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Yao S, Prates K, Freydenzon A, Assante G, McRae AF, Morris MJ, Youngson NA. Liver-specific deletion of de novo DNA methyltransferases protects against glucose intolerance in high-fat diet-fed male mice. FASEB J 2024; 38:e23690. [PMID: 38795327 DOI: 10.1096/fj.202301546rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/27/2024]
Abstract
Alterations to gene transcription and DNA methylation are a feature of many liver diseases including fatty liver disease and liver cancer. However, it is unclear whether the DNA methylation changes are a cause or a consequence of the transcriptional changes. It is even possible that the methylation changes are not required for the transcriptional changes. If DNA methylation is just a minor player in, or a consequence of liver transcriptional change, then future studies in this area should focus on other systems such as histone tail modifications. To interrogate the importance of de novo DNA methylation, we generated mice that are homozygous mutants for both Dnmt3a and Dnmt3b in post-natal liver. These mice are viable and fertile with normal sized livers. Males, but not females, showed increased adipose depots, yet paradoxically, improved glucose tolerance on both control diet and high-fat diets (HFD). Comparison of the transcriptome and methylome with RNA sequencing and whole-genome bisulfite sequencing in adult hepatocytes revealed that widespread loss of methylation in CpG-rich regions in the mutant did not induce loss of homeostatic transcriptional regulation. Similarly, extensive transcriptional changes induced by HFD did not require de novo DNA methylation. The improved metabolic phenotype of the Dnmt3a/3b mutant mice may be mediated through the dysregulation of a subset of glucose and fat metabolism genes which increase both glucose uptake and lipid export by the liver. However, further work is needed to confirm this.
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Affiliation(s)
- S Yao
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - K Prates
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Department of Biotechnology, Genetics, and Cellular Biology, State University of Maringá, Maringá, Brazil
| | - A Freydenzon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - G Assante
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - A F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - M J Morris
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - N A Youngson
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
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2
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Chen Y, Meng L, Xu N, Chen H, Wei X, Lu D, Wang S, Xu X. Ten-eleven translocation-2-mediated macrophage activation promotes liver regeneration. Cell Commun Signal 2024; 22:95. [PMID: 38308318 PMCID: PMC10835877 DOI: 10.1186/s12964-023-01407-7] [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: 09/09/2023] [Accepted: 11/23/2023] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND The remarkable regenerative capacity of the liver enables recovery after radical Hepatocellular carcinoma (HCC) resection. After resection, macrophages secrete interleukin 6 and hepatocyte growth factors to promote liver regeneration. Ten-eleven translocation-2 (Tet2) DNA dioxygenase regulates pro-inflammatory factor secretion in macrophages. In this study, we explored the role of Tet2 in macrophages and its function independent of its enzymatic activity in liver regeneration. METHODS The model of liver regeneration after 70% partial hepatectomy (PHx) is a classic universal model for studying reparative processes in the liver. Mice were euthanized at 0, 24, and 48 h after PHx. Enzyme-linked immunosorbent assays, quantitative reverse transcription-polymerase chain reaction, western blotting, immunofluorescence analysis, and flow cytometry were performed to explore immune cell infiltration and liver regenerative capability. Molecular dynamics simulations were performed to study the interaction between Tet2 and signal transducer and activator of transcription 1 (Stat1). RESULTS Tet2 in macrophages negatively regulated liver regeneration in the partial hepatectomy mice model. Tet2 interacted with Stat1, inhibiting the expression of proinflammatory factors and suppressing liver regeneration. The Tet2 inhibitor attenuated the interaction between Stat1 and Tet2, enhanced Stat1 phosphorylation, and promoted hepatocyte proliferation. The proliferative function of the Tet2 inhibitor relied on macrophages and did not affect hepatocytes directly. CONCLUSION Our findings underscore that Tet2 in macrophages negatively regulates liver regeneration by interacting with Stat1. Targeting Tet2 in macrophages promotes liver regeneration and function after a hepatectomy, presenting a novel target to promote liver regeneration and function.
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Affiliation(s)
- Yiyuan Chen
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Lijun Meng
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Nan Xu
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Huan Chen
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xuyong Wei
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Di Lu
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Shuai Wang
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
- Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China.
| | - Xiao Xu
- Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China.
- Institute of Organ Transplantation, Zhejiang University, Hangzhou, 310003, China.
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3
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Yousof TR, Bouchard CC, Alb M, Lynn EG, Lhoták S, Jiang H, MacDonald M, Li H, Byun JH, Makda Y, Athanasopoulos M, Maclean KN, Cherrington NJ, Naqvi A, Igdoura SA, Krepinsky JC, Steinberg GR, Austin RC. Restoration of the ER stress response protein TDAG51 in hepatocytes mitigates NAFLD in mice. J Biol Chem 2024; 300:105655. [PMID: 38237682 PMCID: PMC10875272 DOI: 10.1016/j.jbc.2024.105655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 02/16/2024] Open
Abstract
Endoplasmic reticulum stress is associated with insulin resistance and the development of nonalcoholic fatty liver disease. Deficiency of the endoplasmic reticulum stress response T-cell death-associated gene 51 (TDAG51) (TDAG51-/-) in mice promotes the development of high-fat diet (HFD)-induced obesity, fatty liver, and hepatic insulin resistance. However, whether this effect is due specifically to hepatic TDAG51 deficiency is unknown. Here, we report that hepatic TDAG51 protein levels are consistently reduced in multiple mouse models of liver steatosis and injury as well as in liver biopsies from patients with liver disease compared to normal controls. Delivery of a liver-specific adeno-associated virus (AAV) increased hepatic expression of a TDAG51-GFP fusion protein in WT, TDAG51-/-, and leptin-deficient (ob/ob) mice. Restoration of hepatic TDAG51 protein was sufficient to increase insulin sensitivity while reducing body weight and fatty liver in HFD fed TDAG51-/- mice and in ob/ob mice. TDAG51-/- mice expressing ectopic TDAG51 display improved Akt (Ser473) phosphorylation, post-insulin stimulation. HFD-fed TDAG51-/- mice treated with AAV-TDAG51-GFP displayed reduced lipogenic gene expression, increased beta-oxidation and lowered hepatic and serum triglycerides, findings consistent with reduced liver weight. Further, AAV-TDAG51-GFP-treated TDAG51-/- mice exhibited reduced hepatic precursor and cleaved sterol regulatory-element binding proteins (SREBP-1 and SREBP-2). In vitro studies confirmed the lipid-lowering effect of TDAG51 overexpression in oleic acid-treated Huh7 cells. These studies suggest that maintaining hepatic TDAG51 protein levels represents a viable therapeutic approach for the treatment of obesity and insulin resistance associated with nonalcoholic fatty liver disease.
