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Hernández-Caballero ME, Sierra-Ramírez JA, De la Peña-Gutierrez M, Galindo-Ramirez F. Investigating the Role of Fat Mass and Obesity-Associated (FTO) Single Nucleotide Polymorphisms and Methylation in Breast Cancer. Cureus 2024; 16:e62851. [PMID: 39040764 PMCID: PMC11260689 DOI: 10.7759/cureus.62851] [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] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Background Fat mass and obesity-associated (FTO) protein is an mRNA demethylase enzyme essential for active genome regulation. The FTO gene codes for a protein that is part of the methylosome complex and has a regulatory role in cancer development. Some studies have shown a relationship between FTO and cancer, where single nucleotide polymorphisms (SNPs) may have some impact on cancer risk. The present study aimed to evaluate the risk of FTO polymorphisms rs9939609, rs1477196, and rs9930506; analyze the methylation status of FTO promoters among Mexican women with breast cancer (BC); and investigate by in silico analysis the methylation status in the region near these polymorphisms. Methods A total of 157 BC patients and 137 healthy controls were genotyped for rs9939609, rs1477196, and rs9930506 FTO polymorphisms by TaqMan SNP Genotyping Assays. Promoter methylation was analyzed by sodium bisulfite and methylation-specific polymerase chain reaction (MSP) for 78 tissue samples. An in silico analysis using The Cancer Genome Atlas Program (TCGA) database was employed to investigate the methylation state in promoter and near polymorphism locations and its relation to survival. Results The AG genotype of FTO rs9930506 was associated with BC protection (P= 0.0025; adjusted OR, 0.27; 95% CI: 0.10-0.70). rs9939609 and rs1477196, according to the results of the present study, had no relation to BC. Promoter methylation status assays by MSP revealed no changes in methylation in BC or healthy tissues. Trying to know more about the methylation in promoters and near polymorphisms' relation to survival, we performed an in silico analysis. Bioinformatics analysis showed a correlation between poor survival and methylation near polymorphisms but not with methylation in the promoter region. Conclusions The AG genotype rs9930506 has a protective function against BC. Whereas high methylation near polymorphisms was related to lower survival, the hypomethylated promoter region does not impact survival.
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Affiliation(s)
| | - Jose Alfredo Sierra-Ramírez
- Postgraduate Studies and Research Section, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, MEX
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Singh S, Kriti M, K.S. A, Sarma DK, Verma V, Nagpal R, Mohania D, Tiwari R, Kumar M. Deciphering the complex interplay of risk factors in type 2 diabetes mellitus: A comprehensive review. Metabol Open 2024; 22:100287. [PMID: 38818227 PMCID: PMC11137529 DOI: 10.1016/j.metop.2024.100287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/15/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
The complex and multidimensional landscape of type 2 diabetes mellitus (T2D) is a major global concern. Despite several years of extensive research, the precise underlying causes of T2D remain elusive, but evidence suggests that it is influenced by a myriad of interconnected risk factors such as epigenetics, genetics, gut microbiome, environmental factors, organelle stress, and dietary habits. The number of factors influencing the pathogenesis is increasing day by day which worsens the scenario; meanwhile, the interconnections shoot up the frame. By gaining deeper insights into the contributing factors, we may pave the way for the development of personalized medicine, which could unlock more precise and impactful treatment pathways for individuals with T2D. This review summarizes the state of knowledge about T2D pathogenesis, focusing on the interplay between various risk factors and their implications for future therapeutic strategies. Understanding these factors could lead to tailored treatments targeting specific risk factors and inform prevention efforts on a population level, ultimately improving outcomes for individuals with T2D and reducing its burden globally.
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Affiliation(s)
- Samradhi Singh
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Mona Kriti
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Anamika K.S.
- Christ Deemed to Be University Bangalore, Karnataka, India
| | - Devojit Kumar Sarma
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Ravinder Nagpal
- Department of Nutrition & Integrative Physiology, College of Health & Human Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Dheeraj Mohania
- Dr. R. P. Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Rajnarayan Tiwari
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Manoj Kumar
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
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Nadiger N, Veed JK, Chinya Nataraj P, Mukhopadhyay A. DNA methylation and type 2 diabetes: a systematic review. Clin Epigenetics 2024; 16:67. [PMID: 38755631 PMCID: PMC11100087 DOI: 10.1186/s13148-024-01670-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVE DNA methylation influences gene expression and function in the pathophysiology of type 2 diabetes mellitus (T2DM). Mapping of T2DM-associated DNA methylation could aid early detection and/or therapeutic treatment options for diabetics. DESIGN A systematic literature search for associations between T2DM and DNA methylation was performed. Prospero registration ID: CRD42020140436. METHODS PubMed and ScienceDirect databases were searched (till October 19, 2023). Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and New Castle Ottawa scale were used for reporting the selection and quality of the studies, respectively. RESULT Thirty-two articles were selected. Four of 130 differentially methylated genes in blood, adipose, liver or pancreatic islets (TXNIP, ABCG1, PPARGC1A, PTPRN2) were reported in > 1 study. TXNIP was hypomethylated in diabetic blood across ethnicities. Gene enrichment analysis of the differentially methylated genes highlighted relevant disease pathways (T2DM, type 1 diabetes and adipocytokine signaling). Three prospective studies reported association of methylation in IGFBP2, MSI2, FTO, TXNIP, SREBF1, PHOSPHO1, SOCS3 and ABCG1 in blood at baseline with incident T2DM/hyperglycemia. Sex-specific differential methylation was reported only for HOOK2 in visceral adipose tissue (female diabetics: hypermethylated, male diabetics: hypomethylated). Gene expression was inversely associated with methylation status in 8 studies, in genes including ABCG1 (blood), S100A4 (adipose tissue), PER2 (pancreatic islets), PDGFA (liver) and PPARGC1A (skeletal muscle). CONCLUSION This review summarizes available evidence for using DNA methylation patterns to unravel T2DM pathophysiology. Further validation studies in diverse populations will set the stage for utilizing this knowledge for identifying early diagnostic markers and novel druggable pathways.
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Affiliation(s)
- Nikhil Nadiger
- Research Scholar, Manipal Academy of Higher Education, Manipal, India
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
| | - Jyothisha Kana Veed
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
| | - Priyanka Chinya Nataraj
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
- Vedantu, Bangalore, India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India.
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Huo W, Hu H, Li T, Yuan L, Zhang J, Feng Y, Wu Y, Fu X, Ke Y, Wang M, Zhang W, Wang L, Chen Y, Gao Y, Li X, Liu J, Huang Z, Hu F, Zhang M, Sun L, Hu D, Zhao Y. Association of methylation risk score with incident type 2 diabetes mellitus: A nested case-control study. J Diabetes 2024; 16:e13512. [PMID: 38062913 PMCID: PMC10940902 DOI: 10.1111/1753-0407.13512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 03/16/2024] Open
Abstract
AIMS To investigate the association of methylation risk score (MRS) and its interactions with environmental factors with type 2 diabetes mellitus (T2DM) risk. METHODS We conducted a nested case-control study with 241 onset cases and 241 matched controls. Conditional logistic regression models were employed to identify risk CpG sites. Simple and weighted MRSs were constructed based on the methylation levels of ATP-binding cassette G1 gene, fat mass and obesity associated gene, potassium voltage-gated channel member 1 gene, and thioredoxin-interacting protein gene previously associated with T2DM to estimate the association of MRS with T2DM risk. Stratified analyses were used to investigate interactions between MRS and environmental factors. RESULTS A total of 10 CpG loci were identified from the aforementioned genes to calculate MRS. After controlling for potential confounding factors, taking tertile 1 as reference, the odds ratios (ORs) and 95% confidence intervals (CIs) for T2DM of tertile 3 was 2.39 (1.36-4.20) for simple MRS and 2.59 (1.45-4.63) for weighted MRS. With per SD score increment in MRS, the OR (95% CI) was 1.66 (1.29-2.14) and 1.60 (1.24-2.08) for simple and weighted MRSs, respectively. J-curved associations were observed between both simple and weighted MRSs and T2DM risks. Additionally, multiplication interactions for smoking and hypertension with simple MRS on the risk of T2DM were found, similarly for smoking and obesity with weighted MRS on the risk of T2DM (all Pinteraction < .05). CONCLUSION Elevated simple and weighted MRSs were associated with increased risk of T2DM. Environmental risk factors may influence the association between MRS and T2DM.
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Affiliation(s)
- Weifeng Huo
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Huifang Hu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Tianze Li
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Lijun Yuan
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Jinli Zhang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yifei Feng
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yuying Wu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Xueru Fu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yamin Ke
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Mengmeng Wang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Wenkai Zhang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Longkang Wang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yaobing Chen
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yajuan Gao
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Xi Li
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Jiong Liu
- Department of Preventive MedicineSchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Zelin Huang
- Department of Preventive MedicineSchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Fulan Hu
- Department of Biostatistics and EpidemiologySchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Ming Zhang
- Department of Biostatistics and EpidemiologySchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Liang Sun
- Department of Social Medicine and Health Service ManagementCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Dongsheng Hu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yang Zhao
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
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Dong H, Sun Y, Nie L, Cui A, Zhao P, Leung WK, Wang Q. Metabolic memory: mechanisms and diseases. Signal Transduct Target Ther 2024; 9:38. [PMID: 38413567 PMCID: PMC10899265 DOI: 10.1038/s41392-024-01755-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Metabolic diseases and their complications impose health and economic burdens worldwide. Evidence from past experimental studies and clinical trials suggests our body may have the ability to remember the past metabolic environment, such as hyperglycemia or hyperlipidemia, thus leading to chronic inflammatory disorders and other diseases even after the elimination of these metabolic environments. The long-term effects of that aberrant metabolism on the body have been summarized as metabolic memory and are found to assume a crucial role in states of health and disease. Multiple molecular mechanisms collectively participate in metabolic memory management, resulting in different cellular alterations as well as tissue and organ dysfunctions, culminating in disease progression and even affecting offspring. The elucidation and expansion of the concept of metabolic memory provides more comprehensive insight into pathogenic mechanisms underlying metabolic diseases and complications and promises to be a new target in disease detection and management. Here, we retrace the history of relevant research on metabolic memory and summarize its salient characteristics. We provide a detailed discussion of the mechanisms by which metabolic memory may be involved in disease development at molecular, cellular, and organ levels, with emphasis on the impact of epigenetic modulations. Finally, we present some of the pivotal findings arguing in favor of targeting metabolic memory to develop therapeutic strategies for metabolic diseases and provide the latest reflections on the consequences of metabolic memory as well as their implications for human health and diseases.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuezhang Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lulingxiao Nie
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Aimin Cui
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Pengfei Zhao
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Wai Keung Leung
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Qi Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Yousri NA, Albagha OME, Hunt SC. Integrated epigenome, whole genome sequence and metabolome analyses identify novel multi-omics pathways in type 2 diabetes: a Middle Eastern study. BMC Med 2023; 21:347. [PMID: 37679740 PMCID: PMC10485955 DOI: 10.1186/s12916-023-03027-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND T2D is of high prevalence in the middle east and thus studying its mechanisms is of a significant importance. Using 1026 Qatar BioBank samples, epigenetics, whole genome sequencing and metabolomics were combined to further elucidate the biological mechanisms of T2D in a population with a high prevalence of T2D. METHODS An epigenome-wide association study (EWAS) with T2D was performed using the Infinium 850K EPIC array, followed by whole genome-wide sequencing SNP-CpG association analysis (> 5.5 million SNPs) and a methylome-metabolome (CpG-metabolite) analysis of the identified T2D sites. RESULTS A total of 66 T2D-CpG associations were identified, including 63 novel sites in pathways of fructose and mannose metabolism, insulin signaling, galactose, starch and sucrose metabolism, and carbohydrate absorption and digestion. Whole genome SNP associations with the 66 CpGs resulted in 688 significant CpG-SNP associations comprising 22 unique CpGs (33% of the 66 CPGs) and included 181 novel pairs or pairs in novel loci. Fourteen of the loci overlapped published GWAS loci for diabetes related traits and were used to identify causal associations of HK1 and PFKFB2 with HbA1c. Methylome-metabolome analysis identified 66 significant CpG-metabolite pairs among which 61 pairs were novel. Using the identified methylome-metabolome associations, methylation QTLs, and metabolic networks, a multi-omics network was constructed which suggested a number of metabolic mechanisms underlying T2D methylated genes. 1-palmitoyl-2-oleoyl-GPE (16:0/18:1) - a triglyceride-associated metabolite, shared a common network with 13 methylated CpGs, including TXNIP, PFKFB2, OCIAD1, and BLCAP. Mannonate - a food component/plant shared a common network with 6 methylated genes, including TXNIP, BLCAP, THBS4 and PEF1, pointing to a common possible cause of methylation in those genes. A subnetwork with alanine, glutamine, urea cycle (citrulline, arginine), and 1-carboxyethylvaline linked to PFKFB2 and TXNIP revealed associations with kidney function, hypertension and triglyceride metabolism. The pathway containing STYXL1-POR was associated with a sphingosine-ceramides subnetwork associated with HDL-C and LDL-C and point to steroid perturbations in T2D. CONCLUSIONS This study revealed several novel methylated genes in T2D, with their genomic variants and associated metabolic pathways with several implications for future clinical use of multi-omics associations in disease and for studying therapeutic targets.
