title: Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease.
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.
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Curtis R
authors.initials: CR
authors.lastname: Warren
authors.affiliation: Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: John F
authors.initials: JF
authors.lastname: O'Sullivan
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Max
authors.initials: M
authors.lastname: Friesen
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Caroline E
authors.initials: CE
authors.lastname: Becker
authors.affiliation: 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.
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Zhang
authors.affiliation: DNA Sequencing and Genomics Core, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
authors.forename: Poching
authors.initials: P
authors.lastname: Liu
authors.affiliation: DNA Sequencing and Genomics Core, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Wakabayashi
authors.affiliation: Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Jordan E
authors.initials: JE
authors.lastname: Morningstar
authors.affiliation: Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Xu
authors.initials: X
authors.lastname: Shi
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Jihoon
authors.initials: J
authors.lastname: Choi
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Fang
authors.initials: F
authors.lastname: Xia
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Derek T
authors.initials: DT
authors.lastname: Peters
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Mary H C
authors.initials: MHC
authors.lastname: Florido
authors.affiliation: 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.
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Tsankov
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Eilene
authors.initials: E
authors.lastname: Duberow
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Comisar
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Shay
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Jiang
authors.affiliation: 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.
authors.forename: Alexander
authors.initials: A
authors.lastname: Meissner
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Kiran
authors.initials: K
authors.lastname: Musunuru
authors.affiliation: Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, CPZN 5.252, Boston, MA 02114, USA.
authors.forename: Sekar
authors.initials: S
authors.lastname: Kathiresan
authors.affiliation: Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Laurence
authors.initials: L
authors.lastname: Daheron
authors.affiliation: DNA Sequencing and Genomics Core, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Gerszten
authors.affiliation: 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.
authors.forename: Rahul C
authors.initials: RC
authors.lastname: Deo
authors.affiliation: 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.
authors.forename: Ramachandran S
authors.initials: RS
authors.lastname: Vasan
authors.affiliation: 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.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: O'Donnell
authors.affiliation: 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.
authors.forename: Chad A
authors.initials: CA
authors.lastname: Cowan
mesh_terms: D052438:Adipocytes, White / Q000166:cytology / Q000378:metabolism; D002454:Cell Differentiation / Q000235:genetics*; D065150:Cellular Reprogramming / Q000235:genetics; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D015331:Cohort Studies; D015536:Down-Regulation / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D022781:Hepatocytes / Q000166:cytology; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D050356:Lipid Metabolism / Q000235:genetics; D008659:Metabolic Diseases / Q000235:genetics*; D055432:Metabolomics; D008957:Models, Genetic; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D014019:Tissue Donors; D059467:Transcriptome / Q000235:genetics
keywords: Framingham Heart Study; RNA sequencing; SORT1; adipocytes; cardiovascular disease; directed differentiation; expression quantitative trait locus; hepatocyte-like cells; induced pluripotent stem cells; metabolomics