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Qadir MMF, Elgamal RM, Song K, Kudtarkar P, Sakamuri SS, Katakam PV, El-Dahr SS, Kolls JK, Gaulton KJ, Mauvais-Jarvis F. Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. RESEARCH SQUARE 2024:rs.3.rs-4607352. [PMID: 39011095 PMCID: PMC11247939 DOI: 10.21203/rs.3.rs-4607352/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Type 2 and type 1 diabetes (T2D, T1D) exhibit sex differences in insulin secretion, the mechanisms of which are unknown. We examined sex differences in human pancreatic islets from 52 donors with and without T2D combining single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), hormone secretion, and bioenergetics. In nondiabetic (ND) donors, sex differences in islet cells gene accessibility and expression predominantly involved sex chromosomes. Islets from T2D donors exhibited similar sex differences in sex chromosomes differentially expressed genes (DEGs), but also exhibited sex differences in autosomal genes. Comparing β cells from T2D vs. ND donors, gene enrichment of female β cells showed suppression in mitochondrial respiration, while male β cells exhibited suppressed insulin secretion. Thus, although sex differences in gene accessibility and expression of ND β cells predominantly affect sex chromosomes, the transition to T2D reveals sex differences in autosomes highlighting mitochondrial failure in females.
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Affiliation(s)
- Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| | - Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Keijing Song
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Siva S.V.P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad V. Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samir S. El-Dahr
- Department of Pediatrics, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Jay K. Kolls
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
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2
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Wang K, Shi M, Luk AOY, Kong APS, Ma RCW, Li C, Chen L, Chow E, Chan JCN. Impaired GK-GKRP interaction rather than direct GK activation worsens lipid profiles and contributes to long-term complications: a Mendelian randomization study. Cardiovasc Diabetol 2024; 23:228. [PMID: 38951793 PMCID: PMC11218184 DOI: 10.1186/s12933-024-02321-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Glucokinase (GK) plays a key role in glucose metabolism. In the liver, GK is regulated by GK regulatory protein (GKRP) with nuclear sequestration at low plasma glucose level. Some GK activators (GKAs) disrupt GK-GKRP interaction which increases hepatic cytoplasmic GK level. Excess hepatic GK activity may exceed the capacity of glycogen synthesis with excess triglyceride formation. It remains uncertain whether hypertriglyceridemia associated with some GKAs in previous clinical trials was due to direct GK activation or impaired GK-GKRP interaction. METHODS Using publicly available genome-wide association study summary statistics, we selected independent genetic variants of GCKR and GCK associated with fasting plasma glucose (FPG) as instrumental variables, to mimic the effects of impaired GK-GKRP interaction and direct GK activation, respectively. We applied two-sample Mendelian Randomization (MR) framework to assess their causal associations with lipid-related traits, risks of metabolic dysfunction-associated steatotic liver disease (MASLD) and cardiovascular diseases. We verified these findings in one-sample MR analysis using individual-level statistics from the Hong Kong Diabetes Register (HKDR). RESULTS Genetically-proxied impaired GK-GKRP interaction increased plasma triglycerides, low-density lipoprotein cholesterol and apolipoprotein B levels with increased odds ratio (OR) of 14.6 (95% CI 4.57-46.4) per 1 mmol/L lower FPG for MASLD and OR of 2.92 (95% CI 1.78-4.81) for coronary artery disease (CAD). Genetically-proxied GK activation was associated with decreased risk of CAD (OR 0.69, 95% CI 0.54-0.88) and not with dyslipidemia. One-sample MR validation in HKDR showed consistent results. CONCLUSIONS Impaired GK-GKRP interaction, rather than direct GK activation, may worsen lipid profiles and increase risks of MASLD and CAD. Development of future GKAs should avoid interfering with GK-GKRP interaction.
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Affiliation(s)
- Ke Wang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Hua Medicine (Shanghai) Co., Ltd., Shanghai, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
| | - Andrea O Y Luk
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Phase 1 Clinical Trial Centre, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
| | - Alice P S Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China
| | - Changhong Li
- Hua Medicine (Shanghai) Co., Ltd., Shanghai, China
| | - Li Chen
- Hua Medicine (Shanghai) Co., Ltd., Shanghai, China
| | - Elaine Chow
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China.
- Phase 1 Clinical Trial Centre, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China.
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region, China.
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3
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Wei C, Zhang G, Li C, Zeng J. Genetic susceptibility to breast cancer increases the risk of neutropenia and agranulocytosis: insights from Mendelian randomization. Support Care Cancer 2024; 32:472. [PMID: 38949722 DOI: 10.1007/s00520-024-08682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/22/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE The causal relationship between breast cancer and its estrogen receptor (ER) subtypes and neutropenia and agranulocytosis is unclear. METHODS In two-sample Mendelian randomization (MR), we used inverse variance weighting (IVW), Bayesian weighted MR (BWMR), MR-Egger, weighted median, simple mode, and weighted mode methods to analyze causality for ER-positive breast cancer, ER-negative breast cancer, overall breast cancer, and drug-induced neutropenia and agranulocytosis. To validate the results, we performed the analysis again using GWAS data on neutropenia from different databases. In multivariable MR (MVMR), we assessed the independent effects of ER-positive and ER-negative breast cancer on causality. RESULTS Two-sample MR analysis showed a causal relationship between ER-positive breast cancer (IVW odds ratio (OR) = 1.319, P = 7.580 × 10-10), ER-negative breast cancer (OR = 1.285, P = 1.263 × 10-4), overall breast cancer (OR = 1.418, P = 2.123 × 10-13), and drug-induced neutropenia and a causal relationship between ER-positive breast cancer (OR = 1.349, P = 1.402 × 10-7), ER-negative breast cancer (OR = 1.235, P = 7.615 × 10-3), overall breast cancer (OR = 1.429, P = 9.111 × 10-10), and neutropenia. Similarly, ER-positive breast cancer (OR = 1.213, P = 5.350 × 10-8), ER-negative breast cancer (OR = 1.179, P = 1.300 × 10-3), and overall breast cancer (OR = 1.275, P = 8.642 × 10-11) also had a causal relationship with agranulocytosis. MVMR analysis showed that ER-positive breast cancer remained causally associated with drug-induced neutropenia (OR = 1.233, P = 4.188 × 10-4), neutropenia (OR = 1.283, P = 6.363 × 10-4), and agranulocytosis (OR = 1.142, P = 4.549 × 10-3). Heterogeneity analysis and pleiotropy test showed that our results were reliable. CONCLUSION Our study provides genetic evidence for a causal association between breast cancer and its estrogen receptor subtypes and neutropenia. In clinical practice, in addition to focusing on therapeutic factors, additional attention should be given to breast cancer patients to avoid severe neutropenia.
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Affiliation(s)
- Changlong Wei
- Department of Breast Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Gongyin Zhang
- Department of Breast Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Changwang Li
- Department of Breast Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Jinsheng Zeng
- Department of Breast Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China.
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Gupta MK, Gouda G, Vadde R. Relation Between Obesity and Type 2 Diabetes: Evolutionary Insights, Perspectives and Controversies. Curr Obes Rep 2024:10.1007/s13679-024-00572-1. [PMID: 38850502 DOI: 10.1007/s13679-024-00572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
PURPOSE OF REVIEW Since the mid-twentieth century, obesity and its related comorbidities, notably insulin resistance (IR) and type 2 diabetes (T2D), have surged. Nevertheless, their underlying mechanisms remain elusive. Evolutionary medicine (EM) sheds light on these issues by examining how evolutionary processes shape traits and diseases, offering insights for medical practice. This review summarizes the pathogenesis and genetics of obesity-related IR and T2D. Subsequently, delving into their evolutionary connections. Addressing limitations and proposing future research directions aims to enhance our understanding of these conditions, paving the way for improved treatments and prevention strategies. RECENT FINDINGS Several evolutionary hypotheses have been proposed to unmask the origin of obesity-related IR and T2D, e.g., the "thrifty genotype" hypothesis suggests that certain "thrifty genes" that helped hunter-gatherer populations efficiently store energy as fat during feast-famine cycles are now maladaptive in our modern obesogenic environment. The "drifty genotype" theory suggests that if thrifty genes were advantageous, they would have spread widely, but proposes genetic drift instead. The "behavioral switch" and "carnivore connection" hypotheses propose insulin resistance as an adaptation for a brain-dependent, low-carbohydrate lifestyle. The thrifty phenotype theory suggests various metabolic outcomes shaped by genes and environment during development. However, the majority of these hypotheses lack experimental validation. Understanding why ancestral advantages now predispose us to diseases may aid in drug development and prevention of disease. EM helps us to understand the evolutionary relation between obesity-related IR and T2D. But still gaps and contradictions persist. Further interdisciplinary research is required to elucidate complete mechanisms.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, 516005, Andhra Pradesh, India.
| | - Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, 753 006, Odisha, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, 516005, Andhra Pradesh, India
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Zhang W, Sun J, Yu H, Shi M, Hu H, Yuan H. Causal relationship between type 2 diabetes mellitus and aortic dissection: insights from two-sample Mendelian randomization and mediation analysis. Front Endocrinol (Lausanne) 2024; 15:1405517. [PMID: 38803481 PMCID: PMC11128602 DOI: 10.3389/fendo.2024.1405517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Objective Some evidence suggests a reduced prevalence of type 2 diabetes mellitus (T2DM) in patients with aortic dissection (AD), a catastrophic cardiovascular illness, compared to general population. However, the conclusions were inconsistent, and the causal relationship between T2DM and AD remains unclear. Methods In this study, we aimed to explore the causal relationship between T2DM and AD using bidirectional Mendelian randomization (MR) analysis. Mediation MR analysis was conducted to explore and quantify the possible mediation effects of 1400 metabolites in T2DM and AD. Results The results of 26 datasets showed no causal relationship between T2DM and AD (P>0.05). Only one dataset (ebi-a-GCST90006934) showed that T2DM was a protective factor for AD (I9-AORTDIS) (OR=0.815, 95%CI: 0.692-0.960, P=0.014), and did not show horizontal pleiotropy (P=0.808) and heterogeneity (P=0.525). Vanillic acid glycine plays a mediator in the causal relationship between T2DM and AD. The mediator effect for vanillic acid glycine levels was -0.023 (95%CI: -0.066-0.021). Conclusion From the perspective of MR analysis, there might not be a causal relationship between T2DM and AD, and T2DM might not be a protective factor for AD. If a causal relationship does exist between T2DM and AD, with T2DM serving as a protective factor, vanillic acid glycine may act as a mediator and enhance such a protective effect.
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Affiliation(s)
| | | | | | | | | | - Hong Yuan
- Department of Cardiovascular, First People’s Hospital of LinPing District, Hangzhou, China
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6
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Sabadell-Basallote J, Astiarraga B, Castaño C, Ejarque M, Repollés-de-Dalmau M, Quesada I, Blanco J, Nuñez-Roa C, Rodríguez-Peña MM, Martínez L, De Jesus DF, Marroqui L, Bosch R, Montanya E, Sureda FX, Tura A, Mari A, Kulkarni RN, Vendrell J, Fernández-Veledo S. SUCNR1 regulates insulin secretion and glucose elevates the succinate response in people with prediabetes. J Clin Invest 2024; 134:e173214. [PMID: 38713514 PMCID: PMC11178533 DOI: 10.1172/jci173214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/26/2024] [Indexed: 05/09/2024] Open
Abstract
Pancreatic β-cell dysfunction is a key feature of type 2 diabetes, and novel regulators of insulin secretion are desirable. Here we report that the succinate receptor (SUCNR1) is expressed in β-cells and is up-regulated in hyperglycemic states in mice and humans. We found that succinate acts as a hormone-like metabolite and stimulates insulin secretion via a SUCNR1-Gq-PKC-dependent mechanism in human β-cells. Mice with β-cell-specific Sucnr1 deficiency exhibit impaired glucose tolerance and insulin secretion on a high-fat diet, indicating that SUCNR1 is essential for preserving insulin secretion in diet-induced insulin resistance. Patients with impaired glucose tolerance show an enhanced nutritional-related succinate response, which correlates with the potentiation of insulin secretion during intravenous glucose administration. These data demonstrate that the succinate/SUCNR1 axis is activated by high glucose and identify a GPCR-mediated amplifying pathway for insulin secretion relevant to the hyperinsulinemia of prediabetic states.