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Affiliation(s)
- Tamana R Yousof
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | - Celeste C Bouchard
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | - Mihnea Alb
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | - Edward G Lynn
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | - Sárka Lhoták
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | - Hua Jiang
- Department of Pediatrics, School of Medicine, University of Colorado Health Sciences Center, Aurora, Colorado, USA
| | - Melissa MacDonald
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | - Hui Li
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona, USA
| | - Jae H Byun
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | - Yumna Makda
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada
| | | | - Kenneth N Maclean
- Department of Pediatrics, School of Medicine, University of Colorado Health Sciences Center, Aurora, Colorado, USA
| | - Nathan J Cherrington
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona, USA
| | - Asghar Naqvi
- Department of Pathology and Molecular Medicine, St. Joseph's Healthcare Hamilton, McMaster University, Hamilton, Ontario, Canada
| | - Suleiman A Igdoura
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Joan C Krepinsky
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada; Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
| | - Gregory R Steinberg
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada; Division of Endocrinology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Richard C Austin
- Division of Nephrology, Department of Medicine, The Research Institute of St. Joe's Hamilton and the Hamilton Centre for Kidney Research, McMaster University, Hamilton, Ontario, Canada; Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada.
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Dashti M, Nizam R, John SE, Melhem M, Channanath A, Alkandari H, Thanaraj TA, Al-Mulla F. ONECUT1 variants beyond type 1 and type 2 diabetes: exploring clinical diversity and epigenetic associations in Arab cohorts. Front Genet 2023; 14:1254833. [PMID: 37941991 PMCID: PMC10628528 DOI: 10.3389/fgene.2023.1254833] [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: 08/08/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
ONECUT1 gene, encoding hepatocyte nuclear factor 6, is involved in pancreas and liver development. ONECUT1 mutations impair the function of pancreatic β-cells and control a transcriptional/epigenetic machinery regulating endocrine development. Homozygous nonsense and missense mutations at ONECUT1_p.E231 and a homozygous frameshift mutation at ONECUT1_p.M289 were reported in neonatal diabetes individuals of French, Turkish, and Indian ethnicity, respectively. Additionally, heterozygous variants were observed in Northern European T2D patients, and Italian patients with neonatal diabetes and early-/late-onset T2D. Examining diverse populations, such as Arabs known for consanguinity, can generalize the ONECUT1 involvement in diabetes. Upon screening the cohorts of Kuwaiti T1D and MODY families, and of Kuwaiti and Qatari T2D individuals, we observed two homozygous variants-the deleterious missense rs202151356_p.H33Q in one MODY, one T1D, and two T2D individuals, and the synonymous rs61735385_p.P94P in two T2D individuals. Heterozygous variants were also observed. Examination of GTEx, NephQTL, mQTLdb and HaploReg highlighted the rs61735385_p.P94P variant as eQTL influencing the tissue-specific expression of ONECUT1, as mQTL influencing methylation at CpG sites in and around ONECUT1 with the nearest site at 677-bases 3' to rs61735385_p.P94P; as overlapping predicted binding sites for NF-kappaB and EBF on ONECUT1. DNA methylation profiles of peripheral blood from 19 MODY-X patients versus eight healthy individuals revealed significant hypomethylation at two CpG sites-one located 617-bases 3' to the p.P94P variant and 8,102 bases away from transcription start; and the other located 14,999 bases away from transcription start. Our study generalizes the association of ONECUT1 with clinical diversity in diabetes.
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Affiliation(s)
- Mohammed Dashti
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Rasheeba Nizam
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Motasem Melhem
- Department of Specialized Services Facility, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Hessa Alkandari
- Department of Population Health, Dasman Diabetes Institute, Kuwait City, Kuwait
- Department of Pediatrics, Farwaniya Hospital, Ministry of Health, Kuwait City, Kuwait
| | | | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
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Bantulà M, Arismendi E, Tubita V, Roca-Ferrer J, Mullol J, de Hollanda A, Sastre J, Valero A, Baos S, Cremades-Jimeno L, Cárdaba B, Picado C. Effect of Obesity on the Expression of Genes Associated with Severe Asthma-A Pilot Study. J Clin Med 2023; 12:4398. [PMID: 37445432 DOI: 10.3390/jcm12134398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Asthma is a complex condition resulting from the interaction of genes and environment. Obesity is a risk factor to develop asthma and contributes to poor response to asthma therapy and severity. The aim of the study was to evaluate the effect of obesity on the expression levels of genes previously associated with severe asthma. Three groups of subjects were studied: non-obese asthmatics (NOA), obese asthma patients (OA), and non-asthmatic obese subjects (O). Previously reported overexpressed (IL-10, MSR1, PHLDA1, SERPINB2, and CD86) and underexpressed genes (CHI3L1, CPA3, IL-8, and PI3) in severe asthma were analyzed by RT-qPCR in peripheral blood mononuclear cells (PBMCs). In the overexpressed genes, obesity significantly decreased the expression of MSR1 and PHLDA1 and had no effects on CD86, IL-10, and SERPINB2. In underexpressed genes, obesity did not affect PI3, CHI3L1, and IL-8 and significantly reduced CPA3 expression. The results of this study show that obesity should be included among the known factors that can contribute toward modifying the expression of genes associated with asthma and, in particular, severe asthma.
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Affiliation(s)
- Marina Bantulà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Ebymar Arismendi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Pulmonology Department, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Valeria Tubita
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Faculty of Medicine, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Jordi Roca-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
| | - Joaquim Mullol
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Rhinology Unit & Smell Clinic, ENT Department, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Ana de Hollanda
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Obesity Unit, Endocrinology and Nutrition Department, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Fisopatología de la Obesidad y Nutrición (CIBEROBN), 28029 Madrid, Spain
| | - Joaquín Sastre
- Centro de Investigaciones Biomédicas en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Allergy Service, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Faculty of Medicine, Universidad Autónoma de Madrid, 28040 Madrid, Spain
| | - Antonio Valero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Allergy Department, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Selene Baos
- Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain
| | - Lucía Cremades-Jimeno
- Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain
| | - Blanca Cárdaba
- Centro de Investigaciones Biomédicas en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain
| | - César Picado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Pulmonology Department, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
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Duarte GCK, Pellenz F, Crispim D, Assmann TS. Integrated bioinformatics approach reveals methylation-regulated differentially expressed genes in obesity. ARCHIVES OF ENDOCRINOLOGY AND METABOLISM 2023; 67:e000604. [PMID: 37252693 PMCID: PMC10665070 DOI: 10.20945/2359-3997000000604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/08/2022] [Indexed: 05/31/2023]
Abstract
Objective To identify DNA methylation and gene expression profiles involved in obesity by implementing an integrated bioinformatics approach. Materials and methods Gene expression (GSE94752, GSE55200, and GSE48964) and DNA methylation (GSE67024 and GSE111632) datasets were obtained from the GEO database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in subcutaneous adipose tissue of patients with obesity were identified using GEO2R. Methylation-regulated DEGs (MeDEGs) were identified by overlapping DEGs and DMGs. The protein-protein interaction (PPI) network was constructed with the STRING database and analyzed using Cytoscape. Functional modules and hub-bottleneck genes were identified by using MCODE and CytoHubba plugins. Functional enrichment analyses were performed based on Gene Ontology terms and KEGG pathways. To prioritize and identify candidate genes for obesity, MeDEGs were compared with obesity-related genes available at the DisGeNET database. Results A total of 54 MeDEGs were identified after overlapping the lists of significant 274 DEGs and 11,556 DMGs. Of these, 25 were hypermethylated-low expression genes and 29 were hypomethylated-high expression genes. The PPI network showed three hub-bottleneck genes (PTGS2, TNFAIP3, and FBXL20) and one functional module. The 54 MeDEGs were mainly involved in the regulation of fibroblast growth factor production, the molecular function of arachidonic acid, and ubiquitin-protein transferase activity. Data collected from DisGeNET showed that 11 of the 54 MeDEGs were involved in obesity. Conclusion This study identifies new MeDEGs involved in obesity and assessed their related pathways and functions. These results data may provide a deeper understanding of methylation-mediated regulatory mechanisms of obesity.
