Intermediate Standstill Clones Trapped in the Reprogramming of Human Fibroblasts to Induced Pluripotent Stem Cells

Factor-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) as a powerful tool for regenerative medicine has gained wide attention in recent years. However, there are certain concerns regarding the efficiency of this reprogramming. Partially reprogrammed iPSCs (piPSCs) are stable cell lines originating from cells that have exited the normal reprogramming route at an early time point. Analysis of the associated global gene expression changes between iPSCs and piPSCs may help understand the barriers to reprogramming. In our study, human fibroblasts were transduced with the four classic transcription factors, OCT4, SOX2, KLF4, and C-MYC. Only a few cells were completely reprogrammed to a fully pluripotent state. Instead, we obtained more number of intermediate standstill clones than human-induced pluripotent stem cells (hiPSCs) during reprogramming. We studied the genome-wide expression profiles of two different fibroblasts, five intermediate standstill clones, and two iPSCs derived from the two fibroblasts. Hierarchical clustering and principal component analysis demonstrated that intermediate standstill clones were on the way to becoming hiPSCs. A remarkable difference in the expression of genes related to cancer and cell adhesion pathway was observed between the intermediate standstill clones and iPSCs. These observations suggest that some cells may become trapped in partially reprogrammed states.