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Ozuynuk-Ertugrul AS, Kirsan CB, Erkan AF, Ekici B, Komurcu-Bayrak E, Coban N. Genetic variants of ANRIL and coronary artery disease: Insights from a Turkish study population. Gene 2024; 917:148475. [PMID: 38631653 DOI: 10.1016/j.gene.2024.148475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND AND AIM Coronary artery disease (CAD) remains a leading cause of morbidity and mortality globally despite advancements in treatment. Long non-coding RNAs (lncRNAs) play crucial roles in the atherosclerotic process, with ANRIL being one such lncRNA. This study explored the association between ANRIL polymorphisms (rs1333049:C > G, rs564398:T > C, and rs10757274:A > G) and CAD along with CAD risk factors in a Turkish patient group. METHODS The study included 1285 participants, consisting of 736 patients diagnosed with CAD (mean age = 63.3 ± 10.5 years) and 549 non-CAD controls (mean age = 57.52 ± 11.01 years). Genotypes for rs1333049, rs564398, and rs10757274 were determined using qRT-PCR. RESULTS G allele carriage of both rs1333049 and rs10757274 polymorphisms were associated with higher Gensini score, SYNTAX score, total cholesterol, and triglyceride levels in female CAD patients and non-CAD males. Females with rs564398 CC genotype were more susceptible to CAD (p = 0.02) and severe CAD (p = 0.05). Moreover, the G and T alleles of rs10757274 and rs564398 were more prevalent among hypertensive males. Also, carrying the C allele for rs564398 was associated with a decreased risk for type 2 diabetes mellitus (T2DM) (p = 0.02). Besides, carriers of the rs1333049 C allele for decreased risk for T2DM (p = 0.03) and CAD complexed with T2DM (p = 0.04) in logistic regression analyses. CONCLUSIONS In conclusion, selected ANRIL polymorphisms were associated with CAD presence/severity and CAD risk factors, T2DM, and hypertension. Notably, this study, the largest sample-sized study examining the effects of selected polymorphisms on CAD and its risk factors among Turkish individuals, supported the findings of previous studies conducted on different ethnicities.
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Affiliation(s)
- Aybike Sena Ozuynuk-Ertugrul
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, Istanbul, Turkey; Istanbul University Institute of Graduate Studies in Health Sciences, Istanbul, Turkey
| | - Cemre Buse Kirsan
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, Istanbul, Turkey; Istanbul University Institute of Graduate Studies in Health Sciences, Istanbul, Turkey
| | - Aycan Fahri Erkan
- Ufuk University, Faculty of Medicine, Department of Cardiology, Ankara, Turkey
| | - Berkay Ekici
- Ufuk University, Faculty of Medicine, Department of Cardiology, Ankara, Turkey
| | - Evrim Komurcu-Bayrak
- Istanbul University, Istanbul Faculty of Medicine, Department of Medical Genetics, Istanbul, Turkey
| | - Neslihan Coban
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, Istanbul, Turkey.
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Li Y, Wu J, Tang H, Jia X, Wang J, Meng C, Wang W, Liu S, Yuan H, Cai J, Wang J, Lu Y. Long-term PM 2.5 exposure and early-onset diabetes: Does BMI link this risk? Sci Total Environ 2024; 913:169791. [PMID: 38176550 DOI: 10.1016/j.scitotenv.2023.169791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
OBJECTIVE Limited studies investigated the association between high-level fine particulate matter (PM2.5) pollution and early-onset diabetes, leaving the possible metabolic mechanisms unclear. We assessed the association of cumulative PM2.5 exposure with diabetes, including early-onset, in high-pollution areas of China and explored whether metabolic factors mediated this association. METHODS 124,204 participants (≥18 years) from 121 counties in Hunan province, China, were enrolled between 2005 and 2020, with follow-up until 2021. The ground-level air pollution concentrations at each participant's residence were calculated using a high-quality dataset in China. The independent association of PM2.5 with incident diabetes and early-onset diabetes was assessed by Cox proportional hazards models. Restricted cubic splines were utilized to establish the exposure-response relationships. The role of metabolism-related mediators was estimated by mediation analysis. RESULTS During a median follow-up of 8.47 (IQR, 6.65-9.82) years, there were 3650 patients with new-onset diabetes. Each 1 μg/m3 increase in the level of cumulative PM2.5 exposure was positively related to an increased incidence of diabetes (HR 1.177, 95 % CI 1.172-1.181) among individuals in the PM2.5 > 50 μg/m3 group after adjusting for multiple variables. The relationship of the PM2.5 dose-response curve for diabetes was non-linear. Significant associations between PM2.5 exposure and early-onset diabetes risk were observed, with this risk showing an increase with the earlier age of early diabetes onset. Males, young individuals (≤45 years), and those with a lower body mass index (BMI <24 kg/m2) appeared to be more susceptible to diabetes. Moreover, change in BMI significantly mediated 31.06 % of the PM2.5-diabetes relationship. CONCLUSIONS Long-term cumulative PM2.5 exposure increased the risk of early-onset diabetes, which is partially mediated by BMI. Sustained air pollution control measures, priority protection of vulnerable individuals, and effective management of BMI should be taken to reduce the burden of diabetes.
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Affiliation(s)
- Yalan Li
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingjing Wu
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haibo Tang
- Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xinru Jia
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie Wang
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Changjiang Meng
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Wang
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shiqi Liu
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong Yuan
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China; Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingjing Cai
- Department of Cardiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jiangang Wang
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China.
| | - Yao Lu
- Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China; Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK.
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Xu Z, He J, Han P, Dai P, Lv W, Liu N, Liu L, Liu L, Pan X, Xiang X, Li H, Ge F, Gao S, Liao Z, Luo Y, Li Y. Plasma extrachromosomal circular DNA is a pathophysiological hallmark of short-term intensive insulin therapy for type 2 diabetes. Clin Transl Med 2023; 13:e1437. [PMID: 37859516 PMCID: PMC10587738 DOI: 10.1002/ctm2.1437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/14/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Extrachromosomal circular DNA (eccDNA) has emerged as a promising biomarker for disease diagnosis and prognosis prediction. However, its role in type 2 diabetes remains unexplored. OBJECTIVE To investigate the characteristics and dynamics of circulating eccDNAs in newly diagnosed type 2 diabetes mellitus (T2DM) patients undergoing short-term intensive insulin therapy (SIIT), a highly effective treatment for inducing long-term glycemic remission. METHODS We conducted Circle-Seq analysis on plasma samples from 35 T2DM patients at three time points: pre-SIIT, post-SIIT, and 1-year post-SIIT. Our analysis encompassed the characterization of eccDNA features, including GC content, eccDNA length distribution, genomic distribution, and the genes in eccDNAs. RESULTS Following SIIT, we observed an increase in plasma eccDNA load, suggesting metabolic alterations during therapy. Notably, a correlation was identified between eccDNA profiles and glycemia in T2DM, both quantitatively and genetically. Our analysis also revealed the frequent presence of metabolism-related genes within T2DM plasma eccDNAs, some of which spanned gene exons and/or fractions. CONCLUSION This study represents the first report of cell-free eccDNA in T2DM and underscores a compelling association between cell-free eccDNA and profound glycemic changes. These findings highlight the potential of eccDNAs as crucial players in the context of T2DM and glycemic control.
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Affiliation(s)
- Zhe Xu
- College of Life SciencesUniversity of Chinese Academy of ScienceBeijingChina
| | - Junyu He
- Department of EndocrinologyThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
| | - Peng Han
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI ResearchQingdaoChina
| | - Peiji Dai
- Department of EndocrinologyThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
| | - Wei Lv
- College of Life SciencesUniversity of Chinese Academy of ScienceBeijingChina
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI ResearchQingdaoChina
| | - Nian Liu
- Department of Biochemistry and Molecular BiologySchool of Basic MedicineQingdao UniversityQingdaoChina
| | - Liyi Liu
- Department of EndocrinologyThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
| | - Liehua Liu
- Department of EndocrinologyThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI ResearchQingdaoChina
| | - Xi Xiang
- Scientific Research CenterThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenPeople's Republic of China
| | | | - Fangfang Ge
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI ResearchQingdaoChina
| | - Shan Gao
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI ResearchQingdaoChina
| | - Zhihong Liao
- Department of EndocrinologyThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI ResearchQingdaoChina
- BGI ResearchShenzhenChina
| | - Yanbing Li
- Department of EndocrinologyThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
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Satyadev N, Rivera MI, Nikolov NK, Fakoya AOJ. Exosomes as biomarkers and therapy in type 2 diabetes mellitus and associated complications. Front Physiol 2023; 14:1241096. [PMID: 37745252 PMCID: PMC10515224 DOI: 10.3389/fphys.2023.1241096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is one of the most prevalent metabolic disorders worldwide. However, T2DM still remains underdiagnosed and undertreated resulting in poor quality of life and increased morbidity and mortality. Given this ongoing burden, researchers have attempted to locate new therapeutic targets as well as methodologies to identify the disease and its associated complications at an earlier stage. Several studies over the last few decades have identified exosomes, small extracellular vesicles that are released by cells, as pivotal contributors to the pathogenesis of T2DM and its complications. These discoveries suggest the possibility of novel detection and treatment methods. This review provides a comprehensive presentation of exosomes that hold potential as novel biomarkers and therapeutic targets. Additional focus is given to characterizing the role of exosomes in T2DM complications, including diabetic angiopathy, diabetic cardiomyopathy, diabetic nephropathy, diabetic peripheral neuropathy, diabetic retinopathy, and diabetic wound healing. This study reveals that the utilization of exosomes as diagnostic markers and therapies is a realistic possibility for both T2DM and its complications. However, the majority of the current research is limited to animal models, warranting further investigation of exosomes in clinical trials. This review represents the most extensive and up-to-date exploration of exosomes in relation to T2DM and its complications.
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Affiliation(s)
- Nihal Satyadev
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, United States
| | - Milagros I. Rivera
- University of Medicine and Health Sciences, Basseterre, St. Kitts and Nevis
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Liu Q, Peng Q, Zhang B, Tan Y. X-ray cross-complementing family: the bridge linking DNA damage repair and cancer. J Transl Med 2023; 21:602. [PMID: 37679817 PMCID: PMC10483876 DOI: 10.1186/s12967-023-04447-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
Genomic instability is a common hallmark of human tumours. As a carrier of genetic information, DNA is constantly threatened by various damaging factors that, if not repaired in time, can affect the transmission of genetic information and lead to cellular carcinogenesis. In response to these threats, cells have evolved a range of DNA damage response mechanisms, including DNA damage repair, to maintain genomic stability. The X-ray repair cross-complementary gene family (XRCC) comprises an important class of DNA damage repair genes that encode proteins that play important roles in DNA single-strand breakage and DNA base damage repair. The dysfunction of the XRCC gene family is associated with the development of various tumours. In the context of tumours, mutations in XRCC and its aberrant expression, result in abnormal DNA damage repair, thus contributing to the malignant progression of tumour cells. In this review, we summarise the significant roles played by XRCC in diverse tumour types. In addition, we discuss the correlation between the XRCC family members and tumour therapeutic sensitivity.
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Affiliation(s)
- Qiang Liu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, Hunan, China
| | - Qiu Peng
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China
| | - Bin Zhang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
| | - Yueqiu Tan
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, Hunan, China.