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Affiliation(s)
- Guilherme Coutinho Kullmann Duarte
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Felipe Pellenz
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Daisy Crispim
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil,
| | - Tais Silveira Assmann
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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Zhao P, Malik S. The phosphorylation to acetylation/methylation cascade in transcriptional regulation: how kinases regulate transcriptional activities of DNA/histone-modifying enzymes. Cell Biosci 2022; 12:83. [PMID: 35659740 PMCID: PMC9164400 DOI: 10.1186/s13578-022-00821-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022] Open
Abstract
Transcription factors directly regulate gene expression by recognizing and binding to specific DNA sequences, involving the dynamic alterations of chromatin structure and the formation of a complex with different kinds of cofactors, like DNA/histone modifying-enzymes, chromatin remodeling factors, and cell cycle factors. Despite the significance of transcription factors, it remains unclear to determine how these cofactors are regulated to cooperate with transcription factors, especially DNA/histone modifying-enzymes. It has been known that DNA/histone modifying-enzymes are regulated by post-translational modifications. And the most common and important modification is phosphorylation. Even though various DNA/histone modifying-enzymes have been classified and partly explained how phosphorylated sites of these enzymes function characteristically in recent studies. It still needs to find out the relationship between phosphorylation of these enzymes and the diseases-associated transcriptional regulation. Here this review describes how phosphorylation affects the transcription activity of these enzymes and other functions, including protein stability, subcellular localization, binding to chromatin, and interaction with other proteins.
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Kim DY, Lim B, Lim D, Park W, Lee KT, Cho ES, Lim KS, Cheon SN, Choi BH, Park JE, Kim JM. Integrative methylome and transcriptome analysis of porcine abdominal fat indicates changes in fat metabolism and immune responses during different development. J Anim Sci 2022; 100:skac302. [PMID: 36074647 PMCID: PMC9733533 DOI: 10.1093/jas/skac302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022] Open
Abstract
Fat is involved in synthesizing fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. The samples were collected from the porcine abdominal fat of different developmental stages (10 and 26 weeks of age). Then, the samples were sequenced using MBD-seq and RNA-seq for profiling DNA methylation and RNA expression. In 26 weeks of age pigs, differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified as 2,251 and 5,768, compared with 10 weeks of age pigs, respectively. Gene functional analysis was performed using GO and KEGG databases. In functional analysis results of DMGs and DEGs, immune responses such as chemokine signaling pathways, B cell receptor signaling pathways, and lipid metabolism terms such as PPAR signaling pathways and fatty acid degradation were identified. It is thought that there is an influence between DNA methylation and gene expression through changes in genes with similar functions. The effects of DNA methylation on gene expression were investigated using cis-regulation and trans-regulation analysis to integrate and interpret different molecular layers. In the cis-regulation analysis using 629 overlapping genes between DEGs and DMGs, immune response functions were identified, while in trans-regulation analysis through the TF-target gene network, the co-expression network of lipid metabolism-related functions was distinguished. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.
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Affiliation(s)
- Do-Young Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
| | - Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Woncheol Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Eun-Seok Cho
- Swine Science Division, National Institute of Animal Science, RDA, Cheonan, Chungcheongnam-do 31000, Republic of Korea
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Si Nae Cheon
- Animal Welfare Research Team, National Institute of Animal Science, RDA, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
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Suzuki Y, Okabayashi K, Hasegawa H, Tsuruta M, Seishima R, Tokuda T, Kitagawa Y. Role of EphB2/ephrin‑B1 signalling in the development and progression of obesity‑associated colorectal cancer. Oncol Lett 2022; 24:316. [PMID: 35949596 PMCID: PMC9353875 DOI: 10.3892/ol.2022.13436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Obesity is a major problem worldwide and has been associated with colorectal cancer development, among other diseases. Ephrin receptors and ligands play an important role in the turnover of the intestinal mucosa and intestinal crypt compartmentalization. It has been hypothesised that obesity-induced inflammation affects ephrin signals, leading to carcinogenesis. Therefore, the aim of the present study was to assess the relationship between Eph-ephrin B signalling, obesity and obesity-associated colorectal cancer. An azoxymethane-induced obesity-associated cancer KKAy mouse model developed in our prior study was used. A total of 46 patients with consecutive colorectal cancer and 48 tumours were analysed. Immunohistological analyses were performed in mouse and human samples, and immunoreactive scores (IRS) were determined. KKAy mice were significantly more prone to cancer development compared with control C57/BL mice (2/15 in C57/BL vs. 10/10 in KKAy; P<0.001). TUNEL assay revealed a lower number of apoptotic cells in normal mucosa of KKAy mice (8.8% in C57/BL vs. 3.2% in KKAy; P<0.001) and obese patients (9.2% with BMI <25 vs. 3.6% with BMI ≥25; P=0.021). Immunohistological analysis revealed that ephrin-B1 was downregulated in normal mucosa from KKAy mice and obese patients (IRS, 2.86 with BMI <25 vs. 6.00 with BMI ≥25; P=0.002). Moreover, EphB2 was downregulated in tumours from KKAy mice and obese patients (IRS, 6.58 with BMI <25 vs. 3.83 with BMI ≥25; P<0.001). The distribution of infiltrated macrophages corresponded to the MCP-1 expression pattern in KKAy mice, and the number of macrophages was also significantly higher in those mice (36.3 in C57/BL vs. 120.0 in KKAy; P=0.029). The findings suggested that obesity results in disruption of EphB2/ephrin-B1 signalling, promoting colorectal cancer development and progression.