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Affiliation(s)
- Joan Sabadell-Basallote
- Unitat de Recerca, Hospital Universitari Joan XXIII, Insitut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Brenno Astiarraga
- Unitat de Recerca, Hospital Universitari Joan XXIII, Insitut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Carlos Castaño
- Unitat de Recerca, Hospital Universitari Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Miriam Ejarque
- Unitat de Recerca, Hospital Universitari Joan XXIII, Insitut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Maria Repollés-de-Dalmau
- Unitat de Recerca, Hospital Universitari Joan XXIII, Insitut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Ivan Quesada
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, ELCHE, Spain
| | - Jordi Blanco
- Departament de Medicina i Cirurgia, Universitat Rovira i Virgili, Reus, Spain
| | - Catalina Nuñez-Roa
- Unitat de Recerca, Hospital Universitari Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - M-Mar Rodríguez-Peña
- Unitat de Recerca, Hospital Universitari Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Laia Martínez
- Unitat de Recerca, Hospital Universitari Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Dario F De Jesus
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
| | - Laura Marroqui
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, ELCHE, Spain
| | - Ramon Bosch
- Unitat de Recerca, Hospital Universitari Joan XXIII, Insitut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Eduard Montanya
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, ELCHE, Spain
| | - Francesc X Sureda
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
| | - Andrea Tura
- Institute of Neuroscience, National Research Council, Padova, Italy
| | - Andrea Mari
- Institute of Neuroscience, National Research Council, Padova, Italy
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
| | - Joan Vendrell
- Unitat de Recerca, Hospital Universitari Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
| | - Sonia Fernández-Veledo
- Unitat de Recerca, Hospital Universitari Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
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Hu M, Kim I, Morán I, Peng W, Sun O, Bonnefond A, Khamis A, Bonàs-Guarch S, Froguel P, Rutter GA. Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function. FASEB J 2024; 38:e23610. [PMID: 38661000 PMCID: PMC11108099 DOI: 10.1096/fj.202301700rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ZnT8. Although this protein-coding variant was previously thought to be the sole driver of T2D risk at this locus, recent studies have provided evidence for lowered expression of SLC30A8 mRNA in protective allele carriers. In the present study, we examined multiple variants that influence SLC30A8 allele-specific expression. Epigenomic mapping has previously identified an islet-selective enhancer cluster at the SLC30A8 locus, hosting multiple T2D risk and cASE associations, which is spatially associated with the SLC30A8 promoter and additional neighboring genes. Here, we show that deletion of variant-bearing enhancer regions using CRISPR-Cas9 in human-derived EndoC-βH3 cells lowers the expression of SLC30A8 and several neighboring genes and improves glucose-stimulated insulin secretion. While downregulation of SLC30A8 had no effect on beta cell survival, loss of UTP23, RAD21, or MED30 markedly reduced cell viability. Although eQTL or cASE analyses in human islets did not support the association between these additional genes and diabetes risk, the transcriptional regulator JQ1 lowered the expression of multiple genes at the SLC30A8 locus and enhanced stimulated insulin secretion.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Innah Kim
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Ignasi Morán
- Life Sciences Department, Barcelona Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
| | - Weicong Peng
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Orien Sun
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Amélie Bonnefond
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, F-59000, France
- University of Lille, Lille University Hospital, Lille, F-59000, France.France
| | - Amna Khamis
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, F-59000, France
- University of Lille, Lille University Hospital, Lille, F-59000, France.France
| | - Sílvia Bonàs-Guarch
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Center for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Philippe Froguel
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, F-59000, France
- University of Lille, Lille University Hospital, Lille, F-59000, France.France
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
- Lee Kong Chian Imperial Medical School, Nanyang Technological University, Singapore
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Yang M, Wan X, Su Y, Xu K, Wen P, Zhang B, Liu L, Yang Z, Xu P. The genetic causal relationship between type 2 diabetes, glycemic traits and venous thromboembolism, deep vein thrombosis, pulmonary embolism: a two-sample Mendelian randomization study. Thromb J 2024; 22:33. [PMID: 38553747 PMCID: PMC10979561 DOI: 10.1186/s12959-024-00600-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
OBJECTIVE To investigate the genetic underpinnings of the association between type 2 diabetes (T2D), glycemic indicators such as fasting glucose (FG), fasting insulin (FI), and glycated hemoglobin (GH), and venous thromboembolism (VTE), encompassing deep vein thrombosis (DVT) and pulmonary embolism (PE), thereby contributing novel insights to the scholarly discourse within this domain. METHODS Genome-wide association study (GWAS) summary data pertaining to exposures (T2D, FG, FI, GH) and outcomes (VTE, DVT, PE) were acquired from the IEU Open GWAS database, encompassing participants of European descent, including both male and female individuals. Two-sample Mendelian randomization (MR) analyses were conducted utilizing the TwoSampleMR and MRPRESSO packages within the R programming environment. The primary analytical approach employed was the random-effects inverse variance weighted (IVW) method. Heterogeneity was assessed via Cochran's Q statistic for MR-IVW and Rucker's Q statistic for MR-Egger. Horizontal pleiotropy was evaluated using the intercept test of MR Egger and MR pleiotropy residual sum and outlier (MR-PRESSO) analysis, with the latter also employed for outlier detection. Additionally, a "Leave one out" analysis was conducted to ascertain the influence of individual single nucleotide polymorphisms (SNPs) on MR results. RESULTS The random-effects IVW analysis revealed a negative genetic causal association between T2D) and VTE (P = 0.008, Odds Ratio [OR] 95% confidence interval [CI] = 0.896 [0.827-0.972]), as well as between FG and VTE (P = 0.002, OR 95% CI = 0.655 [0.503-0.853]), GH and VTE (P = 0.010, OR 95% CI = 0.604 [0.412-0.884]), and GH and DVT (P = 0.002, OR 95% CI = 0.413 [0.235-0.725]). Conversely, the random-effects IVW analysis did not detect a genetic causal relationship between FI and VTE (P > 0.05), nor between T2D, FG, or FI and DVT (P > 0.05), or between T2D, FG, FI, or GH and PE (P > 0.05). Both the Cochran's Q statistic for MR-IVW and Rucker's Q statistic for MR-Egger indicated no significant heterogeneity (P > 0.05). Moreover, the intercept tests of MR Egger and MR-PRESSO suggested the absence of horizontal pleiotropy (P > 0.05). MR-PRESSO analysis identified no outliers, while the "Leave one out" analysis underscored that the MR analysis was not influenced by any single SNP. CONCLUSION Our investigation revealed that T2D, FG, and GH exhibit negative genetic causal relationships with VTE at the genetic level, while GH demonstrates a negative genetic causal relationship with DVT at the genetic level. These findings furnish genetic-level evidence warranting further examination of VTE, DVT, and PE, thereby making a contribution to the advancement of related research domains.
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Affiliation(s)
- Mingyi Yang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Xianjie Wan
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yani Su
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Pengfei Wen
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Binfei Zhang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Lin Liu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Zhi Yang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China.
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Yan Z, Xu Y, Li K, Liu L. Association between high-density lipoprotein cholesterol and type 2 diabetes mellitus: dual evidence from NHANES database and Mendelian randomization analysis. Front Endocrinol (Lausanne) 2024; 15:1272314. [PMID: 38455653 PMCID: PMC10917910 DOI: 10.3389/fendo.2024.1272314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Background Low levels of high-density lipoprotein cholesterol (HDL-C) are commonly seen in patients with type 2 diabetes mellitus (T2DM). However, it is unclear whether there is an independent or causal link between HDL-C levels and T2DM. This study aims to address this gap by using the The National Health and Nutrition Examination Survey (NHANES) database and Mendelian randomization (MR) analysis. Materials and methods Data from the NHANES survey (2007-2018) with 9,420 participants were analyzed using specialized software. Logistic regression models and restricted cubic splines (RCS) were used to assess the relationship between HDL-C and T2DM incidence, while considering covariates. Genetic variants associated with HDL-C and T2DM were obtained from genome-wide association studies (GWAS), and Mendelian randomization (MR) was used to evaluate the causal relationship between HDL-C and T2DM. Various tests were conducted to assess pleiotropy and outliers. Results In the NHANES study, all groups, except the lowest quartile (Q1: 0.28-1.09 mmol/L], showed a significant association between HDL-C levels and reduced T2DM risk (all P < 0.001). After adjusting for covariates, the Q2 [odds ratio (OR) = 0.67, 95% confidence interval (CI): (0.57, 0.79)], Q3 [OR = 0.51, 95% CI: (0.40, 0.65)], and Q4 [OR = 0.29, 95% CI: (0.23, 0.36)] groups exhibited average reductions in T2DM risk of 23%, 49%, and 71%, respectively. In the sensitivity analysis incorporating other lipid levels, the Q4 group still demonstrates a 57% reduction in the risk of T2DM. The impact of HDL-C levels on T2DM varied with age (P for interaction = 0.006). RCS analysis showed a nonlinear decreasing trend in T2DM risk with increasing HDL-C levels (P = 0.003). In the MR analysis, HDL-C levels were also associated with reduced T2DM risk (OR = 0.69, 95% CI = 0.52-0.82; P = 1.41 × 10-13), and there was no evidence of pleiotropy or outliers. Conclusion This study provides evidence supporting a causal relationship between higher HDL-C levels and reduced T2DM risk. Further research is needed to explore interventions targeting HDL-C levels for reducing T2DM risk.
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Affiliation(s)
- Zhaoqi Yan
- Jiangxi University of Traditional Chinese Medicine, Graduate School, Nanchang, Jiangxi, China
| | - Yifeng Xu
- Jiangxi University of Traditional Chinese Medicine, Graduate School, Nanchang, Jiangxi, China
| | - Keke Li
- Jiangxi University of Traditional Chinese Medicine, Graduate School, Nanchang, Jiangxi, China
| | - Liangji Liu
- Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Department of Respiratory and Critical Care Medicine, Nanchang, Jiangxi, China
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10
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Ni X, Tong C, Halengbieke A, Cao T, Tang J, Tao L, Zheng D, Han Y, Li Q, Yang X. Association between nonalcoholic fatty liver disease and type 2 diabetes: A bidirectional two-sample mendelian randomization study. Diabetes Res Clin Pract 2023; 206:110993. [PMID: 37931882 DOI: 10.1016/j.diabres.2023.110993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/22/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
OBJECTIVE The aim of this study was to explore the mutually causal relationship between NAFLD and type 2 diabetes. METHODS Based on the data obtained from GWAS, this study employed bidirectional two-sample MR analysis to investigate the causal relationship between NAFLD and type 2 diabetes, and also examined the causal relationship between liver fat accumulation and type 2 diabetes as well as the relationship between NAFLD and FPG, IR. RESULTS In MR analysis of NAFLD and type 2 diabetes, when NAFLD as an exposure and type 2 diabetes as a result, the OR (95 % CI) was 1.10890 (1.00135-1.22801); in the reverse analysis, the OR value was not statistically significant. In MR analysis of NAFLD, FPG and IR, there was no statistical significance in both directions. In MR analysis of liver fat accumulation and type 2 diabetes, when liver fat as an exposure and type 2 diabetes as a result, the OR (95 % CI) was 1.17516 (1.02054-1.35321); in the reverse analysis, the OR value (95 % CI) was 1.06283 (1.02879-1.09799). CONCLUSION There is a unidirectional causal relationship between NAFLD and type 2 diabetes. Furthermore, a bidirectional causal relationship exists between liver fat accumulation and type 2 diabetes.
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Affiliation(s)
- Xuetong Ni
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Chao Tong
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Aheyeerke Halengbieke
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Tengrui Cao
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Jianmin Tang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Lixin Tao
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Deqiang Zheng
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Yumei Han
- Department of Information, Beijing Physical Examination Center, Beijing, China
| | - Qiang Li
- Department of Information, Beijing Physical Examination Center, Beijing, China
| | - Xinghua Yang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.
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11
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Gómez-Sánchez G, Alonso L, Pérez MÁ, Morán I, Torrents D, Berral JL. Exhaustive Variant Interaction Analysis using Multifactor Dimensionality Reduction. RESEARCH SQUARE 2023:rs.3.rs-3401025. [PMID: 37886566 PMCID: PMC10602162 DOI: 10.21203/rs.3.rs-3401025/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
One of the main goals of human genetics is to understand the connections between genomic variation and the predisposition to develop a complex disorder. These disease-variant associations are usually studied in a single independent manner, disregarding the possible effect derived from the interaction between genomic variants. In particular, in a background of complex diseases, these interactions can be directly linked to the disorder and may play an important role in disease development. Although their study has been suggested to help to complete the understanding of the genetic bases of complex diseases, this still represents a big challenge due to large computing demands. Here, we have taken advantage of High-Performance Computing technologies to tackle this problem using a combination of machine learning methods and statistical approaches. As a result, we have created a containerized framework that uses Multifactor Dimensionality Reduction to detect pairs of variants associated with Type 2 Diabetes (T2D). This methodology has been tested in the Northwestern University NUgene project cohort using a dataset of 1,883,192 variant pairs with a certain degree of association with T2D. Out of the pairs studied, we have identified 104 significant pairs, two of which exhibit a potential functional relationship with T2D.
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Affiliation(s)
- Gonzalo Gómez-Sánchez
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Universitat Politècnica de Catalunya - BarcelonaTECH, Barcelona, Spain
| | - Lorena Alonso
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Ignasi Morán
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats, Barcelona, Spain
| | - Josep Ll. Berral
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Universitat Politècnica de Catalunya - BarcelonaTECH, Barcelona, Spain
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12
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Tan L, Zhong MM, Zhao YQ, Zhao J, Dusenge MA, Feng Y, Ye Q, Hu J, Ou-Yang ZY, Chen NX, Su XL, Zhang Q, Liu Q, Yuan H, Wang MY, Feng YZ, Guo Y. Type 1 diabetes, glycemic traits, and risk of dental caries: a Mendelian randomization study. Front Genet 2023; 14:1230113. [PMID: 37881806 PMCID: PMC10597668 DOI: 10.3389/fgene.2023.1230113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
Background: Regarding past epidemiological studies, there has been disagreement over whether type 1 diabetes (T1DM) is one of the risk factors for dental caries. The purpose of this study was to determine the causative links between genetic susceptibility to T1DM, glycemic traits, and the risk of dental caries using Mendelian randomization (MR) approaches. Methods: Summary-level data were collected on genome-wide association studies (GWAS) of T1DM, fasting glucose (FG), glycated hemoglobin (HbA1c), fasting insulin (FI), and dental caries. MR was performed using the inverse-variance weighting (IVW) method, and sensitivity analyses were conducted using the MR-Egger method, weighted median, weighted mode, replication cohort, and multivariable MR conditioning on potential mediators. Results: The risk of dental caries increased as a result of genetic susceptibility to T1DM [odds ratio (OR) = 1.044; 95% confidence interval (CI) = 1.015-1.074; p = 0.003], with consistent findings in the replication cohort. The relationship between T1DM and dental caries was stable when adjusted for BMI, smoking, alcohol intake, and type 2 diabetes (T2DM) in multivariable MR. However, no significant correlations between the risk of dental caries and FG, HbA1c, or FI were found. Conclusion: These results indicate that T1DM has causal involvement in the genesis of dental caries. Therefore, periodic reinforcement of oral hygiene instructions must be added to the management and early multidisciplinary intervention of T1DM patients, especially among adolescents and teenagers, who are more susceptible to T1DM.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yun-Zhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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13
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Lee RA, Chang M, Yiv N, Tsay A, Tian S, Li D, Poulard C, Stallcup MR, Pufall MA, Wang JC. Transcriptional coactivation by EHMT2 restricts glucocorticoid-induced insulin resistance in a study with male mice. Nat Commun 2023; 14:3143. [PMID: 37253782 PMCID: PMC10229547 DOI: 10.1038/s41467-023-38584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 05/09/2023] [Indexed: 06/01/2023] Open
Abstract
The classical dogma of glucocorticoid-induced insulin resistance is that it is caused by the transcriptional activation of hepatic gluconeogenic and insulin resistance genes by the glucocorticoid receptor (GR). Here, we find that glucocorticoids also stimulate the expression of insulin-sensitizing genes, such as Irs2. The transcriptional coregulator EHMT2 can serve as a transcriptional coactivator or a corepressor. Using male mice that have a defective EHMT2 coactivation function specifically, we show that glucocorticoid-induced Irs2 transcription is dependent on liver EHMT2's coactivation function and that IRS2 play a key role in mediating the limitation of glucocorticoid-induced insulin resistance by EHMT2's coactivation. Overall, we propose a model in which glucocorticoid-regulated insulin sensitivity is determined by the balance between glucocorticoid-modulated insulin resistance and insulin sensitizing genes, in which EHMT2 coactivation is specifically involved in the latter process.
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Affiliation(s)
- Rebecca A Lee
- Endocrinology Graduate Program, University of California Berkeley, Berkeley, CA, 94720, USA
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Maggie Chang
- Endocrinology Graduate Program, University of California Berkeley, Berkeley, CA, 94720, USA
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Nicholas Yiv
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA, 94720, USA
- Metabolic Biology Graduate Program, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Ariel Tsay
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA, 94720, USA
- Metabolic Biology Graduate Program, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sharon Tian
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Danielle Li
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Coralie Poulard
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 28 Rue Laennec, 69000, Lyon, France
| | - Michael R Stallcup
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Miles A Pufall
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Jen-Chywan Wang
- Endocrinology Graduate Program, University of California Berkeley, Berkeley, CA, 94720, USA.
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA, 94720, USA.
