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Grenko CM, Taylor HJ, Bonnycastle LL, Xue D, Lee BN, Weiss Z, Yan T, Swift AJ, Mansell EC, Lee A, Robertson CC, Narisu N, Erdos MR, Chen S, Collins FS, Taylor DL. Single-cell transcriptomic profiling of human pancreatic islets reveals genes responsive to glucose exposure over 24 h. Diabetologia 2024; 67:2246-2259. [PMID: 38967666 PMCID: PMC11447040 DOI: 10.1007/s00125-024-06214-4] [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: 03/04/2024] [Accepted: 05/08/2024] [Indexed: 07/06/2024]
Abstract
AIMS/HYPOTHESIS Disruption of pancreatic islet function and glucose homeostasis can lead to the development of sustained hyperglycaemia, beta cell glucotoxicity and subsequently type 2 diabetes. In this study, we explored the effects of in vitro hyperglycaemic conditions on human pancreatic islet gene expression across 24 h in six pancreatic cell types: alpha; beta; gamma; delta; ductal; and acinar. We hypothesised that genes associated with hyperglycaemic conditions may be relevant to the onset and progression of diabetes. METHODS We exposed human pancreatic islets from two donors to low (2.8 mmol/l) and high (15.0 mmol/l) glucose concentrations over 24 h in vitro. To assess the transcriptome, we performed single-cell RNA-seq (scRNA-seq) at seven time points. We modelled time as both a discrete and continuous variable to determine momentary and longitudinal changes in transcription associated with islet time in culture or glucose exposure. Additionally, we integrated genomic features and genetic summary statistics to nominate candidate effector genes. For three of these genes, we functionally characterised the effect on insulin production and secretion using CRISPR interference to knock down gene expression in EndoC-βH1 cells, followed by a glucose-stimulated insulin secretion assay. RESULTS In the discrete time models, we identified 1344 genes associated with time and 668 genes associated with glucose exposure across all cell types and time points. In the continuous time models, we identified 1311 genes associated with time, 345 genes associated with glucose exposure and 418 genes associated with interaction effects between time and glucose across all cell types. By integrating these expression profiles with summary statistics from genetic association studies, we identified 2449 candidate effector genes for type 2 diabetes, HbA1c, random blood glucose and fasting blood glucose. Of these candidate effector genes, we showed that three (ERO1B, HNRNPA2B1 and RHOBTB3) exhibited an effect on glucose-stimulated insulin production and secretion in EndoC-βH1 cells. CONCLUSIONS/INTERPRETATION The findings of our study provide an in-depth characterisation of the 24 h transcriptomic response of human pancreatic islets to glucose exposure at a single-cell resolution. By integrating differentially expressed genes with genetic signals for type 2 diabetes and glucose-related traits, we provide insights into the molecular mechanisms underlying glucose homeostasis. Finally, we provide functional evidence to support the role of three candidate effector genes in insulin secretion and production. DATA AVAILABILITY The scRNA-seq data from the 24 h glucose exposure experiment performed in this study are available in the database of Genotypes and Phenotypes (dbGap; https://www.ncbi.nlm.nih.gov/gap/ ) with accession no. phs001188.v3.p1. Study metadata and summary statistics for the differential expression, gene set enrichment and candidate effector gene prediction analyses are available in the Zenodo data repository ( https://zenodo.org/ ) under accession number 11123248. The code used in this study is publicly available at https://github.com/CollinsLabBioComp/publication-islet_glucose_timecourse .
