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Müller L, Hoffmann A, Bernhart SH, Ghosh A, Zhong J, Hagemann T, Sun W, Dong H, Noé F, Wolfrum C, Dietrich A, Stumvoll M, Massier L, Blüher M, Kovacs P, Chakaroun R, Keller M. Blood methylation pattern reflects epigenetic remodelling in adipose tissue after bariatric surgery. EBioMedicine 2024; 106:105242. [PMID: 39002385 DOI: 10.1016/j.ebiom.2024.105242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND Studies on DNA methylation following bariatric surgery have primarily focused on blood cells, while it is unclear to which extend it may reflect DNA methylation profiles in specific metabolically relevant organs such as adipose tissue. Here, we investigated whether adipose tissue depots specific methylation changes after bariatric surgery are mirrored in blood. METHODS Using Illumina 850K EPIC technology, we analysed genome-wide DNA methylation in paired blood, subcutaneous and omental visceral AT (SAT/OVAT) samples from nine individuals (N = 6 female) with severe obesity pre- and post-surgery. FINDINGS The numbers and effect sizes of differentially methylated regions (DMRs) post-bariatric surgery were more pronounced in AT (SAT: 12,865 DMRs from -11.5 to 10.8%; OVAT: 14,632 DMRs from -13.7 to 12.8%) than in blood (9267 DMRs from -8.8 to 7.7%). Cross-tissue DMRs implicated immune-related genes. Among them, 49 regions could be validated with similar methylation changes in blood from independent individuals. Fourteen DMRs correlated with differentially expressed genes in AT post bariatric surgery, including downregulation of PIK3AP1 in both SAT and OVAT. DNA methylation age acceleration was significantly higher in AT compared to blood, but remained unaffected after surgery. INTERPRETATION Concurrent methylation pattern changes in blood and AT, particularly in immune-related genes, suggest blood DNA methylation mirrors AT's inflammatory state post-bariatric surgery. FUNDING The funding sources are listed in the Acknowledgments section.
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Affiliation(s)
- Luise Müller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, 04103, Germany
| | - Stephan H Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany; Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany; Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany
| | - Adhideb Ghosh
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Schwerzenbach, Switzerland
| | - Jiawei Zhong
- Department of Medicine Huddinge (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, 141 83, Huddinge, Sweden
| | - Tobias Hagemann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, 04103, Germany
| | - Wenfei Sun
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Schwerzenbach, Switzerland
| | - Hua Dong
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Schwerzenbach, Switzerland
| | - Falko Noé
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Schwerzenbach, Switzerland
| | - Christian Wolfrum
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Schwerzenbach, Switzerland
| | - Arne Dietrich
- Leipzig University Hospital, Department of Visceral, Transplantation, Thoracic and Vascular Surgery, Section of Bariatric Surgery, 04103, Leipzig, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, 04103, Germany; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, 04103, Germany; Deutsches Zentrum für Diabetesforschung e.V., 85764, Neuherberg, Germany
| | - Lucas Massier
- Department of Medicine Huddinge (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, 141 83, Huddinge, Sweden
| | - Matthias Blüher
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, 04103, Germany; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, 04103, Germany; Deutsches Zentrum für Diabetesforschung e.V., 85764, Neuherberg, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, 04103, Germany; Deutsches Zentrum für Diabetesforschung e.V., 85764, Neuherberg, Germany
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, 04103, Germany; The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden
| | - Maria Keller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, 04103, Germany; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, 04103, Germany.
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Cui TT, Huang JX, Ning BL, Mu F, Chen HY, Xing TY, Li H, Wang N. DNA methylation promotes the expression of PPARγ transcript 1 at least in part by preventing NRF1 binding to the promoter P1 of chicken PPARγ gene. Poult Sci 2024; 103:103559. [PMID: 38430780 PMCID: PMC10912915 DOI: 10.1016/j.psj.2024.103559] [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: 10/28/2023] [Revised: 12/16/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a master regulator of adipogenesis. Our previous study revealed that chicken PPARγ has 3 alternative promoters named as P1, P2, and P3, and the DNA methylation of promoter P3 was negatively associated with PPARγ mRNA expression in abdominal adipose tissue (AAT). However, the methylation status of promoters P1 and P2 is unclear. Here we assessed promoter P1 methylation status in AAT of Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). The results showed that promoter P1 methylation differed in AAT between the lean and fat lines of NEAUHLF at 7 wk of age (p < 0.05), and AAT expression of PPARγ transcript 1 (PPARγ1), which was derived from the promoter P1, was greatly higher in fat line than in lean line at 2 and 7 wk of age. The results of the correlation analysis showed that P1 methylation was positively correlated with PPARγ1 expression at 7 wk of age (Pearson's r = 0.356, p = 0.0242), suggesting P1 methylation promotes PPARγ1 expression. To explore the underlying molecular mechanism of P1 methylation on PPARγ1 expression, bioinformatics analysis, dual-luciferase reporter assay, pyrosequencing, and electrophoresis mobility shift assay (EMSA) were performed. The results showed that transcription factor NRF1 repressed the promoter activity of the unmethylated P1, but not the methylated P1. Of all the 4 CpGs (CpG48, CpG49, CpG50, and CpG51), which reside within or nearby the NRF1 binding sites of the P1, only CpG49 methylation in AAT was remarkably higher in the fat line than in lean line at 7 wk of age (3.18 to 0.57, p < 0.05), and CpG49 methylation was positively correlated with PPARγ1 expression (Pearson's r = 0.3716, p = 0.0432). Furthermore, EMSA showed that CpG49 methylation reduced the binding of NRF1 to the P1. Taken together, our findings illustrate that P1 methylation promotes PPARγ1 expression at least in part by preventing NRF1 from binding to the promoter P1.
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Affiliation(s)
- T T Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, 161006, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
| | - J X Huang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
| | - B L Ning
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
| | - F Mu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
| | - H Y Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
| | - T Y Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
| | - H Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
| | - N Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China.
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3
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Argentato PP, Guerra JVDS, Luzia LA, Ramos ES, Maschietto M, Rondó PHDC. Integrative network analysis of differentially methylated regions to study the impact of gestational weight gain on maternal metabolism and fetal-neonatal growth. Genet Mol Biol 2024; 47:e20230203. [PMID: 38530405 PMCID: PMC10993311 DOI: 10.1590/1678-4685-gmb-2023-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/10/2024] [Indexed: 03/28/2024] Open
Abstract
Integrative network analysis (INA) is important for identifying gene modules or epigenetically regulated molecular pathways in diseases. This study evaluated the effect of excessive gestational weight gain (EGWG) on INA of differentially methylated regions, maternal metabolism and offspring growth. Brazilian women from "The Araraquara Cohort Study" with adequate pre-pregnancy body mass index were divided into EGWG (n=30) versus adequate gestational weight gain (AGWG, n=45) groups. The methylome analysis was performed on maternal blood using the Illumina MethylationEPIC BeadChip. Fetal-neonatal growth was assessed by ultrasound and anthropometry, respectively. Maternal lipid and glycemic profiles were investigated. Maternal triglycerides-TG (p=0.030) and total cholesterol (p=0.014); fetus occipito-frontal diameter (p=0.005); neonate head circumference-HC (p=0.016) and thoracic perimeter (p=0.020) were greater in the EGWG compared to the AGWG group. Multiple linear regression analysis showed that maternal DNA methylation was associated with maternal TG and fasting insulin, fetal abdominal circumference, and fetal and neonate HC. The DMRs studied were enriched in 142 biological processes, 21 molecular functions,and 17 cellular components with terms directed for the fatty acids metabolism. Three DMGMs were identified:COL3A1, ITGA4 and KLRK1. INA targeted chronic diseases and maternal metabolism contributing to an epigenetic understanding of the involvement of GWG in maternal metabolism and fetal-neonatal growth.
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Affiliation(s)
- Perla Pizzi Argentato
- Universidade de São Paulo, Faculdade de Saúde Pública, Departamento de Nutrição, São Paulo, SP, Brazil
| | - João Victor da Silva Guerra
- Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Laboratório Nacional de Biociências (LNBio). Campinas, SP, Brazil
- Universidade Estadual de Campinas, Faculdade de Ciências Farmacêuticas, Programa de Pós-Graduação em Ciências Farmacêuticas, Campinas, SP, Brazil
| | - Liania Alves Luzia
- Universidade de São Paulo, Faculdade de Saúde Pública, Departamento de Nutrição, São Paulo, SP, Brazil
| | - Ester Silveira Ramos
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Mariana Maschietto
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Biologia Estrutural e Funcional, Campinas, SP, Brazil
- Centro Infantil Boldrini, Campinas, SP, Brazil
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Nevzorova YA, Cubero FJ. Obesity under the moonlight of c-MYC. Front Cell Dev Biol 2023; 11:1293218. [PMID: 38116204 PMCID: PMC10728299 DOI: 10.3389/fcell.2023.1293218] [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: 09/12/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023] Open
Abstract
The moonlighting protein c-Myc is a master regulator of multiple biological processes including cell proliferation, differentiation, angiogenesis, apoptosis and metabolism. It is constitutively and aberrantly expressed in more than 70% of human cancers. Overwhelming evidence suggests that c-Myc dysregulation is involved in several inflammatory, autoimmune, metabolic and other non-cancerous diseases. In this review, we addressed the role of c-Myc in obesity. Obesity is a systemic disease, accompanied by multi-organ dysfunction apart from white adipose tissue (WAT), such as the liver, the pancreas, and the intestine. c-Myc plays a big diversity of functions regulating cellular proliferation, the maturation of progenitor cells, fatty acids (FAs) metabolism, and extracellular matrix (ECM) remodeling. Moreover, c-Myc drives the expression of a wide range of metabolic genes, modulates the inflammatory response, induces insulin resistance (IR), and contributes to the regulation of intestinal dysbiosis. Altogether, c-Myc is an interesting diagnostic tool and/or therapeutic target in order to mitigate obesity and its consequences.
