101
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Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals. Nat Commun 2021; 12:3117. [PMID: 34035261 PMCID: PMC8149454 DOI: 10.1038/s41467-021-23216-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Hox and ParaHox genes encode transcription factors with similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. Here, we report evidence indicating that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is a likely direct target of Pdx in Pacific oyster adults. We show that one insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue. Transcriptomic comparison suggests that this tissue plays a similar role to the vertebrate pancreas. Using ATAC-seq and ChIP, we identify an upstream regulatory element of the cgILP gene which shows binding interaction with cgPdx protein in oyster hepatopancreas and demonstrate, using a cell culture assay, that the oyster Pdx can act as a transcriptional activator through this site, possibly in synergy with NeuroD. These data argue that a classic homeodomain-target gene interaction dates back to the origin of Bilateria. In vertebrates insulin is a direct transcriptional target of Pdx: the same is true in Pacific oysters and the authors show insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue, showing this gene interaction dates back to the origin of Bilateria.
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102
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Aylward A, Okino ML, Benaglio P, Chiou J, Beebe E, Padilla JA, Diep S, Gaulton KJ. Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes. PLoS Genet 2021; 17:e1009531. [PMID: 33983929 PMCID: PMC8183998 DOI: 10.1371/journal.pgen.1009531] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/07/2021] [Accepted: 04/06/2021] [Indexed: 02/08/2023] Open
Abstract
Glucocorticoids are key regulators of glucose homeostasis and pancreatic islet function, but the gene regulatory programs driving responses to glucocorticoid signaling in islets and the contribution of these programs to diabetes risk are unknown. In this study we used ATAC-seq and RNA-seq to map chromatin accessibility and gene expression from eleven primary human islet samples cultured in vitro with the glucocorticoid dexamethasone at multiple doses and durations. We identified thousands of accessible chromatin sites and genes with significant changes in activity in response to glucocorticoids. Chromatin sites up-regulated in glucocorticoid signaling were prominently enriched for glucocorticoid receptor binding sites and up-regulated genes were enriched for ion transport and lipid metabolism, whereas down-regulated chromatin sites and genes were enriched for inflammatory, stress response and proliferative processes. Genetic variants associated with glucose levels and T2D risk were enriched in glucocorticoid-responsive chromatin sites, including fine-mapped variants at 51 known signals. Among fine-mapped variants in glucocorticoid-responsive chromatin, a likely casual variant at the 2p21 locus had glucocorticoid-dependent allelic effects on beta cell enhancer activity and affected SIX2 and SIX3 expression. Our results provide a comprehensive map of islet regulatory programs in response to glucocorticoids through which we uncover a role for islet glucocorticoid signaling in mediating genetic risk of T2D.
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Affiliation(s)
- Anthony Aylward
- Bioinformatics and Systems Biology graduate program, University of California San Diego, La Jolla, California, United States of America
| | - Mei-Lin Okino
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Paola Benaglio
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Joshua Chiou
- Biomedical Sciences graduate program, University of California San Diego, La Jolla, California, United States of America
| | - Elisha Beebe
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Jose Andres Padilla
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Sharlene Diep
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
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103
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Amorim JP, Gali-Macedo A, Marcelino H, Bordeira-Carriço R, Naranjo S, Rivero-Gil S, Teixeira J, Galhardo M, Marques J, Bessa J. A Conserved Notochord Enhancer Controls Pancreas Development in Vertebrates. Cell Rep 2021; 32:107862. [PMID: 32640228 PMCID: PMC7355232 DOI: 10.1016/j.celrep.2020.107862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/06/2020] [Accepted: 06/09/2020] [Indexed: 12/31/2022] Open
Abstract
The notochord is an evolutionary novelty in vertebrates that functions as an important signaling center during development. Notochord ablation in chicken has demonstrated that it is crucial for pancreas development; however, the molecular mechanism has not been fully described. Here, we show that in zebrafish, the loss of function of nog2, a Bmp antagonist expressed in the notochord, impairs β cell differentiation, compatible with the antagonistic role of Bmp in β cell differentiation. In addition, we show that nog2 expression in the notochord is induced by at least one notochord enhancer and its loss of function reduces the number of pancreatic progenitors and impairs β cell differentiation. Tracing Nog2 diffusion, we show that Nog2 emanates from the notochord to the pancreas progenitor domain. Finally, we find a notochord enhancer in human and mice Nog genomic landscapes, suggesting that the acquisition of a Nog notochord enhancer occurred early in the vertebrate phylogeny and contributes to the development of complex organs like the pancreas.
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Affiliation(s)
- João Pedro Amorim
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Ana Gali-Macedo
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Hugo Marcelino
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Renata Bordeira-Carriço
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Silvia Naranjo
- CABD (Centro Andaluz de Biología del Desarrollo), Universidad Pablo de Olavide, Seville, Spain
| | - Solangel Rivero-Gil
- CABD (Centro Andaluz de Biología del Desarrollo), Universidad Pablo de Olavide, Seville, Spain
| | - Joana Teixeira
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Mafalda Galhardo
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; CIBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Vairão, Portugal
| | - Joana Marques
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - José Bessa
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal.
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104
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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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105
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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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106
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Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation. Sci Rep 2021; 11:8800. [PMID: 33888791 PMCID: PMC8062533 DOI: 10.1038/s41598-021-88003-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Glucose-induced insulin secretion, a hallmark of mature β-cells, is achieved after birth and is preceded by a phase of intense proliferation. These events occurring in the neonatal period are decisive for establishing an appropriate functional β-cell mass that provides the required insulin throughout life. However, key regulators of gene expression involved in functional maturation of β-cells remain to be elucidated. Here, we addressed this issue by mapping open chromatin regions in newborn versus adult rat islets using the ATAC-seq assay. We obtained a genome-wide picture of chromatin accessible sites (~ 100,000) among which 20% were differentially accessible during maturation. An enrichment analysis of transcription factor binding sites identified a group of transcription factors that could explain these changes. Among them, Scrt1 was found to act as a transcriptional repressor and to control β-cell proliferation. Interestingly, Scrt1 expression was controlled by the transcriptional repressor RE-1 silencing transcription factor (REST) and was increased in an in vitro reprogramming system of pancreatic exocrine cells to β-like cells. Overall, this study led to the identification of several known and unforeseen key transcriptional events occurring during β-cell maturation. These findings will help defining new strategies to induce the functional maturation of surrogate insulin-producing cells.
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107
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Huang H, Hu J, Maryam A, Huang Q, Zhang Y, Ramakrishnan S, Li J, Ma H, Ma VWS, Cheuk W, So GYK, Wang W, Cho WCS, Zhang L, Chan KM, Wang X, Chin YR. Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling. Nat Commun 2021; 12:2242. [PMID: 33854062 PMCID: PMC8046763 DOI: 10.1038/s41467-021-22445-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/09/2021] [Indexed: 01/18/2023] Open
Abstract
Breast cancer is a heterogeneous disease, affecting over 3.5 million women worldwide, yet the functional role of cis-regulatory elements including super-enhancers in different breast cancer subtypes remains poorly characterized. Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis. Here we apply integrated epigenomic and transcriptomic profiling to uncover super-enhancer heterogeneity between breast cancer subtypes, and provide clinically relevant biological insights towards TNBC. Using CRISPR/Cas9-mediated gene editing, we identify genes that are specifically regulated by TNBC-specific super-enhancers, including FOXC1 and MET, thereby unveiling a mechanism for specific overexpression of the key oncogenes in TNBC. We also identify ANLN as a TNBC-specific gene regulated by super-enhancer. Our studies reveal a TNBC-specific epigenomic landscape, contributing to the dysregulated oncogene expression in breast tumorigenesis.
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Affiliation(s)
- Hao Huang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Jianyang Hu
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Alishba Maryam
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Qinghua Huang
- Department of Breast Surgery, The Affiliate Tumor Hospital, Guangxi Medical University, Nanning, China
| | - Yuchen Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | | | - Jingyu Li
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Haiying Ma
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Victor W S Ma
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Wah Cheuk
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Grace Y K So
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Wei Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong.
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China.
| | - Y Rebecca Chin
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong.
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China.
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108
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Akerman I, Maestro MA, De Franco E, Grau V, Flanagan S, García-Hurtado J, Mittler G, Ravassard P, Piemonti L, Ellard S, Hattersley AT, Ferrer J. Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene. Cell Rep 2021; 35:108981. [PMID: 33852861 PMCID: PMC8052186 DOI: 10.1016/j.celrep.2021.108981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/04/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their genomic location. This limits our understanding of disease-causing regulatory variants. INS promoter mutations cause recessive neonatal diabetes. We show that all INS promoter point mutations in 60 patients disrupt a CC dinucleotide, whereas none affect other elements important for episomal promoter function. To model CC mutations, we humanized an ∼3.1-kb region of the mouse Ins2 gene. This recapitulated developmental chromatin states and cell-specific transcription. A CC mutant allele, however, abrogated active chromatin formation during pancreas development. A search for transcription factors acting through this element revealed that another neonatal diabetes gene product, GLIS3, has a pioneer-like ability to derepress INS chromatin, which is hampered by the CC mutation. Our in vivo analysis, therefore, connects two human genetic defects in an essential mechanism for developmental activation of the INS gene.
