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Studying the principles of cell identity transitions using naïve pluripotency induction as a model



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Stuart, Hannah Taylor  ORCID logo


In multicellular biology, an astounding array of cellular identities are specified from the same genome, by drawing on a finite pool of transcription factors and signalling pathways in different permutations. How are signal and transcription network interplay computed by the cell to instruct identity? Must a given identity always be established by the same mechanism?

To address these questions, I created defined and tractable systems based on reprogramming from epiblast stem cells to naïve pluripotency. By independent modulation of genetic and signalling parameters followed by isolation of successfully transitioning cells, I showed that naïve pluripotency can be established via distinct routes. These differ in their transcriptional trajectories and in their mechanisms, each with different genetic and signal requirements. Relative to development, one route initially moves forward, with productive cells acquiring mesodermal signature prior to naïve pluripotency induction. In contrast, another route overshoots backwards, transiently resembling the earlier embryo and recapitulating key aspects of naïve epiblast establishment in vivo.

These remarkably distinct routes ultimately converge on the same naïve pluripotent endpoint, revealing surprising flexibility for the establishment of a single identity from a single origin. This provides evidence for cellular identity as a multidimensional attractor state (Kauffman, 1993), and extends the paradigm by which transcription factors and signals are used in different combinations to generate different cell types: they can also be used in different ways to generate the same cell type.

How can the naïve pluripotent identity be reached via such different routes? I reconciled route differences, finding precise Oct4 expression as a unifying, essential and sufficient feature. Different routes achieve this required Oct4 expression by diverse logics, highlighting that successful identity change does not simply require activation of the destination network but instead pivots on the mechanism that permits a transition to occur.

Fixing Oct4 at this level is sufficient to reprogram EpiSCs and more advanced cell types under signal instruction alone, yet is also compatible with bonafide development when returned to the in vivo context. At this expression level, I therefore deem Oct4 to be a ‘transition’ factor, a novel concept that I define as permitting identity change in various directions depending on environmental instruction.

In sum, this thesis furthers our knowledge of naïve pluripotency induction in vitro and in vivo, and provides conceptual advances in our understanding of cell identity transitions.





Silva, José


pluripotency, cell identity, development


Doctor of Philosophy (PhD)

Awarding Institution

University of Cambridge
PhD funded by MRC Studentship 1233706