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Affiliation(s)
- Yulia A. Nevzorova
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Francisco Javier Cubero
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
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Koh J, Woo YD, Yoo HJ, Choi JP, Kim SH, Chang YS, Jung KC, Kim JH, Jeon YK, Kim HY, Chung DH. De novo fatty-acid synthesis protects invariant NKT cells from cell death, thereby promoting their homeostasis and pathogenic roles in airway hyperresponsiveness. eLife 2023; 12:RP87536. [PMID: 37917548 PMCID: PMC10622147 DOI: 10.7554/elife.87536] [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] [Indexed: 11/04/2023] Open
Abstract
Invariant natural-killer T (iNKT) cells play pathogenic roles in allergic asthma in murine models and possibly also humans. While many studies show that the development and functions of innate and adaptive immune cells depend on their metabolic state, the evidence for this in iNKT cells is very limited. It is also not clear whether such metabolic regulation of iNKT cells could participate in their pathogenic activities in asthma. Here, we showed that acetyl-coA-carboxylase 1 (ACC1)-mediated de novo fatty-acid synthesis is required for the survival of iNKT cells and their deleterious functions in allergic asthma. ACC1, which is a key fatty-acid synthesis enzyme, was highly expressed by lung iNKT cells from WT mice that were developing asthma. Cd4-Cre::Acc1fl/fl mice failed to develop OVA-induced and HDM-induced asthma. Moreover, iNKT cell-deficient mice that were reconstituted with ACC1-deficient iNKT cells failed to develop asthma, unlike when WT iNKT cells were transferred. ACC1 deficiency in iNKT cells associated with reduced expression of fatty acid-binding proteins (FABPs) and peroxisome proliferator-activated receptor (PPAR)γ, but increased glycolytic capacity that promoted iNKT-cell death. Furthermore, circulating iNKT cells from allergic-asthma patients expressed higher ACC1 and PPARG levels than the corresponding cells from non-allergic-asthma patients and healthy individuals. Thus, de novo fatty-acid synthesis prevents iNKT-cell death via an ACC1-FABP-PPARγ axis, which contributes to their homeostasis and their pathogenic roles in allergic asthma.
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Affiliation(s)
- Jaemoon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yeon Duk Woo
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Yoo
- Laboratory of Immunology and Vaccine Innovation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jun-Pyo Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sae Hoon Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Council, Seoul, Republic of Korea
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Council, Seoul, Republic of Korea
| | - Kyeong Cheon Jung
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Hyung Kim
- Laboratory of Immunology and Vaccine Innovation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hye Young Kim
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
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Antontseva EV, Degtyareva AO, Korbolina EE, Damarov IS, Merkulova TI. Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis. Vavilovskii Zhurnal Genet Selektsii 2023; 27:662-675. [PMID: 37965371 PMCID: PMC10641029 DOI: 10.18699/vjgb-23-77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 11/16/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most common type of variation in the human genome. The vast majority of SNPs identified in the human genome do not have any effect on the phenotype; however, some can lead to changes in the function of a gene or the level of its expression. Most SNPs associated with certain traits or pathologies are mapped to regulatory regions of the genome and affect gene expression by changing transcription factor binding sites. In recent decades, substantial effort has been invested in searching for such regulatory SNPs (rSNPs) and understanding the mechanisms by which they lead to phenotypic differences, primarily to individual differences in susceptibility to diseases and in sensitivity to drugs. The development of the NGS (next-generation sequencing) technology has contributed not only to the identification of a huge number of SNPs and to the search for their association (genome-wide association studies, GWASs) with certain diseases or phenotypic manifestations, but also to the development of more productive approaches to their functional annotation. It should be noted that the presence of an association does not allow one to identify a functional, truly disease-associated DNA sequence variant among multiple marker SNPs that are detected due to linkage disequilibrium. Moreover, determination of associations of genetic variants with a disease does not provide information about the functionality of these variants, which is necessary to elucidate the molecular mechanisms of the development of pathology and to design effective methods for its treatment and prevention. In this regard, the functional analysis of SNPs annotated in the GWAS catalog, both at the genome-wide level and at the level of individual SNPs, became especially relevant in recent years. A genome-wide search for potential rSNPs is possible without any prior knowledge of their association with a trait. Thus, mapping expression quantitative trait loci (eQTLs) makes it possible to identify an SNP for which - among transcriptomes of homozygotes and heterozygotes for its various alleles - there are differences in the expression level of certain genes, which can be located at various distances from the SNP. To predict rSNPs, approaches based on searches for allele-specific events in RNA-seq, ChIP-seq, DNase-seq, ATAC-seq, MPRA, and other data are also used. Nonetheless, for a more complete functional annotation of such rSNPs, it is necessary to establish their association with a trait, in particular, with a predisposition to a certain pathology or sensitivity to drugs. Thus, approaches to finding SNPs important for the development of a trait can be categorized into two groups: (1) starting from data on an association of SNPs with a certain trait, (2) starting from the determination of allele-specific changes at the molecular level (in a transcriptome or regulome). Only comprehensive use of strategically different approaches can considerably enrich our knowledge about the role of genetic determinants in the molecular mechanisms of trait formation, including predisposition to multifactorial diseases.
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Affiliation(s)
- E V Antontseva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A O Degtyareva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E E Korbolina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I S Damarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T I Merkulova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Vogt G. Phenotypic plasticity in the monoclonal marbled crayfish is associated with very low genetic diversity but pronounced epigenetic diversity. Curr Zool 2023; 69:426-441. [PMID: 37614917 PMCID: PMC10443617 DOI: 10.1093/cz/zoac094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/19/2022] [Indexed: 08/25/2023] Open
Abstract
Clonal organisms are particularly useful to investigate the contribution of epigenetics to phenotypic plasticity, because confounding effects of genetic variation are negligible. In the last decade, the apomictic parthenogenetic marbled crayfish, Procambarus virginalis, has been developed as a model to investigate the relationships between phenotypic plasticity and genetic and epigenetic diversity in detail. This crayfish originated about 30 years ago by autotriploidy from a single slough crayfish Procambarus fallax. As the result of human releases and active spreading, marbled crayfish has established numerous populations in very diverse habitats in 22 countries from the tropics to cold temperate regions. Studies in the laboratory and field revealed considerable plasticity in coloration, spination, morphometric parameters, growth, food preference, population structure, trophic position, and niche width. Illumina and PacBio whole-genome sequencing of marbled crayfish from representatives of 19 populations in Europe and Madagascar demonstrated extremely low genetic diversity within and among populations, indicating that the observed phenotypic diversity and ability to live in strikingly different environments are not due to adaptation by selection on genetic variation. In contrast, considerable differences were found between populations in the DNA methylation patterns of hundreds of genes, suggesting that the environmentally induced phenotypic plasticity is mediated by epigenetic mechanisms and corresponding changes in gene expression. Specific DNA methylation fingerprints persisted in local populations over successive years indicating the existence of epigenetic ecotypes, but there is presently no information as to whether these epigenetic signatures are transgenerationally inherited or established anew in each generation and whether the recorded phenotypic plasticity is adaptive or nonadaptive.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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Accattatis FM, Caruso A, Carleo A, Del Console P, Gelsomino L, Bonofiglio D, Giordano C, Barone I, Andò S, Bianchi L, Catalano S. CEBP-β and PLK1 as Potential Mediators of the Breast Cancer/Obesity Crosstalk: In Vitro and In Silico Analyses. Nutrients 2023; 15:2839. [PMID: 37447165 DOI: 10.3390/nu15132839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Over the last two decades, obesity has reached pandemic proportions in several countries, and expanding evidence is showing its contribution to several types of malignancies, including breast cancer (BC). The conditioned medium (CM) from mature adipocytes contains a complex of secretes that may mimic the obesity condition in studies on BC cell lines conducted in vitro. Here, we report a transcriptomic analysis on MCF-7 BC cells exposed to adipocyte-derived CM and focus on the predictive functional relevance that CM-affected pathways/processes and related biomarkers (BMs) may have in BC response to obesity. CM was demonstrated to increase cell proliferation, motility and invasion as well as broadly alter the transcript profiles of MCF-7 cells by significantly modulating 364 genes. Bioinformatic functional analyses unraveled the presence of five highly relevant central hubs in the direct interaction networks (DIN), and Kaplan-Meier analysis sorted the CCAAT/enhancer binding protein beta (CEBP-β) and serine/threonine-protein kinase PLK1 (PLK1) as clinically significant biomarkers in BC. Indeed, CEBP-β and PLK1 negatively correlated with BC overall survival and were up-regulated by adipocyte-derived CM. In addition to their known involvement in cell proliferation and tumor progression, our work suggests them as a possible "deus ex machina" in BC response to fat tissue humoral products in obese women.
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Affiliation(s)
- Felice Maria Accattatis
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Amanda Caruso
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, Carl-Neuberg-Straße, 30625 Hannover, Germany
| | - Piercarlo Del Console
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Luca Gelsomino
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Daniela Bonofiglio
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Cinzia Giordano
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Ines Barone
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Laura Bianchi
- Section of Functional Proteomics, Department of Life Sciences, Via Aldo Moro, University of Siena, 53100 Siena, Italy
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
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9
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Taatjes DJ, Roth J. In focus in HCB. Histochem Cell Biol 2023; 159:309-311. [PMID: 36977938 DOI: 10.1007/s00418-023-02190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Jürgen Roth
- University of Zurich, CH-8091, Zurich, Switzerland
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10
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High-fat diet induced obesity alters Dnmt1 and Dnmt3a levels and global DNA methylation in mouse ovary and testis. Histochem Cell Biol 2023; 159:339-352. [PMID: 36624173 DOI: 10.1007/s00418-022-02173-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2022] [Indexed: 01/11/2023]
Abstract
Obesity impairs reproductive capacity, and the link between imprinting disorders and obesity has been discussed in many studies. Recent studies indicate that a high-fat diet may cause epigenetic changes in maternal and paternal genes, which may be transmitted to offspring and negatively affect their development. On this basis, our study aims to reveal the changes in DNA methylation and DNA methyltransferase enzymes in the ovaries and testes of C57BL/6 mice fed a high-fat diet and created a model of obesity, by comparing them with the control group. For this purpose, we demonstrated the presence and quantitative differences of DNA methyltransferase 1 and DNA methyltransferase 3a enzymes as well as global DNA methylation in ovaries and testis of C57BL/6 mice fed a high-fat diet by using immunohistochemistry and western blot methods. We found that a high-fat diet induces the levels of Dnmt1 and Dnmt3a proteins (p < 0.05). We observed increased global DNA methylation in testes but, interestingly, decreased global DNA methylation in ovaries. We think that our outcomes have significant value to demonstrate the effects of obesity on ovarian follicle development and testicular spermatogenesis and may bring a new perspective to obesity-induced infertility treatments. Additionally, to the best of our knowledge, this is the first study to document dynamic alteration of Dnmt1 and Dnmt3a as well as global DNA methylation patterns during follicle development in healthy mouse ovaries.