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Affiliation(s)
- Ildem Akerman
- Institute of Metabolism and Systems Research (IMSR), Medical School, University of Birmingham, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), University of Birmingham, Birmingham, UK.
| | - Miguel Angel Maestro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Vanessa Grau
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Sarah Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Javier García-Hurtado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Gerhard Mittler
- Max-Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Philippe Ravassard
- INSERM, CNRS, Paris Brain Institute - Hôpital Pitié-Salpêtrière, Paris, France
| | - Lorenzo Piemonti
- Diabetes Research Institute, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK; Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain; Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
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109
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Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk. Nat Genet 2021; 53:455-466. [PMID: 33795864 PMCID: PMC9037575 DOI: 10.1038/s41588-021-00823-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.
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110
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Shimizu K, Ogiya Y, Yoshinaga K, Kimura H, Michinaga S, Ono M, Taketomi A, Terada T, Sakurai F, Mizuguchi H, Tomita K, Nishinaka T. ZFAND3 Overexpression in the Mouse Liver Improves Glucose Tolerance and Hepatic Insulin Resistance. Exp Clin Endocrinol Diabetes 2021; 130:254-261. [PMID: 33782927 DOI: 10.1055/a-1400-2656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Genome-wide association studies have identified more than 300 loci associated with type 2 diabetes mellitus; however, the mechanisms underlying their role in type 2 diabetes mellitus susceptibility remain largely unknown. Zinc finger AN1-type domain 3 (ZFAND3), known as testis-expressed sequence 27, is a type 2 diabetes mellitus-susceptibility gene. Limited information is available regarding the physiological role of ZFAND3 in vivo. This study aimed to investigate the association between ZFAND3 and type 2 diabetes mellitus. ZFAND3 was significantly upregulated in the liver of diabetic mice compared to wild-type mice. To overexpress ZFAND3, we generated a ZFAND3-expressing adenovirus (Ad) vector using an improved Ad vector exhibiting significantly lower hepatotoxicity (Ad-ZFAND3). Glucose tolerance was significantly improved in Ad-ZFAND3-treated mice compared to the control Ad-treated mice. ZFAND3 overexpression in the mouse liver also improved insulin resistance. Furthermore, gluconeogenic gene expression was significantly lower in primary mouse hepatocytes transduced with Ad-ZFAND3 than those transduced with the control Ad vector. The present results suggest that ZFAND3 improves glucose tolerance by improving insulin resistance and suppressing gluconeogenesis, serving as a potential novel therapeutic target for type 2 diabetes mellitus.
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Affiliation(s)
- Kahori Shimizu
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Yuya Ogiya
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Kaede Yoshinaga
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Hajime Kimura
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Shotaro Michinaga
- Laboratory of Pharmacology, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Moe Ono
- Laboratory of Molecular Biology, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Ayako Taketomi
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Tomoyuki Terada
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Fuminori Sakurai
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Hiroyuki Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,The Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, Japan.,Laboratory of Hepatocyte Differentiation, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan
| | - Koji Tomita
- Laboratory of Molecular Biology, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Toru Nishinaka
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
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111
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Wang Y, Jaime-Lara RB, Roy A, Sun Y, Liu X, Joseph PV. SeqEnhDL: sequence-based classification of cell type-specific enhancers using deep learning models. BMC Res Notes 2021; 14:104. [PMID: 33741075 PMCID: PMC7980595 DOI: 10.1186/s13104-021-05518-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/09/2021] [Indexed: 11/12/2022] Open
Abstract
Objective To address the challenge of computational identification of cell type-specific regulatory elements on a genome-wide scale. Results We propose SeqEnhDL, a deep learning framework for classifying cell type-specific enhancers based on sequence features. DNA sequences of “strong enhancer” chromatin states in nine cell types from the ENCODE project were retrieved to build and test enhancer classifiers. For any DNA sequence, positional k-mer (k = 5, 7, 9 and 11) fold changes relative to randomly selected non-coding sequences across each nucleotide position were used as features for deep learning models. Three deep learning models were implemented, including multi-layer perceptron (MLP), Convolutional Neural Network (CNN) and Recurrent Neural Network (RNN). All models in SeqEnhDL outperform state-of-the-art enhancer classifiers (including gkm-SVM and DanQ) in distinguishing cell type-specific enhancers from randomly selected non-coding sequences. Moreover, SeqEnhDL can directly discriminate enhancers from different cell types, which has not been achieved by other enhancer classifiers. Our analysis suggests that both enhancers and their tissue-specificity can be accurately identified based on their sequence features. SeqEnhDL is publicly available at https://github.com/wyp1125/SeqEnhDL. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05518-7.
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Affiliation(s)
- Yupeng Wang
- BDX Research and Consulting LLC, Herndon, VA, 20171, USA. .,Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Rosario B Jaime-Lara
- Division of Intramural Clinical and Biological Research (DICBR), National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA.,Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Abhrarup Roy
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ying Sun
- BDX Research and Consulting LLC, Herndon, VA, 20171, USA
| | - Xinyue Liu
- BDX Research and Consulting LLC, Herndon, VA, 20171, USA
| | - Paule V Joseph
- Division of Intramural Clinical and Biological Research (DICBR), National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA. .,Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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112
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González-Moro I, Santin I. Long non-coding RNA-regulated pathways in pancreatic β cells: Their role in diabetes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 359:325-355. [PMID: 33832652 DOI: 10.1016/bs.ircmb.2021.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides that have not coding potential, but act as gene expression regulators through several molecular mechanisms. Several studies have identified tons of lncRNAs that are expressed in pancreatic β cells and many of them have been shown to have β cell-specific expression, suggesting a potential role in the regulation of basal β cell functions. Indeed, accumulating evidence based on numerous studies, has highlighted the implication of lncRNAs in the regulation of pancreatic β cell differentiation and proliferation, insulin synthesis and secretion, and apoptosis. In addition, several lncRNAs have shown to be implicated in pancreatic β cell dysfunction linked to different types of diabetes, including type 1 and type 2 diabetes, and monogenic forms of the disease. Pathogenic conditions linked to diabetes (inflammation or lipoglucotoxicity, for example) dysregulate the expression of several lncRNAs, suggesting that changes in lncRNA may alter potentially important pathways for β cell function, and eventually leading to β cell dysfunction and diabetes development. In this sense, functional characterization of some lncRNAs has demonstrated that these non-coding molecules participate in the regulation of several crucial pathways at the pancreatic β cell level, and dysregulation of these pathways leads to pathogenic phenotypes. In this review, we provide an overview of the action mechanisms of functionally characterized lncRNAs in healthy β cells and describe the contribution of some diabetes-associated lncRNAs to pancreatic β cell failure.
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Affiliation(s)
- Itziar González-Moro
- Department of Biochemistry and Molecular biology, University of the Basque Country, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular biology, University of the Basque Country, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; CIBER (Centro de Investigación Biomédica en Red) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
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113
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Shirai Y, Okada Y. Elucidation of disease etiology by trans-layer omics analysis. Inflamm Regen 2021; 41:6. [PMID: 33557957 PMCID: PMC7871538 DOI: 10.1186/s41232-021-00155-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
To date, genome-wide association studies (GWASs) have successfully identified thousands of associations between genetic polymorphisms and human traits. However, the pathways between the associated genotype and phenotype are often poorly understood. The transcriptome, proteome, and metabolome, the omics, are positioned along the pathway and can provide useful information to translate from genotype to phenotype. This review shows useful data resources for connecting each omics and describes how they are combined into a cohesive analysis. Quantitative trait loci (QTL) are useful information for connecting the genome and other omics. QTL represent how much genetic variants have effects on other omics and give us clues to how GWAS risk SNPs affect biological mechanisms. Integration of each omics provides a robust analytical framework for estimating disease causality, discovering drug targets, and identifying disease-associated tissues. Technological advances and the rise of consortia and biobanks have facilitated the analyses of unprecedented data, improving both the quality and quantity of research. Proficient management of these valuable datasets allows discovering novel insights into the genetic background and etiology of complex human diseases and contributing to personalized medicine.
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Affiliation(s)
- Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan.
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114
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Geusz RJ, Wang A, Chiou J, Lancman JJ, Wetton N, Kefalopoulou S, Wang J, Qiu Y, Yan J, Aylward A, Ren B, Dong PDS, Gaulton KJ, Sander M. Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development. eLife 2021; 10:e59067. [PMID: 33544077 PMCID: PMC7864636 DOI: 10.7554/elife.59067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Genetic variants associated with type 2 diabetes (T2D) risk affect gene regulation in metabolically relevant tissues, such as pancreatic islets. Here, we investigated contributions of regulatory programs active during pancreatic development to T2D risk. Generation of chromatin maps from developmental precursors throughout pancreatic differentiation of human embryonic stem cells (hESCs) identifies enrichment of T2D variants in pancreatic progenitor-specific stretch enhancers that are not active in islets. Genes associated with progenitor-specific stretch enhancers are predicted to regulate developmental processes, most notably tissue morphogenesis. Through gene editing in hESCs, we demonstrate that progenitor-specific enhancers harboring T2D-associated variants regulate cell polarity genes LAMA1 and CRB2. Knockdown of lama1 or crb2 in zebrafish embryos causes a defect in pancreas morphogenesis and impairs islet cell development. Together, our findings reveal that a subset of T2D risk variants specifically affects pancreatic developmental programs, suggesting that dysregulation of developmental processes can predispose to T2D.