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Affiliation(s)
- Noha A Yousri
- Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Computer and Systems Engineering, Alexandria University, Alexandria, Egypt.
| | - Omar M E Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Steven C Hunt
- Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
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Jing Z, Zhang H, Wen Y, Cui S, Ren Y, Liu R, Duan S, Zhao W, Fan L. Epigenetic and transcriptomic alterations in the ClC-3-deficient mice consuming a normal diet. Front Cell Dev Biol 2023; 11:1196684. [PMID: 37287451 PMCID: PMC10242048 DOI: 10.3389/fcell.2023.1196684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Introduction: Metabolic disorders are an important health concern that threatens life and burdens society severely. ClC-3 is a member of the chloride voltage-gated channel family, and ClC-3 deletion improved the phenotypes of dysglycemic metabolism and the impairment of insulin sensitivity. However, the effects of a healthy diet on transcriptome and epigenetics in ClC-3-/- mice were not explained in detail. Methods: Here, we performed transcriptome sequencing and Reduced Representation Bisulfite Sequencing for the liver of 3 weeks old WT and ClC-3-/- mice consuming a normal diet to insight into the epigenetic and transcriptomic alterations of ClC-3 deficient mice. Results: In the present study, we found that ClC-3-/- mice that were younger than 8 weeks old had smaller bodies compared to ClC-3+/+ mice with ad libitum self-feeding normal diet, and ClC-3-/- mice that were older than 10 weeks old had a similar body weight. Except for the spleen, lung, and kidney, the average weight of the heart, liver, and brain in ClC-3-/- mice was lower than that in ClC-3+/+ mice. TG, TC, HDL, and LDL in fasting ClC-3-/- mice were not significantly different from those in ClC-3+/+ mice. Fasting blood glucose in ClC-3-/- mice was lower than that in ClC-3+/+ mice; the glucose tolerance test indicated the response to blood glucose increasing for ClC-3-/- mice was torpid, but the efficiency of lowering blood glucose was much higher once started. Transcriptomic sequencing and reduced representation bisulfite sequencing for the liver of unweaned mice indicated that ClC-3 deletion significantly changed transcriptional expression and DNA methylation levels of glucose metabolism-related genes. A total of 92 genes were intersected between DEGs and DMRs-targeted genes, of which Nos3, Pik3r1, Socs1, and Acly were gathered in type II diabetes mellitus, insulin resistance, and metabolic pathways. Moreover, Pik3r1 and Acly expressions were obviously correlated with DNA methylation levels, not Nos3 and Socs1. However, the transcriptional levels of these four genes were not different between ClC-3-/- and ClC-3+/+ mice at the age of 12 weeks. Discussion: ClC-3 influenced the methylated modification to regulate glucose metabolism, of which the gene expressions could be driven to change again by a personalized diet-style intervention.
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Affiliation(s)
- Zhenghui Jing
- Department of Pathology of Basic Medicine College, Xi’an Jiaotong University, Xi’an, China
- Institute of Genetics and Developmental Biology of Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Haifeng Zhang
- Department of Pathology of Basic Medicine College, Xi’an Jiaotong University, Xi’an, China
- Institute of Genetics and Developmental Biology of Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yunjie Wen
- Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, Guangdong, China
| | - Shiyu Cui
- Department of Pathology of Basic Medicine College, Xi’an Jiaotong University, Xi’an, China
- Institute of Genetics and Developmental Biology of Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yuhua Ren
- Department of Pathology of Basic Medicine College, Xi’an Jiaotong University, Xi’an, China
- Institute of Genetics and Developmental Biology of Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Rong Liu
- Department of Pathology of Basic Medicine College, Xi’an Jiaotong University, Xi’an, China
- Institute of Genetics and Developmental Biology of Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Sirui Duan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Wenbao Zhao
- Department of Pathology of Basic Medicine College, Xi’an Jiaotong University, Xi’an, China
| | - Lihong Fan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
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Chen S, Xi M, Gao F, Li M, Dong T, Geng Z, Liu C, Huang F, Wang J, Li X, Wei P, Miao F. Evaluation of mulberry leaves’ hypoglycemic properties and hypoglycemic mechanisms. Front Pharmacol 2023; 14:1045309. [PMID: 37089923 PMCID: PMC10117911 DOI: 10.3389/fphar.2023.1045309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
The effectiveness of herbal medicine in treating diabetes has grown in recent years, but the precise mechanism by which it does so is still unclear to both medical professionals and diabetics. In traditional Chinese medicine, mulberry leaf is used to treat inflammation, colds, and antiviral illnesses. Mulberry leaves are one of the herbs with many medicinal applications, and as mulberry leaf study grows, there is mounting evidence that these leaves also have potent anti-diabetic properties. The direct role of mulberry leaf as a natural remedy in the treatment of diabetes has been proven in several studies and clinical trials. However, because mulberry leaf is a more potent remedy for diabetes, a deeper understanding of how it works is required. The bioactive compounds flavonoids, alkaloids, polysaccharides, polyphenols, volatile oils, sterols, amino acids, and a variety of inorganic trace elements and vitamins, among others, have been found to be abundant in mulberry leaves. Among these compounds, flavonoids, alkaloids, polysaccharides, and polyphenols have a stronger link to diabetes. Of course, trace minerals and vitamins also contribute to blood sugar regulation. Inhibiting alpha glucosidase activity in the intestine, regulating lipid metabolism in the body, protecting pancreatic -cells, lowering insulin resistance, accelerating glucose uptake by target tissues, and improving oxidative stress levels in the body are some of the main therapeutic properties mentioned above. These mechanisms can effectively regulate blood glucose levels. The therapeutic effects of the bioactive compounds found in mulberry leaves on diabetes mellitus and their associated molecular mechanisms are the main topics of this paper’s overview of the state of the art in mulberry leaf research for the treatment of diabetes mellitus.
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Affiliation(s)
- Sikai Chen
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Miaomiao Xi
- The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
- Xi’an TANK Medicinal Biology Institute, Xi’an, China
| | - Feng Gao
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Min Li
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - TaiWei Dong
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Zhixin Geng
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Chunyu Liu
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Fengyu Huang
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jing Wang
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Xingyu Li
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Peifeng Wei
- Shaanxi University of Chinese Medicine, Xianyang, China
- The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
- *Correspondence: Peifeng Wei, ; Feng Miao,
| | - Feng Miao
- The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
- *Correspondence: Peifeng Wei, ; Feng Miao,
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Jung SY, Bhatti P, Pellegrini M. DNA methylation in peripheral blood leukocytes for the association with glucose metabolism and invasive breast cancer. Clin Epigenetics 2023; 15:23. [PMID: 36782224 PMCID: PMC9926571 DOI: 10.1186/s13148-023-01435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Insulin resistance (IR) is a well-established factor for breast cancer (BC) risk in postmenopausal women, but the interrelated molecular pathways on the methylome are not explicitly described. We conducted a population-level epigenome-wide association (EWA) study for DNA methylation (DNAm) probes that are associated with IR and prospectively correlated with BC development, both overall and in BC subtypes among postmenopausal women. METHODS We used data from Women's Health Initiative (WHI) ancillary studies for our EWA analyses and evaluated the associations of site-specific DNAm across the genome with IR phenotypes by multiple regressions adjusting for age and leukocyte heterogeneities. For our analysis of the top 20 IR-CpGs with BC risk, we used the WHI and the Cancer Genomic Atlas (TCGA), using multiple Cox proportional hazards and logit regressions, respectively, accounting for age, diabetes, obesity, leukocyte heterogeneities, and tumor purity (for TCGA). We further conducted a Gene Set Enrichment Analysis. RESULTS We detected several EWA-CpGs in TXNIP, CPT1A, PHGDH, and ABCG1. In particular, cg19693031 in TXNIP was replicated in all IR phenotypes, measured by fasting levels of glucose, insulin, and homeostatic model assessment-IR. Of those replicated IR-genes, 3 genes (CPT1A, PHGDH, and ABCG1) were further correlated with BC risk; and 1 individual CpG (cg01676795 in POR) was commonly detected across the 2 cohorts. CONCLUSIONS Our study contributes to better understanding of the interconnected molecular pathways on the methylome between IR and BC carcinogenesis and suggests potential use of DNAm markers in the peripheral blood cells as preventive targets to detect an at-risk group for IR and BC in postmenopausal women.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, School of Nursing, University of California, Los Angeles, 700 Tiverton Ave, 3-264 Factor Building, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Institute, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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10
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Park SH, Lee J, Hwang JT, Chung MY. Physiologic and epigenetic effects of nutrients on disease pathways. Nutr Res Pract 2023; 17:13-31. [PMID: 36777807 PMCID: PMC9884588 DOI: 10.4162/nrp.2023.17.1.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/06/2022] [Accepted: 07/12/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND/OBJECTIVES Epigenetic regulation by nutrients can influence the development of specific diseases. This study sought to examine the effect of individual nutrients and nutrient families in the context of preventing chronic metabolic diseases via epigenetic regulation. The inhibition of lipid accumulation and inflammation by nutrients including proteins, lipids, vitamins, and minerals were observed, and histone acetylation by histone acetyltransferase (HAT) was measured. Correlative analyses were also performed. MATERIALS/METHODS Nutrients were selected according to information from the Korean Ministry of Food and Drug Safety. Selected nutrient functionalities, including the attenuation of fatty acid-induced lipid accumulation and lipopolysaccharide-mediated acute inflammation were evaluated in mouse macrophage Raw264.7 and mouse hepatocyte AML-12 cells. Effects of the selected nutrients on in vitro HAT inhibition were also evaluated. RESULTS Nitric oxide (NO) production correlated with HAT activity, which was regulated by the amino acids group, suggesting that amino acids potentially contribute to the attenuation of NO production via the inhibition of HAT activity. Unsaturated fatty acids tended to attenuate inflammation by inhibiting NO production, which may be attributable to the inhibition of in vitro HAT activity. In contrast to water-soluble vitamins, the lipid-soluble vitamins significantly decreased NO production. Water- and lipid-soluble vitamins both exhibited significant inhibitory activities against HAT. In addition, calcium and manganese significantly inhibited lipid accumulation, NO production, and HAT activity. CONCLUSIONS Several candidate nutrients and their family members may have roles in the prevention of diseases, including hepatic steatosis and inflammation-related diseases (i.e., nonalcoholic steatohepatitis) via epigenetic regulation. Further studies are warranted to determine which specific amino acids, unsaturated fatty acids and lipid-soluble vitamins or specific minerals influence the development of steatosis and inflammatory-related diseases.
