High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells

Abstract

Summary: Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers the possibility of studying the molecular mechanisms underlying human diseases in cell types difficult to extract from living patients, such as neurons and cardiomyocytes. To date, studies have been published that use small panels of iPSC-derived cell lines to study monogenic diseases. However, to study complex diseases, where the genetic variation underlying the disorder is unknown, a sizable number of patient-specific iPSC lines and controls need to be generated. Currently the methods for deriving and characterizing iPSCs are time consuming, expensive, and, in some cases, descriptive but not quantitative. Here we set out to develop a set of simple methods that reduce cost and increase throughput in the characterization of iPSC lines. Specifically, we outline methods for high-throughput quantification of surface markers, gene expression analysis of in vitro differentiation potential, and evaluation of karyotype with markedly reduced cost. : Working as part of the NHLBI NextGen consortium, D'Antonio and colleagues developed three simple methods that reduce cost and increase throughput in the characterization of iPSCs. These methods include: (1) fluorescent cell barcoding flow cytometry to investigate heterogeneity; (2) gene expression analysis to examine in vitro differentiation potential; and (3) high-resolution digital karyotyping to detect chromosomal aberrations. Keywords: induced pluripotent stem cells, high-throughput methods, pluripotency characterization, differentiation potential, flow cytometry, qPCR, SNP arrays, digital karyotyping, fluorescent cell barcoding