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Affiliation(s)
- Ryan J Geusz
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Sanford Consortium for Regenerative MedicineSan DiegoUnited States
- Biomedical Graduate Studies Program, University of California, San DiegoSan DiegoUnited States
| | - Allen Wang
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Sanford Consortium for Regenerative MedicineSan DiegoUnited States
| | - Joshua Chiou
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
- Biomedical Graduate Studies Program, University of California, San DiegoSan DiegoUnited States
| | - Joseph J Lancman
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery InstituteSan DiegoUnited States
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery InstituteSan DiegoUnited States
| | - Nichole Wetton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Sanford Consortium for Regenerative MedicineSan DiegoUnited States
| | - Samy Kefalopoulou
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Sanford Consortium for Regenerative MedicineSan DiegoUnited States
| | - Jinzhao Wang
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Sanford Consortium for Regenerative MedicineSan DiegoUnited States
| | - Yunjiang Qiu
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Jian Yan
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Anthony Aylward
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
| | - Bing Ren
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Ludwig Institute for Cancer ResearchSan DiegoUnited States
| | - P Duc Si Dong
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery InstituteSan DiegoUnited States
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery InstituteSan DiegoUnited States
| | - Kyle J Gaulton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
| | - Maike Sander
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San DiegoSan DiegoUnited States
- Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Sanford Consortium for Regenerative MedicineSan DiegoUnited States
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115
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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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116
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Isoform-Specific Roles of Mutant p63 in Human Diseases. Cancers (Basel) 2021; 13:cancers13030536. [PMID: 33572532 PMCID: PMC7866788 DOI: 10.3390/cancers13030536] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary The protein p63 belongs to the family of the p53 tumor suppressor. Mouse models have, however, shown that it is not a classical tumor suppressor but instead involved in developmental processes. Mutations in the p63 gene cause several developmental defects in human patients characterized by limb deformation, cleft lip/palate, and ectodermal dysplasia due to p63’s role as a master regulator of epidermal development. In addition, p63 plays a key role as a quality control factor in oocytes and p63 mutations can result either in compromised genetic quality control or premature cell death of all oocytes. Abstract The p63 gene encodes a master regulator of epidermal commitment, development, and differentiation. Heterozygous mutations in the DNA binding domain cause Ectrodactyly, Ectodermal Dysplasia, characterized by limb deformation, cleft lip/palate, and ectodermal dysplasia while mutations in in the C-terminal domain of the α-isoform cause Ankyloblepharon-Ectodermal defects-Cleft lip/palate (AEC) syndrome, a life-threatening disorder characterized by skin fragility, severe, long-lasting skin erosions, and cleft lip/palate. The molecular disease mechanisms of these syndromes have recently become elucidated and have enhanced our understanding of the role of p63 in epidermal development. Here we review the molecular cause and functional consequences of these p63-mutations for skin development and discuss the consequences of p63 mutations for female fertility.
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117
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Nasteska D, Fine NHF, Ashford FB, Cuozzo F, Viloria K, Smith G, Dahir A, Dawson PWJ, Lai YC, Bastidas-Ponce A, Bakhti M, Rutter GA, Fiancette R, Nano R, Piemonti L, Lickert H, Zhou Q, Akerman I, Hodson DJ. PDX1 LOW MAFA LOW β-cells contribute to islet function and insulin release. Nat Commun 2021; 12:674. [PMID: 33514698 PMCID: PMC7846747 DOI: 10.1038/s41467-020-20632-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022] Open
Abstract
Transcriptionally mature and immature β-cells co-exist within the adult islet. How such diversity contributes to insulin release remains poorly understood. Here we show that subtle differences in β-cell maturity, defined using PDX1 and MAFA expression, contribute to islet operation. Functional mapping of rodent and human islets containing proportionally more PDX1HIGH and MAFAHIGH β-cells reveals defects in metabolism, ionic fluxes and insulin secretion. At the transcriptomic level, the presence of increased numbers of PDX1HIGH and MAFAHIGH β-cells leads to dysregulation of gene pathways involved in metabolic processes. Using a chemogenetic disruption strategy, differences in PDX1 and MAFA expression are shown to depend on islet Ca2+ signaling patterns. During metabolic stress, islet function can be restored by redressing the balance between PDX1 and MAFA levels across the β-cell population. Thus, preserving heterogeneity in PDX1 and MAFA expression, and more widely in β-cell maturity, might be important for the maintenance of islet function.
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Affiliation(s)
- Daniela Nasteska
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Nicholas H F Fine
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Fiona B Ashford
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Federica Cuozzo
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Katrina Viloria
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Gabrielle Smith
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Aisha Dahir
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Peter W J Dawson
- School of Sport, Exercise and Rehabilitation Science, University of Birmingham, Edgbaston, UK.,MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, University of Birmingham, Edgbaston, UK
| | - Yu-Chiang Lai
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,School of Sport, Exercise and Rehabilitation Science, University of Birmingham, Edgbaston, UK.,MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, University of Birmingham, Edgbaston, UK
| | - Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), D-85764, Neuherberg, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany.,Technical University of Munich, School of Medicine, Munich, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), D-85764, Neuherberg, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology, and Metabolism, Department of Metabolism, Reproduction, and Digestion, Imperial College London, London, UK.,Lee Kong Chian School of Medicine, Nanyang Technological University, Nanyang, Singapore
| | - Remi Fiancette
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rita Nano
- San Raffaele Diabetes Research Institute, IRCCS Ospedale, San Raffaele, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Lorenzo Piemonti
- San Raffaele Diabetes Research Institute, IRCCS Ospedale, San Raffaele, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), D-85764, Neuherberg, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764, Neuherberg, Germany.,Technical University of Munich, School of Medicine, Munich, Germany
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ildem Akerman
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK. .,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK. .,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK.
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118
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Campbell JE, Newgard CB. Mechanisms controlling pancreatic islet cell function in insulin secretion. Nat Rev Mol Cell Biol 2021; 22:142-158. [PMID: 33398164 DOI: 10.1038/s41580-020-00317-7] [Citation(s) in RCA: 251] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 02/07/2023]
Abstract
Metabolic homeostasis in mammals is tightly regulated by the complementary actions of insulin and glucagon. The secretion of these hormones from pancreatic β-cells and α-cells, respectively, is controlled by metabolic, endocrine, and paracrine regulatory mechanisms and is essential for the control of blood levels of glucose. The deregulation of these mechanisms leads to various pathologies, most notably type 2 diabetes, which is driven by the combined lesions of impaired insulin action and a loss of the normal insulin secretion response to glucose. Glucose stimulates insulin secretion from β-cells in a bi-modal fashion, and new insights about the underlying mechanisms, particularly relating to the second or amplifying phase of this secretory response, have been recently gained. Other recent work highlights the importance of α-cell-produced proglucagon-derived peptides, incretin hormones from the gastrointestinal tract and other dietary components, including certain amino acids and fatty acids, in priming and potentiation of the β-cell glucose response. These advances provide a new perspective for the understanding of the β-cell failure that triggers type 2 diabetes.
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Affiliation(s)
- Jonathan E Campbell
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Endocrinology and Metabolism Division, Duke University Medical Center, Durham, NC, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA. .,Department of Medicine, Endocrinology and Metabolism Division, Duke University Medical Center, Durham, NC, USA. .,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA.
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119
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Ramos-Rodríguez M, Pérez-González B, Pasquali L. The β-Cell Genomic Landscape in T1D: Implications for Disease Pathogenesis. Curr Diab Rep 2021; 21:1. [PMID: 33387073 PMCID: PMC7778620 DOI: 10.1007/s11892-020-01370-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 11/15/2022]
Abstract
PURPOSE OF REVIEW Type 1 diabetes (T1D) develops as a consequence of a combination of genetic predisposition and environmental factors. Combined, these events trigger an autoimmune disease that results in progressive loss of pancreatic β cells, leading to insulin deficiency. This article reviews the current knowledge on the genetics of T1D with a specific focus on genetic variation in pancreatic islet regulatory networks and its implication to T1D risk and disease development. RECENT FINDINGS Accumulating evidence suggest an active role of β cells in T1D pathogenesis. Based on such observation several studies aimed in mapping T1D risk variants acting at the β cell level. Such studies unravel T1D risk loci shared with type 2 diabetes (T2D) and T1D risk variants potentially interfering with β-cell responses to external stimuli. The characterization of regulatory genomics maps of disease-relevant states and cell types can be used to elucidate the mechanistic role of β cells in the pathogenesis of T1D.
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Affiliation(s)
- Mireia Ramos-Rodríguez
- Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, 08003, Barcelona, Spain
| | - Beatriz Pérez-González
- Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, 08003, Barcelona, Spain
| | - Lorenzo Pasquali
- Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, 08003, Barcelona, Spain.
