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Melton HJ, Zhang Z, Deng HW, Wu L, Wu C. MIMOSA: a resource consisting of improved methylome prediction models increases power to identify DNA methylation-phenotype associations. Epigenetics 2024; 19:2370542. [PMID: 38963888 PMCID: PMC11225927 DOI: 10.1080/15592294.2024.2370542] [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: 10/06/2023] [Accepted: 06/12/2024] [Indexed: 07/06/2024] Open
Abstract
Although DNA methylation (DNAm) has been implicated in the pathogenesis of numerous complex diseases, from cancer to cardiovascular disease to autoimmune disease, the exact methylation sites that play key roles in these processes remain elusive. One strategy to identify putative causal CpG sites and enhance disease etiology understanding is to conduct methylome-wide association studies (MWASs), in which predicted DNA methylation that is associated with complex diseases can be identified. However, current MWAS models are primarily trained using the data from single studies, thereby limiting the methylation prediction accuracy and the power of subsequent association studies. Here, we introduce a new resource, MWAS Imputing Methylome Obliging Summary-level mQTLs and Associated LD matrices (MIMOSA), a set of models that substantially improve the prediction accuracy of DNA methylation and subsequent MWAS power through the use of a large summary-level mQTL dataset provided by the Genetics of DNA Methylation Consortium (GoDMC). Through the analyses of GWAS (genome-wide association study) summary statistics for 28 complex traits and diseases, we demonstrate that MIMOSA considerably increases the accuracy of DNA methylation prediction in whole blood, crafts fruitful prediction models for low heritability CpG sites, and determines markedly more CpG site-phenotype associations than preceding methods. Finally, we use MIMOSA to conduct a case study on high cholesterol, pinpointing 146 putatively causal CpG sites.
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Affiliation(s)
- Hunter J. Melton
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Zichen Zhang
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Lang Wu
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Chong Wu
- Cancer Epidemiology Division, University of Hawaii Cancer Center, Honolulu, HI, USA
- Institute for Data Science in Oncology, The UT MD Anderson Cancer Center
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Janez A, Muzurovic E, Bogdanski P, Czupryniak L, Fabryova L, Fras Z, Guja C, Haluzik M, Kempler P, Lalic N, Mullerova D, Stoian AP, Papanas N, Rahelic D, Silva-Nunes J, Tankova T, Yumuk V, Rizzo M. Modern Management of Cardiometabolic Continuum: From Overweight/Obesity to Prediabetes/Type 2 Diabetes Mellitus. Recommendations from the Eastern and Southern Europe Diabetes and Obesity Expert Group. Diabetes Ther 2024; 15:1865-1892. [PMID: 38990471 DOI: 10.1007/s13300-024-01615-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
The increasing global incidence of obesity and type 2 diabetes mellitus (T2D) underscores the urgency of addressing these interconnected health challenges. Obesity enhances genetic and environmental influences on T2D, being not only a primary risk factor but also exacerbating its severity. The complex mechanisms linking obesity and T2D involve adiposity-driven changes in β-cell function, adipose tissue functioning, and multi-organ insulin resistance (IR). Early detection and tailored treatment of T2D and obesity are crucial to mitigate future complications. Moreover, personalized and early intensified therapy considering the presence of comorbidities can delay disease progression and diminish the risk of cardiorenal complications. Employing combination therapies and embracing a disease-modifying strategy are paramount. Clinical trials provide evidence confirming the efficacy and safety of glucagon-like peptide 1 receptor agonists (GLP-1 RAs). Their use is associated with substantial and durable body weight reduction, exceeding 15%, and improved glucose control which further translate into T2D prevention, possible disease remission, and improvement of cardiometabolic risk factors and associated complications. Therefore, on the basis of clinical experience and current evidence, the Eastern and Southern Europe Diabetes and Obesity Expert Group recommends a personalized, polymodal approach (comprising GLP-1 RAs) tailored to individual patient's disease phenotype to optimize diabetes and obesity therapy. We also expect that the increasing availability of dual GLP-1/glucose-dependent insulinotropic polypeptide (GIP) agonists will significantly contribute to the modern management of the cardiometabolic continuum.
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Affiliation(s)
- Andrej Janez
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia.
| | - Emir Muzurovic
- Department of Internal Medicine, Endocrinology Section, Clinical Centre of Montenegro, Faculty of Medicine, University of Montenegro, Podgorica, Montenegro
| | - Pawel Bogdanski
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, University of Medical Sciences, Poznan, Poland
| | - Leszek Czupryniak
- Department of Diabetology and Internal Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Lubomira Fabryova
- MetabolKLINIK sro, Department for Diabetes and Metabolic Disorders, Lipid Clinic, MED PED Centre, Biomedical Research Centre of Slovak Academy of Sciences, Slovak Health University, Bratislava, Slovak Republic
| | - Zlatko Fras
- Preventive Cardiology Unit, Division of Medicine, University Medical Centre Ljubljana and Chair of Internal Medicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Cristian Guja
- Clinic of Diabetes, Nutrition and Metabolic Diseases, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Martin Haluzik
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21, Prague 4, Czech Republic
| | - Peter Kempler
- Department of Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Nebojsa Lalic
- Faculty of Medicine, Clinic for Endocrinology, Diabetes and Metabolic Diseases, Clinical Center of Serbia, University of Belgrade, Belgrade, Serbia
| | - Dana Mullerova
- Faculty of Medicine in Pilsen, Department of Public Health and Preventive Medicine and Faculty Hospital in Pilsen, 1st Internal Clinic, Charles University, Pilsen, Czech Republic
| | - Anca Pantea Stoian
- Diabetes, Nutrition and Metabolic Diseases Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Nikolaos Papanas
- Diabetes Centre, Second Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Dario Rahelic
- Vuk Vrhovac University Clinic for Diabetes, Endocrinology and Metabolic Diseases, Merkur University Hospital, Zagreb, Croatia
- Catholic University of Croatia School of Medicine, Zagreb, Croatia
- Josip Juraj Strossmayer, University of Osijek School of Medicine, Osijek, Croatia
| | - José Silva-Nunes
- NOVA Medical School, New University of Lisbon, Lisbon, Portugal
- Department of Endocrinology, Diabetes and Metabolism, Unidade Local de Saúde São José, Lisbon, Portugal
| | - Tsvetalina Tankova
- Department of Endocrinology, Faculty of Medicine, Medical University, Sofia, Bulgaria
| | - Volkan Yumuk
- Division of Endocrinology, Metabolism and Diabetes, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Manfredi Rizzo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (Promise), School of Medicine, University of Palermo, Palermo, Italy
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3
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Hu Y, Chen J, Li J, Xu Z. Models for depression recognition and efficacy assessment based on clinical and sequencing data. Heliyon 2024; 10:e33973. [PMID: 39130405 PMCID: PMC11315137 DOI: 10.1016/j.heliyon.2024.e33973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 08/13/2024] Open
Abstract
Major depression is a complex psychiatric disorder that includes genetic, neurological, and cognitive factors. Early detection and intervention can prevent progression, and help select the best treatment. Traditional clinical diagnosis tends to be subjective and misdiagnosed. Based on this, this study leverages clinical scale assessments and sequencing data to construct disease prediction models. Firstly, data undergoes preprocessing involving normalization and other requisite procedures. Feature engineering is then applied to curate subsets of features, culminating in the construction of a model through the implementation of machine learning and deep learning algorithms. In this study, 18 features with significant differences between patients and healthy controls were selected. The depression recognition model was constructed by deep learning with an accuracy of 87.26 % and an AUC of 91.56 %, which can effectively distinguish patients with depression from healthy controls. In addition, 33 features selected by recursive feature elimination method were used to construct a prognostic effect model of patients after 2 weeks of treatment, with an accuracy of 75.94 % and an AUC of 83.33 %. The results show that the deep learning algorithm based on clinical and sequencing data has good accuracy and provides an objective and accurate method for the diagnosis and pharmacodynamic prediction of depression. Furthermore, the selected differential features can serve as candidate biomarkers to provide valuable clues for diagnosis and efficacy prediction.
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Affiliation(s)
- Yunyun Hu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, China
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, China
| | - Zhi Xu
- Department of Psychosomatics and Psychiatry, Zhongda Hospital, School of Medicine, Jiangsu Provincial Key Laboratory of Brain Science and Medicine, Southeast University, Nanjing, 210009, China
- Research and Education Centre of General Practice, Zhongda Hospital, Southeast University, Nanjing, 210009, China
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Seo S, Kim YA, Lee Y, Kim YJ, Kim BJ, An JH, Jin H, Do AR, Park K, Won S, Seo JH. Epigenetic link between Agent Orange exposure and type 2 diabetes in Korean veterans. Front Endocrinol (Lausanne) 2024; 15:1375459. [PMID: 39072272 PMCID: PMC11272593 DOI: 10.3389/fendo.2024.1375459] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
Conflicting findings have been reported regarding the association between Agent Orange (AO) exposure and type 2 diabetes. This study aimed to examine whether AO exposure is associated with the development of type 2 diabetes and to verify the causal relationship between AO exposure and type 2 diabetes by combining DNA methylation with DNA genotype analyses. An epigenome-wide association study and DNA genotype analyses of the blood of AO-exposed and AO-unexposed individuals with type 2 diabetes and that of healthy controls were performed. Methylation quantitative trait locus and Mendelian randomisation analyses were performed to evaluate the causal effect of AO-exposure-identified CpGs on type 2 diabetes. AO-exposed individuals with type 2 diabetes were associated with six hypermethylated CpG sites (cg20075319, cg21757266, cg05203217, cg20102280, cg26081717, and cg21878650) and one hypo-methylated CpG site (cg07553761). Methylation quantitative trait locus analysis showed the methylation levels of some CpG sites (cg20075319, cg20102280, and cg26081717) to be significantly different. Mendelian randomisation analysis showed that CpG sites that were differentially methylated in AO-exposed individuals were causally associated with type 2 diabetes; the reverse causal effect was not significant. These findings reflect the need for further epigenetic studies on the causal relationship between AO exposure and type 2 diabetes.
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Affiliation(s)
- Sujin Seo
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Ye An Kim
- Division of Endocrinology, Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Young Lee
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Republic of Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae Hoon An
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Heejin Jin
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyungtaek Park
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Sungho Won
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, Republic of Korea
| | - Je Hyun Seo
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
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Wu Y, Chen W, Zhao Y, Gu M, Gao Y, Ke Y, Wang L, Wang M, Zhang W, Chen Y, Huo W, Fu X, Li X, Zhang D, Qin P, Hu F, Liu Y, Sun X, Zhang M, Hu D. Visit to visit transition in TXNIP gene methylation and the risk of type 2 diabetes mellitus: a nested case-control study. J Hum Genet 2024; 69:311-319. [PMID: 38528048 DOI: 10.1038/s10038-024-01243-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 03/27/2024]
Abstract
Our study aimed to investigate the association between the transition of the TXNIP gene methylation level and the risk of incident type 2 diabetes mellitus (T2DM). This study included 263 incident cases of T2DM and 263 matched non-T2DM participants. According to the methylation levels of five loci (CpG1-5; chr1:145441102-145442001) on the TXNIP gene, the participants were classified into four transition groups: maintained low, low to high, high to low, and maintained high methylation levels. Compared with individuals whose methylation level of CpG2-5 at the TXNIP gene was maintained low, individuals with maintained high methylation levels showed a 61-87% reduction in T2DM risk (66% for CpG2 [OR: 0.34, 95% CI: 0.14, 0.80]; 77% for CpG3 [OR: 0.23, 95% CI: 0.07, 0.78]; 87% for CpG4 [OR: 0.13, 95% CI: 0.03, 0.56]; and 61% for CpG5 [OR: 0.39, 95% CI: 0.16, 0.92]). Maintained high methylation levels of four loci of the TXNIP gene are associated with a reduction of T2DM incident risk in the current study. Our study suggests that preserving hypermethylation levels of the TXNIP gene may hold promise as a potential preventive measure against the onset of T2DM.
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Affiliation(s)
- Yuying Wu
- Department of General Practice, Affiliated Luohu Hospital of Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China
| | - Weiling Chen
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Medical School, 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
| | - Minqi Gu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China
| | - Yajuan Gao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yamin Ke
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Longkang Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Mengmeng Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Wenkai Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yaobing Chen
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Weifeng Huo
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xueru Fu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xi Li
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Dongdong Zhang
- Department of General Practice, Affiliated Luohu Hospital of Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China
| | - Pei Qin
- Department of Medical Record Management, Shenzhen Qianbai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Fulan Hu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China
| | - Yu Liu
- Department of General Practice, Affiliated Luohu Hospital of Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China
| | - Xizhuo Sun
- Department of General Practice, Affiliated Luohu Hospital of Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China
| | - Ming Zhang
- Department of General Practice, Affiliated Luohu Hospital of Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China
| | - Dongsheng Hu
- Department of General Practice, Affiliated Luohu Hospital of Shenzhen University Medical School, Shenzhen, Guangdong, People's Republic of China.