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11
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Chu DT, Bui NL, Vu Thi H, Nguyen Thi YV. Role of DNA methylation in diabetes and obesity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:153-170. [PMID: 37019591 DOI: 10.1016/bs.pmbts.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Due to the fact that the upward trend of several metabolic disorders such as diabetes and obesity, in individuals especially monozygotic twins, who are under the same effects from the environment, are not similar, the role of epigenetic elements like DNA methylation needs taking into account. In this chapter, emerging scientific evidence supporting the strong relationship between changes in DNA methylation and those diseases' development was summarized. Changing in the expression level of diabetes/obesity-related genes through being silenced by methylation can be the underlying mechanism of this phenomenon. Genes with abnormal methylation status are potential biomarkers for early prediction and diagnosis. Moreover, methylation-based molecular targets should be investigated as a new treatment for both T2D and obesity.
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Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
| | - Nhat-Le Bui
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Yen-Vy Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
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12
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Vogt G. Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics. EPIGENOMES 2022; 7:1. [PMID: 36648862 PMCID: PMC9844400 DOI: 10.3390/epigenomes7010001] [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: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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13
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Muacevic A, Adler JR. Obesity: A Doorway to a Molecular Path Leading to Infertility. Cureus 2022; 14:e30770. [PMID: 36320802 PMCID: PMC9612950 DOI: 10.7759/cureus.30770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
The dramatic rise in obesity has recently made it a global health issue. About 1.9 billion were overweight, and 650 million global populations were obese in 2016. Obese women suffer longer conception time, lowered fertility rates, and greater rates of miscarriage. Obesity alters hormones such as adiponectin and leptin, affecting all levels within the hypothalamic-pituitary-gonadal axis. Advanced glycation end products (AGEs) and monocyte chemotactic protein-1 (MCP-1) are inflammatory cytokines that may play an important role in the pathophysiology of ovarian dysfunction in obesity. In obese males, there are altered sperm parameters, reduced testosterone, increased estradiol, hypogonadism, and epigenetic modifications transmitted to offspring. The focus of this article is on the possible adverse effects on reproductive health resulting from obesity and sheds light on different molecular pathways linking obesity with infertility in both female and male subjects. Electronic databases such as Google Scholar, Embase, Science Direct, PubMed, and Google Search Engine were utilized to find obesity and infertility-related papers. The search strategy is detailed in the method section. Even though multiple research work has shown that obesity impacts fertility in both male and female negatively, it is significant to perform extensive research on the molecular mechanisms that link obesity to infertility. This is to find therapeutics that may be developed aiming at these mechanisms to manage and prevent the negative effects of obesity on the reproductive system.
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Thakur S, Vasudev PG. MYB transcription factors and their role in Medicinal plants. Mol Biol Rep 2022; 49:10995-11008. [PMID: 36074230 DOI: 10.1007/s11033-022-07825-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
Transcription factors are multi-domain proteins that regulate gene expression in eukaryotic organisms. They are one of the largest families of proteins, which are structurally and functionally diverse. While there are transcription factors that are plant-specific, such as AP2/ERF, B3, NAC, SBP and WRKY, some transcription factors are present in both plants as well as other eukaryotic organisms. MYB transcription factors are widely distributed among all eukaryotes. In plants, the MYB transcription factors are involved in the regulation of numerous functions such as gene regulation in different metabolic pathways especially secondary metabolic pathways, regulation of different signalling pathways of plant hormones, regulation of genes involved in various developmental and morphological processes etc. Out of the thousands of MYB TFs that have been studied in plants, the majority of them have been studied in the model plants like Arabidopsis thaliana, Oryza sativa etc. The study of MYBs in other plants, especially medicinal plants, has been comparatively limited. But the increasing demand for medicinal plants for the production of biopharmaceuticals and important bioactive compounds has also increased the need to explore more number of these multifaceted transcription factors which play a significant role in the regulation of secondary metabolic pathways. These studies will ultimately contribute to medicinal plants' research and increased production of secondary metabolites, either through transgenic plants or through synthetic biology approaches. This review compiles studies on MYB transcription factors that are involved in the regulation of diverse functions in medicinal plants.
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Affiliation(s)
- Sudipa Thakur
- Plant Biotechnology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, 226015, Lucknow, India.
| | - Prema G Vasudev
- Plant Biotechnology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, 226015, Lucknow, India
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15
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Xu D, Fang H, Liu J, Chen Y, Gu Y, Sun G, Xia B. ChIP-seq assay revealed histone modification H3K9ac involved in heat shock response of the sea cucumber Apostichopus japonicus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153168. [PMID: 35051475 DOI: 10.1016/j.scitotenv.2022.153168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/23/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Heat stress poses an increasing threat for the marine invertebrate Apostichopus japonicus. Histone lysine acetylation is a central chromatin modification for epigenetic regulation of gene expression during stress response. In this study, a genome-wide characterization for acetylated lysine 9 on histone H3 (H3K9ac) binding regions in normal temperature (18 °C) and heat-stress conditions (26 °C) via ChIP-seq were carried out. The results that revealed H3K9ac was an extensive epigenetic modulation in A. japonicus. The GO terms "regulation of transcription, DNA-templated" and "transcription coactivator activity" were significantly enriched in both groups. Particularly, various transcriptional factors (TFs) families showed notable modification of H3K9ac. Differentially acetylated regions (DARs) with H3K9ac modification under heat stress were identified with 24 hyperacetylated and 23 hypoacetylated peaks, respectively. We further examined the transcriptional expression for 13 genes with dysregulated H3K9ac level in the promoter regions by qRT-PCR. Combined H3K9ac ChIP-seq characteristics with the transcriptional expression, 5 up-up genes (ZCCHC3, RPA70, MTRR, β-Gal and PHTF2) and 2 down-down genes (PRPF39 and BSL78_10147) were identified. Surprisingly, the increasing mRNA expression of NECAP1 under heat stress was negatively related to the decreasing H3K9ac level in its promoter region. Our research is the first genome-wide characterization for the epigenetic modification H3K9ac in A. japonicus, and will help to advance the understanding of the roles of H3K9ac in transcriptional regulation under heat-stress condition.
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Affiliation(s)
- Dongxue Xu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Huahua Fang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Ji Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yanru Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yuanxue Gu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, Shandong 264025, China
| | - Bin Xia
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China.
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Zarkesh M, Tabaei K, Akbarzadeh M, Daneshafrooz A, Zadeh-Vakili A. Association of miR-34a and miR-143 levels with PPARγ gene expression in adipose tissues of non-diabetic adults. J Physiol Anthropol 2022; 41:13. [PMID: 35397570 PMCID: PMC8994288 DOI: 10.1186/s40101-022-00286-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/24/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Peroxisome proliferator-activated receptor gamma (PPARγ) is a promising therapeutic molecule. Epigenetic mechanisms, including non-coding RNAs, regulate the expression level of the PPARγ gene. OBJECTIVE We aimed to examine the PPARγ expression in non-diabetic individuals in four body mass index (BMI) categories and its association with miR-34a and miR-143 expression. METHODS Visceral and subcutaneous adipose tissues (VAT and SAT) samples were collected from patients undergoing bariatric or elective open abdominal surgeries. The subjects (mean age: 42±14.8 years) included 18 normal-weight, 19 overweight, 18 obese, and 19 morbidly obese individuals. The RNAs levels were determined by quantitative real-time PCR. RESULTS The PPARγ expression was significantly upregulated in both adipose depots of the morbidly obese subjects compared to the normal group. SAT PPARγ level was significantly increased in the obese group compared to the normal-weight group (P<0.01); this increase was also significant in the SAT of morbidly obese subjects compared to the overweight cases (P=0.02). Differences in the regulation of PPARγ expression in both SAT and VAT were significant between the four groups (P<0.05). While miR-143 was overexpressed in the SAT of obese and morbidly obese individuals compared to the normal-weight group, the pairwise comparison showed no significant difference in the miR-34a expression of SAT between the four BMI groups (P>0.01). After controlling for the confounding factors, the expression of VAT PPARγ was directly associated with the miR-34a level in the normal-weight group (β=0.311, P=0.010). A negative association was observed between the VAT PPARγ expression and miR-34a expression in obese cases (β = - 0.594, P=0.039). CONCLUSION The results also confirmed the regulatory function of microRNAs in the PPARγ expression and adipogenesis.