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Affiliation(s)
- Soo-Hyun Park
- Food Functionality Research Division, Korea Food Research Institute, Wanju 55365, Korea
| | - Jaein Lee
- Food Functionality Research Division, Korea Food Research Institute, Wanju 55365, Korea.,Department of Food Science and Technology, Jeonbuk National University, Jeonju 54896, Korea
| | - Jin-Taek Hwang
- Food Functionality Research Division, Korea Food Research Institute, Wanju 55365, Korea.,Department of Food Biotechnology, University of Science and Technology, Daejeon 34113, Korea
| | - Min-Yu Chung
- Food Functionality Research Division, Korea Food Research Institute, Wanju 55365, Korea
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11
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Hao J, Liu Y. Epigenetics of methylation modifications in diabetic cardiomyopathy. Front Endocrinol (Lausanne) 2023; 14:1119765. [PMID: 37008904 PMCID: PMC10050754 DOI: 10.3389/fendo.2023.1119765] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
Type 2 diabetes is one of the most common metabolic diseases with complications including diabetic cardiomyopathy and atherosclerotic cardiovascular disease. Recently, a growing body of research has revealed that the complex interplay between epigenetic changes and the environmental factors may significantly contribute to the pathogenesis of cardiovascular complications secondary to diabetes. Methylation modifications, including DNA methylation and histone methylation among others, are important in developing diabetic cardiomyopathy. Here we summarized the literatures of studies focusing on the role of DNA methylation, and histone modifications in microvascular complications of diabetes and discussed the mechanism underlying these disorders, to provide the guidance for future research toward an integrated pathophysiology and novel therapeutic strategies to treat or prevent this frequent pathological condition.
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Affiliation(s)
- Jing Hao
- Department of Emergency, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Liu
- Department of Pharmacy, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yao Liu,
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12
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Smail HO, Mohamad DA. Identification of DNA methylation of CAPN10 gene changes in the patients with type 2 diabetes mellitus as a predictive biomarker instead of HbA1c, random blood sugar, lipid profile, kidney function test, and some risk factors. Endocr Regul 2023; 57:221-234. [PMID: 37823570 DOI: 10.2478/enr-2023-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Objective. Nowadays, type 2 diabetes mellitus (T2DM) is the most common chronic endocrine disorder, affecting an estimated 5-10% of adults worldwide and this disease rapidly increases in the Kurdistan region population. This research aims to identify DNA methylation change in the CPAN10 gene as a predictive biomarker in T2DM and the association between DNA methylation status with lipid profile and kidney function test. Methods. The participants (113) were divided into three groups: diabetes group (47), prediabetes group (36), and control group (30). The study was carried out on patients who visited the private clinical sectors between August and December 2021 in the Koya city Kurdistan region of Iraq. To determine DNA methylation status, methylation-specific PCR (MPS) with paired primer for each methylated and unmethylated region was used. The Mann-Whitney U test and Spearman's correlation were performed for statistical analysis of data and a value of p<0.05 was considered significant. Results. The obtained results show that DNA hypermethylation was recorded in the promoter region in the samples of the diabetes and prediabetes groups compared to the healthy group (control). Various factors also affected the level of DNA methylation, such as HbA1c in prediabetes group and body mass index in the control group. Conclusion. These results indicate that DNA methylation changes in the CAPN10 gene promoter region may be used as a potential predictive biomarker to diagnose T2DM; however, this study requires further data to support this evidence.
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Affiliation(s)
- Harem Othman Smail
- 1Department of Biology, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region - F.R. Iraq
| | - Dlnya Asaad Mohamad
- 2Department of Biology, College of Science, University of Sulaimani, Sulaymanyah, Iraq
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13
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Domingo-Relloso A, Gribble MO, Riffo-Campos AL, Haack K, Cole SA, Tellez-Plaza M, Umans JG, Fretts AM, Zhang Y, Fallin MD, Navas-Acien A, Everson TM. Epigenetics of type 2 diabetes and diabetes-related outcomes in the Strong Heart Study. Clin Epigenetics 2022; 14:177. [PMID: 36529747 PMCID: PMC9759920 DOI: 10.1186/s13148-022-01392-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The prevalence of type 2 diabetes has dramatically increased in the past years. Increasing evidence supports that blood DNA methylation, the best studied epigenetic mark, is related to diabetes risk. Few prospective studies, however, are available. We studied the association of blood DNA methylation with diabetes in the Strong Heart Study. We used limma, Iterative Sure Independence Screening and Cox regression to study the association of blood DNA methylation with fasting glucose, HOMA-IR and incident type 2 diabetes among 1312 American Indians from the Strong Heart Study. DNA methylation was measured using Illumina's MethylationEPIC beadchip. We also assessed the biological relevance of our findings using bioinformatics analyses. RESULTS Among the 358 differentially methylated positions (DMPs) that were cross-sectionally associated either with fasting glucose or HOMA-IR, 49 were prospectively associated with incident type 2 diabetes, although no DMPs remained significant after multiple comparisons correction. Multiple of the top DMPs were annotated to genes with relevant functions for diabetes including SREBF1, associated with obesity, type 2 diabetes and insulin sensitivity; ABCG1, involved in cholesterol and phospholipids transport; and HDAC1, of the HDAC family. (HDAC inhibitors have been proposed as an emerging treatment for diabetes and its complications.) CONCLUSIONS: Our results suggest that differences in peripheral blood DNA methylation are related to cross-sectional markers of glucose metabolism and insulin activity. While some of these DMPs were modestly associated with prospective incident type 2 diabetes, they did not survive multiple testing. Common DMPs with diabetes epigenome-wide association studies from other populations suggest a partially common epigenomic signature of glucose and insulin activity.
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Affiliation(s)
- Arce Domingo-Relloso
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain. .,Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA. .,Department of Statistics and Operations Research, University of Valencia, Valencia, Spain.
| | - Matthew O. Gribble
- grid.265892.20000000106344187Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL USA
| | - Angela L. Riffo-Campos
- grid.412163.30000 0001 2287 9552Millennium Nucleus On Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco, Chile ,grid.5338.d0000 0001 2173 938XDepartment of Computer Science, ETSE, University of Valencia, Valencia, Spain
| | - Karin Haack
- grid.250889.e0000 0001 2215 0219Population Health Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Shelley A. Cole
- grid.250889.e0000 0001 2215 0219Population Health Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Maria Tellez-Plaza
- grid.413448.e0000 0000 9314 1427Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Jason G. Umans
- grid.415232.30000 0004 0391 7375MedStar Health Research Institute, Hyattsville, MD USA ,grid.440590.cGeorgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC USA
| | - Amanda M. Fretts
- grid.34477.330000000122986657Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA USA
| | - Ying Zhang
- grid.266902.90000 0001 2179 3618Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - M. Daniele Fallin
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA USA
| | - Ana Navas-Acien
- grid.21729.3f0000000419368729Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY USA
| | - Todd M. Everson
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA USA
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14
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Prevalence and correlates of pre-diabetes in adults of mixed ethnicities in the South African population: A systematic review and meta-analysis. PLoS One 2022; 17:e0278347. [PMID: 36445923 PMCID: PMC9707763 DOI: 10.1371/journal.pone.0278347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
INTRODUCTION Pre-diabetes is a metabolic condition characterised by moderate glycaemic dysregulation and is a frontline risk factor for multiple metabolic complications such as type 2 diabetes mellitus. To the best of our knowledge, this will be the first systematic review and meta-analysis focusing on generating a comprehensive pooling of studies reporting on pre-diabetes prevalence in South Africa. Therefore, the review's purpose will be to screen and select reports that can be used to synthesise and provide the best estimate prevalence of pre-diabetes and its associated correlates in the South African population. METHODS AND ANALYSIS To determine the prevalence and correlates of pre-diabetes in South Africa, we searched PubMed, Web of Science, Google scholar and African Journal online for published or unpublished studies reporting the prevalence of pre-diabetes in South Africa starting from the year 2000 to 2020. Studies were assessed for eligibility by checking if they met the inclusion criteria. RESULTS & CONCLUSION The total number of studies deemed eligible is 13 and from these studies, an overall prevalence of pre-diabetes was reported to be 15,56% in the South African population. Hypertension, obesity and sedentary lifestyle were the common correlates recorded for the population of interest. Therefore, the review highlights the disturbingly high prevalence of pre-diabetes in South Africa and necessitates further investigations into the possible genetics, biochemical and hormonal changes in pre-diabetes. ETHICS AND DISSEMINATION The review will not require ethics clearance because non-identifiable data will be used. The review outcomes will give insight into the current burden that pre-diabetes has in South Africa. PROSPERO REGISTRATION NUMBER CRD42020182430.
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15
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Ibrahim HIM. Epigenetic Regulation of Obesity-Associated Type 2 Diabetes. Medicina (B Aires) 2022; 58:medicina58101366. [PMID: 36295527 PMCID: PMC9607337 DOI: 10.3390/medicina58101366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Obesity is becoming more widespread, and epidemics of this condition are now considered present in all developed countries, leading to public health concerns. The dramatic increases in obesity, type 2 diabetes mellitus (T2DM), and related vascular difficulties are causing a public health crisis. Thus, it is imperative that these trends are curbed. Understanding the molecular underpinnings of these diseases is crucial to aiding in their detection or even management. Thus, understanding the mechanisms underlying the interactions between environment, lifestyle, and genetics is important for developing effective strategies for the management of obesity. The focus is on finding the vital role of epigenetic changes in the etiology of obesity. Genome and epigenome-wide approaches have revealed associations with T2DM. The epigenome indicates that there is a systematic link between genetic variants and environmental factors that put people at risk of obesity. The present review focuses on the epigenetic mechanism linked with obesity-associated T2DM. Although the utilization of epigenetic treatments has been discussed with reference to certain cancers, several challenges remain to be addressed for T2DM.
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Affiliation(s)
- Hairul Islam Mohamed Ibrahim
- Department of Biological Science, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
- Division of Microbiology and Immunology, Pondicherry Centre for Biological Science and Educational Trust, Puducherry 605004, India
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16
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Fernandes V, Preeti K, Sood A, Nair KP, Khan S, Rao BSS, Khatri DK, Singh SB. Neuroepigenetic Changes in DNA Methylation Affecting Diabetes-Induced Cognitive Impairment. Cell Mol Neurobiol 2022:10.1007/s10571-022-01278-5. [PMID: 36138280 DOI: 10.1007/s10571-022-01278-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
Chronic diabetic conditions have been associated with certain cerebral complications, that include neurobehavioral dysfunctional patterns and morphological alterations of neurons, especially the hippocampus. Neuroanatomical studies done by the authors have shown decreased total dendritic length, intersections, dendritic length per branch order and nodes in the CA1 hippocampal region of the diabetic brain as compared to its normal control group, indicating reduced dendritic arborization of the hippocampal CA1 neurons. Epigenetic alterations in the brain are well known to affect age-associated disorders, however its association with the evolving diabetes-induced damage in the brain is still not fully understood. DNA hypermethylation within the neurons, tend to silent the gene expression of several regulatory proteins. The findings in the study have shown an increase in global DNA methylation in palmitic acid-induced lipotoxic Neuro-2a cells as well as within the diabetic mice brain. Inhibiting DNA methylation, restored the levels of HSF1 and certain HSPs, suggesting plausible effect of DNMTs in maintaining the proteostasis and synaptic fidelity. Neuroinflammation, as exhibited by the astrocyte activation (GFAP), were further significantly decreased in the 5-azadeoxycytidine group (DNMT inhibitor). This was further evidenced by decrease in proinflammatory cytokines TNF⍺, IL-6, and mediators iNOS and Phospho-NFkB. Our results suggest that changes in DNA methylation advocate epigenetic dysregulation and its involvement in disrupting the synaptic exactitude in the hippocampus of diabetic mice model, providing an insight into the pathophysiology of diabetes-induced neuroepigenetic changes.
