CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant Journal Article

   

Authors:	Kaplan, S. J.; Wong, W.; Yan, J.; Pulecio, J.; Cho, H. S.; Li, Q.; Zhao, J.; Leslie-Iyer, J.; Kazakov, J.; Murphy, D.; Luo, R.; Dey, K. K.; Apostolou, E.; Leslie, C. S.; Huangfu, D.
Article Title:	CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant
Abstract:	Functional enhancer annotation is critical for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants. However, unbiased enhancer discovery in disease-relevant contexts remains challenging. To identify enhancers pertinent to diabetes, we conducted a CRISPR interference (CRISPRi) screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system. Among the enhancers identified, we focused on an enhancer we named ONECUT1e-664kb, ∼664 kb from the ONECUT1 promoter. Previous studies have linked ONECUT1 coding mutations to pancreatic hypoplasia and neonatal diabetes. We found that homozygous deletion of ONECUT1e-664kb in hPSCs leads to a near-complete loss of ONECUT1 expression and impaired pancreatic differentiation. ONECUT1e-664kb contains a type 2 diabetes-associated variant (rs528350911) disrupting a GATA motif. Introducing the risk variant into hPSCs reduced binding of key pancreatic transcription factors (GATA4, GATA6, and FOXA2), supporting its causal role in diabetes. This work highlights the utility of unbiased enhancer discovery in disease-relevant settings for understanding monogenic and complex disease. © 2024 The Authors
Keywords:	controlled study; human cell; single nucleotide polymorphism; nonhuman; flow cytometry; outcome assessment; animal cell; mouse; animal tissue; gene; gene expression; animal experiment; cell differentiation; immunofluorescence; genetic transfection; chromatin immunoprecipitation; diabetes mellitus; pluripotent stem cell; dna extraction; fluorescence activated cell sorting; non insulin dependent diabetes mellitus; vus; type 2 diabetes; enhancer; transcription factor gata 4; transcription factor gata 6; hepatocyte nuclear factor 3beta; meis1 gene; pancreas islet cell; variant of uncertain significance; human; article; clustered regularly interspaced short palindromic repeat; droplet digital polymerase chain reaction; sox17 gene; rxra gene; pancreas development; gata4 gene; gata6 gene; gsc gene; cp: molecular biology; hhex gene; mafa gene; cp: developmental biology; crispri screen; neonatal diabetes; non-coding variant; onecut1; t2d; gtf3a gene; hnf1b gene; hnf4a gene; isl1 gene; mbd3 gene; nr5a2 gene; nsm1 gene; onecut1 gene; onecut2 gene; pbx1 gene; rfx6 gene; sox13 gene; zbtb20 gene
Journal Title:	Cell Reports
Volume:	43
Issue:	8
ISSN:	2211-1247
Publisher:	Cell Press
Date Published:	2024-08-27
Start Page:	114640
Language:	English
DOI:	10.1016/j.celrep.2024.114640
PROVIDER:	scopus
PUBMED:	39163202
PMCID:	PMC11406439
DOI/URL:	https://www.scopus.com/inward/record.uri?eid=2-s2.0-85201504740&doi=10.1016%2fj.celrep.2024.114640&partnerID=40&md5=69c8464b3a680622b1cad2e25f0a6739
Notes:	Article -- MSK Cancer Center Support Grant (P30 CA008748) acknowledged in PDF -- MSK corresponding author is Danwei Huangfu -- Source: Scopus

https://synapse.mskcc.org/synapse/works/has_related_data_chk/218043