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Affiliation(s)
- Maryam Zarkesh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Tabaei
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdi Akbarzadeh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsoon Daneshafrooz
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azita Zadeh-Vakili
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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He J, Shu Y, Dai Y, Gao Y, Liu S, Wang W, Jiang H, Zhang H, Hong P, Wu H. Microcystin-leucine arginine exposure induced intestinal lipid accumulation and MC-LR efflux disorder in Lithobates catesbeianus tadpoles. Toxicology 2022; 465:153058. [PMID: 34863901 DOI: 10.1016/j.tox.2021.153058] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/05/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Few studies exist on the toxic effects of chronic exposure to microcystins (MCs) on amphibian intestines, and the toxicity mechanisms are unclear. Here, we evaluated the impact of subchronic exposure (30 days) to environmentally realistic microcystin-leucine arginine (MC-LR) concentrations (0 μg/L, 0.5 μg/L and 2 μg/L) on tadpole (Lithobates catesbeianus) intestines by analyzing the histopathological and subcellular microstructural damage, the antioxidative and oxidative enzyme activities, and the transcriptome levels. Histopathological results showed severe damage accompanied by inflammation to the intestinal tissues as the MC-LR exposure concentration increased from 0.5 μg/L to 2 μg/L. RNA-sequencing analysis identified 634 and 1,147 differentially expressed genes (DEGs) after exposure to 0.5 μg/L and 2 μg/L MC-LR, respectively, compared with those of the control group (0 μg/L). Biosynthesis of unsaturated fatty acids and the peroxisome proliferator-activated receptor (PPAR) signaling pathway were upregulated in the intestinal tissues of the exposed groups, with many lipid droplets being observed on transmission electron microscopy, implying that MC-LR may induce lipid accumulation in frog intestines. Moreover, 2 μg/L of MC-LR exposure inhibited the xenobiotic and toxicant biodegradation related to detoxification, implying that the tadpoles' intestinal detoxification ability was weakened after exposure to 2 μg/L MC-LR, which may aggravate intestinal toxicity. Lipid accumulation and toxin efflux disorder may be caused by MC-LR-induced endoplasmic reticular stress. This study presents new evidence that MC-LR harms amphibians by impairing intestinal lipid metabolism and toxin efflux, providing a theoretical basis for evaluating the health risks of MC-LR to amphibians.
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Affiliation(s)
- Jun He
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Yilin Shu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Yue Dai
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Yuxin Gao
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Shuyi Liu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Wenchao Wang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Huiling Jiang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Huijuan Zhang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
| | - Pei Hong
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
| | - Hailong Wu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui Province, China.
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18
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Molecular Mechanisms Underlying the Relationship between Obesity and Male Infertility. Metabolites 2021; 11:metabo11120840. [PMID: 34940598 PMCID: PMC8706114 DOI: 10.3390/metabo11120840] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 01/29/2023] Open
Abstract
In recent decades, the worldwide prevalence of obesity has risen dramatically and is currently estimated to be around 20%. Obesity is linked to an increased risk of comorbidities and premature mortality. Several studies have shown that obesity negatively impacts male fertility through various mechanisms. This review aims to investigate the molecular mechanisms through which obesity impairs male reproduction, including obesity-associated hypogonadism and its effects on spermatogenesis, chronic inflammation, and oxidative stress. Obesity negatively impacts both conventional and biofunctional sperm parameters, and it also induces epigenetic changes that can be transferred to offspring. Moreover, obesity-related diseases are linked to a dysregulation of adipocyte function and micro-environmental inflammatory processes. The dysregulated adipokines significantly influence insulin signaling, and they may also have a detrimental effect on testicular function. Sirtuins can also play an important role in inflammatory and metabolic responses in obese patients. Understanding the molecular mechanisms that are involved in obesity-induced male infertility could increase our ability to identify novel targets for the prevention and treatment of obesity and its related consequences.
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19
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Pierzgalski A, Bryła M, Kanabus J, Modrzewska M, Podolska G. Updated Review of the Toxicity of Selected Fusarium Toxins and Their Modified Forms. Toxins (Basel) 2021; 13:768. [PMID: 34822552 PMCID: PMC8619142 DOI: 10.3390/toxins13110768] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/20/2022] Open
Abstract
Mycotoxins are one of the most dangerous food and feed contaminants, hence they have significant influence on human and animal health. This study reviews the information reported over the last few years on the toxic effects of the most relevant and studied Fusarium toxins and their modified forms. Deoxynivalenol (DON) and its metabolites can induce intracellular oxidative stress, resulting in DNA damage. Recent studies have also revealed the capability of DON and its metabolites to disturb the cell cycle and alter amino acid expression. Several studies have attempted to explore the mechanism of action of T-2 and HT-2 toxins in anorexia induction. Among other findings, two neurotransmitters associated with this process have been identified, namely substance P and serotonin (5-hydroxytryptamine). For zearalenone (ZEN) and its metabolites, the literature points out that, in addition to their generally acknowledged estrogenic and oxidative potentials, they can also modify DNA by altering methylation patterns and histone acetylation. The ability of the compounds to induce alterations in the expression of major metabolic genes suggests that these compounds can contribute to the development of numerous metabolic diseases, including type 2 diabetes.
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Affiliation(s)
- Adam Pierzgalski
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36, 02-532 Warsaw, Poland; (M.B.); (J.K.); (M.M.)
| | - Marcin Bryła
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36, 02-532 Warsaw, Poland; (M.B.); (J.K.); (M.M.)
| | - Joanna Kanabus
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36, 02-532 Warsaw, Poland; (M.B.); (J.K.); (M.M.)
| | - Marta Modrzewska
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36, 02-532 Warsaw, Poland; (M.B.); (J.K.); (M.M.)
| | - Grażyna Podolska
- Department of Cereal Crop Production, Institute of Soil Science and Plant Cultivation–State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland;
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20
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Gire D, Acharya J, Malik S, Inamdar S, Ghaskadbi S. Molecular mechanism of anti-adipogenic effect of vitexin in differentiating hMSCs. Phytother Res 2021; 35:6462-6471. [PMID: 34612537 DOI: 10.1002/ptr.7300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022]
Abstract
In this study, we evaluated a detailed molecular mechanism of anti-adipogenic activity of vitexin, apigenin flavone glucoside, present in germinated fenugreek seeds, in differentiating human mesenchymal stem cells (hMSCs). The lipid content of differentiated adipocytes was estimated by ORO staining. Effect on mitotic clonal expansion was checked by cell cycle analysis. Expression of early and terminal adipocyte differentiation markers, anti- and pro-adipogenic transcription factors and signalling intermediates regulating them was evaluated at RNA and protein level. We found vitexin to be non-cytotoxic up to 20 μM at which intracellular lipid accumulation was significantly decreased. Cell cycle analysis suggested that vitexin does not affect mitotic clonal expansion. Expression of early and late differentiation markers, such as CEBPα, CEBPβ, PPARγ, FABP4, perilipin, adiponectin and Glut4 was significantly reduced in the presence of vitexin. Expression of KLF4 and KLF15, positive regulators of PPARγ, was decreased, whereas that of negative regulators, namely KLF2, GATA2, miR20a, miR27a, miR27b, miR128, miR130a, miR130b, miR182 and miR548 increased with vitexin treatment. This effect was mediated by the activation of the AMP-activated protein kinase (AMPK) pathway via the activation of LepR and additionally by inhibiting ROS. Thus, our results showed that vitexin regulates the expression of PPARγ and inhibits adipogenesis of hMSCs at an early stage of differentiation.
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Affiliation(s)
- Dhananjay Gire
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Jhankar Acharya
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Sajad Malik
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Shrirang Inamdar
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Saroj Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune, India
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21
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Porcuna J, Mínguez-Martínez J, Ricote M. The PPARα and PPARγ Epigenetic Landscape in Cancer and Immune and Metabolic Disorders. Int J Mol Sci 2021; 22:ijms221910573. [PMID: 34638914 PMCID: PMC8508752 DOI: 10.3390/ijms221910573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are ligand-modulated nuclear receptors that play pivotal roles in nutrient sensing, metabolism, and lipid-related processes. Correct control of their target genes requires tight regulation of the expression of different PPAR isoforms in each tissue, and the dysregulation of PPAR-dependent transcriptional programs is linked to disorders, such as metabolic and immune diseases or cancer. Several PPAR regulators and PPAR-regulated factors are epigenetic effectors, including non-coding RNAs, epigenetic enzymes, histone modifiers, and DNA methyltransferases. In this review, we examine advances in PPARα and PPARγ-related epigenetic regulation in metabolic disorders, including obesity and diabetes, immune disorders, such as sclerosis and lupus, and a variety of cancers, providing new insights into the possible therapeutic exploitation of PPAR epigenetic modulation.
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Olaniyi KS, Owolabi MN, Atuma CL, Agunbiade TB, Alabi BY. Acetate rescues defective brain-adipose metabolic network in obese Wistar rats by modulation of peroxisome proliferator-activated receptor-γ. Sci Rep 2021; 11:18967. [PMID: 34556775 PMCID: PMC8460633 DOI: 10.1038/s41598-021-98605-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/09/2021] [Indexed: 02/08/2023] Open
Abstract
We investigated the hypothesis that acetate ameliorates brain-adipose metabolic dysfunction (BAMED) in high fat diet (HFD)-induced obesity, possibly by modulation of peroxisome proliferator-activated receptor-γ (PPAR-γ). Ten-week-old male Wistar rats were randomly assigned into four groups (n = 6/group): Control, acetate and obese with or without acetate groups received vehicle (distilled water; po), acetate (200 mg/kg, po) and 40% HFD with or without acetate respectively. The treatments lasted for 12 weeks. Obese animals showed increase in body weight, visceral fat mass, insulin and triglyceride-glucose index and a reduction in insulin sensitivity. In addition, obese animals also showed increase in plasma/hypothalamic and adipose pyruvate dehydrogenase kinase-4, lactate-pyruvate ratio, malondialdehyde, γ-glutamyl transferase, and a decrease in glucose-6-phosphate dehydrogenase, glutathione, nitric oxide and PPAR-γ. HFD also elevated plasma/hypothalamic lipid and decreased adipose lipid profile, increased hypothalamic and adipose tumor necrosis factor-α, interleukin-6 and histone deacetylase (HDAC), and elevated plasma/adipose leptin. These alterations were reversed by concomitant administration of acetate. The present results demonstrate that obesity is characterized by BAMED, which is accompanied by altered HDAC/PPAR-γ. The results in addition suggest that acetate, an HDAC inhibitor rescues BAMED with consequent normalization of body weight and visceral fat mass by modulation of PPAR-γ and suppression of oxidative stress.