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Affiliation(s)
- Yoshiyuki Suzuki
- Department of Surgery, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Koji Okabayashi
- Department of Surgery, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Hirotoshi Hasegawa
- Department of Surgery, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Masashi Tsuruta
- Department of Surgery, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Ryo Seishima
- Department of Surgery, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Toshiki Tokuda
- Department of Surgery, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo 1608582, Japan
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Qu J, Yang F, Zhu T, Wang Y, Fang W, Ding Y, Zhao X, Qi X, Xie Q, Chen M, Xu Q, Xie Y, Sun Y, Chen D. A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys. Nat Commun 2022; 13:4069. [PMID: 35831300 PMCID: PMC9279386 DOI: 10.1038/s41467-022-31770-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022] Open
Abstract
Non-human primates are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium of cell types across multiple organs in cynomolgus monkeys (Macaca fascicularis) using both single-cell chromatin accessibility and RNA sequencing data. The integrated cell map enables in-depth dissection and comparison of molecular dynamics, cell-type compositions and cellular heterogeneity across multiple tissues and organs. Using single-cell transcriptomic data, we infer pseudotime cell trajectories and cell-cell communications to uncover key molecular signatures underlying their cellular processes. Furthermore, we identify various cell-specific cis-regulatory elements and construct organ-specific gene regulatory networks at the single-cell level. Finally, we perform comparative analyses of single-cell landscapes among mouse, monkey and human. We show that cynomolgus monkey has strikingly higher degree of similarities in terms of immune-associated gene expression patterns and cellular communications to human than mouse. Taken together, our study provides a valuable resource for non-human primate cell biology. Non-human primates are attractive laboratory animal models that can accurately reflect some developmental and pathological features of humans. Here the authors chart a reference cell map of cynomolgus monkeys using both scATAC-seq and scRNA-seq data across multiple organs, providing insights into the molecular dynamics and cellular heterogeneity of this organism.
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Affiliation(s)
- Jiao Qu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Fa Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yingshuo Wang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Wen Fang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yan Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xianjia Qi
- Shanghai XuRan Biotechnology Co., Ltd., 1088 Zhongchun Road, 201109, Shanghai, China
| | - Qiangmin Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yicheng Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China.
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China.
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11
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Zhuo MQ, Chen J, Wu ML, Wang WB. Novel insights for PI3KC3 in mediating lipid accumulation in yellow catfish Pelteobagrus fulvidraco. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:571-583. [PMID: 35389126 DOI: 10.1007/s10695-022-01071-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
In this study, the transcriptional regulation of PI3KC3 by three transcription factors (PPARγ, PPARα, and STAT3) and the potential role of PI3KC3 in mediating lipid accumulation were determined in yellow catfish Pelteobagrus fulvidraco. The 5'-deletion assay, overexpression assay, site-mutation assay, and electrophoretic mobility shift assay suggested that PPARα, PPARγ, and STAT3 negatively regulated the promoter activity of pi3kc3. Moreover, the transcriptional inactivation of pi3kc3 was directly mediated by PPARα and PPARγ under fatty acid (FA) treatment. Using primary hepatocytes from yellow catfish, FA incubation significantly increased triacylglyceride (TG) content, non-esterified fatty acid (NEFA) content, and lipid drops (LDs) content, the mRNA level of pparα, pparγ, stat3, and dnmt3b, the protein level of PPARα, PPARγ, and STAT3, and the methylation level of pi3kc3, but significantly reduced the mRNA and protein level of PI3KC3. Our findings offer new insights into the mechanisms for transcriptional regulation of PI3KC3 and for PI3KC3-mediated lipid accumulation in fish.
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Affiliation(s)
- Mei-Qin Zhuo
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China.
| | - Jun Chen
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China
| | - Mei-Li Wu
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China
| | - Wen-Biao Wang
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430070, China
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12
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Prasad M, Rajagopal P, Devarajan N, Veeraraghavan VP, Palanisamy CP, Cui B, Patil S, Jayaraman S. A comprehensive review on high fat diet-induced diabetes mellitus: An epigenetic view. J Nutr Biochem 2022; 107:109037. [PMID: 35533900 DOI: 10.1016/j.jnutbio.2022.109037] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 01/08/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
Modern lifestyle, genetics, nutritional overload through high-fat diet attributed prevalence and diabetes outcomes with various complications primarily due to obesity in which energy-dense diets frequently affect metabolic health. One possible issue usually associated with elevated chronic fat intake is insulin resistance, and hyperglycaemia constitutes an important function in altering the carbohydrates and lipids metabolism. Similarly, in assessing human susceptibility to weight gain and obesity, genetic variations play a central role, contributing to keen interest in identifying the possible role of epigenetics as a mediator of gene-environmental interactions influencing the production of type 2 diabetes mellitus and its related concerns. Epigenetic modifications associated with the acceptance of a sedentary lifestyle and environmental stress factors in response to energy intake and expenditure imbalances complement genetic alterations and lead to the production and advancement of metabolic disorders such as diabetes and obesity. Methylation of DNA, histone modifications and increases in the expression of non-coding RNAs can result in reduced transcriptional activity of key β-cell genes thus creating insulin resistance. Epigenetics contribute to changes in the expression of the underlying insulin resistance and insufficiency gene networks, along with low-grade obesity-related inflammation, increased ROS generation and DNA damage in multi organs. This review focused on epigenetic mechanisms and metabolic regulations associated with high fat diet (HFD)-induced diabetes mellitus.
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Affiliation(s)
- Monisha Prasad
- Centre for Molecular Medicine and diagnostic (CoMManD), Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600 077, India
| | - Ponnulakshmi Rajagopal
- Central Research Laboratory, Meenakhsi Ammal Dental College and Hospitals, Academy of Higher Education and Research, Chennai, 600 095, India
| | - Nalini Devarajan
- Central Research Laboratory, Meenakhsi Academy of Higher Education and Research, West K.K. Nagar, Chennai, 600 078, India
| | - Vishnu Priya Veeraraghavan
- State Key Laboratory of Biobased Materials and Green Papermaking, College of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, 250353, China
| | - Chella Perumal Palanisamy
- State Key Laboratory of Biobased Materials and Green Papermaking, College of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, 250353, China
| | - Bo Cui
- State Key Laboratory of Biobased Materials and Green Papermaking, College of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, 250353, China
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Saudi Arabia
| | - Selvaraj Jayaraman
- Centre for Molecular Medicine and diagnostic (CoMManD), Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600 077, India.
