hepatol 2024; 30:247-262. [PMID: 38281815 PMCID: PMC11016492 DOI: 10.3350/cmh.2023.0449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/09/2024] [Accepted: 01/26/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND/AIMS Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by fat accumulation in the liver. MASLD encompasses both steatosis and MASH. Since MASH can lead to cirrhosis and liver cancer, steatosis and MASH must be distinguished during patient treatment. Here, we investigate the genomes, epigenomes, and transcriptomes of MASLD patients to identify signature gene set for more accurate tracking of MASLD progression. METHODS Biopsy-tissue and blood samples from patients with 134 MASLD, comprising 60 steatosis and 74 MASH patients were performed omics analysis. SVM learning algorithm were used to calculate most predictive features. Linear regression was applied to find signature gene set that distinguish the stage of MASLD and to validate their application into independent cohort of MASLD. RESULTS After performing WGS, WES, WGBS, and total RNA-seq on 134 biopsy samples from confirmed MASLD patients, we provided 1,955 MASLD-associated features, out of 3,176 somatic variant callings, 58 DMRs, and 1,393 DEGs that track MASLD progression. Then, we used a SVM learning algorithm to analyze the data and select the most predictive features. Using linear regression, we identified a signature gene set capable of differentiating the various stages of MASLD and verified it in different independent cohorts of MASLD and a liver cancer cohort. CONCLUSION We identified a signature gene set (i.e., CAPG, HYAL3, WIPI1, TREM2, SPP1, and RNASE6) with strong potential as a panel of diagnostic genes of MASLD-associated disease.
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Affiliation(s)
- Sumin Oh
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul, Korea
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul, Korea
| | - Yang-Hyun Baek
- Liver Center, Department of Internal Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Sungju Jung
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul, Korea
| | - Sumin Yoon
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul, Korea
| | - Byeonggeun Kang
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- Bio-MAX Institute, Seoul National University, Seoul, Korea
| | - Su-hyang Han
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul, Korea
| | - Gaeul Park
- Division of Rare Cancer, Research Institute, National Cancer Center, Goyang, Korea
| | - Je Yeong Ko
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, Korea
| | | | - Jin-Sook Jeong
- Department of Pathology, Dong-A University Medical Center, Busan, Korea
| | - Jin-Han Cho
- Department of Diagnostic Radiology, Dong-A University Medical Center, Busan, Korea
| | - Young-Hoon Roh
- Department of Surgery, Dong-A University Medical Center, Busan, Korea
| | - Sung-Wook Lee
- Liver Center, Department of Internal Medicine, Dong-A University Medical Center, Busan, Korea
| | - Gi-Bok Choi
- Department of Radiology, On Hospital, Busan, Korea
| | - Yong Sun Lee
- Division of Rare Cancer, Research Institute, National Cancer Center, Goyang, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Won Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Korea
| | - Rho Hyun Seong
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jong Hoon Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, Korea
| | - Yeon-Su Lee
- Division of Rare Cancer, Research Institute, National Cancer Center, Goyang, Korea
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul, Korea
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul, Korea
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Dong H, Sun Y, Nie L, Cui A, Zhao P, Leung WK, Wang Q. Metabolic memory: mechanisms and diseases. Signal Transduct Target Ther 2024; 9:38. [PMID: 38413567 PMCID: PMC10899265 DOI: 10.1038/s41392-024-01755-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Metabolic diseases and their complications impose health and economic burdens worldwide. Evidence from past experimental studies and clinical trials suggests our body may have the ability to remember the past metabolic environment, such as hyperglycemia or hyperlipidemia, thus leading to chronic inflammatory disorders and other diseases even after the elimination of these metabolic environments. The long-term effects of that aberrant metabolism on the body have been summarized as metabolic memory and are found to assume a crucial role in states of health and disease. Multiple molecular mechanisms collectively participate in metabolic memory management, resulting in different cellular alterations as well as tissue and organ dysfunctions, culminating in disease progression and even affecting offspring. The elucidation and expansion of the concept of metabolic memory provides more comprehensive insight into pathogenic mechanisms underlying metabolic diseases and complications and promises to be a new target in disease detection and management. Here, we retrace the history of relevant research on metabolic memory and summarize its salient characteristics. We provide a detailed discussion of the mechanisms by which metabolic memory may be involved in disease development at molecular, cellular, and organ levels, with emphasis on the impact of epigenetic modulations. Finally, we present some of the pivotal findings arguing in favor of targeting metabolic memory to develop therapeutic strategies for metabolic diseases and provide the latest reflections on the consequences of metabolic memory as well as their implications for human health and diseases.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuezhang Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lulingxiao Nie
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Aimin Cui
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Pengfei Zhao
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Wai Keung Leung
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Qi Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Theys C, Ibrahim J, Mateiu L, Mposhi A, García-Pupo L, De Pooter T, De Rijk P, Strazisar M, İnce İA, Vintea I, Rots MG, Vanden Berghe W. Mitochondrial GpC and CpG DNA Hypermethylation Cause Metabolic Stress-Induced Mitophagy and Cholestophagy. Int J Mol Sci 2023; 24:16412. [PMID: 38003603 PMCID: PMC10671279 DOI: 10.3390/ijms242216412] [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: 09/14/2023] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by a constant accumulation of lipids in the liver. This hepatic lipotoxicity is associated with a dysregulation of the first step in lipid catabolism, known as beta oxidation, which occurs in the mitochondrial matrix. Eventually, this dysregulation will lead to mitochondrial dysfunction. To evaluate the possible involvement of mitochondrial DNA methylation in this lipid metabolic dysfunction, we investigated the functional metabolic effects of mitochondrial overexpression of CpG (MSssI) and GpC (MCviPI) DNA methyltransferases in relation to gene expression and (mito)epigenetic signatures. Overall, the results show that mitochondrial GpC and, to a lesser extent, CpG methylation increase bile acid metabolic gene expression, inducing the onset of cholestasis through mito-nuclear epigenetic reprogramming. Moreover, both increase the expression of metabolic nuclear receptors and thereby induce basal overactivation of mitochondrial respiration. The latter promotes mitochondrial swelling, favoring lipid accumulation and metabolic-stress-induced mitophagy and autophagy stress responses. In conclusion, both mitochondrial GpC and CpG methylation create a metabolically challenging environment that induces mitochondrial dysfunction, which may contribute to the progression of MASLD.
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Affiliation(s)
- Claudia Theys
- Lab Protein Chemistry, Proteomics & Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium; (C.T.)
| | - Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Ligia Mateiu
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Archibold Mposhi
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Laura García-Pupo
- Lab Protein Chemistry, Proteomics & Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium; (C.T.)
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Wilrijk, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wirlijk, 2610 Antwerp, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Wilrijk, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wirlijk, 2610 Antwerp, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Wilrijk, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wirlijk, 2610 Antwerp, Belgium
| | - İkbal Agah İnce
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Department of Medical Microbiology, School of Medicine, Acıbadem Mehmet, Ali Aydınlar University, 34752 Ataşehir, İstanbul, Türkiye
| | - Iuliana Vintea
- Pathophysiology Lab, Infla-Med Centre of Excellence, Department of Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Wim Vanden Berghe
- Lab Protein Chemistry, Proteomics & Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium; (C.T.)
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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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Terracciani F, Falcomatà A, Gallo P, Picardi A, Vespasiani-Gentilucci U. Prognostication in NAFLD: physiological bases, clinical indicators, and newer biomarkers. J Physiol Biochem 2023; 79:851-868. [PMID: 36472795 DOI: 10.1007/s13105-022-00934-0] [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: 05/22/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is becoming an epidemic in Western countries. Notably, while the majority of NAFLD patients will not evolve until advanced liver disease, a minority of them will progress towards liver-related events. Therefore, risk stratification and prognostication are emerging as fundamental in order to optimize human and economic resources for the care of these patients.Liver fibrosis has been clearly recognized as the main predictor of poor hepatic and extrahepatic outcomes. However, a prediction based only on the stage of fibrosis is near-sighted and static, as it does not capture the propensity of disease to further progress, the speed of progression and their changes over time. These determinants, which result from the interaction between genetic predisposition and acquired risk factors (obesity, diabetes, etc.), express themselves in disease activity, and can be synthesized by biomarkers of hepatic inflammation and fibrogenesis.In this review, we present the currently available clinical tools for risk stratification and prognostication in NAFLD specifically with respect to the risk of progression towards hard hepatic outcomes, i.e., liver-related events and death. We also discuss about the genetic and acquired drivers of disease progression, together with the physiopathological bases of their come into action. Finally, we introduce the most promising biomarkers in the direction of repeatedly assessing disease activity over time, mainly in response to future therapeutic interventions.