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Affiliation(s)
- Kehinde Samuel Olaniyi
- Cardio/Repro-Metabolic and Microbiome Research Unit, Department of Physiology, College of Medicine and Health Sciences, Afe Babalola University, P.M.B. 5454, Ado-Ekiti, 360101, Nigeria.
| | - Morounkeji Nicole Owolabi
- Cardio/Repro-Metabolic and Microbiome Research Unit, Department of Physiology, College of Medicine and Health Sciences, Afe Babalola University, P.M.B. 5454, Ado-Ekiti, 360101, Nigeria
| | - Chukwubueze Lucky Atuma
- Cardio/Repro-Metabolic and Microbiome Research Unit, Department of Physiology, College of Medicine and Health Sciences, Afe Babalola University, P.M.B. 5454, Ado-Ekiti, 360101, Nigeria
| | - Toluwani Bosede Agunbiade
- Department of Medical Microbiology and Parasitology, College of Medicine and Health Sciences, Afe Babalola University, Ado-Ekiti, 360101, Nigeria
| | - Bolanle Yemisi Alabi
- Department of Hematology and Virology, University of Medical Science Teaching Hospital Complex, Akure, Nigeria
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23
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Gaytán-Pacheco N, Lima-Rogel V, Méndez-Mancilla A, Escalante-Padrón F, Toro-Ortíz JC, Jiménez-Capdeville ME, Zaga-Clavellina V, Portales-Pérez DP, Noyola DE, Salgado-Bustamante M. Changes in PPAR-γ Expression Are Associated with microRNA Profiles during Fetal Programming due to Maternal Overweight and Obesity. Gynecol Obstet Invest 2021; 86:415-426. [PMID: 34547756 DOI: 10.1159/000517116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/10/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND There has been a global increase in the prevalence of obesity in pregnant women in recent years. Animal studies have shown that intrauterine environment associated with maternal obesity leads to epigenetic changes. However, the effects of epigenetic changes occurring before birth in response to maternal conditions have not been clearly characterized in humans. OBJECTIVE The aim of the study was to analyze peroxisome proliferator-activated receptor (PPAR)-γ expression in cell cultures from newborns from mothers with overweight and obesity, in response to in vitro metabolic challenges and their relationship with microRNA profile and cytokine expression. Methods/Study design: The profile of circulating microRNAs from 72 mother-child pairs (including healthy infants born to normal weight [n = 35], overweight [n = 25], and obese [n = 12] mothers) was determined through real-time PCR, and the PPAR-γ expression in peripheral blood mononuclear cell cultures from offspring was analyzed after in vitro challenges. RESULTS miR-146a, miR-155, and miR-378a were upregulated in overweight mothers, while miR-378a was upregulated in obese mothers compared to normal weight mothers. In children from overweight mothers, miR-155 and miR-221 were downregulated and miR-146a was upregulated, while offspring of mothers with obesity showed downregulation of miR-155, miR-221, and miR-1301. These microRNAs have direct or indirect relation with PPAR-γ expression. In vitro exposure to high triglyceride and exposure to miR-378a induced a higher expression of PPAR-γ in cells from offspring of mothers with overweight and obesity. In contrast, cells from offspring of mothers with obesity cultured with high glucose concentrations showed PPAR-γ downregulation. IL-1ß, IL-6, and TNF-α expression in cells of offspring of overweight and obese mothers differed from that of offspring of normal weight mothers. Limitation of our study is the small sample size. CONCLUSION The blood microRNA profile, and in vitro PPAR-γ and inflammatory cytokine expression in cells of newborn infants are associated with maternal obesity indicating that epigenetic marks may be established during intrauterine development. Key Message: Neonatal microRNA profile is associated with maternal weight. Neonatal microRNA profile is independent of maternal microRNA profile. PPAR-γ expression in newborn cell cultures is affected by maternal weight.
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Affiliation(s)
- Noemí Gaytán-Pacheco
- Biochemistry Department, University Autonomous of San Luis Potosí, San Luis Potosi, Mexico
| | - Victoria Lima-Rogel
- Pediatrics Division, Hospital Central "Dr. Ignacio Morones Prieto,", San Luis Potosi, Mexico
| | - Alejandro Méndez-Mancilla
- Cellular and Molecular Immunology Laboratory, Chemistry Faculty, University Autonomous of San Luis Potosí, San Luis Potosi, Mexico
| | | | - Juan Carlos Toro-Ortíz
- Ginecology and Obstetrics Division, Hospital Central "Dr. Ignacio Morones Prieto,", San Luis Potosi, Mexico
| | | | | | - Diana P Portales-Pérez
- Cellular and Molecular Immunology Laboratory, Chemistry Faculty, University Autonomous of San Luis Potosí, San Luis Potosi, Mexico
| | - Daniel E Noyola
- Microbiology Department, Faculty of Medicine, University Autonomous of San Luis Potosí, San Luis Potosi, Mexico
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Comparative Analysis of Genes Associated with Obesity in Humans Using Bioinformatic Data and Tools. Balkan J Med Genet 2021; 24:35-40. [PMID: 34447657 PMCID: PMC8366471 DOI: 10.2478/bjmg-2021-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Obesity has become a serious global problem that still needs a solution. One of the factors that leads to obesity is genetic predisposition. The identity and characteristics of the genes involved have not yet been fully confirmed. Analyzing the genetic contribution to obesity is a major step towards the solution. In this in silico study, using online bioinformatics tools, we evaluate the role of four genes that are believed to contribute to obesity. Data were collected and analyzed for the sequences of four so-called obesity genes: FTO (fat mass and obesity-associated protein), PPARG (peroxisome proliferator activated receptor γ), ADRB3 (adrenergic receptor β 3) and FABP2 (fatty acid binding protein 2). In the first part of the research, information about the genes was collected and organized and data in FASTA, format are extracted from the National Center for Biotechnology Information (NCBI). In the second part, all genes were analyzed by comparing three species of organisms, Homo sapiens (human), Mus musculus (mouse) and Gallus (chicken). In the third part of this study, phylogenetic trees were constructed for each of the four genes, using blast local alignment search tool (BLAST) and molecular evolutionary genetics analysis (MEGA X) software. Our analysis reveals that the functions of all these genes are associated with overweight and obesity.
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25
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Hu C, Jia W. Multi-omics profiling: the way towards precision medicine in metabolic diseases. J Mol Cell Biol 2021; 13:mjab051. [PMID: 34406397 PMCID: PMC8697344 DOI: 10.1093/jmcb/mjab051] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Metabolic diseases including type 2 diabetes mellitus (T2DM), non-alcoholic fatty liver disease (NAFLD), and metabolic syndrome (MetS) are alarming health burdens around the world, while therapies for these diseases are far from satisfying as their etiologies are not completely clear yet. T2DM, NAFLD, and MetS are all complex and multifactorial metabolic disorders based on the interactions between genetics and environment. Omics studies such as genetics, transcriptomics, epigenetics, proteomics, and metabolomics are all promising approaches in accurately characterizing these diseases. And the most effective treatments for individuals can be achieved via omics pathways, which is the theme of precision medicine. In this review, we summarized the multi-omics studies of T2DM, NAFLD, and MetS in recent years, provided a theoretical basis for their pathogenesis and the effective prevention and treatment, and highlighted the biomarkers and future strategies for precision medicine.
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Affiliation(s)
- Cheng Hu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus,
Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth
People's Hospital, Shanghai 200233, China
- Institute for Metabolic Disease, Fengxian Central Hospital, The Third School of
Clinical Medicine, Southern Medical University, Shanghai 201499, China
| | - Weiping Jia
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus,
Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth
People's Hospital, Shanghai 200233, China
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26
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Kramer HM, Cook DE, van den Berg GCM, Seidl MF, Thomma BPHJ. Three putative DNA methyltransferases of Verticillium dahliae differentially contribute to DNA methylation that is dispensable for growth, development and virulence. Epigenetics Chromatin 2021; 14:21. [PMID: 33941240 PMCID: PMC8091789 DOI: 10.1186/s13072-021-00396-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic control mechanism that in many fungi is restricted to genomic regions containing transposable elements (TEs). Two DNA methyltransferases, Dim2 and Dnmt5, are known to perform methylation at cytosines in fungi. While most ascomycete fungi encode both Dim2 and Dnmt5, only few functional studies have been performed in species containing both. METHODS In this study, we report functional analysis of both Dim2 and Dnmt5 in the plant pathogenic fungus Verticillium dahliae. RESULTS Our results show that Dim2, but not Dnmt5 or the putative sexual-cycle-related DNA methyltransferase Rid, is responsible for the majority of DNA methylation under the tested conditions. Single or double DNA methyltransferase mutants did not show altered development, virulence, or transcription of genes or TEs. In contrast, Hp1 and Dim5 mutants that are impacted in chromatin-associated processes upstream of DNA methylation are severely affected in development and virulence and display transcriptional reprogramming in specific hypervariable genomic regions (so-called adaptive genomic regions) that contain genes associated with host colonization. As these adaptive genomic regions are largely devoid of DNA methylation and of Hp1- and Dim5-associated heterochromatin, the differential transcription is likely caused by pleiotropic effects rather than by differential DNA methylation. CONCLUSION Overall, our study suggests that Dim2 is the main DNA methyltransferase in V. dahliae and, in conjunction with work on other fungi, is likely the main active DNMT in ascomycetes, irrespective of Dnmt5 presence. We speculate that Dnmt5 and Rid act under specific, presently enigmatic, conditions or, alternatively, act in DNA-associated processes other than DNA methylation.
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Affiliation(s)
- H Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany.
