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.

Tissue chips – innovative tools for drug development and disease modeling

“…For example, iPSC-derived cardiac and fat tissue was recently produced from peripheral blood cells of 34 donor participants in the Framingham heart study cohort. Genetic variants with known phenotypic signatures were investigated and results were in line with those from previous analyses using different approaches – this being one of the first studies to functionally validate variants found from a GWAS 73 . A number of successful 3D models utilizing human iPS-derived cells have been developed, and include gut and stomach organoids that have allowed investigation of enteric infections such as pathogen-induced diarrhea and stomach ulcers 74, 75 ; iPSC-derived human brain organoids and MPS which illustrate features of human cortical development 76 and can be used to model demyelinating disorders such as multiple sclerosis 77 ; and human embryonic-derived iPS neural constructs described above for developmental neurotoxicity screening 23 .…”

Modeling schizophrenia pathogenesis using patient-derived induced pluripotent stem cells (iPSCs)

“…Recently, with the aim of studying phenotype effect of genotypes with iPSC-derived specific cell types, the NextGen consortium was formed [72]. Their initial proof of principle studies showed that indeed iPSC-derived specific cell types can be used for this purpose, accurately recreating in vivo phenotype [73]. This type of collaborative large-scale study could help reach greater statistical power needed for eQTL studies.…”

Treatment of Dyslipidemia Using CRISPR/Cas9 Genome Editing

“…Additionally, genome editing to introduce specific mutations in iPSCs affords the opportunity to screen for therapies to treat conditions caused by the mutations. A number of examples of the use of iPSCs for the study and treatment of lipid metabolism disorders have recently been reported [27–32]. In one notable example, iPSC-derived hepatocytes from a patient with familial hypercholesterolemia were used to identify cardiac glycosides as a potential treatment for dyslipidemia [31].…”