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Affiliation(s)
- Caleb M Grenko
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
| | - Henry J Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Brian N Lee
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zoe Weiss
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tingfen Yan
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy J Swift
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erin C Mansell
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angela Lee
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine C Robertson
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael R Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - D Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Gupta D, Burstein AW, Schwalbe DC, Shankar K, Varshney S, Singh O, Paul S, Ogden SB, Osborne-Lawrence S, Metzger NP, Richard CP, Campbell JN, Zigman JM. Ghrelin deletion and conditional ghrelin cell ablation increase pancreatic islet size in mice. J Clin Invest 2023; 133:e169349. [PMID: 38099492 PMCID: PMC10721155 DOI: 10.1172/jci169349] [Citation(s) in RCA: 1] [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: 02/02/2023] [Accepted: 10/05/2023] [Indexed: 12/18/2023] Open
Abstract
Ghrelin exerts key effects on islet hormone secretion to regulate blood glucose levels. Here, we sought to determine whether ghrelin's effects on islets extend to the alteration of islet size and β cell mass. We demonstrate that reducing ghrelin - by ghrelin gene knockout (GKO), conditional ghrelin cell ablation, or high-fat diet (HFD) feeding - was associated with increased mean islet size (up to 62%), percentage of large islets (up to 854%), and β cell cross-sectional area (up to 51%). In GKO mice, these effects were more apparent in 10- to 12-week-old mice than in 4-week-old mice. Higher β cell numbers from decreased β cell apoptosis drove the increase in β cell cross-sectional area. Conditional ghrelin cell ablation in adult mice increased the β cell number per islet by 40% within 4 weeks. A negative correlation between islet size and plasma ghrelin in HFD-fed plus chow-fed WT mice, together with even larger islet sizes in HFD-fed GKO mice than in HFD-fed WT mice, suggests that reduced ghrelin was not solely responsible for diet-induced obesity-associated islet enlargement. Single-cell transcriptomics revealed changes in gene expression in several GKO islet cell types, including upregulation of Manf, Dnajc3, and Gnas expression in β cells, which supports decreased β cell apoptosis and/or increased β cell proliferation. These effects of ghrelin reduction on islet morphology might prove useful when designing new therapies for diabetes.
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Affiliation(s)
- Deepali Gupta
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Avi W. Burstein
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Dana C. Schwalbe
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Kripa Shankar
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Salil Varshney
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Omprakash Singh
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Subhojit Paul
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sean B. Ogden
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sherri Osborne-Lawrence
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Nathan P. Metzger
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Corine P. Richard
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - John N. Campbell
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey M. Zigman
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
- Division of Endocrinology and Metabolism, Department of Internal Medicine and
- Department of Psychiatry, UT Southwestern Medical Center, Dallas, Texas, USA
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Xue D, Narisu N, Taylor DL, Zhang M, Grenko C, Taylor HJ, Yan T, Tang X, Sinha N, Zhu J, Vandana JJ, Chong ACN, Lee A, Mansell EC, Swift AJ, Erdos MR, Zhou T, Bonnycastle LL, Zhong A, Chen S, Collins FS. Functional interrogation of twenty type 2 diabetes-associated genes using isogenic hESC-derived β-like cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539774. [PMID: 37214922 PMCID: PMC10197532 DOI: 10.1101/2023.05.07.539774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined β-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-β cells from each knockout line. Analyses of T2D GWAS signals overlapping with HNF4A-dependent ATAC peaks identified a specific SNP as a likely causal variant. In addition, we performed integrative association analyses and identified four genes ( CP, RNASE1, PCSK1N and GSTA2 ) associated with insulin production, and two genes ( TAGLN3 and DHRS2 ) associated with sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental hESC line, to identify a single likely functional variant at each of 23 T2D GWAS signals.
