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Xiao Q, Wang J, Wang L, Ding H. APOA1/C3/A4/A5 Gene Cluster at 11q23.3 and Lipid Metabolism Disorders: From Epigenetic Mechanisms to Clinical Practices. Biomedicines 2024; 12:1224. [PMID: 38927431 PMCID: PMC11201263 DOI: 10.3390/biomedicines12061224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The APOA1/C3/A4/A5 cluster is an essential component in regulating lipoprotein metabolism and maintaining plasma lipid homeostasis. A genome-wide association analysis and Mendelian randomization have revealed potential associations between genetic variants within this cluster and lipid metabolism disorders, including hyperlipidemia and cardiovascular events. An enhanced understanding of the complexity of gene regulation has led to growing recognition regarding the role of epigenetic variation in modulating APOA1/C3/A4/A5 gene expression. Intensive research into the epigenetic regulatory patterns of the APOA1/C3/A4/A5 cluster will help increase our understanding of the pathogenesis of lipid metabolism disorders and facilitate the development of new therapeutic approaches. This review discusses the biology of how the APOA1/C3/A4/A5 cluster affects circulating lipoproteins and the current progress in the epigenetic regulation of the APOA1/C3/A4/A5 cluster.
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Affiliation(s)
- Qianqian Xiao
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Q.X.); (J.W.); (L.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jing Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Q.X.); (J.W.); (L.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Luyun Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Q.X.); (J.W.); (L.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Hu Ding
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Q.X.); (J.W.); (L.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
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Hitzemann R, Ozburn AR, Lockwood D, Phillips TJ. Modeling Brain Gene Expression in Alcohol Use Disorder with Genetic Animal Models. Curr Top Behav Neurosci 2023. [PMID: 37982929 DOI: 10.1007/7854_2023_455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Animal genetic models have and will continue to provide important new information about the behavioral and physiological adaptations associated with alcohol use disorder (AUD). This chapter focuses on two models, ethanol preference and drinking in the dark (DID), their usefulness in interrogating brain gene expression data and the relevance of the data obtained to interpret AUD-related GWAS and TWAS studies. Both the animal and human data point to the importance for AUD of changes in synaptic transmission (particularly glutamate and GABA transmission), of changes in the extracellular matrix (specifically including collagens, cadherins and protocadherins) and of changes in neuroimmune processes. The implementation of new technologies (e.g., cell type-specific gene expression) is expected to further enhance the value of genetic animal models in understanding AUD.
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Affiliation(s)
- Robert Hitzemann
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA.
| | - Angela R Ozburn
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Denesa Lockwood
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Tamara J Phillips
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA
- Veterans Affairs Portland Health Care System, Portland, OR, USA
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Wang S, Zha L, Cui X, Yeh Y, Liu R, Jing J, Shi H, Chen W, Hanover J, Yin J, Yu L, Xue B, Shi H. Epigenetic Regulation of Hepatic Lipid Metabolism by DNA Methylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206068. [PMID: 37282749 PMCID: PMC10369300 DOI: 10.1002/advs.202206068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/25/2023] [Indexed: 06/08/2023]
Abstract
While extensive investigations have been devoted to the study of genetic pathways related to fatty liver diseases, much less is known about epigenetic mechanisms underlying these disorders. DNA methylation is an epigenetic link between environmental factors (e.g., diets) and complex diseases (e.g., non-alcoholic fatty liver disease). Here, it is aimed to study the role of DNA methylation in the regulation of hepatic lipid metabolism. A dynamic change in the DNA methylome in the liver of high-fat diet (HFD)-fed mice is discovered, including a marked increase in DNA methylation at the promoter of Beta-klotho (Klb), a co-receptor for the biological functions of fibroblast growth factor (FGF)15/19 and FGF21. DNA methyltransferases (DNMT) 1 and 3A mediate HFD-induced methylation at the Klb promoter. Notably, HFD enhances DNMT1 protein stability via a ubiquitination-mediated mechanism. Liver-specific deletion of Dnmt1 or 3a increases Klb expression and ameliorates HFD-induced hepatic steatosis. Single-nucleus RNA sequencing analysis reveals pathways involved in fatty acid oxidation in Dnmt1-deficient hepatocytes. Targeted demethylation at the Klb promoter increases Klb expression and fatty acid oxidation, resulting in decreased hepatic lipid accumulation. Up-regulation of methyltransferases by HFD may induce hypermethylation of the Klb promoter and subsequent down-regulation of Klb expression, resulting in the development of hepatic steatosis.