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120
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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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121
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Torres JM, Abdalla M, Payne A, Fernandez-Tajes J, Thurner M, Nylander V, Gloyn AL, Mahajan A, McCarthy MI. A Multi-omic Integrative Scheme Characterizes Tissues of Action at Loci Associated with Type 2 Diabetes. Am J Hum Genet 2020; 107:1011-1028. [PMID: 33186544 PMCID: PMC7820628 DOI: 10.1016/j.ajhg.2020.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/20/2020] [Indexed: 12/30/2022] Open
Abstract
Resolving the molecular processes that mediate genetic risk remains a challenge because most disease-associated variants are non-coding and functional characterization of these signals requires knowledge of the specific tissues and cell-types in which they operate. To address this challenge, we developed a framework for integrating tissue-specific gene expression and epigenomic maps to obtain "tissue-of-action" (TOA) scores for each association signal by systematically partitioning posterior probabilities from Bayesian fine-mapping. We applied this scheme to credible set variants for 380 association signals from a recent GWAS meta-analysis of type 2 diabetes (T2D) in Europeans. The resulting tissue profiles underscored a predominant role for pancreatic islets and, to a lesser extent, adipose and liver, particularly among signals with greater fine-mapping resolution. We incorporated resulting TOA scores into a rule-based classifier and validated the tissue assignments through comparison with data from cis-eQTL enrichment, functional fine-mapping, RNA co-expression, and patterns of physiological association. In addition to implicating signals with a single TOA, we found evidence for signals with shared effects in multiple tissues as well as distinct tissue profiles between independent signals within heterogeneous loci. Lastly, we demonstrated that TOA scores can be directly coupled with eQTL colocalization to further resolve effector transcripts at T2D signals. This framework guides mechanistic inference by directing functional validation studies to the most relevant tissues and can gain power as fine-mapping resolution and cell-specific annotations become richer. This method is generalizable to all complex traits with relevant annotation data and is made available as an R package.
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Affiliation(s)
- Jason M. Torres
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Moustafa Abdalla
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Anthony Payne
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Juan Fernandez-Tajes
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Matthias Thurner
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Anna L. Gloyn
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, 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 School of Medicine, Stanford, CA 94305, USA
| | - Anubha Mahajan
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK,Corresponding author
| | - Mark I. McCarthy
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK,Corresponding author
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122
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Eufrásio A, Perrod C, Ferreira FJ, Duque M, Galhardo M, Bessa J. In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes-Associated Single Nucleotide Polymorphisms. Diabetes 2020; 69:2794-2805. [PMID: 32912862 PMCID: PMC7679775 DOI: 10.2337/db19-1049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 09/02/2020] [Indexed: 12/11/2022]
Abstract
Many single nucleotide polymorphisms (SNPs) associated with type 2 diabetes overlap with putative endocrine pancreatic enhancers, suggesting that these SNPs modulate enhancer activity and, consequently, gene expression. We performed in vivo mosaic transgenesis assays in zebrafish to quantitatively test the enhancer activity of type 2 diabetes-associated loci. Six out of 10 tested sequences are endocrine pancreatic enhancers. The risk variant of two sequences decreased enhancer activity, while in another two incremented it. One of the latter (rs13266634) locates in an SLC30A8 exon, encoding a tryptophan-to-arginine substitution that decreases SLC30A8 function, which is the canonical explanation for type 2 diabetes risk association. However, other type 2 diabetes-associated SNPs that truncate SLC30A8 confer protection from this disease, contradicting this explanation. Here, we clarify this incongruence, showing that rs13266634 boosts the activity of an overlapping enhancer and suggesting an SLC30A8 gain of function as the cause for the increased risk for the disease. We further dissected the functionality of this enhancer, finding a single nucleotide mutation sufficient to impair its activity. Overall, this work assesses in vivo the importance of disease-associated SNPs in the activity of endocrine pancreatic enhancers, including a poorly explored case where a coding SNP modulates the activity of an enhancer.
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Affiliation(s)
- Ana Eufrásio
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, and IBMC-Instituto de Biologia Celular e Molecular, Porto, Portugal
| | - Chiara Perrod
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, and IBMC-Instituto de Biologia Celular e Molecular, Porto, Portugal
| | - Fábio J Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, and IBMC-Instituto de Biologia Celular e Molecular, Porto, Portugal
| | - Marta Duque
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, and IBMC-Instituto de Biologia Celular e Molecular, Porto, Portugal
| | - Mafalda Galhardo
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, and IBMC-Instituto de Biologia Celular e Molecular, Porto, Portugal
| | - José Bessa
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, and IBMC-Instituto de Biologia Celular e Molecular, Porto, Portugal
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123
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Kim H, Kulkarni RN. Epigenetics in β-cell adaptation and type 2 diabetes. Curr Opin Pharmacol 2020; 55:125-131. [PMID: 33232934 DOI: 10.1016/j.coph.2020.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Abstract
Healthy pancreatic β-cells adapt to systemic insulin resistance to maintain normal blood glucose levels, and a failure of this adaptation leads to type 2 diabetes in humans. While genome-wide association studies have uncovered genetic variants that are associated with type 2 diabetes, it is still insufficient to explain the high prevalence of this disease. Epigenetics is the study of gene expression changes that do not involve DNA sequence alterations such as DNA methylation, histone modification, and non-coding RNAs. Over the last decade, a large number of studies have reported on the role of epigenetics in β-cell biology. In this review, we summarize the epigenetic mechanisms in β-cell adaptation and type 2 diabetes, including alterations in three-dimensional chromatin structure and RNA modifications.
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Affiliation(s)
- Hyunki Kim
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Rohit N Kulkarni
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, 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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124
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Zhu H, Bian X, Gong J, Yu P, Lu H. Long noncoding RNAs as novel biomarkers for Type 2 diabetes. Biomark Med 2020; 14:1501-1511. [PMID: 33155821 DOI: 10.2217/bmm-2020-0136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Type 2 diabetes (T2D) is a metabolic disease characterized by disordered glucagon secretion, insulin resistance in target tissues, and decreased islet β-cell mass and function. The routine diagnosis was based on measurements of metabolic markers, while genetic risk factors have been considered to increase the probability of predicting the development of the disease. Recent evidence suggests that long noncoding RNAs (lncRNAs) regulate gene expression in various physiological and pathological processes. As increasing lncRNAs are identified in β cells, understanding the regulatory roles of lncRNAs in T2D becomes indispensable. In this review, we discuss the potential role of lncRNAs contributing to β-cell identity and T2D susceptibility, which provide a perspective insight into the development of novel diagnosis biomarkers for T2D.
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Affiliation(s)
- Han Zhu
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingru Gong
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
| | - Ping Yu
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huiping Lu
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
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125
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Scoville DW, Kang HS, Jetten AM. Transcription factor GLIS3: Critical roles in thyroid hormone biosynthesis, hypothyroidism, pancreatic beta cells and diabetes. Pharmacol Ther 2020; 215:107632. [PMID: 32693112 PMCID: PMC7606550 DOI: 10.1016/j.pharmthera.2020.107632] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/15/2020] [Indexed: 12/16/2022]
Abstract
GLI-Similar 3 (GLIS3) is a member of the GLIS subfamily of Krüppel-like zinc finger transcription factors that functions as an activator or repressor of gene expression. Study of GLIS3-deficiency in mice and humans revealed that GLIS3 plays a critical role in the regulation of several biological processes and is implicated in the development of various diseases, including hypothyroidism and diabetes. This was supported by genome-wide association studies that identified significant associations of common variants in GLIS3 with increased risk of these pathologies. To obtain insights into the causal mechanisms underlying these diseases, it is imperative to understand the mechanisms by which this protein regulates the development of these pathologies. Recent studies of genes regulated by GLIS3 led to the identification of a number of target genes and have provided important molecular insights by which GLIS3 controls cellular processes. These studies revealed that GLIS3 is essential for thyroid hormone biosynthesis and identified a critical function for GLIS3 in the generation of pancreatic β cells and insulin gene transcription. These observations raised the possibility that the GLIS3 signaling pathway might provide a potential therapeutic target in the management of diabetes, hypothyroidism, and other diseases. To develop such strategies, it will be critical to understand the upstream signaling pathways that regulate the activity, expression and function of GLIS3. Here, we review the recent progress on the molecular mechanisms by which GLIS3 controls key functions in thyroid follicular and pancreatic β cells and how this causally relates to the development of hypothyroidism and diabetes.
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Affiliation(s)
- David W Scoville
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Hong Soon Kang
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Anton M Jetten
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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126
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Karakose E, Wang H, Inabnet W, Thakker RV, Libutti S, Fernandez-Ranvier G, Suh H, Stevenson M, Kinoshita Y, Donovan M, Antipin Y, Li Y, Liu X, Jin F, Wang P, Uzilov A, Argmann C, Schadt EE, Stewart AF, Scott DK, Lambertini L. Aberrant methylation underlies insulin gene expression in human insulinoma. Nat Commun 2020; 11:5210. [PMID: 33060578 PMCID: PMC7566641 DOI: 10.1038/s41467-020-18839-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/16/2020] [Indexed: 12/23/2022] Open
Abstract
Human insulinomas are rare, benign, slowly proliferating, insulin-producing beta cell tumors that provide a molecular "recipe" or "roadmap" for pathways that control human beta cell regeneration. An earlier study revealed abnormal methylation in the imprinted p15.5-p15.4 region of chromosome 11, known to be abnormally methylated in another disorder of expanded beta cell mass and function: the focal variant of congenital hyperinsulinism. Here, we compare deep DNA methylome sequencing on 19 human insulinomas, and five sets of normal beta cells. We find a remarkably consistent, abnormal methylation pattern in insulinomas. The findings suggest that abnormal insulin (INS) promoter methylation and altered transcription factor expression create alternative drivers of INS expression, replacing canonical PDX1-driven beta cell specification with a pathological, looping, distal enhancer-based form of transcriptional regulation. Finally, NFaT transcription factors, rather than the canonical PDX1 enhancer complex, are predicted to drive INS transactivation.