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Affiliation(s)
- Valencia Fernandes
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kumari Preeti
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Anika Sood
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kala P Nair
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Sabiya Khan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - B S Shankaranarayana Rao
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
| | - Shashi Bala Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
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17
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Alimohammadi M, Makaremi S, Rahimi A, Asghariazar V, Taghadosi M, Safarzadeh E. DNA methylation changes and inflammaging in aging-associated diseases. Epigenomics 2022; 14:965-986. [PMID: 36043685 DOI: 10.2217/epi-2022-0143] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aging as an inevitable phenomenon is associated with pervasive changes in physiological functions. There is a relationship between aging and the increase of several chronic diseases. Most age-related disorders are accompanied by an underlying chronic inflammatory state, as demonstrated by local infiltration of inflammatory cells and greater levels of proinflammatory cytokines in the bloodstream. Within inflammaging, many epigenetic events, especially DNA methylation, change. During the aging process, due to aberrations of DNA methylation, biological processes are disrupted, leading to the emergence or progression of a variety of human diseases, including cancer, neurodegenerative disorders, cardiovascular disease and diabetes. The focus of this review is on DNA methylation, which is involved in inflammaging-related activities, and how its dysregulation leads to human disorders.
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Affiliation(s)
- Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1983969411, Iran
| | - Shima Makaremi
- School of Medicine & Allied Medical Sciences, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
| | - Ali Rahimi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, 5618985991, Iran
| | - Vahid Asghariazar
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
| | - Mahdi Taghadosi
- Department of Immunology, Kermanshah University of Medical Sciences, Kermanshah, 6714869914, Iran
| | - Elham Safarzadeh
- Department of Microbiology, Parasitology, & Immunology, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
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18
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Hu F, Zhang Y, Qin P, Zhao Y, Liu D, Zhou Q, Tian G, Li Q, Guo C, Wu X, Qie R, Huang S, Han M, Li Y, Hu D, Zhang M. Integrated analysis of probability of type 2 diabetes mellitus with polymorphisms and methylation of SLC30A8 gene: a nested case-control study. J Hum Genet 2022; 67:651-660. [PMID: 35996015 DOI: 10.1038/s10038-022-01067-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/16/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
To estimate the associations between single-nucleotide polymorphisms (SNPs) and methylation of SLC30A8 gene and T2DM risk, and the interactions among SNPs, methylation, and environmental factors on T2DM risk. We genotyped 9 SNPs and tested methylation at 46 CpG loci of SLC30A8 in the baseline DNA of 290 T2DM cases and 290 matched controls nested in the Rural Chinese Cohort Study. A conditional logistic regression model was used to estimate the associations between SNPs and SLC30A8 methylation and T2DM risk. Multifactor Dimensionality Reduction analysis was used to estimate the effect of interactions among SNPs, methylation, and environment on T2DM risk. Probability of T2DM was decreased with rs11558471 (GG vs. AA, OR = 0.55, 95% CI 0.32, 0.96), with rs13266634 (TT vs. CC, OR = 0.55, 95% CI 0.32, 0.94), with rs3802177 (AA vs. GG, OR = 0.54, 95%CI 0.31, 0.94), and its probability was increased with rs2466293 of SLC30A8 (GA vs. AA, OR = 1.63, 95% CI 1.08-2.47). Its probability was also significantly associated with methylation of CG9 and CG45 (OR = 0.56 [95% CI 0.33-0.97] and 1.61 [95%CI 1.03--2.51]). T2DM probability was significantly associated with the interaction effect between rs2466293 and hypertension (p = 0.045). T2DM probability was also significantly associated with the combination effects of rs2466293 with BMI, hypertension, and hypertriglyceridemia, with the combination effects of hypertriglyceridemia with rs11558471, rs13266634, and methylation of CG45.
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Affiliation(s)
- Fulan Hu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yanyan Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Pei Qin
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yang Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Dechen Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Qionggui Zhou
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Gang Tian
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Quanman Li
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Chunmei Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xiaoyan Wu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Ranran Qie
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Shengbing Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Minghui Han
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yang Li
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Dongsheng Hu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Ming Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China.
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19
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Wang D, Kuang Y, Zhang G, Xiao K, Liu Y. Lysine-Specific Demethylase 1 in Energy Metabolism: A Novel Target for Obesity. J Nutr 2022; 152:1611-1620. [PMID: 35380692 DOI: 10.1093/jn/nxac080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/19/2022] [Accepted: 03/29/2022] [Indexed: 11/14/2022] Open
Abstract
Obesity develops from an imbalance of energy homeostasis and is associated with the development of metabolic disorders, including insulin resistance and type 2 diabetes. Identification of the underlying molecular mechanisms and effective therapeutic approaches is highly needed. Lysine-specific demethylase 1 (LSD1), an flavin adenine dinucletide-dependent amine oxidase, is implicated in a wide variety of biological processes, including tumorigenesis, stem cell fate decisions, and embryonic development. Recent studies have suggested a vital role of LSD1 in regulating adaptive thermogenesis, mitochondrial biogenesis, glucose, and lipid metabolism. More recently, LSD1 activity was found to be regulated by nutrients, energy status, and hormonal signals, suggesting that it may act as a novel sensor for nutritional regulation of metabolic health. Here, we first discuss the effects of LSD1 on physiological phenotypes, including body weight, fat mass, body temperature, and glucose homeostasis. We also summarize recent understanding of the physiological roles and underlying mechanisms of LSD1 in controlling metabolic functions of adipose and other tissues. Hopefully, a better understanding of the roles of LSD1 in metabolic regulation may provide new perspectives for the nutritional prevention and treatment of obesity.
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Affiliation(s)
- Dan Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Yanling Kuang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Guolong Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, People's Republic of China.,Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kan Xiao
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Yulan Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, People's Republic of China
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20
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Liu X, Liang Z, Duan H, Yu J, Qin Z, Li J, Zhu L, Wu Q, Xiao W, Shen C, Wan C, Wu K, Ye H, Zhang B, Zhao W. Dengue virus is involved in insulin resistance via the downregulation of IRS-1 by inducing TNF-α secretion. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166472. [PMID: 35752384 DOI: 10.1016/j.bbadis.2022.166472] [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: 03/22/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/29/2022]
Abstract
During the epidemic, the individuals with underlying diseases usually have a higher rate of mortality. Diabetes is highly prevalent worldwide, making it a frequent comorbidity in dengue fever patients. Therefore, understanding the relationship between dengue virus (DENV) infection and diabetes is important. We first demonstrated that DENV-3 infection down-regulated the expression of IRS-1. In vitro, treatment of HepG2 cells with TNF-α inhibitors and siRNA proved that after DENV-3 infection in HepG2 cells, cellular TNF-α secretion was increased, which negatively regulated IRS-1, thereby leading to an insulin-resistant state. In vivo, DENV-3 induced insulin resistance (IR) in hepatocytes by promoting the secretion of TNF-α and inhibiting the expression of IRS-1 was proved. In vivo approaches also showed that after DENV-3 infection, TNF-α levels in the serum of C57BL/6 mice with insulin resistance increased, and upon TNF-α antagonist III treatment, IRS-1 expression in the liver, reduced by infection, was upregulated. In addition, transcriptomic analysis revealed more negative regulatory events in the insulin receptor signaling pathway after DENV-3 infection. This is the first report of a link between DENV-3 infection and insulin resistance, and it lays a foundation for further research.
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Affiliation(s)
- Xuling Liu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zuxin Liang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Hongwei Duan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jianhai Yu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhiran Qin
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jingshu Li
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Li Zhu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Qinghua Wu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Weiwei Xiao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Chengsong Wan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Kefeng Wu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
| | - Hua Ye
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China.
| | - Bao Zhang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China.
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China.
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21
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Jansen RJ, Orr M, Bamlet WR, Petersen GM. A Pilot Study of Blood-Based Methylation Markers Associated With Pancreatic Cancer. Front Genet 2022; 13:849839. [PMID: 35360846 PMCID: PMC8963849 DOI: 10.3389/fgene.2022.849839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/17/2022] [Indexed: 12/14/2022] Open
Abstract
Over the past several decades in the United States, incidence of pancreatic cancer (PCa) has increased, with the 5-year survival rate remaining extremely low at 10.8%. Typically, PCa is diagnosed at an advanced stage, with the consequence that there is more tumor heterogeneity and increased probability that more cells are resistant to treatments. Risk factors for PCa can serve as a way to select a high-risk population and develop biomarkers to improve early detection and treatment. We focus on blood-based methylation as an approach to identify a marker set that can be obtained in a minimally invasive way (through peripheral blood) and could be applied to a high-risk subpopulation [those with recent onset type 2 diabetes (DM)]. Blood samples were collected from 30 patients, 15 had been diagnosed with PCa and 15 had been diagnosed with recent onset DM. HumanMethylationEPIC Beadchip (Illumina, CA, United States) was used to quantify methylation of approximately 850,000 methylation sites across the genome and to analyze methylation markers associated with PCa or DM or both. Exploratory analysis conducted to propose importance of top CpG (5'-C-phosphate-G-3') methylation site associated genes and visualized using boxplots. A methylation-based age predictor was also investigated for ability to distinguish disease groups from controls. No methylation markers were observed to be significantly associated with PCa or new onset diabetes compared with control the respective control groups. In our exploratory analysis, one methylation marker, CpG04969764, found in the Laminin Subunit Alpha 5 (LAMA5) gene region was observed in both PCa and DM Top 100 methylation marker sets. Modification of LAMA5 methylation or LAMA5 gene function may be a way to distinguish those recent DM cases with and without PCa, however, additional studies with larger sample sizes and different study types (e.g., cohort) will be needed to test this hypothesis.
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Affiliation(s)
- Rick J. Jansen
- Department of Public Health, North Dakota State University, Fargo, ND, United States,Genomics, Phenomics, and Bioinformatics Program, North Dakota State University, Fargo, ND, United States,Center for Immunization Research and Education (CIRE), North Dakota State University, Fargo, ND, United States,Center for Diagnostic and Therapeutic Strategies in Pancreatic Cancer, North Dakota State University, Fargo, ND, United States,*Correspondence: Rick J. Jansen,
| | - Megan Orr
- Department of Statistics, North Dakota State University, Fargo, ND, United States
| | - William R. Bamlet
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Gloria M. Petersen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
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22
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Ravari MS, Farrokhi E, Moradi Z, Chaleshtori MH, Jami MS, Zarandi MB. Association between GPX1 and IL-6 promoter methylation and type 2 diabetes. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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How to Slow Down the Ticking Clock: Age-Associated Epigenetic Alterations and Related Interventions to Extend Life Span. Cells 2022; 11:cells11030468. [PMID: 35159278 PMCID: PMC8915189 DOI: 10.3390/cells11030468] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic alterations pose one major hallmark of organismal aging. Here, we provide an overview on recent findings describing the epigenetic changes that arise during aging and in related maladies such as neurodegeneration and cancer. Specifically, we focus on alterations of histone modifications and DNA methylation and illustrate the link with metabolic pathways. Age-related epigenetic, transcriptional and metabolic deregulations are highly interconnected, which renders dissociating cause and effect complicated. However, growing amounts of evidence support the notion that aging is not only accompanied by epigenetic alterations, but also at least in part induced by those. DNA methylation clocks emerged as a tool to objectively determine biological aging and turned out as a valuable source in search of factors positively and negatively impacting human life span. Moreover, specific epigenetic signatures can be used as biomarkers for age-associated disorders or even as targets for therapeutic approaches, as will be covered in this review. Finally, we summarize recent potential intervention strategies that target epigenetic mechanisms to extend healthy life span and provide an outlook on future developments in the field of longevity research.