- Metabolic Biology Graduate Program, University of California Berkeley, Berkeley, CA, 94720, USA.
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14
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Huang J. Mendelian randomization indicates a causal contribution of type 2 diabetes to retinal vein occlusion. Front Endocrinol (Lausanne) 2023; 14:1146185. [PMID: 37223029 PMCID: PMC10200935 DOI: 10.3389/fendo.2023.1146185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/05/2023] [Indexed: 05/25/2023] Open
Abstract
Background Retinal vein occlusion (RVO) is a common retinal vascular disease that can cause severe visual impairment. Many observational studies have shown that type 2 diabetes (T2DM) is associated with RVO, but it remains unknown if the association is causal. The present study aimed to perform Mendelian randomization (MR) analyses to evaluate the causal contribution of genetically predicted T2DM to RVO. Methods We obtained summary-level data from a genome-wide association study meta-analysis including 48,286 cases and 250,671 controls for T2DM and from a genome wide association study of 372 cases and 182,573 controls in the FinnGen project for RVO. To verify the robustness of the results, an independent validation dataset for T2DM (12,931 cases and 57,196 controls) was used. In addition to the main MR analysis using the inverse variance weighted (fixed effect) approach, sensitivity analyses and multivariable MR adjusting for common risk factors of RVO were conducted. Results Genetically predicted T2DM was found to be causally associated with RVO risk (odds ratio (OR)=2.823, 95% confidence interval (CI): 2.072-3.847, P=4.868×10-11). This association was supported by sensitivity analyses using the weighted median (OR=2.415, 95% CI: 1.411-4.132, P=1.294×10-3), weighted mode (OR=2.370, 95% CI: 1.321-4.252, P=5.159×10-3), maximum likelihood (OR=2.871, 95% CI: 2.100-3.924, P=3.719×10-11), MR-PRESSO (OR=2.823, 95% CI: 2.135-3.733, P=5.150×10-10), and MR-Egger (OR=2.441, 95% CI: 1.149-5.184, P=2.335×10-2) methods. In addition, this association persisted in multivariable MR after accounting for common RVO risk factors (OR=1.748, 95% CI: 1.238-2.467, P=1.490×10-3). The MR analyses using the validation dataset obtained consistent results. Conclusion This study indicates that genetically predicted T2DM may have a causal contribution to RVO. Future studies are required to elucidate the underlying mechanisms.
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Hassan N, Gregson CL, Tang H, van der Kamp M, Leo P, McInerney‐Leo AM, Zheng J, Brandi ML, Tang JCY, Fraser W, Stone MD, Grundberg E, Brown MA, Duncan EL, Tobias JH. Rare and Common Variants in GALNT3 May Affect Bone Mass Independently of Phosphate Metabolism. J Bone Miner Res 2023; 38:678-691. [PMID: 36824040 PMCID: PMC10729283 DOI: 10.1002/jbmr.4795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Anabolic treatment options for osteoporosis remain limited. One approach to discovering novel anabolic drug targets is to identify genetic causes of extreme high bone mass (HBM). We investigated a pedigree with unexplained HBM within the UK HBM study, a national cohort of probands with HBM and their relatives. Whole exome sequencing (WES) in a family with HBM identified a rare heterozygous missense variant (NM_004482.4:c.1657C > T, p.Arg553Trp) in GALNT3, segregating appropriately. Interrogation of data from the UK HBM study and the Anglo-Australasian Osteoporosis Genetics Consortium (AOGC) revealed an unrelated individual with HBM with another rare heterozygous variant (NM_004482.4:c.831 T > A, p.Asp277Glu) within the same gene. In silico protein modeling predicted that p.Arg553Trp would disrupt salt-bridge interactions, causing instability of GALNT3, and that p.Asp277Glu would disrupt manganese binding and consequently GALNT3 catalytic function. Bi-allelic loss-of-function GALNT3 mutations alter FGF23 metabolism, resulting in hyperphosphatemia and causing familial tumoral calcinosis (FTC). However, bone mineral density (BMD) in FTC cases, when reported, has been either normal or low. Common variants in the GALNT3 locus show genome-wide significant associations with lumbar, femoral neck, and total body BMD. However, no significant associations with BMD are observed at loci coding for FGF23, its receptor FGFR1, or coreceptor klotho. Mendelian randomization analysis, using expression quantitative trait loci (eQTL) data from primary human osteoblasts and genome-wide association studies data from UK Biobank, suggested increased expression of GALNT3 reduces total body, lumbar spine, and femoral neck BMD but has no effect on phosphate concentrations. In conclusion, rare heterozygous loss-of-function variants in GALNT3 may cause HBM without altering phosphate concentration. These findings suggest that GALNT3 may affect BMD through pathways other than FGF23 regulation, the identification of which may yield novel anabolic drug targets for osteoporosis. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Neelam Hassan
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Celia L. Gregson
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Haotian Tang
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Paul Leo
- Faculty of Health, Translational Genomics Group, Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Aideen M. McInerney‐Leo
- The Faculty of Medicine, Frazer InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
| | - Jie Zheng
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR ChinaShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | | | - Jonathan C. Y. Tang
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Clinical Biochemistry, Departments of Laboratory MedicineNorfolk and Norwich University Hospital NHS Foundation TrustNorwichUK
| | - William Fraser
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Department of Diabetes, Endocrinology and Clinical BiochemistryNorfolk and Norwich University Hospital NHS Foundation TrustNorwichUK
| | - Michael D. Stone
- University Hospital LlandoughCardiff & Vale University Health BoardCardiffUK
| | - Elin Grundberg
- Genomic Medicine CenterChildren's Mercy Kansas CityKansas CityMissouriUSA
| | | | | | - Emma L. Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Jonathan H. Tobias
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
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16
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Cromer SJ, Lakhani CM, Mercader JM, Majarian TD, Schroeder P, Cole JB, Florez JC, Patel CJ, Manning AK, Burnett-Bowie SAM, Merino J, Udler MS. Association and Interaction of Genetics and Area-Level Socioeconomic Factors on the Prevalence of Type 2 Diabetes and Obesity. Diabetes Care 2023; 46:944-952. [PMID: 36787958 PMCID: PMC10154653 DOI: 10.2337/dc22-1954] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/17/2022] [Indexed: 02/16/2023]
Abstract
OBJECTIVE Quantify the impact of genetic and socioeconomic factors on risk of type 2 diabetes (T2D) and obesity. RESEARCH DESIGN AND METHODS Among participants in the Mass General Brigham Biobank (MGBB) and UK Biobank (UKB), we used logistic regression models to calculate cross-sectional odds of T2D and obesity using 1) polygenic risk scores for T2D and BMI and 2) area-level socioeconomic risk (educational attainment) measures. The primary analysis included 26,737 participants of European genetic ancestry in MGBB with replication in UKB (N = 223,843), as well as in participants of non-European ancestry (MGBB N = 3,468; UKB N = 7,459). RESULTS The area-level socioeconomic measure most strongly associated with both T2D and obesity was percent without a college degree, and associations with disease prevalence were independent of genetic risk (P < 0.001 for each). Moving from lowest to highest quintiles of combined genetic and socioeconomic burden more than tripled T2D (3.1% to 22.2%) and obesity (20.9% to 69.0%) prevalence. Favorable socioeconomic risk was associated with lower disease prevalence, even in those with highest genetic risk (T2D 13.0% vs. 22.2%, obesity 53.6% vs. 69.0% in lowest vs. highest socioeconomic risk quintiles). Additive effects of genetic and socioeconomic factors accounted for 13.2% and 16.7% of T2D and obesity prevalence, respectively, explained by these models. Findings were replicated in independent European and non-European ancestral populations. CONCLUSIONS Genetic and socioeconomic factors significantly interact to increase risk of T2D and obesity. Favorable area-level socioeconomic status was associated with an almost 50% lower T2D prevalence in those with high genetic risk.
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Affiliation(s)
- Sara J. Cromer
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Chirag M. Lakhani
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Josep M. Mercader
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Timothy D. Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Philip Schroeder
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Joanne B. Cole
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO
| | - Jose C. Florez
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Alisa K. Manning
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Sherri-Ann M. Burnett-Bowie
- Department of Medicine, Harvard Medical School, Boston, MA
- Endocrine Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
| | - Jordi Merino
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Miriam S. Udler
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
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17
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Kim H, Westerman KE, Smith K, Chiou J, Cole JB, Majarian T, von Grotthuss M, Kwak SH, Kim J, Mercader JM, Florez JC, Gaulton K, Manning AK, Udler MS. High-throughput genetic clustering of type 2 diabetes loci reveals heterogeneous mechanistic pathways of metabolic disease. Diabetologia 2023; 66:495-507. [PMID: 36538063 PMCID: PMC10108373 DOI: 10.1007/s00125-022-05848-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/28/2022] [Indexed: 12/24/2022]
Abstract
AIMS/HYPOTHESIS Type 2 diabetes is highly polygenic and influenced by multiple biological pathways. Rapid expansion in the number of type 2 diabetes loci can be leveraged to identify such pathways. METHODS We developed a high-throughput pipeline to enable clustering of type 2 diabetes loci based on variant-trait associations. Our pipeline extracted summary statistics from genome-wide association studies (GWAS) for type 2 diabetes and related traits to generate a matrix of 323 variants × 64 trait associations and applied Bayesian non-negative matrix factorisation (bNMF) to identify genetic components of type 2 diabetes. Epigenomic enrichment analysis was performed in 28 cell types and single pancreatic cells. We generated cluster-specific polygenic scores and performed regression analysis in an independent cohort (N=25,419) to assess for clinical relevance. RESULTS We identified ten clusters of genetic loci, recapturing the five from our prior analysis as well as novel clusters related to beta cell dysfunction, pronounced insulin secretion, and levels of alkaline phosphatase, lipoprotein A and sex hormone-binding globulin. Four clusters related to mechanisms of insulin deficiency, five to insulin resistance and one had an unclear mechanism. The clusters displayed tissue-specific epigenomic enrichment, notably with the two beta cell clusters differentially enriched in functional and stressed pancreatic beta cell states. Additionally, cluster-specific polygenic scores were differentially associated with patient clinical characteristics and outcomes. The pipeline was applied to coronary artery disease and chronic kidney disease, identifying multiple overlapping clusters with type 2 diabetes. CONCLUSIONS/INTERPRETATION Our approach stratifies type 2 diabetes loci into physiologically interpretable genetic clusters associated with distinct tissues and clinical outcomes. The pipeline allows for efficient updating as additional GWAS become available and can be readily applied to other conditions, facilitating clinical translation of GWAS findings. Software to perform this clustering pipeline is freely available.
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Affiliation(s)
- Hyunkyung Kim
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kenneth E Westerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kirk Smith
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joshua Chiou
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Joanne B Cole
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Marcin von Grotthuss
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Takeda Pharmaceuticals, Cambridge, MA, USA
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- GlaxoSmithKline, Cambridge, MA, USA
| | - Josep M Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jose C Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle Gaulton
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Alisa K Manning
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Miriam S Udler
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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18
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Rottner AK, Ye Y, Navarro-Guerrero E, Rajesh V, Pollner A, Bevacqua RJ, Yang J, Spigelman AF, Baronio R, Bautista A, Thomsen SK, Lyon J, Nawaz S, Smith N, Wesolowska-Andersen A, Fox JEM, Sun H, Kim SK, Ebner D, MacDonald PE, Gloyn AL. A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk. Nat Genet 2023; 55:54-65. [PMID: 36543916 PMCID: PMC9839450 DOI: 10.1038/s41588-022-01261-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Identification of the genes and processes mediating genetic association signals for complex diseases represents a major challenge. As many of the genetic signals for type 2 diabetes (T2D) exert their effects through pancreatic islet-cell dysfunction, we performed a genome-wide pooled CRISPR loss-of-function screen in a human pancreatic beta cell line. We assessed the regulation of insulin content as a disease-relevant readout of beta cell function and identified 580 genes influencing this phenotype. Integration with genetic and genomic data provided experimental support for 20 candidate T2D effector transcripts including the autophagy receptor CALCOCO2. Loss of CALCOCO2 was associated with distorted mitochondria, less proinsulin-containing immature granules and accumulation of autophagosomes upon inhibition of late-stage autophagy. Carriers of T2D-associated variants at the CALCOCO2 locus further displayed altered insulin secretion. Our study highlights how cellular screens can augment existing multi-omic efforts to support mechanistic understanding and provide evidence for causal effects at genome-wide association studies loci.
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Affiliation(s)
- Antje K Rottner
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Yingying Ye
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Elena Navarro-Guerrero
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Varsha Rajesh
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Alina Pollner
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Centre, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Jing Yang
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Aliya F Spigelman
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Roberta Baronio
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Austin Bautista
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Soren K Thomsen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - James Lyon
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Sameena Nawaz
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nancy Smith
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | | | - Jocelyn E Manning Fox
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Han Sun
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Centre, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Daniel Ebner
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
- Stanford Diabetes Research Centre, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK.
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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19
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Lamri A, De Paoli M, De Souza R, Werstuck G, Anand S, Pigeyre M. Insight into genetic, biological, and environmental determinants of sexual-dimorphism in type 2 diabetes and glucose-related traits. Front Cardiovasc Med 2022; 9:964743. [PMID: 36505380 PMCID: PMC9729955 DOI: 10.3389/fcvm.2022.964743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022] Open
Abstract
There is growing evidence that sex and gender differences play an important role in risk and pathophysiology of type 2 diabetes (T2D). Men develop T2D earlier than women, even though there is more obesity in young women than men. This difference in T2D prevalence is attenuated after the menopause. However, not all women are equally protected against T2D before the menopause, and gestational diabetes represents an important risk factor for future T2D. Biological mechanisms underlying sex and gender differences on T2D physiopathology are not yet fully understood. Sex hormones affect behavior and biological changes, and can have implications on lifestyle; thus, both sex-specific environmental and biological risk factors interact within a complex network to explain the differences in T2D risk and physiopathology in men and women. In addition, lifetime hormone fluctuations and body changes due to reproductive factors are generally more dramatic in women than men (ovarian cycle, pregnancy, and menopause). Progress in genetic studies and rodent models have significantly advanced our understanding of the biological pathways involved in the physiopathology of T2D. However, evidence of the sex-specific effects on genetic factors involved in T2D is still limited, and this gap of knowledge is even more important when investigating sex-specific differences during the life course. In this narrative review, we will focus on the current state of knowledge on the sex-specific effects of genetic factors associated with T2D over a lifetime, as well as the biological effects of these different hormonal stages on T2D risk. We will also discuss how biological insights from rodent models complement the genetic insights into the sex-dimorphism effects on T2D. Finally, we will suggest future directions to cover the knowledge gaps.