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Affiliation(s)
- Esra Karakose
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - William Inabnet
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rajesh V Thakker
- The Academic Endocrine Unit, University of Oxford, OX3 7LJ, Oxford, UK
| | - Steven Libutti
- The Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gustavo Fernandez-Ranvier
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hyunsuk Suh
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mark Stevenson
- The Academic Endocrine Unit, University of Oxford, OX3 7LJ, Oxford, UK
| | - Yayoi Kinoshita
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Donovan
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yevgeniy Antipin
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Sema4, Stamford, CT, 06902, USA
| | - Yan Li
- The Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaoxiao Liu
- The Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Fulai Jin
- The Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peng Wang
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Uzilov
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Sema4, Stamford, CT, 06902, USA
| | - Carmen Argmann
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Sema4, Stamford, CT, 06902, USA
| | - Andrew F Stewart
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Donald K Scott
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Luca Lambertini
- From the Diabetes Obesity and Metabolism Institute, The Department of Surgery, The Department of Pathology, The Department of Genetics and Genomics Sciences and The Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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127
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Hu M, Cherkaoui I, Misra S, Rutter GA. Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research. Front Endocrinol (Lausanne) 2020; 11:576632. [PMID: 33162936 PMCID: PMC7580382 DOI: 10.3389/fendo.2020.576632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
The inheritance of variants that lead to coding changes in, or the mis-expression of, genes critical to pancreatic beta cell function can lead to alterations in insulin secretion and increase the risk of both type 1 and type 2 diabetes. Recently developed clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) gene editing tools provide a powerful means of understanding the impact of identified variants on cell function, growth, and survival and might ultimately provide a means, most likely after the transplantation of genetically "corrected" cells, of treating the disease. Here, we review some of the disease-associated genes and variants whose roles have been probed up to now. Next, we survey recent exciting developments in CRISPR/Cas9 technology and their possible exploitation for β cell functional genomics. Finally, we will provide a perspective as to how CRISPR/Cas9 technology may find clinical application in patients with diabetes.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ines Cherkaoui
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shivani Misra
- Metabolic Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
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128
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Scoville DW, Gruzdev A, Jetten AM. Identification of a novel lncRNA (G3R1) regulated by GLIS3 in pancreatic β-cells. J Mol Endocrinol 2020; 65:59-67. [PMID: 32668405 PMCID: PMC7461731 DOI: 10.1530/jme-20-0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022]
Abstract
Recent advances in high throughput RNA sequencing have revealed that, in addition to messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs) play an important role in the regulation of many cell functions and of organ development. While a number of lncRNAs have been identified in pancreatic islets, their function remains largely undetermined. Here, we identify a novel long ncRNA regulated by the transcription factor GLIS3, which we refer to as GLIS3 regulated 1 (G3R1). This lncRNA was identified for its significant loss of expression in GLIS3 knockout mouse pancreatic islets. G3R1 appears to be specifically expressed in mouse pancreatic β-cells and in a β-cell line (βTC-6). ChIP-seq analysis indicated that GLIS3 and other islet-enriched transcription factors bind near the G3R1 gene, suggesting they directly regulate G3R1 transcription. Similarly, an apparent human homolog of G3R1 displays a similar expression pattern, with additional expression seen in human brain. In order to determine the function of G3R1 in mouse pancreatic β-cells, we utilized CRISPR to develop a knockout mouse where ~80% of G3R1 sequence is deleted. Phenotypic analysis of these mice did not reveal any impairment in β-cell function or glucose regulation, indicating the complexity underlying the study of lncRNA function.
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Affiliation(s)
- David W. Scoville
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Artiom Gruzdev
- Knockout Mouse Core, Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Anton M. Jetten
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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129
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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: 72] [Impact Index Per Article: 18.0] [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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130
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Acemel RD, Tena JJ, Gomez-Skarmeta JL, Fibla J, Royo JL. Straightforward protocol for allele-specific chromatin conformation capture. Gene 2020; 767:145185. [PMID: 32998049 DOI: 10.1016/j.gene.2020.145185] [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: 04/29/2020] [Revised: 09/03/2020] [Accepted: 09/23/2020] [Indexed: 11/26/2022]
Abstract
A key advance in our understanding of gene regulation came with the finding that the genome undergoes three-dimensional nuclear folding in a genetically determined process. This 3D conformation directly influences the association between enhancers and their target promoters. This complex interplay has been proven to be essential for gene regulation, and genetic variants affecting this process have been associated to human diseases. The development of new technologies that quantify these DNA interactions represented a revolution in the field. High throughput techniques like HiC provide a general picture of chromatin topology. However, they often lack resolution to evidence subtle effects that single nucleotide polymorphisms exert over the contacts between cis-regulatory regions and target promoters. Here we propose a cost-efficient approach to perform allele-specific chromatin conformation analysis. As a proof of concept, we analyzed the impact of a common deletion mapping between SIRPB1 promoter and one of its downstream enhancers.
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Affiliation(s)
- R D Acemel
- Andalusian Centre for Developmental Biology, University Pablo de Olavide-CSIC-Junta de Andalucia, Sevilla, Spain
| | - J J Tena
- Andalusian Centre for Developmental Biology, University Pablo de Olavide-CSIC-Junta de Andalucia, Sevilla, Spain
| | - J L Gomez-Skarmeta
- Andalusian Centre for Developmental Biology, University Pablo de Olavide-CSIC-Junta de Andalucia, Sevilla, Spain
| | - J Fibla
- Institute of Biomedical Research of Lleida, University of Lleida, Lleida, Spain
| | - J L Royo
- Department of Surgery, Biochemistry, and Immunology, School of Medicine, University of Malaga, 29071 Malaga, Spain.
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131
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Campbell SA, McDonald CL, Krentz NAJ, Lynn FC, Hoffman BG. TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation. Cell Rep 2020; 28:1830-1844.e6. [PMID: 31412250 DOI: 10.1016/j.celrep.2019.07.035] [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: 05/31/2018] [Revised: 06/04/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Appropriate regulation of genes that coordinate pancreas progenitor proliferation and differentiation is required for pancreas development. Here, we explore the role of H3K4 methylation and the Trithorax group (TrxG) complexes in mediating gene expression during pancreas development. Disruption of TrxG complex assembly, but not catalytic activity, prevented endocrine cell differentiation in pancreas progenitor spheroids. In vivo loss of TrxG catalytic activity in PDX1+ cells increased apoptosis and the fraction of progenitors in the G1 phase of the cell cycle. Pancreas progenitors were reallocated to the acinar lineage, primarily at the expense of NEUROG3+ endocrine progenitors. Later in development, acinar and endocrine cell numbers were decreased, and increased gene expression variance and reduced terminal marker activation in acinar cells led to their incomplete differentiation. These findings demonstrate that TrxG co-activator activity is required for gene induction, whereas TrxG catalytic activity and H3K4 methylation help maintain transcriptional stability.
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Affiliation(s)
- Stephanie A Campbell
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Cassandra L McDonald
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada
| | - Nicole A J Krentz
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Francis C Lynn
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Brad G Hoffman
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.
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132
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Allum F, Grundberg E. Capturing functional epigenomes for insight into metabolic diseases. Mol Metab 2020; 38:100936. [PMID: 32199819 PMCID: PMC7300388 DOI: 10.1016/j.molmet.2019.12.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metabolic diseases such as obesity are known to be driven by both environmental and genetic factors. Although genome-wide association studies of common variants and their impact on complex traits have provided some biological insight into disease etiology, identified genetic variants have been found to contribute only a small proportion to disease heritability, and to map mainly to non-coding regions of the genome. To link variants to function, association studies of cellular traits, such as epigenetic marks, in disease-relevant tissues are commonly applied. SCOPE OF THE REVIEW We review large-scale efforts to generate genome-wide maps of coordinated epigenetic marks and their utility in complex disease dissection with a focus on DNA methylation. We contrast DNA methylation profiling methods and discuss the advantages of using targeted methods for single-base resolution assessments of methylation levels across tissue-specific regulatory regions to deepen our understanding of contributing factors leading to complex diseases. MAJOR CONCLUSIONS Large-scale assessments of DNA methylation patterns in metabolic disease-linked study cohorts have provided insight into the impact of variable epigenetic variants in disease etiology. In-depth profiling of epigenetic marks at regulatory regions, particularly at tissue-specific elements, will be key to dissect the genetic and environmental components contributing to metabolic disease onset and progression.
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Affiliation(s)
- Fiona Allum
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0C7, Canada; McGill University and Genome Quebec Innovation Centre, Montréal, Québec, H3A 0G1, Canada
| | - Elin Grundberg
- Children's Mercy Kansas City, Kansas City, MO, 64108, United States.