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24
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Kuzub N, Smialkovska V, Momot V, Moseiko V, Lushchak O, Koliada A. Evaluation of Epigenetic Age Based on DNA Methylation Analysis of Several CpG Sites in Ukrainian Population. Front Genet 2022; 12:772298. [PMID: 35069680 PMCID: PMC8770732 DOI: 10.3389/fgene.2021.772298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetic clocks are the models, which use CpG methylation levels for the age prediction of an organism. Although there were several epigenetic clocks developed there is a demand for development and evaluation of the relatively accurate and sensitive epigenetic clocks that can be used for routine research purposes. In this study, we evaluated two epigenetic clock models based on the 4 CpG sites and 2 CpG sites in the human genome using the pyrosequencing method for their methylation level estimation. The study sample included 153 people from the Ukrainian population with the age from 0 to 101. Both models showed a high correlation with the chronological age in our study sample (R2 = 0.85 for the 2 CpG model and R2 = 0.92 for the 4 CpG model). We also estimated the accuracy metrics of the age prediction in our study sample. For the age group from 18 to 80 MAD was 5.1 years for the 2 CpG model and 4.1 years for the 4 CpG model. In this regard, we can conclude, that the models evaluated in the study have good age predictive accuracy, and can be used for the epigenetic age evaluation due to the relative simplicity and time-effectiveness.
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Affiliation(s)
- N Kuzub
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - V Smialkovska
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - V Momot
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | | | - O Lushchak
- Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - A Koliada
- Diagen Laboratory, Kyiv, Ukraine.,Institute of Food Biotechnology and Genomics NAS of Ukraine, Kyiv, Ukraine
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25
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Nasrullah, Hussain A, Ahmed S, Rasool M, Shah AJ. DNA methylation across the tree of life, from micro to macro-organism. Bioengineered 2022; 13:1666-1685. [PMID: 34986742 PMCID: PMC8805842 DOI: 10.1080/21655979.2021.2014387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a process in which methyl (CH3) groups are added to the DNA molecule. The DNA segment does not change in the sequence, but DNA methylation could alter the action of DNA. Different enzymes like DNA methyltransferases (DNMTs) take part in methylation of cytosine/adenine nucleosides in DNA. In prokaryotes, DNA methylation is performed to prevent the attack of phage and also plays a role in the chromosome replication and repair. In fungi, DNA methylation is studied to see the transcriptional changes, as in insects, the DNA methylation is not that well-known, it plays a different role like other organisms. In mammals, the DNA methylation is related to different types of cancers and plays the most important role in the placental development and abnormal DNA methylation connected with diseases like cancer, autoimmune diseases, and rheumatoid arthritis.
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Affiliation(s)
- Nasrullah
- Center for Advanced Studies in Vaccinology & Biotechnology (Casvab), University of Baluchistan, Quetta- Pakistan. E-mails:
| | - Abrar Hussain
- Department of Biotechnology, Faculty of Life Sciences, Buitems, Quetta-Pakistan. E-mails:
| | - Sagheer Ahmed
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan. E-mails:
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. E-mails:
| | - Abdul Jabbar Shah
- Department of Pharmaceutical Sciences, Comsats University, Abbottabad. E-mails:
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26
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Padilla-Martinez F, Wojciechowska G, Szczerbinski L, Kretowski A. Circulating Nucleic Acid-Based Biomarkers of Type 2 Diabetes. Int J Mol Sci 2021; 23:ijms23010295. [PMID: 35008723 PMCID: PMC8745431 DOI: 10.3390/ijms23010295] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/25/2021] [Accepted: 12/26/2021] [Indexed: 11/23/2022] Open
Abstract
Type 2 diabetes (T2D) is a deficiency in how the body regulates glucose. Uncontrolled T2D will result in chronic high blood sugar levels, eventually resulting in T2D complications. These complications, such as kidney, eye, and nerve damage, are even harder to treat. Identifying individuals at high risk of developing T2D and its complications is essential for early prevention and treatment. Numerous studies have been done to identify biomarkers for T2D diagnosis and prognosis. This review focuses on recent T2D biomarker studies based on circulating nucleic acids using different omics technologies: genomics, transcriptomics, and epigenomics. Omics studies have profiled biomarker candidates from blood, urine, and other non-invasive samples. Despite methodological differences, several candidate biomarkers were reported for the risk and diagnosis of T2D, the prognosis of T2D complications, and pharmacodynamics of T2D treatments. Future studies should be done to validate the findings in larger samples and blood-based biomarkers in non-invasive samples to support the realization of precision medicine for T2D.
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Affiliation(s)
- Felipe Padilla-Martinez
- Clinical Research Centre, Medical University of Bialystok, 15276 Białystok, Poland; (F.P.-M.); (L.S.); (A.K.)
| | - Gladys Wojciechowska
- Clinical Research Centre, Medical University of Bialystok, 15276 Białystok, Poland; (F.P.-M.); (L.S.); (A.K.)
- Correspondence:
| | - Lukasz Szczerbinski
- Clinical Research Centre, Medical University of Bialystok, 15276 Białystok, Poland; (F.P.-M.); (L.S.); (A.K.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15276 Białystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, 15276 Białystok, Poland; (F.P.-M.); (L.S.); (A.K.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15276 Białystok, Poland
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27
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Hu F, Zhang Y, Qin P, Zhao Y, Liu D, Zhou Q, Tian G, Li Q, Guo C, Wu X, Qie R, Huang S, Han M, Li Y, Zhang M, Hu D. Integrated analysis of probability of type 2 diabetes mellitus with polymorphisms and methylation of KCNQ1 gene: A nested case-control study. J Diabetes 2021; 13:975-986. [PMID: 34260825 DOI: 10.1111/1753-0407.13212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/17/2021] [Accepted: 07/07/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND To estimate the associations between single-nucleotide polymorphisms (SNPs) and methylation of KCNQ1 gene and type 2 diabetes mellitus (T2DM) risk and the interactions among SNPs, methylation, and environmental factors on T2DM risk. METHODS We genotyped five SNPs and tested methylation at 39 CpG loci of KCNQ1 in 290 T2DM cases and 290 matched controls nested in the Rural Chinese Cohort Study. Conditional logistic regression model was used to estimate the associations between SNPs and KCNQ1 methylation and T2DM risk. Multifactor dimensionality reduction (MDR) analysis was used to estimate the effect of the interactions SNPs-SNPs, SNPs-methylation, methylation-methylation and SNPs, and methylation-environment on T2DM risk. RESULTS Probability of T2DM was decreased with rs2283228 of KCNQ1 (CA vs AA, odds ratio [OR] = 0.65, 95% confidence interval [CI] 0.42-0.99). T2DM probability was significantly increased with rs2237895 combined with hypertriglyceridemia (OReg = 2.76, 95% CI 1.35-5.62), with hypertension (OReg = 2.23, 95% CI 1.25-3.98), and with body mass index (BMI; OReg = 1.93, 95% CI 1.12-3.34). T2DM probability was associated with methylation of CG11 and CG41 (OR = 1.89, 95% CI 1.23-2.89, P = .003). It was significantly associated with the interaction between BMI, hypertriglyceridemia, and CG5 methylation (P = .028 and .028), and the combined effects of CG11 with hypertriglyceridemia and hypertension. On MDR analysis, no significant interaction was observed. CONCLUSION T2DM probability was reduced 35% with rs2283228 polymorphism. It was associated with rs2237895 combined with hypertension, with BMI and with hypertriglyceridemia. The methylation at two CpG loci of KCNQ1 significantly increased T2DM risk by 89%.
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Affiliation(s)
- Fulan Hu
- Study Team of Shenzhen's Sanming Project, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, China
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yanyan Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Pei Qin
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yang Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Dechen Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Qionggui Zhou
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Gang Tian
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Quanman Li
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Chunmei Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoyan Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ranran Qie
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Shengbing Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Minghui Han
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yang Li
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Ming Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Dongsheng Hu
- Study Team of Shenzhen's Sanming Project, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, China
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28
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DNA Methylation and Type 2 Diabetes: Novel Biomarkers for Risk Assessment? Int J Mol Sci 2021; 22:ijms222111652. [PMID: 34769081 PMCID: PMC8584054 DOI: 10.3390/ijms222111652] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Diabetes is a severe threat to global health. Almost 500 million people live with diabetes worldwide. Most of them have type 2 diabetes (T2D). T2D patients are at risk of developing severe and life-threatening complications, leading to an increased need for medical care and reduced quality of life. Improved care for people with T2D is essential. Actions aiming at identifying undiagnosed diabetes and at preventing diabetes in those at high risk are needed as well. To this end, biomarker discovery and validation of risk assessment for T2D are critical. Alterations of DNA methylation have recently helped to better understand T2D pathophysiology by explaining differences among endophenotypes of diabetic patients in tissues. Recent evidence further suggests that variations of DNA methylation might contribute to the risk of T2D even more significantly than genetic variability and might represent a valuable tool to predict T2D risk. In this review, we focus on recent information on the contribution of DNA methylation to the risk and the pathogenesis of T2D. We discuss the limitations of these studies and provide evidence supporting the potential for clinical application of DNA methylation marks to predict the risk and progression of T2D.
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29
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Gao W, Liu JL, Lu X, Yang Q. Epigenetic regulation of energy metabolism in obesity. J Mol Cell Biol 2021; 13:480-499. [PMID: 34289049 PMCID: PMC8530523 DOI: 10.1093/jmcb/mjab043] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/24/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Obesity has reached epidemic proportions globally. Although modern adoption of a sedentary lifestyle coupled with energy-dense nutrition is considered to be the main cause of obesity epidemic, genetic preposition contributes significantly to the imbalanced energy metabolism in obesity. However, the variants of genetic loci identified from large-scale genetic studies do not appear to fully explain the rapid increase in obesity epidemic in the last four to five decades. Recent advancements of next-generation sequencing technologies and studies of tissue-specific effects of epigenetic factors in metabolic organs have significantly advanced our understanding of epigenetic regulation of energy metabolism in obesity. The epigenome, including DNA methylation, histone modifications, and RNA-mediated processes, is characterized as mitotically or meiotically heritable changes in gene function without alteration of DNA sequence. Importantly, epigenetic modifications are reversible. Therefore, comprehensively understanding the landscape of epigenetic regulation of energy metabolism could unravel novel molecular targets for obesity treatment. In this review, we summarize the current knowledge on the roles of DNA methylation, histone modifications such as methylation and acetylation, and RNA-mediated processes in regulating energy metabolism. We also discuss the effects of lifestyle modifications and therapeutic agents on epigenetic regulation of energy metabolism in obesity.
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Affiliation(s)
- Wei Gao
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Jia-Li Liu
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Xiang Lu
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Qin Yang
- Department of Medicine, Physiology and Biophysics, UC Irvine Diabetes Center, University of California Irvine, Irvine, CA 92697, USA
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30
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Rana S, Sultana A, Bhatti AA. Effect of interaction between obesity-promoting genetic variants and behavioral factors on the risk of obese phenotypes. Mol Genet Genomics 2021; 296:919-938. [PMID: 33966103 DOI: 10.1007/s00438-021-01793-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 01/28/2023]
Abstract
The studies investigating gene-gene and gene-environment (or gene-behavior) interactions provide valuable insight into the pathomechanisms underlying obese phenotypes. The Pakistani population due to its unique characteristics offers numerous advantages for conducting such studies. In this view, the current study was undertaken to examine the effects of gene-gene and gene-environment/behavior interactions on the risk of obesity in a sample of Pakistani population. A total of 578 adult participants including 290 overweight/obese cases and 288 normal-weight controls were involved. The five key obesity-associated genetic variants namely MC4R rs17782313, BDNF rs6265, FTO rs1421085, TMEM18 rs7561317, and NEGR1 rs2815752 were genotyped using the TaqMan allelic discrimination assays. The data related to behavioral factors, such as eating pattern, diet consciousness, the tendency toward fat-dense food (TFDF), sleep duration, sleep-wake cycle (SWC), shift work (SW), and physical activity levels were collected via a questionnaire. Gene-gene and gene-behavior interactions were analyzed by multifactor dimensionality reduction and linear regression, respectively. In our study, only TMEM18 rs7561317 was found to be significantly associated with anthropometric traits with no significant effect of gene-gene interactions were observed on obesity-related phenotypes. However, the genetic variants were found to interact with the behavioral factors to significantly influence various obesity-related anthropometric traits including BMI, waist circumference, hip circumference, waist-to-hip ratio, waist-to-height ratio, and percentage of body fat. In conclusion, the interaction between genetic architecture and behavior/environment determines the outcome of obesity-related anthropometric phenotypes. Thus, gene-environment/behavior interaction studies should be promoted to explore the risk of complex and multifactorial disorders, such as obesity.
