Analysis of Differential Epigenetic Reprogramming Potential among Pluripotent, Germ and Somatic Cell Types

In vitro spermatogenesis from induced pluripotent stem cells (iPSCs) represents a potential solution for male infertility. However, despite significant progress, in vitro spermatogenesis remains an unfulfilled challenge. Epigenetic aberrations can accrue during the reprogramming processes associated with the derivation of iPSCs and/or germ cell-like cells. I sought to test the hypothesis that residual epigenetic programming from source cell types limits the extent to which complete epigenetic reprogramming can be achieved upon induction of transitions in cell fate in vitro. To test this hypothesis, I derived iPSC lines from differentiated somatic and germ cell types, and then induced those to differentiate into primordial germ cell-like cells (PGCLCs). I analyzed each population of iPSCs or PGCLCs by bulk RNA-seq and whole-genome bisulfite sequencing to identify residual gene expression or epigenetic programming patterns retained from the source cell types. Our results show that epigenetic/transcriptional memory was inherited by iPSCs derived from different types of differentiated source cells. However, very little of the epigenetic/transcriptional memory retained during iPSC reprogramming was retained when iPSCs were induced to differentiate into PGCLCs. This appears to reflect the fact that the transition from differentiated source cell types to iPSCs recapitulates embryonic epigenetic reprogramming that normally occurs in the preimplantation embryo in vivo, whereas the transition from iPSCs to PGCLCs recapitulates germline epigenetic reprogramming that normally occurs during the fetal stages in vivo. Because, in vivo, germline reprogramming is known to erase and reset epigenetic programming more extensively than embryonic reprogramming, we conclude that this difference is recapitulated in vitro by the iPSC to PGCLC and differentiated source cell type to iPSC transitions, respectively.