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133
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Manning AK, Goustin AS, Kleinbrink EL, Thepsuwan P, Cai J, Ju D, Leong A, Udler MS, Brown JB, Goodarzi MO, Rotter JI, Sladek R, Meigs JB, Lipovich L. A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1- PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus. Front Genet 2020; 11:615. [PMID: 32754192 PMCID: PMC7367044 DOI: 10.3389/fgene.2020.00615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/20/2020] [Indexed: 01/08/2023] Open
Abstract
AIMS Causal transcripts at genomic loci associated with type 2 diabetes (T2D) are mostly unknown. The chr8p23.1 variant rs4841132, associated with an insulin-resistant diabetes risk phenotype, lies in the second exon of a long non-coding RNA (lncRNA) gene, LOC157273, located 175 kilobases from PPP1R3B, which encodes a key protein regulating insulin-mediated hepatic glycogen storage in humans. We hypothesized that LOC157273 regulates expression of PPP1R3B in human hepatocytes. METHODS We tested our hypothesis using Stellaris fluorescent in situ hybridization to assess subcellular localization of LOC157273; small interfering RNA (siRNA) knockdown of LOC157273, followed by RT-PCR to quantify LOC157273 and PPP1R3B expression; RNA-seq to quantify the whole-transcriptome gene expression response to LOC157273 knockdown; and an insulin-stimulated assay to measure hepatocyte glycogen deposition before and after knockdown. RESULTS We found that siRNA knockdown decreased LOC157273 transcript levels by approximately 80%, increased PPP1R3B mRNA levels by 1.7-fold, and increased glycogen deposition by >50% in primary human hepatocytes. An A/G heterozygous carrier (vs. three G/G carriers) had reduced LOC157273 abundance due to reduced transcription of the A allele and increased PPP1R3B expression and glycogen deposition. CONCLUSION We show that the lncRNA LOC157273 is a negative regulator of PPP1R3B expression and glycogen deposition in human hepatocytes and a causal transcript at an insulin-resistant T2D risk locus.
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Affiliation(s)
- Alisa K. Manning
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Anton Scott Goustin
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Erica L. Kleinbrink
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Pattaraporn Thepsuwan
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Juan Cai
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Donghong Ju
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute at Wayne State University, Detroit, MI, United States
| | - Aaron Leong
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Miriam S. Udler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, United States
| | - James Bentley Brown
- Department of Statistics, University of California, Berkeley, Berkeley, CA, United States
- Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
- Computational Biosciences Group, Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - 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, United States
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Medicine, McGill University, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada
| | - James B. Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Leonard Lipovich
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
- Department of Neurology, School of Medicine, Wayne State University, Detroit, MI, United States
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134
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Guay C, Jacovetti C, Bayazit MB, Brozzi F, Rodriguez-Trejo A, Wu K, Regazzi R. Roles of Noncoding RNAs in Islet Biology. Compr Physiol 2020; 10:893-932. [PMID: 32941685 DOI: 10.1002/cphy.c190032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The discovery that most mammalian genome sequences are transcribed to ribonucleic acids (RNA) has revolutionized our understanding of the mechanisms governing key cellular processes and of the causes of human diseases, including diabetes mellitus. Pancreatic islet cells were found to contain thousands of noncoding RNAs (ncRNAs), including micro-RNAs (miRNAs), PIWI-associated RNAs, small nucleolar RNAs, tRNA-derived fragments, long non-coding RNAs, and circular RNAs. While the involvement of miRNAs in islet function and in the etiology of diabetes is now well documented, there is emerging evidence indicating that other classes of ncRNAs are also participating in different aspects of islet physiology. The aim of this article will be to provide a comprehensive and updated view of the studies carried out in human samples and rodent models over the past 15 years on the role of ncRNAs in the control of α- and β-cell development and function and to highlight the recent discoveries in the field. We not only describe the role of ncRNAs in the control of insulin and glucagon secretion but also address the contribution of these regulatory molecules in the proliferation and survival of islet cells under physiological and pathological conditions. It is now well established that most cells release part of their ncRNAs inside small extracellular vesicles, allowing the delivery of genetic material to neighboring or distantly located target cells. The role of these secreted RNAs in cell-to-cell communication between β-cells and other metabolic tissues as well as their potential use as diabetes biomarkers will be discussed. © 2020 American Physiological Society. Compr Physiol 10:893-932, 2020.
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Affiliation(s)
- Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Cécile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Mustafa Bilal Bayazit
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Flora Brozzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Adriana Rodriguez-Trejo
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Kejing Wu
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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135
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Papanicolaou N, Bonetti A. The New Frontier of Functional Genomics: From Chromatin Architecture and Noncoding RNAs to Therapeutic Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:568-580. [PMID: 32486876 PMCID: PMC7309355 DOI: 10.1177/2472555220926158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
Common diseases are complex, multifactorial disorders whose pathogenesis is influenced by the interplay of genetic predisposition and environmental factors. Genome-wide association studies have interrogated genetic polymorphisms across genomes of individuals to test associations between genotype and susceptibility to specific disorders, providing insights into the genetic architecture of several complex disorders. However, genetic variants associated with the susceptibility to common diseases are often located in noncoding regions of the genome, such as tissue-specific enhancers or long noncoding RNAs, suggesting that regulatory elements might play a relevant role in human diseases. Enhancers are cis-regulatory genomic sequences that act in concert with promoters to regulate gene expression in a precise spatiotemporal manner. They can be located at a considerable distance from their cognate target promoters, increasing the difficulty of their identification. Genomes are organized in domains of chromatin folding, namely topologically associating domains (TADs). Identification of enhancer-promoter interactions within TADs has revealed principles of cell-type specificity across several organisms and tissues. The vast majority of mammalian genomes are pervasively transcribed, accounting for a previously unappreciated complexity of the noncoding RNA fraction. Particularly, long noncoding RNAs have emerged as key players for the establishment of chromatin architecture and regulation of gene expression. In this perspective, we describe the new advances in the fields of transcriptomics and genome organization, focusing on the role of noncoding genomic variants in the predisposition of common diseases. Finally, we propose a new framework for the identification of the next generation of pharmacological targets for common human diseases.
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Affiliation(s)
- Natali Papanicolaou
- Division of Biomaterials, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alessandro Bonetti
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
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136
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Eizirik DL, Pasquali L, Cnop M. Pancreatic β-cells in type 1 and type 2 diabetes mellitus: different pathways to failure. Nat Rev Endocrinol 2020; 16:349-362. [PMID: 32398822 DOI: 10.1038/s41574-020-0355-7] [Citation(s) in RCA: 380] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Loss of functional β-cell mass is the key mechanism leading to the two main forms of diabetes mellitus - type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM). Understanding the mechanisms behind β-cell failure is critical to prevent or revert disease. Basic pathogenic differences exist in the two forms of diabetes mellitus; T1DM is immune mediated and T2DM is mediated by metabolic mechanisms. These mechanisms differentially affect early β-cell dysfunction and eventual fate. Over the past decade, major advances have been made in the field, mostly delivered by studies on β-cells in human disease. These advances include studies of islet morphology and human β-cell gene expression in T1DM and T2DM, the identification and characterization of the role of T1DM and T2DM candidate genes at the β-cell level and the endoplasmic reticulum stress signalling that contributes to β-cell failure in T1DM (mostly IRE1 driven) and T2DM (mostly PERK-eIF2α dependent). Here, we review these new findings, focusing on studies performed on human β-cells or on samples obtained from patients with diabetes mellitus.
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Affiliation(s)
- Décio L Eizirik
- ULB Center for Diabetes Research, Welbio Investigator, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium.
- Indiana Biosciences Research Institute (IBRI), Indianapolis, IN, USA.
| | - Lorenzo Pasquali
- Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, Barcelona, Spain.
- Germans Trias i Pujol University Hospital and Research Institute, Badalona, Spain.
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain.
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium.
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium.
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137
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Abstract
Background Pancreatic Islets of Langerhans are heterogeneous tissues consisting of multiple endocrine cell types that carry out distinct yet coordinated roles to regulate blood glucose homeostasis. Islet dysfunction and specifically failure of the beta cells to secrete adequate insulin are known precursors to type 2 diabetes (T2D) onset. However, the exact genetic, (epi)genomic, and environmental mechanisms that contribute to islet failure, and ultimately to T2D pathogenesis, require further elucidation. Scope of review This review summarizes efforts and advances in dissection of the complex genetic underpinnings of islet function and resilience in T2D pathogenesis. In this review, we will highlight results of the latest T2D genome-wide association study (GWAS) and discuss how these data are being combined with clinical measures in patients to uncover putative T2D subtypes and with functional (epi)genomic studies in islets to understand the genetic programming of islet cell identity, function, and adaptation. Finally, we discuss new and important opportunities to address major knowledge gaps in our understanding of islet (dys)function in T2D risk and progression. Major conclusions Genetic variation exerts clear effects on the islet epigenome, regulatory element usage, and gene expression. Future (epi)genomic comparative analyses between T2D and normal islets should incorporate genetics to distinguish patient-specific from disease-specific differences. Incorporating genotype information into future analyses and studies will also enable more precise insights into the molecular genetics of islet deficiency and failure in T2D risk, and should ultimately contribute to a stratified view of T2D and more precise treatment strategies. Islet cellular heterogeneity continues to remain a challenge for understanding the associations between islet failure and T2D development. Further efforts to obtain purified islet cell type populations and determine the specific genetic and environmental effects on each will help address this. Beyond observation of islets at steady state conditions, more research of islet stress and stimulation responses are needed to understand the transition of these tissues from a healthy to diseased state. Together, focusing on these objectives will provide more opportunities to prevent, treat, and manage T2D.