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Affiliation(s)
- Sobia Rana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan.
| | - Ayesha Sultana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Adil Anwar Bhatti
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
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31
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Zampieri M, Bacalini MG, Barchetta I, Scalea S, Cimini FA, Bertoccini L, Tagliatesta S, De Matteis G, Zardo G, Cavallo MG, Reale A. Increased PARylation impacts the DNA methylation process in type 2 diabetes mellitus. Clin Epigenetics 2021; 13:114. [PMID: 34001206 PMCID: PMC8130175 DOI: 10.1186/s13148-021-01099-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Background Epigenetic modifications, such as DNA methylation, can influence the genetic susceptibility to type 2 diabetes mellitus (T2DM) and the progression of the disease. Our previous studies demonstrated that the regulation of the DNA methylation pattern involves the poly(ADP-ribosyl)ation (PARylation) process, a post-translational modification of proteins catalysed by the poly(ADP-ribose) polymerase (PARP) enzymes. Experimental data showed that the hyperactivation of PARylation is associated with impaired glucose metabolism and the development of T2DM. Aims of this case–control study were to investigate the association between PARylation and global and site-specific DNA methylation in T2DM and to evaluate metabolic correlates. Results Data were collected from 61 subjects affected by T2DM and 48 healthy individuals, recruited as controls. Global levels of poly(ADP-ribose) (PAR, a surrogate of PARP activity), cytosine methylation (5-methylcytosine, 5mC) and de-methylation intermediates 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) were determined in peripheral blood cells by ELISA-based methodologies. Site-specific DNA methylation profiling of SOCS3, SREBF1 and TXNIP candidate genes was performed by mass spectrometry-based bisulfite sequencing, methyl-sensitive endonucleases digestion and by DNA immuno-precipitation. T2DM subjects presented higher PAR levels than controls. In T2DM individuals, increased PAR levels were significantly associated with higher HbA1c levels and the accumulation of the de-methylation intermediates 5hmC and 5fC in the genome. In addition, T2DM patients with higher PAR levels showed reduced methylation with increased 5hmC and 5fC levels in specific SOCS3 sites, up-regulated SOCS3 expression compared to both T2DM subjects with low PAR levels and controls. Conclusions This study demonstrates the activation of PARylation processes in patients with T2DM, particularly in those with poor glycaemic control. PARylation is linked to dysregulation of DNA methylation pattern via activation of the DNA de-methylation cascade and may be at the basis of the differential gene expression observed in presence of diabetes. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01099-1.
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Affiliation(s)
- Michele Zampieri
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | | | - Ilaria Barchetta
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Stefania Scalea
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Flavia Agata Cimini
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Laura Bertoccini
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Stefano Tagliatesta
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Giovanna De Matteis
- Research Centre for Animal Production and Aquaculture, Consiglio Per La Ricerca in Agricoltura E L'Analisi Dell'Economia Agraria (CREA), 00015, Monterotondo, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Maria Gisella Cavallo
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy.
| | - Anna Reale
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy.
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Parveen N, Dhawan S. DNA Methylation Patterning and the Regulation of Beta Cell Homeostasis. Front Endocrinol (Lausanne) 2021; 12:651258. [PMID: 34025578 PMCID: PMC8137853 DOI: 10.3389/fendo.2021.651258] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic beta cells play a central role in regulating glucose homeostasis by secreting the hormone insulin. Failure of beta cells due to reduced function and mass and the resulting insulin insufficiency can drive the dysregulation of glycemic control, causing diabetes. Epigenetic regulation by DNA methylation is central to shaping the gene expression patterns that define the fully functional beta cell phenotype and regulate beta cell growth. Establishment of stage-specific DNA methylation guides beta cell differentiation during fetal development, while faithful restoration of these signatures during DNA replication ensures the maintenance of beta cell identity and function in postnatal life. Lineage-specific transcription factor networks interact with methylated DNA at specific genomic regions to enhance the regulatory specificity and ensure the stability of gene expression patterns. Recent genome-wide DNA methylation profiling studies comparing islets from diabetic and non-diabetic human subjects demonstrate the perturbation of beta cell DNA methylation patterns, corresponding to the dysregulation of gene expression associated with mature beta cell state in diabetes. This article will discuss the molecular underpinnings of shaping the islet DNA methylation landscape, its mechanistic role in the specification and maintenance of the functional beta cell phenotype, and its dysregulation in diabetes. We will also review recent advances in utilizing beta cell specific DNA methylation patterns for the development of biomarkers for diabetes, and targeting DNA methylation to develop translational approaches for supplementing the functional beta cell mass deficit in diabetes.
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Affiliation(s)
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, United States
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Huang S, Qin P, Chen Q, Zhang D, Cheng C, Guo C, Li Q, Zhou Q, Tian G, Qie R, Han M, Wu X, Yang X, Feng Y, Li Y, Zhang Y, Wu Y, Liu D, Lu J, Zhang M, Zhao Y, Hu D. Association of FTO gene methylation with incident type 2 diabetes mellitus: A nested case-control study. Gene 2021; 786:145585. [PMID: 33753148 DOI: 10.1016/j.gene.2021.145585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVES This study aimed to investigate the association of FTO methylation level with type 2 diabetes mellitus (T2DM) in a nested case-control study. METHODS This nested case-control study included 287 pairs of T2DM cases and controls identified from a rural Chinese cohort study with a 6-year follow-up. Controls were matched to the cases on a 1:1 basis by age, sex, ethnicity, marital status, and residence. Conditional multivariate logistic regression models were used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for the association of cytosine guanine (CpG) locus and tag-single nucleotide polymorphisms (Tag-SNPs) with T2DM. Spearman correlation analysis was used to evaluate the association between FTO methylation and possible risk factors for T2DM in the control group. RESULTS The methylation level on the CpG9 site significantly differs between cases and controls, with a significant association between the CpG9 site methylation and probability of T2DM: OR 2.19 (95%CI: 1.31-3.65) after adjusting for potential confounders. The Tag-SNPs (rs72803657, rs1558902, rs17817449, rs11076023) were not associated with T2DM. Further, FTO methylation was associated with some risk factors for T2DM. CONCLUSIONS A CpG locus of FTO was positively associated with T2DM, but SNPs were not. FTO methylation were also associated with some T2DM risk factors. Further study with a large sample size and data on metabolic product are needed to confirm the association.
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Affiliation(s)
- Shengbing Huang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Pei Qin
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Qing Chen
- Department of Mental Health, Bao'an Chronic Diseases Prevent and Cure Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Dongdong Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Cheng Cheng
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Chunmei Guo
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Quanman Li
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Qionggui Zhou
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Gang Tian
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Ranran Qie
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Minghui Han
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xiaoyan Wu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Xingjin Yang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yifei Feng
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yang Li
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yanyan Zhang
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yuying Wu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Dechen Liu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Jie Lu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Ming Zhang
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
| | - Dongsheng Hu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
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Qie R, Han M, Huang S, Li Q, Liu L, Zhang D, Cheng C, Zhao Y, Liu D, Qin P, Guo C, Zhou Q, Tian G, Zhang Y, Wu X, Wu Y, Li Y, Yang X, Zhao Y, Feng Y, Hu F, Zhang M, Hu D, Lu J. Association of TCF7L2 gene polymorphisms, methylation, and gene-environment interaction with type 2 diabetes mellitus risk: A nested case-control study in the Rural Chinese Cohort Study. J Diabetes Complications 2021; 35:107829. [PMID: 33419631 DOI: 10.1016/j.jdiacomp.2020.107829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/08/2020] [Accepted: 12/01/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND To assess the associations of single-nucleotide polymorphisms (SNPs) and methylation of transcription factor 7-like 2 (TCF7L2) gene with type 2 diabetes mellitus (T2DM) risk and further explore the interactions among SNPs, methylation, and environmental factors involved in T2DM risk. METHODS We conducted a nested case-control study with 290 pairs of T2DM cases and matched controls. We genotyped 3 SNPs of TCF7L2 in all included participants and tested 14 CpG loci of TCF7L2 in 76 pairs of cases and controls. Conditional logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (95% CIs) for T2DM risk according to SNPs and methylation of TCF7L2. Multifactor dimensionality reduction (MDR) analysis was used to explore the potential TCF7L2 gene-environment interactions in T2DM risk. RESULTS We found no statistically significant association between the TCF7L2 polymorphisms and T2DM risk. We observed significant positive associations of methylation at CpG5 and CpG7_8 with T2DM risk. For each 1% increase in DNA methylation at CpG5 and CpG7_8, T2DM risk increased 12% (OR 1.12, 95% CI 1.01-1.25) and 32% (OR 1.32, 95% CI 1.07-1.63), respectively. Additionally, MDR analyses identified significant SNP-environment interactions among rs290487, alcohol drinking, and hypertension and methylation-environment interactions among CpG5, CpG7_8 and hypertension (P <0.05). CONCLUSIONS TCF7L2 polymorphisms were not independently associated with T2DM risk. However, TCF7L2 methylation were positively associated with T2DM risk in rural Chinese adults. Interactions among TCF7L2 polymorphisms, TCF7L2 methylation and environmental factors also suggest a possible etiologic pattern for T2DM.
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Affiliation(s)
- Ranran Qie
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Minghui Han
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Shengbing Huang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Quanman Li
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Leilei Liu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Dongdong Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Cheng Cheng
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Dechen Liu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Pei Qin
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Chunmei Guo
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Qionggui Zhou
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Gang Tian
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yanyan Zhang
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Xiaoyan Wu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yuying Wu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yang Li
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Xingjin Yang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yifei Feng
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Fulan Hu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Ming Zhang
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Dongsheng Hu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
| | - Jie Lu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
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Andrade S, Morais T, Sandovici I, Seabra AL, Constância M, Monteiro MP. Adipose Tissue Epigenetic Profile in Obesity-Related Dysglycemia - A Systematic Review. Front Endocrinol (Lausanne) 2021; 12:681649. [PMID: 34290669 PMCID: PMC8288106 DOI: 10.3389/fendo.2021.681649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/26/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Obesity is a major risk factor for dysglycemic disorders, including type 2 diabetes (T2D). However, there is wide phenotypic variation in metabolic profiles. Tissue-specific epigenetic modifications could be partially accountable for the observed phenotypic variability. SCOPE The aim of this systematic review was to summarize the available data on epigenetic signatures in human adipose tissue (AT) that characterize overweight or obesity-related insulin resistance (IR) and dysglycemia states and to identify potential underlying mechanisms through the use of unbiased bioinformatics approaches. METHODS Original data published in the last decade concerning the comparison of epigenetic marks in human AT of individuals with metabolically unhealthy overweight/obesity (MUHO) versus normal weight individuals or individuals with metabolically healthy overweight/obesity (MHO) was assessed. Furthermore, association of these epigenetic marks with IR/dysglycemic traits, including T2D, was compiled. RESULTS We catalogued more than two thousand differentially methylated regions (DMRs; above the cut-off of 5%) in the AT of individuals with MUHO compared to individuals with MHO. These DNA methylation changes were less likely to occur around the promoter regions and were enriched at loci implicated in intracellular signaling (signal transduction mediated by small GTPases, ERK1/2 signaling and intracellular trafficking). We also identified a network of seven transcription factors that may play an important role in targeting DNA methylation changes to specific genes in the AT of subjects with MUHO, contributing to the pathogeny of obesity-related IR/T2D. Furthermore, we found differentially methylated CpG sites at 8 genes that were present in AT and whole blood, suggesting that DMRs in whole blood could be potentially used as accessible biomarkers of MUHO. CONCLUSIONS The overall evidence linking epigenetic alterations in key tissues such AT to metabolic complications in human obesity is still very limited, highlighting the need for further studies, particularly those focusing on epigenetic marks other than DNA methylation. Our initial analysis suggests that DNA methylation patterns can potentially discriminate between MUHO from MHO and provide new clues into why some people with obesity are less susceptible to dysglycemia. Identifying AT-specific epigenetic targets could also lead to novel approaches to modify the progression of individuals with obesity towards metabolic disease. SYSTEMATIC REVIEW REGISTRATION PROSPERO, identifier CRD42021227237.