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Affiliation(s)
- Francesca Terracciani
- Hepatology and Clinical Medicine Unit, University Campus Bio-Medico of Rome, Rome, Italy
| | - Andrea Falcomatà
- Hepatology and Clinical Medicine Unit, University Campus Bio-Medico of Rome, Rome, Italy
| | - Paolo Gallo
- Hepatology and Clinical Medicine Unit, University Campus Bio-Medico of Rome, Rome, Italy.
| | - Antonio Picardi
- Hepatology and Clinical Medicine Unit, University Campus Bio-Medico of Rome, Rome, Italy
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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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Sarnowski C, Huan T, Ma Y, Joehanes R, Beiser A, DeCarli CS, Heard-Costa NL, Levy D, Lin H, Liu CT, Liu C, Meigs JB, Satizabal CL, Florez JC, Hivert MF, Dupuis J, De Jager PL, Bennett DA, Seshadri S, Morrison AC. Multi-tissue epigenetic analysis identifies distinct associations underlying insulin resistance and Alzheimer's disease at CPT1A locus. Clin Epigenetics 2023; 15:173. [PMID: 37891690 PMCID: PMC10612362 DOI: 10.1186/s13148-023-01589-4] [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: 07/17/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Insulin resistance (IR) is a major risk factor for Alzheimer's disease (AD) dementia. The mechanisms by which IR predisposes to AD are not well-understood. Epigenetic studies may help identify molecular signatures of IR associated with AD, thus improving our understanding of the biological and regulatory mechanisms linking IR and AD. METHODS We conducted an epigenome-wide association study of IR, quantified using the homeostatic model assessment of IR (HOMA-IR) and adjusted for body mass index, in 3,167 participants from the Framingham Heart Study (FHS) without type 2 diabetes at the time of blood draw used for methylation measurement. We identified DNA methylation markers associated with IR at the genome-wide level accounting for multiple testing (P < 1.1 × 10-7) and evaluated their association with neurological traits in participants from the FHS (N = 3040) and the Religious Orders Study/Memory and Aging Project (ROSMAP, N = 707). DNA methylation profiles were measured in blood (FHS) or dorsolateral prefrontal cortex (ROSMAP) using the Illumina HumanMethylation450 BeadChip. Linear regressions (ROSMAP) or mixed-effects models accounting for familial relatedness (FHS) adjusted for age, sex, cohort, self-reported race, batch, and cell type proportions were used to assess associations between DNA methylation and neurological traits accounting for multiple testing. RESULTS We confirmed the strong association of blood DNA methylation with IR at three loci (cg17901584-DHCR24, cg17058475-CPT1A, cg00574958-CPT1A, and cg06500161-ABCG1). In FHS, higher levels of blood DNA methylation at cg00574958 and cg17058475 were both associated with lower IR (P = 2.4 × 10-11 and P = 9.0 × 10-8), larger total brain volumes (P = 0.03 and P = 9.7 × 10-4), and smaller log lateral ventricular volumes (P = 0.07 and P = 0.03). In ROSMAP, higher levels of brain DNA methylation at the same two CPT1A markers were associated with greater risk of cognitive impairment (P = 0.005 and P = 0.02) and higher AD-related indices (CERAD score: P = 5 × 10-4 and 0.001; Braak stage: P = 0.004 and P = 0.01). CONCLUSIONS Our results suggest potentially distinct epigenetic regulatory mechanisms between peripheral blood and dorsolateral prefrontal cortex tissues underlying IR and AD at CPT1A locus.
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Affiliation(s)
- Chloé Sarnowski
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
| | - Yiyi Ma
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Alexa Beiser
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | | | - Nancy L Heard-Costa
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Daniel Levy
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia L Satizabal
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Harvard University, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Josée Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montreal, Canada
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Jung SY, Bhatti P, Pellegrini M. DNA methylation in peripheral blood leukocytes for the association with glucose metabolism and invasive breast cancer. Clin Epigenetics 2023; 15:23. [PMID: 36782224 PMCID: PMC9926571 DOI: 10.1186/s13148-023-01435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Insulin resistance (IR) is a well-established factor for breast cancer (BC) risk in postmenopausal women, but the interrelated molecular pathways on the methylome are not explicitly described. We conducted a population-level epigenome-wide association (EWA) study for DNA methylation (DNAm) probes that are associated with IR and prospectively correlated with BC development, both overall and in BC subtypes among postmenopausal women. METHODS We used data from Women's Health Initiative (WHI) ancillary studies for our EWA analyses and evaluated the associations of site-specific DNAm across the genome with IR phenotypes by multiple regressions adjusting for age and leukocyte heterogeneities. For our analysis of the top 20 IR-CpGs with BC risk, we used the WHI and the Cancer Genomic Atlas (TCGA), using multiple Cox proportional hazards and logit regressions, respectively, accounting for age, diabetes, obesity, leukocyte heterogeneities, and tumor purity (for TCGA). We further conducted a Gene Set Enrichment Analysis. RESULTS We detected several EWA-CpGs in TXNIP, CPT1A, PHGDH, and ABCG1. In particular, cg19693031 in TXNIP was replicated in all IR phenotypes, measured by fasting levels of glucose, insulin, and homeostatic model assessment-IR. Of those replicated IR-genes, 3 genes (CPT1A, PHGDH, and ABCG1) were further correlated with BC risk; and 1 individual CpG (cg01676795 in POR) was commonly detected across the 2 cohorts. CONCLUSIONS Our study contributes to better understanding of the interconnected molecular pathways on the methylome between IR and BC carcinogenesis and suggests potential use of DNAm markers in the peripheral blood cells as preventive targets to detect an at-risk group for IR and BC in postmenopausal women.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, School of Nursing, University of California, Los Angeles, 700 Tiverton Ave, 3-264 Factor Building, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Institute, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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9
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Melton PE, Burton MA, Lillycrop KA, Godfrey KM, Rauschert S, Anderson D, Burdge GC, Mori TA, Beilin LJ, Ayonrinde OT, Craig JM, Olynyk JK, Holbrook JD, Pennell CE, Oddy WH, Moses EK, Adams LA, Huang RC. Differential DNA methylation of steatosis and non-alcoholic fatty liver disease in adolescence. Hepatol Int 2023; 17:584-594. [PMID: 36737504 PMCID: PMC9897882 DOI: 10.1007/s12072-022-10469-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/11/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND AIMS Epigenetic modifications are associated with hepatic fat accumulation and non-alcoholic fatty liver disease (NAFLD). However, few epigenetic modifications directly implicated in such processes have been identified during adolescence, a critical developmental window where physiological changes could influence future disease trajectory. To investigate the association between DNA methylation and NAFLD in adolescence, we undertook discovery and validation of novel methylation marks, alongside replication of previously reported marks. APPROACH AND RESULTS We performed a DNA methylation epigenome-wide association study (EWAS) on DNA from whole blood from 707 Raine Study adolescents phenotyped for steatosis score and NAFLD by ultrasound at age 17. Next, we performed pyrosequencing validation of loci within the most 100 strongly associated differentially methylated CpG sites (dmCpGs) for which ≥ 2 probes per gene remained significant across four statistical models with a nominal p value < 0.007. EWAS identified dmCpGs related to three genes (ANK1, MIR10a, PTPRN2) that met our criteria for pyrosequencing. Of the dmCpGs and surrounding loci that were pyrosequenced (ANK1 n = 6, MIR10a n = 7, PTPRN2 n = 3), three dmCpGs in ANK1 and two in MIR10a were significantly associated with NAFLD in adolescence. After adjustment for waist circumference only dmCpGs in ANK1 remained significant. These ANK1 CpGs were also associated with γ-glutamyl transferase and alanine aminotransferase concentrations. Three of twenty-two differentially methylated dmCpGs previously associated with adult NAFLD were associated with NAFLD in adolescence (all adjusted p < 2.3 × 10-3). CONCLUSIONS We identified novel DNA methylation loci associated with NAFLD and serum liver biochemistry markers during adolescence, implicating putative dmCpG/gene regulatory pathways and providing insights for future mechanistic studies.