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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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Agyemang C, van der Linden EL, Chilunga F, van den Born BH. International Migration and Cardiovascular Health: Unraveling the Disease Burden Among Migrants to North America and Europe. J Am Heart Assoc 2024; 13:e030228. [PMID: 38686900 PMCID: PMC11179927 DOI: 10.1161/jaha.123.030228] [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: 07/03/2023] [Accepted: 12/26/2023] [Indexed: 05/02/2024]
Abstract
Europe and North America are the 2 largest recipients of international migrants from low-resource regions in the world. Here, large differences in cardiovascular disease (CVD) morbidity and death exist between migrants and the host populations. This review discusses the CVD burden and its most important contributors among the largest migrant groups in Europe and North America as well as the consequences of migration to high-income countries on CVD diagnosis and therapy. The available evidence indicates that migrants in Europe and North America generally have a higher CVD risk compared with the host populations. Cardiometabolic, behavioral, and psychosocial factors are important contributors to their increased CVD risk. However, despite these common denominators, there are important ethnic differences in the propensity to develop CVD that relate to pre- and postmigration factors, such as socioeconomic status, cultural factors, lifestyle, psychosocial stress, access to health care and health care usage. Some of these pre- and postmigration environmental factors may interact with genetic (epigenetics) and microbial factors, which further influence their CVD risk. The limited number of prospective cohorts and clinical trials in migrant populations remains an important culprit for better understanding pathophysiological mechanism driving health differences and for developing ethnic-specific CVD risk prediction and care. Only by improved understanding of the complex interaction among human biology, migration-related factors, and sociocultural determinants of health influencing CVD risk will we be able to mitigate these differences and truly make inclusive personalized treatment possible.
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Affiliation(s)
- Charles Agyemang
- Department of Public and Occupational Health, Amsterdam UMCUniversity of Amsterdam, Amsterdam Public Health Research InstituteAmsterdamThe Netherlands
- Division of Endocrinology, Diabetes, and Metabolism, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Eva L. van der Linden
- Department of Public and Occupational Health, Amsterdam UMCUniversity of Amsterdam, Amsterdam Public Health Research InstituteAmsterdamThe Netherlands
- Department of Vascular Medicine, Amsterdam UMCUniversity of Amsterdam, Amsterdam Cardiovascular SciencesAmsterdamThe Netherlands
| | - Felix Chilunga
- Department of Public and Occupational Health, Amsterdam UMCUniversity of Amsterdam, Amsterdam Public Health Research InstituteAmsterdamThe Netherlands
| | - Bert‐Jan H. van den Born
- Department of Public and Occupational Health, Amsterdam UMCUniversity of Amsterdam, Amsterdam Public Health Research InstituteAmsterdamThe Netherlands
- Department of Vascular Medicine, Amsterdam UMCUniversity of Amsterdam, Amsterdam Cardiovascular SciencesAmsterdamThe Netherlands
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9
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Christiansen C, Potier L, Martin TC, Villicaña S, Castillo-Fernandez JE, Mangino M, Menni C, Tsai PC, Campbell PJ, Mullin S, Ordoñana JR, Monteagudo O, Sachdev PS, Mather KA, Trollor JN, Pietilainen KH, Ollikainen M, Dalgård C, Kyvik K, Christensen K, van Dongen J, Willemsen G, Boomsma DI, Magnusson PKE, Pedersen NL, Wilson SG, Grundberg E, Spector TD, Bell JT. Enhanced resolution profiling in twins reveals differential methylation signatures of type 2 diabetes with links to its complications. EBioMedicine 2024; 103:105096. [PMID: 38574408 PMCID: PMC11004697 DOI: 10.1016/j.ebiom.2024.105096] [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: 05/22/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) susceptibility is influenced by genetic and environmental factors. Previous findings suggest DNA methylation as a potential mechanism in T2D pathogenesis and progression. METHODS We profiled DNA methylation in 248 blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. FINDINGS We find and replicate 3 previously unreported T2D differentially methylated CpG positions (T2D-DMPs) at FDR 5% in RGL3, NGB and OTX2, and 20 signals at FDR 25%, of which 14 replicated. Integrating genetic variation and T2D-discordant monozygotic twin analyses, we identify both genetic-based and genetic-independent T2D-DMPs. The signals annotate to genes with established GWAS and EWAS links to T2D and its complications, including blood pressure (RGL3) and eye disease (OTX2). INTERPRETATION The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications. FUNDING Funding acknowledgements for each cohort can be found in the Supplementary Note.
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Affiliation(s)
| | - Louis Potier
- APHP, Paris Cité University, INSERM, Paris, France
| | | | | | | | | | | | - Pei-Chien Tsai
- King's College London, UK; Department of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Purdey J Campbell
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Shelby Mullin
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | | | | | | | | | | | - Kirsi H Pietilainen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Finland; HealthyWeightHub, Abdominal Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Miina Ollikainen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Finland
| | | | | | | | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | | | | | - Scott G Wilson
- King's College London, UK; Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
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10
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Kopfnagel V, Klopp N, Bernemann I, Nizhegorodtseva N, Wilson R, Gronauer R, Seifert M, Illig T. Effects of Repeated Freeze and Thaw Cycles on the Genome-Wide DNA Methylation Profile of Isolated Genomic DNA. Biopreserv Biobank 2024; 22:110-114. [PMID: 37074140 DOI: 10.1089/bio.2022.0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
The characterization of DNA methylation patterns to identify epigenetic markers for complex human diseases is an important and rapidly evolving part in biomedical research. DNA samples collected and stored in clinical biobanks over the past years are an important source for future epigenetic studies. Isolated gDNA is considered stable when stored at low temperatures for several years. However, the effect of multiple use and the associated repeated thawing of long-term stored DNA samples on DNA methylation patterns has not yet been investigated. In this study, we examined the influence of up to 10 freeze and thaw cycles on global DNA methylation by comparing genome-wide methylation profiles. DNA samples from 19 healthy volunteers were either frozen at -80°C or subjected to up to 10 freeze and thaw cycles. Genome-wide DNA methylation was analyzed after 0, 1, 3, 5, or 10 thaw cycles using the Illumina Infinium MethylationEPIC BeadChip. Evaluation of the global DNA methylation profile by beta-value density plots and multidimensional scaling plots revealed an expected clear participant-dependent variability, but a very low variability depending on the freeze and thaw cycles. In accordance, no significant difference in any of the methylated cytosine/guanine sites studied could be detected in the performed statistical analyses. Our results suggest that long-term frozen DNA samples are still suitable for epigenetic studies after multiple thaw cycles.
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Affiliation(s)
- Verena Kopfnagel
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Norman Klopp
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Inga Bernemann
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | | | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
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11
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Feng J, Zhu Z, Zhou R, Liu H, Hu Z, Wu F, Wang H, Yue J, Zhou T, Yang L, Wu F. Differential methylation patterns from clusters associated with glucose metabolism: evidence from a Shanghai twin study. Epigenomics 2024; 16:445-459. [PMID: 38410918 DOI: 10.2217/epi-2023-0449] [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] [Indexed: 02/28/2024] Open
Abstract
Aim: To assess the associations between genome-wide DNA methylation (DNAm) and glucose metabolism among a Chinese population, in particular the multisite correlation. Materials & methods: Epigenome-wide associations with fasting plasma glucose (FPG) and hemoglobin A1c (HbA1c) were analyzed among 100 Shanghai monozygotic (MZ) twin pairs using the Infinium HumanMethylationEPIC v2.0 BeadChip. We conducted a Pearson's correlation test, hierarchical cluster and pairwise analysis to examine the differential methylation patterns from clusters. Results: Cg01358804 (TXNIP) was identified as the most significant site associated with FPG and HbA1c. Two clusters with hypermethylated and hypomethylated patterns were observed for both FPG and HbA1c. Conclusion: Differential methylation patterns from clusters may provide new clues for epigenetic changes and biological mechanisms in glucose metabolism.
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Affiliation(s)
- Jingyuan Feng
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Zhenni Zhu
- Division of Health Risk Factors Monitoring & Control, Shanghai Municipal Center for Disease Control & Prevention, 200336, Shanghai, China
| | - Rongfei Zhou
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Hongwei Liu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Zihan Hu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Fei Wu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Huiting Wang
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Junhong Yue
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Tong Zhou
- Shanghai Precision Medicine Co. Ltd, Shanghai, 201406, China
| | - Li Yang
- Shanghai Precision Medicine Co. Ltd, Shanghai, 201406, China
| | - Fan Wu
- School of Public Health, Fudan University, Shanghai, 200032, China
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12
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Yu G, Tam HCH, Huang C, Shi M, Lim CKP, Chan JCN, Ma RCW. Lessons and Applications of Omics Research in Diabetes Epidemiology. Curr Diab Rep 2024; 24:27-44. [PMID: 38294727 PMCID: PMC10874344 DOI: 10.1007/s11892-024-01533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
PURPOSE OF REVIEW Recent advances in genomic technology and molecular techniques have greatly facilitated the identification of disease biomarkers, advanced understanding of pathogenesis of different common diseases, and heralded the dawn of precision medicine. Much of these advances in the area of diabetes have been made possible through deep phenotyping of epidemiological cohorts, and analysis of the different omics data in relation to detailed clinical information. In this review, we aim to provide an overview on how omics research could be incorporated into the design of current and future epidemiological studies. RECENT FINDINGS We provide an up-to-date review of the current understanding in the area of genetic, epigenetic, proteomic and metabolomic markers for diabetes and related outcomes, including polygenic risk scores. We have drawn on key examples from the literature, as well as our own experience of conducting omics research using the Hong Kong Diabetes Register and Hong Kong Diabetes Biobank, as well as other cohorts, to illustrate the potential of omics research in diabetes. Recent studies highlight the opportunity, as well as potential benefit, to incorporate molecular profiling in the design and set-up of diabetes epidemiology studies, which can also advance understanding on the heterogeneity of diabetes. Learnings from these examples should facilitate other researchers to consider incorporating research on omics technologies into their work to advance the field and our understanding of diabetes and its related co-morbidities. Insights from these studies would be important for future development of precision medicine in diabetes.
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Affiliation(s)
- Gechang Yu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Henry C H Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Cadmon K P Lim
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
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13
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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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14
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Linares-Pineda TM, Fragoso-Bargas N, Picón MJ, Molina-Vega M, Jenum AK, Sletner L, Lee-Ødegård S, Opsahl JO, Moen GH, Qvigstad E, Prasad RB, Birkeland KI, Morcillo S, Sommer C. DNA methylation risk score for type 2 diabetes is associated with gestational diabetes. Cardiovasc Diabetol 2024; 23:68. [PMID: 38350951 PMCID: PMC10865541 DOI: 10.1186/s12933-024-02151-z] [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: 12/14/2023] [Accepted: 02/02/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) and type 2 diabetes mellitus (T2DM) share many pathophysiological factors including genetics, but whether epigenetic marks are shared is unknown. We aimed to test whether a DNA methylation risk score (MRS) for T2DM was associated with GDM across ancestry and GDM criteria. METHODS In two independent pregnancy cohorts, EPIPREG (n = 480) and EPIDG (n = 32), DNA methylation in peripheral blood leukocytes was measured at a gestational age of 28 ± 2. We constructed an MRS in EPIPREG and EPIDG based on CpG hits from a published epigenome-wide association study (EWAS) of T2DM. RESULTS With mixed models logistic regression of EPIPREG and EPIDG, MRS for T2DM was associated with GDM: odd ratio (OR)[95% CI]: 1.3 [1.1-1.8], P = 0.002 for the unadjusted model, and 1.4 [1.1-1.7], P = 0.00014 for a model adjusted by age, pre-pregnant BMI, family history of diabetes and smoking status. Also, we found 6 CpGs through a meta-analysis (cg14020176, cg22650271, cg14870271, cg27243685, cg06378491, cg25130381) associated with GDM, and some of their methylation quantitative loci (mQTLs) were related to T2DM and GDM. CONCLUSION For the first time, we show that DNA methylation marks for T2DM are also associated with GDM, suggesting shared epigenetic mechanisms between GDM and T2DM.
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Affiliation(s)
- Teresa M Linares-Pineda
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
- Department of Biochemistry and Molecular Biology 2, University of Granada, Granada, Spain
- Centre for Biomedical Research Network on Obesity Physiopathology and Nutrition (CIBEROBN), Madrid, Spain
| | - Nicolas Fragoso-Bargas
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - María José Picón
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
| | - Maria Molina-Vega
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
| | - Anne Karen Jenum
- General Practice Research Unit (AFE), Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Line Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Sindre Lee-Ødegård
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Julia O Opsahl
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Haukeland University Hospital, Bergen, Norway
| | - Gunn-Helen Moen
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, Australia
- K. G Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Elisabeth Qvigstad
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rashmi B Prasad
- Lund University Diabetes Centre, Malmo, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Kåre I Birkeland
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sonsoles Morcillo
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
- Centre for Biomedical Research Network on Obesity Physiopathology and Nutrition (CIBEROBN), Madrid, Spain
| | - Christine Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway.