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27
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Fischer J, Ardakani FB, Kattler K, Walter J, Schulz MH. CpG content-dependent associations between transcription factors and histone modifications. PLoS One 2021; 16:e0249985. [PMID: 33857234 PMCID: PMC8049299 DOI: 10.1371/journal.pone.0249985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/30/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the factors that underlie the epigenetic regulation of genes is crucial to understand the gene regulatory machinery as a whole. Several experimental and computational studies examined the relationship between different factors involved. Here we investigate the relationship between transcription factors (TFs) and histone modifications (HMs), based on ChIP-seq data in cell lines. As it was shown that gene regulation by TFs differs depending on the CpG class of a promoter, we study the impact of the CpG content in promoters on the associations between TFs and HMs. We suggest an approach based on sparse linear regression models to infer associations between TFs and HMs with respect to CpG content. A study of the partial correlation of HMs for the two classes of high and low CpG content reveals possible CpG dependence and potential candidates for confounding factors in our models. We show that the models are accurate, inferred associations reflect known biological relationships, and we give new insight into associations with respect to CpG content. Moreover, analysis of a ChIP-seq dataset in HepG2 cells of the HM H3K122ac, an HM about little is known, reveals novel TF associations and supports a previously established link to active transcription.
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Affiliation(s)
- Jonas Fischer
- Max Planck Institute for Informatics, Databases and Information Systems, Saarbrücken, Germany
- Cluster of Excellence for Multimodal Computing and Interaction, High Throughput Genomics and Systems Biology, Saarbrücken, Germany
- * E-mail:
| | - Fatemeh Behjati Ardakani
- Max Planck Institute for Informatics, Computational Biology and Applied Algorithmics, Saarbrücken, Germany
- Cluster of Excellence for Multimodal Computing and Interaction, High Throughput Genomics and Systems Biology, Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
| | - Kathrin Kattler
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Marcel H. Schulz
- Max Planck Institute for Informatics, Computational Biology and Applied Algorithmics, Saarbrücken, Germany
- Cluster of Excellence for Multimodal Computing and Interaction, High Throughput Genomics and Systems Biology, Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
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28
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Wang J, Wang Z, Yuan J, Wang Q, Shen X. Upregulation of miR-137 Expression Suppresses Tumor Growth and Progression via Interacting with DNMT3a Through Inhibiting the PTEN/Akt Signaling in HCC. Onco Targets Ther 2021; 14:165-176. [PMID: 33447058 PMCID: PMC7802901 DOI: 10.2147/ott.s268570] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/27/2020] [Indexed: 01/05/2023] Open
Abstract
Background Downregulation of miR-137 regulates tumor growth in hepatocellular carcinoma (HCC). Yet, the underlying molecular mechanisms stay unclear. Materials and Methods miR-137 and DNA methyltransferase 3a (DNMT3a) expression levels were detected by Western blot, immunohistochemistry and qRT-PCR assays. Luciferase reporter and Western blot assays were also carried out to explore the correlation of miR-137 and DNMT3a. Flow cytometry assay, MTT analysis, transwell and wound healing assay were used to evaluate cell apoptosis, proliferation, as well as invasive and migratory abilities. Western blot was used to examine the caspase-3, cleaved caspase-3, PCNA, MMP-2, and MMP-7 protein levels, as well as PTEN/Akt signaling alternations. Methylation-specific PCR was applied to detect the PTEN promoter methylation status. Xenograft tumor assay, Western blot and immunohistochemistry analyses were taken to confirm the miR-137 regulation in vivo. Results Downregulation of miR-137, upregulation of DNMT3a, as well as an inverse correlation between them were observed in HCC clinical samples and cells. Moreover, miR-137 targeted directly and inhibited DNMT3a in HCC cells, which further retarded cell proliferative, migratory and invasive capabilities, while promoted apoptotic ones. Additionally, miR-137 overexpression inactivated the PTEN/Akt pathway in HCC cell by decreasing DNMT3a expression. Furthermore, miR-137 overexpression inhibited tumor growth in vivo in HCC via interacting with DNMT3a through inhibiting the PTEN/Akt cascades. Conclusion Our findings suggested that miR-137 inhibited HCC tumor growth and progression via interacting with DNMT3a and suppressing the PTEN/Akt signaling in vitro and in vivo.
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Affiliation(s)
- Jiachen Wang
- Department of Minimally Invasive Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
| | - Zhao Wang
- Department of Minimally Invasive Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
| | - Jiaxiang Yuan
- Department of Minimally Invasive Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
| | - Qun Wang
- Department of Minimally Invasive Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
| | - Xinsheng Shen
- Department of Minimally Invasive Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
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29
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D’Anneo A, Bavisotto CC, Gammazza AM, Paladino L, Carlisi D, Cappello F, de Macario EC, Macario AJL, Lauricella M. Lipid chaperones and associated diseases: a group of chaperonopathies defining a new nosological entity with implications for medical research and practice. Cell Stress Chaperones 2020; 25:805-820. [PMID: 32856199 PMCID: PMC7591661 DOI: 10.1007/s12192-020-01153-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/16/2020] [Accepted: 08/10/2020] [Indexed: 02/08/2023] Open
Abstract
Fatty acid-binding proteins (FABPs) are lipid chaperones assisting in the trafficking of long-chain fatty acids with functions in various cell compartments, including oxidation, signaling, gene-transcription regulation, and storage. The various known FABP isoforms display distinctive tissue distribution, but some are active in more than one tissue. Quantitative and/or qualitative changes of FABPs are associated with pathological conditions. Increased circulating levels of FABPs are biomarkers of disorders such as obesity, insulin resistance, cardiovascular disease, and cancer. Deregulated expression and malfunction of FABPs can result from genetic alterations or posttranslational modifications and can be pathogenic. We have assembled the disorders with abnormal FABPs as chaperonopathies in a distinct nosological entity. This entity is similar but separate from that encompassing the chaperonopathies pertaining to protein chaperones. In this review, we discuss the role of FABPs in the pathogenesis of metabolic syndrome, cancer, and neurological diseases. We highlight the opportunities for improving diagnosis and treatment that open by encompassing all these pathological conditions within of a coherent nosological group, focusing on abnormal lipid chaperones as biomarkers of disease and etiological-pathogenic factors.
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Affiliation(s)
- Antonella D’Anneo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), Laboratory of Biochemistry, University of Palermo, 90127 Palermo, Italy
| | - Celeste Caruso Bavisotto
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Letizia Paladino
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Daniela Carlisi
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Biochemistry, University of Palermo, 90127 Palermo, Italy
| | - Francesco Cappello
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Everly Conway de Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202 USA
| | - Alberto J. L. Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202 USA
| | - Marianna Lauricella
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Biochemistry, University of Palermo, 90127 Palermo, Italy
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30
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Xiao Y, Liu D, Cline MA, Gilbert ER. Chronic stress, epigenetics, and adipose tissue metabolism in the obese state. Nutr Metab (Lond) 2020; 17:88. [PMID: 33088334 PMCID: PMC7574417 DOI: 10.1186/s12986-020-00513-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
In obesity, endocrine and metabolic perturbations, including those induced by chronic activation of the hypothalamus-pituitary-adrenal axis, are associated with the accumulation of adipose tissue and inflammation. Such changes are attributable to a combination of genetic and epigenetic factors that are influenced by the environment and exacerbated by chronic activation of the hypothalamus-pituitary-adrenal axis. Stress exposure at different life stages can alter adipose tissue metabolism directly through epigenetic modification or indirectly through the manipulation of hypothalamic appetite regulation, and thereby contribute to endocrine changes that further disrupt whole-body energy balance. This review synthesizes current knowledge, with an emphasis on human clinical trials, to describe metabolic changes in adipose tissue and associated endocrine, genetic and epigenetic changes in the obese state. In particular, we discuss epigenetic changes induced by stress exposure and their contribution to appetite and adipocyte dysfunction, which collectively promote the pathogenesis of obesity. Such knowledge is critical for providing future directions of metabolism research and targets for treating metabolic disorders.
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Affiliation(s)
- Yang Xiao
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - Dongmin Liu
- Department of Human Nutrition, Foods, and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - Mark A Cline
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA USA.,School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - Elizabeth R Gilbert
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA USA.,School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
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31
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Genario R, Cipolla-Neto J, Bueno AA, Santos HO. Melatonin supplementation in the management of obesity and obesity-associated disorders: A review of physiological mechanisms and clinical applications. Pharmacol Res 2020; 163:105254. [PMID: 33080320 DOI: 10.1016/j.phrs.2020.105254] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/11/2020] [Accepted: 10/11/2020] [Indexed: 02/08/2023]
Abstract
Despite the evolving advances in clinical approaches to obesity and its inherent comorbidities, the therapeutic challenge persists. Among several pharmacological tools already investigated, recent studies suggest that melatonin supplementation could be an efficient therapeutic approach in the context of obesity. In the present review, we have amalgamated the evidence so far available on physiological effects of melatonin supplementation in obesity therapies, addressing its effects upon neuroendocrine systems, cardiometabolic biomarkers and body composition. Most studies herein appraised employed melatonin supplementation at dosages ranging from 1 to 20 mg/day, and most studies followed up participants for periods from 3 weeks to 12 months. Overall, it was observed that melatonin plays an important role in glycaemic homeostasis, in addition to modulation of white adipose tissue activity and lipid metabolism, and mitochondrial activity. Additionally, melatonin increases brown adipose tissue volume and activity, and its antioxidant and anti-inflammatory properties have also been demonstrated. There appears to be a role for melatonin in adiposity reduction; however, several questions remain unanswered, for example melatonin baseline levels in obesity, and whether any seeming hypomelatonaemia or melatonin irresponsiveness could be clarifying factors. Supplementation dosage studies and more thorough clinical trials are needed to ascertain not only the relevance of such findings but also the efficacy of melatonin supplementation.
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Affiliation(s)
- Rafael Genario
- School of Medicine, University of Sao Paulo (USP), São Paulo, Brazil.
| | - José Cipolla-Neto
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Allain A Bueno
- College of Health, Life and Environmental Sciences, University of Worcester, Worcester, United Kingdom
| | - Heitor O Santos
- School of Medicine, Federal University of Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil.