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Affiliation(s)
- Sara Andrade
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Tiago Morais
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Ionel Sandovici
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre L. Seabra
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Miguel Constância
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- National Institute of Health Research, Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Mariana P. Monteiro
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- *Correspondence: Mariana P. Monteiro,
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Sharma NK, Comeau ME, Montoya D, Pellegrini M, Howard TD, Langefeld CD, Das SK. Integrative Analysis of Glucometabolic Traits, Adipose Tissue DNA Methylation, and Gene Expression Identifies Epigenetic Regulatory Mechanisms of Insulin Resistance and Obesity in African Americans. Diabetes 2020; 69:2779-2793. [PMID: 32928872 PMCID: PMC7679782 DOI: 10.2337/db20-0117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022]
Abstract
Decline in insulin sensitivity due to dysfunction of adipose tissue (AT) is one of the earliest pathogenic events in type 2 diabetes. We hypothesize that differential DNA methylation (DNAm) controls insulin sensitivity and obesity by modulating transcript expression in AT. Integrating AT DNAm profiles with transcript profile data measured in a cohort of 230 African Americans (AAs) from the African American Genetics of Metabolism and Expression cohort, we performed cis-expression quantitative trait methylation (cis-eQTM) analysis to identify epigenetic regulatory loci for glucometabolic trait-associated transcripts. We identified significantly associated cytosine-guanine dinucleotide regions for 82 transcripts (false discovery rate [FDR]-P < 0.05). The strongest eQTM locus was observed for the proopiomelanocortin (POMC; ρ = -0.632, P = 4.70 × 10-27) gene. Epigenome-wide association studies (EWAS) further identified 155, 46, and 168 cytosine-guanine dinucleotide regions associated (FDR-P < 0.05) with the Matsuda index, SI, and BMI, respectively. Intersection of EWAS, transcript level to trait association, and eQTM results, followed by causal inference test identified significant eQTM loci for 23 genes that were also associated with Matsuda index, SI, and/or BMI in EWAS. These associated genes include FERMT3, ITGAM, ITGAX, and POMC In summary, applying an integrative multiomics approach, our study provides evidence for DNAm-mediated regulation of gene expression at both previously identified and novel loci for many key AT transcripts influencing insulin resistance and obesity.
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Affiliation(s)
- Neeraj K Sharma
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC
| | - Mary E Comeau
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Dennis Montoya
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Timothy D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Swapan K Das
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC
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Xu S, Shi Q, Li B, Han L, Xu G, Peng X, Chen H, Dai S, Ma W, Wang C, Ma J. High MTHFR promoter methylation levels in men confer protection against ischemic stroke. Bosn J Basic Med Sci 2020; 20:477-486. [PMID: 32358951 PMCID: PMC7664794 DOI: 10.17305/bjbms.2020.4636] [Citation(s) in RCA: 5] [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: 02/04/2020] [Accepted: 04/29/2020] [Indexed: 02/05/2023] Open
Abstract
The MTHFR gene encodes methylenetetrahydrofolate reductase required for the metabolism of homocysteine (Hcy) - a previously reported independent risk factor for ischemic stroke (IS). In this study, we first aimed to clarify the association between DNA methylation levels in the MTHFR promoter and the risk of IS, followed by the analysis of potential interactions between environmental factors and DNA methylation levels that affect IS risk. We recruited 164 patients with hypertension and IS (case group) and 345 age-matched and sex-matched patients with hypertension only (control group). Demographic and clinical information was obtained using questionnaires, and blood samples were collected for biochemical analyses. Fluorescence quantitative methylation-specific PCR (qMSP) was used to detect MTHFR promoter methylation levels. A logistic regression analysis was performed to determine the relationship between environmental factors, MTHFR promoter methylation levels, and IS risk. We finally generated a receiver operating characteristic curve to determine whether MTHFR promoter methylation levels can predict IS. The mean MTHFR methylation levels in the case group (8.10 ± 6.14) were significantly lower than those in the control group (17.44 ± 3.16; p < 0.05). MTHFR promoter methylation levels were also lower in patients with plasma Hcy levels ≥15 μmol/L (10.65 ± 4.05) than in those with Hcy levels <15 μmol/L (16.74 ± 4.26, p < 0.001). Finally, we found that MTHFR hypermethylation is a protective factor for IS, particular in men (OR in men: 0.07; 95% CI: 0.02-0.16; p < 0.001). Further, sex and MTHFR promoter methylation levels exhibited a preliminary interaction effect on IS risk. These results indicate that MTHFR promoter methylation status might have diagnostic value in IS.
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Affiliation(s)
- Shan Xu
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Qianping Shi
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
| | - Bo Li
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Liyuan Han
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Guodong Xu
- Medical Record Statistics Room, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Xiaolin Peng
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Hongen Chen
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Shuhong Dai
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Wancheng Ma
- Luohu Center for Chronic Disease Control, Shenzhen, China
| | - Changyi Wang
- Nanshan Center for Chronic Disease Control, Shenzhen, China
- Corresponding authors: Changyi Wang and Jianping Ma, Nanshan Center for Chronic Disease Control, 5 Huaming Road, Shenzhen, China. E-mail:
| | - Jianping Ma
- Nanshan Center for Chronic Disease Control, Shenzhen, China
- Corresponding authors: Changyi Wang and Jianping Ma, Nanshan Center for Chronic Disease Control, 5 Huaming Road, Shenzhen, China. E-mail:
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Preliminary indications that the Attachment and Biobehavioral Catch-up Intervention alters DNA methylation in maltreated children. Dev Psychopathol 2020; 32:1486-1494. [PMID: 31854285 DOI: 10.1017/s0954579419001421] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Maltreatment during development is associated with epigenetic changes to the genome. Enhancing caregiving may mitigate these effects. Attachment and Biobehavioral Catch-Up (ABC) is an intervention that has been shown to improve parent-child relationships and a variety of biological and behavioral outcomes among children that are involved in Child Protective Services. This preliminary study, using a small sample size, explored whether children who received ABC exhibit different methylation patterns than those who received a control intervention. The participants included 23 children aged 6-21 months who were randomized to receive ABC (n = 12) or a control intervention (n = 11). While the children displayed similar methylation patterns preintervention, DNA methylation varied between the ABC and control groups at 14,828 sites postintervention. Functional pathway analyses indicated that these differences were associated with gene pathways that are involved in cell signaling, metabolism, and neuronal development. This study is one of the first to explore parenting intervention effects on children's DNA methylation at the whole genome level in infancy. These preliminary findings provide a basis for hypothesis generation in further research with larger-scale studies regarding the malleability of epigenetic states that are associated with maltreatment.
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Chen YT, Lin WD, Liao WL, Tsai YC, Liao JW, Tsai FJ. NT5C2 methylation regulatory interplay between DNMT1 and insulin receptor in type 2 diabetes. Sci Rep 2020; 10:16087. [PMID: 32999320 PMCID: PMC7527562 DOI: 10.1038/s41598-020-71336-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 08/12/2020] [Indexed: 11/29/2022] Open
Abstract
Epigenetics alternation of non-genetic variation and genome-wide association study proven allelic variants may associate with insulin secretion in type 2 diabetes (T2D) development. We analyzed promoter DNA methylation array to evaluate the associated with increased susceptibility to T2D (30 cases, 10 controls) and found 1,091 gene hypermethylated in promoter regions. We performed the association study of T2D and found 698 single nucleotide polymorphisms in exon and promoter sites by using 2,270 subjects (560 cases, 1,710 controls). A comparison of DNA hypermethylation and gene silencing of mouse T2D results in our T2D patients’ results showed that the 5′-nucleotidase, cytosolic II (NT5C2) and fucosyltransferase 8 (FUT8) genes were strongly associated with increased susceptibility to T2D. DNA hypermethylation in promoter regions reduced NT5C2 gene expression, but not FUT8 in T2D patients. NT5C2 protein expression was decreased in pancreatic β-cells from T2D mice. Transient transfection NT5C2 into RIN-m5F cells down-regulated DNA methyltransferase I (DNMT1) expression and up-regulation of the insulin receptor. Moreover, NT5C2 knockdown induced in DNMT1 overexpression and insulin receptor inhibition. Taken together, these results showed that NT5C2 epigenetically regulated insulin receptor in patients and mice with T2D, and maybe provide for T2D therapy strategy.
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Affiliation(s)
- Yng-Tay Chen
- Graduate Institute of Food Safety, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.
| | - Wei-De Lin
- Human Genetic Center, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.,School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.,Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ya-Ching Tsai
- Human Genetic Center, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Jiunn-Wang Liao
- Graduate Institute of Veterinary Pathobiology, National Chung Hsing University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Human Genetic Center, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan. .,School of Chinese Medicine, China Medical University, Taichung, Taiwan. .,Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan.
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Kucher AN. The FTO Gene and Diseases: The Role of Genetic Polymorphism, Epigenetic Modifications, and Environmental Factors. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420090136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Lecamwasam A, Ekinci EI, Saffery R, Dwyer KM. Potential for Novel Biomarkers in Diabetes-Associated Chronic Kidney Disease: Epigenome, Metabolome, and Gut Microbiome. Biomedicines 2020; 8:E341. [PMID: 32927866 PMCID: PMC7555227 DOI: 10.3390/biomedicines8090341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022] Open
Abstract
Diabetes-associated chronic kidney disease is a pandemic issue. Despite the global increase in the number of individuals with this chronic condition together with increasing morbidity and mortality, there are currently only limited therapeutic options to slow disease progression. One of the reasons for this is that the current-day "gold standard" biomarkers lack adequate sensitivity and specificity to detect early diabetic chronic kidney disease (CKD). This review focuses on the rapidly evolving areas of epigenetics, metabolomics, and the gut microbiome as potential sources of novel biomarkers in diabetes-associated CKD and discusses their relevance to clinical practice. However, it also highlights the problems associated with many studies within these three areas-namely, the lack of adequately powered longitudinal studies, and the lack of reproducibility of results which impede biomarker development and clinical validation in this complex and susceptible population.
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Affiliation(s)
- Ashani Lecamwasam
- Epigenetics Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Endocrinology, Austin Health, Ivanhoe, VIC 3079, Australia;
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds, VIC 3220, Australia;
| | - Elif I. Ekinci
- Department of Endocrinology, Austin Health, Ivanhoe, VIC 3079, Australia;
- Department of Medicine, University of Melbourne, Parkville, VIC 3010, Australia
| | - Richard Saffery
- Epigenetics Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Karen M. Dwyer
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds, VIC 3220, Australia;
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42
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Geurtsen ML, Jaddoe VWV, Gaillard R, Felix JF. Associations of maternal early-pregnancy blood glucose and insulin concentrations with DNA methylation in newborns. Clin Epigenetics 2020; 12:134. [PMID: 32894192 PMCID: PMC7487846 DOI: 10.1186/s13148-020-00924-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/25/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Intrauterine exposure to a disturbed maternal glucose metabolism is associated with adverse offspring outcomes. DNA methylation is a potential mechanism underlying these associations. We examined whether maternal early-pregnancy glucose and insulin concentrations are associated with newborn DNA methylation. In a population-based prospective cohort study among 935 pregnant women, maternal plasma concentrations of non-fasting glucose and insulin were measured at a median of 13.1 weeks of gestation (95% range 9.4-17.4). DNA methylation was measured using the Infinium HumanMethylation450 BeadChip (Ilumina). We analyzed associations of maternal early-pregnancy glucose and insulin concentrations with single-CpG DNA methylation using robust linear regression models. Differentially methylated regions were analyzed using the dmrff package in R. We stratified the analyses on normal weight versus overweight or obese women. We also performed a look-up of CpGs and differently methylated regions from previous studies to be associated with maternal gestational diabetes, hyperglycemia or hyperinsulinemia, or with type 2 diabetes in adults. RESULTS Maternal early-pregnancy glucose and insulin concentrations were not associated with DNA methylation at single CpGs nor with differentially methylated regions in the total group. In analyses stratified on maternal BMI, maternal early-pregnancy glucose concentrations were associated with DNA methylation at one CpG (cg03617420, XKR6) among normal weight women and at another (cg12081946, IL17D) among overweight or obese women. No stratum-specific associations were found for maternal early-pregnancy insulin concentrations. The two CpGs were not associated with birth weight or childhood glycemic measures (p values > 0.1). Maternal early-pregnancy insulin concentrations were associated with one CpG known to be related to adult type 2 diabetes. Enrichment among nominally significant findings in our maternal early-pregnancy glucose concentrations was found for CpGs identified in a previous study on adult type 2 diabetes. CONCLUSIONS Maternal early-pregnancy glucose concentrations, but not insulin concentrations, were associated with DNA methylation at one CpG each in the subgroups of normal weight and of overweight or obese women. No associations were present in the full group. The role of these CpGs in mechanisms underlying offspring health outcomes needs further study. Future studies should replicate our results in larger samples with early-pregnancy information on maternal fasting glucose metabolism.