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15
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Luong RAM, Guan W, Vue FC, Dai J. Literary Identification of Differentially Hydroxymethylated DNA Regions for Type 2 Diabetes Mellitus: A Scoping Minireview. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:177. [PMID: 38397668 PMCID: PMC10887687 DOI: 10.3390/ijerph21020177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024]
Abstract
Type 2 diabetes mellitus (T2DM) is a public health condition where environmental and genetic factors can intersect through hydroxymethylation. It was unclear which blood DNA regions were hydroxymethylated in human T2DM development. We aimed to identify the regions from the literature as designed in the ongoing Twins Discordant for Incident T2DM Study. A scoping review was performed using Medical Subject Headings (MeSH) and keyword methods to search PubMed for studies published in English and before 1 August 2022, following our registered protocol. The keyword and MeSH methods identified 12 and 3 records separately, and the keyword-identified records included all from the MeSH. Only three case-control studies met the criteria for the full-text review, including one MeSH-identified record. Increased global levels of 5-hydroxymethylated cytosine (5hmC) in T2DM patients versus healthy controls in blood or peripheral blood mononuclear cells were consistently reported (p < 0.05 for all). Among candidate DNA regions related to the human SOCS3, SREBF1, and TXNIP genes, only the SOCS3 gene yielded higher 5hmC levels in T2DM patients with high poly-ADP-ribosylation than participants combined from those with low PARylation and healthy controls (p < 0.05). Hydroxymethylation in the SOCS3-related region of blood DNA is promising to investigate for its mediation in the influences of environment on incident T2DM.
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Affiliation(s)
- Ryan Anh Minh Luong
- Doctoral Program of Osteopathic Medicine, College of Osteopathic Medicine, Des Moines University, West Des Moines, IA 50266, USA; (R.A.M.L.); (F.C.V.)
| | - Weihua Guan
- Division of Biostatistics & Health Data Science, University of Minnesota School of Public Health, Minneapolis, MN 55414, USA;
| | - Fue Chee Vue
- Doctoral Program of Osteopathic Medicine, College of Osteopathic Medicine, Des Moines University, West Des Moines, IA 50266, USA; (R.A.M.L.); (F.C.V.)
| | - Jun Dai
- Department of Public Health, College of Health Sciences, Des Moines University, West Des Moines, IA 50266, USA
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16
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Wu Z, Zhang W, Qu J, Liu GH. Emerging epigenetic insights into aging mechanisms and interventions. Trends Pharmacol Sci 2024; 45:157-172. [PMID: 38216430 DOI: 10.1016/j.tips.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Epigenetic dysregulation emerges as a critical hallmark and driving force of aging. Although still an evolving field with much to explore, it has rapidly gained significance by providing valuable insights into the mechanisms of aging and potential therapeutic opportunities for age-related diseases. Recent years have witnessed remarkable strides in our understanding of the epigenetic landscape of aging, encompassing pivotal elements, such as DNA methylation, histone modifications, RNA modifications, and noncoding (nc) RNAs. Here, we review the latest discoveries that shed light on new epigenetic mechanisms and critical targets for predicting and intervening in aging and related disorders. Furthermore, we explore burgeoning interventions and exemplary clinical trials explicitly designed to foster healthy aging, while contemplating the potential ramifications of epigenetic influences.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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17
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Domínguez-Barragán J, Fernández-Sanlés A, Hernáez Á, Llauradó-Pont J, Marrugat J, Robinson O, Tzoulaki I, Elosua R, Lassale C. Blood DNA methylation signature of diet quality and association with cardiometabolic traits. Eur J Prev Cardiol 2024; 31:191-202. [PMID: 37793095 PMCID: PMC10809172 DOI: 10.1093/eurjpc/zwad317] [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: 05/30/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
AIMS Diet quality might influence cardiometabolic health through epigenetic changes, but this has been little investigated in adults. Our aims were to identify cytosine-phosphate-guanine (CpG) dinucleotides associated with diet quality by conducting an epigenome-wide association study (EWAS) based on blood DNA methylation (DNAm) and to assess how diet-related CpGs associate with inherited susceptibility to cardiometabolic traits: body mass index (BMI), systolic blood pressure (SBP), triglycerides, type 2 diabetes (T2D), and coronary heart disease (CHD). METHODS AND RESULTS Meta-EWAS including 5274 participants in four cohorts from Spain, the USA, and the UK. We derived three dietary scores (exposures) to measure adherence to a Mediterranean diet, to a healthy plant-based diet, and to the Dietary Approaches to Stop Hypertension. Blood DNAm (outcome) was assessed with the Infinium arrays Human Methylation 450K BeadChip and MethylationEPIC BeadChip. For each diet score, we performed linear EWAS adjusted for age, sex, blood cells, smoking and technical variables, and BMI in a second set of models. We also conducted Mendelian randomization analyses to assess the potential causal relationship between diet-related CpGs and cardiometabolic traits. We found 18 differentially methylated CpGs associated with dietary scores (P < 1.08 × 10-7; Bonferroni correction), of which 12 were previously associated with cardiometabolic traits. Enrichment analysis revealed overrepresentation of diet-associated genes in pathways involved in inflammation and cardiovascular disease. Mendelian randomization analyses suggested that genetically determined methylation levels corresponding to lower diet quality at cg02079413 (SNORA54), cg02107842 (MAST4), and cg23761815 (SLC29A3) were causally associated with higher BMI and at cg05399785 (WDR8) with greater SBP, and methylation levels associated with higher diet quality at cg00711496 (PRMT1) with lower BMI, T2D risk, and CHD risk and at cg0557921 (AHRR) with lower CHD risk. CONCLUSION Diet quality in adults was related to differential methylation in blood at 18 CpGs, some of which related to cardiometabolic health.
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Affiliation(s)
- Jorge Domínguez-Barragán
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
| | - Alba Fernández-Sanlés
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Álvaro Hernáez
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo 0463, Norway
- Blanquerna School of Health Sciences, Universitat Ramon Llull, 08025 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
| | - Joana Llauradó-Pont
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
| | - Jaume Marrugat
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Oliver Robinson
- μedical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Ioanna Tzoulaki
- Centre for Systems Biology, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Roberto Elosua
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic—Central University of Catalunya, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Camille Lassale
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003, Barcelona, Spain
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18
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Yang X, Xue C, Chen K, Gao D, Wang H, Tang C. Characteristics of elderly diabetes patients: focus on clinical manifestation, pathogenic mechanism, and the role of traditional Chinese medicine. Front Pharmacol 2024; 14:1339744. [PMID: 38273819 PMCID: PMC10808572 DOI: 10.3389/fphar.2023.1339744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/28/2023] [Indexed: 01/27/2024] Open
Abstract
Diabetes mellitus has become a major public health issue globally, putting an enormous burden on global health systems and people. Among all diseased groups, a considerable part of patients are elderly, while their clinical features, pathogenic processes, and medication regimens are different from patients of other ages. Despite the availability of multiple therapies and techniques, there are still numerous elderly diabetes patients suffering from poor blood glucose control, severe complications, and drug adverse effects, which negatively affect the quality of life in their golden years. Traditional Chinese Medicine (TCM) has been widely used in the treatment of diabetes for several decades, and its relevant clinical practice has confirmed that it has a satisfactory effect on alleviating clinical symptoms and mitigating the progression of complications. Chinese herbal medicine and its active components were used widely with obvious clinical advantages by multiple targets and signaling pathways. However, due to the particular features of elderly diabetes, few studies were conducted to explore Traditional Chinese Medicine intervention on elderly diabetic patients. This study reviews the research on clinical features, pathogenic processes, treatment principles, and TCM treatments, hoping to provide fresh perspectives on the prevention and management strategies for elderly diabetes.
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Affiliation(s)
- Xiaofei Yang
- Beijing University of Chinese Medicine, Beijing, China
- Institute of Metabolic Diseases, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chongxiang Xue
- Beijing University of Chinese Medicine, Beijing, China
- Institute of Metabolic Diseases, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Keyu Chen
- Institute of Metabolic Diseases, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dongyang Gao
- Institute of Metabolic Diseases, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Han Wang
- Beijing University of Chinese Medicine, Beijing, China
| | - Cheng Tang
- Beijing University of Chinese Medicine, Beijing, China
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19
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Reynolds LM, Houston DK, Skiba MB, Whitsel EA, Stewart JD, Li Y, Zannas AS, Assimes TL, Horvath S, Bhatti P, Baccarelli AA, Tooze JA, Vitolins MZ. Diet Quality and Epigenetic Aging in the Women's Health Initiative. J Acad Nutr Diet 2024:S2212-2672(24)00002-9. [PMID: 38215906 PMCID: PMC11236955 DOI: 10.1016/j.jand.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 12/05/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024]
Abstract
BACKGROUND Higher diet quality scores are associated with a lower risk for many chronic diseases and all-cause mortality; however, it is unclear if diet quality is associated with aging biology. OBJECTIVE This study aimed to examine the association between diet quality and a measure of biological aging known as epigenetic aging. DESIGN A cross-sectional data analysis was used to examine the association between three diet quality scores based on self-reported food frequency questionnaire data and five measures of epigenetic aging based on DNA methylation (DNAm) data from peripheral blood. PARTICIPANTS/SETTING This study included 4,500 postmenopausal women recruited from multiple sites across the United States (1993-98), aged 50 to 79 years, with food frequency questionnaire and DNAm data available from the Women's Health Initiative baseline visit. MAIN OUTCOME MEASURES Five established epigenetic aging measures were generated from HumanMethylation450 Beadchip DNAm data, including AgeAccelHannum, AgeAccelHorvath, AgeAccelPheno, AgeAccelGrim, and DunedinPACE. STATISTICAL ANALYSES PERFORMED Linear mixed models were used to test for associations between three diet quality scores (Healthy Eating Index, Dietary Approaches to Stop Hypertension, and alternate Mediterranean diet scores) and epigenetic aging measures, adjusted for age, race and ethnicity, education, tobacco smoking, physical activity, Women's Health Initiative substudy from which DNAm data were obtained, and DNAm-based estimates of leukocyte proportions. RESULTS Healthy Eating Index, Dietary Approaches to Stop Hypertension, and alternate Mediterranean diet scores were all inversely associated with AgeAccelPheno, AgeAccelGrim, and DunedinPACE (P < 0.05), with the largest effects with DunedinPACE. A one standard deviation increment in diet quality scores was associated with a decrement (β ± SE) in DunedinPACE z score of -0.097 ± 0.014 (P = 9.70 x 10-13) for Healthy Eating Index, -0.107 ± 0.014 (P = 1.53 x 10-14) for Dietary Approaches to Stop Hypertension, and -0.068 ± 0.013 (P = 2.31 x 10-07) for the alternate Mediterranean diet. CONCLUSIONS In postmenopausal women, diet quality scores were inversely associated with DNAm-based measures of biological aging, particularly DunedinPACE.
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Affiliation(s)
- Lindsay M Reynolds
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina.
| | - Denise K Houston
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Meghan B Skiba
- Division of Biobehavioral Health Science, University of Arizona Cancer Center, University of Arizona, Tucson, Arizona
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - James D Stewart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina; Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Yun Li
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Anthony S Zannas
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - Themistocles L Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Steve Horvath
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California; Altos Labs, San Diego, California
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada; School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Janet A Tooze
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Mara Z Vitolins
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina
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20
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Dokuru DR, Horwitz TB, Freis SM, Stallings MC, Ehringer MA. South Asia: The Missing Diverse in Diversity. Behav Genet 2024; 54:51-62. [PMID: 37917228 PMCID: PMC11129896 DOI: 10.1007/s10519-023-10161-y] [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: 04/23/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023]
Abstract
South Asia, making up around 25% of the world's population, encompasses a wide range of individuals with tremendous genetic and environmental diversity. This region, which spans eight countries, is home to over 4500 anthropologically defined groups that speak numerous languages and have an array of religious beliefs and cultures, making it one of the most diverse places in the world. Much of the region's rich genetic diversity and structure is the result of a complex combination of population history, migration patterns, and endogamous practices. Despite the overwhelming size and diversity, South Asians have often been underrepresented in genetic research, making up less than 2% of the participants in genetic studies. This has led to a lack of population specific understanding of genetic disease risks. We aim to raise awareness about underlying genetic diversity in this ancestry group, call attention to the lack of representation of the group, and to highlight strategies for future studies in South Asians.
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Affiliation(s)
- Deepika R Dokuru
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA.
