Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease

Curtis R Warren; John F O'Sullivan; Max Friesen; Caroline E Becker; Xiaoling Zhang; Poching Liu; Yoshiyuki Wakabayashi; Jordan E Morningstar; Xu Shi; Jihoon Choi; Fang Xia; Derek T Peters; Mary H C Florido; Alexander M Tsankov; Eilene Duberow; Lauren Comisar; Jennifer Shay; Xin Jiang; Alexander Meissner; Kiran Musunuru; Sekar Kathiresan; Laurence Daheron; Jun Zhu; Robert E Gerszten; Rahul C Deo; Ramachandran S Vasan; Christopher J O'Donnell; Chad A Cowan

doi:10.1016/j.stem.2017.01.010

Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease

Cell Stem Cell. 2017 Apr 6;20(4):547-557.e7. doi: 10.1016/j.stem.2017.01.010.

Authors

Curtis R Warren¹, John F O'Sullivan², Max Friesen¹, Caroline E Becker¹, Xiaoling Zhang³, Poching Liu⁴, Yoshiyuki Wakabayashi⁴, Jordan E Morningstar², Xu Shi², Jihoon Choi¹, Fang Xia¹, Derek T Peters¹, Mary H C Florido¹, Alexander M Tsankov⁵, Eilene Duberow¹, Lauren Comisar¹, Jennifer Shay¹, Xin Jiang¹, Alexander Meissner⁵, Kiran Musunuru¹, Sekar Kathiresan⁶, Laurence Daheron¹, Jun Zhu⁴, Robert E Gerszten², Rahul C Deo⁷, Ramachandran S Vasan⁸, Christopher J O'Donnell⁹, Chad A Cowan¹⁰

Affiliations

¹ Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
² Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
³ School of Medicine, Boston University, Boston, MA 02118, USA; The Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 01702, USA.
⁴ DNA Sequencing and Genomics Core, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
⁵ Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁶ Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, CPZN 5.252, Boston, MA 02114, USA.
⁷ Cardiovascular Research Institute, Department of Medicine and Institute for Human Genetics, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94143, USA.
⁸ The Framingham Heart Study, Sections of Preventive Medicine and Epidemiology and Cardiology, Framingham, MA 01702, USA; School of Medicine, Boston University, Boston, MA 02118, USA; School of Public Health, Boston University, Boston, MA 02118, USA.
⁹ The Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 01702, USA; Cardiology Section, Department of Medicine, Boston Veterans Administration Healthcare and Brigham and Women's Hospital, Boston, MA 02114, USA.
¹⁰ Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address: chad_cowan@harvard.edu.

PMID: 28388431
DOI: 10.1016/j.stem.2017.01.010

Abstract

Genome-wide association studies (GWAS) have highlighted a large number of genetic variants with potential disease association, but functional analysis remains a challenge. Here we describe an approach to functionally validate identified variants through differentiation of induced pluripotent stem cells (iPSCs) to study cellular pathophysiology. We collected peripheral blood cells from Framingham Heart Study participants and reprogrammed them to iPSCs. We then differentiated 68 iPSC lines into hepatocytes and adipocytes to investigate the effect of the 1p13 rs12740374 variant on cardiometabolic disease phenotypes via transcriptomics and metabolomic signatures. We observed a clear association between rs12740374 and lipid accumulation and gene expression in differentiated hepatocytes, in particular, expression of SORT1, CELSR2, and PSRC1, consistent with previous analyses of this variant using other approaches. Initial investigation of additional SNPs also highlighted correlations with gene expression. These findings suggest that iPSC-based population studies hold promise as tools for the functional validation of GWAS variants.

Keywords: Framingham Heart Study; RNA sequencing; SORT1; adipocytes; cardiovascular disease; directed differentiation; expression quantitative trait locus; hepatocyte-like cells; induced pluripotent stem cells; metabolomics.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

MeSH terms

Adipocytes, White / cytology
Adipocytes, White / metabolism
Cell Differentiation / genetics*
Cellular Reprogramming / genetics
Chromosomes, Human, Pair 1 / genetics
Cohort Studies
Down-Regulation / genetics
Genome-Wide Association Study*
Genotype
Hepatocytes / cytology
Humans
Induced Pluripotent Stem Cells / cytology*
Induced Pluripotent Stem Cells / metabolism
Leukocytes, Mononuclear / metabolism
Lipid Metabolism / genetics
Metabolic Diseases / genetics*
Metabolomics
Models, Genetic
Phenotype
Quantitative Trait Loci / genetics
Reproducibility of Results
Sequence Analysis, RNA
Tissue Donors
Transcriptome / genetics

Abstract

Publication types

MeSH terms

Grants and funding