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Kang RB, Li Y, Rosselot C, Zhang T, Siddiq M, Rajbhandari P, Stewart AF, Scott DK, Garcia-Ocana A, Lu G. Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles. Genome Med 2023; 15:30. [PMID: 37127706 PMCID: PMC10150516 DOI: 10.1186/s13073-023-01179-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) provides valuable insights into human islet cell types and their corresponding stable gene expression profiles. However, this approach requires cell dissociation that complicates its utility in vivo. On the other hand, single-nucleus RNA sequencing (snRNA-seq) has compatibility with frozen samples, elimination of dissociation-induced transcriptional stress responses, and affords enhanced information from intronic sequences that can be leveraged to identify pre-mRNA transcripts. METHODS We obtained nuclear preparations from fresh human islet cells and generated snRNA-seq datasets. We compared these datasets to scRNA-seq output obtained from human islet cells from the same donor. We employed snRNA-seq to obtain the transcriptomic profile of human islets engrafted in immunodeficient mice. In both analyses, we included the intronic reads in the snRNA-seq data with the GRCh38-2020-A library. RESULTS First, snRNA-seq analysis shows that the top four differentially and selectively expressed genes in human islet endocrine cells in vitro and in vivo are not the canonical genes but a new set of non-canonical gene markers including ZNF385D, TRPM3, LRFN2, PLUT (β-cells); PTPRT, FAP, PDK4, LOXL4 (α-cells); LRFN5, ADARB2, ERBB4, KCNT2 (δ-cells); and CACNA2D3, THSD7A, CNTNAP5, RBFOX3 (γ-cells). Second, by integrating information from scRNA-seq and snRNA-seq of human islet cells, we distinguish three β-cell sub-clusters: an INS pre-mRNA cluster (β3), an intermediate INS mRNA cluster (β2), and an INS mRNA-rich cluster (β1). These display distinct gene expression patterns representing different biological dynamic states both in vitro and in vivo. Interestingly, the INS mRNA-rich cluster (β1) becomes the predominant sub-cluster in vivo. CONCLUSIONS In summary, snRNA-seq and pre-mRNA analysis of human islet cells can accurately identify human islet cell populations, subpopulations, and their dynamic transcriptome profile in vivo.
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Affiliation(s)
- Randy B Kang
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Yansui Li
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carolina Rosselot
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Mustafa Siddiq
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Rajbhandari
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew F Stewart
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donald K Scott
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adolfo Garcia-Ocana
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Present address: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Geming Lu
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Present address: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Overview of Transcriptomic Research on Type 2 Diabetes: Challenges and Perspectives. Genes (Basel) 2022; 13:genes13071176. [PMID: 35885959 PMCID: PMC9319211 DOI: 10.3390/genes13071176] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Type 2 diabetes (T2D) is a common chronic disease whose etiology is known to have a strong genetic component. Standard genetic approaches, although allowing for the detection of a number of gene variants associated with the disease as well as differentially expressed genes, cannot fully explain the hereditary factor in T2D. The explosive growth in the genomic sequencing technologies over the last decades provided an exceptional impetus for transcriptomic studies and new approaches to gene expression measurement, such as RNA-sequencing (RNA-seq) and single-cell technologies. The transcriptomic analysis has the potential to find new biomarkers to identify risk groups for developing T2D and its microvascular and macrovascular complications, which will significantly affect the strategies for early diagnosis, treatment, and preventing the development of complications. In this article, we focused on transcriptomic studies conducted using expression arrays, RNA-seq, and single-cell sequencing to highlight recent findings related to T2D and challenges associated with transcriptome experiments.
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Uniken Venema WTC, Ramírez-Sánchez AD, Bigaeva E, Withoff S, Jonkers I, McIntyre RE, Ghouraba M, Raine T, Weersma RK, Franke L, Festen EAM, van der Wijst MGP. Gut mucosa dissociation protocols influence cell type proportions and single-cell gene expression levels. Sci Rep 2022; 12:9897. [PMID: 35701452 PMCID: PMC9197976 DOI: 10.1038/s41598-022-13812-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/27/2022] [Indexed: 01/15/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of the cellular landscape of organs. Most single-cell protocols require fresh material, which limits sample size per experiment, and consequently, introduces batch effects. This is especially true for samples acquired through complex medical procedures, such as intestinal mucosal biopsies. Moreover, the tissue dissociation procedure required for obtaining single cells is a major source of noise; different dissociation procedures applied to different compartments of the tissue induce artificial gene expression differences between cell subsets. To overcome these challenges, we have developed a one-step dissociation protocol and demonstrated its use on cryopreserved gut mucosal biopsies. Using flow cytometry and scRNA-seq analysis, we compared this one-step dissociation protocol with the current gold standard, two-step collagenase digestion, and an adaptation of a recently published alternative, three-step cold-active Bacillus licheniformus protease digestion. Both cell viability and cell type composition were comparable between the one-step and two-step collagenase dissociation, with the former being more time-efficient. The cold protease digestion resulted in equal cell viability, but better preserves the epithelial cell types. Consequently, to analyze the rarer cell types, such as glial cells, larger total biopsy cell numbers are required as input material. The multi-step protocols affected cell types spanning multiple compartments differently. In summary, we show that cryopreserved gut mucosal biopsies can be used to overcome the logistical challenges and batch effects in large scRNA-seq studies. Furthermore, we demonstrate that using cryopreserved biopsies digested using a one-step collagenase protocol enables large-scale scRNA-seq, FACS, organoid generation and intraepithelial lymphocyte expansion.