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32
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Nie Y, Shu C, Sun X. Cooperative binding of transcription factors in the human genome. Genomics 2020; 112:3427-3434. [DOI: 10.1016/j.ygeno.2020.06.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 04/16/2020] [Accepted: 06/17/2020] [Indexed: 01/24/2023]
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Yan K, Wang X, Zhu H, Pan H, Wang L, Yang H, Liu M, Jin M, Zang B, Gong F. Safflower yellow improves insulin sensitivity in high-fat diet-induced obese mice by promoting peroxisome proliferator-activated receptor-γ2 expression in subcutaneous adipose tissue. J Diabetes Investig 2020; 11:1457-1469. [PMID: 32356607 PMCID: PMC7610129 DOI: 10.1111/jdi.13285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 12/13/2022] Open
Abstract
Aims/Introduction Safflower yellow (SY) and its main component, hydroxysafflor yellow A, have been demonstrated to show anti‐obesity effects. Peroxisome proliferator‐activated receptor‐γ2 (PPARγ2) is a critical transcription factor in adipose tissue metabolism. The aim of the present study was to explore the effects of SY in high‐fat diet‐induced obese mice, and further investigate the mechanism involving PPARγ2. Methods High‐fat diet‐induced obese mice were given 120 mg/kg/day SY for 8 weeks. Glucose and insulin tolerance tests were carried out. Fat mass and serum levels of glucose and insulin were measured. The expression of insulin signaling pathway‐related genes and PPARγ2 in the adipose tissue was measured. In vitro, the effects of SY (0–500 mg/L) and hydroxysafflor yellow A (0–100 mg/L) on PPARγ2 promoter activities and PPARγ2 messenger ribonucleic acid (mRNA) levels in 3T3‐L1 preadipocytes or adipocytes were also detected. Results Safflower yellow reduced fat mass, decreased glucose levels and improved insulin sensitivity in obese mice. SY also increased the mRNA levels of insulin signaling pathway‐related genes, and increased PPARγ2 mRNA levels by 39.1% in subcutaneous adipose tissue (P < 0.05). In vitro, SY and hydroxysafflor yellow A significantly enhanced PPARγ2 promoter activities by 1.3–2.1‐fold, and increased PPARγ2 mRNA levels by 1.2–1.6‐fold in 3T3‐L1 preadipocytes or adipocytes (P < 0.05). Conclusions SY could reduce fat mass, decrease glucose levels and improve insulin sensitivity in high‐fat diet‐induced obese mice. The probable mechanism is to increase PPARγ2 expression by stimulating PPARγ2 promoter activities, further increasing the expression of insulin signaling pathway‐related genes in subcutaneous adipose tissue.
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Affiliation(s)
- Kemin Yan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiangqing Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Huijuan Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hui Pan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linjie Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hongbo Yang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Meijuan Liu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ming Jin
- Department of Pharmacology, China-Beijing Institute of Heart, Lung and Blood Vessel Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Baoxia Zang
- Department of Pharmacology, China-Beijing Institute of Heart, Lung and Blood Vessel Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Fengying Gong
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Moradifard S, Saghiri R, Ehsani P, Mirkhani F, Ebrahimi-Rad M. A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites. Mol Genet Genomic Med 2020; 8:e1219. [PMID: 32155318 PMCID: PMC7216802 DOI: 10.1002/mgg3.1219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/25/2020] [Indexed: 11/12/2022] Open
Abstract
Background In the human genome, the transcription factors (TFs) and transcription factor‐binding sites (TFBSs) network has a great regulatory function in the biological pathways. Such crosstalk might be affected by the single‐nucleotide polymorphisms (SNPs), which could create or disrupt a TFBS, leading to either a disease or a phenotypic defect. Many computational resources have been introduced to predict the TFs binding variations due to SNPs inside TFBSs, sTRAP being one of them. Methods A literature review was performed and the experimental data for 18 TFBSs located in 12 genes was provided. The sequences of TFBS motifs were extracted using two different strategies; in the size similar with synthetic target sites used in the experimental techniques, and with 60 bp upstream and downstream of the SNPs. The sTRAP (http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) was applied to compute the binding affinity scores of their cognate TFs in the context of reference and mutant sequences of TFBSs. The alternative bioinformatics model used in this study was regulatory analysis of variation in enhancers (RAVEN; http://www.cisreg.ca/cgi-bin/RAVEN/a). The bioinformatics outputs of our study were compared with experimental data, electrophoretic mobility shift assay (EMSA). Results In 6 out of 18 TFBSs in the following genes COL1A1, Hb ḉᴪ, TF, FIX, MBL2, NOS2A, the outputs of sTRAP were inconsistent with the results of EMSA. Furthermore, no p value of the difference between the two scores of binding affinity under the wild and mutant conditions of TFBSs was presented. Nor, were any criteria for preference or selection of any of the measurements of different matrices used for the same analysis. Conclusion Our preliminary study indicated some paradoxical results between sTRAP and experimental data. However, to link the data of sTRAP to the biological functions, its optimization via experimental procedures with the integration of expanded data and applying several other bioinformatics tools might be required.
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Affiliation(s)
| | - Reza Saghiri
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran
| | - Parastoo Ehsani
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Mirkhani
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran
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Karaman EF, Zeybel M, Ozden S. Evaluation of the epigenetic alterations and gene expression levels of HepG2 cells exposed to zearalenone and α-zearalenol. Toxicol Lett 2020; 326:52-60. [PMID: 32119988 DOI: 10.1016/j.toxlet.2020.02.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/30/2023]
Abstract
Zearalenone, produced by various Fusarium species, is a non-steroidal estrogenic mycotoxin that contaminates cereals, resulting in adverse effects on human health. We investigated the effects of zearalenone and its metabolite alpha zearalenol on epigenetic modifications and its relationship with metabolic pathways in human hepatocellular carcinoma cells following 24 h of exposure. Zearalenone and alpha zearalenol at the concentrations of 1, 10 and 50 μM significantly increased global levels of DNA methylation and global histone modifications (H3K27me3, H3K9me3, H3K9ac). Expression levels of the chromatin modifying enzymes EHMT2, ESCO1, HAT1, KAT2B, PRMT6 and SETD8 were upregulated by 50 μM of zearalenone exposure using PCR arrays, consistent with the results of global histone modifications. Zearalenone and alpha zearalenol also changed expression levels of the AhR, LXRα, PPARα, PPARɣ, L-fabp, LDLR, Glut2, Akt1 and HK2 genes, which are related to nuclear receptors and metabolic pathways. PPARɣ, a key regulator of lipid metabolism, was selected from among these genes for further analysis. The PPARɣ promoter reduced methylation significantly following zearalenone exposure. Taken together, the epigenetic mechanisms of DNA methylation and histone modifications may be key mechanisms in zearalenone toxicity. Furthermore, effects of zearalenone in metabolic pathways could be mediated by epigenetic modifications.
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Affiliation(s)
- Ecem Fatma Karaman
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkey
| | - Müjdat Zeybel
- Department of Gastroenterology and Hepatology, School of Medicine, Koç University, 34010, Topkapi, Istanbul, Turkey
| | - Sibel Ozden
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkey.
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Guo W, Zhang H, Yang A, Ma P, Sun L, Deng M, Mao C, Xiong J, Sun J, Wang N, Ma S, Nie L, Jiang Y. Homocysteine accelerates atherosclerosis by inhibiting scavenger receptor class B member1 via DNMT3b/SP1 pathway. J Mol Cell Cardiol 2020; 138:34-48. [PMID: 31733201 DOI: 10.1016/j.yjmcc.2019.11.145] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/04/2019] [Indexed: 12/25/2022]
Abstract
Homocysteine (Hcy) is an independent risk factor for atherosclerosis, which is characterized by lipid accumulation in the atherosclerotic plaque. Increasing evidence supports that as the main receptor of high-density lipoprotein, scavenger receptor class B member 1 (SCARB1) is protective against atherosclerosis. However, the underlying mechanism regarding it in Hcy-mediated atherosclerosis remains unclear. Here, we found the remarkable inhibition of SCARB1 expression in atherosclerotic plaque and Hcy-treated foam cells, whereas overexpression of SCARB1 can suppress lipid accumulation in foam cells following Hcy treatment. Analysis of SCARB1 promoter showed that no significant change of methylation level was observed both in vivo and in vitro under Hcy treatment. Moreover, it was found that the negative regulation of DNMT3b on SCARB1 was due to the decreased recruitment of SP1 to SCARB1 promoter. Thus, we concluded that inhibition of SCARB1 expression induced by DNMT3b at least partly accelerated Hcy-mediated atherosclerosis through promoting lipid accumulation in foam cells, which was attributed to the decreased binding of SP1 to SCARB1 promoter. In our point, these findings will provide novel insight into an epigenetic mechanism for atherosclerosis.
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Affiliation(s)
- Wei Guo
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China
| | - Huiping Zhang
- Prenatal Diagnosis Center of Ningxia Medical University General Hospital, Yinchuan, China
| | - Anning Yang
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China
| | - Pengjun Ma
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China
| | - Lei Sun
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China
| | - Mei Deng
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China
| | - Caiyan Mao
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China
| | - Jiantuan Xiong
- College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Jianmin Sun
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Nan Wang
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Shengchao Ma
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China
| | - Lihong Nie
- Department of Physiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Yideng Jiang
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China; Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China; NHC Key Laboratory of Metabolic Cardiovascular Diseases Research (NingXia Medical University), Yinchuan, China.