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Affiliation(s)
- Amel Lamri
- Department of Medicine, McMaster University, Hamilton, ON, Canada,Population Health Research Institute (PHRI), Hamilton, ON, Canada
| | - Monica De Paoli
- Department of Medicine, McMaster University, Hamilton, ON, Canada,Thrombosis and Atherosclerosis Research Institute (TaARI), Hamilton, ON, Canada
| | - Russell De Souza
- Population Health Research Institute (PHRI), Hamilton, ON, Canada,Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Geoff Werstuck
- Department of Medicine, McMaster University, Hamilton, ON, Canada,Thrombosis and Atherosclerosis Research Institute (TaARI), Hamilton, ON, Canada
| | - Sonia Anand
- Department of Medicine, McMaster University, Hamilton, ON, Canada,Population Health Research Institute (PHRI), Hamilton, ON, Canada,Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Marie Pigeyre
- Department of Medicine, McMaster University, Hamilton, ON, Canada,Population Health Research Institute (PHRI), Hamilton, ON, Canada,*Correspondence: Marie Pigeyre
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20
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Wang K, Shi M, Huang C, Fan B, Luk AOY, Kong APS, Ma RCW, Chan JCN, Chow E. Evaluating the impact of glucokinase activation on risk of cardiovascular disease: a Mendelian randomisation analysis. Cardiovasc Diabetol 2022; 21:192. [PMID: 36151532 PMCID: PMC9503210 DOI: 10.1186/s12933-022-01613-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glucokinase activators (GKAs) are an emerging class of glucose lowering drugs that activate the glucose-sensing enzyme glucokinase (GK). Pending formal cardiovascular outcome trials, we applied two-sample Mendelian randomisation (MR) to investigate the impact of GK activation on risk of cardiovascular diseases. METHODS We used independent genetic variants in or around the glucokinase gene meanwhile associated with HbA1c at genome-wide significance (P < 5 × 10-8) in the Meta-Analyses of Glucose and Insulin-related traits Consortium study (N = 146,806; European ancestry) as instrumental variables (IVs) to mimic the effects of GK activation. We assessed the association between genetically proxied GK activation and the risk of coronary artery disease (CAD; 122,733 cases and 424,528 controls), peripheral arterial disease (PAD; 7098 cases and 206,541 controls), stroke (40,585 cases and 406,111 controls) and heart failure (HF; 47,309 cases and 930,014 controls), using genome-wide association study summary statistics of these outcomes in Europeans. We compared the effect estimates of genetically proxied GK activation with estimates of genetically proxied lower HbA1c on the same outcomes. We repeated our MR analyses in East Asians as validation. RESULTS Genetically proxied GK activation was associated with reduced risk of CAD (OR 0.38 per 1% lower HbA1c, 95% CI 0.29-0.51, P = 8.77 × 10-11) and HF (OR 0.54 per 1% lower HbA1c, 95% CI 0.41-0.73, P = 3.55 × 10-5). The genetically proxied protective effects of GKA on CAD and HF exceeded those due to non-targeted HbA1c lowering. There was no causal relationship between genetically proxied GK activation and risk of PAD or stroke. The estimates in sensitivity analyses and in East Asians were generally consistent. CONCLUSIONS GKAs may protect against CAD and HF which needs confirmation by long-term clinical trials.
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Affiliation(s)
- Ke Wang
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Mai Shi
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Baoqi Fan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Andrea O Y Luk
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Phase 1 Clinical Trial Centre, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Alice P S Kong
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.,Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Elaine Chow
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China. .,Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China. .,Phase 1 Clinical Trial Centre, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
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21
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Bennett AN, Rainford J, Huang X, He Q, Chan KHK. Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files. BMC Bioinformatics 2022; 23:304. [PMID: 35896971 PMCID: PMC9327220 DOI: 10.1186/s12859-022-04822-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022] Open
Abstract
Background Previous studies have demonstrated the value of re-analysing publicly available genetics data with recent analytical approaches. Publicly available datasets, such as the Women’s Health Initiative (WHI) offered by the database of genotypes and phenotypes (dbGaP), provide a wealthy resource for researchers to perform multiple analyses, including Genome-Wide Association Studies. Often, the genetic information of individuals in these datasets are stored in imputed dosage files output by MaCH; mldose and mlinfo files. In order for researchers to perform GWAS studies with this data, they must first be converted to a file format compatible with their tool of choice e.g., PLINK. Currently, there is no published tool which easily converts the datasets provided in MACH dosage files into PLINK-ready files.
Results Herein, we present Canary a singularity-based tool which converts MaCH dosage files into PLINK-compatible files with a single line of user input at the command line. Further, we provide a detailed tutorial on preparation of phenotype files. Moreover, Canary comes with preinstalled software often used during GWAS studies, to further increase the ease-of-use of HPC systems for researchers. Conclusions Until now, conversion of imputed data in the form of MaCH mldose and mlinfo files needed to be completed manually. Canary uses singularity container technology to allow users to automatically convert these MaCH files into PLINK compatible files. Additionally, Canary provides researchers with a platform to conduct GWAS analysis more easily as it contains essential software needed for conducting GWAS studies, such as PLINK and Bioconductor. We hope that this tool will greatly increase the ease at which researchers can perform GWAS with imputed data, particularly on HPC environments.
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Affiliation(s)
- Adam N Bennett
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | | | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
| | - Qian He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Kei Hang Katie Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China. .,Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR, China. .,Department of Epidemiology, Centre for Global Cardiometabolic Health, Brown University, Providence, RI, USA.
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22
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Sujana C, Salomaa V, Kee F, Seissler J, Jousilahti P, Neville C, Then C, Koenig W, Kuulasmaa K, Reinikainen J, Blankenberg S, Zeller T, Herder C, Mansmann U, Peters A, Thorand B. Associations of the vasoactive peptides CT-proET-1 and MR-proADM with incident type 2 diabetes: results from the BiomarCaRE Consortium. Cardiovasc Diabetol 2022; 21:99. [PMID: 35681200 PMCID: PMC9185875 DOI: 10.1186/s12933-022-01513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/28/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Endothelin-1 (ET-1) and adrenomedullin (ADM) are commonly known as vasoactive peptides that regulate vascular homeostasis. Less recognised is the fact that both peptides could affect glucose metabolism. Here, we investigated whether ET-1 and ADM, measured as C-terminal-proET-1 (CT-proET-1) and mid-regional-proADM (MR-proADM), respectively, were associated with incident type 2 diabetes. METHODS Based on the population-based Biomarkers for Cardiovascular Risk Assessment in Europe (BiomarCaRE) Consortium data, we performed a prospective cohort study to examine associations of CT-proET-1 and MR-proADM with incident type 2 diabetes in 12,006 participants. During a median follow-up time of 13.8 years, 862 participants developed type 2 diabetes. The associations were examined in Cox proportional hazard models. Additionally, we performed two-sample Mendelian randomisation analyses using published data. RESULTS CT-proET-1 and MR-proADM were positively associated with incident type 2 diabetes. The multivariable hazard ratios (HRs) [95% confidence intervals (CI)] were 1.10 [1.03; 1.18], P = 0.008 per 1-SD increase of CT-proET-1 and 1.11 [1.02; 1.21], P = 0.016 per 1-SD increase of log MR-proADM, respectively. We observed a stronger association of MR-proADM with incident type 2 diabetes in obese than in non-obese individuals (P-interaction with BMI < 0.001). The HRs [95%CIs] were 1.19 [1.05; 1.34], P = 0.005 and 1.02 [0.90; 1.15], P = 0.741 in obese and non-obese individuals, respectively. Our Mendelian randomisation analyses yielded a significant association of CT-proET-1, but not of MR-proADM with type 2 diabetes risk. CONCLUSIONS Higher concentrations of CT-proET-1 and MR-proADM are associated with incident type 2 diabetes, but our Mendelian randomisation analysis suggests a probable causal link for CT-proET-1 only. The association of MR-proADM seems to be modified by body composition.
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Affiliation(s)
- Chaterina Sujana
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Pettenkofer School of Public Health, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Diabetes Research (DZD), Partner München-Neuherberg, Neuherberg, Germany
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Frank Kee
- Centre for Public Health, Queens University of Belfast, Belfast, Northern Ireland, UK
| | - Jochen Seissler
- Diabetes Zentrum, Medizinische Klinik Und Poliklinik IV, Klinikum Der Ludwig-Maximilians-Universität München, Munich, Germany
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Charlotte Neville
- Centre for Public Health, Queens University of Belfast, Belfast, Northern Ireland, UK
| | - Cornelia Then
- Diabetes Zentrum, Medizinische Klinik Und Poliklinik IV, Klinikum Der Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Koenig
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- German Centre for Cardiovascular Research (DZHK E.V.), Partner Site Munich Heart Alliance, Munich, Germany
| | - Kari Kuulasmaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jaakko Reinikainen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Stefan Blankenberg
- Department for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
- German Centre for Cardiovascular Research (DZHK E.V.), Partner site Hamburg, Lübeck, Kiel, Hamburg, Germany
| | - Tanja Zeller
- Department for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
- German Centre for Cardiovascular Research (DZHK E.V.), Partner site Hamburg, Lübeck, Kiel, Hamburg, Germany
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, Neuherberg, Germany
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Pettenkofer School of Public Health, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Partner München-Neuherberg, Neuherberg, Germany
- German Centre for Cardiovascular Research (DZHK E.V.), Partner Site Munich Heart Alliance, Munich, Germany
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Partner München-Neuherberg, Neuherberg, Germany.
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Gao N, Kong M, Li X, Wei D, Zhu X, Hong Z, Ni M, Wang Y, Dong A. Systemic Lupus Erythematosus and Cardiovascular Disease: A Mendelian Randomization Study. Front Immunol 2022; 13:908831. [PMID: 35734181 PMCID: PMC9207262 DOI: 10.3389/fimmu.2022.908831] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022] Open
Abstract
Background Previous studies have shown that patients with systemic lupus erythematosus (SLE) tend to have a higher risk of cardiovascular disease (CVD), but the potential causal relationship between genetic susceptibility to SLE and CVD risk is not clear. This study systematically investigated the potential association between genetically determined SLE and the risk of CVD. Methods The genetic tools were obtained from genome-wide association studies of SLE and CVD, with no overlap between their participating populations. Mendelian randomization (MR) analysis was performed using inverse variance weighting as the primary method. Simultaneously, a series of repeated analyses, sensitivity analyses, and instrumental variable strength evaluations were performed to verify the reliability of our results. Results MR analysis showed that genetic susceptibility to SLE was associated with a higher risk of heart failure (OR=1.025, 95% CI [1.009-1.041], P=0.002), ischemic stroke (OR=1.020, 95% CI [1.005-1.034], P=0.009), and venous thromboembolism (OR=1.001, 95% CI [1.000-1.002], P=0.014). However, genetic susceptibility to SLE was negatively correlated with the risk of type 2 diabetes (OR=0.968, 95% CI [0.947-0.990], P=0.004). Sensitivity analysis found no evidence of horizontal pleiotropy or heterogeneity. Conclusion Our MR study explored the causal role of SLE in the etiology of CVD, which would help improve our understanding of the basic disease mechanisms of SLE and provide comprehensive CVD assessment and treatment for SLE patients.
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24
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Thompson WD, Beaumont RN, Kuang A, Warrington NM, Ji Y, Tyrrell J, Wood AR, Scholtens DM, Knight BA, Evans DM, Lowe Jr WL, Santorelli G, Azad R, Mason D, Hattersley AT, Frayling TM, Yaghootkar H, Borges MC, Lawlor DA, Freathy RM. Fetal alleles predisposing to metabolically favorable adiposity are associated with higher birth weight. Hum Mol Genet 2022; 31:1762-1775. [PMID: 34897462 PMCID: PMC9169452 DOI: 10.1093/hmg/ddab356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Higher birthweight is associated with higher adult body mass index (BMI). Alleles that predispose to greater adult adiposity might act in fetal life to increase fetal growth and birthweight. Whether there are fetal effects of recently identified adult metabolically favorable adiposity alleles on birthweight is unknown. AIM We aimed to test the effect on birthweight of fetal genetic predisposition to higher metabolically favorable adult adiposity and compare that with the effect of fetal genetic predisposition to higher adult BMI. METHODS We used published genome wide association study data (n = upto 406 063) to estimate fetal effects on birthweight (adjusting for maternal genotype) of alleles known to raise metabolically favorable adult adiposity or BMI. We combined summary data across single nucleotide polymorphisms (SNPs) with random effects meta-analyses. We performed weighted linear regression of SNP-birthweight effects against SNP-adult adiposity effects to test for a dose-dependent association. RESULTS Fetal genetic predisposition to higher metabolically favorable adult adiposity and higher adult BMI were both associated with higher birthweight (3 g per effect allele (95% CI: 1-5) averaged over 14 SNPs; P = 0.002; 0.5 g per effect allele (95% CI: 0-1) averaged over 76 SNPs; P = 0.042, respectively). SNPs with greater effects on metabolically favorable adiposity tended to have greater effects on birthweight (R2 = 0.2912, P = 0.027). There was no dose-dependent association for BMI (R2 = -0.0019, P = 0.602). CONCLUSIONS Fetal genetic predisposition to both higher adult metabolically favorable adiposity and BMI is associated with birthweight. Fetal effects of metabolically favorable adiposity-raising alleles on birthweight are modestly proportional to their effects on future adiposity, but those of BMI-raising alleles are not.
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Affiliation(s)
- William D Thompson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Alan Kuang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicole M Warrington
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
- University of Queensland Diamantina Institute, University of Queensland, Brisbane QLD 4102, Australia
- Department of Public Health and Nursing, NTNU, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Postboks 8905, N-7491, Norway
| | - Yingjie Ji
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Denise M Scholtens
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bridget A Knight
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - David M Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
- University of Queensland Diamantina Institute, University of Queensland, Brisbane QLD 4102, Australia
| | - William L Lowe Jr
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Gillian Santorelli
- Bradford Institute for Health Research, Bradford Royal Infirmary, Duckworth Lane, Bradford BD9 6RJ, UK
| | - Raq Azad
- Department of Biochemistry, Bradford Royal Infirmary, Bradford BD9 6DA, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Royal Infirmary, Duckworth Lane, Bradford BD9 6RJ, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Maria Carolina Borges
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
- Population Health, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
- Population Health, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Bristol NIHR Biomedical Research Centre, Bristol BS8 2BN, UK
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
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25
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Bouland GA, Beulens JWJ, Nap J, van der Slik AR, Zaldumbide A, 't Hart LM, Slieker RC. Diabetes risk loci-associated pathways are shared across metabolic tissues. BMC Genomics 2022; 23:368. [PMID: 35568807 PMCID: PMC9107144 DOI: 10.1186/s12864-022-08587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/23/2022] [Indexed: 11/28/2022] Open
Abstract
Aims/hypothesis Numerous genome-wide association studies have been performed to understand the influence of genetic variation on type 2 diabetes etiology. Many identified risk variants are located in non-coding and intergenic regions, which complicates understanding of how genes and their downstream pathways are influenced. An integrative data approach will help to understand the mechanism and consequences of identified risk variants. Methods In the current study we use our previously developed method CONQUER to overlap 403 type 2 diabetes risk variants with regulatory, expression and protein data to identify tissue-shared disease-relevant mechanisms. Results One SNP rs474513 was found to be an expression-, protein- and metabolite QTL. Rs474513 influenced LPA mRNA and protein levels in the pancreas and plasma, respectively. On the pathway level, in investigated tissues most SNPs linked to metabolism. However, in eleven of the twelve tissues investigated nine SNPs were linked to differential expression of the ribosome pathway. Furthermore, seven SNPs were linked to altered expression of genes linked to the immune system. Among them, rs601945 was found to influence multiple HLA genes, including HLA-DQA2, in all twelve tissues investigated. Conclusion Our results show that in addition to the classical metabolism pathways, other pathways may be important to type 2 diabetes that show a potential overlap with type 1 diabetes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08587-5.