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13
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Yang X, Xiao X, Zhang L, Wang B, Li P, Cheng B, Liang C, Ma M, Guo X, Zhang F, Wen Y. An integrative analysis of DNA methylation and transcriptome showed the dysfunction of MAPK pathway was involved in the damage of human chondrocyte induced by T-2 toxin. BMC Mol Cell Biol 2022; 23:4. [PMID: 35038982 PMCID: PMC8762874 DOI: 10.1186/s12860-021-00404-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/28/2021] [Indexed: 12/05/2022] Open
Abstract
Background T-2 toxin is thought to induce the growth plate and articular cartilage damage of Kashin-Beck disease (KBD), an endemic osteochondropathy in China. This study aims to explore the potential underlying mechanism of such toxic effects by integrating DNA methylation and gene expression profiles. Methods In this study, C28/I2 chondrocytes were treated with T-2 toxin (5 ng/mL) for 24 h and 72 h. Global DNA methylation level of chondrocyte was tested by Enzyme-Linked Immuno Sorbent Assay. Genome-wide DNA methylation and expression profiles were detected using Illumina Infinium HumanMethylation850 BeadChip and RNA-seq technique, respectively. Differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified mainly for two stages including 24 h group versus Control group and 72 h group versus 24 h group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed by Metascape. DMGs and DEGs were further validated by Sequenom MassARRAY system and quantitative real-time polymerase chain reaction. Results The global DNA methylation levels of chondrocytes exposed to T-2 toxin were significantly increased (P < 0.05). For 24 h group versus Control group (24 VS C), 189 DEGs and 590 DMGs were identified, and 4 of them were overlapping. For 72 h group versus 24 h group (72 VS 24), 1671 DEGs and 637 DMGs were identified, and 45 of them were overlapping. The enrichment analysis results of DMGs and DEGs both showed that MAPK was the one of the mainly involved signaling pathways in the regulation of chondrocytes after T-2 toxin exposure (DEGs: P24VSc = 1.62 × 10− 7; P72VS24 = 1.20 × 10− 7; DMGs: P24VSc = 0.0056; P72VS24 = 3.80 × 10− 5). Conclusions The findings depicted a landscape of genomic methylation and transcriptome changes of chondrocytes after T-2 toxin exposure and suggested that dysfunction of MAPK pathway may play important roles in the chondrocytes damage induced by T-2 toxin, which could provide new clues for understanding the potential biological mechanism of KBD cartilage damage induced by T-2 toxin. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00404-3.
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Affiliation(s)
- Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Xue Xiao
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Bo Wang
- HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaan'xi, 710061, People's Republic of China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.
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14
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Liao S, He H, Zeng Y, Yang L, Liu Z, An Z, Zhang M. A nomogram for predicting metabolic steatohepatitis: The combination of NAMPT, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. Open Med (Wars) 2021; 16:773-785. [PMID: 34041361 PMCID: PMC8130015 DOI: 10.1515/med-2021-0286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/17/2021] [Accepted: 04/17/2021] [Indexed: 02/05/2023] Open
Abstract
Objective To identify differentially expressed and clinically significant mRNAs and construct a potential prediction model for metabolic steatohepatitis (MASH). Method We downloaded four microarray datasets, GSE89632, GSE24807, GSE63067, and GSE48452, from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis were performed to screen significant genes. Finally, we constructed a nomogram of six hub genes in predicting MASH and assessed it through receiver operating characteristic (ROC) curve, calibration plot, and decision curve analysis (DCA). In addition, qRT-PCR was used for relative quantitative detection of RNA in QSG-7011 cells to further verify the expression of the selected mRNA in fatty liver cells. Results Based on common DEGs and brown and yellow modules, seven hub genes were identified, which were NAMPT, PHLDA1, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. After logistic regression analysis, six hub genes were used to establish the nomogram, which were NAMPT, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. The area under the ROC of the nomogram was 0.897. The DCA showed that when the threshold probability of MASH was 0–0.8, the prediction model was valuable to GSE48452. In QSG-7011 fatty liver model cells, the relative expression levels of NAMPT, GADD45B, FOSL2, RTP3, RASD1 and RALGDS were lower than the control group. Conclusion We identified seven hub genes NAMPT, PHLDA1, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. The nomogram showed good performance in the prediction of MASH and it had clinical utility in distinguishing MASH from simple steatosis.
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Affiliation(s)
- Shenling Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - He He
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuping Zeng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Lidan Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhi Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhenmei An
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
| | - Mei Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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Oral Bisphenol A Worsens Liver Immune-Metabolic and Mitochondrial Dysfunction Induced by High-Fat Diet in Adult Mice: Cross-Talk between Oxidative Stress and Inflammasome Pathway. Antioxidants (Basel) 2020; 9:antiox9121201. [PMID: 33265944 PMCID: PMC7760359 DOI: 10.3390/antiox9121201] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022] Open
Abstract
Lines of evidence have shown the embryogenic and transgenerational impact of bisphenol A (BPA), an endocrine-disrupting chemical, on immune-metabolic alterations, inflammation, and oxidative stress, while BPA toxic effects in adult obese mice are still overlooked. Here, we evaluate BPA’s worsening effect on several hepatic maladaptive processes associated to high-fat diet (HFD)-induced obesity in mice. After 12 weeks HFD feeding, C57Bl/6J male mice were exposed daily to BPA (50 μg/kg per os) along with HFD for 3 weeks. Glucose tolerance and lipid metabolism were examined in serum and/or liver. Hepatic oxidative damage (reactive oxygen species, malondialdehyde, antioxidant enzymes), and mitochondrial respiratory capacity were evaluated. Moreover, liver damage progression and inflammatory/immune response were determined by histological and molecular analysis. BPA amplified HFD-induced alteration of key factors involved in glucose and lipid metabolism, liver triglycerides accumulation, and worsened mitochondrial dysfunction by increasing oxidative stress and reducing antioxidant defense. The exacerbation by BPA of hepatic immune-metabolic dysfunction induced by HFD was shown by increased toll-like receptor-4 and its downstream pathways (i.e., NF-kB and NLRP3 inflammasome) amplifying inflammatory cytokine transcription and promoting fibrosis progression. This study evidences that BPA exposure represents an additional risk factor for the progression of fatty liver diseases strictly related to the cross-talk between oxidative stress and immune-metabolic impairment due to obesity.
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16
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The function and regulation of TET2 in innate immunity and inflammation. Protein Cell 2020; 12:165-173. [PMID: 33085059 PMCID: PMC7895883 DOI: 10.1007/s13238-020-00796-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/15/2020] [Indexed: 02/08/2023] Open
Abstract
TET2, a member of ten-eleven translocation (TET) family as α-ketoglutarate- and Fe2+-dependent dioxygenase catalyzing the iterative oxidation of 5-methylcytosine (5mC), has been widely recognized to be an important regulator for normal hematopoiesis especially myelopoiesis. Mutation and dysregulation of TET2 contribute to the development of multiple hematological malignancies. Recent studies reveal that TET2 also plays an important role in innate immune homeostasis by promoting DNA demethylation or independent of its enzymatic activity. Here, we focus on the functions of TET2 in the initiation and resolution of inflammation through epigenetic regulation and signaling network. In addition, we highlight regulation of TET2 at various molecular levels as well as the correlated inflammatory diseases, which will provide the insight to intervene in the pathological process caused by TET2 dysregulation.
