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Yang W, Lyu Y, Xiang R, Yang J. Long Noncoding RNAs in the Pathogenesis of Insulin Resistance. Int J Mol Sci 2022; 23:ijms232416054. [PMID: 36555704 PMCID: PMC9785789 DOI: 10.3390/ijms232416054] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has been increasing evidence that lncRNAs participated in the pathogenesis of IR, and the dysregulated lncRNA profile played important roles in the pathogenesis of metabolic diseases including obesity, diabetes and NAFLD. For example, the lncRNAs MEG3, H19, MALAT1, GAS5, lncSHGL and several other lncRNAs have been shown to regulate insulin signaling and glucose/lipid metabolism in various tissues. In this review, we briefly introduced the general features of lncRNA and the methods for lncRNA research, and then summarized and discussed the recent advances on the roles and mechanisms of lncRNAs in IR, particularly focused on liver, skeletal muscle and adipose tissues.
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Affiliation(s)
- Weili Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yixiang Lyu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Rui Xiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
- Correspondence:
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Song MA, Seffernick AE, Archer KJ, Mori KM, Park SY, Chang L, Ernst T, Tiirikainen M, Peplowska K, Wilkens LR, Le Marchand L, Lim U. Race/ethnicity-associated blood DNA methylation differences between Japanese and European American women: an exploratory study. Clin Epigenetics 2021; 13:188. [PMID: 34635168 PMCID: PMC8507376 DOI: 10.1186/s13148-021-01171-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Racial/ethnic disparities in health reflect a combination of genetic and environmental causes, and DNA methylation may be an important mediator. We compared in an exploratory manner the blood DNA methylome of Japanese Americans (JPA) versus European Americans (EUA). METHODS Genome-wide buffy coat DNA methylation was profiled among healthy Multiethnic Cohort participant women who were Japanese (JPA; n = 30) or European (EUA; n = 28) Americans aged 60-65. Differentially methylated CpGs by race/ethnicity (DM-CpGs) were identified by linear regression (Bonferroni-corrected P < 0.1) and analyzed in relation to corresponding gene expression, a priori selected single nucleotide polymorphisms (SNPs), and blood biomarkers of inflammation and metabolism using Pearson or Spearman correlations (FDR < 0.1). RESULTS We identified 174 DM-CpGs with the majority of hypermethylated in JPA compared to EUA (n = 133), often in promoter regions (n = 48). Half (51%) of the genes corresponding to the DM-CpGs were involved in liver function and liver disease, and the methylation in nine genes was significantly correlated with gene expression for DM-CpGs. A total of 156 DM-CpGs were associated with rs7489665 (SH2B1). Methylation of DM-CpGs was correlated with blood levels of the cytokine MIP1B (n = 146). We confirmed some of the DM-CpGs in the TCGA adjacent non-tumor liver tissue of Asians versus EUA. CONCLUSION We found a number of differentially methylated CpGs in blood DNA between JPA and EUA women with a potential link to liver disease, specific SNPs, and systemic inflammation. These findings may support further research on the role of DNA methylation in mediating some of the higher risk of liver disease among JPA.
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Affiliation(s)
- Min-Ae Song
- Division of Environmental Health Science, College of Public Health, The Ohio State University, 404 Cunz Hall, 1841 Neil Ave., Columbus, OH, 43210, USA.
| | - Anna Eames Seffernick
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Kellie J Archer
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Kellie M Mori
- Division of Environmental Health Science, College of Public Health, The Ohio State University, 404 Cunz Hall, 1841 Neil Ave., Columbus, OH, 43210, USA
| | - Song-Yi Park
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Linda Chang
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Thomas Ernst
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Maarit Tiirikainen
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Karolina Peplowska
- Genomics and Bioinformatics Shared Resources, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Lynne R Wilkens
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Loïc Le Marchand
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Unhee Lim
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
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Goodrich JM, Hector EC, Tang L, LaBarre JL, Dolinoy DC, Mercado-Garcia A, Cantoral A, Song PX, Téllez-Rojo MM, Peterson KE. Integrative Analysis of Gene-Specific DNA Methylation and Untargeted Metabolomics Data from the ELEMENT Cohort. Epigenet Insights 2020; 13:2516865720977888. [PMID: 33354655 PMCID: PMC7734565 DOI: 10.1177/2516865720977888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/04/2020] [Indexed: 12/18/2022] Open
Abstract
Epigenetic modifications, such as DNA methylation, influence gene expression and cardiometabolic phenotypes that are manifest in developmental periods in later life, including adolescence. Untargeted metabolomics analysis provide a comprehensive snapshot of physiological processes and metabolism and have been related to DNA methylation in adults, offering insights into the regulatory networks that influence cellular processes. We analyzed the cross-sectional correlation of blood leukocyte DNA methylation with 3758 serum metabolite features (574 of which are identifiable) in 238 children (ages 8-14 years) from the Early Life Exposures in Mexico to Environmental Toxicants (ELEMENT) study. Associations between these features and percent DNA methylation in adolescent blood leukocytes at LINE-1 repetitive elements and genes that regulate early life growth (IGF2, H19, HSD11B2) were assessed by mixed effects models, adjusting for sex, age, and puberty status. After false discovery rate correction (FDR q < 0.05), 76 metabolites were significantly associated with LINE-1 DNA methylation, 27 with HSD11B2, 103 with H19, and 4 with IGF2. The ten identifiable metabolites included dicarboxylic fatty acids (five associated with LINE-1 or H19 methylation at q < 0.05) and 1-octadecanoyl-rac-glycerol (q < 0.0001 for association with H19 and q = 0.04 for association with LINE-1). We then assessed the association between these ten known metabolites and adiposity 3 years later. Two metabolites, dicarboxylic fatty acid 17:3 and 5-oxo-7-octenoic acid, were inversely associated with measures of adiposity (P < .05) assessed approximately 3 years later in adolescence. In stratified analyses, sex-specific and puberty-stage specific (Tanner stage = 2 to 5 vs Tanner stage = 1) associations were observed. Most notably, hundreds of statistically significant associations were observed between H19 and LINE-1 DNA methylation and metabolites among children who had initiated puberty. Understanding relationships between subclinical molecular biomarkers (DNA methylation and metabolites) may increase our understanding of genes and biological pathways contributing to metabolic changes that underlie the development of adiposity during adolescence.
