Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach

Matteo D’Antonio,Paola Benaglio,David Jakubosky,William W Greenwald,Hiroko Matsui,Margaret K.R Donovan,He Li,Erin N Smith,Agnieszka D’Antonio-Chronowska,Kelly A Frazer

doi:10.1016/j.celrep.2018.06.091

Matteo D’Antonio, Paola Benaglio + Show 8 more

Open Access

https://doi.org/10.1016/j.celrep.2018.06.091

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Journal: Cell Reports	Publication Date: Jul 1, 2018
Citations: 79	License type: cc-by

Affiliation: University of California, San Diego

Abstract

To understand the mutational burden of human induced pluripotent stem cells (iPSCs), we sequenced genomes of 18 fibroblast-derived iPSC lines and identified different classes of somatic mutations based on structure, origin, and frequency. Copy-number alterations affected 295 kb in each sample and strongly impacted gene expression. UV-damage mutations were present in ∼45% of the iPSCs and accounted for most of the observed heterogeneity in mutation rates across lines. Subclonal mutations (not present in all iPSCs within a line) composed 10% of point mutations and, compared with clonal variants, showed an enrichment in active promoters and increased association with altered gene expression. Our study shows that, by combining WGS, transcriptome, and epigenome data, we can understand the mutational burden of each iPSC line on an individual basis and suggests that this information could be used to prioritize iPSC lines for models of specific human diseases and/or transplantation therapy.

Highlights

In the genomes of the 18 induced pluripotent stem cells (iPSCs), we found 49,388 somatic mutations: 44,441 single nucleotide variants (SNVs), 2,171 dinucleotide variants (DNVs), 2,170 small deletions, and 606 small insertions (1–51 nucleotides) (Table S2)
This difference was most likely due to the fact that these previous studies compared the whole-genome sequencing (WGS) of the iPSC lines to the parental cell population, and most somatic mutations present in the parental cell were excluded from the analysis; here, we instead compared the WGS of the skin-fibroblast-derived iPSC lines to blood DNA
Members of the same family displayed large differences in the number of somatic mutations, for instance, between the two identical twins; there was a 4-fold difference. These data show that iPSC lines have a greater number of mutations than indicated by previous studies and suggest that the heterogeneity in mutation rates across iPSC lines is heavily influenced by a factor(s) other than donor age, ethnicity, gender, or genetic background

Summary

Introduction

Somatic mutations in induced pluripotent stem cell (iPSCs) have been previously analyzed using a variety of approaches (Bhutani et al, 2016; Cheng et al, 2012; Gore et al, 2011; Laurent et al, 2011; Lo Sardo et al, 2017); a more complete understanding of mutational burden in iPSCs could increase their utility as a model system for human disease as well as for transplantation therapy. It is still unknown how to identify which somatic alterations—including those derived from the parental cell of origin as well as those that arose during reprogramming—influence molecular phenotypes in iPSCs and may have an impact on the utility of iPSC-derived tissues as an experimental model of human disease and/or influence their safety for transplantation therapy

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Conclusion