Autocrine FGF feedback can establish distinct states of Nanog expression in pluripotent stem cells: a computational analysis

Abstract

BackgroundThe maintenance of stem cell pluripotency is controlled by a core cluster of transcription factors, NANOG, OCT4 and SOX2 – genes that jointly regulate each other’s expression. The expression of some of these genes, especially of Nanog, is heterogeneous in a population of undifferentiated stem cells in culture. Transient changes in expression levels, as well as heterogeneity of the population is not restricted to this core regulator, but involve a large number of other genes that include growth factors, transcription factors or signal transduction proteins.ResultsAs the molecular mechanisms behind NANOG expression heterogeneity is not yet understood, we explore by computational modeling the core transcriptional regulatory circuit and its input from autocrine FGF signals that act through the MAP kinase cascade. We argue that instead of negative feedbacks within the core NANOG-OCT4-SOX2 transcriptional regulatory circuit, autocrine signaling loops such as the Esrrb - FGF - ERK feedback considered here are likely to generate distinct sub-states within the “ON” state of the core Nanog switch. Thus, the experimentally observed fluctuations in Nanog transcription levels are best explained as noise-induced transitions between negative feedback-generated sub-states. We also demonstrate that ERK phosphorilation is altered and being anti-correlated with fluctuating Nanog expression – in accord with model simulations. Our modeling approach assigns an empirically testable function to the transcriptional regulators Klf4 and Esrrb, and predict differential regulation of FGF family members.ConclusionsWe argue that slow fluctuations in Nanog expression likely reflect individual cell-specific changes in parameters of an autocrine feedback loop, such as changes in ligand capture efficiency, receptor numbers or the presence of crosstalks within the MAPK signal transduction pathway. We proposed a model that operates with binding affinities of multiple transcriptional regulators of pluripotency, and the activity of an autocrine signaling pathway. The resulting model produces varied expression levels of several components of pluripotency regulation, largely consistent with empirical observations reported previously and in this present work.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-014-0112-4) contains supplementary material, which is available to authorized users.

Pluripotency gene network dynamics: System views from parametric analysis

“…The heterogeneity is dynamically maintained, with individual cells exhibiting transient changes in expression levels. Nanog heterogeneity has been widely studied by mathematical modeling approach and it was shown that the phenomenon may be inferred from properties of OSN interaction circuit, activity of signal transduction pathways or transcriptional stochasticity induced transitions [ 12 , 36 , 40 , 43 , 76 ]. Our model also describes this behavior in domains D 2 and D 3 , in which all revealed states are unstable ( Fig 3A ).…”

“…Comparing sustained oscillations and stochastic fluctuations in an agent-based model suggested that the noise-driven model more consistently explain Nanog expression dynamics in mESC populations. Coupling in simulations the OSN network to extracellular signals provided evidence that stochastic autocrine feedback loops might also generate fluctuations in Nanog expression [ 43 ]. Meanwhile, a single-molecule fluorescent in situ hybridization used to detect Nanog mRNA in mESCs, cultured in serum/LIF or 2i/LIF media, offered evidence for the stochastic nature of Nanog expression in pluripotent mESCs, independently of the culture conditions implying that NANOG fluctuations are not dependent on autocrine ERK signaling mediated by FGF4 [ 44 ].…”

Three-dimensional cell neighbourhood impacts differentiation in the inner mass cells of the mouse blastocyst

“…It has been proposed that Epi fate reinforces PrE fate in neighbouring cells via FGF4 in mid blastocysts 4,22,45,46 . NANOG expressing cells would secrete FGF4, inducing GATA6 expression in the neighbouring cells.…”

An extended model for culture-dependent heterogenous gene expression and proliferation dynamics in mouse embryonic stem cells

“…Interactions between the core network genes Nanog, Oct4 and Sox2 were kept the same as in, 31 where the authors considered the Oct4-Sox2 heterodimer complex, 40 rather than the two single genes, regulating Nanog. Modelling the former regulation only has already been proven to enable good reproduction of mESC dynamics in serum/LIF 30 , 31 , 41 – 44 and reduces the number of unknown parameters in the model. In the NIA bank analysis we found that Oct4 represses Nanog; consistently, in our network, the complex both activates Nanog, 40 and also indirectly represses Nanog via the Fgf/Erk module (see below).…”