Modeling Epigenetic Reprogramming of Mammalian Cells

While combinatorial transcription factor (TF) ‘codes’ for specifying cell types during mammalian development in vivo have been previously described [e.g., neural patterning; Jessell], several recent discoveries demonstrate that combinations of only 3-10 TFs can also mediate cell state transitions in vitro when expressed transiently: Oct4-Sox2-cMyc-Klf4 for somatic cells to induced pluripotent stem cells [iPSCs; Yamanaka]; Ascl1-Brn2-Myt1l for fibroblasts to induced neurons [Wernig]; and, Gata4-Mef2c-Tbx5 for fibroblasts to induced cardiomyocytes [Srivastava]. These efforts ‘epigenetically reprogram’ mammalian cells for anticipated cell therapy and disease modeling applications, but detailed understanding of the molecular mechanisms driving reprogramming is lacking.

In this work, we monitored the somatic to iPSC transition quantitatively and found that the process is stochastic and inefficient, with long multiple-day-timescales for rate-limiting processes to occur.  We also discovered that somatic cells can be reprogrammed to distinct pluripotent states – naïve and primed - corresponding to the inner cell mass and epiblast embryonic developmental stages, respectively. The induction of specific cell types (e.g., naïve or primed) are, in general, highly sensitive to the specific in vitro culture conditions during reprogramming. The observed dynamics of these processes suggest that the conversion from a somatic cell to an iPSC upon continued growth and TF expression can be thought of as a drift in cell state. This cell state can be defined by a gene expression or epigenetic pattern, whose fluctuations drive the conversion to an iPSC. Such quantitative parameterization and modeling of cell state may provide a general framework to molecularly track and dissect epigenetic reprogramming processes in mammalian cells.