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Villeneuve T, Guilleminault L. [Asthma and obesity in adults]. Rev Mal Respir 2019; 37:60-74. [PMID: 31866123 DOI: 10.1016/j.rmr.2019.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/06/2019] [Indexed: 12/31/2022]
Abstract
Asthma is a chronic inflammatory airway disorder characterized by a multitude of phenotypes. Epidemiological studies show an increase in asthma prevalence in obese patients regardless of age. The association of asthma and obesity is now considered as a phenotype with its own clinical, biological and functional characteristics. Regarding the pathophysiology of asthma and obesity, numerous factors such as nutrition, genetic predisposition, microbiome, ventilatory mechanics and the role of adipose tissue have been identified to explain the heterogeneous characteristics of patients with asthma and obesity. In adult patients with asthma and obesity, respiratory symptoms are particularly prominent and atopy and eosinophilic inflammation is uncommon compared to normal weight asthma patients. Obese asthma patients experience more hospitalizations and use more rescue medications than normal weight asthmatics. Management of asthma in obese patients is complex because these patients have less response to the usual anti-asthmatic treatments. Weight loss through caloric restriction combined with exercise is the main intervention to obtain improvement of asthma outcomes. Bariatric surgery is an invasive procedure with interesting results.
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Affiliation(s)
- T Villeneuve
- Pôles des voies respiratoires, hôpital Larrey, CHU de Toulouse, 24, chemin de Pouvourville, TSA 30030, 31059 Toulouse cedex 9, France
| | - L Guilleminault
- Pôles des voies respiratoires, hôpital Larrey, CHU de Toulouse, 24, chemin de Pouvourville, TSA 30030, 31059 Toulouse cedex 9, France; Centre de physiopathologie de Toulouse Purpan (CPTP-U1043, Inserm, équipe 12), UPS, Toulouse, France.
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Yang Y, Liu L, Li M, Cheng X, Fang M, Zeng Q, Xu Y. The chromatin remodeling protein BRG1 links ELOVL3 trans-activation to prostate cancer metastasis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:834-845. [PMID: 31154107 DOI: 10.1016/j.bbagrm.2019.05.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/20/2019] [Accepted: 05/25/2019] [Indexed: 10/26/2022]
Abstract
Prostate cancer malignancies are intimately correlated with deregulated fatty acid metabolism. The underlying epigenetic mechanism is not fully understood. In the present study we investigated the mechanism whereby the chromatin remodeling protein BRG1 regulates the transcription of long-chain fatty acid elongase 3 (Elovl3) in prostate cancer cells. We report that in response to pro-metastatic cues (androgen and TGF-β) BRG1 expression was up-regulated along with Elvol3 in prostate cancer cells. BRG1 over-expression potentiated whereas BRG1 knockdown attenuated prostate cancer cell migration and invasion. Coincidently, Elovl3 was up-regulated following BRG1 over-expression and down-regulated after BRG1 knockdown in prostate cancer cells. Further analysis revealed that BRG1 interacted with and was recruited by retinoic acid receptor-related orphan receptor (RORγ) to the Elovl3 promoter to activate transcription. Chromatin immunoprecipitation (ChIP) profiling demonstrated that BRG1 interacted with histone acetyltransferase p300 to activate Elovl3 transcription. Depletion of p300 by siRNA or inhibition of p300 by curcumin attenuated Elovl3 trans-activation in prostate cancer cells. Together, our data identify a novel epigenetic pathway that links Elovl3 transcription to prostate cancer cell migration and invasion.
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Affiliation(s)
- Yuyu Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China; Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Li Liu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Min Li
- Center for Male Reproductive Medicine, Department of Clinical Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Xian Cheng
- Jiangsu Institute of Nuclear Medicine, Wuxi, China
| | - Mingming Fang
- Center for Male Reproductive Medicine, Department of Clinical Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Qingqi Zeng
- Center for Male Reproductive Medicine, Department of Clinical Medicine, Jiangsu Health Vocational College, Nanjing, China.
| | - Yong Xu
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.
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Overexpression of DNMT3A promotes proliferation and inhibits differentiation of porcine intramuscular preadipocytes by methylating p21 and PPARg promoters. Gene 2019; 696:54-62. [DOI: 10.1016/j.gene.2019.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
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Samblas M, Milagro FI, Martínez A. DNA methylation markers in obesity, metabolic syndrome, and weight loss. Epigenetics 2019; 14:421-444. [PMID: 30915894 DOI: 10.1080/15592294.2019.1595297] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The fact that not all individuals exposed to the same environmental risk factors develop obesity supports the hypothesis of the existence of underlying genetic and epigenetic elements. There is suggestive evidence that environmental stimuli, such as dietary pattern, particularly during pregnancy and early life, but also in adult life, can induce changes in DNA methylation predisposing to obesity and related comorbidities. In this context, the DNA methylation marks of each individual have emerged not only as a promising tool for the prediction, screening, diagnosis, and prognosis of obesity and metabolic syndrome features, but also for the improvement of weight loss therapies in the context of precision nutrition. The main objectives in this field are to understand the mechanisms involved in transgenerational epigenetic inheritance, and featuring the nutritional and lifestyle factors implicated in the epigenetic modifications. Likewise, DNA methylation modulation caused by diet and environment may be a target for newer therapeutic strategies concerning the prevention and treatment of metabolic diseases.
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Affiliation(s)
- Mirian Samblas
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain
| | - Fermín I Milagro
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain.,b CIBERobn, CIBER Fisiopatología de la Obesidad y Nutrición , Instituto de Salud Carlos III. Madrid , Spain.,c IdiSNA, Instituto de Investigación Sanitaria de Navarra (IdiSNA) , Pamplona , Spain
| | - Alfredo Martínez
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain.,b CIBERobn, CIBER Fisiopatología de la Obesidad y Nutrición , Instituto de Salud Carlos III. Madrid , Spain.,c IdiSNA, Instituto de Investigación Sanitaria de Navarra (IdiSNA) , Pamplona , Spain.,d IMDEA, Research Institute on Food & Health Sciences , Madrid , Spain
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Trojnar M, Patro-Małysza J, Kimber-Trojnar Ż, Leszczyńska-Gorzelak B, Mosiewicz J. Associations between Fatty Acid-Binding Protein 4⁻A Proinflammatory Adipokine and Insulin Resistance, Gestational and Type 2 Diabetes Mellitus. Cells 2019; 8:cells8030227. [PMID: 30857223 PMCID: PMC6468522 DOI: 10.3390/cells8030227] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/03/2019] [Accepted: 03/03/2019] [Indexed: 12/12/2022] Open
Abstract
There is ample scientific evidence to suggest a link between the fatty acid-binding protein 4 (FABP4) and insulin resistance, gestational (GDM), and type 2 (T2DM) diabetes mellitus. This novel proinflammatory adipokine is engaged in the regulation of lipid metabolism at the cellular level. The molecule takes part in lipid oxidation, the regulation of transcription as well as the synthesis of membranes. An involvement of FABP4 in the pathogenesis of obesity and insulin resistance seems to be mediated via FABP4-dependent peroxisome proliferator-activated receptor γ (PPARγ) inhibition. A considerable number of studies have shown that plasma concentrations of FABP4 is increased in obesity and T2DM, and that circulating FABP4 levels are correlated with certain clinical parameters, such as body mass index, insulin resistance, and dyslipidemia. Since plasma-circulating FABP4 has the potential to modulate the function of several types of cells, it appears to be of extreme interest to try to develop potential therapeutic strategies targeting the pathogenesis of metabolic diseases in this respect. In this manuscript, representing a detailed review of the literature on FABP4 and the abovementioned metabolic disorders, various mechanisms of the interaction of FABP4 with insulin signaling pathways are thoroughly discussed. Clinical aspects of insulin resistance in diabetic patients, including women diagnosed with GDM, are analyzed as well.
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Affiliation(s)
- Marcin Trojnar
- Chair and Department of Internal Medicine, Medical University of Lublin, 20-081 Lublin, Poland.
| | - Jolanta Patro-Małysza
- Chair and Department of Obstetrics and Perinatology, Medical University of Lublin, 20-090 Lublin, Poland.
| | - Żaneta Kimber-Trojnar
- Chair and Department of Obstetrics and Perinatology, Medical University of Lublin, 20-090 Lublin, Poland.
| | | | - Jerzy Mosiewicz
- Chair and Department of Internal Medicine, Medical University of Lublin, 20-081 Lublin, Poland.
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An T, Zhang J, Lv B, Liu Y, Huang J, Lian J, Wu Y, Gao S, Jiang G. Salvianolic acid B plays an anti-obesity role in high fat diet-induced obese mice by regulating the expression of mRNA, circRNA, and lncRNA. PeerJ 2019; 7:e6506. [PMID: 30842902 PMCID: PMC6397762 DOI: 10.7717/peerj.6506] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
Background Adipose tissue plays a central role in obesity-related metabolic diseases such as type 2 diabetes. Salvianolic acid B (Sal B), a water-soluble ingredient derived from Salvia miltiorrhiza, has been shown to reduce obesity and obesity-related metabolic diseases by suppressing adipogenesis. However, the role of Sal B in white adipose tissue (WAT) is not yet clear. Methods Illumina Hiseq 4000 was used to study the effects of Sal B on the expression of long non-coding RNA (lncRNA) and circular RNA (circRNA) in epididymal white adipose tissue induced by a high fat diet in obese mice. Results RNA-Seq data showed that 234 lncRNAs, 19 circRNAs, and 132 mRNAs were differentially expressed in WAT under Sal B treatment. The up-regulated protein-coding genes in WAT of the Sal B-treated group were involved in the insulin resistance pathway, while the down-regulated genes mainly participated in the IL-17 signaling pathway. Other pathways may play an important role in the formation and differentiation of adipose tissue, such as B cell receptor signaling. Analysis of the lncRNA–mRNA network provides potential targets for lncRNAs in energy metabolism. We speculate that Sal B may serve as a potential therapeutic approach for obesity.
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Affiliation(s)
- Tian An
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Jing Zhang
- Department of Endocrinology, Tangshan Workers Hospital, Tangshan, China
| | - Bohan Lv
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yufei Liu
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | | | - Juan Lian
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yanxiang Wu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Sihua Gao
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Guangjian Jiang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
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