Comprehensive Proteogenomic Analysis of Human Embryonic and Induced Pluripotent Stem Cells

Although the concepts of reprogramming and human induced pluripotent stem cells (hiPSCs) generation have undergone to several analysis to strengthen the usefulness of these cells in research and clinic, it still remains controversial whether the hiPSCs are really equivalent to human embryonic stem cells, pointing to the need of further characterizations in order to gain a more comprehensive understanding of human stem cells pluripotency. Most of the experimental evidence comes from the transcriptome analysis, while a little information is available on protein data, and even less is known about the post-translational modifications. Here we report a combined strategy of nLC-MS/MS and gene expression profiling for proteogenomic analysis of two distinct stem cell lines, the commercially available hESCs H9 and the hiPSCs, obtained in our laboratory by reprogramming of peripheral blood T-lymphocytes with the Sendai virus-driven Yamanaka’s 4-transcription factors cocktail. The analysis was further enriched by the study of the phosphoproteomic profile of the two PSC lines. The results obtained through this integrated, multi -“omics” approach, indicate that a small number of distinct pathways is enriched in reprogrammed versus naïve pluripotent stem cells, supporting the view that pluripotency is an extremely complex, multifaceted phenomenon, with peculiarities that are characteristic of each cell type. human induced pluripotent stem cells (hiPSCs) and H9 cells; triplicates