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Affiliation(s)
- Phillip E. Melton
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Private Bag 23, Hobart, TAS 7000 Australia ,grid.1012.20000 0004 1936 7910School of Global and Population Health, The University of Western Australia, Crawley, WA Australia
| | - M. A. Burton
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - K. A. Lillycrop
- grid.5491.90000 0004 1936 9297Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK ,grid.430506.40000 0004 0465 4079NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - K. M. Godfrey
- grid.430506.40000 0004 0465 4079NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK ,grid.5491.90000 0004 1936 9297MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - S. Rauschert
- grid.1012.20000 0004 1936 7910Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - D. Anderson
- grid.1012.20000 0004 1936 7910Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - G. C. Burdge
- grid.5491.90000 0004 1936 9297School of Human Health and Development, Faculty of Medicine, University of Southampton, Southampton, UK
| | - T. A. Mori
- grid.1012.20000 0004 1936 7910Medical School, The University of Western Australia, Perth, Australia
| | - L. J. Beilin
- grid.1012.20000 0004 1936 7910Medical School, The University of Western Australia, Perth, Australia
| | - O. T. Ayonrinde
- grid.1012.20000 0004 1936 7910Medical School, The University of Western Australia, Perth, Australia ,Department of Gastroenterology and Hepatology, Fiona Stanley and Fremantle Hospitals, Murdoch, WA Australia
| | - J. M. Craig
- grid.416107.50000 0004 0614 0346MCRI, Royal Children’s Hospital, Flemington Road, Parkville, VIC Australia ,grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC Australia
| | - J. K. Olynyk
- Department of Gastroenterology and Hepatology, Fiona Stanley and Fremantle Hospitals, Murdoch, WA Australia ,grid.1038.a0000 0004 0389 4302School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA Australia
| | - J. D. Holbrook
- grid.5491.90000 0004 1936 9297MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - C. E. Pennell
- grid.266842.c0000 0000 8831 109XUniversity of Newcastle, Newcastle, NSW Australia
| | - W. H. Oddy
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Private Bag 23, Hobart, TAS 7000 Australia
| | - E. K. Moses
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Private Bag 23, Hobart, TAS 7000 Australia ,grid.1012.20000 0004 1936 7910School of Biomedical Sciences, University of Western Australia, Crawley, WA Australia
| | - L. A. Adams
- grid.1012.20000 0004 1936 7910Medical School, The University of Western Australia, Perth, Australia
| | - R. C. Huang
- grid.1012.20000 0004 1936 7910Telethon Kids Institute, The University of Western Australia, Perth, Australia
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10
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Lee KC, Wu PS, Lin HC. Pathogenesis and treatment of non-alcoholic steatohepatitis and its fibrosis. Clin Mol Hepatol 2023; 29:77-98. [PMID: 36226471 PMCID: PMC9845678 DOI: 10.3350/cmh.2022.0237] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/11/2022] [Indexed: 02/02/2023] Open
Abstract
The initial presentation of non-alcoholic steatohepatitis (NASH) is hepatic steatosis. The dysfunction of lipid metabolism within hepatocytes caused by genetic factors, diet, and insulin resistance causes lipid accumulation. Lipotoxicity, oxidative stress, mitochondrial dysfunction, and endoplasmic reticulum stress would further contribute to hepatocyte injury and death, leading to inflammation and immune dysfunction in the liver. During the healing process, the accumulation of an excessive amount of fibrosis might occur while healing. During the development of NASH and liver fibrosis, the gut-liver axis, adipose-liver axis, and renin-angiotensin system (RAS) may be dysregulated and impaired. Translocation of bacteria or its end-products entering the liver could activate hepatocytes, Kupffer cells, and hepatic stellate cells, exacerbating hepatic steatosis, inflammation, and fibrosis. Bile acids regulate glucose and lipid metabolism through Farnesoid X receptors in the liver and intestine. Increased adipose tissue-derived non-esterified fatty acids would aggravate hepatic steatosis. Increased leptin also plays a role in hepatic fibrogenesis, and decreased adiponectin may contribute to hepatic insulin resistance. Moreover, dysregulation of peroxisome proliferator-activated receptors in the liver, adipose, and muscle tissues may impair lipid metabolism. In addition, the RAS may contribute to hepatic fatty acid metabolism, inflammation, and fibrosis. The treatment includes lifestyle modification, pharmacological therapy, and non-pharmacological therapy. Currently, weight reduction by lifestyle modification or surgery is the most effective therapy. However, vitamin E, pioglitazone, and obeticholic acid have also been suggested. In this review, we will introduce some new clinical trials and experimental therapies for the treatment of NASH and related fibrosis.
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Affiliation(s)
- Kuei-Chuan Lee
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan,Department of Medicine, National Yang Ming Chiao Tung University School of Medicine, Taipei, Taiwan,Corresponding author : Kuei-Chuan Lee Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei 11217, Taiwan Tel: +886 2 2871 2121, Fax: +886 2 2873 9318, E-mail:
| | - Pei-Shan Wu
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan,Department of Medicine, National Yang Ming Chiao Tung University School of Medicine, Taipei, Taiwan,Endoscopy Center for Diagnosis and Treatment, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Han-Chieh Lin
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan,Department of Medicine, National Yang Ming Chiao Tung University School of Medicine, Taipei, Taiwan,Corresponding author : Kuei-Chuan Lee Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei 11217, Taiwan Tel: +886 2 2871 2121, Fax: +886 2 2873 9318, E-mail:
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11
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Sokolowska KE, Maciejewska-Markiewicz D, Bińkowski J, Palma J, Taryma-Leśniak O, Kozlowska-Petriczko K, Borowski K, Baśkiewicz-Hałasa M, Hawryłkowicz V, Załęcka P, Ufnal M, Strapagiel D, Jarczak J, Skonieczna-Żydecka K, Ryterska K, Machaliński B, Wojdacz TK, Stachowska E. Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade. Clin Epigenetics 2022; 14:157. [PMID: 36447285 PMCID: PMC9710135 DOI: 10.1186/s13148-022-01377-6] [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: 04/12/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND High caloric diet and lack of physical activity are considered main causes of NAFLD, and a change in the diet is still the only effective treatment of this disease. However, molecular mechanism of the effectiveness of diet change in treatment of NAFLD is poorly understood. We aimed to assess the involvement of epigenetic mechanisms of gene expression regulation in treatment of NAFLD. Eighteen participants with medium- to high-grade steatosis were recruited and trained to follow the Mediterranean diet modified to include fibre supplements. At three timepoints (baseline, after 30 and 60 days), we evaluated adherence to the diet and measured a number of physiological parameters such as anthropometry, blood and stool biochemistry, liver steatosis and stiffness. We also collected whole blood samples for genome-wide methylation profiling and histone acetylation assessment. RESULTS The diet change resulted in a decrease in liver steatosis along with statistically significant, but a minor change in BMI and weight of our study participants. The epigenetic profiling of blood cells identified significant genome-wide changes of methylation and acetylation with the former not involving regions directly regulating gene expression. Most importantly, we were able to show that identified blood methylation changes occur also in liver cells of NAFLD patients and the machine learning-based classifier that we build on those methylation changes was able to predict the stage of liver fibrosis with ROC AUC = 0.9834. CONCLUSION Methylomes of blood cells from NAFLD patients display a number of changes that are most likely a consequence of unhealthy diet, and the diet change appears to reverse those epigenetic changes. Moreover, the methylation status at CpG sites undergoing diet-related methylation change in blood cells stratifies liver biopsies from NAFLD patients according to fibrosis grade.
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Affiliation(s)
- Katarzyna Ewa Sokolowska
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Dominika Maciejewska-Markiewicz
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Jan Bińkowski
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Joanna Palma
- grid.107950.a0000 0001 1411 4349Department of Biochemical Sciences, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Olga Taryma-Leśniak
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Katarzyna Kozlowska-Petriczko
- grid.107950.a0000 0001 1411 4349Translational Medicine Group, Pomeranian Medical University, 70-204 Szczecin, Poland ,Department of Gastroenterology and Internal Medicine, SPWSZ Hospital, 71-455 Szczecin, Poland
| | - Konrad Borowski
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Magdalena Baśkiewicz-Hałasa
- grid.107950.a0000 0001 1411 4349Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Viktoria Hawryłkowicz
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Patrycja Załęcka
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Marcin Ufnal
- grid.13339.3b0000000113287408Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Dominik Strapagiel
- grid.10789.370000 0000 9730 2769Biobank Laboratory, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Justyna Jarczak
- grid.10789.370000 0000 9730 2769Biobank Laboratory, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland ,grid.413454.30000 0001 1958 0162Laboratory of Molecular Basis of Behavior, Nencki Institute of Experimental Biology, Polish Academy of Science, Warsaw, Poland
| | - Karolina Skonieczna-Żydecka
- grid.107950.a0000 0001 1411 4349Department of Biochemical Sciences, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Karina Ryterska
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Bogusław Machaliński
- grid.107950.a0000 0001 1411 4349Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Tomasz Kazimierz Wojdacz
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Ewa Stachowska
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
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12
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Szukiewicz D, Trojanowski S, Kociszewska A, Szewczyk G. Modulation of the Inflammatory Response in Polycystic Ovary Syndrome (PCOS)-Searching for Epigenetic Factors. Int J Mol Sci 2022; 23:ijms232314663. [PMID: 36498989 PMCID: PMC9736994 DOI: 10.3390/ijms232314663] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in women of reproductive age. Despite its incidence, the syndrome is poorly understood and remains underdiagnosed, and female patients are diagnosed with a delay. The heterogenous nature of this complex disorder results from the combined occurrence of genetic, environmental, endocrine, and behavioral factors. Primary clinical manifestations of PCOS are derived from the excess of androgens (anovulation, polycystic ovary morphology, lack of or scanty, irregular menstrual periods, acne and hirsutism), whereas the secondary manifestations include multiple metabolic, cardiovascular, and psychological disorders. Dietary and lifestyle factors play important roles in the development and course of PCOS, which suggests strong epigenetic and environmental influences. Many studies have shown a strong association between PCOS and chronic, low-grade inflammation both in the ovarian tissue and throughout the body. In the vast majority of PCOS patients, elevated values of inflammatory markers or their gene markers have been reported. Development of the vicious cycle of the chronic inflammatory state in PCOS is additionally stimulated by hyperinsulinemia and obesity. Changes in DNA methylation, histone acetylation and noncoding RNA levels are presented in this review in the context of oxidative stress, reactive oxygen species, and inflammatory signaling in PCOS. Epigenetic modulation of androgenic activity in response to inflammatory signaling is also discussed.
