Single-cell transcriptional landscape of human embryonic limb development

How the limb bud gives rise to the limb is a classic paradigm of model organism developmental biology, which is uncharted in human, and incompletely understood at the molecular and cellular levels. Here, we analyze the transcriptomes of 27,426 cells from 5 human embryonic limbs between 5 and 8 weeks post-conception to build a high-resolution single-cell transcriptome atlas of embryonic limb development. We developed a new toolkit, “PLOGS”, to visualize genes guiding cell fate decisions. Using this approach, we decipher the developmental trajectories of the major mesodermal lineages, and identify regulatory factors in limb development. For the skeletal muscle lineage, we show how Pax3+ cells directly differentiate towards embryonic myocytes, as well as give rise to the Pax7+ stem cell reservoir. For the osteoblast lineage, we reveal development out of the perichondrium for the first time. Moreover, we constructed a global cell–cell signaling map, and identified an interaction between endothelial cells and muscle stem cells which directs myocyte differentiation. We highlight the importance of the cell signaling circuitry to mechanisms underlying human developmental diseases. Overall, this study illustrates the first whole human body structure charted comprehensively by single cell transcriptomics, and provides a valuable resource for the community accessible via an online portal.