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Affiliation(s)
- Gerard A Bouland
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands
| | - Joline W J Beulens
- Department of Epidemiology and Data Science, Amsterdam UMC, Location VUMC, Amsterdam Public Health Institute, Amsterdam, the Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joey Nap
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands
| | - Arno R van der Slik
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands
| | - Leen M 't Hart
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands.,Department of Epidemiology and Data Science, Amsterdam UMC, Location VUMC, Amsterdam Public Health Institute, Amsterdam, the Netherlands.,Molecular Epidemiology Section, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands. .,Department of Epidemiology and Data Science, Amsterdam UMC, Location VUMC, Amsterdam Public Health Institute, Amsterdam, the Netherlands.
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26
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Yang M, Huang L, Huang H, Tang H, Zhang N, Yang H, Wu J, Mu F. Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution. Nucleic Acids Res 2022; 50:e81. [PMID: 35536244 PMCID: PMC9371931 DOI: 10.1093/nar/gkac326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
Interpretation of non-coding genome remains an unsolved challenge in human genetics due to impracticality of exhaustively annotating biochemically active elements in all conditions. Deep learning based computational approaches emerge recently to help interpret non-coding regions. Here, we present LOGO (Language of Genome), a self-attention based contextualized pre-trained language model containing only two self-attention layers with 1 million parameters as a substantially light architecture that applies self-supervision techniques to learn bidirectional representations of the unlabelled human reference genome. LOGO is then fine-tuned for sequence labelling task, and further extended to variant prioritization task via a special input encoding scheme of alternative alleles followed by adding a convolutional module. Experiments show that LOGO achieves 15% absolute improvement for promoter identification and up to 4.5% absolute improvement for enhancer-promoter interaction prediction. LOGO exhibits state-of-the-art multi-task predictive power on thousands of chromatin features with only 3% parameterization benchmarking against the fully supervised model, DeepSEA and 1% parameterization against a recent BERT-based DNA language model. For allelic-effect prediction, locality introduced by one dimensional convolution shows improved sensitivity and specificity for prioritizing non-coding variants associated with human diseases. In addition, we apply LOGO to interpret type 2 diabetes (T2D) GWAS signals and infer underlying regulatory mechanisms. We make a conceptual analogy between natural language and human genome and demonstrate LOGO is an accurate, fast, scalable, and robust framework to interpret non-coding regions for global sequence labeling as well as for variant prioritization at base-resolution.
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Affiliation(s)
- Meng Yang
- MGI, BGI-Shenzhen, Shenzhen 518083, China.,Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | | | | | - Hui Tang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Nan Zhang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jihong Wu
- Department of Ophthalmology, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Feng Mu
- MGI, BGI-Shenzhen, Shenzhen 518083, China
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27
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Merson L, Ndwandwe D, Malinga T, Paparella G, Oneil K, Karam G, Terry RF. Promotion of data sharing needs more than an emergency: An analysis of trends across clinical trials registered on the International Clinical Trials Registry Platform. Wellcome Open Res 2022; 7:101. [PMID: 35419494 PMCID: PMC8980676 DOI: 10.12688/wellcomeopenres.17700.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND: A growing body of evidence shows that sharing health research data with other researchers for secondary analyses can contribute to better health. This is especially important in the context of a public health emergency when stopping a pandemic depends on accelerating science. METHODS: We analysed the information on data sharing collected by the 18 clinical trial registries included in the WHO International Clinical Trials Registry Platform (ICTRP) to understand the reporting of data sharing plans and which studies were and were not planning to share data. Data on sponsor and funder organisations, country of recruitment, registry, and condition of study were standardised to compare the sharing of information and data across these facets. This represents the first ever comprehensive study of the complete data set contained in ICTRP. RESULTS: Across 132,545 studies registered between January 2019 and December 2020, 11.2% of studies stated that individual patient data (IPD) would be shared. Plans to share IPD varied across the 18 contributing registries– information on data sharing was missing in >95% of study records across 7/18 registries. In the 26,851 (20.3%) studies that were funded or sponsored by a commercial entity, intention to share IPD was similar to those that were not (11.5% vs 11.2%). Intention to share IPD was most common in studies recruiting across both high-income and low- or middle-income countries (21.4%) and in those recruiting in Sub-Saharan Africa (50.3%). Studies of COVID-19 had similar levels of data sharing to studies of other non-pandemic diseases in 2020 (13.7% vs 11.7%). CONCLUSIONS: Rates of planned IPD sharing vary between clinical trial registries and economic regions, and are similar whether commercial or non-commercial agencies are involved. Despite many calls to action, plans to share IPD have not increased significantly and remain below 14% for diseases causing public health emergencies.
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Affiliation(s)
- Laura Merson
- Infectious Diseases Data Observatory, University of Oxford, Oxford, OX3 7FZ, UK
| | - Duduzile Ndwandwe
- Cochrane South Africa, South African Medical Research Council, Cape Town, 7505, South Africa
| | - Thobile Malinga
- Cochrane South Africa, South African Medical Research Council, Cape Town, 7505, South Africa
| | | | - Kwame Oneil
- Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Robert F. Terry
- Special Programme for Research and Training in Tropical Diseases (TDR), Geneva, Switzerland
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28
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O’Connor MJ, Schroeder P, Huerta-Chagoya A, Cortés-Sánchez P, Bonàs-Guarch S, Guindo-Martínez M, Cole JB, Kaur V, Torrents D, Veerapen K, Grarup N, Kurki M, Rundsten CF, Pedersen O, Brandslund I, Linneberg A, Hansen T, Leong A, Florez JC, Mercader JM. Recessive Genome-Wide Meta-analysis Illuminates Genetic Architecture of Type 2 Diabetes. Diabetes 2022; 71:554-565. [PMID: 34862199 PMCID: PMC8893948 DOI: 10.2337/db21-0545] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/28/2021] [Indexed: 11/13/2022]
Abstract
Most genome-wide association studies (GWAS) of complex traits are performed using models with additive allelic effects. Hundreds of loci associated with type 2 diabetes have been identified using this approach. Additive models, however, can miss loci with recessive effects, thereby leaving potentially important genes undiscovered. We conducted the largest GWAS meta-analysis using a recessive model for type 2 diabetes. Our discovery sample included 33,139 case subjects and 279,507 control subjects from 7 European-ancestry cohorts, including the UK Biobank. We identified 51 loci associated with type 2 diabetes, including five variants undetected by prior additive analyses. Two of the five variants had minor allele frequency of <5% and were each associated with more than a doubled risk in homozygous carriers. Using two additional cohorts, FinnGen and a Danish cohort, we replicated three of the variants, including one of the low-frequency variants, rs115018790, which had an odds ratio in homozygous carriers of 2.56 (95% CI 2.05-3.19; P = 1 × 10-16) and a stronger effect in men than in women (for interaction, P = 7 × 10-7). The signal was associated with multiple diabetes-related traits, with homozygous carriers showing a 10% decrease in LDL cholesterol and a 20% increase in triglycerides; colocalization analysis linked this signal to reduced expression of the nearby PELO gene. These results demonstrate that recessive models, when compared with GWAS using the additive approach, can identify novel loci, including large-effect variants with pathophysiological consequences relevant to type 2 diabetes.
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Affiliation(s)
- Mark J. O’Connor
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Philip Schroeder
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Alicia Huerta-Chagoya
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | | | - Joanne B. Cole
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Center for Basic and Translations Obesity Research, Boston Children’s Hospital, Boston, MA
| | - Varinderpal Kaur
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Kumar Veerapen
- Department of Medicine, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mitja Kurki
- Department of Medicine, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Carsten F. Rundsten
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aaron Leong
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Jose C. Florez
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Josep M. Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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Bailetti D, Sentinelli F, Prudente S, Cimini FA, Barchetta I, Totaro M, Di Costanzo A, Barbonetti A, Leonetti F, Cavallo MG, Baroni MG. Deep Resequencing of 9 Candidate Genes Identifies a Role for ARAP1 and IGF2BP2 in Modulating Insulin Secretion Adjusted for Insulin Resistance in Obese Southern Europeans. Int J Mol Sci 2022; 23:ijms23031221. [PMID: 35163144 PMCID: PMC8835579 DOI: 10.3390/ijms23031221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
Type 2 diabetes is characterized by impairment in insulin secretion, with an established genetic contribution. We aimed to evaluate common and low-frequency (1–5%) variants in nine genes strongly associated with insulin secretion by targeted sequencing in subjects selected from the extremes of insulin release measured by the disposition index. Collapsing data by gene and/or function, the association between disposition index and nonsense variants were significant, also after adjustment for confounding factors (OR = 0.25, 95% CI = 0.11–0.59, p = 0.001). Evaluating variants individually, three novel variants in ARAP1, IGF2BP2 and GCK, out of eight reaching significance singularly, remained associated after adjustment. Constructing a genetic risk model combining the effects of the three variants, only carriers of the ARAP1 and IGF2BP2 variants were significantly associated with a reduced probability to be in the lower, worst, extreme of insulin secretion (OR = 0.223, 95% CI = 0.105–0.473, p < 0.001). Observing a high number of normal glucose tolerance between carriers, a regression posthoc analysis was performed. Carriers of genetic risk model variants had higher probability to be normoglycemic, also after adjustment (OR = 2.411, 95% CI = 1.136–5.116, p = 0.022). Thus, in our southern European cohort, nonsense variants in all nine candidate genes showed association with better insulin secretion adjusted for insulin resistance, and we established the role of ARAP1 and IGF2BP2 in modulating insulin secretion.
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Affiliation(s)
- Diego Bailetti
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
- Correspondence: (D.B.); (M.G.B.); Tel.: +39-862-433327 (M.G.B.)
| | - Federica Sentinelli
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Sabrina Prudente
- Research Unit of Metabolic and Cardiovascular Diseases, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Flavia Agata Cimini
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Ilaria Barchetta
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Maria Totaro
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
| | - Alessia Di Costanzo
- Department of Translational and Precision Medicine, Sapienza University of Rome, 00185 Rome, Italy;
| | - Arcangelo Barbonetti
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
| | - Frida Leonetti
- Diabetes Unit, Department of Medical-Surgical Sciences and Biotechnologies, Santa Maria Goretti Hospital, Sapienza University of Rome, 04100 Latina, Italy;
| | - Maria Gisella Cavallo
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Marco Giorgio Baroni
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
- Neuroendocrinology and Metabolic Diseases, IRCCS Neuromed, 86077 Pozzilli, Italy
- Correspondence: (D.B.); (M.G.B.); Tel.: +39-862-433327 (M.G.B.)
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30
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Dai M, Guo W, Zhu S, Gong G, Chen M, Zhong Z, Guo J, Zhang Y. Type 2 diabetes mellitus and the risk of abnormal spermatozoa: A Mendelian randomization study. Front Endocrinol (Lausanne) 2022; 13:1035338. [PMID: 36407300 PMCID: PMC9666365 DOI: 10.3389/fendo.2022.1035338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/06/2022] [Indexed: 12/01/2022] Open
Abstract
Abnormal spermatozoa can not only reduce the fertilization rate, but also prolong the natural conception time and even increase the risk of spontaneous miscarriage. Diabetes mellitus (DM) has become a major global health problem, and its incidence continues to rise, while affecting an increasing number of men in their reproductive years. Type 2 Diabetes Mellitus (T2DM), accounting for about 85-95% of DM, is closely related to the development of sperm. However, the exact association between T2DM and abnormal spermatozoa remains unclear. Herein, we designed a Two-sample Mendelian randomization (MR) study to explore the causal association between T2DM and abnormal spermatozoa risk in European population data which come from the GWAS summary datasets. We selected 9 single nucleotide polymorphisms (SNPs) of T2DM (exposure data) as instrumental variables (IVs), and then retrieved the suitable abnormal spermatozoa genome-wide association study (GWAS) data of European from Ieu Open GWAS Project database which includes 915 cases and 209,006 control as the outcome data. Our results indicate that strict T2DM might not result in a higher risk of abnormal spermatozoa genetically in Europeans (OR: 1.017, 95% confidence interval (CI): 0.771-1.342, p=0.902). Our findings demonstrate that only T2DM may not explain the relatively higher risk of abnormal spermatozoa in men with it in Europeans. In subsequent studies, more comprehensive and larger samples need to be studied to reveal the relationship and potential mechanism between T2DM and abnormal spermatozoa.
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Affiliation(s)
- Mengyuan Dai
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Weijie Guo
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - San Zhu
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Guidong Gong
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Mei Chen
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Zhuoling Zhong
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Junling Guo
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China
| | - Yaoyao Zhang
- Department of Obstetrics and Gynecology of West China Second University Hospital, BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- *Correspondence: Yaoyao Zhang,
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Wang F, Luo D, Chen J, Pan C, Wang Z, Fu H, Xu J, Yang M, Mo S, Zhuang L, Ye L, Wang W. Genome-Wide Association Analysis to Search for New Loci Associated with Lifelong Premature Ejaculation Risk in Chinese Male Han Population. World J Mens Health 2022; 40:330-339. [PMID: 35021295 PMCID: PMC8987137 DOI: 10.5534/wjmh.210084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/23/2021] [Accepted: 07/31/2021] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Genetic factors play an indispensable role in the pathogenesis of lifelong premature ejaculation (LPE). The susceptibility genes/SNPs that have been discovered are very limited and can only explain part of the genetic effects of LPE. Therefore, discovering more genetic polymorphisms associated with the occurrence and development of LPE will help reveal the pathogenesis of LPE. MATERIALS AND METHODS We conducted a genome-wide association study of LPE in 486 Chinese male Han people (cases and controls). We used Gene Titan multi-channel instrument and Axiom Analysis Suite 6.0 software for genotyping. Imputation was performed by IMPUTE2 software and the 1000 Genomes Project (Phase3) was used as reference for haplotype. Finally, logistic regression analysis was performed on all loci that passed the quality control. The odds ratio and 95% confidence interval were calculated to determine the association between each SNPs and Chinese male Han population LPE risk. RESULTS The results showed that a total of 33 genetic variants in 13 genes (LACTBL1, SSBP3, ACOT11, LINC02486, TMEM154, LINC01098, NONE, HCG27, HLA-C, TNFSF8, TNC, FAM53B, SULF2) have a suggestively significant genome-wide association with LPE risk (p<5×10-6). CONCLUSIONS This study is the first to conduct a GWAS on LPE in Chinese male Han population 33 genetic polymorphisms have a suggestive genome-wide association with LPE risk. This study have provided data supplement for the genetic loci of LPE risk, and laid a scientific foundation for the pathogenesis and the targeted therapy of LPE.
