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Piron, A.* ; Szymczak, F.* ; Folon, L.* ; Crouch, D.J.M.* ; Papadopoulou, T.* ; Lytrivi, M.* ; Tong, Y.* ; Alvelos, M.I.* ; Colli, M.L.* ; Yi, X.* ; Pekalski, M.L.* ; Hatzikotoulas, K. ; Huerta-Chagoya, A.* ; Taylor, H.J.* ; Defrance, M.* ; Todd, J.A.* ; Eizirik, D.L.* ; Mercader, J.M.* ; Cnop, M.*

Identification of novel type 1 and type 2 diabetes genes by co-localization of human islet eQTL and GWAS variants with colocRedRibbon.

Cell Genom. 5:101004 (2025)

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	Open Access Gold

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Over 1,000 genetic variants have been associated with diabetes by genome-wide association studies (GWASs), but for most, their functional impact is unknown; only 7% alter gene expression in pancreatic islets in expression quantitative trait locus (eQTL) studies. To fill this gap, we developed a co-localization pipeline, colocRedRibbon, that prefilters eQTLs by the direction of effect on gene expression and shortlists overlapping eQTL and GWAS variants prior to co-localization. Applying colocRedRibbon to recent diabetes and glycemic trait GWASs, we identified 292 co-localizing gene regions, including 24 co-localizations for type 1 diabetes and 268 for type 2 diabetes and glycemic traits, representing a 4-fold increase. A low-frequency type 2 diabetes protective variant increases islet MYO5C expression, and a type 1 diabetes protective variant increases FUT2 expression. These novel co-localizations advance the understanding of diabetes genetics and its impact on human islet biology. colocRedRibbon has broad applicability to co-localize GWASs and various QTLs.

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Publication type Article: Journal article

Document type Scientific Article

Keywords Gwas ; Co-localization ; Colocredribbon ; Diabetes ; Eqtl ; Genetics ; Glycemic Traits ; Insulin ; Meqtl ; Multi-ancestry ; Pqtl ; Pancreatic Islets ; β Cells; Expression; Insights; Genetics; Adipose; Loci

ISSN (print) / ISBN 2666-979X

e-ISSN 2666-979X

Journal Cell Genomics

Quellenangaben Volume: 5, Issue: 11, Article Number: 101004

Publisher Elsevier

Publishing Place 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa

Reviewing status Peer reviewed

Institute(s) Institute of Translational Genomics (ITG)

Grants Medical University of Bialystok (MUB) grant from the Ministry of Science and Higher Education (Poland)
Leona M. and Harry B. Helmsley Charitable Trust
European Federation of Pharmaceutical Industries and Associations, JDRF
European Union's Horizon 2020 research and innovation programme
Innovative Medicines Initiative 2 Joint Undertaking
Walloon Region strategic axis FRFS-WELBIO
FRS-FNRS under the Excellence of Science (EOS) programme
FWO
Fonds National de la Recherche Scientifique (FNRS)
Fonds David et Alice Van Buuren
Fondation Jaumotte-Demoulin
Fondation Wiener-Anspach
National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health
American Diabetes Association
National Institutes of Health NIDDK
National Institutes of Health Human Islet Research Network Consortium on Beta Cell Death & Survival from Pancreatic beta-Cell Gene Networks
JDRF (now Breakthrough T1D)
Research Fellow FNRS fellowship
FNRS
European Union's Horizon 2020 research and innovation programme T2DSystems