Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

Abstract

A whole-genome and transcriptome analysis of 20 human induced pluripotent stem-cell lines shows that reprogramming does not necessarily add de novo copy number variants to what is already present in the somatic cells from which they originated. The ability to derive induced pluripotent stem cells (iPSCs) from somatic cells raises exciting possibilities for the study of human development and regenerative medicine. These applications require that the clonal cells maintain the genetic background of the individual from whom they are derived, so reports of chromosomal copy number variations (CNVs) in reprogrammed cells carry serious implications for their translational utility. Flora Vaccarino and colleagues now report a whole-genome and transcriptome analysis of 20 human iPSC lines from seven individuals. They found that reprogramming does not necessarily add de novo CNVs to those already present in the somatic genome. Interestingly, they also found a mosaic CNV pattern within individuals, confirming previous findings from cultured human fibroblasts. This work shows that iPSCs can be used as a discovery tool for the investigation of genomic mosaicism due to low-frequency CNVs in human tissues. Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) has been suspected of causing de novo copy number variation1,2,3,4. To explore this issue, here we perform a whole-genome and transcriptome analysis of 20 human iPSC lines derived from the primary skin fibroblasts of seven individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two copy number variants (CNVs) not apparent in the fibroblasts from which the iPSC was derived. Using PCR and digital droplet PCR, we show that at least 50% of those CNVs are present as low-frequency somatic genomic variants in parental fibroblasts (that is, the fibroblasts from which each corresponding human iPSC line is derived), and are manifested in iPSC lines owing to their clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSCs, because most of the line-manifested CNVs reflect somatic mosaicism in the human skin. Moreover, our findings demonstrate that clonal expansion, and iPSC lines in particular, can be used as a discovery tool to reliably detect low-frequency CNVs in the tissue of origin. Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs in their genomes, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.