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Jackson JT, Nutt SL, McCormack MP. The Haematopoietically-expressed homeobox transcription factor: roles in development, physiology and disease. Front Immunol 2023; 14:1197490. [PMID: 37398663 PMCID: PMC10313424 DOI: 10.3389/fimmu.2023.1197490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
The Haematopoietically expressed homeobox transcription factor (Hhex) is a transcriptional repressor that is of fundamental importance across species, as evident by its evolutionary conservation spanning fish, amphibians, birds, mice and humans. Indeed, Hhex maintains its vital functions throughout the lifespan of the organism, beginning in the oocyte, through fundamental stages of embryogenesis in the foregut endoderm. The endodermal development driven by Hhex gives rise to endocrine organs such as the pancreas in a process which is likely linked to its role as a risk factor in diabetes and pancreatic disorders. Hhex is also required for the normal development of the bile duct and liver, the latter also importantly being the initial site of haematopoiesis. These haematopoietic origins are governed by Hhex, leading to its crucial later roles in definitive haematopoietic stem cell (HSC) self-renewal, lymphopoiesis and haematological malignancy. Hhex is also necessary for the developing forebrain and thyroid gland, with this reliance on Hhex evident in its role in endocrine disorders later in life including a potential role in Alzheimer's disease. Thus, the roles of Hhex in embryological development throughout evolution appear to be linked to its later roles in a variety of disease processes.
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Affiliation(s)
- Jacob T. Jackson
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Stephen L. Nutt
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Matthew P. McCormack
- The Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
- iCamuno Biotherapeutics, Melbourne, VIC, Australia
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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: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Abu Seman N, Othman SH. Recent Progress in Genetics and Epigenetics Research on Diabetic Nephropathy in Malaysia. J Diabetes Res 2023; 2023:9053580. [PMID: 37187702 PMCID: PMC10181909 DOI: 10.1155/2023/9053580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/15/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Diabetic nephropathy is a multifactorial disease. Gene susceptibility, as well as environmental exposure, plays an important role in disease progression. Malaysia is reported to be among the world's second-fastest-growing rates of kidney failure. Diabetic nephropathy has become the main cause of end-stage renal disease in Malaysia. This article is aimed at reviewing genetic studies conducted among diabetic nephropathy patients in the Malaysian population. This review was conducted by searching PubMed, MEDLINE, and Google Scholar databases to identify all relevant papers published in English from March 2022 to April 2022, using the following keywords: diabetes, type 2 diabetes, diabetic nephropathy, diabetic kidney disease, and Malaysia. The case-control study among diabetic patients with and without diabetic nephropathy showed a significant association with diabetic nephropathy in CNDP1, NOS3, and MnSOD genes. In the ethnic subgroup analysis, significant differences for diabetic nephropathy in terms of diabetes duration (≥10 years) were observed for CCL2 rs3917887, CCR5 rs1799987, ELMO1 rs74130, and IL8 rs4073. The IL8 rs4073 was associated only with the Indians, while the CCR5 rs1799987 was associated with the Chinese. In Malays, SLC12A3 Arg913Gln polymorphism and ICAM1 K469E (A/G) polymorphism were found to be associated with diabetic nephropathy. Studies on gene-environment interactions have suggested significant genetic and environmental factors such as smoking, waist circumference, and sex for eNOS rs2070744, PPARGC1A rs8192678, KCNQ1 rs2237895, and KCNQ1 rs2283228 with kidney disease. The genetic variants' contributions differed across ethnic groups. Therefore, a study to validate the genetic variants that are found to be associated with different ethnicities in Malaysia may be important in future studies.
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Affiliation(s)
- Norhashimah Abu Seman
- Endocrine and Metabolic Unit, Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Siti Haslina Othman
- Endocrine and Metabolic Unit, Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
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Chaar DL, Nguyen K, Wang Y, Ratliff SM, Mosley TH, Kardia SLR, Smith JA, Zhao W. SNP-by-CpG Site Interactions in ABCA7 Are Associated with Cognition in Older African Americans. Genes (Basel) 2022; 13:2150. [DOI: 10.3390/genes13112150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
SNPs in ABCA7 confer the largest genetic risk for Alzheimer’s Disease (AD) in African Americans (AA) after APOE ε4. However, the relationship between ABCA7 and cognitive function has not been thoroughly examined. We investigated the effects of five known AD risk SNPs and 72 CpGs in ABCA7, as well as their interactions, on general cognitive function (cognition) in 634 older AA without dementia from Genetic Epidemiology Network of Arteriopathy (GENOA). Using linear mixed models, no SNP or CpG was associated with cognition after multiple testing correction, but five CpGs were nominally associated (p < 0.05). Four SNP-by-CpG interactions were associated with cognition (FDR q < 0.1). Contrast tests show that methylation is associated with cognition in some genotype groups (p < 0.05): a 1% increase at cg00135882 and cg22271697 is associated with a 0.68 SD decrease and 0.14 SD increase in cognition for those with the rs3764647 GG/AG (p = 0.004) and AA (p = 2 × 10−4) genotypes, respectively. In addition, a 1% increase at cg06169110 and cg17316918 is associated with a 0.37 SD decrease (p = 2 × 10−4) and 0.33 SD increase (p = 0.004), respectively, in cognition for those with the rs115550680 GG/AG genotype. While AD risk SNPs in ABCA7 were not associated with cognition in this sample, some have interactions with proximal methylation on cognition.
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Abstract
Data generated over nearly two decades clearly demonstrate the importance of epigenetic modifications and mechanisms in the pathogenesis of type 2 diabetes. However, the role of pharmacoepigenetics in type 2 diabetes is less well established. The field of pharmacoepigenetics covers epigenetic biomarkers that predict response to therapy, therapy-induced epigenetic alterations as well as epigenetic therapies including inhibitors of epigenetic enzymes. Not all individuals with type 2 diabetes respond to glucose-lowering therapies in the same way, and there is therefore a need for clinically useful biomarkers that discriminate responders from non-responders. Blood-based epigenetic biomarkers may be useful for this purpose. There is also a need for a better understanding of whether existing glucose-lowering therapies exert their function partly through therapy-induced epigenetic alterations. Finally, epigenetic enzymes may be drug targets for type 2 diabetes. Here, I discuss whether pharmacoepigenetics is clinically relevant for type 2 diabetes based on studies addressing this topic.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
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Goyal Y, Verma AK, Kumar S, Bhatt D, Ahmad F, Dev K. Association of SLC30A8 (rs13266634) and GLIS3 (rs7034200) gene variant in development of type 2 diabetes mellitus in Indian population: A case-control study. Gene Reports 2022. [DOI: 10.1016/j.genrep.2022.101655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Hu F, Zhang Y, Qin P, Zhao Y, Liu D, Zhou Q, Tian G, Li Q, Guo C, Wu X, Qie R, Huang S, Han M, Li Y, Hu D, Zhang M. Integrated analysis of probability of type 2 diabetes mellitus with polymorphisms and methylation of SLC30A8 gene: a nested case-control study. J Hum Genet 2022; 67:651-660. [PMID: 35996015 DOI: 10.1038/s10038-022-01067-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/16/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
To estimate the associations between single-nucleotide polymorphisms (SNPs) and methylation of SLC30A8 gene and T2DM risk, and the interactions among SNPs, methylation, and environmental factors on T2DM risk. We genotyped 9 SNPs and tested methylation at 46 CpG loci of SLC30A8 in the baseline DNA of 290 T2DM cases and 290 matched controls nested in the Rural Chinese Cohort Study. A conditional logistic regression model was used to estimate the associations between SNPs and SLC30A8 methylation and T2DM risk. Multifactor Dimensionality Reduction analysis was used to estimate the effect of interactions among SNPs, methylation, and environment on T2DM risk. Probability of T2DM was decreased with rs11558471 (GG vs. AA, OR = 0.55, 95% CI 0.32, 0.96), with rs13266634 (TT vs. CC, OR = 0.55, 95% CI 0.32, 0.94), with rs3802177 (AA vs. GG, OR = 0.54, 95%CI 0.31, 0.94), and its probability was increased with rs2466293 of SLC30A8 (GA vs. AA, OR = 1.63, 95% CI 1.08-2.47). Its probability was also significantly associated with methylation of CG9 and CG45 (OR = 0.56 [95% CI 0.33-0.97] and 1.61 [95%CI 1.03--2.51]). T2DM probability was significantly associated with the interaction effect between rs2466293 and hypertension (p = 0.045). T2DM probability was also significantly associated with the combination effects of rs2466293 with BMI, hypertension, and hypertriglyceridemia, with the combination effects of hypertriglyceridemia with rs11558471, rs13266634, and methylation of CG45.
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Affiliation(s)
- Fulan Hu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yanyan Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Pei Qin
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yang Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Dechen Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Qionggui Zhou
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Gang Tian
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Quanman Li
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Chunmei Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xiaoyan Wu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Ranran Qie
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Shengbing Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Minghui Han
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yang Li
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Dongsheng Hu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Ming Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China.
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Li W, Wang Y, Huang R, Lian F, Xu G, Wang W, Xue S. Association of lipid metabolism-related gene promoter methylation with risk of coronary artery disease. Mol Biol Rep 2022. [PMID: 35941416 DOI: 10.1007/s11033-022-07789-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND Coronary artery disease (CAD) is a complex disease that is influenced by environmental and genetic factors. Lipid levels are regarded as a major risk factor for CAD, and epigenetic mechanisms might be involved in the regulation of CAD development. This study was designed to investigate the association between the DNA methylation status of 8 lipid metabolism-related genes and the risk of CAD in the Chinese Han population. METHODS A total of 260 individuals were sampled in this study, including 120 CAD cases and 140 normal healthy controls. DNA methylation status was tested via targeted bisulfite sequencing. RESULTS The results indicated a significant association between hypomethylation of the APOC3, CETP and APOC1 gene promoters and the risk of CAD. Individuals with higher methylation levels of the APOA5 and LIPC gene promoters had increased risks for CAD. In addition, ANGPTL4 methylation level was significantly associated with CAD in males but not females. There were no significant differences in the methylation levels of the APOB and PCSK9 gene promoters between CAD patients and controls. CONCLUSIONS The methylation status of the APOC3, APOA5, LIPC, CETP and APOC1 gene promoters may be associated with the development of CAD.
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Abstract
Pioneering studies performed over the past few decades demonstrate links between epigenetics and type 2 diabetes mellitus (T2DM), the metabolic disorder with the most rapidly increasing prevalence in the world. Importantly, these studies identified epigenetic modifications, including altered DNA methylation, in pancreatic islets, adipose tissue, skeletal muscle and the liver from individuals with T2DM. As non-genetic factors that affect the risk of T2DM, such as obesity, unhealthy diet, physical inactivity, ageing and the intrauterine environment, have been associated with epigenetic modifications in healthy individuals, epigenetics probably also contributes to T2DM development. In addition, genetic factors associated with T2DM and obesity affect the epigenome in human tissues. Notably, causal mediation analyses found DNA methylation to be a potential mediator of genetic associations with metabolic traits and disease. In the past few years, translational studies have identified blood-based epigenetic markers that might be further developed and used for precision medicine to help patients with T2DM receive optimal therapy and to identify patients at risk of complications. This Review focuses on epigenetic mechanisms in the development of T2DM and the regulation of body weight in humans, with a special focus on precision medicine.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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Ortega-Contreras B, Armella A, Appel J, Mennickent D, Araya J, González M, Castro E, Obregón AM, Lamperti L, Gutiérrez J, Guzmán-Gutiérrez E. Pathophysiological Role of Genetic Factors Associated With Gestational Diabetes Mellitus. Front Physiol 2022; 13:769924. [PMID: 35450164 PMCID: PMC9016477 DOI: 10.3389/fphys.2022.769924] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Gestational Diabetes Mellitus (GDM) is a highly prevalent maternal pathology characterized by maternal glucose intolerance during pregnancy that is, associated with severe complications for both mother and offspring. Several risk factors have been related to GDM; one of the most important among them is genetic predisposition. Numerous single nucleotide polymorphisms (SNPs) in genes that act at different levels on various tissues, could cause changes in the expression levels and activity of proteins, which result in glucose and insulin metabolism dysfunction. In this review, we describe various SNPs; which according to literature, increase the risk of developing GDM. These SNPs include: (1) those associated with transcription factors that regulate insulin production and excretion, such as rs7903146 (TCF7L2) and rs5015480 (HHEX); (2) others that cause a decrease in protective hormones against insulin resistance such as rs2241766 (ADIPOQ) and rs6257 (SHBG); (3) SNPs that cause modifications in membrane proteins, generating dysfunction in insulin signaling or cell transport in the case of rs5443 (GNB3) and rs2237892 (KCNQ1); (4) those associated with enzymes such as rs225014 (DIO2) and rs9939609 (FTO) which cause an impaired metabolism, resulting in an insulin resistance state; and (5) other polymorphisms, those are associated with growth factors such as rs2146323 (VEGFA) and rs755622 (MIF) which could cause changes in the expression levels of these proteins, producing endothelial dysfunction and an increase of pro-inflammatory cytokines, characteristic on GDM. While the pathophysiological mechanism is unclear, this review describes various potential effects of these polymorphisms on the predisposition to develop GDM.