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Metabolic Flexibility Assists Reprograming of Central and Peripheral Innate Immunity During Neurodevelopment. Mol Neurobiol 2020; 58:703-718. [PMID: 33006752 DOI: 10.1007/s12035-020-02154-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/28/2020] [Indexed: 01/03/2023]
Abstract
Central innate immunity assists time-dependent neurodevelopment by recruiting and interacting with peripheral immune cells. Microglia are the major player of central innate immunity integrating peripheral signals arising from the circumventricular regions lacking the blood-brain barrier (BBB), via neural afferent pathways such as the vagal nerve and also by choroid plexus into the brain ventricles. Defective and/or unrestrained activation of central and peripheral immunity during embryonic development might set an aberrant connectome establishment and brain function, leading to major psychiatric disorders in postnatal stages. Molecular candidates leading to central and peripheral innate immune overactivation identified metabolic substrates and lipid species as major contributors of immunological priming, supporting the role of a metabolic flexibility node during trained immunity. Mechanistically, trained immunity is established by an epigenetic program including DNA methylation and histone acetylation, as the major molecular epigenetic signatures to set immune phenotypes. By definition, immunological training sets reprogramming of innate immune cells, enhancing or repressing immune responses towards a second challenge which potentially might contribute to neurodevelopment disorders. Notably, the innate immune training might be set during pregnancy by maternal immune activation stimuli. In this review, we integrate the most valuable scientific evidence supporting the role of metabolic cues assisting metabolic flexibility, leading to innate immune training during development and its effects on aberrant neurological phenotypes in the offspring. We also add reports supporting the role of methylation and histone acetylation signatures as a major epigenetic mechanism regulating immune training.
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18
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Cronjé HT, Elliott HR, Nienaber-Rousseau C, Pieters M. Leveraging the urban-rural divide for epigenetic research. Epigenomics 2020; 12:1071-1081. [PMID: 32657149 DOI: 10.2217/epi-2020-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Urbanization coincides with a complex change in environmental exposure and a rapid increase in noncommunicable diseases (NCDs). Epigenetics, including DNA methylation (DNAm), is thought to mediate part of the association between genetic/environmental exposure and NCDs. The urban-rural divide provides a unique opportunity to investigate the effect of the combined presence of multiple forms of environmental exposure on DNAm and the related increase in disease risk. This review evaluates the ability of three epidemiological study designs (migration, income-comparative and urban-rural designs) to investigate the role of DNAm in the association between urbanization and the rise in NCD prevalence. We also discuss the ability of each study design to address the gaps in the current literature, including the complex methylation-mediated risk attributable to the cluster of forms of exposure characterizing urban and rural living, while providing a platform for developing countries to leverage their demographic discrepancies in future research ventures.
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Affiliation(s)
- Héléne T Cronjé
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Cornelie Nienaber-Rousseau
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Marlien Pieters
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
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19
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Schulze KV, Swaminathan S, Howell S, Jajoo A, Lie NC, Brown O, Sadat R, Hall N, Zhao L, Marshall K, May T, Reid ME, Taylor-Bryan C, Wang X, Belmont JW, Guan Y, Manary MJ, Trehan I, McKenzie CA, Hanchard NA. Edematous severe acute malnutrition is characterized by hypomethylation of DNA. Nat Commun 2019; 10:5791. [PMID: 31857576 PMCID: PMC6923441 DOI: 10.1038/s41467-019-13433-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
Edematous severe acute childhood malnutrition (edematous SAM or ESAM), which includes kwashiorkor, presents with more overt multi-organ dysfunction than non-edematous SAM (NESAM). Reduced concentrations and methyl-flux of methionine in 1-carbon metabolism have been reported in acute, but not recovered, ESAM, suggesting downstream DNA methylation changes could be relevant to differences in SAM pathogenesis. Here, we assess genome-wide DNA methylation in buccal cells of 309 SAM children using the 450 K microarray. Relative to NESAM, ESAM is characterized by multiple significantly hypomethylated loci, which is not observed among SAM-recovered adults. Gene expression and methylation show both positive and negative correlation, suggesting a complex transcriptional response to SAM. Hypomethylated loci link to disorders of nutrition and metabolism, including fatty liver and diabetes, and appear to be influenced by genetic variation. Our epigenetic findings provide a potential molecular link to reported aberrant 1-carbon metabolism in ESAM and support consideration of methyl-group supplementation in ESAM.
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Affiliation(s)
- Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Shanker Swaminathan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Sharon Howell
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Aarti Jajoo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Natasha C Lie
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Orgen Brown
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Roa Sadat
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Nancy Hall
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Shiyan City, China
| | - Kwesi Marshall
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Thaddaeus May
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Marvin E Reid
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Carolyn Taylor-Bryan
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Xueqing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Yongtao Guan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Mark J Manary
- Departments of Paediatrics and Child Health and Community Health, University of Malawi, Blantyre, Malawi
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Indi Trehan
- Departments of Paediatrics and Child Health and Community Health, University of Malawi, Blantyre, Malawi
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
- Departments of Pediatrics and Global Health, University of Washington, Seattle, WA, USA
| | - Colin A McKenzie
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA.
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20
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Nutritional Factors Modulating Alu Methylation in an Italian Sample from The Mark-Age Study Including Offspring of Healthy Nonagenarians. Nutrients 2019; 11:nu11122986. [PMID: 31817660 PMCID: PMC6950565 DOI: 10.3390/nu11122986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/11/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
Alu hypomethylation promotes genomic instability and is associated with aging and age-related diseases. Dietary factors affect global DNA methylation, leading to changes in genomic stability and gene expression with an impact on longevity and the risk of disease. This preliminary study aims to investigate the relationship between nutritional factors, such as circulating trace elements, lipids and antioxidants, and Alu methylation in elderly subjects and offspring of healthy nonagenarians. Alu DNA methylation was analyzed in sixty RASIG (randomly recruited age-stratified individuals from the general population) and thirty-two GO (GeHA offspring) enrolled in Italy in the framework of the MARK-AGE project. Factor analysis revealed a different clustering between Alu CpG1 and the other CpG sites. RASIG over 65 years showed lower Alu CpG1 methylation than those of GO subjects in the same age class. Moreover, Alu CpG1 methylation was associated with fruit and whole-grain bread consumption, LDL2-Cholesterol and plasma copper. The preserved Alu methylation status in GO, suggests Alu epigenetic changes as a potential marker of aging. Our preliminary investigation shows that Alu methylation may be affected by food rich in fibers and antioxidants, or circulating LDL subfractions and plasma copper.