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Affiliation(s)
- Werna T C Uniken Venema
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emilia Bigaeva
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Tim Raine
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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7
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Malhi NK, Luo Y, Tang X, Sriram K, Calandrelli R, Zhong S, Chen ZB. Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level. J Vis Exp 2022:10.3791/63307. [PMID: 35343966 PMCID: PMC9180814 DOI: 10.3791/63307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023] Open
Abstract
Endothelial cells (ECs) are crucial for vascular and whole-body function through their dynamic response to environmental cues. Elucidating the transcriptome and epigenome of ECs is paramount to understanding their roles in development, health, and disease, but is limited in the availability of isolated primary cells. Recent technologies have enabled the high-throughput profiling of EC transcriptome and epigenome, leading to the identification of previously unknown EC cell subpopulations and developmental trajectories. While EC cultures are a useful tool in the exploration of EC function and dysfunction, the culture conditions and multiple passages can introduce external variables that alter the properties of native EC, including morphology, epigenetic state, and gene expression program. To overcome this limitation, the present paper demonstrates a method of isolating human primary ECs from donor mesenteric arteries aiming to capture their native state. ECs in the intimal layer are dissociated mechanically and biochemically with the use of particular enzymes. The resultant cells can be directly used for bulk RNA or single-cell RNA-sequencing or plated for culture. In addition, a workflow is described for the preparation of human arterial tissue for spatial transcriptomics, specifically for a commercially available platform, although this method is also suitable for other spatial transcriptome profiling techniques. This methodology can be applied to different vessels collected from a variety of donors in health or disease states to gain insights into EC transcriptional and epigenetic regulation, a pivotal aspect of endothelial cell biology.
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Affiliation(s)
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, City of Hope
| | - Xiaofang Tang
- Department of Diabetes Complications and Metabolism, City of Hope
| | - Kiran Sriram
- Department of Diabetes Complications and Metabolism, City of Hope; Irell and Manella Graduate School of Biological Sciences, City of Hope
| | | | - Sheng Zhong
- Department of Bioengineering, University of California San Diego
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, City of Hope; Irell and Manella Graduate School of Biological Sciences, City of Hope;
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8
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Basile G, Kahraman S, Dirice E, Pan H, Dreyfuss JM, Kulkarni RN. Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets. Genome Med 2021; 13:128. [PMID: 34376240 PMCID: PMC8356387 DOI: 10.1186/s13073-021-00941-8] [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: 07/17/2020] [Accepted: 07/13/2021] [Indexed: 01/09/2023] Open
Abstract
Background Human pancreatic islets are a central focus of research in metabolic studies. Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing (scRNA-seq). We introduce single-nucleus RNA-sequencing (snRNA-seq) as an alternative approach for investigating transplanted human islets. Methods The Nuclei EZ protocol was used to obtain nuclear preparations from fresh and frozen human islet cells. Such preparations were first used to generate snRNA-seq datasets and compared to scRNA-seq output obtained from cells from the same donor. Finally, we employed snRNA-seq to obtain the transcriptomic profile of archived human islets engrafted in immunodeficient animals. Results We observed virtually complete concordance in identifying cell types and gene proportions as well as a strong association of global and islet cell type gene signatures between scRNA-seq and snRNA-seq applied to fresh and frozen cultured or transplanted human islet samples. Conclusions We propose snRNA-seq as a reliable strategy to probe transcriptomic profiles of freshly harvested or frozen sources of transplanted human islet cells especially when scRNA-seq is not ideal. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00941-8.
