CRISPR Gene Editing in Stem Cells

Cell Stem Cell

Article

An Isogenic Human ESC Platform for Functional

Evaluation of Genome-wide-Association-Study-

Identified Diabetes Genes and Drug Discovery

Hui Zeng,

1,3,9

Min Guo,

2,3,9

Ting Zhou,

Lei Tan,

Chi Nok Chong,

Tuo Zhang,

Xue Dong,

Jenny Zhaoying Xiang,

Albert S. Yu,

Lixia Yue,

Qibin Qi,

Todd Evans,

Johannes Graumann,

4,8

and Shuibing Chen

3,4,

Department of Hematology in Xiangya Hospital

Department of Endocrinology in Xiangya Hospital

Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China

Department of Surgery

Department of Biochemistry

Genomic Core

Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA

Calhoun Cardiology Center and Department of Cell Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington,

CT 06030, USA

Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA

Research Division, Weill Cornell Medical College in Qatar, Doha, State of Qatar

Co-first author

*Correspondence:

shc2034@med.cornell.edu http://dx.doi.org/10.1016/j.stem.2016.07.002

SUMMARY

Genome-wide association studies (GWASs) have

increased our knowledge of loci associated with

a range of human diseases. However, applying

such findings to elucidate pathophysiology and pro-

mote drug discovery remains challenging. Here, we

created isogenic human ESCs (hESCs) with muta-

tions in GWAS-identified susceptibility genes for

type 2 diabetes. In pancreatic beta-like cells differ-

entiated from these lines, we found that muta-

tions in CDKAL1, KCNQ1, and KCNJ11 led to

impaired glucose secretion in vitro and in vivo, coin-

ciding with defective glucose homeostasis. CDKAL1

mutant insulin+ cells were also hypersensitive to

glucolipotoxicity. A high-content chemical screen

identified a candidate drug that rescued CDKAL1-

specific defects in vitro and in vivo by inhibiting

the FOS/JUN pathway. Our approach of a proof-of-

principle platform, which uses isogenic hESCs for

functional evaluation of GWAS-identified loci and

identification of a drug candidate that rescues

gene-specific defects, paves the way for precision

therapy of metabolic diseases.

INTRODUCTION

Multiple genome-wide association studies (GWASs) have

correlated type 2 diabetes mellitus (T2DM) with genetic vari-

ants, yielding a large number of loci and associated gene

products that are linked to the disease phenotype—often

with little or no insight into the mechanism underlying

that link (Hivert et al., 2014). The current challenge is to

establish robust systems to systematically evaluate the role

of these loci using disease-relevant cells. Previous studies

have used patient samples, cell lines, or animal models to

seek mechanistic insight but with significant limitations. Large

variation is observed in primary patient samples, perhaps due

to genetic heterogeneity, whereas animal models present

major physiological and metabolic differences that hamper

understanding of the precise function of human genes in

T2DM. Therefore, a robust system to systematically evaluate

the role of T2DM-associated genes using disease-relevant

human cells will provide an important tool for diabetes

research and spur the development of precision (allele-spe-

cific) therapies, exemplified by the use of sulfonylurea drugs

to treat patients carrying certain

KCNJ11

mutations (Gloyn

et al., 2004).

Human embryonic stem cells (hESCs) and human induced

pluripotent stem cells (hiPSCs) provide platforms to recapitu-

late cellular pathology of human diseases. Whereas two iPSC

models have been used to mimic pancreatic beta cell defects

in neonatal and inherited forms of diabetes, maturity onset dia-

betes of young 2 (Hua et al., 2013) and Wolfram syndrome pa-

tients (Shang et al., 2014), there is no robust model reported

for T2DM-associated loci in the literature. Here, we focused on

CDKAL1

KCNQ1

, and

KCNJ11

loci that were identified and

confirmed through the first wave of T2DM GWASs. Risk alleles

of the genetic variants at these loci are associated with aspects

of beta cell function (HOMA-B) rather than insulin resistance

(HOMA-IR) (Saxena et al., 2007; Scott et al., 2007; Steinthorsdot-

tir et al., 2007; Unoki et al., 2008; Yasuda et al., 2008). Some

studies suggested potential roles of these genes in pancreatic

beta cell function or survival. For example, knockdown of

Cdkal1

enhanced endoplasmic reticulum (ER) stress in insulinoma

cells (Brambillasca et al., 2012), whereas

Cdkal1

mice show

reduced first-phase insulin exocytosis (Ohara-Imaizumi et al.,

326

Cell Stem Cell

, 326–340, September 1, 2016

2016 Elsevier Inc.