A quantitative comparison of human embryonic and induced stem cell proteomes

Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. However, a clear overview of their differences at the protein level is still incomplete. In this study we characterise the proteomes of hiPSC and hESC lines, where we find that they express a similar set of proteins but show consistent quantitative differences that can be masked by the normalisation methods. hiPSCs have a higher protein content, with over 1,500 proteins showing over two-fold increased expression. They also display proteomic differences in their mitochondria, with increased expression of mitochondrial transporters and metabolic proteins as well as mitochondrial translation machinery. The hiPSCs also show higher expression of important amino acid transporters, secreted proteins, and growth factors with potential to affect neighbouring cells, coupled with a systematic reduction in the expression levels of H1 histone variants. We conclude that despite hiPSCs and hESCs being highly similar cell types, they show important differences in protein expression that may be relevant for their use in clinical research.