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Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
- Correspondence:
| | - Seweryn Trojanowski
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Anna Kociszewska
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Grzegorz Szewczyk
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
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13
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Moylan CA, Mavis AM, Jima D, Maguire R, Bashir M, Hyun J, Cabezas MN, Parish A, Niedzwiecki D, Diehl AM, Murphy SK, Abdelmalek MF, Hoyo C. Alterations in DNA methylation associate with fatty liver and metabolic abnormalities in a multi-ethnic cohort of pre-teenage children. Epigenetics 2022; 17:1446-1461. [PMID: 35188871 PMCID: PMC9586600 DOI: 10.1080/15592294.2022.2039850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Non-Alcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease in children. Epigenetic alterations, such as through DNA methylation (DNAm), may link adverse childhood exposures and fatty liver and provide non-invasive methods for identifying children at high risk for NAFLD and associated metabolic dysfunction. We investigated the association between differential DNAm and liver fat content (LFC) and liver injury in pre-adolescent children. Leveraging data from the Newborn Epigenetics Study (NEST), we enrolled 90 mother-child dyads and used linear regression to identify CpG sites and differentially methylated regions (DMRs) in peripheral blood associated with LFC and alanine aminotransferase (ALT) levels in 7-12yo children. DNAm was measured using Infinium HumanMethylationEPIC BeadChips (Illumina). LFC and fibrosis were quantified by magnetic resonance imaging proton density fat fraction and elastography. Median LFC was 1.4% (range, 0.3-13.4%) and MRE was 2.5 kPa (range, 1.5-3.6kPa). Three children had LFC ≥ 5%, while six (7.6%) met our definition of NAFLD (LFC ≥ 3.7%). All children with NAFLD were obese and five were Black. LFC was associated with 88 DMRs and 106 CpGs (FDR<5%). The top two CpGs, cg25474373 and cg07264203, mapped to or near RFTN2 and PRICKLE2 genes. These two CpG sites were also significantly associated with a NAFLD diagnosis. As higher LFC associates with an adverse cardiometabolic profile already in childhood, altered DNAm may identify these children early in disease course for targeted intervention. Larger, longitudinal studies are needed to validate these findings and determine mechanistic relevance.
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Affiliation(s)
- Cynthia A. Moylan
- Department of Medicine, Duke University Medical Center, Durham, NC, United States,Contact Cynthia A. Moylan 905 South LaSalle Street, Division of Gastroenterology, Duke University Medical Center, Durham27710NC, United States
| | - Alisha M. Mavis
- Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Dereje Jima
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Rachel Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Mustafa Bashir
- Department of Radiology, Center of Advanced Magnetic Resonance Development, Duke University Medical Center, Durham, NC, United States
| | - Jeongeun Hyun
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Melanie N. Cabezas
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Alice Parish
- Biostatistics and Bioinformatics, Duke University, Durham, NC, United States
| | - Donna Niedzwiecki
- Biostatistics and Bioinformatics, Duke University, Durham, NC, United States
| | - Anna Mae Diehl
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | | | - Manal F. Abdelmalek
- Department of Radiology, Center of Advanced Magnetic Resonance Development, Duke University Medical Center, Durham, NC, United States
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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14
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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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15
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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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16
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Zheng Y, Joyce B, Hwang SJ, Ma J, Liu L, Allen N, Krefman A, Wang J, Gao T, Nannini D, Zhang H, Jacobs DR, Gross M, Fornage M, Lewis CE, Schreiner PJ, Sidney S, Chen D, Greenland P, Levy D, Hou L, Lloyd-Jones D. Association of Cardiovascular Health Through Young Adulthood With Genome-Wide DNA Methylation Patterns in Midlife: The CARDIA Study. Circulation 2022; 146:94-109. [PMID: 35652342 PMCID: PMC9348746 DOI: 10.1161/circulationaha.121.055484] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cardiovascular health (CVH) from young adulthood is strongly associated with an individual's future risk of cardiovascular disease (CVD) and total mortality. Defining epigenomic biomarkers of lifelong CVH exposure and understanding their roles in CVD development may help develop preventive and therapeutic strategies for CVD. METHODS In 1085 CARDIA study (Coronary Artery Risk Development in Young Adults) participants, we defined a clinical cumulative CVH score that combines body mass index, blood pressure, total cholesterol, and fasting glucose measured longitudinally from young adulthood through middle age over 20 years (mean age, 25-45). Blood DNA methylation at >840 000 methylation markers was measured twice over 5 years (mean age, 40 and 45). Epigenome-wide association analyses on the cumulative CVH score were performed in CARDIA and compared in the FHS (Framingham Heart Study). We used penalized regression to build a methylation-based risk score to evaluate the risk of incident coronary artery calcification and clinical CVD events. RESULTS We identified 45 methylation markers associated with cumulative CVH at false discovery rate <0.01 (P=4.7E-7-5.8E-17) in CARDIA and replicated in FHS. These associations were more pronounced with methylation measured at an older age. CPT1A, ABCG1, and SREBF1 appeared as the most prominent genes. The 45 methylation markers were mostly located in transcriptionally active chromatin and involved lipid metabolism, insulin secretion, and cytokine production pathways. Three methylation markers located in genes SARS1, SOCS3, and LINC-PINT statistically mediated 20.4% of the total effect between CVH and risk of incident coronary artery calcification. The methylation risk score added information and significantly (P=0.004) improved the discrimination capacity of coronary artery calcification status versus CVH score alone and showed association with risk of incident coronary artery calcification 5 to 10 years later independent of cumulative CVH score (odds ratio, 1.87; P=9.66E-09). The methylation risk score was also associated with incident clinical CVD in FHS (hazard ratio, 1.28; P=1.22E-05). CONCLUSIONS Cumulative CVH from young adulthood contributes to midlife epigenetic programming over time. Our findings demonstrate the role of epigenetic markers in response to CVH changes and highlight the potential of epigenomic markers for precision CVD prevention, and earlier detection of subclinical CVD, as well.
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Affiliation(s)
- Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Brian Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiantao Ma
- Tufts University Friedman School of Nutrition Science and Policy, Boston, Massachusetts, USA
| | - Lei Liu
- Division of Biostatistics, Washington University, St. Louis, Missouri, USA
| | - Norrina Allen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amy Krefman
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jun Wang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Drew Nannini
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, China
| | - David R. Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Cora E. Lewis
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Pamela J. Schreiner
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Stephen Sidney
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Dongquan Chen
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Donald Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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17
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Riccio S, Melone R, Vitulano C, Guida P, Maddaluno I, Guarino S, Marzuillo P, Miraglia del Giudice E, Di Sessa A. Advances in pediatric non-alcoholic fatty liver disease: From genetics to lipidomics. World J Clin Pediatr 2022; 11:221-238. [PMID: 35663007 PMCID: PMC9134151 DOI: 10.5409/wjcp.v11.i3.221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
As a result of the obesity epidemic, non-alcoholic fatty liver disease (NAFLD) represents a global medical concern in childhood with a closely related increased cardiometabolic risk. Knowledge on NAFLD pathophysiology has been largely expanded over the last decades. Besides the well-known key NAFLD genes (including the I148M variant of the PNPLA3 gene, the E167K allele of the TM6SF2, the GCKR gene, the MBOAT7-TMC4 rs641738 variant, and the rs72613567:TA variant in the HSD17B13 gene), an intriguing pathogenic role has also been demonstrated for the gut microbiota. More interestingly, evidence has added new factors involved in the “multiple hits” theory. In particular, omics determinants have been highlighted as potential innovative markers for NAFLD diagnosis and treatment. In fact, different branches of omics including metabolomics, lipidomics (in particular sphingolipids and ceramides), transcriptomics (including micro RNAs), epigenomics (such as DNA methylation), proteomics, and glycomics represent the most attractive pathogenic elements in NAFLD development, by providing insightful perspectives in this field. In this perspective, we aimed to provide a comprehensive overview of NAFLD pathophysiology in children, from the oldest pathogenic elements (including genetics) to the newest intriguing perspectives (such as omics branches).
