Assessment of spatiotemporal development of cell lineages in the mouse blastocyst using bespoke cell neighbourhood analysis approaches

This work demonstrates the efficiency of the software IVEN (Internal Versus External Neighbourhood) in describing the dynamic changes in neighbourhoods of all cell lineages in the mammalian blastocyst. In the mouse model, the primitive endoderm (PrE)/epiblast (Epi) dichotomy is established during blastocyst formation, which results in a seemingly random distribution of cells from both lineages within the ICM (‘salt and pepper’ model). Nevertheless, differences in cell potency, plasticity and distribution suggest that specific cell traits, such as environment, might be defining the ultimate fate acquisition. We have tested the new functionalities in the latest IVEN version and its efficiency to explore the changes in cell distribution within cell lineages and sub-populations. For this purpose, we have developed pipelines that combine functionalities from the imaging software (IMARIS) with IVEN internal algorithms to provide an insight into the dynamic cell neighbourhood within the early blastocyst. IVEN returns detailed reconstructions and numerical arrays that can be interpreted to describe the evolution of cell neighbourhoods within and between lineages. Thus, we have been able to identify specific subsets of cells within the TE and the ICM lineages depending on their relative position to the blastocyst cavity and revealed distinct neighbourhood features. IVEN analyses were essential to provide quantitative understanding of the intrinsic dynamics of the mouse blastocyst. Our approach demonstrates the accuracy of IVEN as a descriptive analytical tool and offers the possibility of applying it on to other systems to uncover differences between species.