Atlas of lymphangiogenesis [scRNA-Seq]

During development, lymphatic vasculature forms as a second and distinct network that derives from embryonic blood vessels. Transdifferentiation of venous endothelial cells into specified lymphatic endothelial cells (LECs) is the first step in this process. Transdifferentiation and specification of LEC fate requires Prox1, but how Prox1 regulates transdifferentiation and differentiation is not fully understood. We present a single cell transcriptomic atlas of lymphangiogenesis spanning four key developmental stages that reveals new markers and functional regulators of lymphatic development. We extend this to comprehensively profile single cell transcriptomic and chromatin changes controlled by Prox1 using zygotic prox1a mutants, which form lymphatics that then dedifferentiate. Combining this with single cell analysis of Prox1-null, double prox1a/prox1b maternal zygotic mutants, we reveal in depth the role of Prox1 in control of LEC fate specification and differentiation. This resource reveals dual and progressive functions for Prox1, blocking blood vascular and hematopoietic fate while simultaneously up-regulating a small number of early acting genes that include tspan18a/b and lgals3a/b which are essential for lymphangiogenesis. This embryonic developmental resource will serve as a baseline to better understand both developmental and pathological lymphangiogenesis in the future. [Citations in sample metadata correspond to reference numbers in the associated publication.] Single cell RNA profiles of endothelial cells from wild type developing zebrafish across 4 stages of development (40hpf, 3dpf, 4dpf, 5dpf), Zprox-/- mutant and matched WT siblings at 4dpf, and MZprox-/- mutant and matched WT siblings at 40hpf. All code associated with this data and publication are publicly available under an open source software license at: https://atlassian.petermac.org.au/bitbucket/users/tyrone.chen/repos/hogan_lab/browse/2022_Grimm_Mason_et_al_PROX1_NatCellBiol/