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA.
| | - Tanya B Horwitz
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Samantha M Freis
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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21
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Priyadarshini A, Madan R, Das S. Genetics and epigenetics of diabetes and its complications in India. Hum Genet 2024; 143:1-17. [PMID: 37999799 DOI: 10.1007/s00439-023-02616-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/17/2023] [Indexed: 11/25/2023]
Abstract
Diabetes mellitus (DM) has become a significant health concern with an increasing rate of morbidity and mortality worldwide. India ranks second in the number of diabetes cases in the world. The increasing burden of DM can be explained by genetic predisposition of Indians to type 2 diabetes mellitus (T2DM) coupled with rapid urbanization and socio-economic development in the last 3 decades leading to drastic changes in lifestyle. Environment and lifestyle changes contribute to T2DM development by altering epigenetic processes such as DNA methylation, histone post-translational modifications, and long non-coding RNAs, all of which regulate chromatin structure and gene expression. Although the genetic predisposition of Indians to T2DM is well established, how environmental and genetic factors interact and lead to T2DM is not well understood. In this review, we discuss the prevalence of diabetes and its complications across different states in India and how various risk factors contribute to its pathogenesis. The review also highlights the role of genetic predisposition among the Indian population and epigenetic factors involved in the etiology of diabetes. Lastly, we review current treatments and emphasize the knowledge gap with respect to genetic and epigenetic factors in the Indian context. Further understanding of the genetic and epigenetic determinants will help in risk prediction and prevention as well as therapeutic interventions, which will improve the clinical management of diabetes and associated macro- and micro-vascular complications.
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Affiliation(s)
- Ankita Priyadarshini
- Diabetic Vascular Complications Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, 140306, India
| | - Riya Madan
- Diabetic Vascular Complications Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, 140306, India
| | - Sadhan Das
- Diabetic Vascular Complications Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, 140306, India.
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22
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Rönn T, Ofori JK, Perfilyev A, Hamilton A, Pircs K, Eichelmann F, Garcia-Calzon S, Karagiannopoulos A, Stenlund H, Wendt A, Volkov P, Schulze MB, Mulder H, Eliasson L, Ruhrmann S, Bacos K, Ling C. Genes with epigenetic alterations in human pancreatic islets impact mitochondrial function, insulin secretion, and type 2 diabetes. Nat Commun 2023; 14:8040. [PMID: 38086799 PMCID: PMC10716521 DOI: 10.1038/s41467-023-43719-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Epigenetic dysregulation may influence disease progression. Here we explore whether epigenetic alterations in human pancreatic islets impact insulin secretion and type 2 diabetes (T2D). In islets, 5,584 DNA methylation sites exhibit alterations in T2D cases versus controls and are associated with HbA1c in individuals not diagnosed with T2D. T2D-associated methylation changes are found in enhancers and regions bound by β-cell-specific transcription factors and associated with reduced expression of e.g. CABLES1, FOXP1, GABRA2, GLR1A, RHOT1, and TBC1D4. We find RHOT1 (MIRO1) to be a key regulator of insulin secretion in human islets. Rhot1-deficiency in β-cells leads to reduced insulin secretion, ATP/ADP ratio, mitochondrial mass, Ca2+, and respiration. Regulators of mitochondrial dynamics and metabolites, including L-proline, glycine, GABA, and carnitines, are altered in Rhot1-deficient β-cells. Islets from diabetic GK rats present Rhot1-deficiency. Finally, RHOT1methylation in blood is associated with future T2D. Together, individuals with T2D exhibit epigenetic alterations linked to mitochondrial dysfunction in pancreatic islets.
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Affiliation(s)
- Tina Rönn
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Jones K Ofori
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Alexander Perfilyev
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Alexander Hamilton
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
- Department of Biology, University of Copenhagen, København, Denmark
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
- HCEMM-Su, Neurobiology and Neurodegenerative Diseases Research Group, Budapest, Hungary
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Fabian Eichelmann
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sonia Garcia-Calzon
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
- Department of Food Science and Physiology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Alexandros Karagiannopoulos
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Hans Stenlund
- Swedish Metabolomics Centre, Umeå University, Umeå, Sweden
| | - Anna Wendt
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Petr Volkov
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Hindrik Mulder
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Lena Eliasson
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Karl Bacos
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
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23
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Muniyappa R, Narayanappa SBK. Disentangling Dual Threats: Premature Coronary Artery Disease and Early-Onset Type 2 Diabetes Mellitus in South Asians. J Endocr Soc 2023; 8:bvad167. [PMID: 38178904 PMCID: PMC10765382 DOI: 10.1210/jendso/bvad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Indexed: 01/06/2024] Open
Abstract
South Asian individuals (SAs) face heightened risks of premature coronary artery disease (CAD) and early-onset type 2 diabetes mellitus (T2DM), with grave health, societal, and economic implications due to the region's dense population. Both conditions, influenced by cardiometabolic risk factors such as insulin resistance, hypertension, and central adiposity, manifest earlier and with unique thresholds in SAs. Epidemiological, demographic, nutritional, environmental, sociocultural, and economic transitions in SA have exacerbated the twin epidemic. The coupling of premature CAD and T2DM arises from increased obesity due to limited adipose storage, early-life undernutrition, distinct fat thresholds, reduced muscle mass, and a predisposition for hepatic fat accumulation from certain dietary choices cumulatively precipitating a decline in insulin sensitivity. As T2DM ensues, the β-cell adaptive responses are suboptimal, precipitating a transition from compensatory hyperinsulinemia to β-cell decompensation, underscoring a reduced functional β-cell reserve in SAs. This review delves into the interplay of these mechanisms and highlights a prediabetes endotype tied to elevated vascular risk. Deciphering these mechanistic interconnections promises to refine stratification paradigms, surpassing extant risk-prediction strategies.
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Affiliation(s)
- Ranganath Muniyappa
- Clinical Endocrine Section, Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Satish Babu K Narayanappa
- Department of Medicine, Sri Madhusudan Sai Institute of Medical Sciences and Research, Muddenahalli, Karnataka 562101, India
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24
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Li X, Shao X, Kou M, Wang X, Ma H, Grundberg E, Bazzano LA, Smith SR, Bray GA, Sacks FM, Qi L. DNA Methylation at ABCG1 and Long-term Changes in Adiposity and Fat Distribution in Response to Dietary Interventions: The POUNDS Lost Trial. Diabetes Care 2023; 46:2201-2207. [PMID: 37770056 DOI: 10.2337/dc23-0748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE To examine whether participants with different levels of diabetes-related DNA methylation at ABCG1 might respond differently to dietary weight loss interventions with long-term changes in adiposity and body fat distribution. RESEARCH DESIGN AND METHODS The current study included overweight/obese participants from the POUNDS Lost trial. Blood levels of regional DNA methylation at ABCG1 were profiled by high-resolution methylC-capture sequencing at baseline among 673 participants, of whom 598 were followed up at 6 months and 543 at 2 years. Two-year changes in adiposity and computed tomography-measured body fat distribution were calculated. RESULTS Regional DNA methylation at ABCG1 showed significantly different associations with long-term changes in body weight and waist circumference at 6 months and 2 years in dietary interventions varying in protein intake (interaction P < 0.05 for all). Among participants assigned to an average-protein (15%) diet, lower baseline regional DNA methylation at ABCG1 was associated with greater reductions in body weight and waist circumference at 6 months and 2 years, whereas opposite associations were found among those assigned to a high-protein (25%) diet. Similar interaction patterns were also observed for body fat distribution, including visceral adipose tissue, subcutaneous adipose tissue, deep subcutaneous adipose tissue, and total adipose tissue at 6 months and 2 years (interaction P < 0.05 for all). CONCLUSIONS Baseline DNA methylation at ABCG1 interacted with dietary protein intake on long-term decreases in adiposity and body fat distribution. Participants with lower methylation at ABCG1 benefitted more in long-term reductions in body weight, waist circumference, and body fat distribution when consuming an average-protein diet.
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Affiliation(s)
- Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Lydia A Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | | | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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25
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Sumida K, Mozhui K, Liang X, Mallisetty Y, Han Z, Kovesdy CP. Association of DNA methylation signatures with premature ageing and cardiovascular death in patients with end-stage kidney disease: a pilot epigenome-wide association study. Epigenetics 2023; 18:2214394. [PMID: 37207321 PMCID: PMC10202091 DOI: 10.1080/15592294.2023.2214394] [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: 12/29/2022] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023] Open
Abstract
Patients with end-stage kidney disease (ESKD) display features of premature aging. There is strong evidence that changes in DNA methylation (DNAm) contribute to age-related pathologies; however, little is known about their association with premature aging and cardiovascular mortality in patients with ESKD. We assayed genome-wide DNAm in a pilot case-control study of 60 hemodialysis patients with (n=30, cases) and without (n=30, controls) a fatal cardiovascular event. DNAm was profiled on the Illumina EPIC BeadChip. Four established DNAm clocks (i.e., Horvath-, Hannum-, Pheno-, and GrimAge) were used to estimate epigenetic age (DNAmAge). Epigenetic age acceleration (EAA) was derived as the residuals of regressing DNAmAge on chronological age (chroAge), and its association with cardiovascular death was examined using multivariable conditional logistic regression. An epigenome-wide association study (EWAS) was performed to identify differentially methylated CpGs associated with cardiovascular death. All clocks performed well at predicting chroAge (correlation between DNAmAges and chroAge of r=0.76-0.89), with GrimAge showing the largest deviation from chroAge (a mean of +21.3 years). There was no significant association of EAAs with cardiovascular death. In the EWAS, a CpG (cg22305782) in the FBXL19 gene had the strongest association with cardiovascular death with significantly lower DNAm in cases vs. controls (PFDR=2.0x10-6). FBXL19 is involved in cell apoptosis, inflammation, and adipogenesis. Overall, we observed more accelerated aging in patients with ESKD, although there was no significant association of EAAs with cardiovascular death. EWAS suggests a potential novel DNAm biomarker for premature cardiovascular mortality in ESKD.
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Affiliation(s)
- Keiichi Sumida
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Xiaoyu Liang
- Department of Epidemiology and Biostatistics, Michigan State University College of Human Medicine, East Lansing, MI, USA
| | - Yamini Mallisetty
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Zhongji Han
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Csaba P Kovesdy
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
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26
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Keller M, Svensson SIA, Rohde-Zimmermann K, Kovacs P, Böttcher Y. Genetics and Epigenetics in Obesity: What Do We Know so Far? Curr Obes Rep 2023; 12:482-501. [PMID: 37819541 DOI: 10.1007/s13679-023-00526-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE OF REVIEW Enormous progress has been made in understanding the genetic architecture of obesity and the correlation of epigenetic marks with obesity and related traits. This review highlights current research and its challenges in genetics and epigenetics of obesity. RECENT FINDINGS Recent progress in genetics of polygenic traits, particularly represented by genome-wide association studies, led to the discovery of hundreds of genetic variants associated with obesity, which allows constructing polygenic risk scores (PGS). In addition, epigenome-wide association studies helped identifying novel targets and methylation sites being important in the pathophysiology of obesity and which are essential for the generation of methylation risk scores (MRS). Despite their great potential for predicting the individual risk for obesity, the use of PGS and MRS remains challenging. Future research will likely discover more loci being involved in obesity, which will contribute to better understanding of the complex etiology of human obesity. The ultimate goal from a clinical perspective will be generating highly robust and accurate prediction scores allowing clinicians to predict obesity as well as individual responses to body weight loss-specific life-style interventions.
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Affiliation(s)
- Maria Keller
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig, University Hospital Leipzig, 04103, Leipzig, Germany
| | - Stina Ingrid Alice Svensson
- EpiGen, Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway
| | - Kerstin Rohde-Zimmermann
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig, University Hospital Leipzig, 04103, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
| | - Yvonne Böttcher
- EpiGen, Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway.
- EpiGen, Medical Division, Akershus University Hospital, 1478, Lørenskog, Norway.
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27
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Yu W, Drzymalla E, Gyorfy MF, Khoury MJ, Sun YV, Gwinn M. Navigating epigenetic epidemiology publications. EPIGENETICS COMMUNICATIONS 2023; 3:8. [PMID: 38414576 PMCID: PMC10895989 DOI: 10.1186/s43682-023-00023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 02/29/2024]
Affiliation(s)
- Wei Yu
- Office of Genomics and Precision Public Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Emily Drzymalla
- Office of Genomics and Precision Public Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Muin J Khoury
- Office of Genomics and Precision Public Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Xue X, Wang Z, Wang Y, Zhou X. Disease Diagnosis Based on Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2114-2127. [PMID: 37527510 DOI: 10.1021/acschembio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid modifications include a wide range of epigenetic and epitranscriptomic factors and impact a wide range of nucleic acids due to their profound influence on biological inheritance, growth, and metabolism. The recently developed methods of mapping and characterizing these modifications have promoted their discovery as well as large-scale studies in eukaryotes, especially in humans. Because of these pioneering strategies, nucleic acid modifications have been shown to have a great impact on human disorders such as cancer. Therefore, whether nucleic acid modifications could become a new type of biomarker remains an open question. In this review, we briefly look back at classical nucleic acid modifications and then focus on the progress made in investigating these modifications as diagnostic biomarkers in clinical therapy and present our perspective on their development prospects.
