Exploring coherence and disorder: an analysis of spatial patterning within the neuromesodermal progenitor niche

Abstract

How regulatory frameworks control cellular identity and organisation via cell-cell communication is a poorly understood yet fundamental process in development. Different signalling pathway regulatory mechanisms can create a variety of spatial patterns of transcription factor (TF) expression and differentiation, however quantitatively assessing multicellular organisation in 3D has only recently been made possible due to advances in imaging and image analysis tools. Downstream analysis methods are still in their infancy and require further development to utilise the newly available information.

Neuromesodermal progenitors (NMPs) are a bipotent population of cells in the post gastrulation epiblast that self-renew while allocating cells to neural and mesodermal tissues of the trunk. Gradients of Retinoic acid, Wnt, and FGF signalling direct the neural vs mesoderm cell fate decision and regionalise the axial progenitor niches, but the spatial patterning of TF expression has not been quantified. Further, previous work shows that the Notch signalling pathway also regulates the cell fate decision in NMPs, but this is not well characterised and it’s unknown if Notch contributes to any TF patterning.

I aimed to use systems biology inspired analysis methods to investigate the role of Notch signalling in NMP fate and patterning. First, I investigated the pro-neural effect of Notch inhibition in NMPs and identified which Notch components are expressed.

Then, I developed quantitative analysis methods that show differential spatial patterning of key TF fate markers in NMP niches in vitro and in vivo. Finally, I explored how Notch influences this patterning, overall providing a framework for future work to analyse spatial gene expression data.