Pluripotent cells can be subdivided into two distinct states, the naïve and
the primed state, the latter being further advanced on the path of
differentiation. There are substantial differences in the regulation of
pluripotency between human and mouse, and in humans only stem cells that
resemble the primed state in mouse are readily available. Reprogramming of
human stem cells into a more naïve-like state is an important research focus.
Here, we developed a pipeline to reanalyze transcriptomics data sets that
describe both states, naïve and primed pluripotency, in human and mouse. The
pipeline consists of identifying regulated start-ups/shut-downs in terms of
molecular interactions, followed by functional annotation of the genes
involved and aggregation of results across conditions, yielding sets of
mechanisms that are consistently regulated in transitions towards similar
states of pluripotency. Our results suggest that one published protocol for
naïve human cells gave rise to human cells that indeed share putative
mechanisms with the prototypical naïve mouse pluripotent cells, such as DNA
damage response and histone acetylation. However, cellular response and
differentiation-related mechanisms are similar between the naïve human state
and the primed mouse state, so the naïve human state did not fully reflect the
naïve mouse state