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Affiliation(s)
- Jaclyn M Goodrich
- Deptartment of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Emily C Hector
- Deptartment of Biostatistics, University of Michigan, Ann Arbor, MI, USA.,Deptartment of Statistics, North Carolina State University, USA
| | - Lu Tang
- Deptartment of Biostatistics, University of Pittsburgh, USA
| | - Jennifer L LaBarre
- Deptartment of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Deptartment of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA.,Deptartment of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Adriana Mercado-Garcia
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, México
| | - Alejandra Cantoral
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, México
| | - Peter Xk Song
- Deptartment of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Martha Maria Téllez-Rojo
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, México
| | - Karen E Peterson
- Deptartment of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA.,Deptartment of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
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Perera BP, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC. The role of environmental exposures and the epigenome in health and disease. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:176-192. [PMID: 31177562 PMCID: PMC7252203 DOI: 10.1002/em.22311] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
The genetic material of every organism exists within the context of regulatory networks that govern gene expression, collectively called the epigenome. Epigenetics has taken center stage in the study of diseases such as cancer and diabetes, but its integration into the field of environmental health is still emerging. As the Environmental Mutagenesis and Genomics Society (EMGS) celebrates its 50th Anniversary this year, we have come together to review and summarize the seminal advances in the field of environmental epigenomics. Specifically, we focus on the role epigenetics may play in multigenerational and transgenerational transmission of environmentally induced health effects. We also summarize state of the art techniques for evaluating the epigenome, environmental epigenetic analysis, and the emerging field of epigenome editing. Finally, we evaluate transposon epigenetics as they relate to environmental exposures and explore the role of noncoding RNA as biomarkers of environmental exposures. Although the field has advanced over the past several decades, including being recognized by EMGS with its own Special Interest Group, recently renamed Epigenomics, we are excited about the opportunities for environmental epigenetic science in the next 50 years. Environ. Mol. Mutagen. 61:176-192, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Bambarendage P.U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Correspondence to: Dana C. Dolinoy, Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan.
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Qin L, Huang CC, Yan XM, Wang Y, Li ZY, Wei XC. Long non-coding RNA H19 is associated with polycystic ovary syndrome in Chinese women: a preliminary study. Endocr J 2019; 66:587-595. [PMID: 30982795 DOI: 10.1507/endocrj.ej19-0004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) represents a serious reproductive and endocrine condition and is associated with high incidence rates. H19 is a compelling long noncoding RNA (lncRNA) which carries out a range of biological functions. However, prior to this study, little was known as to whether there was an association between lncRNA H19 and PCOS. In the current study, we used quantitative real-time polymerase chain reaction (qRT-PCR) to determine lncRNA H19 expression levels in peripheral blood leukocytes from patients with PCOS and compared this data with that derived from normal controls. We also screened data for potential relationships between lncRNA H19 and a range of endocrine variables in PCOS. The expression of lncRNA H19 was significantly higher in cases of PCOS than in controls. Individuals exhibiting higher expression levels of lncRNA H19 were associated with a significantly higher risk of PCOS than those with lower expression levels. Moreover, lncRNA H19 expression was positively correlated with fasting plasma glucose levels; this was the case with both raw data, and after adjustment for age and BMI in the PCOS group. However, lncRNA H19 expression showed no significant correlation with total testosterone or insulin resistance in either PCOS cases or the controls. In conclusion, we demonstrate the first evidence to indicate that lncRNA H19 is associated with PCOS, suggesting that elevated lncRNA H19 levels are a risk factor for PCOS. For susceptible individuals, lncRNA H19 may represent a useful biomarker of the early stages of endocrine and metabolic disorders in PCOS.
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Affiliation(s)
- Li Qin
- Department of Obstetrics and Gynecology, the First Clinical Medical College of Jinan University, Guangzhou, Guangdong 510632, China
- Center for Reproductive Medicine, the Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Chui-Can Huang
- Department of Obstetrics and Gynecology, the First Clinical Medical College of Jinan University, Guangzhou, Guangdong 510632, China
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiu-Min Yan
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yao Wang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Zhong-Yi Li
- Department of Obstetrics and Gynecology, the First Clinical Medical College of Jinan University, Guangzhou, Guangdong 510632, China
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiang-Cai Wei
- Department of Obstetrics and Gynecology, the First Clinical Medical College of Jinan University, Guangzhou, Guangdong 510632, China
- Guangdong Women and Children Hospital, Guangzhou, Guangdong 510000, China
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