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Affiliation(s)
- Simona Riccio
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Rosa Melone
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Caterina Vitulano
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Pierfrancesco Guida
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Ivan Maddaluno
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Stefano Guarino
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Pierluigi Marzuillo
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Emanuele Miraglia del Giudice
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Anna Di Sessa
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
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18
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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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19
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Lohoff FW, Clarke TK, Kaminsky ZA, Walker RM, Bermingham ML, Jung J, Morris SW, Rosoff D, Campbell A, Barbu M, Charlet K, Adams M, Lee J, Howard DM, O'Connell EM, Whalley H, Porteous DJ, McIntosh AM, Evans KL. Epigenome-wide association study of alcohol consumption in N = 8161 individuals and relevance to alcohol use disorder pathophysiology: identification of the cystine/glutamate transporter SLC7A11 as a top target. Mol Psychiatry 2022; 27:1754-1764. [PMID: 34857913 PMCID: PMC9095480 DOI: 10.1038/s41380-021-01378-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/22/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022]
Abstract
Alcohol misuse is common in many societies worldwide and is associated with extensive morbidity and mortality, often leading to alcohol use disorders (AUD) and alcohol-related end-organ damage. The underlying mechanisms contributing to the development of AUD are largely unknown; however, growing evidence suggests that alcohol consumption is strongly associated with alterations in DNA methylation. Identification of alcohol-associated methylomic variation might provide novel insights into pathophysiology and novel treatment targets for AUD. Here we performed the largest single-cohort epigenome-wide association study (EWAS) of alcohol consumption to date (N = 8161) and cross-validated findings in AUD populations with relevant endophenotypes, as well as alcohol-related animal models. Results showed 2504 CpGs significantly associated with alcohol consumption (Bonferroni p value < 6.8 × 10-8) with the five leading probes located in SLC7A11 (p = 7.75 × 10-108), JDP2 (p = 1.44 × 10-56), GAS5 (p = 2.71 × 10-47), TRA2B (p = 3.54 × 10-42), and SLC43A1 (p = 1.18 × 10-40). Genes annotated to associated CpG sites are implicated in liver and brain function, the cellular response to alcohol and alcohol-associated diseases, including hypertension and Alzheimer's disease. Two-sample Mendelian randomization confirmed the causal relationship of consumption on AUD risk (inverse variance weighted (IVW) p = 5.37 × 10-09). A methylation-based predictor of alcohol consumption was able to discriminate AUD cases in two independent cohorts (p = 6.32 × 10-38 and p = 5.41 × 10-14). The top EWAS probe cg06690548, located in the cystine/glutamate transporter SLC7A11, was replicated in an independent cohort of AUD and control participants (N = 615) and showed strong hypomethylation in AUD (p < 10-17). Decreased CpG methylation at this probe was consistently associated with clinical measures including increased heavy drinking days (p < 10-4), increased liver function enzymes (GGT (p = 1.03 × 10-21), ALT (p = 1.29 × 10-6), and AST (p = 1.97 × 10-8)) in individuals with AUD. Postmortem brain analyses documented increased SLC7A11 expression in the frontal cortex of individuals with AUD and animal models showed marked increased expression in liver, suggesting a mechanism by which alcohol leads to hypomethylation-induced overexpression of SLC7A11. Taken together, our EWAS discovery sample and subsequent validation of the top probe in AUD suggest a strong role of abnormal glutamate signaling mediated by methylomic variation in SLC7A11. Our data are intriguing given the prominent role of glutamate signaling in brain and liver and might provide an important target for therapeutic intervention.
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Affiliation(s)
- Falk W Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Zachary A Kaminsky
- Royal's Institute of Mental Health Research, University of Ottawa, Ottawa, ON, Canada
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mairead L Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Miruna Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Katrin Charlet
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mark Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - David M Howard
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Emma M O'Connell
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Heather Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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20
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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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21
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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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22
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Zhu X, Xia M, Gao X. Update on genetics and epigenetics in metabolic associated fatty liver disease. Ther Adv Endocrinol Metab 2022; 13:20420188221132138. [PMID: 36325500 PMCID: PMC9619279 DOI: 10.1177/20420188221132138] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/25/2022] [Indexed: 11/06/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is becoming the most frequent chronic liver disease worldwide. Metabolic (dysfunction) associated fatty liver disease (MAFLD) is suggested to replace the nomenclature of NAFLD. For individuals with metabolic dysfunction, multiple NAFLD-related factors also contribute to the development and progression of MAFLD including genetics and epigenetics. The application of genome-wide association study (GWAS) and exome-wide association study (EWAS) uncovers single-nucleotide polymorphisms (SNPs) in MAFLD. In addition to the classic SNPs in PNPLA3, TM6SF2, and GCKR, some new SNPs have been found recently to contribute to the pathogenesis of liver steatosis. Epigenetic factors involving DNA methylation, histone modifications, non-coding RNAs regulations, and RNA methylation also play a critical role in MAFLD. DNA methylation is the most reported epigenetic modification. Developing a non-invasion biomarker to distinguish metabolic steatohepatitis (MASH) or liver fibrosis is ongoing. In this review, we summarized and discussed the latest progress in genetic and epigenetic factors of NAFLD/MAFLD, in order to provide potential clues for MAFLD treatment.
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Affiliation(s)
- Xiaopeng Zhu
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan Institute for Metabolic Diseases, Fudan University, Shanghai, China
| | | | - Xin Gao
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan Institute for Metabolic Diseases, Fudan University, Shanghai, China
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23
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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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24
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Dongiovanni P, Paolini E, Corsini A, Sirtori CR, Ruscica M. Nonalcoholic fatty liver disease or metabolic dysfunction-associated fatty liver disease diagnoses and cardiovascular diseases: From epidemiology to drug approaches. Eur J Clin Invest 2021; 51:e13519. [PMID: 33583033 DOI: 10.1111/eci.13519] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND A consensus of experts has proposed to replace the term nonalcoholic fatty liver disease (NAFLD), whose global prevalence is 25%, with metabolic dysfunction-associated fatty liver disease (MAFLD), to describe more appropriately the liver disease related to metabolic derangements. MAFLD is closely intertwined with type 2 diabetes, obesity, dyslipidaemia, all linked to a rise in the risk of cardiovascular disease (CVDs). Since controversy still stands on whether or not NAFLD/MAFLD raises the odds of CVD, the present review aims to evaluate the impact of NAFLD/MAFLD aetiologies on CV health and the potential correction by dietary and drug approaches. RESULTS Epidemiological studies indicate that NAFLD raises risk of fatal or non-fatal CVD events. NAFLD patients have a higher prevalence of arterial plaques and stiffness, coronary calcification, and endothelial dysfunction. Although genetic and environmental factors strongly contribute to NAFLD pathogenesis, a Mendelian randomization analysis indicated that the PNPLA3 genetic variant leading to NAFLD may not be causally associated with CVD risk. Among other genetic variants related to NAFLD, TM6SF2 appears to be protective, whereas MBOAT7 may favour venous thromboembolism. CONCLUSIONS NAFLD is correlated to a higher CVD risk which may be ameliorated by dietary interventions. This is not surprising, since new criteria defining MAFLD include other metabolic risk abnormalities fuelling development of serious adverse extrahepatic outcomes, for example CVD. The present lack of a targeted pharmacological approach makes the identification of patients with liver disease at higher CVD risk (eg diabetes, hypertension, obesity or high levels of C-reactive protein) of major clinical interest.
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Affiliation(s)
- Paola Dongiovanni
- General Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Erika Paolini
- General Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alberto Corsini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy.,Multimedica IRCCS, Sesto San Giovanni (MI), Milan, Italy
| | - Cesare R Sirtori
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Ruscica
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
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25
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Jhun MA, Mendelson M, Wilson R, Gondalia R, Joehanes R, Salfati E, Zhao X, Braun KVE, Do AN, Hedman ÅK, Zhang T, Carnero-Montoro E, Shen J, Bartz TM, Brody JA, Montasser ME, O'Connell JR, Yao C, Xia R, Boerwinkle E, Grove M, Guan W, Liliane P, Singmann P, Müller-Nurasyid M, Meitinger T, Gieger C, Peters A, Zhao W, Ware EB, Smith JA, Dhana K, van Meurs J, Uitterlinden A, Ikram MA, Ghanbari M, Zhi D, Gustafsson S, Lind L, Li S, Sun D, Spector TD, Chen YDI, Damcott C, Shuldiner AR, Absher DM, Horvath S, Tsao PS, Kardia S, Psaty BM, Sotoodehnia N, Bell JT, Ingelsson E, Chen W, Dehghan A, Arnett DK, Waldenberger M, Hou L, Whitsel EA, Baccarelli A, Levy D, Fornage M, Irvin MR, Assimes TL. A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids. Nat Commun 2021; 12:3987. [PMID: 34183656 PMCID: PMC8238961 DOI: 10.1038/s41467-021-23899-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Here we examine the association between DNA methylation in circulating leukocytes and blood lipids in a multi-ethnic sample of 16,265 subjects. We identify 148, 35, and 4 novel associations among Europeans, African Americans, and Hispanics, respectively, and an additional 186 novel associations through a trans-ethnic meta-analysis. We observe a high concordance in the direction of effects across racial/ethnic groups, a high correlation of effect sizes between high-density lipoprotein and triglycerides, a modest overlap of associations with epigenome-wide association studies of other cardio-metabolic traits, and a largely non-overlap with lipid loci identified to date through genome-wide association studies. Thirty CpGs reached significance in at least 2 racial/ethnic groups including 7 that showed association with the expression of an annotated gene. CpGs annotated to CPT1A showed evidence of being influenced by triglycerides levels. DNA methylation levels of circulating leukocytes show robust and consistent association with blood lipid levels across multiple racial/ethnic groups.
