Journal Article

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

Erdos, Michael R., Orchard, Peter, Krus, Ulrika, Viñuela, Ana, Varshney, Arushi, Boehnke, Michael, Vadlamudi, Swarooparani, Bennett, Amanda, Welch, Ryan, Hansson, Ola, Johnson, Paul, Narisu, Narisu, Gloyn, Anna L., Dermitzakis, Emmanouil T., Iyengar, Apoorva K., MacDonald, Patrick E., Nylander, Vibe, Fadista, João, Payne, Anthony, Collins, Francis S., Stitzel, Michael L., Mohlke, Karen L., Hatem, Gad, Scott, Laura J., Panousis, Nikolaos I., Brown, Andrew A., Prasad, Rashmi B., Groop, Leif, Manning Fox, Jocelyn E., McCarthy, Mark I., van de Bunt, Martijn, Oskolkov, Nikolay, Asplund, Olof, Mahajan, Anubha, Parker, Stephen C. J., Howald, Cédric

2020

Overview

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. Mechanistic inference following GWAS is hampered by the lack of tissue-specific transcriptomic resources. Here the authors combine genetic variants predisposing to type 2 diabetes with human pancreatic islet RNA-seq data. They identify 7741 islet expression quantitative trait loci (eQTLs), providing a resource for functional interpretation of association signals mapping to non-coding sequence.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38 / 38/39 / 38/43 / 45 / 45/91 / 49 / 49/91 / 631/114/2400 / 631/208/200 / 631/208/205 / 692/699/2743/137/773 / Adolescent / Adult / Aged / Aged, 80 and over / Animals / Blood Glucose - genetics / Blood Glucose - metabolism / Cell Line, Tumor / Clinical Medicine / Cohort Studies / Diabetes / Diabetes mellitus (non-insulin dependent) / Diabetes Mellitus, Type 2 - blood / Diabetes Mellitus, Type 2 - genetics / Diacylglycerol Kinase - genetics / Diacylglycerol Kinase - metabolism / Endocrinology and Diabetes / Endokrinologi och diabetes / Enhancer Elements, Genetic / Enhancers / Female / Gene expression / Gene Expression Regulation / Gene mapping / Gene regulation / Genetic diversity / Genetic Predisposition to Disease / Genetic variance / Genome-wide association studies / Genome-Wide Association Study / Genomes / Humanities and Social Sciences / Humans / Inference / Islets of Langerhans - metabolism / Klinisk medicin / Male / Mapping / Medical and Health Sciences / Medicin och hälsovetenskap / Mice / Middle Aged / multidisciplinary / Nucleotide sequence / Pancreas / Polymorphism, Single Nucleotide / Quantitative Trait Loci / Regulatory sequences / Ribonucleic acid / RNA / RNA-Seq / Science / Science (multidisciplinary) / Sequence Analysis, DNA / Tissues / Transcription / Transcription Factor 7-Like 2 Protein - genetics / Transcription Factor 7-Like 2 Protein - metabolism / Transcriptomics / Young Adult