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Affiliation(s)
- Fei Wang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Defan Luo
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital to University of South China, Hengyang, Hunan, China
| | - Jianxiang Chen
- Department of Urology, Affiliated Hospital of Xiangnan University, Chenzhou, Hunan, China
| | - Cuiqing Pan
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Zhongyao Wang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Housheng Fu
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jianbing Xu
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Meng Yang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Shaowei Mo
- Ministry of Science and education, Hainan Women and Children's Medical Center, Haikou, Hainan, China
| | - Liying Zhuang
- Library, Hainan Medical University, Haikou, Hainan, China
| | - Liefu Ye
- Department of Urology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China, China.
| | - Weifu Wang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China.
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Alonso L, Piron A, Morán I, Guindo-Martínez M, Bonàs-Guarch S, Atla G, Miguel-Escalada I, Royo R, Puiggròs M, Garcia-Hurtado X, Suleiman M, Marselli L, Esguerra JLS, Turatsinze JV, Torres JM, Nylander V, Chen J, Eliasson L, Defrance M, Amela R, Mulder H, Gloyn AL, Groop L, Marchetti P, Eizirik DL, Ferrer J, Mercader JM, Cnop M, Torrents D. TIGER: The gene expression regulatory variation landscape of human pancreatic islets. Cell Rep 2021; 37:109807. [PMID: 34644572 PMCID: PMC8864863 DOI: 10.1016/j.celrep.2021.109807] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/23/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies (GWASs) identified hundreds of signals associated with type 2 diabetes (T2D). To gain insight into their underlying molecular mechanisms, we have created the translational human pancreatic islet genotype tissue-expression resource (TIGER), aggregating >500 human islet genomic datasets from five cohorts in the Horizon 2020 consortium T2DSystems. We impute genotypes using four reference panels and meta-analyze cohorts to improve the coverage of expression quantitative trait loci (eQTL) and develop a method to combine allele-specific expression across samples (cASE). We identify >1 million islet eQTLs, 53 of which colocalize with T2D signals. Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identify eight cASE colocalizations, among which we found a T2D-associated SLC30A8 variant. We make all data available through the TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translates into therapeutic insight and precision medicine for T2D.
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Affiliation(s)
- Lorena Alonso
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Anthony Piron
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels 1050, Belgium
| | - Ignasi Morán
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Marta Guindo-Martínez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Sílvia Bonàs-Guarch
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Goutham Atla
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Irene Miguel-Escalada
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Romina Royo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Montserrat Puiggròs
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Xavier Garcia-Hurtado
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Jonathan L S Esguerra
- Unit of Islet Cell Exocytosis, Lund University Diabetes Centre, Malmö 214 28, Sweden
| | | | - Jason M Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LE, UK
| | - Ji Chen
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, Exeter EX4 4PY, UK
| | - Lena Eliasson
- Unit of Islet Cell Exocytosis, Lund University Diabetes Centre, Malmö 214 28, Sweden
| | - Matthieu Defrance
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Ramon Amela
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Hindrik Mulder
- Unit of Molecular Metabolism, Lund University Diabetes Centre, Malmö 214 28, Sweden
| | - Anna L Gloyn
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK; Oxford Centre for Diabetes, Endocrinology, and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LE, UK; Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA; NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford OX3 7DQ, UK; Stanford Diabetes Research Centre, Stanford University, Stanford, CA 94305, USA
| | - Leif Groop
- Unit of Islet Cell Exocytosis, Lund University Diabetes Centre, Malmö 214 28, Sweden; Unit of Molecular Metabolism, Lund University Diabetes Centre, Malmö 214 28, Sweden; Finnish Institute of Molecular Medicine Finland (FIMM), Helsinki University, Helsinki 00014, Finland
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; WELBIO, Université Libre de Bruxelles, Brussels 1050, Belgium
| | - Jorge Ferrer
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain; Section of Epigenomics and Disease, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Josep M Mercader
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain; Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels 1070, Belgium.
| | - David Torrents
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
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Meeks KAC, Bentley AR, Gouveia MH, Chen G, Zhou J, Lei L, Adeyemo AA, Doumatey AP, Rotimi CN. Genome-wide analyses of multiple obesity-related cytokines and hormones informs biology of cardiometabolic traits. Genome Med 2021; 13:156. [PMID: 34620218 PMCID: PMC8499470 DOI: 10.1186/s13073-021-00971-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A complex set of perturbations occur in cytokines and hormones in the etiopathogenesis of obesity and related cardiometabolic conditions such as type 2 diabetes (T2D). Evidence for the genetic regulation of these cytokines and hormones is limited, particularly in African-ancestry populations. In order to improve our understanding of the biology of cardiometabolic traits, we investigated the genetic architecture of a large panel of obesity- related cytokines and hormones among Africans with replication analyses in African Americans. METHODS We performed genome-wide association studies (GWAS) in 4432 continental Africans, enrolled from Ghana, Kenya, and Nigeria as part of the Africa America Diabetes Mellitus (AADM) study, for 13 obesity-related cytokines and hormones, including adipsin, glucose-dependent insulinotropic peptide (GIP), glucagon-like peptide-1 (GLP-1), interleukin-1 receptor antagonist (IL1-RA), interleukin-6 (IL-6), interleukin-10 (IL-10), leptin, plasminogen activator inhibitor-1 (PAI-1), resistin, visfatin, insulin, glucagon, and ghrelin. Exact and local replication analyses were conducted in African Americans (n = 7990). The effects of sex, body mass index (BMI), and T2D on results were investigated through stratified analyses. RESULTS GWAS identified 39 significant (P value < 5 × 10-8) loci across all 13 traits. Notably, 14 loci were African-ancestry specific. In this first GWAS for adipsin and ghrelin, we detected 13 and 4 genome-wide significant loci respectively. Stratified analyses by sex, BMI, and T2D showed a strong effect of these variables on detected loci. Eight novel loci were successfully replicated: adipsin (3), GIP (1), GLP-1 (1), and insulin (3). Annotation of these loci revealed promising links between these adipocytokines and cardiometabolic outcomes as illustrated by rs201751833 for adipsin and blood pressure and locus rs759790 for insulin level and T2D in lean individuals. CONCLUSIONS Our study identified genetic variants underlying variation in multiple adipocytokines, including the first loci for adipsin and ghrelin. We identified population differences in variants associated with adipocytokines and highlight the importance of stratification for discovery of loci. The high number of African-specific loci detected emphasizes the need for GWAS in African-ancestry populations, as these loci could not have been detected in other populations. Overall, our work contributes to the understanding of the biology linking adipocytokines to cardiometabolic traits.
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Affiliation(s)
- Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Lin Lei
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA.
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA.
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34
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Kim DS, Gloyn AL, Knowles JW. Genetics of Type 2 Diabetes: Opportunities for Precision Medicine: JACC Focus Seminar. J Am Coll Cardiol 2021; 78:496-512. [PMID: 34325839 PMCID: PMC8328195 DOI: 10.1016/j.jacc.2021.03.346] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022]
Abstract
Type 2 diabetes (T2D) is highly prevalent and is a strong contributor for cardiovascular disease. However, there is significant heterogeneity in disease pathogenesis and the risk of complications. Enormous progress has been made in our ability to catalog genetic variation associated with T2D risk and variation in disease-relevant quantitative traits. These discoveries hold the potential to shed light on tractable targets and pathways for safe and effective therapeutic development, but the promise of precision medicine has been slow to be realized. Recent studies have identified subgroups of individuals with differential risk for intermediate phenotypes (eg, lipid levels, fasting insulin, body mass index) that contribute to T2D risk, helping to account for the observed clinical heterogeneity. These "partitioned genetic risk scores" not only have the potential to identify patients at greatest risk of cardiovascular disease and rapid disease progression, but also could aid patient stratification bridging the gap toward precision medicine for T2D.
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Affiliation(s)
- Daniel Seung Kim
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Anna L Gloyn
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA; Stanford Diabetes Research Center, Stanford University, Stanford, California, USA
| | - Joshua W Knowles
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA; Stanford Diabetes Research Center, Stanford University, Stanford, California, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, California, USA.
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35
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Sticht J, Álvaro-Benito M, Konigorski S. Type 1 Diabetes and the HLA Region: Genetic Association Besides Classical HLA Class II Genes. Front Genet 2021; 12:683946. [PMID: 34220961 PMCID: PMC8248358 DOI: 10.3389/fgene.2021.683946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023] Open
Abstract
Type 1 diabetes is an autoimmune disease with rising incidence in high-income countries. Genetic and environmental predisposing factors contribute to the etiology of the disease, although their interaction is not sufficiently understood to allow for preventive action. Strongest known associations with genetic variation map to classical HLA class II genes. Because of its genetic complexity, the HLA region has been under-represented in genome-wide association studies, having potentially hindered the identification of relevant associations underlying the etiology of the disease. Here, we performed a comprehensive HLA-wide genetic association analysis of type 1 diabetes including multi-allelic and rare variants. We used high-density whole-exome sequencing data of the HLA region in the large UK Biobank dataset to apply gene-based association tests with a carefully defined type 1 diabetes phenotype (97 cases and 48,700 controls). Exon-based and single-variant association tests were used to complement the analysis. We replicated the known association of type 1 diabetes with the classical HLA-DQ gene. Tailoring the analysis toward rare variants, we additionally identified the lysine methyl transferase EHMT2 as associated. Deeper insight into genetic variation associated with disease as presented and discussed in detail here can help unraveling mechanistic details of the etiology of type 1 diabetes. More specifically, we hypothesize that genetic variation in EHMT2 could impact autoimmunity in type 1 diabetes development.
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Affiliation(s)
- Jana Sticht
- Digital Health and Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, Potsdam, Germany.,Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Miguel Álvaro-Benito
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Stefan Konigorski
- Digital Health and Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, Potsdam, Germany
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36
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Bevacqua RJ, Dai X, Lam JY, Gu X, Friedlander MSH, Tellez K, Miguel-Escalada I, Bonàs-Guarch S, Atla G, Zhao W, Kim SH, Dominguez AA, Qi LS, Ferrer J, MacDonald PE, Kim SK. CRISPR-based genome editing in primary human pancreatic islet cells. Nat Commun 2021; 12:2397. [PMID: 33893274 PMCID: PMC8065166 DOI: 10.1038/s41467-021-22651-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023] Open
Abstract
Gene targeting studies in primary human islets could advance our understanding of mechanisms driving diabetes pathogenesis. Here, we demonstrate successful genome editing in primary human islets using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9). CRISPR-based targeting efficiently mutated protein-coding exons, resulting in acute loss of islet β-cell regulators, like the transcription factor PDX1 and the KATP channel subunit KIR6.2, accompanied by impaired β-cell regulation and function. CRISPR targeting of non-coding DNA harboring type 2 diabetes (T2D) risk variants revealed changes in ABCC8, SIX2 and SIX3 expression, and impaired β-cell function, thereby linking regulatory elements in these target genes to T2D genetic susceptibility. Advances here establish a paradigm for genetic studies in human islet cells, and reveal regulatory and genetic mechanisms linking non-coding variants to human diabetes risk.
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Affiliation(s)
- Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaoqing Dai
- Alberta Diabetes Institute and Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
| | - Jonathan Y Lam
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xueying Gu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mollie S H Friedlander
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Krissie Tellez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Irene Miguel-Escalada
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Silvia Bonàs-Guarch
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Goutham Atla
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Weichen Zhao
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Seung Hyun Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Antonia A Dominguez
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Chem-H, Stanford University, Stanford, CA, USA
| | - Jorge Ferrer
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
- Section of Genetics and Genomics, Imperial College London, London, UK
| | - Patrick E MacDonald
- Alberta Diabetes Institute and Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine (Endocrinology), Stanford University School of Medicine, Stanford, CA, USA.
- Northern California JDRF Center of Excellence, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA.
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37
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Guindo-Martínez M, Amela R, Bonàs-Guarch S, Puiggròs M, Salvoro C, Miguel-Escalada I, Carey CE, Cole JB, Rüeger S, Atkinson E, Leong A, Sanchez F, Ramon-Cortes C, Ejarque J, Palmer DS, Kurki M, Aragam K, Florez JC, Badia RM, Mercader JM, Torrents D. The impact of non-additive genetic associations on age-related complex diseases. Nat Commun 2021; 12:2436. [PMID: 33893285 PMCID: PMC8065056 DOI: 10.1038/s41467-021-21952-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/09/2021] [Indexed: 01/19/2023] Open
Abstract
Genome-wide association studies (GWAS) are not fully comprehensive, as current strategies typically test only the additive model, exclude the X chromosome, and use only one reference panel for genotype imputation. We implement an extensive GWAS strategy, GUIDANCE, which improves genotype imputation by using multiple reference panels and includes the analysis of the X chromosome and non-additive models to test for association. We apply this methodology to 62,281 subjects across 22 age-related diseases and identify 94 genome-wide associated loci, including 26 previously unreported. Moreover, we observe that 27.7% of the 94 loci are missed if we use standard imputation strategies with a single reference panel, such as HRC, and only test the additive model. Among the new findings, we identify three novel low-frequency recessive variants with odds ratios larger than 4, which need at least a three-fold larger sample size to be detected under the additive model. This study highlights the benefits of applying innovative strategies to better uncover the genetic architecture of complex diseases.
