Periodic Reporting for period 2 - CROSSINGSCALES (Reverse Scale-Crossing Effects In Biology)
Période du rapport: 2022-03-01 au 2023-08-31
can be quantitatively compared in terms of their size, shape, molecular composition and relative spatial organization. Using high-resolution multiplexed immunofuorescence, this reveals how subcellular organization changes upon perturbation of RNA synthesis, RNA processing or cell size, and uncovers links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates. By capturing interpretable cellular phenotypes, we anticipate that CAMPA will greatly accelerate the systematic mapping of multiscale atlases of biological organization to identify the rules by which context shapes physiology and disease. This work was published in Spitzer et al., 2023 (PMID 37248388). In addition, we also started to apply these approaches to in vitro grown multicellular systems, or organoids, and in particular to retinal organoids that recapitulate the development of the human retina created from human induced pluripotent stem cells. To study how context across scales influences the development of these systems, we generated multiplexed protein maps over a retinal organoid time course and primary adult human retinal tissue. We developed a toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components and global patterning in each organoid and primary tissue. In addition, we generated a single-cell transcriptome and chromatin accessibility timecourse dataset and inferred a gene regulatory network underlying organoid development. We integrated genomic data with spatially segmented nuclei into a multimodal atlas to explore organoid patterning and retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death and showing that mosaic genetic perturbations in retinal organoids provide insight into cell fate regulation. This work was published in Wahle et al., 2023 (PMID 37156914).