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Affiliation(s)
- Giorgio Basile
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Sevim Kahraman
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Ercument Dirice
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA.,Current Address: Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY, 10595, USA
| | - Hui Pan
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center and Harvard Medical School, Boston, MA, USA
| | - Jonathan M Dreyfuss
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center and Harvard Medical School, Boston, MA, USA
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA. .,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.
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9
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Rocque B, Barbetta A, Singh P, Goldbeck C, Helou DG, Loh YHE, Ung N, Lee J, Akbari O, Emamaullee J. Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis. Front Immunol 2021; 12:679521. [PMID: 34335581 PMCID: PMC8322955 DOI: 10.3389/fimmu.2021.679521] [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: 03/12/2021] [Accepted: 06/28/2021] [Indexed: 01/16/2023] Open
Abstract
The liver is unique in both its ability to maintain immune homeostasis and in its potential for immune tolerance following solid organ transplantation. Single-cell RNA sequencing (scRNA seq) is a powerful approach to generate highly dimensional transcriptome data to understand cellular phenotypes. However, when scRNA data is produced by different groups, with different data models, different standards, and samples processed in different ways, it can be challenging to draw meaningful conclusions from the aggregated data. The goal of this study was to establish a method to combine ‘human liver’ scRNA seq datasets by 1) characterizing the heterogeneity between studies and 2) using the meta-atlas to define the dominant phenotypes across immune cell subpopulations in healthy human liver. Publicly available scRNA seq data generated from liver samples obtained from a combined total of 17 patients and ~32,000 cells were analyzed. Liver-specific immune cells (CD45+) were extracted from each dataset, and immune cell subpopulations (myeloid cells, NK and T cells, plasma cells, and B cells) were examined using dimensionality reduction (UMAP), differential gene expression, and ingenuity pathway analysis. All datasets co-clustered, but cell proportions differed between studies. Gene expression correlation demonstrated similarity across all studies, and canonical pathways that differed between datasets were related to cell stress and oxidative phosphorylation rather than immune-related function. Next, a meta-atlas was generated via data integration and compared against PBMC data to define gene signatures for each hepatic immune subpopulation. This analysis defined key features of hepatic immune homeostasis, with decreased expression across immunologic pathways and enhancement of pathways involved with cell death. This method for meta-analysis of scRNA seq data provides a novel approach to broadly define the features of human liver immune homeostasis. Specific pathways and cellular phenotypes described in this human liver immune meta-atlas provide a critical reference point for further study of immune mediated disease processes within the liver.
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Affiliation(s)
- Brittany Rocque
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Arianna Barbetta
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Pranay Singh
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Cameron Goldbeck
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Doumet Georges Helou
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Yong-Hwee Eddie Loh
- Norris Medical Library, University of Southern California, Los Angeles, CA, United States
| | - Nolan Ung
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jerry Lee
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Chemical Engineering and Materials Sciences, University of Southern California, Los Angeles, CA, United States
| | - Omid Akbari
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Juliet Emamaullee
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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10
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Domínguez-Bendala J, Qadir MMF, Pastori RL. Temporal single-cell regeneration studies: the greatest thing since sliced pancreas? Trends Endocrinol Metab 2021; 32:433-443. [PMID: 34006411 PMCID: PMC8239162 DOI: 10.1016/j.tem.2021.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/12/2021] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
The application of single-cell analytic techniques to the study of stem/progenitor cell niches supports the emerging view that pancreatic cell lineages are in a state of flux between differentiation stages. For all their value, however, such analyses merely offer a snapshot of the cellular palette of the tissue at any given time point. Conclusions about potential developmental/regeneration paths are solely based on bioinformatics inferences. In this context, the advent of new techniques for the long-term culture and lineage tracing of human pancreatic slices offers a virtual window into the native organ and presents the field with a unique opportunity to serially resolve pancreatic regeneration dynamics at the single-cell level.