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Affiliation(s)
- Min-A Jhun
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Michael Mendelson
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Rory Wilson
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Rahul Gondalia
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Roby Joehanes
- Hebrew SeniorLife, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Elias Salfati
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaoping Zhao
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Anh Nguyet Do
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Åsa K Hedman
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tao Zhang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Jincheng Shen
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeff R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Chen Yao
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rui Xia
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, Huston, TX, USA
| | - Megan Grove
- School of Public Health, University of Texas Health Science Center at Houston, Huston, TX, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Pfeiffer Liliane
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Paula Singmann
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Meitinger
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Wei Zhao
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Erin B Ware
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, USA
| | - Klodian Dhana
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Mohammad Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Deugi Zhi
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Shengxu Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Dianjianyi Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Yii-der Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Coleen Damcott
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Philip S Tsao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Sharon Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine, and Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Erik Ingelsson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Wei Chen
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Biostatistics and Epidemiology, MRC Centre for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Donna K Arnett
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eric A Whitsel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Myriam Fornage
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- VA Palo Alto Healthcare System, Palo Alto, CA, USA.
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
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26
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Karabegović I, Portilla-Fernandez E, Li Y, Ma J, Maas SCE, Sun D, Hu EA, Kühnel B, Zhang Y, Ambatipudi S, Fiorito G, Huang J, Castillo-Fernandez JE, Wiggins KL, de Klein N, Grioni S, Swenson BR, Polidoro S, Treur JL, Cuenin C, Tsai PC, Costeira R, Chajes V, Braun K, Verweij N, Kretschmer A, Franke L, van Meurs JBJ, Uitterlinden AG, de Knegt RJ, Ikram MA, Dehghan A, Peters A, Schöttker B, Gharib SA, Sotoodehnia N, Bell JT, Elliott P, Vineis P, Relton C, Herceg Z, Brenner H, Waldenberger M, Rebholz CM, Voortman T, Pan Q, Fornage M, Levy D, Kayser M, Ghanbari M. Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption. Nat Commun 2021; 12:2830. [PMID: 33990564 PMCID: PMC8121846 DOI: 10.1038/s41467-021-22752-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023] Open
Abstract
Coffee and tea are extensively consumed beverages worldwide which have received considerable attention regarding health. Intake of these beverages is consistently linked to, among others, reduced risk of diabetes and liver diseases; however, the mechanisms of action remain elusive. Epigenetics is suggested as a mechanism mediating the effects of dietary and lifestyle factors on disease onset. Here we report the results from epigenome-wide association studies (EWAS) on coffee and tea consumption in 15,789 participants of European and African-American ancestries from 15 cohorts. EWAS meta-analysis of coffee consumption reveals 11 CpGs surpassing the epigenome-wide significance threshold (P-value <1.1×10-7), which annotated to the AHRR, F2RL3, FLJ43663, HDAC4, GFI1 and PHGDH genes. Among them, cg14476101 is significantly associated with expression of the PHGDH and risk of fatty liver disease. Knockdown of PHGDH expression in liver cells shows a correlation with expression levels of genes associated with circulating lipids, suggesting a role of PHGDH in hepatic-lipid metabolism. EWAS meta-analysis on tea consumption reveals no significant association, only two CpGs annotated to CACNA1A and PRDM16 genes show suggestive association (P-value <5.0×10-6). These findings indicate that coffee-associated changes in DNA methylation levels may explain the mechanism of action of coffee consumption in conferring risk of diseases.
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Affiliation(s)
- Irma Karabegović
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, the Netherlands
- Epidemiology and Microbial Genomics, National Health Laboratory, Dudelange, Luxembourg
| | | | - Yang Li
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jiantao Ma
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland and the Framingham Heart Study, Framingham, MA, USA
| | - Silvana C E Maas
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Daokun Sun
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Emily A Hu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Srikant Ambatipudi
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, Cedex 08, France
| | - Giovanni Fiorito
- Laboratory of Biostatistics, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
| | - Jian Huang
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- UK Dementia Research Institute at Imperial College London, London, UK
- Imperial College NIHR Biomedical Research Centre, London, UK
| | - Juan E Castillo-Fernandez
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, CHRU, Seattle, WA, USA
| | - Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sara Grioni
- Epidemiology and Prevention Unit, IRCCS National Cancer Institute Foundation, Milan, Italy
| | - Brenton R Swenson
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, CHRU, Seattle, WA, USA
| | - Silvia Polidoro
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- Italian Institute for Genomic Medicine (IIGM, former HuGeF), c/o IRCCS Candiolo, Candiolo, Italy
| | - Jorien L Treur
- Department of Psychiatry, Amsterdam UMC, Amsterdam, the Netherlands
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, Cedex 08, France
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Veronique Chajes
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Kim Braun
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Niek Verweij
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Genomics plc, Park End St, Oxford, UK
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert J de Knegt
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Abbas Dehghan
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- UK Dementia Research Institute at Imperial College London, London, UK
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sina A Gharib
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, CHRU, Seattle, WA, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Paul Elliott
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- UK Dementia Research Institute at Imperial College London, London, UK
- Imperial College NIHR Biomedical Research Centre, London, UK
- Health Data Research UK-London, London, UK
| | - Paolo Vineis
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, Cedex 08, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland and the Framingham Heart Study, Framingham, MA, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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27
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Zhang X, Asllanaj E, Amiri M, Portilla-Fernandez E, Bramer WM, Nano J, Voortman T, Pan Q, Ghanbari M. Deciphering the role of epigenetic modifications in fatty liver disease: A systematic review. Eur J Clin Invest 2021; 51:e13479. [PMID: 33350463 PMCID: PMC8243926 DOI: 10.1111/eci.13479] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fatty liver disease (FLD), primarily nonalcoholic fatty liver disease (NAFLD), is the most common liver disorder that affects a quarter of the global population. NAFLD is a spectrum of disease ranging from simple steatosis to nonalcoholic steatohepatitis, which is associated with increased risk of developing liver cancer. Given that the pathogenic mechanisms of fatty liver remain largely elusive, it is important to further investigate potential underlying mechanisms including epigenetic modifications. Here, we performed a systematic review of human epigenetic studies on FLD presence. METHODS Five bibliographic databases were screened until 28 August 2020. We included cross-sectional, case-control and cohort studies in humans that examined the association of epigenetic modifications including global, candidate or epigenome-wide methylation of DNA, noncoding RNAs and histone modifications with FLD. RESULTS In total 36 articles, based on 33 unique studies, consisting of 12 112 participants met the inclusion criteria. Among these, two recent epigenome-wide association studies conducted among large population-based cohorts have reported the association between cg06690548 (SLC7A11) and FLD. Moreover, several studies have demonstrated the association between microRNAs (miRNAs) and FLD, in which miR-122, miR-34a and miR-192 were recognized as the most relevant miRNAs as biomarkers for FLD. We did not find any studies examining histone modifications in relation to FLD. CONCLUSIONS Cumulative evidence suggests a link between epigenetic mechanisms, specifically DNA methylation and miRNAs, and FLD. Further efforts should investigate the molecular pathways by which these epigenetic markers may regulate FLD and also the potential role of histone modifications in FLD.
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Affiliation(s)
- Xiaofang Zhang
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eralda Asllanaj
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Masoud Amiri
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eliana Portilla-Fernandez
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wichor M Bramer
- Medical Library, Erasmus MC, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Diabetes Center, München-Neuherberg, Germany
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
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28
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Maude H, Sanchez-Cabanillas C, Cebola I. Epigenetics of Hepatic Insulin Resistance. Front Endocrinol (Lausanne) 2021; 12:681356. [PMID: 34046015 PMCID: PMC8147868 DOI: 10.3389/fendo.2021.681356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 01/14/2023] Open
Abstract
Insulin resistance (IR) is largely recognized as a unifying feature that underlies metabolic dysfunction. Both lifestyle and genetic factors contribute to IR. Work from recent years has demonstrated that the epigenome may constitute an interface where different signals may converge to promote IR gene expression programs. Here, we review the current knowledge of the role of epigenetics in hepatic IR, focusing on the roles of DNA methylation and histone post-translational modifications. We discuss the broad epigenetic changes observed in the insulin resistant liver and its associated pathophysiological states and leverage on the wealth of 'omics' studies performed to discuss efforts in pinpointing specific loci that are disrupted by these changes. We envision that future studies, with increased genomic resolution and larger cohorts, will further the identification of biomarkers of early onset hepatic IR and assist the development of targeted interventions. Furthermore, there is growing evidence to suggest that persistent epigenetic marks may be acquired over prolonged exposure to disease or deleterious exposures, highlighting the need for preventative medicine and long-term lifestyle adjustments to avoid irreversible or long-term alterations in gene expression.