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Affiliation(s)
- B. Ortega-Contreras
- Pregnancy Diseases Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
| | - A. Armella
- Pregnancy Diseases Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
| | - J. Appel
- Pregnancy Diseases Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
| | - D. Mennickent
- Pregnancy Diseases Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
- Department of Instrumental Analysis, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
| | - J. Araya
- Department of Instrumental Analysis, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
| | - M. González
- Department of Obstetrics and Gynecology, Faculty of Medicine, Universidad de Concepción, Concepción, Chile
| | - E. Castro
- Departamento de Obstetricia y Puericultura, Facultad de Ciencias de la Salud, Universidad de Atacama, Copiapó, Chile
| | - A. M. Obregón
- Faculty of Health Care, Universidad San Sebastián, Concepción, Chile
| | - L. Lamperti
- Pregnancy Diseases Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
| | - J. Gutiérrez
- Faculty of Health Sciences, Universidad San Sebastián, Santiago,Chile
| | - E. Guzmán-Gutiérrez
- Pregnancy Diseases Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepción, Concepción, Chile
- *Correspondence: E. Guzmán-Gutiérrez,
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Akhlaghipour I, Bina AR, Mogharrabi MR, Fanoodi A, Ebrahimian AR, Khojasteh Kaffash S, Babazadeh Baghan A, Khorashadizadeh ME, Taghehchian N, Moghbeli M. Single-nucleotide polymorphisms as important risk factors of diabetes among Middle East population. Hum Genomics 2022; 16:11. [PMID: 35366956 PMCID: PMC8976361 DOI: 10.1186/s40246-022-00383-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/23/2022] [Indexed: 12/16/2022] Open
Abstract
Diabetes is a chronic metabolic disorder that leads to the dysfunction of various tissues and organs, including eyes, kidneys, and cardiovascular system. According to the World Health Organization, diabetes prevalence is 8.8% globally among whom about 90% of cases are type 2 diabetes. There are not any significant clinical manifestations in the primary stages of diabetes. Therefore, screening can be an efficient way to reduce the diabetic complications. Over the recent decades, the prevalence of diabetes has increased alarmingly among the Middle East population, which has imposed exorbitant costs on the health care system in this region. Given that the genetic changes are among the important risk factors associated with predisposing people to diabetes, we examined the role of single-nucleotide polymorphisms (SNPs) in the pathogenesis of diabetes among Middle East population. In the present review, we assessed the molecular pathology of diabetes in the Middle East population that paves the way for introducing an efficient SNP-based diagnostic panel for diabetes screening among the Middle East population. Since, the Middle East has a population of 370 million people; the current review can be a reliable model for the introduction of SNP-based diagnostic panels in other populations and countries around the world.
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Shyamala N, Kongettira CL, Puranam K, Kupsal K, Kummari R, Padala C, Hanumanth SR. In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size. Sci Rep 2022; 12:3574. [PMID: 35246549 PMCID: PMC8897451 DOI: 10.1038/s41598-022-05198-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/03/2022] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between -2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.
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Affiliation(s)
- Nivas Shyamala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chaitra Lava Kongettira
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Kaushik Puranam
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Keerthi Kupsal
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Ramanjaneyulu Kummari
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chiranjeevi Padala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana State, India
| | - Surekha Rani Hanumanth
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India.
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Tian G, He L, Gu R, Sun J, Chen W, Qian Y, Ma X, Yan W, Zhao Z, Xu Z, Suo M, Sheng W, Huang G. CpG site hypomethylation at ETS1‑binding region regulates DLK1 expression in Chinese patients with Tetralogy of Fallot. Mol Med Rep 2022; 25:93. [PMID: 35059744 PMCID: PMC8809049 DOI: 10.3892/mmr.2022.12609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart malformation accounting for ~10% of cases. Although the pathogenesis of TOF is complex and largely unknown, epigenetics plays a huge role, specifically DNA methylation. The protein δ like non-canonical Notch ligand 1 (DLK1) gene encodes a non-canonical ligand of the Notch signaling pathway, which is involved in heart development. However, the epigenetic mechanism of DLK1 in the pathogenesis of TOF is yet to be elucidated. Therefore, the present study aimed to clarify its specific mechanism. In this study, immunohistochemistry was used to detect the protein expression of DLK1 and the methylation status of the DLK1 promoter was measured via bisulfite sequencing PCR. Dual-luciferase reporter assays were performed to examine the influence of transcription factor ETS proto-oncogene 1 (ETS1) on DLK1 gene expression. The electrophoretic mobility shift assay and chromatin immunoprecipitation assay, both in vivo and in vitro, were used to verify the binding of the ETS1 transcription factor to the DLK1 promoter as well as the influence of methylation status of DLK1 promoter on this binding affinity. The expression of DLK1 in the right ventricular outflow tract was significantly lower in patients with Tetralogy of Fallot (TOF) than that in controls (P<0.001). Moreover, the methylation level of CpG site 10 and CpG site 11 in the DLK1_R region was significantly decreased in TOF cases compared with controls (P<0.01). The integral methylation levels of DLK1_R and the methylation status of the CpG site 11 were both positively associated with DLK1 protein expression in TOF cases. ETS1 was found to inhibit DLK1 transcriptional activity by binding to the CpG site 11 and this affinity could be influenced by the methylation level of the DLK1 promoter. These findings demonstrated that the hypomethylation of the DLK1 promoter could increase the binding affinity of ETS1 transcription factor, which in turn inhibited DLK1 gene transcriptional activity and contributed to the development of TOF.
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Affiliation(s)
- Guixiang Tian
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Lili He
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Ruoyi Gu
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Jingwei Sun
- Pediatrics Department, Bengbu First People's Hospital, Bengbu, Anhui 233000, P.R. China
| | - Weicheng Chen
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Yanyan Qian
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Xiaojing Ma
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Weili Yan
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Zhenshan Zhao
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Ziqing Xu
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Meijiao Suo
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Wei Sheng
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Guoying Huang
- Department of Ultrasound, Cardiovascular Center, Pediatrics Research Institute, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
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Kaimala S, Kumar CA, Allouh MZ, Ansari SA, Emerald BS. Epigenetic modifications in pancreas development, diabetes, and therapeutics. Med Res Rev 2022; 42:1343-1371. [PMID: 34984701 PMCID: PMC9306699 DOI: 10.1002/med.21878] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 11/24/2021] [Accepted: 12/18/2021] [Indexed: 12/26/2022]
Abstract
A recent International Diabetes Federation report suggests that more than 463 million people between 20 and 79 years have diabetes. Of the 20 million women affected by hyperglycemia during pregnancy, 84% have gestational diabetes. In addition, more than 1.1 million children or adolescents are affected by type 1 diabetes. Factors contributing to the increase in diabetes prevalence are complex and include contributions from genetic, environmental, and epigenetic factors. However, molecular regulatory mechanisms influencing the progression of an individual towards increased susceptibility to metabolic diseases such as diabetes are not fully understood. Recent studies suggest that the pathogenesis of diabetes involves epigenetic changes, resulting in a persistently dysregulated metabolic phenotype. This review summarizes the role of epigenetic mechanisms, mainly DNA methylation and histone modifications, in the development of the pancreas, their contribution to the development of diabetes, and the potential employment of epigenetic modulators in diabetes treatment.
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Affiliation(s)
- Suneesh Kaimala
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Challagandla Anil Kumar
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Mohammed Z Allouh
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE.,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE.,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
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Bartolomé A. Stem Cell-Derived β Cells: A Versatile Research Platform to Interrogate the Genetic Basis of β Cell Dysfunction. Int J Mol Sci 2022; 23:501. [PMID: 35008927 PMCID: PMC8745644 DOI: 10.3390/ijms23010501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic β cell dysfunction is a central component of diabetes progression. During the last decades, the genetic basis of several monogenic forms of diabetes has been recognized. Genome-wide association studies (GWAS) have also facilitated the identification of common genetic variants associated with an increased risk of diabetes. These studies highlight the importance of impaired β cell function in all forms of diabetes. However, how most of these risk variants confer disease risk, remains unanswered. Understanding the specific contribution of genetic variants and the precise role of their molecular effectors is the next step toward developing treatments that target β cell dysfunction in the era of personalized medicine. Protocols that allow derivation of β cells from pluripotent stem cells, represent a powerful research tool that allows modeling of human development and versatile experimental designs that can be used to shed some light on diabetes pathophysiology. This article reviews different models to study the genetic basis of β cell dysfunction, focusing on the recent advances made possible by stem cell applications in the field of diabetes research.
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Affiliation(s)
- Alberto Bartolomé
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
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Hu F, Zhang Y, Qin P, Zhao Y, Liu D, Zhou Q, Tian G, Li Q, Guo C, Wu X, Qie R, Huang S, Han M, Li Y, Zhang M, Hu D. Integrated analysis of probability of type 2 diabetes mellitus with polymorphisms and methylation of KCNQ1 gene: A nested case-control study. J Diabetes 2021; 13:975-986. [PMID: 34260825 DOI: 10.1111/1753-0407.13212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/17/2021] [Accepted: 07/07/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND To estimate the associations between single-nucleotide polymorphisms (SNPs) and methylation of KCNQ1 gene and type 2 diabetes mellitus (T2DM) risk and the interactions among SNPs, methylation, and environmental factors on T2DM risk. METHODS We genotyped five SNPs and tested methylation at 39 CpG loci of KCNQ1 in 290 T2DM cases and 290 matched controls nested in the Rural Chinese Cohort Study. Conditional logistic regression model was used to estimate the associations between SNPs and KCNQ1 methylation and T2DM risk. Multifactor dimensionality reduction (MDR) analysis was used to estimate the effect of the interactions SNPs-SNPs, SNPs-methylation, methylation-methylation and SNPs, and methylation-environment on T2DM risk. RESULTS Probability of T2DM was decreased with rs2283228 of KCNQ1 (CA vs AA, odds ratio [OR] = 0.65, 95% confidence interval [CI] 0.42-0.99). T2DM probability was significantly increased with rs2237895 combined with hypertriglyceridemia (OReg = 2.76, 95% CI 1.35-5.62), with hypertension (OReg = 2.23, 95% CI 1.25-3.98), and with body mass index (BMI; OReg = 1.93, 95% CI 1.12-3.34). T2DM probability was associated with methylation of CG11 and CG41 (OR = 1.89, 95% CI 1.23-2.89, P = .003). It was significantly associated with the interaction between BMI, hypertriglyceridemia, and CG5 methylation (P = .028 and .028), and the combined effects of CG11 with hypertriglyceridemia and hypertension. On MDR analysis, no significant interaction was observed. CONCLUSION T2DM probability was reduced 35% with rs2283228 polymorphism. It was associated with rs2237895 combined with hypertension, with BMI and with hypertriglyceridemia. The methylation at two CpG loci of KCNQ1 significantly increased T2DM risk by 89%.