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Affiliation(s)
- Juan Domínguez-Bendala
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ricardo Luis Pastori
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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11
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Ng NHJ, Neo CWY, Ding SSL, Teo AKK. Insights from single cell studies of human pancreatic islets and stem cell-derived islet cells to guide functional beta cell maturation in vitro. VITAMINS AND HORMONES 2021; 116:193-233. [PMID: 33752818 DOI: 10.1016/bs.vh.2021.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
There is now a sizeable number of single cell transcriptomics studies performed on human and rodent pancreatic islets that have shed light on the unique gene signatures and level of heterogeneity within each individual islet cell type. Following closely from these studies, there is also rapidly-growing activity on characterizing islet-like cells derived from in vitro differentiation of human pluripotent stem cells (hPSCs) at the single cell level. The overall consensus across the studies so far suggests that the first few stages of differentiation are largely uniform, whereas during pancreatic endocrine commitment, cell trajectories start to diverge, resulting in multiple end-stage pancreatic cells that include progenitor-like, endocrine and non-endocrine cells. Comprehensive transcriptional profiling is important for understanding how and why islet cells, especially the insulin-secreting beta cells, exist in subpopulations that differ in maturity, proliferation rate, sensitivity to stress, and insulin secretion function. For hPSC-derived beta cells to be used confidently for cell therapy, optimal differentiation and thorough characterization is required. The key questions to address are-What is the trajectory of differentiation? Is heterogeneity a natural occurrence or is it a consequence of imperfect differentiation protocols? Can lessons be drawn from the extensive single cell transcriptomic data to help guide maturation of beta cells in vitro? This book chapter seeks to address some of these questions, and facilitate ongoing efforts in improving the beta cell differentiation pipeline or enriching for desired beta cell populations following differentiation, to make way for better mechanistic studies and future clinical translation.
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Affiliation(s)
- Natasha Hui Jin Ng
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, Singapore, Singapore
| | - Claire Wen Ying Neo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shirley Suet Lee Ding
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, Singapore, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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12
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Teitelman G. Human Islets Contain a Beta Cell Type That Expresses Proinsulin But Not the Enzyme That Converts the Precursor to Insulin. J Histochem Cytochem 2021; 68:691-702. [PMID: 32998631 DOI: 10.1369/0022155420961361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In pancreatic beta cells, proinsulin (ProIN) undergoes folding in endoplasmic reticulum/Golgi system and is translocated to secretory vesicles for processing into insulin and C-peptide by the proprotein convertases (PC)1/3 and PC2, and carboxypeptidase E. Human beta cells show significant variation in the level of expression of PC1/3, the critical proconvertase involved in proinsulin processing. To ascertain whether this heterogeneity is correlated with the level of expression of the prohormone and mature hormone, the expression of proinsulin, insulin, and PC1/3 in human beta cells was examined. This analysis identified a human beta cell type that expressed proinsulin but lacked PC1/3 (ProIN+PC1/3-). This beta cell type is absent in rodent islets and is abundant in human islets of adults but scarce in islets from postnatal donors. Human islets also contained a beta cell type that expressed both proinsulin and variable levels of PC1/3 (ProIN+PC1/3+) and a less abundant cell type that lacked proinsulin but expressed the convertase (ProIN-PC1/3+). These cell phenotypes were altered by type 2 diabetes. These data suggest that these three cell types represent different stages of a dynamic process with proinsulin folding in ProIN+PC1/3- cells, proinsulin conversion into insulin in ProIN+PC1/3+cells, and replenishment of the proinsulin content in ProIN-PC1/3+ cells.
