Transcriptome analysis of OSKM- or RAS-induced senescent IMR90 fibroblasts treated with Rapamycin.

Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a. In this study, we have screened for shRNAs blunting reprogramming-induced senescence. We found that mTOR depletion bypasses OSKM-indced senescence but not RAS-induced senescence. To investigate the differences between the two types of senescence, we performed RNA-sequencing (RNA-Seq). Cells were transduced with OSKM or RAS expression and treated with 2 doses of the mTOR inhibitor Rapaycin for 10 days. Overall design: 7 samples in triplicate: IMR90 + MSCV + DMSO (Prolif), IMR90 + OSKM + DMSO (OSKM), IMR90 + OSKM + 1nM Rapamycin (OSKM1nM), IMR90 + OSKM + 10nM Rapamycin (OSKM10nM), IMR90 + RAS + DMSO (RAS), IMR90 + RAS + 1nM Rapamycin (RAS1nM) and IMR90 + RAS + 10nM Rapamycin (RAS10nM).