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Affiliation(s)
- Fulan Hu
- Study Team of Shenzhen's Sanming Project, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, China
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yanyan Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Pei Qin
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yang Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Dechen Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Qionggui Zhou
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Gang Tian
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Quanman Li
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Chunmei Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoyan Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ranran Qie
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Shengbing Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Minghui Han
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yang Li
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Ming Zhang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Dongsheng Hu
- Study Team of Shenzhen's Sanming Project, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, China
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22
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Aguilera-Venegas IG, Mora-Peña JDS, Velazquez-Villafaña M, Gonzalez-Dominguez MI, Barbosa-Sabanero G, Gomez-Zapata HM, Lazo-de-la-Vega-Monroy ML. Association of diabetes-related variants in ADCY5 and CDKAL1 with neonatal insulin, C-peptide, and birth weight. Endocrine 2021; 74:318-331. [PMID: 34169461 DOI: 10.1007/s12020-021-02799-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND PURPOSE Neonates at the highest and lowest percentiles of birth weight present an increased risk of developing metabolic diseases in adult life. While environmental events in utero may play an important role in this association, some genetic variants are associated both with birth weight and type 2 diabetes mellitus (T2DM), suggesting a genetic link between intrauterine growth and metabolism in adult life. Variants rs11708067 in ADCY5 and rs7754840 in CDKAL1 are associated with low birth weight, risk of T2DM, and lower insulin secretion in adults. We aimed to investigate whether, besides birth weight, these polymorphisms were related to insulin secretion at birth. METHODS A cohort of 218 healthy term newborns from uncomplicated pregnancies were evaluated for anthropometric and biochemical variables. Cord blood insulin and C-peptide were analyzed by ELISA. Genotyping of rs11708067 in ADCY5 and rs7754840 in CDKAL1 was performed. RESULTS Newborns carrying the A allele of ADCY5 rs11708067 had lower cord blood insulin and C-peptide, even after adjusting by maternal glycemia, HbA1c, and pregestational BMI. Lower birth weight was found for AA-AG genotypes compared to GG, but no differences were seen in adjusted birth weight or z-score. Variant rs7754840 in CDKAL1 was not associated with birth weight, neonatal insulin, or C-peptide for any genotype or genetic model. CONCLUSIONS The variant rs11708067 in ADCY5 is associated with lower neonatal insulin and C-peptide concentrations. Our results suggest that the genetic influence on insulin secretion may be evident from birth, even in healthy newborns, independently of maternal glycemia and BMI.
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Affiliation(s)
| | | | | | - Martha-Isabel Gonzalez-Dominguez
- Universidad de la Cienega del Estado de Michoacan de Ocampo, Trayectoria de Ingenieria en Nanotecnologia, Sahuayo, Michoacan, Mexico
| | - Gloria Barbosa-Sabanero
- Medical Sciences Department, Health Sciences Division, University of Guanajuato, Guanajuato, Mexico
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23
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Dallio M, Romeo M, Gravina AG, Masarone M, Larussa T, Abenavoli L, Persico M, Loguercio C, Federico A. Nutrigenomics and Nutrigenetics in Metabolic- (Dysfunction) Associated Fatty Liver Disease: Novel Insights and Future Perspectives. Nutrients 2021; 13:nu13051679. [PMID: 34063372 PMCID: PMC8156164 DOI: 10.3390/nu13051679] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Metabolic- (dysfunction) associated fatty liver disease (MAFLD) represents the predominant hepatopathy and one of the most important systemic, metabolic-related disorders all over the world associated with severe medical and socio-economic repercussions due to its growing prevalence, clinical course (steatohepatitis and/or hepatocellular-carcinoma), and related extra-hepatic comorbidities. To date, no specific medications for the treatment of this condition exist, and the most valid recommendation for patients remains lifestyle change. MAFLD has been associated with metabolic syndrome; its development and progression are widely influenced by the interplay between genetic, environmental, and nutritional factors. Nutrigenetics and nutrigenomics findings suggest nutrition’s capability, by acting on the individual genetic background and modifying the specific epigenetic expression as well, to influence patients’ clinical outcome. Besides, immunity response is emerging as pivotal in this multifactorial scenario, suggesting the interaction between diet, genetics, and immunity as another tangled network that needs to be explored. The present review describes the genetic background contribution to MAFLD onset and worsening, its possibility to be influenced by nutritional habits, and the interplay between nutrients and immunity as one of the most promising research fields of the future in this context.
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Affiliation(s)
- Marcello Dallio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy; (M.R.); (A.G.G.); (C.L.); (A.F.)
- Correspondence: ; Tel.: +39-0815666740
| | - Mario Romeo
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy; (M.R.); (A.G.G.); (C.L.); (A.F.)
| | - Antonietta Gerarda Gravina
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy; (M.R.); (A.G.G.); (C.L.); (A.F.)
| | - Mario Masarone
- Department of Medicine and Surgery, University of Salerno, Via Allende, 84081 Baronissi, Italy; (M.M.); (M.P.)
| | - Tiziana Larussa
- Department of Health Sciences, University Magna Graecia, viale Europa, 88100 Catanzaro, Italy; (T.L.); (L.A.)
| | - Ludovico Abenavoli
- Department of Health Sciences, University Magna Graecia, viale Europa, 88100 Catanzaro, Italy; (T.L.); (L.A.)
| | - Marcello Persico
- Department of Medicine and Surgery, University of Salerno, Via Allende, 84081 Baronissi, Italy; (M.M.); (M.P.)
| | - Carmelina Loguercio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy; (M.R.); (A.G.G.); (C.L.); (A.F.)
| | - Alessandro Federico
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via S. Pansini 5, 80131 Naples, Italy; (M.R.); (A.G.G.); (C.L.); (A.F.)
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24
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Sinnott-Armstrong N, Sousa IS, Laber S, Rendina-Ruedy E, Nitter Dankel SE, Ferreira T, Mellgren G, Karasik D, Rivas M, Pritchard J, Guntur AR, Cox RD, Lindgren CM, Hauner H, Sallari R, Rosen CJ, Hsu YH, Lander ES, Kiel DP, Claussnitzer M. A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density. Cell Metab 2021; 33:615-628.e13. [PMID: 33513366 PMCID: PMC7928941 DOI: 10.1016/j.cmet.2021.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/14/2019] [Accepted: 12/31/2020] [Indexed: 02/07/2023]
Abstract
Skeletal and glycemic traits have shared etiology, but the underlying genetic factors remain largely unknown. To identify genetic loci that may have pleiotropic effects, we studied Genome-wide association studies (GWASs) for bone mineral density and glycemic traits and identified a bivariate risk locus at 3q21. Using sequence and epigenetic modeling, we prioritized an adenylate cyclase 5 (ADCY5) intronic causal variant, rs56371916. This SNP changes the binding affinity of SREBP1 and leads to differential ADCY5 gene expression, altering the chromatin landscape from poised to repressed. These alterations result in bone- and type 2 diabetes-relevant cell-autonomous changes in lipid metabolism in osteoblasts and adipocytes. We validated our findings by directly manipulating the regulator SREBP1, the target gene ADCY5, and the variant rs56371916, which together imply a novel link between fatty acid oxidation and osteoblast differentiation. Our work, by systematic functional dissection of pleiotropic GWAS loci, represents a framework to uncover biological mechanisms affecting pleiotropic traits.
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Affiliation(s)
- Nasa Sinnott-Armstrong
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Stanford University, Stanford 94305 CA, USA
| | - Isabel S Sousa
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Samantha Laber
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Big Data Institute, University of Oxford, Oxford, UK
| | - Elizabeth Rendina-Ruedy
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Simon E Nitter Dankel
- University of Bergen, Bergen 5020, Norway; Mohn Nutrition Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; Hormone Laboratory, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Gunnar Mellgren
- University of Bergen, Bergen 5020, Norway; Mohn Nutrition Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway; Hormone Laboratory, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA 02131, USA; Faculty of Medicine of the Galilee, Bar-Ilan University, Safed, Israel
| | - Manuel Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Pritchard
- Department of Genetics, Stanford University, Stanford 94305 CA, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Anyonya R Guntur
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Roger D Cox
- Medical Research Council Harwell, Oxfordshire, UK
| | - Cecilia M Lindgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Big Data Institute, University of Oxford, Oxford, UK
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising 85354, Germany; Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Freising 85354, Germany; Clinical Cooperation Group "Nutrigenomics and Type 2 Diabetes" of the German Center of Diabetes Research, Helmholtz Center Munich, Munich 85764, Germany
| | - Richard Sallari
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clifford J Rosen
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074, USA
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA 02131, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02131, USA
| | - Eric S Lander
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas P Kiel
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA 02131, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02131, USA
| | - Melina Claussnitzer
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02131, USA; University of Hohenheim, Institute of Nutritional Science, Stuttgart 70599, Germany.
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25
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Abstract
Psychiatric disorders are common, complex, and heritable conditions estimated to be the leading cause of disability worldwide. The last decade of research in genomics of psychiatry, performed by multinational, and multicenter collaborative efforts on hundreds of thousands of mental disorder cases and controls, provided invaluable insight into the genetic risk variants of these conditions. With increasing cohort sizes, more risk variants are predicted to be identified in the near future, but there appears to be a knowledge gap in understanding how these variants contribute to the pathophysiology of psychiatric disorders. Majority of the identified common risk single-nucleotide polymorphisms (SNPs) are non-coding but are enriched in regulatory regions of the genome. It is therefore of great interest to study the impact of identified psychiatric disorders' risk SNPs on DNA methylation, the best studied epigenetic modification, playing a pivotal role in the regulation of transcriptomic processes, brain development, and functioning. This work outlines the mechanisms through which risk SNPs can impact DNA methylation levels and provides a summary of current evidence on the role of DNA methylation in mediating the genetic risk of psychiatric disorders.
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Affiliation(s)
- Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
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26
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Aftabi Y, Khoshkam Z, Amiri-sadeghan A, Khalili Y, Ichihara G. An introduction to EpiPol (Epigenetic affecting Polymorphism) concept with an in silico identification of CpG-affecting SNPs in the upstream regulatory sequences of human AHR gene. Meta Gene 2020; 26:100805. [DOI: 10.1016/j.mgene.2020.100805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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Asif S, Morrow NM, Mulvihill EE, Kim KH. Understanding Dietary Intervention-Mediated Epigenetic Modifications in Metabolic Diseases. Front Genet 2020; 11:590369. [PMID: 33193730 PMCID: PMC7593700 DOI: 10.3389/fgene.2020.590369] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
The global prevalence of metabolic disorders, such as obesity, diabetes and fatty liver disease, is dramatically increasing. Both genetic and environmental factors are well-known contributors to the development of these diseases and therefore, the study of epigenetics can provide additional mechanistic insight. Dietary interventions, including caloric restriction, intermittent fasting or time-restricted feeding, have shown promising improvements in patients' overall metabolic profiles (i.e., reduced body weight, improved glucose homeostasis), and an increasing number of studies have associated these beneficial effects with epigenetic alterations. In this article, we review epigenetic changes involved in both metabolic diseases and dietary interventions in primary metabolic tissues (i.e., adipose, liver, and pancreas) in hopes of elucidating potential biomarkers and therapeutic targets for disease prevention and treatment.
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Affiliation(s)
- Shaza Asif
- University of Ottawa Heart Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Nadya M. Morrow
- University of Ottawa Heart Institute, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Erin E. Mulvihill
- University of Ottawa Heart Institute, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kyoung-Han Kim
- University of Ottawa Heart Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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28
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Cruz JDO, Conceição IMCA, Tosatti JAG, Gomes KB, Luizon MR. Global DNA methylation in placental tissues from pregnant with preeclampsia: A systematic review and pathway analysis. Placenta 2020; 101:97-107. [PMID: 32942147 DOI: 10.1016/j.placenta.2020.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 12/28/2022]
Abstract
Pre-eclampsia (PE) is the major cause of fetal and maternal mortality and can be classified according to gestational age of onset into early-onset (EOPE, <34 weeks of gestation) and late- (LOPE, ≥34 weeks of gestation). DNA methylation (DNAm) may help to understand the abnormal placentation in PE. Therefore, we performed a systematic review to assess the role of global DNAm on pathophysiology of PE, focused on fetal and maternal tissues of placenta from pregnant with PE, including EOPE and LOPE. We searched the databases EMBASE, Medline/PubMed, Cochrane Central Register of Controlled Trials, Scopus, Lilacs, Scielo and Google Scholar, and followed the MOOSE guidelines. Moreover, we performed pathway analysis with the overlapping genes from the included studies. Twelve out of 24 included studies in the qualitative analysis considered the classification into EOPE and LOPE. We did not found heterogeneity in the criteria used for diagnosis of PE, and a few studies evaluated whether confounding factors would influence placental DNAm. Fourteen out of 24 included studies showed hypomethylation in placental tissue from pregnant with PE compared to controls. The differences in DNAm are specific to genes or differentially methylated regions, and more evident in EOPE and preterm PE compared to controls, rather than LOPE and term PE. The overlapping genes from included studies revealed pathways relevant to pathophysiology of PE. Our findings highlighted the heterogeneous results of the included studies, mainly focused on North America and China. Replication studies in different populations should use the same placental tissues, techniques to assess DNAm and pipelines for bioinformatic analysis.