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21
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Rosselot C, Kumar A, Lakshmipathi J, Zhang P, Lu G, Katz LS, Prochownik EV, Stewart AF, Lambertini L, Scott DK, Garcia-Ocaña A. Myc Is Required for Adaptive β-Cell Replication in Young Mice but Is Not Sufficient in One-Year-Old Mice Fed With a High-Fat Diet. Diabetes 2019; 68:1934-1949. [PMID: 31292135 PMCID: PMC6754239 DOI: 10.2337/db18-1368] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 07/02/2019] [Indexed: 12/18/2022]
Abstract
Failure to expand pancreatic β-cells in response to metabolic stress leads to excessive workload resulting in β-cell dysfunction, dedifferentiation, death, and development of type 2 diabetes. In this study, we demonstrate that induction of Myc is required for increased pancreatic β-cell replication and expansion during metabolic stress-induced insulin resistance with short-term high-fat diet (HFD) in young mice. β-Cell-specific Myc knockout mice fail to expand adaptively and show impaired glucose tolerance and β-cell dysfunction. Mechanistically, PKCζ, ERK1/2, mTOR, and PP2A are key regulators of the Myc response in this setting. DNA methylation analysis shows hypomethylation of cell cycle genes that are Myc targets in islets from young mice fed with a short-term HFD. Importantly, DNA hypomethylation of Myc response elements does not occur in islets from 1-year-old mice fed with a short-term HFD, impairing both Myc recruitment to cell cycle regulatory genes and β-cell replication. We conclude that Myc is required for metabolic stress-mediated β-cell expansion in young mice, but with aging, Myc upregulation is not sufficient to induce β-cell replication by, at least partially, an epigenetically mediated resistance to Myc action.
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Affiliation(s)
- Carolina Rosselot
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Anil Kumar
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jayalakshmi Lakshmipathi
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Pili Zhang
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Geming Lu
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Liora S Katz
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Edward V Prochownik
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA
- Department of Microbiology & Molecular Genetics, University of Pittsburgh Medical Center, Hillman Cancer Center, and Pittsburgh Liver Research Center, Pittsburgh, PA
| | - Andrew F Stewart
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Luca Lambertini
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Donald K Scott
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Adolfo Garcia-Ocaña
- Division of Endocrinology, Diabetes and Bone Diseases, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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22
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Nicoletti CF, Pinhel MAS, Diaz-Lagares A, Casanueva FF, Jácome A, Pinhanelli VC, de Oliveira BAP, Crujeiras AB, Nonino CB. DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se. BMC Med Genomics 2019; 12:72. [PMID: 31133015 PMCID: PMC6537208 DOI: 10.1186/s12920-019-0522-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Background/objectives Obesity has been associated with gene methylation regulation. Recent studies have shown that epigenetic signature plays a role in metabolic homeostasis after Roux-en Y gastric bypass (RYGB). To conduct a genome-wide epigenetic analysis in peripheral blood to investigate whether epigenetic changes following RYGB stem from weight loss or the surgical procedure per se. Subjects/methods By means of the Infinium Human Methylation 450 BeadChip array, global methylation was analyzed in blood of 24 severely obese women before and 6 months after RYGB and in 24 normal-weight women (controls). Results In blood cells, nine DMCpG sites showed low methylation levels before surgery, methylation levels increased after RYGB and neared the levels measured in the controls. Additionally, 44 CpG sites associated with the Wnt and p53 signaling pathways were always differently methylated in the severely obese patients as compared to the controls and were not influenced by RYGB. Finally, 1638 CpG sites related to inflammation, angiogenesis, and apoptosis presented distinct methylation in the post-surgery patients as compared to the controls. Conclusion Bariatric surgery per se acts on CpGs related to inflammation, angiogenesis, and endothelin-signaling. However, the gene cluster associated with obesity remains unchanged, suggesting that weight loss 6 months after RYGB surgery cannot promote this effect. Graphical abstract ![]()
Electronic supplementary material The online version of this article (10.1186/s12920-019-0522-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C F Nicoletti
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - M A S Pinhel
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - A Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - F F Casanueva
- Epigenomics in Endocrinology and Nutrition, Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - A Jácome
- Department of Mathematics, MODES group, CITIC, Universidade da Coruña, Faculty of Science, A Coruña, Spain
| | - V C Pinhanelli
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - B A P de Oliveira
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - A B Crujeiras
- Epigenomics in Endocrinology and Nutrition, Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain. .,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.
| | - C B Nonino
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil.
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23
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Effect of Age, High-Fat Diet, and Rat Strain on Serum Biomarkers and Telomere Length and Global DNA Methylation in Peripheral Blood Mononuclear Cells. Sci Rep 2019; 9:1996. [PMID: 30760804 PMCID: PMC6374545 DOI: 10.1038/s41598-018-38192-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022] Open
Abstract
The objective of the current study was to determine if age, diet, and genetic disposition (animal strain) in an animal model had early effects on specific molecular markers in circulating peripheral blood mononuclear cells (PBMCs). Three strains [Sprague-Dawley (SD), Fischer 344 (F344), and Brown-Norway (BN)] of male rats were maintained on a high-fat (HF) or regular diet. Blood was collected at 4, 12, and 24 wk to assess chemistry and to recover PBMCs. Triglycerides and body weight gain increased at all time points in the HF diet group for each strain. Telomere length in PBMCs decreased in the HF diet group compared to the regular diet group up to 24 wk in all strains. Telomere length decreased in PBMCs at 24 wk compared to baseline in all strains, indicating an age-related effect. These findings highlight that diet and age cause changes in PBMCs recovered from different strains of rats. The next tier of studies will examine the contribution of an occupational exposure (e.g., welding fume inhalation) in combination with diet, age, and strain, to assess changes in the molecular responses of isolated PBMCs. In addition, studies involving lifestyle exposure (e.g., tobacco smoke) are in the planning stages and will assess the long-term effects of exposure in our animal model.