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Affiliation(s)
| | - Ramon Amela
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Silvia Bonàs-Guarch
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | | | | | - Irene Miguel-Escalada
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Caitlin E Carey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joanne B Cole
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Sina Rüeger
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elizabeth Atkinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Leong
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Jorge Ejarque
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Duncan S Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- GENOMICS plc, Oxford, UK
| | - Mitja Kurki
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Krishna Aragam
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Rosa M Badia
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Josep M Mercader
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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38
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Natarajan P, Pampana A, Graham SE, Ruotsalainen SE, Perry JA, de Vries PS, Broome JG, Pirruccello JP, Honigberg MC, Aragam K, Wolford B, Brody JA, Antonacci-Fulton L, Arden M, Aslibekyan S, Assimes TL, Ballantyne CM, Bielak LF, Bis JC, Cade BE, Do R, Doddapaneni H, Emery LS, Hung YJ, Irvin MR, Khan AT, Lange L, Lee J, Lemaitre RN, Martin LW, Metcalf G, Montasser ME, Moon JY, Muzny D, O'Connell JR, Palmer ND, Peralta JM, Peyser PA, Stilp AM, Tsai M, Wang FF, Weeks DE, Yanek LR, Wilson JG, Abecasis G, Arnett DK, Becker LC, Blangero J, Boerwinkle E, Bowden DW, Chang YC, Chen YDI, Choi WJ, Correa A, Curran JE, Daly MJ, Dutcher SK, Ellinor PT, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, He J, Hveem K, Jarvik GP, Kaplan RC, Kardia SLR, Kenny E, Kim RW, Kooperberg C, Laurie CC, Lee S, Lloyd-Jones DM, Loos RJF, Lubitz SA, Mathias RA, Martinez KAV, McGarvey ST, Mitchell BD, Nickerson DA, North KE, Palotie A, Park CJ, Psaty BM, Rao DC, Redline S, Reiner AP, Seo D, Seo JS, Smith AV, Tracy RP, Vasan RS, Kathiresan S, Cupples LA, Rotter JI, Morrison AC, Rich SS, Ripatti S, Willer C, Peloso GM. Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. Nat Commun 2021; 12:2182. [PMID: 33846329 PMCID: PMC8042019 DOI: 10.1038/s41467-021-22339-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Autosomal genetic analyses of blood lipids have yielded key insights for coronary heart disease (CHD). However, X chromosome genetic variation is understudied for blood lipids in large sample sizes. We now analyze genetic and blood lipid data in a high-coverage whole X chromosome sequencing study of 65,322 multi-ancestry participants and perform replication among 456,893 European participants. Common alleles on chromosome Xq23 are strongly associated with reduced total cholesterol, LDL cholesterol, and triglycerides (min P = 8.5 × 10-72), with similar effects for males and females. Chromosome Xq23 lipid-lowering alleles are associated with reduced odds for CHD among 42,545 cases and 591,247 controls (P = 1.7 × 10-4), and reduced odds for diabetes mellitus type 2 among 54,095 cases and 573,885 controls (P = 1.4 × 10-5). Although we observe an association with increased BMI, waist-to-hip ratio adjusted for BMI is reduced, bioimpedance analyses indicate increased gluteofemoral fat, and abdominal MRI analyses indicate reduced visceral adiposity. Co-localization analyses strongly correlate increased CHRDL1 gene expression, particularly in adipose tissue, with reduced concentrations of blood lipids.
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Affiliation(s)
- Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Akhil Pampana
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Sarah E Graham
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Sanni E Ruotsalainen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - James A Perry
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - James P Pirruccello
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael C Honigberg
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Krishna Aragam
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Brooke Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lucinda Antonacci-Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Moscati Arden
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Christie M Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX, USA
- Houston Methodist Debakey Heart and Vascular Center, Houston, TX, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan branch, Taipei, Taiwan
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alyna T Khan
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jiwon Lee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa W Martin
- Division of Cardiology, George Washington University School of Medicine and Healthcare Sciences, Washington, DC, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - May E Montasser
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R O'Connell
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Michael Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Fei Fei Wang
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Daniel E Weeks
- Departments of Human Genetics and Biostatistics, University of Pittsburgh, Pittsburgh, Pittsburgh, PA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Donna K Arnett
- Deans office, School of Public Health, University of Kentucky, Lexington, KY, USA
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yi-Cheng Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yii-Der I Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Won Jung Choi
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Susan K Dutcher
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital, Boston, MA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-, Salem, NC, USA
| | - Stacey Gabriel
- Genomics Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, and Tulane University Translational Science Institute, Tulane University, New Orleans, LA, USA
| | - Kristian Hveem
- Department of Public Health and General Practice, HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Dept of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Eimear Kenny
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan W Kim
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Seonwook Lee
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Don M Lloyd-Jones
- Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital, Boston, MA, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Stephen T McGarvey
- Department of Epidemiology and International Health Institute, Brown University, Providence, RI, USA
| | - Braxton D Mitchell
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aarno Palotie
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cheol Joo Park
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Departments of Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daekwan Seo
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Jeong-Sun Seo
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- The Icelandic Heart Association, Kopavogur, Iceland
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larrner College of Medicine, University of Vermont, Colchester, VT, USA
| | - Ramachandran S Vasan
- Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - L Adrienne Cupples
- NHLBI Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Samuli Ripatti
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Cristen Willer
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
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39
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Liu W, Zhang L, Li S, Liu C, Tong Y, Fang H, Zhang R, Song B, Xia Z, Xu Y. A Mendelian Randomization Study of Plasma Homocysteine Levels and Cerebrovascular and Neurodegenerative Diseases. Front Genet 2021; 12:653032. [PMID: 33868384 PMCID: PMC8047106 DOI: 10.3389/fgene.2021.653032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Homocysteine (Hcy) is a toxic amino acid and hyperhomocysteinemia (HHcy) was reported to be associated with both cerebrovascular disease and neurodegenerative disease. Our aim was to assess the causal link between plasma Hcy level and cerebrovascular and neurodegenerative diseases through a Mendelian randomization (MR) study. Methods: A two-sample MR study was performed to infer the causal link. We extracted the genetic variants (SNPs) associated with plasma Hcy level from a large genome-wide association study (GWAS) meta-analysis. The main MR analysis was performed using the inverse variance-weighted method. Additional analyses were further performed using MR-Egger intercept and Cochran’s Q statistic to detect the heterogeneity or pleiotropy of our findings. Results: Thirteen Hcy-associated SNPs were selected as instrumental variables. The results showed evidence of a causal link between plasma Hcy level and ischemic stroke (IS) caused by small artery occlusion (SAS, OR = 1.329, 95% CI 1.047–1.612, p = 0.048). Meanwhile, there was no evidence of association between plasma Hcy level and other types of IS, transient ischemic attack (TIA), or neurodegenerative disease. The MR-Egger intercept test indicated no evidence of directional pleiotropy. Results of additional MR analysis indicated that blood pressure (BP) and type 2 diabetes mellitus (T2DM) serve as influencers in the association. Conclusion: The MR study found a little causal link between plasma Hcy level and SAS. The link is likely to be influenced by other risk factors like BP and T2DM.
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Affiliation(s)
- Weishi Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Luyang Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shen Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chen Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Tong
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Fang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Rui Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Song
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongping Xia
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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40
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Pang H, Xia Y, Luo S, Huang G, Li X, Xie Z, Zhou Z. Emerging roles of rare and low-frequency genetic variants in type 1 diabetes mellitus. J Med Genet 2021; 58:289-296. [PMID: 33753534 PMCID: PMC8086251 DOI: 10.1136/jmedgenet-2020-107350] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 12/12/2022]
Abstract
Type 1 diabetes mellitus (T1DM) is defined as an autoimmune disorder and has enormous complexity and heterogeneity. Although its precise pathogenic mechanisms are obscure, this disease is widely acknowledged to be precipitated by environmental factors in individuals with genetic susceptibility. To date, the known susceptibility loci, which have mostly been identified by genome-wide association studies, can explain 80%–85% of the heritability of T1DM. Researchers believe that at least a part of its missing genetic component is caused by undetected rare and low-frequency variants. Most common variants have only small to modest effect sizes, which increases the difficulty of dissecting their functions and restricts their potential clinical application. Intriguingly, many studies have indicated that rare and low-frequency variants have larger effect sizes and play more significant roles in susceptibility to common diseases, including T1DM, than common variants do. Therefore, better recognition of rare and low-frequency variants is beneficial for revealing the genetic architecture of T1DM and for providing new and potent therapeutic targets for this disease. Here, we will discuss existing challenges as well as the great significance of this field and review current knowledge of the contributions of rare and low-frequency variants to T1DM.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ying Xia
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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41
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Hu M, Cebola I, Carrat G, Jiang S, Nawaz S, Khamis A, Canouil M, Froguel P, Schulte A, Solimena M, Ibberson M, Marchetti P, Cardenas-Diaz FL, Gadue PJ, Hastoy B, Almeida-Souza L, McMahon H, Rutter GA. Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a regulator of insulin secretion. Cell Rep 2021; 34:108703. [PMID: 33535042 PMCID: PMC7856552 DOI: 10.1016/j.celrep.2021.108703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
Using chromatin conformation capture, we show that an enhancer cluster in the STARD10 type 2 diabetes (T2D) locus forms a defined 3-dimensional (3D) chromatin domain. A 4.1-kb region within this locus, carrying 5 T2D-associated variants, physically interacts with CTCF-binding regions and with an enhancer possessing strong transcriptional activity. Analysis of human islet 3D chromatin interaction maps identifies the FCHSD2 gene as an additional target of the enhancer cluster. CRISPR-Cas9-mediated deletion of the variant region, or of the associated enhancer, from human pancreas-derived EndoC-βH1 cells impairs glucose-stimulated insulin secretion. Expression of both STARD10 and FCHSD2 is reduced in cells harboring CRISPR deletions, and lower expression of STARD10 and FCHSD2 is associated, the latter nominally, with the possession of risk variant alleles in human islets. Finally, CRISPR-Cas9-mediated loss of STARD10 or FCHSD2, but not ARAP1, impairs regulated insulin secretion. Thus, multiple genes at the STARD10 locus influence β cell function.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Gaelle Carrat
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Shuying Jiang
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Sameena Nawaz
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LE, UK
| | - Amna Khamis
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Mickaël Canouil
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Philippe Froguel
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Anke Schulte
- Sanofi-Aventis Deutschland GmbH, 65926 Frankfurt am Main, Germany
| | - Michele Solimena
- Paul Langerhans Institute of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Piero Marchetti
- Department of Endocrinology and Metabolism, University of Pisa, 56126 Pisa, Italy
| | - Fabian L Cardenas-Diaz
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Centre for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Gadue
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Centre for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benoit Hastoy
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LE, UK
| | - Leonardo Almeida-Souza
- HiLIFE Institute of Biotechnology & Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Harvey McMahon
- MRC MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK; Lee Kong Chian School of Medicine, Nan Yang Technological University, Singapore, Singapore.
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42
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Chu H, Xin J, Yuan Q, Wu Y, Du M, Zheng R, Liu H, Wu S, Zhang Z, Wang M. A prospective study of the associations among fine particulate matter, genetic variants, and the risk of colorectal cancer. ENVIRONMENT INTERNATIONAL 2021; 147:106309. [PMID: 33338681 DOI: 10.1016/j.envint.2020.106309] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/17/2020] [Accepted: 11/26/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Fine particulate matter (PM2.5) is suspected to increase the risk of colorectal cancer, but the mechanism remains unknown. We aimed to investigate the association between PM2.5 exposure, genetic variants and colorectal cancer risk in the Prostate, Lung, Colon and Ovarian (PLCO) Cancer Screening trial. METHODS We included a prospective cohort of 139,534 cancer-free individuals from 10 United States research centers with over ten years of follow-up. We used a Cox regression model to assess the association between PM2.5 exposure and colorectal cancer incidence by calculating the hazard ratio (HR) and 95% confidence interval (CI) with adjustment for potential confounders. The polygenic risk score (PRS) and genome-wide interaction analysis (GWIA) were used to evaluate the multiplicative interaction between PM2.5 exposure and genetic variants in regard to colorectal cancer risk. RESULTS After a median of 10.43 years of follow-up, 1,666 participants had been diagnosed with colorectal cancer. PM2.5 exposure was significantly associated with an increased risk of colorectal cancer (HR = 1.27; 95% CI = 1.17-1.37 per 5 μg/m3 increase). Five independent susceptibility loci reached statistical significance at P < 1.22 × 10-8 in the interaction analysis. Furthermore, a joint interaction was observed between PM2.5 exposure and the PRS based on these five loci with colorectal cancer risk (P = 3.11 × 10-29). The Gene Ontology analysis showed that the vascular endothelial growth factor (VEGF) receptor signaling pathway was involved in the biological process of colorectal cancer. CONCLUSIONS Our large-scale analysis has shown for the first time that long-term PM2.5 exposure potential increases colorectal cancer risk, which might be modified by genetic variants.
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Affiliation(s)
- Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, 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
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, 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
| | - Qi Yuan
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Yanling Wu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, 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, Nanjing Medical University, Nanjing, China
| | - Rui Zheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hanting Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Shaowei Wu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, 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, 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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Balboa D, Iworima DG, Kieffer TJ. Human Pluripotent Stem Cells to Model Islet Defects in Diabetes. Front Endocrinol (Lausanne) 2021; 12:642152. [PMID: 33828531 PMCID: PMC8020750 DOI: 10.3389/fendo.2021.642152] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
Diabetes mellitus is characterized by elevated levels of blood glucose and is ultimately caused by insufficient insulin production from pancreatic beta cells. Different research models have been utilized to unravel the molecular mechanisms leading to the onset of diabetes. The generation of pancreatic endocrine cells from human pluripotent stem cells constitutes an approach to study genetic defects leading to impaired beta cell development and function. Here, we review the recent progress in generating and characterizing functional stem cell-derived beta cells. We summarize the diabetes disease modeling possibilities that stem cells offer and the challenges that lie ahead to further improve these models.
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Affiliation(s)
- Diego Balboa
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- *Correspondence: Diego Balboa,
| | - Diepiriye G. Iworima
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Timothy J. Kieffer
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
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44
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Brenner LN, Mercader JM, Robertson CC, Cole J, Chen L, Jacobs SBR, Rich SS, Florez JC. Analysis of Glucocorticoid-Related Genes Reveal CCHCR1 as a New Candidate Gene for Type 2 Diabetes. J Endocr Soc 2020; 4:bvaa121. [PMID: 33150273 PMCID: PMC7594651 DOI: 10.1210/jendso/bvaa121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
Glucocorticoids have multiple therapeutic benefits and are used both for immunosuppression and treatment purposes. Notwithstanding their benefits, glucocorticoid use often leads to hyperglycemia. Owing to the pathophysiologic overlap in glucocorticoid-induced hyperglycemia (GIH) and type 2 diabetes (T2D), we hypothesized that genetic variation in glucocorticoid pathways contributes to T2D risk. To determine the genetic contribution of glucocorticoid action on T2D risk, we conducted multiple genetic studies. First, we performed gene-set enrichment analyses on 3 collated glucocorticoid-related gene sets using publicly available genome-wide association and whole-exome data and demonstrated that genetic variants in glucocorticoid-related genes are associated with T2D and related glycemic traits. To identify which genes are driving this association, we performed gene burden tests using whole-exome sequence data. We identified 20 genes within the glucocorticoid-related gene sets that are nominally enriched for T2D-associated protein-coding variants. The most significant association was found in coding variants in coiled-coil α-helical rod protein 1 (CCHCR1) in the HLA region (P = .001). Further analyses revealed that noncoding variants near CCHCR1 are also associated with T2D at genome-wide significance (P = 7.70 × 10-14), independent of type 1 diabetes HLA risk. Finally, gene expression and colocalization analyses demonstrate that variants associated with increased T2D risk are also associated with decreased expression of CCHCR1 in multiple tissues, implicating this gene as a potential effector transcript at this locus. Our discovery of a genetic link between glucocorticoids and T2D findings support the hypothesis that T2D and GIH may have shared underlying mechanisms.