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Affiliation(s)
- Juliana de O Cruz
- Graduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Izabela M C A Conceição
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Jéssica A G Tosatti
- Department of Clinical and Toxicological Analyzes, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Karina B Gomes
- Department of Clinical and Toxicological Analyzes, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Marcelo R Luizon
- Graduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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29
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Hess R, Henthorn P, Devoto M, Wang F, Feng R. An Exploratory Association Analysis of the Insulin Gene Region With Diabetes Mellitus in Two Dog Breeds. J Hered 2020; 110:793-800. [PMID: 31587057 PMCID: PMC6916661 DOI: 10.1093/jhered/esz059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Samoyeds and Australian Terriers are the 2 dog breeds at highest risk (>10-fold) for diabetes mellitus in the United States. It is unknown if the insulin (INS) gene is involved in the pathophysiology of diabetes in Samoyeds and Australian Terriers. It was hypothesized that the INS gene region provides a common genetic causality for diabetes in Samoyeds and Australian Terriers. We conducted a 2-stage genetic association study involving both breeds. In the discovery stage (Stage 1), Samoyeds with and without diabetes were compared in the frequencies of 447 tagging single-nucleotide polymorphisms (SNPs) within 2.5 megabases (Mb) up- and downstream of the INS gene on the Illumina CanineHD BeadChip. SNPs yielding a P-value < 0.005 were selected for further follow-up. In the validation stage (Stage 2), Australian Terriers with and without diabetes were compared in the SNPs genotyped by the Affymetrix GeneChip Canine Genome 2.0 Array and within 1 Mb up- and downstream of the selected SNPs from Stage 1. Two SNPs that were in high linkage disequilibrium (LD, r2 = 0.7) were selected from Stage 1. In Stage 2, among the 76 SNPs examined, 5 were significantly associated with diabetes after Bonferroni's correction for multiple comparisons. Three of these 5 SNPs were in complete LD (r2 = 1 for all associations) and the 2 remaining SNPs were in moderate LD (r2 = 0.4). In conclusion, an association between the INS gene region and diabetes was suggested in 2 dog breeds of different clades. This region could have importance in diabetes in other breeds or in canine diabetes at large.
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Affiliation(s)
- Rebecka Hess
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Paula Henthorn
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Translational and Precision Medicine, University of Rome Sapienza, Rome, Italy
| | - Fan Wang
- Department of Molecular Cardiology, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Rui Feng
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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30
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Vohra M, Adhikari P, Souza SC, Nagri SK, Umakanth S, Satyamoorthy K, Rai PS. CpG-SNP site methylation regulates allele-specific expression of MTHFD1 gene in type 2 diabetes. J Transl Med 2020; 100:1090-101. [PMID: 32238907 DOI: 10.1038/s41374-020-0422-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/12/2020] [Accepted: 03/12/2020] [Indexed: 12/30/2022] Open
Abstract
The interaction of genetic and epigenetic mechanisms is one of the underlying causes of phenotypic variability in complex diseases such as type 2 diabetes (T2D). To explore the influence of genetic and epigenetic changes in T2D, we examined the effect of methylation of CpG-SNP sites on allele-specific expression (ASE) in one-carbon metabolism pathway genes in T2D. Case-control study was conducted on 860 individuals (430 T2D and 430 controls). CpG-SNPs shortlisted through in silico analysis were genotyped using tetra ARMS PCR and validated using Sanger DNA sequencing. Global DNA methylation was carried out using RP-HPLC. Promoter DNA methylation and CpG site-specific methylation were carried out using bisulfite sequencing. mRNA expression and ASE were examined by SYBR green and TaqMan assay, respectively. Four exonic CpG-SNPs of MTHFD1, MTRR, and GGH genes were identified in folate pathway genes. Among these, MTHFD1 rs2236225 showed significant association with T2D independent of obesity, displayed ASE, and correlated with CpG-SNP site-specific methylation when compared with controls. Our results demonstrate that SNP rs2236225 in the CpG site of MTHFD1, which regulates allele-specific gene expression in PBMCs is methylation dependent and may perturb one-carbon metabolism pathway in T2D subjects.
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31
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Ling C. Epigenetic regulation of insulin action and secretion - role in the pathogenesis of type 2 diabetes. J Intern Med 2020; 288:158-167. [PMID: 32363639 DOI: 10.1111/joim.13049] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/21/2022]
Abstract
The prevalence of type 2 diabetes (T2D) is rapidly increasing worldwide. Obesity, physical inactivity and ageing increase the risk of T2D. Epigenetic modifications can change due to environmental exposures and may thereby predispose to disease. This review aims at summarizing recent advances in epigenetics related to T2D, with a special focus on impaired insulin action and secretion in humans. There will be an emphasis on analyses in human tissues; both from T2D case-control cohorts and intervention studies. Current data support an important role for epigenetics in the pathogenesis of T2D. Numerous studies have found differential DNA methylation and gene expression in skeletal muscle, adipose tissue, the liver and pancreatic islets from subjects with T2D compared with nondiabetic controls. For example, PDX1 has increased DNA methylation and decreased expression in pancreatic islets from patients with T2D compared with nondiabetic controls. Nongenetic risk factors for T2D such as ageing, unhealthy diets and physical activity do also impact the epigenome in human tissues. Interestingly, physical activity altered DNA methylation of candidate genes for T2D such as THADA in muscle and FTO, KCNQ1 and TCF7L2 in adipose tissue. There is also a strong interaction between genetic and epigenetic factors that together seem to affect T2D. mQTL studies in human adipose tissue and pancreatic islets showed that SNPs associated with DNA methylation levels in numerous sites. Several of these SNPs are also associated with T2D. Recent data also support that DNA methylation of some sites in blood may be developed into biomarkers that predict T2D since methylation of, for example TXNIP, ABCG1 and SREBF1 associated with future T2D. Future studies should use this information for development of new therapies and biomarkers and thereby improve prediction, prevention and treatment of T2D and its complications.
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Affiliation(s)
- C Ling
- From the, Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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32
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Ahmed SAH, Ansari SA, Mensah-Brown EPK, Emerald BS. The role of DNA methylation in the pathogenesis of type 2 diabetes mellitus. Clin Epigenetics 2020; 12:104. [PMID: 32653024 PMCID: PMC7353744 DOI: 10.1186/s13148-020-00896-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Diabetes mellitus (DM) is a chronic condition characterised by β cell dysfunction and persistent hyperglycaemia. The disorder can be due to the absence of adequate pancreatic insulin production or a weak cellular response to insulin signalling. Among the three types of DM, namely, type 1 DM (T1DM), type 2 DM (T2DM), and gestational DM (GDM); T2DM accounts for almost 90% of diabetes cases worldwide. Epigenetic traits are stably heritable phenotypes that result from certain changes that affect gene function without altering the gene sequence. While epigenetic traits are considered reversible modifications, they can be inherited mitotically and meiotically. In addition, epigenetic traits can randomly arise in response to environmental factors or certain genetic mutations or lesions, such as those affecting the enzymes that catalyse the epigenetic modification. In this review, we focus on the role of DNA methylation, a type of epigenetic modification, in the pathogenesis of T2DM.
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Affiliation(s)
- Sanabil Ali Hassan Ahmed
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Eric P K Mensah-Brown
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates.
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Ali N, Niaz S, Khan NU, Gohar A, Khattak I, Dong Y, Khattak T, Ahmad I, Wang Y, Usman T. Polymorphisms in JAK2 Gene are Associated with Production Traits and Mastitis Resistance in Dairy Cattle. Annals of Animal Science 2020; 20:409-23. [DOI: 10.2478/aoas-2019-0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The present study was designed to investigate the effects of single nucleotide polymorphisms (SNPs) in the JAK2 gene on the production and mastitis related traits in dairy cattle. Blood and milk samples were collected from 201 lactating dairy cattle of three breeds, i.e. Holstein Friesian (HF), Jersey (J) and Achai (A) and their crosses maintained at well-established dairy farms in Khyber Pakhtunkhwa, Pakistan. Generalized linear model was used to evaluate the association between genotypes and the studied traits. A DNA pool was made from randomly selected 30 samples which revealed three SNPs, i.e. SNP 1 in 5’ upstream region (G>A, rs379754157), SNP 2 in intron 15 (A>G, rs134192265), and SNP 3 in exon 20 (A>G, rs110298451) that were further validated in the population under study using SNaPshot technique. Of the three SNPs, SNP 1 did not obey Hardy-Weinberg equilibrium (P<0.05). SNP 2 and SNP 3 were found to be in strong linkage disequilibrium and allele G was highly prevalent compared to allele A in these SNPs. in SNP 1, the GG genotype was associated with significantly (P<0.01) higher SCC, whereas SNP 2 and SNP 3 were significantly (P<0.01) associated with higher lactose percentage compared to the other geno-types. The haplogroups association analysis revealed that H1H2 (GG GG AG) has significantly lower SCC than H2H2 (GG GG GG). The results infer that JAK2 could be an important candidate gene and the studied SNPs might be useful genetic markers for production and mastitis related traits.
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Coassin S, Hermann-Kleiter N, Haun M, Wahl S, Wilson R, Paulweber B, Kunze S, Meitinger T, Strauch K, Peters A, Waldenberger M, Kronenberg F, Lamina C. A genome-wide analysis of DNA methylation identifies a novel association signal for Lp(a) concentrations in the LPA promoter. PLoS One 2020; 15:e0232073. [PMID: 32343731 PMCID: PMC7188291 DOI: 10.1371/journal.pone.0232073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022] Open
Abstract
Lipoprotein(a) [Lp(a)] is a major cardiovascular risk factor, which is largely genetically determined by one major gene locus, the LPA gene. Many aspects of the transcriptional regulation of LPA are poorly understood and the role of epigenetics has not been addressed yet. Therefore, we conducted an epigenome-wide analysis of DNA methylation on Lp(a) levels in two population-based studies (total n = 2208). We identified a CpG site in the LPA promoter which was significantly associated with Lp(a) concentrations. Surprisingly, the identified CpG site was found to overlap the SNP rs76735376. We genotyped this SNP de-novo in three studies (total n = 7512). The minor allele of rs76735376 (1.1% minor allele frequency) was associated with increased Lp(a) values (p = 1.01e-59) and explained 3.5% of the variation of Lp(a). Statistical mediation analysis showed that the effect on Lp(a) is rather originating from the base change itself and is not mediated by DNA methylation levels. This finding is supported by eQTL data from 208 liver tissue samples from the GTEx project, which shows a significant association of the rs76735376 minor allele with increased LPA expression. To evaluate, whether the association signal at rs76735376 may actually be derived from a stronger eQTL signal in LD with this SNP, eQTL association results of all correlated SNPs (r2≥0.1) were integrated with genetic association results. This analysis pinpointed to rs10455872 as the potential trigger of the effect of rs76735376. Furthermore, both SNPs coincide with short apo(a) isoforms. Adjusting for both, rs10455872 and the apo(a) isoforms diminished the effect size of rs76735376 to 5.38 mg/dL (p = 0.0463). This indicates that the effect of rs76735376 can be explained by both an independent effect of the SNP and a strong correlation with rs10455872 and apo(a) isoforms.