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138
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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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139
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Russell R, Carnese PP, Hennings TG, Walker EM, Russ HA, Liu JS, Giacometti S, Stein R, Hebrok M. Loss of the transcription factor MAFB limits β-cell derivation from human PSCs. Nat Commun 2020; 11:2742. [PMID: 32488111 PMCID: PMC7265500 DOI: 10.1038/s41467-020-16550-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Next generation sequencing studies have highlighted discrepancies in β-cells which exist between mice and men. Numerous reports have identified MAF BZIP Transcription Factor B (MAFB) to be present in human β-cells postnatally, while its expression is restricted to embryonic and neo-natal β-cells in mice. Using CRISPR/Cas9-mediated gene editing, coupled with endocrine cell differentiation strategies, we dissect the contribution of MAFB to β-cell development and function specifically in humans. Here we report that MAFB knockout hPSCs have normal pancreatic differentiation capacity up to the progenitor stage, but favor somatostatin- and pancreatic polypeptide–positive cells at the expense of insulin- and glucagon-producing cells during endocrine cell development. Our results describe a requirement for MAFB late in the human pancreatic developmental program and identify it as a distinguishing transcription factor within islet cell subtype specification. We propose that hPSCs represent a powerful tool to model human pancreatic endocrine development and associated disease pathophysiology. The MAF bZIP transcription factor B (MAFB) is present in postnatal human beta cells but its role is unclear. Here, the authors show that MAFB regulates endocrine pancreatic cell fate specification.
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Affiliation(s)
- Ronan Russell
- UCSF Diabetes Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Phichitpol P Carnese
- UCSF Diabetes Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Thomas G Hennings
- UCSF Diabetes Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Emily M Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Holger A Russ
- UCSF Diabetes Center, University of California San Francisco, San Francisco, CA, 94143, USA.,Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Jennifer S Liu
- UCSF Diabetes Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Simone Giacometti
- UCSF Diabetes Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Matthias Hebrok
- UCSF Diabetes Center, University of California San Francisco, San Francisco, CA, 94143, USA.
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140
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Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism. Nat Commun 2020; 11:2695. [PMID: 32483258 PMCID: PMC7264154 DOI: 10.1038/s41467-020-16537-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Obesity and type 2 diabetes (T2D) are metabolic disorders influenced by lifestyle and genetic factors that are characterized by insulin resistance in skeletal muscle, a prominent site of glucose disposal. Numerous genetic variants have been associated with obesity and T2D, of which the majority are located in non-coding DNA regions. This suggests that most variants mediate their effect by altering the activity of gene-regulatory elements, including enhancers. Here, we map skeletal muscle genomic enhancer elements that are dynamically regulated after exposure to the free fatty acid palmitate or the inflammatory cytokine TNFα. By overlapping enhancer positions with the location of disease-associated genetic variants, and resolving long-range chromatin interactions between enhancers and gene promoters, we identify target genes involved in metabolic dysfunction in skeletal muscle. The majority of these genes also associate with altered whole-body metabolic phenotypes in the murine BXD genetic reference population. Thus, our combined genomic investigations identified genes that are involved in skeletal muscle metabolism. Obesity and type 2 diabetes (T2D) are metabolic disorders characterized by insulin resistance in skeletal muscle. Here, the authors map skeletal muscle enhancer elements dynamically regulated after exposure to free fatty acid palmitate or inflammatory cytokine TNFα and identify target genes involved in metabolic dysfunction in skeletal muscle.
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141
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Levings D, Shaw KE, Lacher SE. Genomic resources for dissecting the role of non-protein coding variation in gene-environment interactions. Toxicology 2020; 441:152505. [PMID: 32450112 DOI: 10.1016/j.tox.2020.152505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022]
Abstract
The majority of single nucleotide variants (SNVs) identified in Genome Wide Association Studies (GWAS) fall within non-protein coding DNA and have the potential to alter gene expression. Non-protein coding DNA can control gene expression by acting as transcription factor (TF) binding sites or by regulating the organization of DNA into chromatin. SNVs in non-coding DNA sequences can disrupt TF binding and chromatin structure and this can result in pathology. Further, environmental health studies have shown that exposure to xenobiotics can disrupt the ability of TFs to regulate entire gene networks and result in pathology. However, there is a large amount of interindividual variability in exposure-linked health outcomes. One explanation for this heterogeneity is that genetic variation and exposure combine to disrupt gene regulation, and this eventually manifests in disease. Many resources exist that annotate common variants from GWAS and combine them with conservation, functional genomics, and TF binding data. These annotation tools provide clues regarding the biological implications of an SNV, as well as lead to the generation of hypotheses regarding potentially disrupted target genes, epigenetic markers, pathways, and cell types. Collectively this information can be used to predict how SNVs can alter an individual's response to exposure and disease risk. A basic understanding of the regulatory information contained within non-protein coding DNA is needed to predict the biological consequences of SNVs, and to determine how these SNVs impact exposure-related disease. We hope that this review will aid in the characterization of disease-associated genetic variation in the non-protein coding genome.
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Affiliation(s)
- Daniel Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, 1035 University Drive, Duluth, MN, 55812, USA
| | - Kirsten E Shaw
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, 1035 University Drive, Duluth, MN, 55812, USA
| | - Sarah E Lacher
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, 1035 University Drive, Duluth, MN, 55812, USA.
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142
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Bai X, Shi S, Ai B, Jiang Y, Liu Y, Han X, Xu M, Pan Q, Wang F, Wang Q, Zhang J, Li X, Feng C, Li Y, Wang Y, Song Y, Feng K, Li C. ENdb: a manually curated database of experimentally supported enhancers for human and mouse. Nucleic Acids Res 2020; 48:D51-D57. [PMID: 31665430 PMCID: PMC7145688 DOI: 10.1093/nar/gkz973] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022] Open
Abstract
Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, are highly associated with human disease and biological processes. Although some enhancer databases have been published, most only focus on enhancers identified by high-throughput experimental techniques. Therefore, it is highly desirable to construct a comprehensive resource of manually curated enhancers and their related information based on low-throughput experimental evidences. Here, we established a comprehensive manually-curated enhancer database for human and mouse, which provides a resource for experimentally supported enhancers, and to annotate the detailed information of enhancers. The current release of ENdb documents 737 experimentally validated enhancers and their related information, including 384 target genes, 263 TFs, 110 diseases and 153 functions in human and mouse. Moreover, the enhancer-related information was supported by experimental evidences, such as RNAi, in vitro knockdown, western blotting, qRT-PCR, luciferase reporter assay, chromatin conformation capture (3C) and chromosome conformation capture-on-chip (4C) assays. ENdb provides a user-friendly interface to query, browse and visualize the detailed information of enhancers. The database is available at http://www.licpathway.net/ENdb.
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Affiliation(s)
- Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Shanshan Shi
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yuejuan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xiaole Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Mingcong Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yanyu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yiwei Song
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Ke Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
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143
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Cano-Gamez E, Trynka G. From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases. Front Genet 2020; 11:424. [PMID: 32477401 PMCID: PMC7237642 DOI: 10.3389/fgene.2020.00424] [Citation(s) in RCA: 264] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/06/2020] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have successfully mapped thousands of loci associated with complex traits. These associations could reveal the molecular mechanisms altered in common complex diseases and result in the identification of novel drug targets. However, GWAS have also left a number of outstanding questions. In particular, the majority of disease-associated loci lie in non-coding regions of the genome and, even though they are thought to play a role in gene expression regulation, it is unclear which genes they regulate and in which cell types or physiological contexts this regulation occurs. This has hindered the translation of GWAS findings into clinical interventions. In this review we summarize how these challenges have been addressed over the last decade, with a particular focus on the integration of GWAS results with functional genomics datasets. Firstly, we investigate how the tissues and cell types involved in diseases can be identified using methods that test for enrichment of GWAS variants in genomic annotations. Secondly, we explore how to find the genes regulated by GWAS loci using methods that test for colocalization of GWAS signals with molecular phenotypes such as quantitative trait loci (QTLs). Finally, we highlight potential future research avenues such as integrating GWAS results with single-cell sequencing read-outs, designing functionally informed polygenic risk scores (PRS), and validating disease associated genes using genetic engineering. These tools will be crucial to identify new drug targets for common complex diseases.
