(A) Mean DNA methylation age (calculated using the multi-tissue clock; Horvath, 2013) throughout the reprogramming process where cells were transduced with our tetO-GFP-hOKMS vector and treated continuously with 2 µg/ml of doxycycline. Reprogramming is divided in three distinct phases: initiation phase (IP), maturation phase (MP), and stabilization phase (SP). DNA methylation age decreased substantially during the MP of reprogramming in cells that were successfully reprogramming (magenta line) but not in control cells (yellow and orange lines represent non-transduced cells and cells expressing hOKMS but failing to reprogram as indicated by cell surface markers, respectively). Points represent the mean and error bars the standard deviation. N=3 biological replicates per condition, where fibroblasts were derived from different donors. N=2 biological replicates for the iPSC time point (day 51). (B) Experimental scheme for maturation phase transient reprogramming (MPTR). The tetO-GFP-hOKMS reprogramming construct was introduced into fibroblasts from older donors by lentiviral transduction. Alternatively, cells were ‘mock infected’ as a negative control. Following this, cells were grown in the presence of 2 µg/ml doxycycline to initiate reprogramming. At several time points during the MP, cells were flow sorted and successfully reprogramming cells (CD13− SSEA4+) and cells that were failing to reprogram (CD13+ SSEA4−) were collected for analysis. These were termed ‘transient reprogramming intermediate’ and ‘failing to transiently reprogram intermediate,’ respectively. Sorted cells were also further cultured, and grown in the absence of doxycycline for at least 4 weeks—these were termed ‘transiently reprogrammed’ (CD13− SSEA4+) or ‘failed to transiently reprogram’ (CD13+ SSEA4−). (C) Phase-contrast microscope images of cells after doxycycline treatment (transient reprogramming intermediate) and after withdrawal of doxycycline (transiently reprogrammed) as described in (B). The morphology of some cells changed after doxycycline treatment. These cells appeared to form colonies, which became larger with longer exposure to doxycycline. After sorting, these cells were cultured in medium no longer containing doxycycline, and appeared to return to their initial fibroblast morphology. (D) Roundness ratio of cells before, during, and after MPTR (with 13 days of reprogramming). Roundness ratio was calculated by dividing maximum length by perpendicular width. Fibroblasts became significantly rounder during MPTR and returned to a more elongated state upon the completion of MPTR. Values from individual cells have been represented as violin plots. Points represent mean values and are connected with lines. Significance was calculated with a Tukey’s range test. Representative 3D renderings of cells (generated using Volocity) before, during, and after successful transient reprogramming are included below the plot. CD13 is colored in green, SSEA4 is colored in red, and DAPI staining is colored in blue. White scale bars represent a distance of 20 µm. (E) Principal component analysis of transient reprogramming and reference reprogramming sample transcriptomes (light blue to dark blue and black crosses, data from Banovich et al., 2018, Fleischer et al., 2018 and our novel Sendai reprogramming data set). Reference samples form a reprogramming trajectory along PC1. In the Sendai reprogramming reference data set, cells that were not reprogramming (CD13+ SSEA4−) were also profiled and clustered midway along PC1 suggesting some transcriptional changes had still occurred in these cells. Transient reprogramming samples moved along this trajectory with continued exposure to doxycycline (light magenta points) and returned to the beginning of the trajectory after withdrawal of doxycycline (magenta points). Control samples (yellow and orange points) remained at the beginning of the trajectory throughout the experiment. (F) Mean gene expression levels for the fibroblast specific gene FSP1 and the iPSC specific gene NANOG. Transiently reprogrammed samples expressed these genes at levels similar to control fibroblasts. Bars represent the mean and error bars the standard deviation. Samples transiently reprogrammed for 10, 13, 15, or 17 days were pooled. The number of distinct samples in each group is indicated in brackets. (G) Principal component analysis of transient reprogramming (magenta points) and reference reprogramming sample methylomes (light blue to dark blue and black crosses, data from Banovich et al., 2018, Ohnuki et al., 2014 and our novel Sendai reprogramming data set). Reference samples formed a reprogramming trajectory along PC1. Transient reprogramming samples moved along this trajectory with continued exposure to doxycycline (light magenta points) and returned to the beginning of the trajectory after withdrawal of doxycycline (magenta points). Control samples (yellow and orange points) remained at the beginning of the trajectory throughout the experiment. (H) Mean DNA methylation levels across the fibroblast-specific gene FSP1 and the iPSC-specific gene POU5F1 (encoding OCT4). Transiently reprogrammed samples had methylation profiles across these genes that resemble those found in fibroblasts. Gray bars and black bars indicate the locations of Ensembl annotated promoters and genes, respectively. Samples transiently reprogrammed for 10, 13, 15, or 17 days were pooled for visualization purposes. The number of distinct samples in each group is indicated in brackets. iPSC, induced pluripotent stem cell; MPTR, maturation phase transient reprogramming.