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Affiliation(s)
- Stefan Coassin
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Natascha Hermann-Kleiter
- Department of Genetics and Pharmacology, Institute of Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Margot Haun
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Private Medical University, Salzburg, Austria
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- German Research Center for Environmental Health, Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Konstantin Strauch
- German Research Center for Environmental Health, Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Medical Informatics, Biometry, and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudia Lamina
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
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Nassan M, Veldic M, Winham S, Frye MA, Larrabee B, Colby C, Biernacka J, Bellia F, Pucci M, Terenius L, Vukojevic V, D'Addario C. Methylation of Brain Derived Neurotrophic Factor (BDNF) Val66Met CpG site is associated with early onset bipolar disorder. J Affect Disord 2020; 267:96-102. [PMID: 32063579 DOI: 10.1016/j.jad.2020.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/21/2020] [Accepted: 02/01/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The brain-derived neurotrophic factor (BDNF) rs6265 (Val66Met) Met allele is associated with early onset (≤ 19 years old) bipolar disorder (BD). Val66Met (G196A) creates a CpG site when the Val/G allele is present. We sought to study the methylation of the BDNF promoter and its interaction with Val66Met genotype in BD. METHODS Sex/age-matched previously genotyped DNA samples from BD-Type 1 cases [N = 166: early onset (≤ 19 years old) n = 79, late onset (> 20 years old) n = 87] and controls (N = 162) were studied. Pyrosequencing of four CpGs in Promoter-I, four CpGs in promoter-IV, and two CpGs in Promoter-IX (CpG2 includes G= Val allele) was performed. Logistic regression adjusting for batch effect was used to compare cases vs. controls. Analyses also included stratification by disease onset and adjustment for Val66Met genotype. Secondary exploratory analyses for the association of life stressors, comorbid substance abuse, and psychotropic use with methylation patterns were performed. RESULTS Comparing all BD cases vs. controls and adjusting for Val66Met genotype, BD cases had significantly higher methylation in promoter -IX/CPG-2 (p = 0.0074). This was driven by early onset cases vs. controls (p = 0.00039) and not late onset cases vs. controls (p = 0.2). LIMITATION Relatively small sample size. CONCLUSION Early onset BD is associated with increased methylation of CpG site created by Val=G allele of the Val66Met variance. Further studies could include larger sample size and postmortem brain samples in an attempt to replicate these findings.
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Affiliation(s)
- Malik Nassan
- Mayo Clinic, Psychiatry & Psychology, Rochester, MN, USA
| | - Marin Veldic
- Mayo Clinic, Psychiatry & Psychology, Rochester, MN, USA
| | - Stacey Winham
- Mayo Clinic, Psychiatry & Psychology, Rochester, MN, USA
| | - Mark A Frye
- Mayo Clinic, Psychiatry & Psychology, Rochester, MN, USA
| | - Beth Larrabee
- Mayo Clinic, Psychiatry & Psychology, Rochester, MN, USA
| | - Colin Colby
- Mayo Clinic, Psychiatry & Psychology, Rochester, MN, USA
| | | | | | | | - Lars Terenius
- Karolinska Institute, Clinical Neuroscience, Solna, Sweden
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Wang Z, Qiu C, Lin X, Zhao LJ, Liu Y, Wu X, Wang Q, Liu W, Li K, Deng HW, Tang SY, Shen H. Identification of novel functional CpG-SNPs associated with type 2 diabetes and coronary artery disease. Mol Genet Genomics 2020; 295:607-19. [PMID: 32162118 DOI: 10.1007/s00438-020-01651-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/03/2020] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D) and coronary artery disease (CAD), respectively. Nevertheless, these studies were generally performed for single-trait/disease and failed to assess the pleiotropic role of the identified variants. To identify novel functional loci and the pleiotropic relationship between CAD and T2D, the targeted cFDR analysis on CpG-SNPs was performed by integrating two independent large and multi-centered GWASs with summary statistics of T2D (26,676 cases and 132,532 controls) and CAD (60,801 cases and 123,504 controls). Applying the cFDR significance threshold of 0.05, we observed a pleiotropic enrichment between T2D and CAD by incorporating pleiotropic effects into a conditional analysis framework. We identified 79 novel CpG-SNPs for T2D, 61 novel CpG-SNPs for CAD, and 18 novel pleiotropic loci for both traits. Among these novel CpG-SNPs, 33 of them were annotated as methylation quantitative trait locus (meQTL) in whole blood, and ten of them showed expression QTL (eQTL), meQTL, and metabolic QTL (metaQTL) effects simultaneously. To the best of our knowledge, we performed the first targeted cFDR analysis on CpG-SNPs, and our findings provided novel insights into the shared biological mechanisms and overlapped genetic heritability between T2D and CAD.
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Li X, Chan LWC, Li X, Liu C, Yang G, Gao J, Dai M, Wang Y, Xie Z, Liu J, Zhou F, Zheng T, Feng D, Guo S, Li H, Sun K, Yang S. Obesity-Induced Regulator of Calcineurin 1 Overexpression Leads to β-Cell Failure Through Mitophagy Pathway Inhibition. Antioxid Redox Signal 2020; 32:413-428. [PMID: 31822118 DOI: 10.1089/ars.2019.7806] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aims: Type 2 diabetes (T2D) is associated with pancreatic β-cell dysfunction, manifested by reduced glucose-stimulated insulin secretion (GSIS). The regulator of calcineurin 1 (RCAN1) in islets is an endogenous inhibitor of calcium-activated protein phosphatase. Previous studies have indicated that global RCAN1 overexpression under high nutrient stress is involved in insulin resistance in T2D. However, the specific role and mechanism of this gene's overexpression in pancreatic β-cells have not been thoroughly elucidated to date. Results: In this study, we showed that mice overexpressing islet-specific RCAN1 exhibited a prediabetic phenotype with markedly reduced GSIS under nutrient stress. Overexpression of RCAN1 increased the autophagy-associated DNA methylation level of Beclin-1 suppressing the induction of autophagy, affected the protein kinase B, and downregulated the activation of mammalian target of rapamycin, leading to Miro1-mediated mitophagy deficiency. Furthermore, the exacerbated impairment of autophagy induction and mitophagy flux failures induced β-cell apoptosis, resulting in GSIS impairment, lipid imbalance, and NOD-like receptor 3 proinflammation under high nutrient stress in mice. Innovation: Our present data identify a detrimental effect of RCAN1 overexpression on Miro1-mediated mitophagy deficiency and β-cell dysfunction in high-fat diet-fed RCAN1 overexpressing mice. Conclusion: Our results revealed that strategies targeting RCAN1 in vivo may provide a therapeutic target to enhance β-cell mitophagy quality and may determine the crucial factor in T2D development.
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Affiliation(s)
- Xujun Li
- ABSL-3 Laboratory at the Center for Animal Experiment, Institute of Animal Model for Human Disease, Wuhan University School of Medicine, Wuhan, People's Republic of China
| | - Lawrence W C Chan
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Xianyu Li
- Department of Pathophysiology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, People's Republic of China
| | - Chunyan Liu
- ABSL-3 Laboratory at the Center for Animal Experiment, Institute of Animal Model for Human Disease, Wuhan University School of Medicine, Wuhan, People's Republic of China
| | - Guohua Yang
- Demonstration Center for Experimental Basic Medicine Education, School of Basic Medical Science, Wuhan University, Wuhan, People's Republic of China
| | - Jianfeng Gao
- ABSL-3 Laboratory at the Center for Animal Experiment, Institute of Animal Model for Human Disease, Wuhan University School of Medicine, Wuhan, People's Republic of China
| | - Ming Dai
- ABSL-3 Laboratory at the Center for Animal Experiment, Institute of Animal Model for Human Disease, Wuhan University School of Medicine, Wuhan, People's Republic of China
| | - Yunxin Wang
- School of Medical Technology, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Zhiwen Xie
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Junli Liu
- Shanghai Diabetes Research Institute, Shanghai JiaoTong University Affiliated 6th People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, People's Republic of China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Tian Zheng
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Du Feng
- Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Shaodong Guo
- Department of Nutrition and Food Science, Texas A&M University, College Station, Texas
| | - Haojie Li
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Kai Sun
- Center for Metabolic and Degenerative Diseases, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Sijun Yang
- ABSL-3 Laboratory at the Center for Animal Experiment, Institute of Animal Model for Human Disease, Wuhan University School of Medicine, Wuhan, People's Republic of China
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Li Y, Wang K, Zhang P, Huang J, Liu Y, Wang Z, Lu Y, Tan S, Yang F, Tan Y. Pyrosequencing analysis of IRS1 methylation levels in schizophrenia with tardive dyskinesia. Mol Med Rep 2020; 21:1702-1708. [PMID: 32319643 PMCID: PMC7057828 DOI: 10.3892/mmr.2020.10984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/17/2020] [Indexed: 12/16/2022] Open
Abstract
Tardive dyskinesia (TD) is a serious side effect of certain antipsychotic medications that are used to treat schizophrenia (SCZ) and other mental illnesses. The methylation status of the insulin receptor substrate 1 (IRS1) gene is reportedly associated with SCZ; however, no study, to the best of the authors' knowledge, has focused on the quantitative DNA methylation levels of the IRS1 gene using pyrosequencing in SCZ with or without TD. The present study aimed to quantify DNA methylation levels of 4 CpG sites in the IRS1 gene using a Chinese sample including SCZ patients with TD and without TD (NTD) and healthy controls (HCs). The general linear model (GLM) was used to detect DNA methylation levels among the 3 proposed groups (TD vs. NTD vs. HC). Mean DNA methylation levels of 4 CpG sites demonstrated normal distribution. Pearson's correlation analysis did not reveal any significant correlations between the DNA methylation levels of the 4 CpG sites and the severity of SCZ. GLM revealed significant differences between the 3 groups for CpG site 1 and the average of the 4 CpG sites (P=0.0001 and P=0.0126, respectively). Furthermore, the TD, NTD and TD + NTD groups demonstrated lower methylation levels in CpG site 1 (P=0.0003, P<0.0001 and P<0.0001, respectively) and the average of 4 CpG sites (P=0.0176, P=0.0063 and P=0.003, respectively) compared with the HC group. The results revealed that both NTD and TD patients had significantly decreased DNA methylation levels compared with healthy controls, which indicated a significant association between the DNA methylation levels of the IRS1 gene with SCZ and TD.
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Affiliation(s)
- Yanli Li
- Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing 100096, P.R. China
| | - Kesheng Wang
- Department of Family and Community Health, School of Nursing, Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA
| | - Ping Zhang
- Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing 100096, P.R. China
| | - Junchao Huang
- Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing 100096, P.R. China
| | - Ying Liu
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN 37614, USA
| | - Zhiren Wang
- Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing 100096, P.R. China
| | - Yongke Lu
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
| | - Shuping Tan
- Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing 100096, P.R. China
| | - Fude Yang
- Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing 100096, P.R. China
| | - Yunlong Tan
- Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing 100096, P.R. China
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Liu M, Li S, Du M, Chu H, Wang M, Zhang Z. Novel CpG-SNPs in the gastric acid secretion pathway GNAI3 and susceptibility to gastric cancer. Gene 2020; 736:144447. [PMID: 32032744 DOI: 10.1016/j.gene.2020.144447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Previous studies indicated that gastric acid secretion was associated with gastric cancer risk. However, it still needs to explore whether the related pathway genetic variation affects GC risk. METHODS A bioinformatics study in 1625 gastric cancer cases and 2100 controls was conducted to investigate the relationship of genetic variants in eleven gastric acid secretion pathway genes and gastric cancer risk. We used logistic regression model with odds ratios (ORs) and 95% confidence intervals (CIs) to estimate the effect of 38 single nucleotide polymorphisms (SNPs) on gastric cancer susceptibility. Expression quantitative trait loci (eQTL) analysis and the methylation eQTL (meQTL) analysis were used to calculate the genetic effect on gene expression. RESULTS We identified that the CpG-SNP rs11810577 in GNAI3 was significantly increased gastric cancer risk (OR = 1.19, 95% CI = 1.07-1.32, P = 1.12 × 10-3). Furthermore, rs11810577 T allele had a negative effect on adhesion molecule with Ig like domain 1 (AMIGO1) expression in gastric tissues and increased the methylation levels of cg18220030 and cg15694127 in the promoter region of AMIGO1. Moreover, we found AMIGO1 had a lower expression levels in gastric cancer tissues than normal tissues (P = 0.037), in agreement with the data results from The Cancer Genome Atlas (TCGA) database (P < 1.0 × 10-4). CONCLUSION The CpG-SNP rs11810577 in GNAI3 in the gastric acid secretion pathway was significantly associated with susceptibility to gastric cancer.
