Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

Abstract

Human iPS cells have been generated using a diverse range of tissues from a variety of donors using different reprogramming vectors. However, these cell lines are heterogeneous, which presents a limitation for their use in disease modeling and personalized medicine. To explore the basis of this heterogeneity we generated 25 iPS cell lines under normalised conditions from the same set of somatic tissues across a number of donors. RNA-seq data sets from each cell line were compared to identify the majority contributors to transcriptional heterogeneity. We found that genetic differences between individual donors were the major cause of transcriptional variation between lines. In contrast, residual signatures from the somatic cell of origin, so called epigenetic memory, contributed relatively little to transcriptional variation. Thus, underlying genetic background variation is responsible for most heterogeneity between human iPS cell lines. We conclude that epigenetic effects in hIPSCs are minimal, and that hIPSCs are a stable, robust and powerful platform for large-scale studies of the function of genetic differences between individuals. Our data also suggest that future studies using hIPSCs as a model system should focus most effort on collection of large numbers of donors, rather than generating large numbers of lines from the same donor.

An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion

“…31 It is now evident that differences in the quality of iPSC clones are largely due to technical variables relating to reprogramming approaches and culture conditions. 4,8,27,32 Additionally, some uncontrolled stochastic events during reprogramming undoubtedly influence gene expression and DNA methylation patterns in even functionally identical iPSC lines. Therefore, the evaluation of parameters that make iPSC line(s) indistinguishable from currently virtual but pre-existing ESCs, as well as the selection process, will be essential for identifying iPSC clones that are suitable for medical applications.…”

Transcriptional Regulation of Platelet Formation: Harnessing the Complexity for Efficient Platelet Production In Vitro

“…The emergence of genome-editing technologies such as transcription activator-like endonucleases (TALENs) and Cas9/clustered regularly interspaced short palindromic repeats (CRISPR) also offers the opportunity to introduce specific mutations in the genome of an hPSC line from which the phenotype and MK output are known using a specific differentiation protocol. The latter approach has the advantage to eliminate potential bias of interpretation due to inter-donor cell line variability [243].…”

Present and future challenges of induced pluripotent stem cells

“…On the other hand, many other reports have demonstrated that no distinct differences (including differences in epigenetic memory) exist between ESCs and iPSCs [54,[74][75][76]. The number of cells used in such studies may influence conclusions.…”