iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation

Kara Quaid, Xiaoyun Xing, Yi-Hsien Chen, Yong Miao, Amber Neilson, Vijayalingam Selvamani, Aaron Tran, Xiaoxia Cui (), Ming Hu () and Ting Wang ()
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Kara Quaid: Washington University in St. Louis
Xiaoyun Xing: Washington University in St. Louis
Yi-Hsien Chen: Washington University School of Medicine in St. Louis
Yong Miao: Washington University School of Medicine in St. Louis
Amber Neilson: Washington University School of Medicine in St. Louis
Vijayalingam Selvamani: Washington University School of Medicine in St. Louis
Aaron Tran: Washington University in St. Louis
Xiaoxia Cui: Washington University School of Medicine in St. Louis
Ming Hu: Cleveland Clinic Foundation
Ting Wang: Washington University in St. Louis

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Understanding the interaction between genetic and epigenetic variation remains a challenge due to confounding environmental factors. We propose that human induced Pluripotent Stem Cells (iPSCs) are an excellent model to study the relationship between genetic and epigenetic variation while controlling for environmental factors. In this study, we have created a comprehensive resource of high-quality genomic, epigenomic, and transcriptomic data from iPSC lines and three iPSC-derived cell types (neural stem cell (NSC), motor neuron, monocyte) from three healthy donors. We find that epigenetic variation is most strongly associated with genetic variation at the iPSC stage, and that relationship weakens as epigenetic variation increases in differentiated cells. Additionally, cell type is a stronger source of epigenetic variation than genetic variation. Further, we elucidate a utility of studying epigenetic variation in iPSCs and their derivatives for identifying important loci for GWAS studies and the cell types in which they may be acting.

Date: 2025
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DOI: 10.1038/s41467-025-56569-4

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