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24
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Luna RCP, Dos Santos Nunes MK, Monteiro MGCA, da Silva CSO, do Nascimento RAF, Lima RPA, Pimenta FCF, de Oliveira NFP, Persuhn DC, de Almeida ATC, da Silva Diniz A, Pissetti CW, Vianna RPT, de Lima Ferreira FEL, Rodrigues Gonçalves MDC, de Carvalho Costa MJ. α-Tocopherol influences glycaemic control and miR-9-3 DNA methylation in overweight and obese women under an energy-restricted diet: a randomized, double-blind, exploratory, controlled clinical trial. Nutr Metab (Lond) 2018; 15:49. [PMID: 30008789 PMCID: PMC6042339 DOI: 10.1186/s12986-018-0286-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/03/2018] [Indexed: 12/14/2022] Open
Abstract
Background Excess weight is a strong risk factor for the development of dysglycaemia. It has been suggested that changes in the metabolism microRNAs, small non-coding RNAs that regulate gene expression, could precede late glycaemic changes. Vitamin E in turn may exert important functions in methylation and gene expression processes. This study aimed to determine the effect of α-tocopherol on glycaemic variables and miR-9-1 and miR-9-3 promoter DNA methylation in overweight women. Methods A randomized, double-blind, exploratory, placebo-controlled study was conducted in overweight and obese adult women (n = 44) who ingested synthetic vitamin E (all-rac-α-tocopherol), natural source vitamin E (RRR-rac-α-tocopherol) or placebo capsules and were followed up for a period of 8 weeks. Supplemented groups also received dietary guidance for an energy-restricted diet. An additional group that received no supplementation and did not follow an energy-restricted diet was also followed up. The intervention effect was evaluated by DNA methylation levels (quantitative real-time PCR assay) and anthropometric and biochemical variables (fasting plasma glucose, haemoglobin A1C, insulin, and vitamin E). Results Increased methylation levels of the miR-9-3 promoter region (P < 0.001) and reduced haemoglobin A1C (P < 0.05) were observed in the natural source vitamin E group after intervention. Increased fasting plasma glucose was observed in the synthetic vitamin E group, despite the significant reduction of anthropometric variables compared to the other groups. Conclusions α-Tocopherol from natural sources increased methylation levels of the miR-9-3 promoter region and reduced haemoglobin A1C in overweight women following an energy-restricted diet. These results provide novel information about the influence of vitamin E on DNA methylation. Trial registration ClinicalTrials.gov, NCT02922491. Registered 4 October, 2016. Electronic supplementary material The online version of this article (10.1186/s12986-018-0286-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rafaella Cristhine Pordeus Luna
- 1Postgraduate in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil.,10Postgraduate in Nutrition Sciences, Health Sciences Center, Health and Nutrition Studies Interdisciplinary Center (NIESN), Federal University of Paraíba (Universidade Federal da Paraíba), Castelo Branco, João Pessoa, Paraíba 58051-900 Brazil
| | - Mayara Karla Dos Santos Nunes
- 2Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58059-900 Brazil
| | - Mussara Gomes Cavalcante Alves Monteiro
- 1Postgraduate in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Cássia Surama Oliveira da Silva
- 3Health and Nutrition Studies Interdisciplinary Center, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Rayner Anderson Ferreira do Nascimento
- 2Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58059-900 Brazil
| | - Raquel Patrícia Ataíde Lima
- 1Postgraduate in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Flávia Cristina Fernandes Pimenta
- 4Department of Internal Medicine, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Naila Francis Paulo de Oliveira
- 5Departament of Molecular Biology, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, 58059-900 Paraíba Brasil
| | - Darlene Camati Persuhn
- 1Postgraduate in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil.,2Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58059-900 Brazil.,5Departament of Molecular Biology, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, 58059-900 Paraíba Brasil
| | - Aléssio Tony Cavalcanti de Almeida
- 6Department of Economics, Postgraduate Program in Applied Economics and Economics of the Public Sector, Center for Applied Social Sciences, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58059-900 Brazil
| | - Alcides da Silva Diniz
- 7Department of Nutrition, Graduate Program in Nutrition, Health Sciences Center, Federal University of Pernambuco, Recife, Pernambuco 50670901 Brazil
| | - Cristina Wide Pissetti
- 8Department of Obstetrics and Gynecology, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Rodrigo Pinheiro Toledo Vianna
- 9Department of Nutrition, Graduate Program in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Flavia Emília Leite de Lima Ferreira
- 9Department of Nutrition, Graduate Program in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Maria da Conceição Rodrigues Gonçalves
- 1Postgraduate in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil.,9Department of Nutrition, Graduate Program in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
| | - Maria José de Carvalho Costa
- 1Postgraduate in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil.,9Department of Nutrition, Graduate Program in Nutrition Sciences, Health Sciences Center, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Paraíba 58051-900 Brazil
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25
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Abstract
The aim of the present review paper is to survey the literature related to DNA methylation, and its association with cancer and ageing. The review will outline the key factors, including diet, which modulate DNA methylation. Our rationale for conducting this review is that ageing and diseases, including cancer, are often accompanied by aberrant DNA methylation, a key epigenetic process, which is crucial to the regulation of gene expression. Significantly, it has been observed that with age and certain disease states, DNA methylation status can become disrupted. For instance, a broad array of cancers are associated with promoter-specific hypermethylation and concomitant gene silencing. This review highlights that hypermethylation, and gene silencing, of the EN1 gene promoter, a crucial homeobox gene, has been detected in various forms of cancer. This has led to this region being proposed as a potential biomarker for diseases such as cancer. We conclude the review by describing a recently developed novel electrochemical method that can be used to quantify the level of methylation within the EN1 promoter and emphasise the growing trend in the use of electrochemical techniques for the detection of aberrant DNA methylation.
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26
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Cao J, Zhu Q, Liu L, Glazier BJ, Hinkel BC, Liang C, Shi H. Global Transcriptome Analysis of Brown Adipose Tissue of Diet-Induced Obese Mice. Int J Mol Sci 2018; 19:ijms19041095. [PMID: 29642370 PMCID: PMC5979511 DOI: 10.3390/ijms19041095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/17/2018] [Accepted: 03/24/2018] [Indexed: 12/16/2022] Open
Abstract
Consumption of a high-fat diet (HFD) promotes the development of obesity, a disease resulting from an imbalance between energy intake and energy expenditure. Brown adipose tissue (BAT) has thermogenic capacity that burns calories to produce heat, and it is a potential target for the treatment and prevention of obesity. There is limited information regarding the impact of HFD on the BAT transcriptome. We hypothesized that HFD-induced obesity would lead to transcriptional regulation of BAT genes. RNA sequencing was used to generate global transcriptome profiles from BAT of lean mice fed with a low-fat diet (LFD) and obese mice fed with a HFD. Gene Ontology (GO) analysis identified increased expression of genes involved in biological processes (BP) related to immune responses, which enhanced molecular function (MF) in chemokine activity; decreased expression of genes involved in BP related to ion transport and muscle structure development, which reduced MF in channel and transporter activity and structural binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathway analysis indicated that pathways associated with innate immunity were enhanced by HFD, while pathways associated with muscle contraction and calcium signaling were suppressed by HFD. Collectively, these results suggest that diet-induced obesity changes transcriptomic signatures of BAT, leading to dysfunction involving inflammation, calcium signaling, ion transport, and cell structural development.
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Affiliation(s)
- Jingyi Cao
- Program of Physiology and Neuroscience, Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Qi Zhu
- Program of Physiology and Neuroscience, Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Lin Liu
- Program of Bioinformatics, Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Bradley J Glazier
- Program of Physiology and Neuroscience, Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Benjamin C Hinkel
- Program of Physiology and Neuroscience, Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Chun Liang
- Program of Bioinformatics, Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Haifei Shi
- Program of Physiology and Neuroscience, Department of Biology, Miami University, Oxford, OH 45056, USA.
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