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Affiliation(s)
| | | | - Inês Cebola
- *Correspondence: Hannah Maude, ; Inês Cebola,
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29
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Jonas W, Schürmann A. Genetic and epigenetic factors determining NAFLD risk. Mol Metab 2020; 50:101111. [PMID: 33160101 PMCID: PMC8324682 DOI: 10.1016/j.molmet.2020.101111] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/27/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hepatic steatosis is a common chronic liver disease that can progress into more severe stages of NAFLD or promote the development of life-threatening secondary diseases for some of those affected. These include the liver itself (nonalcoholic steatohepatitis or NASH; fibrosis and cirrhosis, and hepatocellular carcinoma) or other organs such as the vessels and the heart (cardiovascular disease) or the islets of Langerhans (type 2 diabetes). In addition to elevated caloric intake and a sedentary lifestyle, genetic and epigenetic predisposition contribute to the development of NAFLD and the secondary diseases. SCOPE OF REVIEW We present data from genome-wide association studies (GWAS) and functional studies in rodents which describe polymorphisms identified in genes relevant for the disease as well as changes caused by altered DNA methylation and gene regulation via specific miRNAs. The review also provides information on the current status of the use of genetic and epigenetic factors as risk markers. MAJOR CONCLUSION With our overview we provide an insight into the genetic and epigenetic landscape of NAFLD and argue about the applicability of currently defined risk scores for risk stratification and conclude that further efforts are needed to make the scores more usable and meaningful.
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Affiliation(s)
- Wenke Jonas
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, D-14558, Nuthetal, Germany; German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, D-85764, München-Neuherberg, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, D-14558, Nuthetal, Germany; German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, D-85764, München-Neuherberg, Germany; University of Potsdam, Institute of Nutritional Sciences, Arthur-Scheunert-Allee 114-116, D-14558, Nuthetal, Germany; Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology, Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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30
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Hyun J, Jung Y. DNA Methylation in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2020; 21:ijms21218138. [PMID: 33143364 PMCID: PMC7662478 DOI: 10.3390/ijms21218138] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a widespread hepatic disorder in the United States and other Westernized countries. Nonalcoholic steatohepatitis (NASH), an advanced stage of NAFLD, can progress to end-stage liver disease, including cirrhosis and liver cancer. Poor understanding of mechanisms underlying NAFLD progression from simple steatosis to NASH has limited the development of effective therapies and biomarkers. An accumulating body of studies has suggested the importance of DNA methylation, which plays pivotal roles in NAFLD pathogenesis. DNA methylation signatures that can affect gene expression are influenced by environmental and lifestyle experiences such as diet, obesity, and physical activity and are reversible. Hence, DNA methylation signatures and modifiers in NAFLD may provide the basis for developing biomarkers indicating the onset and progression of NAFLD and therapeutics for NAFLD. Herein, we review an update on the recent findings in DNA methylation signatures and their roles in the pathogenesis of NAFLD and broaden people’s perspectives on potential DNA methylation-related treatments and biomarkers for NAFLD.
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Affiliation(s)
- Jeongeun Hyun
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea;
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
- Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Korea
- Cell and Matter Institute, Dankook University, Cheonan 31116, Korea
| | - Youngmi Jung
- Department of Integrated Biological Science, Pusan National University, Pusan 46241, Korea
- Department of Biological Sciences, Pusan National University, Pusan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2262
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31
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Palanivel R, Vinayachandran V, Biswal S, Deiuliis JA, Padmanabhan R, Park B, Gangwar RS, Durieux JC, Ebreo Cara EA, Das L, Bevan G, Fayad ZA, Tawakol A, Jain MK, Rao S, Rajagopalan S. Exposure to Air Pollution Disrupts Circadian Rhythm through Alterations in Chromatin Dynamics. iScience 2020; 23:101728. [PMID: 33241196 PMCID: PMC7672280 DOI: 10.1016/j.isci.2020.101728] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/21/2020] [Accepted: 10/21/2020] [Indexed: 11/27/2022] Open
Abstract
Particulate matter ≤2.5μm (PM2.5) air pollution is a leading environmental risk factor contributing disproportionately to the global burden of non-communicable disease. We compared impact of chronic exposure to PM2.5 alone, or with light at night exposure (LL) on metabolism. PM2.5 induced peripheral insulin resistance, circadian rhythm (CR) dysfunction, and metabolic and brown adipose tissue (BAT) dysfunction, akin to LL (with no additive interaction between PM2.5 and LL). Transcriptomic analysis of liver and BAT revealed widespread but unique alterations in CR genes, with evidence for differentially accessible promoters and enhancers of CR genes in response to PM2.5 by ATAC-seq. The histone deacetylases 2, 3, and 4 were downregulated with PM2.5 exposure, with increased promoter occupancy by the histone acetyltransferase p300 as evidenced by ChIP-seq. These findings suggest a previously unrecognized role of PM2.5 in promoting CR disruption and metabolic dysfunction through epigenetic regulation of circadian targets. Air pollution disrupts the circadian rhythm (CR) similar to light at night Dysregulated circadian genes result in insulin resistance and metabolic diseases PM2.5 alters chromatin structure of circadian genes at regulatory regions PM2.5 alters chromatin structure by recruiting histone acetyl transferase (HAT), p300
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Affiliation(s)
- Rengasamy Palanivel
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Vinesh Vinayachandran
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Shyam Biswal
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey A Deiuliis
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Roshan Padmanabhan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bongsoo Park
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Roopesh Singh Gangwar
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Jared C Durieux
- Harrington Heart and Vascular Institute, University Hospital Cleveland Medical Center, Cleveland, OH, USA
| | - Elaine Ann Ebreo Cara
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Lopa Das
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Graham Bevan
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Zahi A Fayad
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ahmed Tawakol
- Cardiology Division and Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mukesh K Jain
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA.,Harrington Heart and Vascular Institute, University Hospital Cleveland Medical Center, Cleveland, OH, USA
| | - Sujata Rao
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Sanjay Rajagopalan
- Cardiovascular Research Institute, Department of Medicine, University Hospitals/Case Western Reserve University, Cleveland, OH, USA.,Harrington Heart and Vascular Institute, University Hospital Cleveland Medical Center, Cleveland, OH, USA
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32
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Perakakis N, Stefanakis K, Mantzoros CS. The role of omics in the pathophysiology, diagnosis and treatment of non-alcoholic fatty liver disease. Metabolism 2020; 111S:154320. [PMID: 32712221 PMCID: PMC7377759 DOI: 10.1016/j.metabol.2020.154320] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/15/2020] [Accepted: 07/18/2020] [Indexed: 12/12/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a multifaceted metabolic disorder, whose spectrum covers clinical, histological and pathophysiological developments ranging from simple steatosis to non-alcoholic steatohepatitis (NASH) and liver fibrosis, potentially evolving into cirrhosis, hepatocellular carcinoma and liver failure. Liver biopsy remains the gold standard for diagnosing NAFLD, while there are no specific treatments. An ever-increasing number of high-throughput Omics investigations on the molecular pathobiology of NAFLD at the cellular, tissue and system levels produce comprehensive biochemical patient snapshots. In the clinical setting, these applications are considerably enhancing our efforts towards obtaining a holistic insight on NAFLD pathophysiology. Omics are also generating non-invasive diagnostic modalities for the distinct stages of NAFLD, that remain though to be validated in multiple, large, heterogenous and independent cohorts, both cross-sectionally as well as prospectively. Finally, they aid in developing novel therapies. By tracing the flow of information from genomics to epigenomics, transcriptomics, proteomics, metabolomics, lipidomics and glycomics, the chief contributions of these techniques in understanding, diagnosing and treating NAFLD are summarized herein.
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Affiliation(s)
- Nikolaos Perakakis
- Department of Internal Medicine, Boston VA Healthcare system and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA..
| | - Konstantinos Stefanakis
- Department of Internal Medicine, Boston VA Healthcare system and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christos S Mantzoros
- Department of Internal Medicine, Boston VA Healthcare system and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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33
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Belsky DW, Caspi A, Arseneault L, Baccarelli A, Corcoran DL, Gao X, Hannon E, Harrington HL, Rasmussen LJH, Houts R, Huffman K, Kraus WE, Kwon D, Mill J, Pieper CF, Prinz JA, Poulton R, Schwartz J, Sugden K, Vokonas P, Williams BS, Moffitt TE. Quantification of the pace of biological aging in humans through a blood test, the DunedinPoAm DNA methylation algorithm. eLife 2020; 9:e54870. [PMID: 32367804 PMCID: PMC7282814 DOI: 10.7554/elife.54870] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022] Open
Abstract
Biological aging is the gradual, progressive decline in system integrity that occurs with advancing chronological age, causing morbidity and disability. Measurements of the pace of aging are needed as surrogate endpoints in trials of therapies designed to prevent disease by slowing biological aging. We report a blood-DNA-methylation measure that is sensitive to variation in pace of biological aging among individuals born the same year. We first modeled change-over-time in 18 biomarkers tracking organ-system integrity across 12 years of follow-up in n = 954 members of the Dunedin Study born in 1972-1973. Rates of change in each biomarker over ages 26-38 years were composited to form a measure of aging-related decline, termed Pace-of-Aging. Elastic-net regression was used to develop a DNA-methylation predictor of Pace-of-Aging, called DunedinPoAm for Dunedin(P)ace(o)f(A)ging(m)ethylation. Validation analysis in cohort studies and the CALERIE trial provide proof-of-principle for DunedinPoAm as a single-time-point measure of a person's pace of biological aging.