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Affiliation(s)
- Shirong Wang
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Lin Zha
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
- The Northern Medical DistrictChinese PLA General HospitalBeijing100094China
| | - Xin Cui
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Yu‐Te Yeh
- Department of Internal MedicineUniversity of Maryland School of MedicineBaltimoreMD21201USA
| | - Ruochuan Liu
- Department of Chemistry and the Center for Diagnosis and TherapeuticsGeorgia State UniversityAtlantaGA30303
| | - Jia Jing
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Huidong Shi
- GRU Cancer Center and Department of Biochemistry and Molecular BiologyMedical College of GeorgiaAugusta UniversityAugustaGA30912USA
| | - Weiping Chen
- Genomic Core Lab of National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD20855USA
| | - John Hanover
- Genomic Core Lab of National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD20855USA
| | - Jun Yin
- Department of Chemistry and the Center for Diagnosis and TherapeuticsGeorgia State UniversityAtlantaGA30303
| | - Liqing Yu
- Department of Internal MedicineUniversity of Maryland School of MedicineBaltimoreMD21201USA
| | - Bingzhong Xue
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Hang Shi
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
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Anderson JQ, Darakjian P, Hitzemann R, Lockwood DR, Phillips TJ, Ozburn AR. Brain gene expression differences related to ethanol preference in the collaborative cross founder strains. Front Behav Neurosci 2022; 16:992727. [PMID: 36212197 PMCID: PMC9539754 DOI: 10.3389/fnbeh.2022.992727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
The collaborative cross (CC) founder strains include five classical inbred laboratory strains [129S1/SvlmJ (S129), A/J (AJ), C57BL/6J (B6), NOD/ShiLtJ (NOD), and NZO/HILtJ (NZO)] and three wild-derived strains [CAST/EiJ (CAST), PWK/PhJ (PWK), and WSB/EiJ (WSB)]. These strains encompass 89% of the genetic diversity available in Mus musculus and ∼10-20 times more genetic diversity than found in Homo sapiens. For more than 60 years the B6 strain has been widely used as a genetic model for high ethanol preference and consumption. However, another of the CC founder strains, PWK, has been identified as a high ethanol preference/high consumption strain. The current study determined how the transcriptomes of the B6 and PWK strains differed from the 6 low preference CC strains across 3 nodes of the brain addiction circuit. RNA-Seq data were collected from the central nucleus of the amygdala (CeA), the nucleus accumbens core (NAcc) and the prelimbic cortex (PrL). Differential expression (DE) analysis was performed in each of these brain regions for all 28 possible pairwise comparisons of the CC founder strains. Unique genes for each strain were identified by selecting for genes that differed significantly [false discovery rate (FDR) < 0.05] from all other strains in the same direction. B6 was identified as the most distinct classical inbred laboratory strain, having the highest number of total differently expressed genes (DEGs) and DEGs with high log fold change, and unique genes compared to other CC strains. Less than 50 unique DEGs were identified in common between B6 and PWK within all three brain regions, indicating the strains potentially represent two distinct genetic signatures for risk for high ethanol-preference. 338 DEGs were found to be commonly different between B6, PWK and the average expression of the remaining CC strains within all three regions. The commonly different up-expressed genes were significantly enriched (FDR < 0.001) among genes associated with neuroimmune function. These data compliment findings showing that neuroimmune signaling is key to understanding alcohol use disorder (AUD) and support use of these 8 strains and the highly heterogeneous mouse populations derived from them to identify alcohol-related brain mechanisms and treatment targets.
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Affiliation(s)
- Justin Q. Anderson
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Priscila Darakjian
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Robert Hitzemann
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Denesa R. Lockwood
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Tamara J. Phillips
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Angela R. Ozburn
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
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Meneghel P, Pinto E, Russo FP. Physiopathology of nonalcoholic fatty liver disease: from diet to nutrigenomics. Curr Opin Clin Nutr Metab Care 2022; 25:329-333. [PMID: 35920204 PMCID: PMC10878452 DOI: 10.1097/mco.0000000000000859] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Nonalcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease worldwide and is strongly associated with metabolic disorders, such as obesity, type 2 diabetes mellitus, and metabolic syndrome, to the extent that a new definition of metabolic associated fatty liver disease has been proposed. RECENT FINDINGS Insulin resistance, worsened by a high-fat and high-carbohydrate diet, is the key to the physiopathology of hepatic steatosis. This is driven by several mechanisms that are mostly activated at a genetic level, such as de-novo lipogenesis and triglyceride synthesis. Therefore, many diet regimens have been studied, although significant controversies remain regarding their metabolic effects and long-term sustainability. SUMMARY In this review, we summarized the role and effects of the main macronutrients on the development of NAFLD and discussed the molecular mechanisms involved. We also discussed the importance of genetic polymorphisms, epigenetic alterations, and dysbiosis to determine if lifestyle modification and a specific dietary regimen could be an essential part of NAFLD treatment.
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Affiliation(s)
- Paola Meneghel
- Department of Surgery, Oncology and Gastroenterology, University Hospital Padua, Padova, Italy
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