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Affiliation(s)
- Xiaochen Xue
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiying Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Department of Chemistry, College of Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
- Cross Research Institute of Zhongnan Hospital, Wuhan University, Wuhan 430071, China
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29
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Topriceanu CC, Dev E, Ahmad M, Hughes R, Shiwani H, Webber M, Direk K, Wong A, Ugander M, Moon JC, Hughes AD, Maddock J, Schlegel TT, Captur G. Accelerated DNA methylation age plays a role in the impact of cardiovascular risk factors on the human heart. Clin Epigenetics 2023; 15:164. [PMID: 37853450 PMCID: PMC10583368 DOI: 10.1186/s13148-023-01576-9] [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: 06/27/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) age acceleration (AgeAccel) and cardiac age by 12-lead advanced electrocardiography (A-ECG) are promising biomarkers of biological and cardiac aging, respectively. We aimed to explore the relationships between DNAm age and A-ECG heart age and to understand the extent to which DNAm AgeAccel relates to cardiovascular (CV) risk factors in a British birth cohort from 1946. RESULTS We studied four DNAm ages (AgeHannum, AgeHorvath, PhenoAge, and GrimAge) and their corresponding AgeAccel. Outcomes were the results from two publicly available ECG-based cardiac age scores: the Bayesian A-ECG-based heart age score of Lindow et al. 2022 and the deep neural network (DNN) ECG-based heart age score of Ribeiro et al. 2020. DNAm AgeAccel was also studied relative to results from two logistic regression-based A-ECG disease scores, one for left ventricular (LV) systolic dysfunction (LVSD), and one for LV electrical remodeling (LVER). Generalized linear models were used to explore the extent to which any associations between biological cardiometabolic risk factors (body mass index, hypertension, diabetes, high cholesterol, previous cardiovascular disease [CVD], and any CV risk factor) and the ECG-based outcomes are mediated by DNAm AgeAccel. We derived the total effects, average causal mediation effects (ACMEs), average direct effects (ADEs), and the proportion mediated [PM] with their 95% confidence intervals [CIs]. 498 participants (all 60-64 years) were included, with the youngest ECG heart age being 27 and the oldest 90. When exploring the associations between cardiometabolic risk factors and Bayesian A-ECG cardiac age, AgeAccelPheno appears to be a partial mediator, as ACME was 0.23 years [0.01, 0.52] p = 0.028 (i.e., PM≈18%) for diabetes, 0.34 [0.03, 0.74] p = 0.024 (i.e., PM≈15%) for high cholesterol, and 0.34 [0.03, 0.74] p = 0.024 (PM≈15%) for any CV risk factor. Similarly, AgeAccelGrim mediates ≈30% of the relationship between diabetes or high cholesterol and the DNN ECG-based heart age. When exploring the link between cardiometabolic risk factors and the A-ECG-based LVSD and LVER scores, it appears that AgeAccelPheno or AgeAccelGrim mediate 10-40% of these associations. CONCLUSION By the age of 60, participants with accelerated DNA methylation appear to have older, weaker, and more electrically impaired hearts. We show that the harmful effects of CV risk factors on cardiac age and health, appear to be partially mediated by DNAm AgeAccelPheno and AgeAccelGrim. This highlights the need to further investigate the potential cardioprotective effects of selective DNA methyltransferases modulators.
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Affiliation(s)
- Constantin-Cristian Topriceanu
- UCL MRC Unit for Lifelong Health and Ageing, University College London, 1-19 Torrington Place, London, UK
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK
- Cardiac MRI Unit, Barts Heart Centre, West Smithfield, London, UK
| | - Eesha Dev
- UCL Medical School, Gower Street, London, UK
| | - Mahmood Ahmad
- Centre for Inherited Heart Muscle Conditions, The Royal Free Hospital, Pond Street, Hampstead, London, UK
| | - Rebecca Hughes
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK
- Cardiac MRI Unit, Barts Heart Centre, West Smithfield, London, UK
| | - Hunain Shiwani
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK
- Cardiac MRI Unit, Barts Heart Centre, West Smithfield, London, UK
| | - Matthew Webber
- UCL MRC Unit for Lifelong Health and Ageing, University College London, 1-19 Torrington Place, London, UK
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK
| | - Kenan Direk
- UCL MRC Unit for Lifelong Health and Ageing, University College London, 1-19 Torrington Place, London, UK
| | - Andrew Wong
- UCL MRC Unit for Lifelong Health and Ageing, University College London, 1-19 Torrington Place, London, UK
| | - Martin Ugander
- Kolling Institute Royal North Shore Hospital, and Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Department of Clinical Physiology, Karolinska University Hospital, and Karolinska Institutet, Stockholm, Sweden
| | - James C Moon
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK
- Cardiac MRI Unit, Barts Heart Centre, West Smithfield, London, UK
| | - Alun D Hughes
- UCL MRC Unit for Lifelong Health and Ageing, University College London, 1-19 Torrington Place, London, UK
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK
| | - Jane Maddock
- UCL MRC Unit for Lifelong Health and Ageing, University College London, 1-19 Torrington Place, London, UK
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK
| | - Todd T Schlegel
- Department of Clinical Physiology, Karolinska University Hospital, and Karolinska Institutet, Stockholm, Sweden
- Nicollier-Schlegel SARL, Trélex, Switzerland
| | - Gabriella Captur
- UCL MRC Unit for Lifelong Health and Ageing, University College London, 1-19 Torrington Place, London, UK.
- UCL Institute of Cardiovascular Science, University College London, 62 Huntley St, London, WC1E 6BT, UK.
- Centre for Inherited Heart Muscle Conditions, The Royal Free Hospital, Pond Street, Hampstead, London, UK.
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Tan K, Foo R, Loh M. Cardiomyopathy in Asian Cohorts: Genetic and Epigenetic Insights. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:496-506. [PMID: 37589150 DOI: 10.1161/circgen.123.004079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Previous studies on cardiomyopathies have been particularly valuable for clarifying pathological mechanisms in heart failure, an etiologically heterogeneous disease. In this review, we specifically focus on cardiomyopathies in Asia, where heart failure is particularly pertinent. There has been an increase in prevalence of cardiomyopathies in Asia, in sharp contrast with the decline observed in Western countries. Indeed, important disparities in cardiomyopathy incidence, clinical characteristics, and prognosis have been reported in Asian versus White cohorts. These have been accompanied by emerging descriptions of a distinct rare and common genetic basis for disease among Asian cardiomyopathy patients marked by an increased burden of variants with uncertain significance, reclassification of variants deemed pathogenic based on evidence from predominantly White cohorts, and the discovery of Asian-specific cardiomyopathy-associated loci with underappreciated pathogenicity under conventional classification criteria. Findings from epigenetic studies of heart failure, particularly DNA methylation studies, have complemented genetic findings in accounting for the phenotypic variability in cardiomyopathy. Though extremely limited, findings from Asian ancestry-focused DNA methylation studies of cardiomyopathy have shown potential to contribute to general understanding of cardiomyopathy pathophysiology by proposing disease and cause-relevant pathophysiological mechanisms. We discuss the value of multiomics study designs incorporating genetic, methylation, and transcriptomic information for future DNA methylation studies in Asian cardiomyopathy cohorts to yield Asian ancestry-specific insights that will improve risk stratification in the Asian population.
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Affiliation(s)
- Konstanze Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore (K.T., M.L.)
| | - Roger Foo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore (R.F.)
- Department of Cardiology, National University Heart Centre, National University Health System, Singapore (R.F.)
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore (K.T., M.L.)
- Genome Institute of Singapore, Singapore (GIS), Agency for Science, Technology and Research (A*STAR) (M.L.)
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, United Kingdom (M.L.)
- National Skin Centre, Singapore (M.L.)
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31
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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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Di Pietrantonio N, Cappellacci I, Mandatori D, Baldassarre MPA, Pandolfi A, Pipino C. Role of Epigenetics and Metabolomics in Predicting Endothelial Dysfunction in Type 2 Diabetes. Adv Biol (Weinh) 2023; 7:e2300172. [PMID: 37616517 DOI: 10.1002/adbi.202300172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/15/2023] [Indexed: 08/26/2023]
Abstract
Type 2 diabetes (T2D) is a worldwide health problem and cardiovascular disease (CVD) is a leading cause of morbidity and mortality in T2D patients, making the prevention of CVD onset a major priority. It is therefore crucial to optimize diagnosis and treatment to reduce this burden. Endothelial dysfunction is one of the most important prognostic factors for CVD progression, thus novel approaches to identify the early phase of endothelial dysfunction may lead to specific preventive measures to reduce the occurrence of CVD. Nowadays, multiomics approaches have provided unprecedented opportunities to stratify T2D patients into endotypes, improve therapeutic treatment and outcome and amend the survival prediction. Among omics strategies, epigenetics and metabolomics are gaining increasing interest. Recently, a dynamic correlation between metabolic pathways and gene expression through chromatin remodeling, such as DNA methylation, has emerged, indicating new perspectives on the regulatory networks impacting cellular processes. Thus, a better understanding of epigenetic-metabolite relationships can provide insight into the physiological processes altered early in the endothelium that ultimately head to disease development. Here, recent studies on epigenetics and metabolomics related to CVD prevention potentially useful to identify disease biomarkers, as well as new therapies hopefully targeting the early phase of endothelial dysfunction are highlighted.
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Affiliation(s)
- Nadia Di Pietrantonio
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Ilaria Cappellacci
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Domitilla Mandatori
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Maria Pompea Antonia Baldassarre
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Department of Medicine and Aging Sciences, "G. d'Annunzio" University Chieti-Pescara, Chieti, 66100, Italy
| | - Assunta Pandolfi
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Caterina Pipino
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
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Issarapu P, Arumalla M, Elliott HR, Nongmaithem SS, Sankareswaran A, Betts M, Sajjadi S, Kessler NJ, Bayyana S, Mansuri SR, Derakhshan M, Krishnaveni GV, Shrestha S, Kumaran K, Di Gravio C, Sahariah SA, Sanderson E, Relton CL, Ward KA, Moore SE, Prentice AM, Lillycrop KA, Fall CHD, Silver MJ, Chandak GR. DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood. Nat Commun 2023; 14:5200. [PMID: 37626025 PMCID: PMC10457295 DOI: 10.1038/s41467-023-40607-0] [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: 01/14/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Human height is strongly influenced by genetics but the contribution of modifiable epigenetic factors is under-explored, particularly in low and middle-income countries (LMIC). We investigate links between blood DNA methylation and child height in four LMIC cohorts (n = 1927) and identify a robust association at three CpGs in the suppressor of cytokine signaling 3 (SOCS3) gene which replicates in a high-income country cohort (n = 879). SOCS3 methylation (SOCS3m)-height associations are independent of genetic effects. Mendelian randomization analysis confirms a causal effect of SOCS3m on height. In longitudinal analysis, SOCS3m explains a maximum 9.5% of height variance in mid-childhood while the variance explained by height polygenic risk score increases from birth to 21 years. Children's SOCS3m is associated with prenatal maternal folate and socio-economic status. In-vitro characterization confirms a regulatory effect of SOCS3m on gene expression. Our findings suggest epigenetic modifications may play an important role in driving child height in LMIC.
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Affiliation(s)
- Prachand Issarapu
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Manisha Arumalla
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Suraj S Nongmaithem
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Alagu Sankareswaran
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Modupeh Betts
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Sara Sajjadi
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Noah J Kessler
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Swati Bayyana
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Sohail R Mansuri
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Maria Derakhshan
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - G V Krishnaveni
- Epidemiology Research Unit, CSI Holdsworth Memorial Hospital, Mysore, Karnataka, India
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Kalyanaraman Kumaran
- Epidemiology Research Unit, CSI Holdsworth Memorial Hospital, Mysore, Karnataka, India
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Chiara Di Gravio
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Eleanor Sanderson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kate A Ward
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
- Department of Women & Children's Health, King's College London, London, UK
| | - Sophie E Moore
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
- Department of Women & Children's Health, King's College London, London, UK
| | - Andrew M Prentice
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Karen A Lillycrop
- School of Medicine, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Caroline H D Fall
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Matt J Silver
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India.
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India.
