GSE195511
Triple transgenic reprogrammable mouse model reveals no evidence of epigenetic memory in reprogrammed cells/induced pluripotent stem cells
Virtually any nucleated somatic cell can be reprogrammed to an induced pluripotent stem cell (iPSC). The process of reprogramming involves epigenetic remodelling to turn on pluripotency-associated genes and turn off lineage-specific genes. Some evidence shows that iPSC retain epigenetic marks of their cell of origin and this “epigenetic memory” influences differentiation potential, with a preference towards their cell of origin. Here, we reprogrammed proximal tubule cells (PTC) and tail tip fibroblasts (TTF), from a reprogrammable mouse, to iPSC and differentiated the iPSC to renal progenitors to understand if epigenetic memory plays a role in renal differentiation. The reprogrammable mouse model allowed us to eliminate the variability due to different cell donors and transfection of the reprogramming factors. We showed that early passage PTC iPSC and TTF iPSC expressed low levels of renal progenitor genes and high levels of pluripotency-associated genes, and the transcriptional levels of these genes were not significantly different between PTC iPSC and TTF iPSC. In agreement with this, we used ChIP-seq to demonstrate that the H3K4me3, H3K27 and H3K36me3 profiles of PTC iPSC and TTF iPSC were not different from each other for kidney developmental genes and pluripotency-associated genes. DNA methylation also demonstrated no difference between PTC iPSC and TTF iPSC. However, when the iPSC were differentiated to renal progenitors, the progenitors derived from PTC iPSC expressed higher levels of some renal progenitor genes compared to progenitors derived from TTF iPSC. This demonstrates that although PTC iPSC and TTF iPSC are epigenetically identical, there are still differences in their response and sensitivity to differentiation cues and this ultimately influences their differentiation propensity. Overall design: iPSCs were obtained from reprogramming of either mouse proximal tubule cells (PTC) or tail tip fibroblasts (TTF) from triple transgenic reprogrammable mice. Samples were generated in duplicates from two separate mice. Epigenetic memory was assessed through Oxford Nanopore Technologies long-read DNA sequencing (lrDNAseq), treated in duplicates, followed by DNA methylation analyis using the Nanopolish software. Chromatin Immunoprecipitation sequencing (ChIP-seq) was also performed for H3K4me3, H3K36me3 and H3K27me3.