Journal Article

A human embryonic limb cell atlas resolved in space and time

Zhang, Hui, Firth, Helen, Dean, Andrew, Fu, Yixi, Yang, Hao, He, Xiaoling, Zhang, Hongbo, Mamanova, Lira, Fasouli, Eirini S., Teichmann, Sarah A., Tuck, Elizabeth, Marioni, John C., Bolt, Liam, Chedotal, Alain, Wang, Shuaiyu, Li, Tong, Williams, Brian A., Storer, Mekayla A., Roberts, Kenny, Zhang, Bao, Kleshchevnikov, Vitalii, Bayraktar, Omer Ali, Liang, Chen, Polanski, Krzysztof, Barker, Roger A., Elmentaite, Rasa, Wold, Barbara J., Yayon, Nadav, He, Peng, Blain, Raphael, Lawrence, John E. G., Prete, Martin, FitzPatrick, David R.

2024

Overview

Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed limbs over the subsequent months 1 . This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common 2 . Decades of work with model organisms have defined the fundamental mechanisms underlying vertebrate limb development, but an in-depth characterization of this process in humans has yet to be performed. Here we detail human embryonic limb development across space and time using single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells from a few multipotent progenitors to myriad differentiated cell states, including several novel cell populations. We uncover two waves of human muscle development, each characterized by different cell states regulated by separate gene expression programmes, and identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity. Through assembly of multiple anatomically continuous spatial transcriptomic samples using VisiumStitcher, we map cells across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of the mesenchyme in the autopod. Finally, we perform single-cell RNA sequencing on mouse embryonic limbs to facilitate cross-species developmental comparison, finding substantial homology between the two species. Using single-cell and spatial transcriptomics, human embryonic limb development across space and time and the diversification and cross-species conservation of cells are demonstrated.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 13 / 13/1 / 13/109 / 13/51 / 14/32 / 14/5 / 38/109 / 38/39 / 38/62 / 38/77 / 38/91 / 631/136/2060/2433 / 631/208/212/2019 / 631/61/191/2018 / 64/60 / Animals / Atlases as Topic / Basic Helix-Loop-Helix Transcription Factors - metabolism / Brachydactyly / Brachydactyly - genetics / Cell differentiation / Cell Differentiation - genetics / Cells / Embryogenesis / Extremities - embryology / Female / Fetus - cytology / Fetus - embryology / Fetuses / Fibroblasts / Gene expression / Gene Expression Regulation, Developmental / Gene sequencing / Homology / Human performance / Humanities and Social Sciences / Humans / Leg - embryology / Life Sciences / Limb buds / Limb Buds - cytology / Limb Buds - embryology / Limb Buds - metabolism / Limbs / Mesenchyme / Mesoderm - cytology / Mesoderm - embryology / Mesoderm - metabolism / Mice / Morphogenesis / multidisciplinary / Muscle Development - genetics / Muscles / Organisms / Phenotypes / Populations / Progenitor cells / Quality control / Quorum sensing / Repressor Proteins - metabolism / Science / Science (multidisciplinary) / Single-Cell Analysis - standards / Single-Cell Gene Expression Analysis / Smooth muscle / Spatio-Temporal Analysis / Stem cells / Stem Cells - cytology / Stem Cells - metabolism / Syndactyly - genetics / Transcriptome / Transcriptomics / Vertebrates