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Affiliation(s)
- Mengting Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Biostatistics, School of Health, Nanjing Medical University, Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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Souza AMD, Lopes OS, Liberato ADL, Oliveira PJRD, Herrero SST, Nascimento ALD, Longui CA, Carvalho Filho IRD, Soares LF, Silva RBD, Burbano RR, Delatorre P, Lima EM. Association between SNPs and Loss of Methylation Site on the CpG island of the Promoter Region of the Smoothened Gene, Potential Molecular Markers for Susceptibility to the Development of Basal Cell Carcinoma in the Brazilian Population. Asian Pac J Cancer Prev 2020; 21:25-29. [PMID: 31983159 PMCID: PMC7294008 DOI: 10.31557/apjcp.2020.21.1.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
Objective: Perform genotyping of SNPs in the promoter region of the SMO gene in BCC samples from patients from northeastern Brazil, and to determine if there is an association of these SNPs of the gene in question with the susceptibility to the development of the BCC. Methods: 100 samples of paraffined tissue from patients with histopathological diagnosis of BCC and 100 control samples were analyzed for each polymorphism by a newly developed genotyping method, the Dideoxy Single Allele Specific – PCR. The software Bioestat - version 5.3 and Haploview 4.2 were used for the statistical analysis. For all tests a P-value <0.05 was considered significant. Results: The SNP rs538312246 is the Hardy-Weinberg equilibrium, therefore, it did not present significant association with the BCC (X² =2.343 and P<0.158). However, the CpG-SNPs rs375350898 and rs75827493 were significantly associated to the BCC in the analyzed samples (X2 = 27,740/21,500 and P <0001), the SNP rs75827493 showed a significant association with the BCC of the nodular subtype (P <0.0069). Therefore, our results suggest that SNPs rs375350898 and rs75827493 are potential molecular markers for susceptibility to BCC. Conclusion: The ability to detect SNP in a population, especially in promoter regions, has profoundly changed human genetic studies. This study allowed the understanding of the relationship between the presence of SNPs in CpG islands of the promoter region of the SMO gene can modify the methylation pattern and provide susceptibility to BCC in the population.
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Affiliation(s)
- Augusto Monteiro de Souza
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Otávio Sérgio Lopes
- Department of Dermatology, Dermatological Clinic Santa Catarina, João Pessoa - PB - Brazil.,Postgraduate Program in Health Sciences; Santa Casa School of Medical Sciences of São Paulo; Sao Paulo - SP, Brazil
| | - Andressa de Lima Liberato
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Paulo Junior Ribeiro de Oliveira
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Sylvia Satomi Takeno Herrero
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Agnaldo Luiz do Nascimento
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Carlos Alberto Longui
- Postgraduate Program in Health Sciences; Santa Casa School of Medical Sciences of São Paulo; Sao Paulo - SP, Brazil
| | | | | | - Renally Barbosa da Silva
- Postgraduate Program in Natural Sciences and Biotechnology, Federal University of Campina Grande - UFCG, Campus de Cuité - PB, Brazil
| | | | - Plínio Delatorre
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil.,Molecular Biology Department; Federal University of Paraiba; João Pessoa - PB, Brazil
| | - Eleonidas Moura Lima
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil.,Molecular Biology Department; Federal University of Paraiba; João Pessoa - PB, Brazil
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Goyal Y, Verma AK, Joshi P, Dev K. Contemplating the role of genetic variants of HHEX, CDKAL1, WFS1 and SLC30A8 genes of TYPE-2 diabetes in Asians ethnic groups. Gene Reports 2019; 17:100465. [DOI: 10.1016/j.genrep.2019.100465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Cantrell B, Friedman S, Lachance H, Bernier C, Murdoch B, Frattini S, Talenti A, Crepaldi P, McKay S. A novel understanding of global DNA methylation in bobcat ( Lynx rufus). Genome 2019; 63:125-130. [PMID: 31770025 DOI: 10.1139/gen-2019-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Epigenetic mechanisms may provide a novel prospective of bobcat (Lynx rufus) adaptation to habitat loss/fragmentation. Previous research has focused on bobcat behavior and genetics, but epigenetics has not been studied in bobcat. The aim of this study was to determine the quantity of global DNA methylation in the liver of 30 bobcats. DNA was extracted from liver samples obtained from the Vermont Fish and Wildlife Department. The percent of global DNA methylation was quantified and calculated using the MethylFlashTM Methylated DNA 5-mC Quantification Kit from Epigentek (Farmingdale, NY, USA). Age, sex, and carcass weight data were collected at sampling and analyzed with percent of global DNA methylation. Global DNA methylation was found to range from 0.46% to 2.76%. Age ranged from <1 to 12 years old and weight ranged from 3.18 to 13.61 kg. Further analysis of differential methylation may provide insight into novel means of bobcat conservation within different regions of Vermont. These results reinforce the need for genome-wide epigenetic studies in conservation biology.
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Affiliation(s)
- Bonnie Cantrell
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Sydney Friedman
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Hannah Lachance
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Chris Bernier
- Vermont Fish and Wildlife Department, Springfield, VT 05156, USA
| | - Brenda Murdoch
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID 83844, USA
| | - Stefano Frattini
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Andrea Talenti
- Department of Veterinary Medicine, University of Milan, Milan, Italy.,The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - Paola Crepaldi
- Department of Veterinary Medicine, University of Milan, Milan, Italy.,Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Stephanie McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA
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43
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Juvinao-Quintero DL, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA Methylation and Type 2 Diabetes: the Use of Mendelian Randomization to Assess Causality. Curr Genet Med Rep 2019; 7:191-207. [PMID: 32274260 PMCID: PMC7145450 DOI: 10.1007/s40142-019-00176-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarises recent advances in the field of epigenetics in order to understand the aetiology of type 2 diabetes (T2D). Recent Findings DNA methylation at a number of loci has been shown to be robustly associated with T2D, including TXNIP, ABCG1, CPT1A, and SREBF1. However, due to the cross-sectional nature of many epidemiological studies and predominant analysis in samples derived from blood rather than disease relevant tissues, inferring causality is difficult. We therefore outline the use of Mendelian randomisation (MR) as one method able to assess causality in epigenetic studies of T2D. Summary Epidemiological studies have been fruitful in identifying epigenetic markers of T2D. Triangulation of evidence including utilisation of MR is essential to delineate causal from non-causal biomarkers of disease. Understanding the causality of epigenetic markers in T2D more fully will aid prioritisation of CpG sites as early biomarkers to detect disease or in drug development to target epigenetic mechanisms in order to treat patients.
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Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, USA
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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Nazari Z, Shahryari A, Ghafari S, Nabiuni M, Golalipour MJ. In Utero Exposure to Gestational Diabetes Alters DNA Methylation and Gene Expression of CDKN2A/B in Langerhans Islets of Rat Offspring. Cell J 2019; 22:203-211. [PMID: 31721535 PMCID: PMC6874789 DOI: 10.22074/cellj.2020.6699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/09/2019] [Indexed: 12/14/2022]
Abstract
Objective DNA methylation, a major epigenetic reprogramming mechanism, contributes to the increased prevalence of type 2 diabetes mellitus (T2DM). Based on genome-wide association studies, polymorphisms in CDKN2A/B are associated with T2DM. Our previous studies showed that gestational diabetes mellitus (GDM) causes apoptosis in β-cells, leading to a reduction in their number in pancreatic tissue of GDM-exposed adult rat offspring. The aim of this study was to examine the impact of intrauterine exposure to GDM on DNA methylation, mRNA transcription, as well as protein expression of these factors in the pancreatic islets of Wistar rat offspring. Our hypothesis was that the morphological changes seen in our previous study might have been caused by aberrant methylation and expression of CDKN2A/B. Materials and Methods In this experimental study, we delineated DNA methylation patterns, mRNA transcription and protein expression level of CDKN2A/B in the pancreatic islets of 15-week-old rat offspring of streptozotocin-induced GDM dams. We performed bisulfite sequencing to determine the DNA methylation patterns of CpGs in candidate promoter regions of CDKN2A/B. Furthermore, we compared the levels of mRNA transcripts as well as the cell cycle inhibitory proteins P15 and P16 in two groups by qPCR and western blotting, respectively. Results Our results demonstrated that hypomethylation of CpG sites in the vicinity of CDKN2A and CDKN2B genes is positively related to increased levels of CDKN2A/B mRNA and protein in islets of Langerhans in the GDM offspring. The average percentage of CDKN2A promoter methylation was significantly lower in GDM group compared to the controls (P<0.01). Conclusion We postulate that GDM is likely to exert its adverse effects on pancreatic β-cells of offspring through hypomethylation of the CDKN2A/B promoter. Abnormal methylation of these genes may have a link with β-cell dysfunction and diabetes. These data potentially lead to a novel approach to the treatment of T2DM.
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Affiliation(s)
- Zahra Nazari
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, Iran
| | - Alireza Shahryari
- Stem Cell Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Soraya Ghafari
- Congenital Malformations Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammad Nabiuni
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Jafar Golalipour
- Congenital Malformations Research Center, Golestan University of Medical Sciences, Gorgan, Iran. Electronic Address:
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45
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Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One 2019; 14:e0222329. [PMID: 31513639 PMCID: PMC6742455 DOI: 10.1371/journal.pone.0222329] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Methylation patterns established and maintained at CpG sites may be altered by single nucleotide polymorphisms (SNPs) within these sites and may affect the regulation of nearby genes. Our aims were to: 1) identify and generate a database of SNPs potentially subject to epigenetic control by DNA methylation via their involvement in creating, removing or displacing CpG sites (meSNPs), and; 2) investigate the association of these meSNPs with CpG islands (CGIs), and with methylation profiles of DNA extracted from tissues from cattle with divergent feed efficiencies detected using MIRA-Seq. Using the variant annotation for 56,969,697 SNPs identified in Run5 of the 1000 Bull Genomes Project and the UMD3.1.1 bovine reference genome sequence assembly, we identified and classified 12,836,763 meSNPs according to the nature of variation created at CpGs. The majority of the meSNPs were located in intergenic regions (68%) or introns (26.3%). We found an enrichment (p<0.01) of meSNPs located in CGIs relative to the genome as a whole, and also in differentially methylated sequences in tissues from animals divergent for feed efficiency. Seven meSNPs, located in differentially methylated regions, were fixed for methylation site creating (MSC) or destroying (MSD) alleles in the differentially methylated genomic sequences of animals differing in feed efficiency. These meSNPs may be mechanistically responsible for creating or deleting methylation targets responsible for the differential expression of genes underlying differences in feed efficiency. Our methyl SNP database (dbmeSNP) is useful for identifying potentially functional "epigenetic polymorphisms" underlying variation in bovine phenotypes.
