Plate IV.40 · Publications
An integrated single cell and spatial omics atlas of human prenatal development
Preprint in bioRxiv, 1 April 2026.
Abstract
Single cell genomics has enabled analysis of human prenatal development at unprecedented resolution. However, most studies have relied on dissociated tissues during restricted windows of development, limiting insights into how spatially distributed networks of cells, and multicellular niches emerge and adapt to distinct organ microenvironments in situ. Moreover, existing human developmental atlases have not yet been harmonised, and we thus lack a comprehensive catalogue of known cell types in the developing human body. Here, we introduce the Human Developmental Cell Atlas (HDCA), a unified structural, cellular and molecular resource for prenatal human development. The HDCA integrates published and unpublished single cell/nucleus RNAseq atlases across prenatal organs, and includes a newly generated, spatially resolved, multimodal cell atlas of intact human embryos. Spanning 4-22 post conceptional weeks, capturing embryonic and early to mid fetal stages, the HDCA contains ∼4.6 million cells/nuclei which resolve into ∼450 cell types, explorable with a bespoke web portal. For a global overview of the human embryo’s multicellular communities, we applied unsupervised deep learning to our intact human embryo spatial data, charting 114 tissue niches that are structural and signalling hubs for the cellular interactions of the embryo. Guided by these niches, we profiled cellular networks over space and time, not examinable using single-organ atlases. In so doing, we revealed tissue-specific fibroblast patterning from previously undescribed mesenchyme progenitors, early diversification of organ-specific blood capillaries and lymphatic vasculature, emergence of neural crest cell fates, the formation of placode-and neural crest-derived peripheral sensory neurons, and how tissue niches guide peripheral neuron maturation and axonal migration. The HDCA thus serves as a comprehensive step towards a comprehensive understanding of human prenatal development, and a template towards unravelling the biology of congenital disorders.
Cite
@misc{webb2026integrated,
title = {{An integrated single cell and spatial omics atlas of human prenatal development}},
author = {Webb, Simone and Rose, Antony and Xu, Chuan and Steele, Lloyd and Kuri, Masami A and Stephenson, Emily and Inecik, Kemal and Jafree, Daniyal and Foster, April R and Basurto-Lozada, Daniela and Chipampe, Nana-Jane and Pournara, Anna V and Jacques, Marc-Antoine and To, Ken and Admane, Chloe and Kritikaki, Efpraxia and Chroscik, Marta A and Horsfall, David and Foreman, Julia and Rademaker, Koen and Karjalainen, Julia and Laddach, Anna and Madad, Shaista and Lawrence, John E G and Kleshchevnikov, Vitalii and Lisgo, Steven and Lee, Jimmy Tsz Hang and Blevinal, Joséphine and Alqahtani, Ahlam and Makarchuk, Stanislaw and Jackson, Jake and Ucuncu, Ekin and Silva, Teresa P and Lorenzi, Valentina and Torabi, Fereshteh and Botting, Rachel A and Roberts, Kenny and Olabi, Bayanne and Chakala, Keerthi P and Dony, Leander and Dall’Aglio, Gabriele and Cujba, Ana-Maria and Whitfield, Holly J and Hale, Christine and Engelbert, Justin and Li, Tong and Prigmore, Elena and Gopee, Nusayhah Hudaa and Mather, Michael W and Talks, Ben and Fei, Lijiang and Pereira, Diana and Moldovan, Corina and Elmentaite, Rasa and Polanski, Krzysztof and Predeus, Alexander V and Mazin, Pasha and Rowe, Vicky and Bayraktar, Semih and Knight-Schrijver, Vincent R and Clatworthy, Menna and Kanemaru, Kazumasa and Cranley, James and Guo, Andrew and Sinha, Sanjay and McDonald, David and Filby, Andrew and Kerwin, Janet and He, Peng and Sequeira, Inês and Vento-Tormo, Roser and Luecken, Malte D. and Chédotal, Alain and Taylor, Deanne and Martin-Almedina, Silvia and Ostergaard, Pia and Behjati, Sam and Robertson, Elizabeth and Wilson, Nicola K and Marioni, John and Firth, Helen V and Wright, Caroline F and Pourquie, Olivier and Gambardella, Laure and Alexandre, Paula and Gottgens, Berthold and Meyer, Kerstin B and Vijayabaskar, MS and Lotfollahi, Mo and Teichmann, Sarah A and Theis, Fabian J and Progatzky, Fränze and Bayraktar, Omer Ali and Haniffa, Muzlifah},
howpublished = {bioRxiv},
publisher = {openRxiv},
year = {2026},
month = apr,
doi = {10.64898/2026.03.30.714220},
url = {https://doi.org/10.64898/2026.03.30.714220},
note = {Preprint}
}