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Affiliation(s)
- Laura N Brenner
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Boston, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Josep M Mercader
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Catherine C Robertson
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Joanne Cole
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Ling Chen
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Suzanne B R Jacobs
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Jose C Florez
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts
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45
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Vujkovic M, Keaton JM, Lynch JA, Miller DR, Zhou J, Tcheandjieu C, Huffman JE, Assimes TL, Lorenz K, Zhu X, Hilliard AT, Judy RL, Huang J, Lee KM, Klarin D, Pyarajan S, Danesh J, Melander O, Rasheed A, Mallick NH, Hameed S, Qureshi IH, Afzal MN, Malik U, Jalal A, Abbas S, Sheng X, Gao L, Kaestner KH, Susztak K, Sun YV, DuVall SL, Cho K, Lee JS, Gaziano JM, Phillips LS, Meigs JB, Reaven PD, Wilson PW, Edwards TL, Rader DJ, Damrauer SM, O'Donnell CJ, Tsao PS, Chang KM, Voight BF, Saleheen D. Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis. Nat Genet 2020; 52:680-691. [PMID: 32541925 PMCID: PMC7343592 DOI: 10.1038/s41588-020-0637-y] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/29/2020] [Indexed: 12/19/2022]
Abstract
We investigated type 2 diabetes (T2D) genetic susceptibility via multi-ethnic meta-analysis of 228,499 cases and 1,178,783 controls in the Million Veteran Program, DIAMANTE, Biobank Japan, and other studies. We report 568 associations, including 286 autosomal, 7 X chromosomal, and 25 identified in ancestry-specific analyses that were previously unreported. Transcriptome-wide association analysis detected 3,568 T2D-associations with genetically predicted gene expression in 687 novel genes; of these, 54 are known to interact with FDA-approved drugs. A polygenic risk score was strongly associated with increased risk of T2D-related retinopathy and modestly associated with chronic kidney disease (CKD), peripheral artery disease (PAD), and neuropathy. We investigated the genetic etiology of T2D-related vascular outcomes in MVP and observed statistical SNP-T2D interactions at 13 variants, including coronary heart disease, CKD, PAD, and neuropathy. These findings may help to identify potential therapeutic targets for T2D and genomic pathways that link T2D to vascular outcomes.
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Affiliation(s)
- Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacob M Keaton
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie A Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA.,College of Nursing and Health Sciences, University of Massachusetts, Lowell, MA, USA
| | - Donald R Miller
- Edith Nourse Rogers Memorial VA Hospital, Bedford, MA, USA.,Center for Population Health, University of Massachusetts, Lowell, MA, USA
| | - Jin Zhou
- Phoenix VA Health Care System, Phoenix, AZ, USA.,Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Catherine Tcheandjieu
- VA Palo Alto Health Care System, Palo Alto, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pediatric Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kimberly Lorenz
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.,Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Xiang Zhu
- VA Palo Alto Health Care System, Palo Alto, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Austin T Hilliard
- VA Palo Alto Health Care System, Palo Alto, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Renae L Judy
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.,Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jie Huang
- VA Boston Healthcare System, Boston, MA, USA.,Department of Global Health, Peking University School of Public Health, Beijing, China
| | - Kyung M Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Derek Klarin
- VA Boston Healthcare System, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Vascular Surgery and Endovascular Therapy, University of Florida School of Medicine, Gainesville, FL, USA
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, MA, USA.,Department of Medicine, Brigham Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Sindh, Pakistan
| | | | - Shahid Hameed
- Punjab Institute of Cardiology, Lahore, Punjab, Pakistan
| | - Irshad H Qureshi
- Department of Medicine, King Edward Medical University, Lahore, Punjab, Pakistan.,Mayo Hospital, Lahore, Punjab, Pakistan
| | - Muhammad Naeem Afzal
- Department of Medicine, King Edward Medical University, Lahore, Punjab, Pakistan.,Mayo Hospital, Lahore, Punjab, Pakistan
| | - Uzma Malik
- Department of Medicine, King Edward Medical University, Lahore, Punjab, Pakistan.,Mayo Hospital, Lahore, Punjab, Pakistan
| | - Anjum Jalal
- Department of Cardiology, Faisalabad Institute of Cardiology, Faisalabad, Punjab, Pakistan
| | - Shahid Abbas
- Department of Cardiology, Faisalabad Institute of Cardiology, Faisalabad, Punjab, Pakistan
| | - Xin Sheng
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Long Gao
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yan V Sun
- Atlanta VA Medical Center, Decatur, GA, USA.,Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Scott L DuVall
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA.,Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA.,Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Jennifer S Lee
- VA Palo Alto Health Care System, Palo Alto, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA, USA.,Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Lawrence S Phillips
- Atlanta VA Medical Center, Decatur, GA, USA.,Division of Endocrinology, Emory University School of Medicine, Atlanta, GA, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, USA.,College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - Peter W Wilson
- Atlanta VA Medical Center, Decatur, GA, USA.,Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Todd L Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Nashville VA Medical Center, Nashville, TN, USA
| | - Daniel J Rader
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.,Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, USA.,Department of Medicine, Brigham Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,South Texas Veterans Health Care System, San Antonio, TX, USA
| | - Benjamin F Voight
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA. .,Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Sindh, Pakistan. .,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA.
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González JR, Ruiz-Arenas C, Cáceres A, Morán I, López-Sánchez M, Alonso L, Tolosana I, Guindo-Martínez M, Mercader JM, Esko T, Torrents D, González J, Pérez-Jurado LA. Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases. Am J Hum Genet 2020; 106:846-858. [PMID: 32470372 DOI: 10.1016/j.ajhg.2020.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/28/2020] [Indexed: 11/25/2022] Open
Abstract
The burden of several common diseases including obesity, diabetes, hypertension, asthma, and depression is increasing in most world populations. However, the mechanisms underlying the numerous epidemiological and genetic correlations among these disorders remain largely unknown. We investigated whether common polymorphic inversions underlie the shared genetic influence of these disorders. We performed an inversion association analysis including 21 inversions and 25 obesity-related traits on a total of 408,898 Europeans and validated the results in 67,299 independent individuals. Seven inversions were associated with multiple diseases while inversions at 8p23.1, 16p11.2, and 11q13.2 were strongly associated with the co-occurrence of obesity with other common diseases. Transcriptome analysis across numerous tissues revealed strong candidate genes for obesity-related traits. Analyses in human pancreatic islets indicated the potential mechanism of inversions in the susceptibility of diabetes by disrupting the cis-regulatory effect of SNPs from their target genes. Our data underscore the role of inversions as major genetic contributors to the joint susceptibility to common complex diseases.
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Goodarzi MO, Palmer ND, Cui J, Guo X, Chen YDI, Taylor KD, Raffel LJ, Wagenknecht LE, Buchanan TA, Hsueh WA, Rotter JI. Classification of Type 2 Diabetes Genetic Variants and a Novel Genetic Risk Score Association With Insulin Clearance. J Clin Endocrinol Metab 2020; 105:dgz198. [PMID: 31714576 PMCID: PMC7059988 DOI: 10.1210/clinem/dgz198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022]
Abstract
CONTEXT Genome-wide association studies have identified more than 450 single nucleotide polymorphisms (SNPs) for type 2 diabetes (T2D). OBJECTIVE To facilitate use of these SNPs in future genetic risk score (GRS)-based analyses, we aimed to classify the SNPs based on physiology. We also sought to validate GRS associations with insulin-related traits in deeply phenotyped Mexican Americans. DESIGN, SETTING, AND PARTICIPANTS A total of 457 T2D SNPs from the literature were assigned physiologic function based on association studies and cluster analyses. All SNPs (All-GRS), beta-cell (BC-GRS), insulin resistance (IR-GRS), lipodystrophy (Lipo-GRS), and body mass index plus lipids (B + L-GRS) were evaluated for association with diabetes and indices of insulin secretion (from oral glucose tolerance test), insulin sensitivity and insulin clearance (from euglycemic clamp), and adiposity and lipid markers in 1587 Mexican Americans. RESULTS Of the 457 SNPs, 52 were classified as BC, 30 as IR, 12 as Lipo, 12 as B + L, whereas physiologic function of 351 was undefined. All-GRS was strongly associated with T2D. Among nondiabetic Mexican Americans, BC-GRS was associated with reduced insulinogenic index, IR-GRS was associated with reduced insulin sensitivity, and Lipo-GRS was associated with reduced adiposity. B + L-GRS was associated with increased insulin clearance. The latter did not replicate in an independent cohort wherein insulin clearance was assessed by a different method. CONCLUSIONS Supporting their utility, BC-GRS, IR-GRS, and Lipo-GRS, based on SNPs discovered largely in Europeans, exhibited expected associations in Mexican Americans. The novel association of B + L-GRS with insulin clearance suggests that impaired ability to reduce insulin clearance in compensation for IR may play a role in the pathogenesis of T2D. Whether this applies to other ethnic groups remains to be determined.
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Affiliation(s)
- Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, US
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, US
| | - Jinrui Cui
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, US
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California, US
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California, US
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California, US
| | - Leslie J Raffel
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California, Irvine, US
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, US
| | - Thomas A Buchanan
- Department of Physiology and Biophysics and Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, US
| | - Willa A Hsueh
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Wexner Medical Center, The Ohio State University, Columbus, US
| | - Jerome I Rotter
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, US
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Deligiannidou GE, Philippou E, Vidakovic M, Berghe WV, Heraclides A, Grdovic N, Mihailovic M, Kontogiorgis C. Natural Products Derived from the Mediterranean Diet with Antidiabetic Activity: from Insulin Mimetic Hypoglycemic to Nutriepigenetic Modulator Compounds. Curr Pharm Des 2020; 25:1760-1782. [PMID: 31298162 DOI: 10.2174/1381612825666190705191000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND The Mediterranean diet is a healthy eating pattern that protects against the development of Type 2 diabetes mellitus (T2DM), a metabolic disease characterized by elevated blood sugar levels due to pancreatic beta-cell functional impairment and insulin resistance in various tissues. Inspired by the ancient communities, this diet emphasizes eating primarily plant-based foods, including vegetables, legumes, fruits, cereals, and nuts. Importantly, virgin olive oil is used as the principal source of fat. Red meat is consumed in low amounts while wine and fish are consumed moderately. OBJECTIVE Here, we review the most beneficial components of the Mediterranean Diet and tentative mechanisms of action for prevention and/or management of T2DM, based on research conducted within the last decade. METHODS The references over the last five years have been reviewed and they have been selected properly according to inclusion/ exclusion criteria. RESULTS Several bioactive diet components were evaluated to prevent inflammation and cytokine-induced oxidative damage, reduce glucose concentration, carbohydrate absorption and increase insulin sensitivity and related gene expression. CONCLUSION The adherence to a healthy lifestyle, including diet, exercise and habits remains the best approach for the prevention of diabetes as well as frequent check-ups and education. Though diabetes has a strong genetic component, in recent years many reports strongly point to the critical role of lifestyle specific epigenetic modifications in the development of T2DM. It remains to be established how different components of the Mediterranean Diet interact and influence the epigenetic landscape to prevent or treat the disease.
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Affiliation(s)
- Georgia-Eirini Deligiannidou
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Elena Philippou
- Department of Life and Health Sciences, University of Nicosia, Makedonitissis, Nicosia 2417, Cyprus.,Diabetes and Nutritional Sciences Division, King's College London, London, United Kingdom
| | - Melita Vidakovic
- Department of Molecular Biology, Institute for Biological Research, University of Belgrade, Bulevar despota Stefana 142, 11000 Belgrade, Serbia
| | - Wim V Berghe
- Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Wilrijk, Belgium
| | - Alexandros Heraclides
- Department of Primary Care and Population Health, University of Nicosia Medical School, Ayiou Nikolaou Street, Egkomi, Cyprus
| | - Nevena Grdovic
- Department of Molecular Biology, Institute for Biological Research, University of Belgrade, Bulevar despota Stefana 142, 11000 Belgrade, Serbia
| | - Mirjana Mihailovic
- Department of Molecular Biology, Institute for Biological Research, University of Belgrade, Bulevar despota Stefana 142, 11000 Belgrade, Serbia
| | - Christos Kontogiorgis
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, 68100, Greece
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Li-Gao R, Carlotti F, de Mutsert R, van Hylckama Vlieg A, de Koning EJP, Jukema JW, Rosendaal FR, Willems van Dijk K, Mook-Kanamori DO. Genome-Wide Association Study on the Early-Phase Insulin Response to a Liquid Mixed Meal: Results From the NEO Study. Diabetes 2019; 68:2327-2336. [PMID: 31537524 DOI: 10.2337/db19-0378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/09/2019] [Indexed: 11/13/2022]
Abstract
Early-phase insulin secretion is a determinant of postprandial glucose homeostasis. In this study, we aimed to identify novel genetic variants associated with the early-phase insulin response to a liquid mixed meal by a genome-wide association study using a discovery and replication design embedded in the Netherlands Epidemiology of Obesity (NEO) study. The early-phase insulin response was defined as the difference between the natural logarithm-transformed insulin concentrations of the postprandial state at 30 min after a meal challenge and the fasting state (Δinsulin). After Bonferroni correction, rs505922 (β: -6.5% [minor allele frequency (MAF) 0.32, P = 3.3 × 10-8]) located in the ABO gene reached genome-wide significant level (P < 5 × 10-8) and was also replicated successfully (β: -7.8% [MAF 0.32, P = 7.2 × 10-5]). The function of the ABO gene was assessed using in vitro shRNA-mediated knockdown of gene expression in the murine pancreatic β-cell line MIN6. Knocking down the ABO gene led to decreased insulin secretion in the murine pancreatic β-cell line. These data indicate that the previously identified elevated risk of type 2 diabetes for carriers of the ABO rs505922:C allele may be caused by decreased early-phase insulin secretion.
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Affiliation(s)
- Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Françoise Carlotti
- Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Eelco J P de Koning
- Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
- University Medical Center Utrecht, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, the Netherlands
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - J Wouter Jukema
- Einthoven Laboratory for Experimental Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ko Willems van Dijk
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
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Abstract
PURPOSE OF REVIEW Common genetic variants that associate with type 2 diabetes risk are markedly enriched in pancreatic islet transcriptional enhancers. This review discusses current advances in the annotation of islet enhancer variants and their target genes. RECENT FINDINGS Recent methodological advances now allow genetic and functional mapping of diabetes causal variants at unprecedented resolution. Mapping of enhancer-promoter interactions in human islets has provided a unique appreciation of the complexity of islet gene regulatory processes and enabled direct association of noncoding diabetes risk variants to their target genes. The recently improved human islet enhancer annotations constitute a framework for the interpretation of diabetes genetic signals in the context of pancreatic islet gene regulation. In the future, integration of existing and yet to come regulatory maps with genetic fine-mapping efforts and in-depth functional characterization will foster the discovery of novel diabetes molecular risk mechanisms.
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Affiliation(s)
- Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, ICTEM 5th floor, Du Cane Road, London, W12 0NN, UK.
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