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Affiliation(s)
| | | | - Sheila T Nagamatsu
- Genomics and Expression Laboratory, University of Campinas, Campinas, São Paulo, Brazil.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Marcelo F Carazzolle
- Genomics and Expression Laboratory, University of Campinas, Campinas, São Paulo, Brazil.,National Center for High Performance Computing (CENAPAD-SP), University of Campinas, Campinas, São Paulo, Brazil
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Lynsey K Whitacre
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.,Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Stephanie D McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, Vermont, United States of America
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Flavia L Lopes
- São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
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Kubi JA, Chen ACH, Fong SW, Lai KP, Wong CKC, Yeung WSB, Lee KF, Lee YL. Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the differentiation of embryonic stem cells towards pancreatic lineage and pancreatic beta cell function. Environ Int 2019; 130:104885. [PMID: 31195220 DOI: 10.1016/j.envint.2019.05.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Animal and epidemiological studies demonstrated association of persistent exposure of TCDD, an endocrine disrupting chemical, to susceptibility of type 2 diabetes (T2D). High doses of TCDD were commonly employed in experimental animals to illustrate its diabetogenic effects. Data linking the epigenetic effects of low doses of TCDD on embryonic cells to T2D susceptibility risks is very limited. To address whether low dose exposure to TCDD would affect pancreatic development, hESCs pretreated with TCDD at concentrations similar to human exposure were differentiated towards pancreatic lineage cells, and their global DNA methylation patterns were determined. Our results showed that TCDD-treated hESCs had impaired pancreatic lineage differentiation potentials and altered global DNA methylation patterns. Four of the hypermethylated genes (PRKAG1, CAPN10, HNF-1B and MAFA) were validated by DNA bisulfite sequencing. PRKAG1, a regulator in the AMPK signaling pathway critical for insulin secretion, was selected for further functional study in the rat insulinoma cell line, INS-1E cells. TCDD treatment induced PRKAG1 hypermethylation in hESCs, and the hypermethylation was maintained after pancreatic progenitor cells differentiation. Transient Prkag1 knockdown in the INS-1E cells elevated glucose stimulated insulin secretions (GSIS), possibly through mTOR signaling pathway. The current study suggested that early embryonic exposure to TCDD might alter pancreatogenesis, increasing the risk of T2D.
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Affiliation(s)
- John A Kubi
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China
| | - Andy C H Chen
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Sze Wan Fong
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China
| | - Keng Po Lai
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Chris K C Wong
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - William S B Yeung
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Kai Fai Lee
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong Shenzhen Hospital, Shenzhen, China.
| | - Yin Lau Lee
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong Shenzhen Hospital, Shenzhen, China.
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47
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Ding T, Zhou Y, Long R, Chen C, Zhao J, Cui P, Guo M, Liang G, Xu L. DUSP8 phosphatase: structure, functions, expression regulation and the role in human diseases. Cell Biosci 2019; 9:70. [PMID: 31467668 PMCID: PMC6712826 DOI: 10.1186/s13578-019-0329-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/12/2019] [Indexed: 12/28/2022] Open
Abstract
Dual-specificity phosphatases (DUSPs) are a subset of protein tyrosine phosphatases (PTPs), many of which dephosphorylate the residues of phosphor-serine/threonine and phosphor-tyrosine on mitogen-activated protein kinases (MAPKs), and hence are also referred to as MAPK phosphatases (MKPs). Homologue of Vaccinia virus H1 phosphatase gene clone 5 (HVH-5), also known as DUSP8, is a unique member of the DUSPs family of phosphatases. Accumulating evidence has shown that DUSP8 plays an important role in phosphorylation-mediated signal transduction of MAPK signaling ranging from cell oxidative stress response, cell apoptosis and various human diseases. It is generally believed that DUSP8 exhibits significant dephosphorylation activity against JNK, however, with the deepening of research, plenty of new literature reports that DUSP8 also has effective dephosphorylation activity on p38 MAPK and ERKs, successfully affects the transduction of MAPKs pathway, indicating that DUSP8 presents a unknown diversity of DUSPs family on distinct corresponding dephosphorylated substrates in different biological events. Therefore, the in-depth study of DUSP8 not only throws a new light on the multi-biological function of DUSPs, but also is much valuable for the reveal of complex pathobiology of clinical diseases. In this review, we provide a detail overview of DUSP8 phosphatase structure, biological function and expression regulation, as well as its role in related clinical human diseases, which might be help for the understanding of biological function of DUSP8 and the development of prevention, diagnosis and therapeutics in related human diseases.
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Affiliation(s)
- Tao Ding
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi, 563000 Guizhou China.,2Department of Immunology, Zunyi Medical University, Zunyi, 563000 Guizhou China
| | - Ya Zhou
- 3Department of Medical Physics, Zunyi Medical University, Zunyi, 563000 Guizhou China
| | - Runying Long
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi, 563000 Guizhou China.,2Department of Immunology, Zunyi Medical University, Zunyi, 563000 Guizhou China
| | - Chao Chen
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi, 563000 Guizhou China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi, 563000 Guizhou China
| | - Panpan Cui
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi, 563000 Guizhou China
| | - Mengmeng Guo
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi, 563000 Guizhou China
| | - Guiyou Liang
- 4Department of Cardiovascular Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004 Guizhou China.,5Department of Cardiovascular Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000 Guizhou China
| | - Lin Xu
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi, 563000 Guizhou China.,2Department of Immunology, Zunyi Medical University, Zunyi, 563000 Guizhou China
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Stenz L, Rahban R, Prados J, Nef S, Paoloni-Giacobino A. Genetic resistance to DEHP-induced transgenerational endocrine disruption. PLoS One 2019; 14:e0208371. [PMID: 31181066 DOI: 10.1371/journal.pone.0208371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/15/2019] [Indexed: 02/07/2023] Open
Abstract
Di(2-ethylhexyl)phthalate (DEHP) interferes with sex hormones signaling pathways (SHP). C57BL/6J mice prenatally exposed to 300 mg/kg/day DEHP develop a testicular dysgenesis syndrome (TDS) at adulthood, but similarly-exposed FVB/N mice are not affected. Here we aim to understand the reasons behind this drastic difference that should depend on the genome of the strain. In both backgrounds, pregnant female mice received per os either DEHP or corn oil vehicle and the male filiations were examined. Computer-assisted sperm analysis showed a DEHP-induced decreased sperm count and velocities in C57BL/6J. Sperm RNA sequencing experiments resulted in the identification of the 62 most differentially expressed RNAs. These RNAs, mainly regulated by hormones, produced strain-specific transcriptional responses to prenatal exposure to DEHP; a pool of RNAs was increased in FVB, another pool of RNAs was decreased in C57BL/6J. In FVB/N, analysis of non-synonymous single nucleotide polymorphisms (SNP) impacting SHP identified rs387782768 and rs29315913 respectively associated with absence of the Forkhead Box A3 (Foxa3) RNA and increased expression of estrogen receptor 1 variant 4 (NM_001302533) RNA. Analysis of the role of SNPs modifying SHP binding sites in function of strain-specific responses to DEHP revealed a DEHP-resistance allele in FVB/N containing an additional FOXA1-3 binding site at rs30973633 and four DEHP-induced beta-defensins (Defb42, Defb30, Defb47 and Defb48). A DEHP-susceptibility allele in C57BL/6J contained five SNPs (rs28279710, rs32977910, rs46648903, rs46677594 and rs48287999) affecting SHP and six genes (Svs2, Svs3b, Svs4, Svs3a, Svs6 and Svs5) epigenetically silenced by DEHP. Finally, targeted experiments confirmed increased methylation in the Svs3ab promoter with decreased SEMG2 persisting across generations, providing a molecular explanation for the transgenerational sperm velocity decrease found in C57BL/6J after DEHP exposure. We conclude that the existence of SNP-dependent mechanisms in FVB/N inbred mice may confer resistance to transgenerational endocrine disruption.
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Guo K, Elzinga S, Eid S, Figueroa-Romero C, Hinder LM, Pacut C, Feldman EL, Hur J. Genome-wide DNA methylation profiling of human diabetic peripheral neuropathy in subjects with type 2 diabetes mellitus. Epigenetics 2019; 14:766-779. [PMID: 31132961 PMCID: PMC6615525 DOI: 10.1080/15592294.2019.1615352] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is an epigenetic mechanism important for the regulation of gene expression, which plays a vital role in the interaction between genetic and environmental factors. Aberrant epigenetic changes are implicated in the pathogenesis of diabetes and diabetic complications, but the role of DNA methylation in diabetic peripheral neuropathy (DPN) is not well understood. Therefore, our aim in this study was to explore the role of DNA methylation in the progression of DPN in type 2 diabetes. We compared genome-wide DNA methylation profiles of human sural nerve biopsies from subjects with stable or improving nerve fibre counts to biopsies from subjects with progressive loss of nerve fibres. Nerve fibre counts were determined by comparing myelinated nerve fibre densities between an initial and repeat biopsy separated by 52 weeks. Subjects with significant nerve regeneration (regenerators) and subjects with significant nerve degeneration (degenerators) represent the two extreme DPN phenotypes. Using reduced representation bisulfite sequencing, we identified 3,460 differentially methylated CpG dinucleotides between the two groups. The genes associated with differentially methylated CpGs were highly enriched in biological processes that have previously been implicated in DPN such as nervous system development, neuron development, and axon guidance, as well as glycerophospholipid metabolism and mitogen-activated protein kinase (MAPK) signalling. These findings are the first to provide a comprehensive analysis of DNA methylation profiling in human sural nerves of subjects with DPN and suggest that epigenetic regulation has an important role in the progression of this prevalent diabetic complication.
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Affiliation(s)
- Kai Guo
- a Department of Biomedical Sciences, School of Medicine and Health Sciences , University of North Dakota , Grand Forks , ND , USA
| | - Sarah Elzinga
- b Department of Neurology, School of Medicine , University of Michigan , Ann Arbor , MI , USA
| | - Stephanie Eid
- b Department of Neurology, School of Medicine , University of Michigan , Ann Arbor , MI , USA
| | - Claudia Figueroa-Romero
- b Department of Neurology, School of Medicine , University of Michigan , Ann Arbor , MI , USA
| | - Lucy M Hinder
- b Department of Neurology, School of Medicine , University of Michigan , Ann Arbor , MI , USA
| | - Crystal Pacut
- b Department of Neurology, School of Medicine , University of Michigan , Ann Arbor , MI , USA
| | - Eva L Feldman
- b Department of Neurology, School of Medicine , University of Michigan , Ann Arbor , MI , USA
| | - Junguk Hur
- a Department of Biomedical Sciences, School of Medicine and Health Sciences , University of North Dakota , Grand Forks , ND , USA
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50
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Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C. ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes. Sci Rep 2019; 9:7785. [PMID: 31123324 PMCID: PMC6533306 DOI: 10.1038/s41598-019-44076-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 05/08/2019] [Indexed: 01/08/2023] Open
Abstract
Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and rs878521 near TCF7L2, KCNQ1, HNF1B, ADCY5 and GCK, respectively) and with additional 67 SNPs in LD with known T2D SNPs (e.g. SNPs annotated to GIPR, KCNJ11, GLIS3, IGF2BP2, FTO and PPARG). There was enrichment of open chromatin regions near highly expressed genes in human islets. Moreover, 1,078 open chromatin peaks, annotated to 898 genes, differed in prevalence between diabetic and non-diabetic islet donors. Some of these peaks are annotated to candidate genes for T2D and islet dysfunction (e.g. HHEX, HMGA2, GLIS3, MTNR1B and PARK2) and some overlap with SNPs associated with T2D (e.g. rs3821943 near WFS1 and rs508419 near ANK1). Enhancer regions and motifs specific to key TFs including BACH2, FOXO1, FOXA2, NEUROD1, MAFA and PDX1 were enriched in differential islet ATAC-seq peaks of T2D versus non-diabetic donors. Our study provides new understanding into how T2D alters the chromatin landscape, and thereby accessibility for TFs and gene expression, in human pancreatic islets.
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Affiliation(s)
- Madhusudhan Bysani
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Rasmus Agren
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Göteborg, Sweden
| | - Cajsa Davegårdh
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
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