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Affiliation(s)
- Gladys Teitelman
- Department of Cell Biology, SUNY Downstate Health Science University, Brooklyn, New York
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13
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Viñuela A, Varshney A, van de Bunt M, Prasad RB, Asplund O, Bennett A, Boehnke M, Brown AA, Erdos MR, Fadista J, Hansson O, Hatem G, Howald C, Iyengar AK, Johnson P, Krus U, MacDonald PE, Mahajan A, Manning Fox JE, Narisu N, Nylander V, Orchard P, Oskolkov N, Panousis NI, Payne A, Stitzel ML, Vadlamudi S, Welch R, Collins FS, Mohlke KL, Gloyn AL, Scott LJ, Dermitzakis ET, Groop L, Parker SCJ, McCarthy MI. Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. Nat Commun 2020; 11:4912. [PMID: 32999275 PMCID: PMC7528108 DOI: 10.1038/s41467-020-18581-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/12/2020] [Indexed: 02/08/2023] Open
Abstract
Most signals detected by genome-wide association studies map to non-coding sequence and their tissue-specific effects influence transcriptional regulation. However, key tissues and cell-types required for functional inference are absent from large-scale resources. Here we explore the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using data from 420 donors. We find: (a) 7741 cis-eQTLs in islets with a replication rate across 44 GTEx tissues between 40% and 73%; (b) marked overlap between islet cis-eQTL signals and active regulatory sequences in islets, with reduced eQTL effect size observed in the stretch enhancers most strongly implicated in GWAS signal location; (c) enrichment of islet cis-eQTL signals with T2D risk variants identified in genome-wide association studies; and (d) colocalization between 47 islet cis-eQTLs and variants influencing T2D or glycemic traits, including DGKB and TCF7L2. Our findings illustrate the advantages of performing functional and regulatory studies in disease relevant tissues.
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Affiliation(s)
- Ana Viñuela
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland ,grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE1 4EP Newcastle, UK
| | - Arushi Varshney
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Martijn van de Bunt
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK ,grid.410556.30000 0001 0440 1440Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE UK
| | - Rashmi B. Prasad
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Olof Asplund
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Amanda Bennett
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK
| | - Michael Boehnke
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Andrew A. Brown
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland ,grid.8241.f0000 0004 0397 2876Population Health and Genomics, University of Dundee, Dundee, Scotland, DD1 9SY UK
| | - Michael R. Erdos
- grid.280128.10000 0001 2233 9230Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - João Fadista
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden ,grid.6203.70000 0004 0417 4147Department of Epidemiology Research, Statens Serum Institut, Copenhagen, DK 2300 Denmark ,grid.7737.40000 0004 0410 2071Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Ola Hansson
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden ,grid.7737.40000 0004 0410 2071Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Gad Hatem
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Cédric Howald
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Apoorva K. Iyengar
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Paul Johnson
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK
| | - Ulrika Krus
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Patrick E. MacDonald
- grid.17089.37Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta Canada
| | - Anubha Mahajan
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.418158.10000 0004 0534 4718Present Address: Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Jocelyn E. Manning Fox
- grid.17089.37Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta Canada
| | - Narisu Narisu
- grid.280128.10000 0001 2233 9230Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vibe Nylander
- grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK
| | - Peter Orchard
- grid.214458.e0000000086837370Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Nikolay Oskolkov
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Nikolaos I. Panousis
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Anthony Payne
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK
| | - Michael L. Stitzel
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA ,grid.63054.340000 0001 0860 4915Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032 USA
| | - Swarooparani Vadlamudi
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Ryan Welch
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Francis S. Collins
- grid.280128.10000 0001 2233 9230Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Karen L. Mohlke
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Anna L. Gloyn
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK ,grid.410556.30000 0001 0440 1440Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE UK ,grid.168010.e0000000419368956Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA USA
| | - Laura J. Scott
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Emmanouil T. Dermitzakis
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Leif Groop
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden ,grid.7737.40000 0004 0410 2071Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Stephen C. J. Parker
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Mark I. McCarthy
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK ,grid.410556.30000 0001 0440 1440Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE UK ,grid.418158.10000 0004 0534 4718Present Address: Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
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