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Atla G, Bonàs-Guarch S, Cuenca-Ardura M, Beucher A, Crouch DJM, Garcia-Hurtado J, Moran I, Irimia M, Prasad RB, Gloyn AL, Marselli L, Suleiman M, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Todd JA, Piemonti L, Ferrer J. Genetic regulation of RNA splicing in human pancreatic islets. Genome Biol 2022; 23:196. [PMID: 36109769 PMCID: PMC9479353 DOI: 10.1186/s13059-022-02757-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 08/23/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Non-coding genetic variants that influence gene transcription in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D), and likely also contribute to type 1 diabetes (T1D) risk. For many loci, however, the mechanisms through which non-coding variants influence diabetes susceptibility are unknown. RESULTS We examine splicing QTLs (sQTLs) in pancreatic islets from 399 human donors and observe that common genetic variation has a widespread influence on the splicing of genes with established roles in islet biology and diabetes. In parallel, we profile expression QTLs (eQTLs) and use transcriptome-wide association as well as genetic co-localization studies to assign islet sQTLs or eQTLs to T2D and T1D susceptibility signals, many of which lack candidate effector genes. This analysis reveals biologically plausible mechanisms, including the association of T2D with an sQTL that creates a nonsense isoform in ERO1B, a regulator of ER-stress and proinsulin biosynthesis. The expanded list of T2D risk effector genes reveals overrepresented pathways, including regulators of G-protein-mediated cAMP production. The analysis of sQTLs also reveals candidate effector genes for T1D susceptibility such as DCLRE1B, a senescence regulator, and lncRNA MEG3. CONCLUSIONS These data expose widespread effects of common genetic variants on RNA splicing in pancreatic islets. The results support a role for splicing variation in diabetes susceptibility, and offer a new set of genetic targets with potential therapeutic benefit.
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Affiliation(s)
- Goutham Atla
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Silvia Bonàs-Guarch
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Mirabai Cuenca-Ardura
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
| | - Anthony Beucher
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Daniel J M Crouch
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Javier Garcia-Hurtado
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
| | - Ignasi Moran
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Present Address: Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rashmi B Prasad
- Lund University Diabetes Centre, Clinical Research Center, Malmö, Sweden
- Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Thierry Berney
- Cell Isolation and Transplantation Center, University of Geneva, Geneva, Switzerland
| | - Eelco J P de Koning
- Department of Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Hubrecht Institute/KNAW, Utrecht, the Netherlands
| | - Julie Kerr-Conte
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), Institute Pasteur Lille, U1190 -European Genomic Institute for Diabetes (EGID), F59000, Lille, France
| | - Francois Pattou
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), Institute Pasteur Lille, U1190 -European Genomic Institute for Diabetes (EGID), F59000, Lille, France
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lorenzo Piemonti
- Diabetes Research Institute, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Jorge Ferrer
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
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