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Affiliation(s)
- Eddie Cano-Gamez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Open Targets, Wellcome Genome Campus, Cambridge, United Kingdom
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144
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Ogara MF, Rodríguez-Seguí SA, Marini M, Nacht AS, Stortz M, Levi V, Presman DM, Vicent GP, Pecci A. The glucocorticoid receptor interferes with progesterone receptor-dependent genomic regulation in breast cancer cells. Nucleic Acids Res 2020; 47:10645-10661. [PMID: 31598691 PMCID: PMC6846950 DOI: 10.1093/nar/gkz857] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 09/19/2019] [Accepted: 10/04/2019] [Indexed: 12/30/2022] Open
Abstract
The glucocorticoid and progesterone receptors (GR and PR) are closely related members of the steroid receptor family. Despite sharing similar structural and functional characteristics; the cognate hormones display very distinct physiological responses. In mammary epithelial cells, PR activation is associated with the incidence and progression of breast cancer, whereas the GR is related to growth suppression and differentiation. Despite their pharmacological relevance, only a few studies have compared GR and PR activities in the same system. Using a PR+/GR+ breast cancer cell line, here we report that either glucocorticoid-free or dexamethasone (DEX)-activated GR inhibits progestin-dependent gene expression associated to epithelial-mesenchymal-transition and cell proliferation. When both receptors are activated with their cognate hormones, PR and GR can form part of the same complex according to co-immunoprecipitation, quantitative microscopy and sequential ChIP experiments. Moreover, genome-wide studies in cells treated with either DEX or R5020, revealed the presence of several regions co-bound by both receptors. Surprisingly, GR also binds novel genomic sites in cells treated with R5020 alone. This progestin-induced GR binding was enriched in REL DNA motifs and located close to genes coding for chromatin remodelers. Understanding GR behavior in the context of progestin-dependent breast cancer could provide new targets for tumor therapy.
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Affiliation(s)
- Maria F Ogara
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Santiago A Rodríguez-Seguí
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Melisa Marini
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Ana Silvina Nacht
- Centro de Regulación Genómica, Barcelona 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Martin Stortz
- Departamento de Fisiología, Biología Molecular y Celular, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.,Departamento de Química Biológica, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Guillermo P Vicent
- Centro de Regulación Genómica, Barcelona 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.,Department of Molecular Genomics, Institute of Molecular Biology of Barcelona, IBMB-CSIC. Baldiri Reixac 4, Barcelona 08028, Spain
| | - Adali Pecci
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.,Departamento de Química Biológica, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
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145
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Ohnmacht J, May P, Sinkkonen L, Krüger R. Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. J Neural Transm (Vienna) 2020; 127:729-748. [PMID: 32248367 PMCID: PMC7242266 DOI: 10.1007/s00702-020-02184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by a complex interplay of genetic and environmental factors. For the stratification of PD patients and the development of advanced clinical trials, including causative treatments, a better understanding of the underlying genetic architecture of PD is required. Despite substantial efforts, genome-wide association studies have not been able to explain most of the observed heritability. The majority of PD-associated genetic variants are located in non-coding regions of the genome. A systematic assessment of their functional role is hampered by our incomplete understanding of genotype-phenotype correlations, for example through differential regulation of gene expression. Here, the recent progress and remaining challenges for the elucidation of the role of non-coding genetic variants is reviewed with a focus on PD as a complex disease with multifactorial origins. The function of gene regulatory elements and the impact of non-coding variants on them, and the means to map these elements on a genome-wide level, will be delineated. Moreover, examples of how the integration of functional genomic annotations can serve to identify disease-associated pathways and to prioritize disease- and cell type-specific regulatory variants will be given. Finally, strategies for functional validation and considerations for suitable model systems are outlined. Together this emphasizes the contribution of rare and common genetic variants to the complex pathogenesis of PD and points to remaining challenges for the dissection of genetic complexity that may allow for better stratification, improved diagnostics and more targeted treatments for PD in the future.
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Affiliation(s)
- Jochen Ohnmacht
- LCSB, University of Luxembourg, Belvaux, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- LCSB, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- LCSB, University of Luxembourg, Belvaux, Luxembourg.
- Luxembourg Institute of Health (LIH), Transversal Translational Medicine, Strassen, Luxembourg.
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
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146
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Lawlor N, Márquez EJ, Orchard P, Narisu N, Shamim MS, Thibodeau A, Varshney A, Kursawe R, Erdos MR, Kanke M, Gu H, Pak E, Dutra A, Russell S, Li X, Piecuch E, Luo O, Chines PS, Fuchbserger C, Sethupathy P, Aiden AP, Ruan Y, Aiden EL, Collins FS, Ucar D, Parker SCJ, Stitzel ML. Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function. Cell Rep 2020; 26:788-801.e6. [PMID: 30650367 PMCID: PMC6389269 DOI: 10.1016/j.celrep.2018.12.083] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/26/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of β cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-βH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) β cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or β cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-βH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing β cell identity and (dys)function in diabetes. EndoC-βH1 is becoming an important cellular model to study genes and pathways governing human β cell identity and function, but its (epi)genomic similarity to primary human islets is unknown. Lawlor et al. complete and compare extensive EndoC and primary human islet multiomic maps to identify shared and distinct genomic circuitry.
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Affiliation(s)
- Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eladio J Márquez
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Narisu Narisu
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Muhammad Saad Shamim
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael R Erdos
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Huiya Gu
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Evgenia Pak
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amalia Dutra
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sheikh Russell
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Xingwang Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Emaly Piecuch
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA
| | - Oscar Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Peter S Chines
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Christian Fuchbserger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Aviva Presser Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Francis S Collins
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
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147
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Krentz NAJ, Gloyn AL. Insights into pancreatic islet cell dysfunction from type 2 diabetes mellitus genetics. Nat Rev Endocrinol 2020; 16:202-212. [PMID: 32099086 DOI: 10.1038/s41574-020-0325-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/17/2020] [Indexed: 12/30/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is an increasingly prevalent multifactorial disease that has both genetic and environmental risk factors, resulting in impaired glucose homeostasis. Genome-wide association studies (GWAS) have identified over 400 genetic signals that are associated with altered risk of T2DM. Human physiology and epigenomic data support a central role for the pancreatic islet in the pathogenesis of T2DM. This Review focuses on the promises and challenges of moving from genetic associations to molecular mechanisms and highlights efforts to identify the causal variant and effector transcripts at T2DM GWAS susceptibility loci. In addition, we examine current human models that are used to study both β-cell development and function, including EndoC-β cell lines and human induced pluripotent stem cell-derived β-like cells. We use examples of four T2DM susceptibility loci (CDKAL1, MTNR1B, SLC30A8 and PAM) to emphasize how a holistic approach involving genetics, physiology, and cellular and developmental biology can disentangle disease mechanisms at T2DM GWAS signals.
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Affiliation(s)
- Nicole A J Krentz
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Anna L Gloyn
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK.
- Stanford Diabetes Research Centre, Stanford University, Stanford, CA, USA.
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148
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Zeng Y, Cao Y, Halevy RS, Nguyen P, Liu D, Zhang X, Ahituv N, Han JDJ. Characterization of functional transposable element enhancers in acute myeloid leukemia. SCIENCE CHINA-LIFE SCIENCES 2020; 63:675-687. [PMID: 32170627 DOI: 10.1007/s11427-019-1574-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
Transposable elements (TEs) have been shown to have important gene regulatory functions and their alteration could lead to disease phenotypes. Acute myeloid leukemia (AML) develops as a consequence of a series of genetic changes in hematopoietic precursor cells, including mutations in epigenetic factors. Here, we set out to study the gene regulatory role of TEs in AML. We first explored the epigenetic landscape of TEs in AML patients using ATAC-seq data. We show that a large number of TEs in general, and more specifically mammalian-wide interspersed repeats (MIRs), are more enriched in AML cells than in normal blood cells. We obtained a similar finding when analyzing histone modification data in AML patients. Gene Ontology enrichment analysis showed that genes near MIRs in open chromatin regions are involved in leukemogenesis. To functionally validate their regulatory role, we selected 19 MIR regions in AML cells, and tested them for enhancer activity in an AML cell line (Kasumi-1) and a chronic myeloid leukemia (CML) cell line (K562); the results revealed several MIRs to be functional enhancers. Taken together, our results suggest that TEs are potentially involved in myeloid leukemogenesis and highlight these sequences as potential candidates harboring AML-associated variation.
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Affiliation(s)
- Yingying Zeng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rivka Sukenik Halevy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA.,Sackler School of Medicine, Tel-Aviv University, Tel Aviv, 6997801, Israel
| | - Picard Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA
| | - Denghui Liu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaoli Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA.
| | - Jing-Dong J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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149
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Mattis KK, Gloyn AL. From Genetic Association to Molecular Mechanisms for Islet-cell Dysfunction in Type 2 Diabetes. J Mol Biol 2020; 432:1551-1578. [PMID: 31945378 DOI: 10.1016/j.jmb.2019.12.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/30/2022]
Abstract
Genome-wide association studies (GWAS) have identified over 400 signals robustly associated with risk for type 2 diabetes (T2D). At the vast majority of these loci, the lead single nucleotide polymorphisms (SNPs) reside in noncoding regions of the genome, which hampers biological inference and translation of genetic discoveries into disease mechanisms. The study of these T2D risk variants in normoglycemic individuals has revealed that a significant proportion are exerting their disease risk through islet-cell dysfunction. The central role of the islet is also demonstrated by numerous studies, which have shown an enrichment of these signals in islet-specific epigenomic annotations. In recent years the emergence of authentic human beta-cell lines, and advances in genome-editing technologies coupled with improved protocols differentiating human pluripotent stem cells into beta-like cells has opened up new opportunities for T2D disease modeling. Here we review the current understanding on the genetic basis of T2D focusing on approaches, which have facilitated the identification of causal variants and their effector transcripts in human islets. We will present examples of functional studies based on animal and conventional cellular systems and highlight the potential of novel stem cell-based T2D disease models.
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Affiliation(s)
- Katia K Mattis
- Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, UK
| | - Anna L Gloyn
- Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, UK; National Institute of Health Research, Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.
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150
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Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
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Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
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