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Venkataraghavan S, Pankow JS, Boerwinkle E, Fornage M, Selvin E, Ray D. Epigenome-wide association study of incident type 2 diabetes in Black and White participants from the Atherosclerosis Risk in Communities Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.09.23293896. [PMID: 37609313 PMCID: PMC10441493 DOI: 10.1101/2023.08.09.23293896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
DNA methylation studies of incident type 2 diabetes in US populations are limited, and to our knowledge none included individuals of African descent living in the US. We performed an epigenome-wide association analysis of blood-based methylation levels at CpG sites with incident type 2 diabetes using Cox regression in 2,091 Black and 1,029 White individuals from the Atherosclerosis Risk in Communities study. At an epigenome-wide significance threshold of 10-7, we detected 7 novel diabetes-associated CpG sites in C1orf151 (cg05380846: HR= 0.89, p = 8.4 × 10-12), ZNF2 (cg01585592: HR= 0.88, p = 1.6 × 10-9), JPH3 (cg16696007: HR= 0.87, p = 7.8 × 10-9), GPX6 (cg02793507: HR= 0.85, p = 2.7 × 10-8 and cg00647063: HR= 1.20, p = 2.5 × 10-8), chr17q25 (cg16865890: HR= 0.8, p = 6.9 × 10-8), and chr11p15 (cg13738793: HR= 1.11, p = 7.7 × 10-8). The CpG sites at C1orf151, ZNF2, JPH3 and GPX6, were identified in Black adults, chr17q25 was identified in White adults, and chr11p15 was identified upon meta-analyzing the two groups. The CpG sites at JPH3 and GPX6 were likely associated with incident type 2 diabetes independent of BMI. All the CpG sites, except at JPH3, were likely consequences of elevated glucose at baseline. We additionally replicated known type 2 diabetes-associated CpG sites including cg19693031 at TXNIP, cg00574958 at CPT1A, cg16567056 at PLBC2, cg11024682 at SREBF1, cg08857797 at VPS25, and cg06500161 at ABCG1, 3 of which were replicated in Black adults at the epigenome-wide threshold. We observed modest increase in type 2 diabetes variance explained upon addition of the significantly associated CpG sites to a Cox model that included traditional type 2 diabetes risk factors and fasting glucose (increase from 26.2% to 30.5% in Black adults; increase from 36.9% to 39.4% in White adults). We examined if groups of proximal CpG sites were associated with incident type 2 diabetes using a gene-region specific and a gene-region agnostic differentially methylated region (DMR) analysis. Our DMR analyses revealed several clusters of significant CpG sites, including a DMR consisting of a previously discovered CpG site at ADCY7 and promoter regions of TP63 which were differentially methylated across all race groups. This study illustrates improved discovery of CpG sites/regions by leveraging both individual CpG site and DMR analyses in an unexplored population. Our findings include genes linked to diabetes in experimental studies (e.g., GPX6, JPH3, and TP63), and future gene-specific methylation studies could elucidate the link between genes, environment, and methylation in the pathogenesis of type 2 diabetes.
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Affiliation(s)
- Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of American
| | - Eric Boerwinkle
- The UTHealth School of Public Health, Houston, Texas, United States of America
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Elizabeth Selvin
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology, & Clinical Research, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
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35
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Giri AK, Prasad G, Parekatt V, Rajashekar D, Tandon N, Bharadwaj D. Epigenome-wide methylation study identified two novel CpGs associated with T2DM risk and a network of co-methylated CpGs capable of patient's classifications. Hum Mol Genet 2023; 32:2576-2586. [PMID: 37184252 DOI: 10.1093/hmg/ddad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023] Open
Abstract
Prevention of Type 2 diabetes mellitus (T2DM) pandemic needs markers that can precisely predict the disease risk in an individual. Alterations in DNA methylations due to exposure towards environmental risk factors are widely sought markers for T2DM risk prediction. To identify such individual DNA methylation signatures and their effect on disease risk, we performed an epigenome-wide association study (EWAS) in 844 Indian individuals of Indo-European origin. We identified and validated methylation alterations at two novel CpG sites in MIR1287 (cg01178710) and EDN2-SCMH1 (cg04673737) genes associated with T2DM risk at the epigenome-wide-significance-level (P < 1.2 × 10-7). Further, we also replicated the association of two known CpG sites in TXNIP, and CPT1A in the Indian population. With 535 EWAS significant CpGs (P < 1.2 × 10-7) identified in the discovery phase samples, we created a co-methylation network using weighted correlation network analysis and identified four modules among the CpGs. We observed that methylation of one of the module associates with T2DM risk factors (e.g. BMI, insulin and C-peptide) and can be used as markers to segregate T2DM patients with good glycemic control (e.g. low HbA1c) and dyslipidemia (low HDL and high TG) from the other patients. Additionally, an intronic SNP (rs6503650) in the JUP gene, a member of the same module, associated with methylation at all the 14 hub CpG sites of that module as methQTL. Our network-assisted EWAS is the first to systematically explore DNA methylation variations conferring risks to T2DM in Indians and use the identified risk CpG sites for patient segregation with different clinical outcomes. These findings can be useful for better stratification of patients to improve the clinical management and treatment effects.
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Affiliation(s)
- Anil K Giri
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gauri Prasad
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vaisak Parekatt
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Donaka Rajashekar
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Nikhil Tandon
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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Ma H, Wang X, Liang Z, Li X, Heianza Y, He J, Chen W, Bazzano L, Qi L. BMI change during childhood, DNA methylation change at TXNIP, and glucose change during midlife. Obesity (Silver Spring) 2023; 31:2150-2158. [PMID: 37415079 PMCID: PMC10524171 DOI: 10.1002/oby.23806] [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: 01/18/2023] [Revised: 03/28/2023] [Accepted: 04/29/2023] [Indexed: 07/08/2023]
Abstract
OBJECTIVE This study investigated whether changes in DNA methylation (DNAm) at TXNIP are associated with glycemic changes and whether such an association differs with early-life adiposity changes. METHODS A total of 594 Bogalusa Heart Study participants who had blood DNAm measurements at two time points in midlife were included. Of them, 353 participants had at least four BMI measurements during childhood and adolescence. The incremental area under the curve was calculated as a measure of long-term trends of BMI during childhood and adolescence. RESULTS Increase in DNAm at TXNIP was significantly associated with decrease in fasting plasma glucose (FPG) independent of covariates (p < 0.001). The study found that the strength of this relationship was significantly modified by a trend of increasing BMI during childhood and adolescence (p-interaction = 0.003). Each 1% increase in DNAm at TXNIP was associated with a 2.90- (0.77) mg/dL decrease in FPG among participants with the highest tertile of BMI incremental area under the curve and a 0.96- (0.38) mg/dL decrease among those with the middle tertile, whereas no association was observed among participants with the lowest tertile. CONCLUSIONS These results indicate that changes in blood DNAm at TXNIP are significantly associated with changes in FPG in midlife, and this association was modified by BMI trends during childhood and adolescence.
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Affiliation(s)
- Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Zhaoxia Liang
- Obstetrical Department, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Jiang He
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Wei Chen
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Lydia Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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Jin J, Zhao X, Zhu C, Li M, Wang J, Fan Y, Liu C, Shen C, Yang R. Hypomethylation of ABCG1 in peripheral blood as a potential marker for the detection of coronary heart disease. Clin Epigenetics 2023; 15:120. [PMID: 37507725 PMCID: PMC10375639 DOI: 10.1186/s13148-023-01533-6] [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: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Novel molecular biomarkers for the risk assessment and early detection of coronary heart disease (CHD) are urgently needed for disease prevention. Altered methylation of ATP-binding cassette subfamily G member 1 (ABCG1) has been implicated in CHD but was mostly studied in Caucasians. Exploring the potential relationship between ABCG1 methylation in blood and CHD among the Chinese population would yield valuable insights. METHODS Peripheral blood samples were obtained from a case-control study (287 CHD patients vs. 277 controls) and a prospective nested case-control study (171 CHD patients and 197 matched controls). DNA extraction and bisulfite-specific PCR amplification techniques were employed for sample processing. Quantitative assessment of methylation levels was conducted using mass spectrometry. Statistical analyses involved the utilization of logistic regression and nonparametric tests. RESULTS We found hypomethylation of ABCG1 in whole blood was associated with the risk of CHD in both studies, which was enhanced in heart failure (HF) patients, female and younger subjects. When combined with baseline characteristics, altered ABCG1 methylation showed improved predictive effect for differentiating CHD cases, ischemic cardiomyopathy (ICM) cases, younger than 60 years CHD cases, and female CHD cases from healthy controls (area under the curve (AUC) = 0.68, 0.71, 0.74, and 0.73, respectively). CONCLUSIONS We demonstrated a robust link between ABCG1 hypomethylation in whole blood and CHD risk in the Chinese population and provided novel evidence indicating that aberrant ABCG1 methylation in peripheral blood can serve as an early detection biomarker for CHD patients.
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Affiliation(s)
- Jialie Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Xiaojing Zhao
- Military Translational Medicine Lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100000, People's Republic of China
- Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100000, People's Republic of China
| | - Chao Zhu
- Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100000, People's Republic of China
| | - Mengxia Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Jinxin Wang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, Beijing, 100000, People's Republic of China
| | - Yao Fan
- Division of Clinical Epidemiology, Affiliated Geriatric Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Chong Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China.
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, 211166, Nanjing, China.
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China.
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Wang W, Yao W, Tan Q, Li S, Duan H, Tian X, Xu C, Zhang D. Identification of key DNA methylation changes on fasting plasma glucose: a genome-wide DNA methylation analysis in Chinese monozygotic twins. Diabetol Metab Syndr 2023; 15:159. [PMID: 37461060 PMCID: PMC10351111 DOI: 10.1186/s13098-023-01136-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Elevated fasting plasma glucose (FPG) levels can increase morbidity and mortality even when it is below the diagnostic threshold of type 2 diabetes mellitus (T2DM). We conducted a genome-wide DNA methylation analysis to detect DNA methylation (DNAm) variants potentially related to FPG in Chinese monozygotic twins. METHODS Genome-wide DNA methylation profiling in whole blood of twins was performed using Reduced Representation Bisulfite Sequencing (RRBS), yielding 551,447 raw CpGs. Association between DNAm of single CpG and FPG was tested using a generalized estimation equation. Differentially methylated regions (DMRs) were identified using comb-P approach. ICE FALCON method was utilized to perform the causal inference. Candidate CpGs were quantified and validated using Sequenom MassARRAY platform in a community population. Weighted gene co-expression network analysis (WGCNA) was conducted using gene expression data from twins. RESULTS The mean age of 52 twin pairs was 52 years (SD: 7). The relationship between DNAm of 142 CpGs and FPG reached the genome-wide significance level. Thirty-two DMRs within 24 genes were identified, including TLCD1, MRPS31P5, CASZ1, and CXADRP3. The causal relationship of top CpGs mapped to TLCD1, MZF1, PTPRN2, SLC6A18, ASTN2, IQCA1, GRIN1, and PDE2A genes with FPG were further identified using ICE FALCON method. Pathways potentially related to FPG were also identified, such as phospholipid-hydroperoxide glutathione peroxidase activity and mitogen-activated protein kinase p38 binding. Three CpGs mapped to SLC6A18 gene were validated in a community population, with a hypermethylated direction in diabetic patients. The expression levels of 18 genes (including SLC6A18 and TLCD1) were positively correlated with FPG levels. CONCLUSIONS We detect many DNAm variants that may be associated with FPG in whole blood, particularly the loci within SLC6A18 gene. Our findings provide important reference for the epigenetic regulation of elevated FPG levels and diabetes.
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Affiliation(s)
- Weijing Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, No. 308 Ningxia Road, Qingdao, 266071 Shandong Province China
| | - Wenqin Yao
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, No. 308 Ningxia Road, Qingdao, 266071 Shandong Province China
- Shandong Province Center for Disease Control and Prevention, Shandong, China
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Shuxia Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention/Qingdao Institute of Preventive Medicine, Qingdao, Shandong China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention/Qingdao Institute of Preventive Medicine, Qingdao, Shandong China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention/Qingdao Institute of Preventive Medicine, Qingdao, Shandong China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, No. 308 Ningxia Road, Qingdao, 266071 Shandong Province China
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Li X, Shao X, Xue Q, Kou M, Champagne CM, Koseva BS, Heianza Y, Grundberg E, Bazzano LA, Bray GA, Sacks FM, Qi L. DNA Methylation Near CPT1A and Changes in Triglyceride-rich Lipoproteins in Response to Weight-loss Diet Interventions. J Clin Endocrinol Metab 2023; 108:e542-e549. [PMID: 36800272 PMCID: PMC10348458 DOI: 10.1210/clinem/dgad086] [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: 09/20/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
CONTEXT Carnitine palmitoyltransferase-1A, encoded by the CPT1A gene, plays a key role in the oxidation of long-chain fatty acids in the mitochondria and may be important in triglyceride metabolism. Previous work has shown that high fat intake was negatively associated with CPT1A methylation and positively associated with CPT1A expression. OBJECTIVE We aim to investigate the association of DNA methylation (DNAm) at the CPT1A gene with reductions in triglycerides and triglyceride-rich lipoproteins (TRLs) in response to weight-loss diet interventions. METHODS The current study included 538 White participants, who were randomly assigned to 1 of 4 diets varying in macronutrient components. We defined the regional DNAm at CPT1A as the average methylation level over CpGs within 500 bp of the 3 triglyceride-related DNAm sites. RESULTS Dietary fat intake significantly modified the association between baseline DNAm at CPT1A and 2-year changes in total plasma triglycerides, independent of concurrent weight loss. Among participants assigned to a low-fat diet, a higher regional DNAm level at CPT1A was associated with a greater reduction in total plasma triglycerides at 2 years (P = .01), compared with those assigned to a high-fat diet (P = .64) (P interaction = .018). Further investigation on lipids and apolipoproteins in very low-density lipoprotein (VLDL) revealed similar interaction patterns for 2-year changes in VLDL-triglycerides, VLDL-cholesterol, and VLDL-apolipoprotein B (P interaction = .009, .002, and .016, respectively), but not for VLDL-apoC-III (P interaction = .36). CONCLUSION Participants with a higher regional DNAm level at CPT1A benefit more in long-term improvement in triglycerides, particularly in the TRLs and related apolipoproteins when consuming a low-fat weight-loss diet.
