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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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Hu M, Kim I, Morán I, Peng W, Sun O, Bonnefond A, Khamis A, Bonas-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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548906. [PMID: 37502937 PMCID: PMC10369998 DOI: 10.1101/2023.07.13.548906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
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, combined allele-specific expression (cASE) analysis in human islets revealed multiple variants that influence SLC30A8 expression. Epigenomic mapping 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 neighbouring genes. Deletions of variant-bearing enhancer regions using CRISPR-Cas9 in human-derived EndoC-βH3 cells lowered the expression of SLC30A8 and several neighbouring genes, and improved insulin secretion. Whilst down-regulation 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
| | - Silvia Bonas-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 MN, Huang R, Zheng T, Dong Y, Wang WJ, Xu YJ, Mehra V, Zhou GD, Liu X, He H, Fang F, Li F, Fan JG, Zhang J, Ouyang F, Briollais L, Li J, Luo ZC. Genome-wide placental DNA methylations in fetal overgrowth and associations with leptin, adiponectin and fetal growth factors. Clin Epigenetics 2022; 14:192. [PMID: 36585686 PMCID: PMC9801645 DOI: 10.1186/s13148-022-01412-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 12/15/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Fetal overgrowth "programs" an elevated risk of type 2 diabetes in adulthood. Epigenetic alterations may be a mechanism in programming the vulnerability. We sought to characterize genome-wide alterations in placental gene methylations in fetal overgrowth and the associations with metabolic health biomarkers including leptin, adiponectin and fetal growth factors. RESULTS Comparing genome-wide placental gene DNA methylations in large-for-gestational-age (LGA, an indicator of fetal overgrowth, n = 30) versus optimal-for-gestational-age (OGA, control, n = 30) infants using the Illumina Infinium Human Methylation-EPIC BeadChip, we identified 543 differential methylation positions (DMPs; 397 hypermethylated, 146 hypomethylated) at false discovery rate < 5% and absolute methylation difference > 0.05 after adjusting for placental cell-type heterogeneity, maternal age, pre-pregnancy BMI and HbA1c levels during pregnancy. Twenty-five DMPs annotated to 20 genes (QSOX1, FCHSD2, LOC101928162, ADGRB3, GCNT1, TAP1, MYO16, NAV1, ATP8A2, LBXCOR1, EN2, INCA1, CAMTA2, SORCS2, SLC4A4, RPA3, UMAD1,USP53, OR2L13 and NR3C2) could explain 80% of the birth weight variations. Pathway analyses did not detect any statistically significant pathways after correcting for multiple tests. We validated a newly discovered differentially (hyper-)methylated gene-visual system homeobox 1 (VSX1) in an independent pyrosequencing study sample (LGA 47, OGA 47). Our data confirmed a hypermethylated gene-cadherin 13 (CDH13) reported in a previous epigenome-wide association study. Adiponectin in cord blood was correlated with its gene methylation in the placenta, while leptin and fetal growth factors (insulin, IGF-1, IGF-2) were not. CONCLUSIONS Fetal overgrowth may be associated with a large number of altered placental gene methylations. Placental VSX1 and CDH13 genes are hypermethylated in fetal overgrowth. Placental ADIPOQ gene methylations and fetal circulating adiponectin levels were correlated, suggesting the contribution of placenta-originated adiponectin to cord blood adiponectin.
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Affiliation(s)
- Meng-Nan Yang
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China ,grid.17063.330000 0001 2157 2938Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, L5-240, Murray Street 60, Toronto, ON M5G 1X5 Canada
| | - Rong Huang
- grid.17063.330000 0001 2157 2938Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, L5-240, Murray Street 60, Toronto, ON M5G 1X5 Canada
| | - Tao Zheng
- grid.16821.3c0000 0004 0368 8293Department of Obstetrics and Gynecology, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Yu Dong
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Wen-Juan Wang
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Ya-Jie Xu
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Vrati Mehra
- grid.17063.330000 0001 2157 2938Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, L5-240, Murray Street 60, Toronto, ON M5G 1X5 Canada
| | - Guang-Di Zhou
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Xin Liu
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Hua He
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Fang Fang
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Fei Li
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Jian-Gao Fan
- grid.16821.3c0000 0004 0368 8293Center for Fatty Liver, Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Jun Zhang
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Fengxiu Ouyang
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China
| | - Laurent Briollais
- grid.17063.330000 0001 2157 2938Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, L5-240, Murray Street 60, Toronto, ON M5G 1X5 Canada
| | - Jiong Li
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine-Department of Clinical Epidemiology, Aarhus University, Olof Palmes Allé 43-45, 8200 Aathus, Denmark
| | - Zhong-Cheng Luo
- grid.16821.3c0000 0004 0368 8293Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200092 China ,grid.17063.330000 0001 2157 2938Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, L5-240, Murray Street 60, Toronto, ON M5G 1X5 Canada
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Bartolomé A. Stem Cell-Derived β Cells: A Versatile Research Platform to Interrogate the Genetic Basis of β Cell Dysfunction. Int J Mol Sci 2022; 23:501. [PMID: 35008927 PMCID: PMC8745644 DOI: 10.3390/ijms23010501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic β cell dysfunction is a central component of diabetes progression. During the last decades, the genetic basis of several monogenic forms of diabetes has been recognized. Genome-wide association studies (GWAS) have also facilitated the identification of common genetic variants associated with an increased risk of diabetes. These studies highlight the importance of impaired β cell function in all forms of diabetes. However, how most of these risk variants confer disease risk, remains unanswered. Understanding the specific contribution of genetic variants and the precise role of their molecular effectors is the next step toward developing treatments that target β cell dysfunction in the era of personalized medicine. Protocols that allow derivation of β cells from pluripotent stem cells, represent a powerful research tool that allows modeling of human development and versatile experimental designs that can be used to shed some light on diabetes pathophysiology. This article reviews different models to study the genetic basis of β cell dysfunction, focusing on the recent advances made possible by stem cell applications in the field of diabetes research.
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Affiliation(s)
- Alberto Bartolomé
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
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Claussnitzer M, Susztak K. Gaining insight into metabolic diseases from human genetic discoveries. Trends Genet 2021; 37:1081-1094. [PMID: 34315631 PMCID: PMC8578350 DOI: 10.1016/j.tig.2021.07.005] [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] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022]
Abstract
Human large-scale genetic association studies have identified sequence variations at thousands of genetic risk loci that are more common in patients with diverse metabolic disease compared with healthy controls. While these genetic associations have been replicated in multiple large cohorts and sometimes can explain up to 50% of heritability, the molecular and cellular mechanisms affected by common genetic variation associated with metabolic disease remains mostly unknown. A variety of new genome-wide data types, in conjunction with novel biostatistical and computational analytical methodologies and foundational experimental technologies, are paving the way for a principled approach to systematic variant-to-function (V2F) studies for metabolic diseases, turning associated regions into causal variants, cell types and states of action, effector genes, and cellular and physiological mechanisms. Identification of new target genes and cellular programs for metabolic risk loci will improve mechanistic understanding of disease biology and identification of novel therapeutic strategies.
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Affiliation(s)
- Melina Claussnitzer
- Beth Israel Deaconess Medical Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Katalin Susztak
- Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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