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Affiliation(s)
- Madelon L Geurtsen
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000, CA, Rotterdam, The Netherlands.
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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de la Rocha C, Zaina S, Lund G. Is Any Cardiovascular Disease-Specific DNA Methylation Biomarker Within Reach? Curr Atheroscler Rep 2020; 22:62. [DOI: 10.1007/s11883-020-00875-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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44
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Wang LJ, Han X, Qiu JG, Jiang B, Zhang CY. Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level. Chem Sci 2020; 11:9675-9684. [PMID: 34094232 PMCID: PMC8161687 DOI: 10.1039/d0sc03240a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/25/2020] [Indexed: 12/28/2022] Open
Abstract
DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3-signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10-3 U mL-1 for M.SssI MTase and 3.39 × 10-3 U mL-1 for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
| | - Xiao Han
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - BingHua Jiang
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
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45
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New Mechanisms of Vascular Dysfunction in Cardiometabolic Patients: Focus on Epigenetics. High Blood Press Cardiovasc Prev 2020; 27:363-371. [PMID: 32740853 DOI: 10.1007/s40292-020-00400-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/21/2020] [Indexed: 12/28/2022] Open
Abstract
Epigenetic processing takes centre stage in cardiometabolic diseases (obesity, metabolic syndrome, type 2 diabetes, hypertension), where it participates in adiposity, inflammation, endothelial dysfunction, vascular insulin resistance and atherosclerosis. Epigenetic modifications, defined as heritable changes in gene expression that do not entail mutation in the DNA sequence, are mainly induced by environmental stimuli (stress, pollution, cigarette smoking) and are gaining considerable interest due to their causal role in cardiovascular disease, and their amenability to pharmacological intervention. Importantly, epigenetic modifications acquired during life can be transmitted to the offspring and exert their biological effects across multiple generations. Indeed, such transgenerational transmission of epigenetic signals may contribute to anticipating cardiovascular and metabolic disease phenotypes already in children and young adults. A deeper understanding of environmental factors and their effects on the epigenetic machinery and transcriptional programs is warranted to develop effective mechanism-based therapeutic strategies. The clinical application of epigenetic drugs-also known as "epi-drugs"-is currently exploding in the field of cardiovascular disease. The present review describes the main epigenetic networks underlying cardiometabolic alterations and sheds light on specific points of intervention for pharmacological reprogramming in this setting.
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Chen Z, Miao F, Braffett BH, Lachin JM, Zhang L, Wu X, Roshandel D, Carless M, Li XA, Tompkins JD, Kaddis JS, Riggs AD, Paterson AD, Natarajan R. DNA methylation mediates development of HbA1c-associated complications in type 1 diabetes. Nat Metab 2020; 2:744-762. [PMID: 32694834 PMCID: PMC7590966 DOI: 10.1038/s42255-020-0231-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/29/2020] [Indexed: 01/09/2023]
Abstract
Metabolic memory, the persistent benefits of early glycaemic control on preventing and/or delaying the development of diabetic complications, has been observed in the Diabetes Control and Complications Trial (DCCT) and in the Epidemiology of Diabetes Interventions and Complications (EDIC) follow-up study, but the underlying mechanisms remain unclear. Here, we show the involvement of epigenetic DNA methylation (DNAme) in metabolic memory by examining its associations with preceding glycaemic history, and with subsequent development of complications over an 18-yr period in the blood DNA of 499 randomly selected DCCT participants with type 1 diabetes who are also followed up in EDIC. We demonstrate the associations between DNAme near the closeout of DCCT and mean HbA1c during DCCT (mean-DCCT HbA1c) at 186 cytosine-guanine dinucleotides (CpGs) (FDR < 15%, including 43 at FDR < 5%), many of which were located in genes related to complications. Exploration studies into biological function reveal that these CpGs are enriched in binding sites for the C/EBP transcription factor, as well as enhancer/transcription regions in blood cells and haematopoietic stem cells, and open chromatin states in myeloid cells. Mediation analyses show that, remarkably, several CpGs in combination explain 68-97% of the association of mean-DCCT HbA1c with the risk of complications during EDIC. In summary, DNAme at key CpGs appears to mediate the association between hyperglycaemia and complications in metabolic memory, through modifying enhancer activity at myeloid and other cells.
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Affiliation(s)
- Zhuo Chen
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Feng Miao
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Barbara H Braffett
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - John M Lachin
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - Lingxiao Zhang
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melanie Carless
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Xuejun Arthur Li
- Biostatistics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Joshua D Tompkins
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - John S Kaddis
- Department of Diabetes Immunology, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Department of Diabetes and Cancer Discovery Science, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Arthur D Riggs
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Andrew D Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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Ahmed SAH, Ansari SA, Mensah-Brown EPK, Emerald BS. The role of DNA methylation in the pathogenesis of type 2 diabetes mellitus. Clin Epigenetics 2020; 12:104. [PMID: 32653024 PMCID: PMC7353744 DOI: 10.1186/s13148-020-00896-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Diabetes mellitus (DM) is a chronic condition characterised by β cell dysfunction and persistent hyperglycaemia. The disorder can be due to the absence of adequate pancreatic insulin production or a weak cellular response to insulin signalling. Among the three types of DM, namely, type 1 DM (T1DM), type 2 DM (T2DM), and gestational DM (GDM); T2DM accounts for almost 90% of diabetes cases worldwide. Epigenetic traits are stably heritable phenotypes that result from certain changes that affect gene function without altering the gene sequence. While epigenetic traits are considered reversible modifications, they can be inherited mitotically and meiotically. In addition, epigenetic traits can randomly arise in response to environmental factors or certain genetic mutations or lesions, such as those affecting the enzymes that catalyse the epigenetic modification. In this review, we focus on the role of DNA methylation, a type of epigenetic modification, in the pathogenesis of T2DM.
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Affiliation(s)
- Sanabil Ali Hassan Ahmed
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Eric P K Mensah-Brown
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates.
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Guo G, Wang H, Shi X, Ye L, Yan K, Chen Z, Zhang H, Jin Z, Xue X. Disease Activity-Associated Alteration of mRNA m 5 C Methylation in CD4 + T Cells of Systemic Lupus Erythematosus. Front Cell Dev Biol 2020; 8:430. [PMID: 32582707 PMCID: PMC7291606 DOI: 10.3389/fcell.2020.00430] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/08/2020] [Indexed: 01/17/2023] Open
Abstract
Epigenetic processes including RNA methylation, post-translational modifications, and non-coding RNA expression have been associated with the heritable risks of systemic lupus erythematosus (SLE). In this study, we aimed to explore the dysregulated expression of 5-methylcytosine (m5C) in CD4+ T cells from patients with SLE and the potential function of affected mRNAs in SLE pathogenesis. mRNA methylation profiles were ascertained through chromatography-coupled triple quadrupole mass spectrometry in CD4+ T cells from two pools of patients with SLE exhibiting stable activity, two pools with moderate-to-major activity, and two pools of healthy controls (HCs). Simultaneously, mRNA methylation profiles and expression profiling were performed using RNA-Bis-Seq and RNA-Seq, respectively. Integrated mRNA methylation and mRNA expression bioinformatics analysis was comprehensively performed. mRNA methyltransferase NSUN2 expression was validated in CD4+ T cells from 27 patients with SLE and 28 HCs using real-time polymerase chain reaction and western blot analyses. Hypomethylated-mRNA profiles of NSUN2-knockdown HeLa cells and of CD4+ T cells of patients with SLE were jointly analyzed using bioinformatics. Eleven methylation modifications (including elevated Am, 3′OMeA, m1A, and m6A and decreased Ψ, m3C, m1G, m5U, and t6A levels) were detected in CD4+ T cells of patients with SLE. Additionally, decreased m5C levels, albeit increased number of m5C-containing mRNAs, were observed in CD4+ T cells of patients with SLE compared with that in CD4+ T cells of HCs. m5C site distribution in mRNA transcripts was highly conserved and enriched in mRNA translation initiation sites. In particular, hypermethylated m5C or/and significantly up-regulated genes in SLE were significantly involved in immune-related and inflammatory pathways, including immune system, cytokine signaling pathway, and interferon signaling. Compared to that in HCs, NSUN2 expression was significantly lower in SLE CD4+ T cells. Notably, hypomethylated m5C genes in SLE and in NSUN2-knockdown HeLa cells revealed linkage between eukaryotic translation elongation and termination, and mRNA metabolism. Our study identified novel aberrant m5C mRNAs relevant to critical immune pathways in CD4+ T cells from patients with SLE. These data provide valuable perspectives for future studies of the multifunctionality and post-transcriptional significance of mRNA m5C modification in SLE.
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Affiliation(s)
- Gangqiang Guo
- School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huijing Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xinyu Shi
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Gynecologic Oncology, Wenzhou Central Hospital, Wenzhou, China
| | - Kejing Yan
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhiyuan Chen
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zibing Jin
- Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
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49
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Sexually dimorphic DNA-methylation in cardiometabolic health: A systematic review. Maturitas 2020; 135:6-26. [DOI: 10.1016/j.maturitas.2020.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
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50
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Evans LW, Stratton MS, Ferguson BS. Dietary natural products as epigenetic modifiers in aging-associated inflammation and disease. Nat Prod Rep 2020; 37:653-676. [PMID: 31993614 PMCID: PMC7577396 DOI: 10.1039/c9np00057g] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2020Chronic, low-grade inflammation is linked to aging and has been termed "inflammaging". Inflammaging is considered a key contributor to the development of metabolic dysfunction and a broad spectrum of diseases or disorders including declines in brain and heart function. Genome-wide association studies (GWAS) coupled with epigenome-wide association studies (EWAS) have shown the importance of diet in the development of chronic and age-related diseases. Moreover, dietary interventions e.g. caloric restriction can attenuate inflammation to delay and/or prevent these diseases. Common themes in these studies entail the use of phytochemicals (plant-derived compounds) or the production of short chain fatty acids (SCFAs) as epigenetic modifiers of DNA and histone proteins. Epigenetic modifications are dynamically regulated and as such, serve as potential therapeutic targets for the treatment or prevention of age-related disease. In this review, we will focus on the role for natural products that include phytochemicals and short chain fatty acids (SCFAs) as regulators of these epigenetic adaptations. Specifically, we discuss regulators of methylation, acetylation and acylation, in the protection from chronic inflammation driven metabolic dysfunction and deterioration of neurocognitive and cardiac function.
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Affiliation(s)
- Levi W Evans
- Department of Nutrition, University of Nevada, Reno, NV 89557, USA.
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