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Affiliation(s)
- Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1C 0R6, Canada
| | - Qiaochu Xue
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Catherine M Champagne
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Boryana S Koseva
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Lydia A Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Juvinao-Quintero DL, Sharp GC, Sanderson ECM, Relton CL, Elliott HR. Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation. Diabetologia 2023; 66:1247-1259. [PMID: 37202507 PMCID: PMC10244277 DOI: 10.1007/s00125-023-05914-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/25/2023] [Indexed: 05/20/2023]
Abstract
AIMS/HYPOTHESIS Several studies have identified associations between type 2 diabetes and DNA methylation (DNAm). However, the causal role of these associations remains unclear. This study aimed to provide evidence for a causal relationship between DNAm and type 2 diabetes. METHODS We used bidirectional two-sample Mendelian randomisation (2SMR) to evaluate causality at 58 CpG sites previously detected in a meta-analysis of epigenome-wide association studies (meta-EWAS) of prevalent type 2 diabetes in European populations. We retrieved genetic proxies for type 2 diabetes and DNAm from the largest genome-wide association study (GWAS) available. We also used data from the Avon Longitudinal Study of Parents and Children (ALSPAC, UK) when associations of interest were not available in the larger datasets. We identified 62 independent SNPs as proxies for type 2 diabetes, and 39 methylation quantitative trait loci as proxies for 30 of the 58 type 2 diabetes-related CpGs. We applied the Bonferroni correction for multiple testing and inferred causality based on p<0.001 for the type 2 diabetes to DNAm direction and p<0.002 for the opposing DNAm to type 2 diabetes direction in the 2SMR analysis. RESULTS We found strong evidence of a causal effect of DNAm at cg25536676 (DHCR24) on type 2 diabetes. An increase in transformed residuals of DNAm at this site was associated with a 43% (OR 1.43, 95% CI 1.15, 1.78, p=0.001) higher risk of type 2 diabetes. We inferred a likely causal direction for the remaining CpG sites assessed. In silico analyses showed that the CpGs analysed were enriched for expression quantitative trait methylation sites (eQTMs) and for specific traits, dependent on the direction of causality predicted by the 2SMR analysis. CONCLUSIONS/INTERPRETATION We identified one CpG mapping to a gene related to the metabolism of lipids (DHCR24) as a novel causal biomarker for risk of type 2 diabetes. CpGs within the same gene region have previously been associated with type 2 diabetes-related traits in observational studies (BMI, waist circumference, HDL-cholesterol, insulin) and in Mendelian randomisation analyses (LDL-cholesterol). Thus, we hypothesise that our candidate CpG in DHCR24 may be a causal mediator of the association between known modifiable risk factors and type 2 diabetes. Formal causal mediation analysis should be implemented to further validate this assumption.
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Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eleanor C M Sanderson
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
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Hillary RF, McCartney DL, Smith HM, Bernabeu E, Gadd DA, Chybowska AD, Cheng Y, Murphy L, Wrobel N, Campbell A, Walker RM, Hayward C, Evans KL, McIntosh AM, Marioni RE. Blood-based epigenome-wide analyses of 19 common disease states: A longitudinal, population-based linked cohort study of 18,413 Scottish individuals. PLoS Med 2023; 20:e1004247. [PMID: 37410739 PMCID: PMC10325072 DOI: 10.1371/journal.pmed.1004247] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/25/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND DNA methylation is a dynamic epigenetic mechanism that occurs at cytosine-phosphate-guanine dinucleotide (CpG) sites. Epigenome-wide association studies (EWAS) investigate the strength of association between methylation at individual CpG sites and health outcomes. Although blood methylation may act as a peripheral marker of common disease states, previous EWAS have typically focused only on individual conditions and have had limited power to discover disease-associated loci. This study examined the association of blood DNA methylation with the prevalence of 14 disease states and the incidence of 19 disease states in a single population of over 18,000 Scottish individuals. METHODS AND FINDINGS DNA methylation was assayed at 752,722 CpG sites in whole-blood samples from 18,413 volunteers in the family-structured, population-based cohort study Generation Scotland (age range 18 to 99 years). EWAS tested for cross-sectional associations between baseline CpG methylation and 14 prevalent disease states, and for longitudinal associations between baseline CpG methylation and 19 incident disease states. Prevalent cases were self-reported on health questionnaires at the baseline. Incident cases were identified using linkage to Scottish primary (Read 2) and secondary (ICD-10) care records, and the censoring date was set to October 2020. The mean time-to-diagnosis ranged from 5.0 years (for chronic pain) to 11.7 years (for Coronavirus Disease 2019 (COVID-19) hospitalisation). The 19 disease states considered in this study were selected if they were present on the World Health Organisation's 10 leading causes of death and disease burden or included in baseline self-report questionnaires. EWAS models were adjusted for age at methylation typing, sex, estimated white blood cell composition, population structure, and 5 common lifestyle risk factors. A structured literature review was also conducted to identify existing EWAS for all 19 disease states tested. The MEDLINE, Embase, Web of Science, and preprint servers were searched to retrieve relevant articles indexed as of March 27, 2023. Fifty-four of approximately 2,000 indexed articles met our inclusion criteria: assayed blood-based DNA methylation, had >20 individuals in each comparison group, and examined one of the 19 conditions considered. First, we assessed whether the associations identified in our study were reported in previous studies. We identified 69 associations between CpGs and the prevalence of 4 conditions, of which 58 were newly described. The conditions were breast cancer, chronic kidney disease, ischemic heart disease, and type 2 diabetes mellitus. We also uncovered 64 CpGs that associated with the incidence of 2 disease states (COPD and type 2 diabetes), of which 56 were not reported in the surveyed literature. Second, we assessed replication across existing studies, which was defined as the reporting of at least 1 common site in >2 studies that examined the same condition. Only 6/19 disease states had evidence of such replication. The limitations of this study include the nonconsideration of medication data and a potential lack of generalizability to individuals that are not of Scottish and European ancestry. CONCLUSIONS We discovered over 100 associations between blood methylation sites and common disease states, independently of major confounding risk factors, and a need for greater standardisation among EWAS on human disease.
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Affiliation(s)
- Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Hannah M. Smith
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Aleksandra D. Chybowska
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- School of Psychology, University of Exeter, Exeter, United Kingdom
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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Kou M, Li X, Shao X, Grundberg E, Wang X, Ma H, Heianza Y, Martinez JA, Bray GA, Sacks FM, Qi L. DNA Methylation of Birthweight-Blood Pressure Genes and Changes of Blood Pressure in Response to Weight-Loss Diets in the POUNDS Lost Trial. Hypertension 2023; 80:1223-1230. [PMID: 37039021 PMCID: PMC10192077 DOI: 10.1161/hypertensionaha.123.20864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/26/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND DNA methylation (DNAm) may play a critical role in bridging prenatal adverse events and cardiometabolic disorders including hypertension in later life. METHODS We included 672 adult participants with overweight or obesity, who participated in a 2-year randomized weight-loss dietary intervention study. We defined the regional DNAm levels as the average methylation level of 5'-cytosine-phosphate-guanine-3' within 500 bp of LINC00319 (cg01820192), ATP2B1 (cg00508575), and LMNA (cg12593793), respectively. Generalized linear regression models were used to assess the association between the regional DNAm and 2-year blood pressure changes. Trajectory analysis was used to identify subgroups that shared a similar underlying trajectory of 2-year blood pressure changes. RESULTS The regional DNAm at LINC00319, showed significantly different associations with 2-year changes in systolic blood pressure and diastolic blood pressure among participants assigned to low- or high-fat diets (P for interaction<0.05 for all). In response to the low-fat diet, per SD higher regional DNAm at LINC00319 was associated with greater reductions in both 2-year changes in systolic blood pressure (β, -1.481; P=0.020) and diastolic blood pressure (β, -1.096; P=0.009). Three trajectories of changes in systolic blood pressure or diastolic blood pressure were identified, and participants with higher regional DNAm at LINC00319 were more likely to experience and maintain decreased systolic blood pressure and diastolic blood pressure (odds ratio of being in decrease-stable versus stable [95% CI], 1.542 [1.146-2.076] and 1.463 [1.125-1.902]). CONCLUSIONS Our findings suggest that DNAm could be a metabolic memory bridging early and later life, and an indicator of more benefits from eating a low-fat weight-loss diet.
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Affiliation(s)
- Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, United States
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - J. Alfredo Martinez
- Madrid Institute of Advance Studies (IMDEA), Research Institute on Food & Health Sciences, Precision Nutrition Program, Madrid, Spain
| | - George A. Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, United States
| | - Frank M. Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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Johansson SE, Jansåker F, Sundquist K, Bygren LO. A longitudinal study of the association between attending cultural events and coronary heart disease. COMMUNICATIONS MEDICINE 2023; 3:72. [PMID: 37225790 DOI: 10.1038/s43856-023-00301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The experiences of art and music are an essential part of human life and this study aimed to examine the longitudinal association between cultural participation and coronary heart disease. METHODS This was a longitudinal study on a randomly selected representative adult cohort (n = 3296) of the Swedish population. The study period was over 36 years (1982-2017) with three separate eight-year interval measurements of cultural exposure (for example, visiting theatres and museums) starting in 1982/83. The outcome was coronary heart disease during the study period. Marginal structural Cox models with inverse probability weighting were used to account for time-varying weights of the exposure and potential confounders during the follow-up. The associations were also examined through a time-varying Cox proportional hazard regression model. RESULTS Cultural participation shows a graded association, the higher the exposure the lower the risk of coronary heart disease; the hazard ratio was 0.66 (95% confidence interval, 0.50 to 0.86) for coronary heart disease in participants with the highest level of cultural exposure compared with the lowest level. CONCLUSION Although causality cannot be determined due to the remaining risk of residual confounding and bias, the use of marginal structural Cox models with inverse probability weighting strengthens the evidence for a potentially causal association with cardiovascular health, which warrants further studies.
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Affiliation(s)
- Sven-Erik Johansson
- Center for Primary Health Care Research, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Filip Jansåker
- Center for Primary Health Care Research, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden.
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Kristina Sundquist
- Center for Primary Health Care Research, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, USA
- Center for Community-based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Shimane, Japan
| | - Lars Olov Bygren
- Community Medicine and Rehabilitation, Umeå University, Umeå, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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Li KY, Tam CHT, Liu H, Day S, Lim CKP, So WY, Huang C, Jiang G, Shi M, Lee HM, Lan HY, Szeto CC, Hanson RL, Nelson RG, Susztak K, Chan JCN, Yip KY, Ma RCW. DNA methylation markers for kidney function and progression of diabetic kidney disease. Nat Commun 2023; 14:2543. [PMID: 37188670 PMCID: PMC10185566 DOI: 10.1038/s41467-023-37837-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
Epigenetic markers are potential biomarkers for diabetes and related complications. Using a prospective cohort from the Hong Kong Diabetes Register, we perform two independent epigenome-wide association studies to identify methylation markers associated with baseline estimated glomerular filtration rate (eGFR) and subsequent decline in kidney function (eGFR slope), respectively, in 1,271 type 2 diabetes subjects. Here we show 40 (30 previously unidentified) and eight (all previously unidentified) CpG sites individually reach epigenome-wide significance for baseline eGFR and eGFR slope, respectively. We also develop a multisite analysis method, which selects 64 and 37 CpG sites for baseline eGFR and eGFR slope, respectively. These models are validated in an independent cohort of Native Americans with type 2 diabetes. Our identified CpG sites are near genes enriched for functional roles in kidney diseases, and some show association with renal damage. This study highlights the potential of methylation markers in risk stratification of kidney disease among type 2 diabetes individuals.
