Cancer-Related Mutations Are Not Enriched in Naive Human Pluripotent Stem Cells.

Giuliano Giuseppe Stirparo,Ge Guo,Austin Smith

doi:10.1016/j.stem.2020.11.014

Abstract

SummaryPrevious analysis of RNA sequencing (RNA-seq) data from human naive pluripotent stem cells reported multiple point “mutations” in cancer-related genes and implicated selective culture conditions. We observed, however, that those mutations were only present in co-cultures with mouse feeder cells. Inspection of reads containing the polymorphisms revealed complete identity to the mouse reference genome. After we filtered reads to remove sequences of mouse origin, the actual incidence of oncogenic polymorphisms arising in naive pluripotent stem cells is close to zero.

Highlights

An important consideration for the use of human pluripotent stem cells in biomedical research and regenerative medicine is the acquisition of mutations, in particular in genes associated with cancer
We reasoned that failure to detect these point mutations may have been attributable to our use of the optional variants hard-filtering step, which was designed to increase the stringency of single nucleotide polymorphisms (SNPs) calls
Culture on mouse embryo fibroblasts (MEFs) feeder layers results in the presence of mouse gene sequences in human pluripotent stem cells (hPSCs) RNA sequencing (RNA-seq) datasets, which can lead to erroneous SNP calls

Summary

Introduction

An important consideration for the use of human pluripotent stem cells (hPSCs) in biomedical research and regenerative medicine is the acquisition of mutations, in particular in genes associated with cancer. This issue was highlighted in a recent study that reported point mutations in many cancer-related genes in one-third of hPSC lines (Avior et al, 2019). The authors highlighted a 4-fold higher incidence of these mutations in naive hPSCs than in primed hPSCs. Naive cells are maintained by chemical inhibition of several signaling pathways (Dong et al, 2019), and Avior et al (2019) proposed that oncogenic mutations are selected for because they confer a growth advantage in the presence of the inhibitors. The finding of mutations in genes linked to growth and cancer raises potentially grave concerns about consequences for in vitro phenotypes and in vivo tumorigenicity

Results

Discussion

Conclusion