Quantification and reconstruction of prototypic three-dimensional brain growth using a friendly digital interface (3D-BRAIN) Quantification and reconstruction of prototypic three-dimensional brain growth using a friendly digital interface (3D-BRAIN)

Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-atlas to monitor the changes in the growth of the neuronal differentiation domain in the zebrafish hindbrain upon time (Blanc et al, eLife 2022). DAMAKER integrates spatial and temporal data of cell populations, neuronal differentiation and brain morphogenesis, through in vivo imaging techniques paired with image analyses and segmentation tools. We quantified the dynamic growth of the neuronal differentiation domain by in vivo neuronal birthdating experiments in zebrafish embryos and generated digital neuronal birthdating 3D-maps. They revealed that the temporal order of neuronal differentiation prefigured the spatial distribution of neurons in the tissue, with an inner-outer  differentiation gradient. We applied it to specific differentiated neuronal populations such as glutamatergic and GABAergic neurons, as proof-of-concept that the digital birthdating 3D-maps could be used as a proxy to infer neuronal birthdate. 

The aim of the proposal is deciphering the contribution of distinct neural progenitor pools to specific neuronal circuits. We will seek the contribution to the i) whole differentiated neuronal domain, and ii) specific functional neuronal populations according to neurotransmitter expression, during hindbrain morphogenesis. For this we will combine intersectional fate mapping, in vivo imaging and the 3D-atlas of temporal differentiation. We will use the DAMAKER to register the experimental whole 3D hindbrain images and map the neuronal differentiation patterns at different temporal stages with a unified spatial representation.


Blanc, M, Dalmasso, G, Udina, F, Pujades, C. A dynamic and expandable Digital 3D-Atlas MAKER for monitoring the temporal changes in tissue growth during hindbrain morphogenesis; eLife, 2022 in press


Hevia, CF, Engel-Pizcueta, C, Udina, F, Pujades C. The neurogenic fate of the hindbrain boundaries relies on Notch3-dependent asymmetric cell divisions. Cell Reports Jun 7; 39(10): 110915. doi:10.1016/j.celrep.2022.110915, 2022


Belmonte-Mateos, C, Pujades, C. From cell states to cell fates: how cell proliferation and neuronal differentiation are coordinated? Invited review, Frontiers in Neurosciences, 15:781160. doi:10.3389/fnins.2021.781160, 2022


Engel-Pizcueta, C, Pujades C. The interplay between mechanical cues and Notch-pathway in the regulation of cell fate during embryo development. Invited review, Frontiers in Cell and Developmental Biology 9: 711531.
doi: 10.3389/fcell.2021.711531, 2021;