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Affiliation(s)
- Kelly Yichen Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Claudia Ha Ting Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Samantha Day
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies and Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Cadmon King Poo Lim
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Heung Man Lee
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Cheuk-Chun Szeto
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert G Nelson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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Conole ELS, Vaher K, Cabez MB, Sullivan G, Stevenson AJ, Hall J, Murphy L, Thrippleton MJ, Quigley AJ, Bastin ME, Miron VE, Whalley HC, Marioni RE, Boardman JP, Cox SR. Immuno-epigenetic signature derived in saliva associates with the encephalopathy of prematurity and perinatal inflammatory disorders. Brain Behav Immun 2023; 110:322-338. [PMID: 36948324 DOI: 10.1016/j.bbi.2023.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/12/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Preterm birth is closely associated with a phenotype that includes brain dysmaturation and neurocognitive impairment, commonly termed Encephalopathy of Prematurity (EoP), of which systemic inflammation is considered a key driver. DNA methylation (DNAm) signatures of inflammation from peripheral blood associate with poor brain imaging outcomes in adult cohorts. However, the robustness of DNAm inflammatory scores in infancy, their relation to comorbidities of preterm birth characterised by inflammation, neonatal neuroimaging metrics of EoP, and saliva cross-tissue applicability are unknown. METHODS Using salivary DNAm from 258 neonates (n = 155 preterm, gestational age at birth 23.28 - 34.84 weeks, n = 103 term, gestational age at birth 37.00 - 42.14 weeks), we investigated the impact of a DNAm surrogate for C-reactive protein (DNAm CRP) on brain structure and other clinically defined inflammatory exposures. We assessed i) if DNAm CRP estimates varied between preterm infants at term equivalent age and term infants, ii) how DNAm CRP related to different types of inflammatory exposure (maternal, fetal and postnatal) and iii) whether elevated DNAm CRP associated with poorer measures of neonatal brain volume and white matter connectivity. RESULTS Higher DNAm CRP was linked to preterm status (-0.0107 ± 0.0008, compared with -0.0118 ± 0.0006 among term infants; p < 0.001), as well as perinatal inflammatory diseases, including histologic chorioamnionitis, sepsis, bronchopulmonary dysplasia, and necrotising enterocolitis (OR range |2.00 | to |4.71|, p < 0.01). Preterm infants with higher DNAm CRP scores had lower brain volume in deep grey matter, white matter, and hippocampi and amygdalae (β range |0.185| to |0.218|). No such associations were observed for term infants. Association magnitudes were largest for measures of white matter microstructure among preterms, where elevated epigenetic inflammation associated with poorer global measures of white matter integrity (β range |0.206| to |0.371|), independent of other confounding exposures. CONCLUSIONS Inflammatory-related DNAm captures the allostatic load of inflammatory burden in preterm infants. Such DNAm measures complement biological and clinical metrics when investigating the determinants of neurodevelopmental differences.
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Affiliation(s)
- Eleanor L S Conole
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Kadi Vaher
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Manuel Blesa Cabez
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Gemma Sullivan
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jill Hall
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael J Thrippleton
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alan J Quigley
- Imaging Department, Royal Hospital for Children and Young People, Edinburgh, EH16 4TJ, UK
| | - Mark E Bastin
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Veronique E Miron
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Heather C Whalley
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - James P Boardman
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
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Cheng Y, Gadd DA, Gieger C, Monterrubio-Gómez K, Zhang Y, Berta I, Stam MJ, Szlachetka N, Lobzaev E, Wrobel N, Murphy L, Campbell A, Nangle C, Walker RM, Fawns-Ritchie C, Peters A, Rathmann W, Porteous DJ, Evans KL, McIntosh AM, Cannings TI, Waldenberger M, Ganna A, McCartney DL, Vallejos CA, Marioni RE. Development and validation of DNA methylation scores in two European cohorts augment 10-year risk prediction of type 2 diabetes. NATURE AGING 2023; 3:450-458. [PMID: 37117793 DOI: 10.1038/s43587-023-00391-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/27/2023] [Indexed: 04/30/2023]
Abstract
Type 2 diabetes mellitus (T2D) presents a major health and economic burden that could be alleviated with improved early prediction and intervention. While standard risk factors have shown good predictive performance, we show that the use of blood-based DNA methylation information leads to a significant improvement in the prediction of 10-year T2D incidence risk. Previous studies have been largely constrained by linear assumptions, the use of cytosine-guanine pairs one-at-a-time and binary outcomes. We present a flexible approach (via an R package, MethylPipeR) based on a range of linear and tree-ensemble models that incorporate time-to-event data for prediction. Using the Generation Scotland cohort (training set ncases = 374, ncontrols = 9,461; test set ncases = 252, ncontrols = 4,526) our best-performing model (area under the receiver operating characteristic curve (AUC) = 0.872, area under the precision-recall curve (PRAUC) = 0.302) showed notable improvement in 10-year onset prediction beyond standard risk factors (AUC = 0.839, precision-recall AUC = 0.227). Replication was observed in the German-based KORA study (n = 1,451, ncases = 142, P = 1.6 × 10-5).
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Affiliation(s)
- Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Karla Monterrubio-Gómez
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Yufei Zhang
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Imrich Berta
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Michael J Stam
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | | | - Evgenii Lobzaev
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Cliff Nangle
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Chloe Fawns-Ritchie
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, München, Germany
| | - Wolfgang Rathmann
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Institute for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Catalina A Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- The Alan Turing Institute, London, UK.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Feng B, Wang L, Wei D, Huo W, Jing T, Wang C, Mao Z. Combined Effects of ESRα DNA Methylation and Progesterone on Glucose Metabolic Disorders: The Henan Rural Cohort Study. Nutrients 2023; 15:nu15071659. [PMID: 37049500 PMCID: PMC10096615 DOI: 10.3390/nu15071659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
To explore the independent and combined effects of ESRα methylation and progesterone on impaired fasting glucose (IFG) and type 2 diabetes mellitus (T2DM), a case-control study including 901 subjects was conducted. Generalized linear models were performed to assess the independent and combined effects of ESRα methylation and progesterone on IFG or T2DM. Methylation level of cytosine-phosphoguanine (CpG) 1 in the estrogen receptor α (ESRα) gene was positively related to IFG in both men (odds ratio (OR) (95% confidence interval (CI)): 1.77 (1.05, 3.00)) and postmenopausal women (OR (95% CI): 1.82 (1.09, 3.04)), whereas the association between CpG 1 and T2DM was not significant. Positive associations of progesterone with IFG and T2DM were observed in both men (OR (95% CI): 2.03 (1.18, 3.49) and 3.00 (1.63, 5.52)) and postmenopausal women (OR (95% CI): 2.13 (1.27, 3.56) and 3.30 (1.85, 5.90)). Participants with high CpG 1 methylation plus high progesterone had an increased risk of IFG and T2DM, both in men and postmenopausal women. ESRα methylation and progesterone were positively associated with IFG, and the positive association between progesterone and T2DM was also found. Importantly, we firstly found the combined effects of ESRα methylation and progesterone on IFG and T2DM.
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48
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Narayan KMV, Varghese JS, Beyh YS, Bhattacharyya S, Khandelwal S, Krishnan GS, Siegel KR, Thomas T, Kurpad AV. A Strategic Research Framework for Defeating Diabetes in India: A 21st-Century Agenda. J Indian Inst Sci 2023; 103:1-22. [PMID: 37362852 PMCID: PMC10029804 DOI: 10.1007/s41745-022-00354-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/14/2022] [Indexed: 03/24/2023]
Abstract
Indian people are at high risk for type 2 diabetes (T2DM) even at younger ages and lower body weights. Already 74 million people in India have the disease, and the proportion of those with T2DM is increasing across all strata of society. Unique aspects, related to lower insulin secretion or function, and higher hepatic fat deposition, accompanied by the rise in overweight (related to lifestyle changes) may all be responsible for this unrelenting epidemic of T2DM. Yet, research to understand the causes, pathophysiology, phenotypes, prevention, treatment, and healthcare delivery of T2DM in India seriously lags behind. There are major opportunities for scientific discovery and technological innovation, which if tapped can generate solutions for T2DM relevant to the country's context and make leading contributions to global science. We analyze the situation of T2DM in India, and present a four-pillar (etiology, precision medicine, implementation research, and health policy) strategic research framework to tackle the challenge. We offer key research questions for each pillar, and identify infrastructure needs. India offers a fertile environment for shifting the paradigm from imprecise late-stage diabetes treatment toward early-stage precision prevention and care. Investing in and leveraging academic and technological infrastructures, across the disciplines of science, engineering, and medicine, can accelerate progress toward a diabetes-free nation.
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Affiliation(s)
- K. M. Venkat Narayan
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Emory Global Diabetes Research Center, Woodruff Health Sciences Center, Emory University, Atlanta, GA 30322 USA
| | - Jithin Sam Varghese
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Emory Global Diabetes Research Center, Woodruff Health Sciences Center, Emory University, Atlanta, GA 30322 USA
| | - Yara S. Beyh
- Laney Graduate School, Nutrition and Health Sciences Doctoral Program, Emory University, Atlanta, USA
| | | | | | - Gokul S. Krishnan
- Robert Bosch Centre for Data Science and Artificial Intelligence, Indian Institute of Technology Madras, Chennai, India
| | - Karen R. Siegel
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Emory Global Diabetes Research Center, Woodruff Health Sciences Center, Emory University, Atlanta, GA 30322 USA
| | - Tinku Thomas
- Department of Biostatistics, St. John’s Medical College, Bengaluru, India
| | - Anura V. Kurpad
- Department of Physiology, St. John’s Medical College, Bengaluru, India
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49
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Wu YL, Lin ZJ, Li CC, Lin X, Shan SK, Guo B, Zheng MH, Li F, Yuan LQ, Li ZH. Epigenetic regulation in metabolic diseases: mechanisms and advances in clinical study. Signal Transduct Target Ther 2023; 8:98. [PMID: 36864020 PMCID: PMC9981733 DOI: 10.1038/s41392-023-01333-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/02/2023] [Accepted: 01/18/2023] [Indexed: 03/04/2023] Open
Abstract
Epigenetics regulates gene expression and has been confirmed to play a critical role in a variety of metabolic diseases, such as diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), osteoporosis, gout, hyperthyroidism, hypothyroidism and others. The term 'epigenetics' was firstly proposed in 1942 and with the development of technologies, the exploration of epigenetics has made great progresses. There are four main epigenetic mechanisms, including DNA methylation, histone modification, chromatin remodelling, and noncoding RNA (ncRNA), which exert different effects on metabolic diseases. Genetic and non-genetic factors, including ageing, diet, and exercise, interact with epigenetics and jointly affect the formation of a phenotype. Understanding epigenetics could be applied to diagnosing and treating metabolic diseases in the clinic, including epigenetic biomarkers, epigenetic drugs, and epigenetic editing. In this review, we introduce the brief history of epigenetics as well as the milestone events since the proposal of the term 'epigenetics'. Moreover, we summarise the research methods of epigenetics and introduce four main general mechanisms of epigenetic modulation. Furthermore, we summarise epigenetic mechanisms in metabolic diseases and introduce the interaction between epigenetics and genetic or non-genetic factors. Finally, we introduce the clinical trials and applications of epigenetics in metabolic diseases.
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Affiliation(s)
- Yan-Lin Wu
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Zheng-Jun Lin
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Chang-Chun Li
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Xiao Lin
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Su-Kang Shan
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Bei Guo
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Ming-Hui Zheng
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Fuxingzi Li
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Ling-Qing Yuan
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Zhi-Hong Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
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Fragoso-Bargas N, Elliott HR, Lee-Ødegård S, Opsahl JO, Sletner L, Jenum AK, Drevon CA, Qvigstad E, Moen GH, Birkeland KI, Prasad RB, Sommer C. Cross-Ancestry DNA Methylation Marks of Insulin Resistance in Pregnancy: An Integrative Epigenome-Wide Association Study. Diabetes 2023; 72:415-426. [PMID: 36534481 PMCID: PMC9935495 DOI: 10.2337/db22-0504] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Although there are some epigenome-wide association studies (EWAS) of insulin resistance, for most of them authors did not replicate their findings, and most are focused on populations of European ancestry, limiting the generalizability. In the Epigenetics in Pregnancy (EPIPREG; n = 294 Europeans and 162 South Asians) study, we conducted an EWAS of insulin resistance in maternal peripheral blood leukocytes, with replication in the Born in Bradford (n = 879; n = 430 Europeans and 449 South Asians), Methyl Epigenome Network Association (MENA) (n = 320), and Botnia (n = 56) cohorts. In EPIPREG, we identified six CpG sites inversely associated with insulin resistance across ancestry, of which five were replicated in independent cohorts (cg02988288, cg19693031, and cg26974062 in TXNIP; cg06690548 in SLC7A11; and cg04861640 in ZSCAN26). From methylation quantitative trait loci analysis in EPIPREG, we identified gene variants related to all five replicated cross-ancestry CpG sites, which were associated with several cardiometabolic phenotypes. Mediation analyses suggested that the gene variants regulate insulin resistance through DNA methylation. To conclude, our cross-ancestry EWAS identified five CpG sites related to lower insulin resistance.
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Affiliation(s)
- Nicolas Fragoso-Bargas
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hannah R. Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Sindre Lee-Ødegård
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Julia O. Opsahl
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Line Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Anne Karen Jenum
- General Practice Research Unit (AFE), Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Christian A. Drevon
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Vitas Ltd. Analytical Services, Oslo Science Park, Oslo, Norway
| | - Elisabeth Qvigstad
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Institute of Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kåre I. Birkeland
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rashmi B. Prasad
- Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Christine Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
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