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New Studies Demonstrate Utility of iPSC Technology for Genetic Research

NEW YORK (GenomeWeb) – The Next Generation Genetic Association Studies (NextGen) Consortium today published 11 studies in Cell Stem Cell, Stem Cell Reports, and EBioMedicine that show the utility of large-scale applications of induced pluripotent stem cells (iPSC) to probe the role of genetic variation in human cells, biology, and disease in the heart, liver, lung, blood, and fat systems.

The NextGen consortium is funded through a grant from the National Institutes of Health's National Heart, Lung, and Blood Institute (NHLBI) awarded in 2010. The studies are led by researchers from multiple institutions, including Boston University, Harvard University, University of Pennsylvania, Medical College of Wisconsin, Stanford University, and the University of California, San Diego.

The researchers were tasked with deriving iPSC lines for use in functional genomic research from more than 1,500 individuals, representing various conditions such as diabetes and cardiovascular disease and including healthy controls. In 2015, NHLBI designated WiCell, a Wisconsin-based nonprofit stem cell organization, to store and distribute the cell lines developed by the consortium. All cell lines used in these studies are publicly available through WiCell.

In one of four studies, led by UCSD's Kelly Frazer, the researchers used whole-genome sequencing and RNA sequencing to map expression quantitative trait loci to 215 human iPSC lines. Upon analysis, they were able to predict causal variants for these eQ trait loci, identify copy-number variant eQ trait loci, and identify effects on gene expression of rare genetic CNVs and regulatory single-nucleotide variants. Another study led by Frazer investigated variable methylation patterns in iPSC lines by looking at monozygotic twins to investigate how genetic background, clone, and passage number contribute. The researchers found reason to believe that there are non-genetic biological mechanisms that underlie aberrant methylation in iPSCs.

A third UCSD study resulted in the iPSCORE, a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals. The researchers wrote in the paper that the collection demonstrates particular utility in examining how genetic variants influence molecular and physiological traits in non-European sectors of the human population. The fourth UCSD study outlined the methods for reduced cost, high-throughput quantification of surface markers, gene expression analysis of in vitro differentiation potential, and evaluation of karyotype in iPSCs.

A study led by Harvard researchers used iPSCs to validate variants identified in genome-wide association studies. The team differentiated 68 iPSC lines into hepatocytes and adipocytes to investigate the effect of the 1p13 rs12740374 variant on cardiometabolic disease phenotypes. They saw a clear association between rs12740374 and lipid accumulation, and gene expression in differentiated hepatocytes, particularly SORT1, CELSR2, and PSRC1 in differentiated hepatocytes.

Researchers from the Medical College of Wisconsin determined the possibility of using iPSCs to find potential treatments for hypercholesterolemia. Studying hepatocyte-like cells generated from homozygous familial hypercholesterolemia iPSCs led them to the discovery that cardiac glycosides could reduce the production of apolipoprotein B which causes higher LDL-C levels, which they confirmed by reviewing medical records.

Meanwhile, a UPenn-led study developed iPSCs and hepatocyte-like cells from a multi-ethnic cohort of healthy volunteers. The researchers analyzed the developed cells, and established s2277862-CPNE1, rs10889356-DOCK7, rs10889356-ANGPTL3, and rs10872142-FRK as functional SNP-gene sets. They also found HLC eGenes CPNE1, VKORC1, UBE2L3, and ANGPTL3, and HLC ASE gene ACAA2 to be lipid-functional genes in mouse models. A second UPenn-led team generated iPSCs to define the functional effects of human hepatocyte ABCA1 deficiency. Upon analysis, the researchers found that human HLCs deficient in ABCA1 lack the ability to form nascent HDL, secrete elevated levels of VLDL-TG, and express and secrete increased amounts of ANGPTL3, an inhibitor of LPL activity.

Stanford researchers used iPSC-derived endothelial cells to uncover pathways that protect BMPR2 mutation carriers against pulmonary hypertension. Their analysis identified novel modifiers in unaffected UMC iPSC-ECs that result in a protective pattern of gene expression, and found gene candidates that might act as biomarkers for reduced risk of inherited pulmonary hypertension.

A Boston University-led study that created an ethnically diverse library of sickle cell disease-specific iPSCs, identified novel haplotype-specific polymorphisms that affect disease severity, and which could be used to develop patient-specific therapeutics for the disorder.

The final study, a collaboration between researchers at Stanford and the Icahn School of Medicine at Mount Sinai, analyzed transcriptional variability in 317 human iPSC lines. The researchers' analysis determined that approximately 50 percent of this variability could be explained by variation across individuals, indicating a donor-specific gene expression pattern that is retained in each line.

Overall, the researchers also came away with key takeaways for future iPSC studies: the number of stem cell lines needed to analyze polygenetic disease may not require hundreds of samples; very small changes in gene expression could yield surprisingly dramatic changes in a cell; and some of the effects mutations have on cells manifest before the stem cells are differentiated.

In an editorial about the Consortium's new publications, Cell Stem Cell Editor Deborah Sweet wrote, "While iPSCs show considerable promise as a complement to genome-wide association studies in understanding the functional basis of variation, there is still quite a lot of work to do in terms of standardization of protocols and understanding of best practices to make this type of approach a reliable discovery tool."