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

Summary Previous 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 • Culture conditions for naive stem cells do not select for cancer-related mutations • Contaminating sequences in RNA-seq data can be misidentified as point mutations • Filtering to remove mouse sequences eliminates most mutations • Remaining mutations in naive stem cells are carried over from primed stem cells
Acquisition of pathogenic mutations during in vitro propagation is a concern for applications of pluripotent stem cells. In this paper, Stirparo and colleagues show that detection of multiple mutations in naïve stem cells by RNA-seq analysis is due to contamination with mouse sequences. The actual cancer mutation incidence is low.