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Affiliation(s)
- Daniel W Belsky
- Department of Epidemiology, Columbia University Mailman School of Public HealthNew YorkUnited States
- Butler Columbia Aging Center, Columbia University Mailman School of Public HealthNew YorkUnited States
| | - Avshalom Caspi
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College LondonLondonUnited Kingdom
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
- Department of Psychiatry and Behavioral Sciences, Duke University School of MedicineDurhamUnited States
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - Louise Arseneault
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College LondonLondonUnited Kingdom
| | - Andrea Baccarelli
- Laboratory of Precision Environmental Health, Mailman School of Public Health, Columbia UniversityNew YorkUnited States
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - Xu Gao
- Laboratory of Precision Environmental Health, Mailman School of Public Health, Columbia UniversityNew YorkUnited States
| | - Eiliss Hannon
- University of Exeter Medical School, College of Medicine and HealthExeterUnited Kingdom
| | - Hona Lee Harrington
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Line JH Rasmussen
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
- Clinical Research Centre, Copenhagen University Hospital Amager and HvidovreHvidovreDenmark
| | - Renate Houts
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Kim Huffman
- Duke Molecular Physiology Institute, Duke UniversityDurhamUnited States
- Duke University Center for the Study of Aging, Duke UniversityDurhamUnited States
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke UniversityDurhamUnited States
- Duke University Center for the Study of Aging, Duke UniversityDurhamUnited States
| | - Dayoon Kwon
- Butler Columbia Aging Center, Columbia University Mailman School of Public HealthNew YorkUnited States
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and HealthExeterUnited Kingdom
| | - Carl F Pieper
- Duke University Center for the Study of Aging, Duke UniversityDurhamUnited States
- Department of Biostatistics, Duke University School of MedicineDurhamUnited States
| | - Joseph A Prinz
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - Richie Poulton
- Department of Psychology and Dunedin Multidisciplinary Health and Development Research Unit, University of OtagoOtagoNew Zealand
| | - Joel Schwartz
- Department of Environmental Health Sciences, Harvard TH Chan School of Public HealthBostonUnited States
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Pantel Vokonas
- Veterans Affairs Normative Aging Study, Veterans Affairs Boston Healthcare System, Department of Medicine, Boston University School of MedicineBostonUnited States
| | - Benjamin S Williams
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Terrie E Moffitt
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College LondonLondonUnited Kingdom
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
- Department of Psychiatry and Behavioral Sciences, Duke University School of MedicineDurhamUnited States
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
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34
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Ikram MA, Brusselle G, Ghanbari M, Goedegebure A, Ikram MK, Kavousi M, Kieboom BCT, Klaver CCW, de Knegt RJ, Luik AI, Nijsten TEC, Peeters RP, van Rooij FJA, Stricker BH, Uitterlinden AG, Vernooij MW, Voortman T. Objectives, design and main findings until 2020 from the Rotterdam Study. Eur J Epidemiol 2020; 35:483-517. [PMID: 32367290 PMCID: PMC7250962 DOI: 10.1007/s10654-020-00640-5] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/23/2020] [Indexed: 12/19/2022]
Abstract
The Rotterdam Study is an ongoing prospective cohort study that started in 1990 in the city of Rotterdam, The Netherlands. The study aims to unravel etiology, preclinical course, natural history and potential targets for intervention for chronic diseases in mid-life and late-life. The study focuses on cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. Since 2016, the cohort is being expanded by persons aged 40 years and over. The findings of the Rotterdam Study have been presented in over 1700 research articles and reports. This article provides an update on the rationale and design of the study. It also presents a summary of the major findings from the preceding 3 years and outlines developments for the coming period.
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Affiliation(s)
- M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Guy Brusselle
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - André Goedegebure
- Department of Otorhinolaryngology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Kamran Ikram
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Brenda C T Kieboom
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert J de Knegt
- Department of Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemarie I Luik
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Tamar E C Nijsten
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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35
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Eslam M, Sanyal AJ, George J, Neuschwander-Tetri B, Tiribelli C, Kleiner DE, Brunt E, Bugianesi E, Yki-Järvinen H, Grønbæk H, Cortez-Pinto H, George J, Fan J, Valenti L, Abdelmalek M, Romero-Gomez M, Rinella M, Arrese M, Eslam M, Bedossa P, Newsome PN, Anstee QM, Jalan R, Bataller R, Loomba R, Sookoian S, Sarin SK, Harrison S, Kawaguchi T, Wong VWS, Ratziu V, Yilmaz Y, Younossi Z. MAFLD: A Consensus-Driven Proposed Nomenclature for Metabolic Associated Fatty Liver Disease. Gastroenterology 2020; 158:1999-2014.e1. [PMID: 32044314 DOI: 10.1053/j.gastro.2019.11.312] [Citation(s) in RCA: 1735] [Impact Index Per Article: 433.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/27/2019] [Accepted: 11/05/2019] [Indexed: 12/02/2022]
Abstract
Fatty liver associated with metabolic dysfunction is common, affects a quarter of the population, and has no approved drug therapy. Although pharmacotherapies are in development, response rates appear modest. The heterogeneous pathogenesis of metabolic fatty liver diseases and inaccuracies in terminology and definitions necessitate a reappraisal of nomenclature to inform clinical trial design and drug development. A group of experts sought to integrate current understanding of patient heterogeneity captured under the acronym nonalcoholic fatty liver disease (NAFLD) and provide suggestions on terminology that more accurately reflects pathogenesis and can help in patient stratification for management. Experts reached consensus that NAFLD does not reflect current knowledge, and metabolic (dysfunction) associated fatty liver disease "MAFLD" was suggested as a more appropriate overarching term. This opens the door for efforts from the research community to update the nomenclature and subphenotype the disease to accelerate the translational path to new treatments.
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Affiliation(s)
- Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
| | - Arun J Sanyal
- Virginia Commonwealth University School of Medicine, Richmond, Virginia.
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
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36
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Bayoumi A, Grønbæk H, George J, Eslam M. The Epigenetic Drug Discovery Landscape for Metabolic-associated Fatty Liver Disease. Trends Genet 2020; 36:429-441. [PMID: 32396836 DOI: 10.1016/j.tig.2020.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Abstract
Despite decades of research, effective therapies for metabolic (dysfunction)-associated fatty liver disease (MAFLD) are lacking. An increasing body of evidence suggests that epigenetic dysregulation is frequent in MAFLD, and orchestrates many aspects of its development and progression. Furthermore, the high plasticity of epigenetic modifications in response to environmental cues renders epigenetics a novel area for therapeutic drug discovery. Over recent years, several epigenetics-based drugs and diagnostic biomarkers have entered clinical development and/or obtained regulatory approval. Here, we review recent advances in our understanding of epigenetic regulation and programming during MAFLD, including DNA methylation, histone modifications, chromatin remodelling, transcriptional control, and noncoding (nc)RNAs. We also discuss the potential translational implications and challenges of epigenetics in the context of MAFLD.
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Affiliation(s)
- Ali Bayoumi
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Henning Grønbæk
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
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Geurtsen ML, Jaddoe VWV, Salas LA, Santos S, Felix JF. Newborn and childhood differential DNA methylation and liver fat in school-age children. Clin Epigenetics 2019; 12:3. [PMID: 31892367 PMCID: PMC6938624 DOI: 10.1186/s13148-019-0799-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/19/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease is the most common chronic liver disease in children in western countries. Adverse early-life exposures are associated with higher liver fat percentages in children. Differential DNA methylation may underlie these associations. We aimed to identify differential DNA methylation in newborns and children associated with liver fat accumulation in childhood. We also examined whether DNA methylation at 22 cytosine-phosphate-guanine sites (CpGs) associated with adult non-alcoholic fatty liver disease is associated with liver fat in children. Within a population-based prospective cohort study, we analyzed epigenome-wide DNA methylation data of 785 newborns and 344 10-year-old children in relation to liver fat fraction at 10 years. DNA methylation was measured using the Infinium HumanMethylation450 BeadChip (Illumina). We measured liver fat fraction by Magnetic Resonance Imaging. Associations of single CpG DNA methylation at the two-time points with liver fat accumulation were analyzed using robust linear regression models. We also analyzed differentially methylation regions using the dmrff package. We looked-up associations of 22 known adult CpGs at both ages with liver fat at 10 years. RESULTS The median liver fat fraction was 2.0% (95% range 1.3, 5.1). No single CpGs and no differentially methylated regions were associated with liver fat accumulation. None of the 22 known adult CpGs were associated with liver fat in children. CONCLUSIONS DNA methylation at birth and in childhood was not associated with liver fat accumulation in 10-year-old children in this study. This may be due to modest sample sizes or DNA methylation changes being a consequence rather than a determinant of liver fat.
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Affiliation(s)
- Madelon L Geurtsen
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, Rotterdam, 3000 CA, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, Rotterdam, 3000 CA, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Lucas A Salas
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Susana Santos
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, Rotterdam, 3000 CA, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, Rotterdam, 3000 CA, the Netherlands. .,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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