Normal and pathological human embryology

Principal investigator: Alain CHEDOTAL

Embryo | Fetus | Development | Tissue clearing | Cell atlas | 3D imaging | Evolution | Developmental disorders | Light sheet microscopy | Cell Atlas

 Our team uses cutting-edge 3D imaging techniques, powerful image analysis pipelines and transcriptomics to study the development of several human organs and address long-standing questions in developmental biology.

Developmental diseases are a major public healthcare burden and today the molecular and cellular mechanisms that ensure correct tissue morphogenesis in humans remain largely unknown. We are trying to build high-resolution cellular maps of human embryonic organs including the nervous system, muscles, vasculature, skeleton and branched organs. This should help Understanding human development and the etiology of ontogenic diseases.

A tridimensional atlas of the developing human head

3D visualization of the tongue and larynx muscles and their innervation in a PCW7.5 human embryo; 3D visualization of extraocular muscles and oculomotor nerves in a PCW8.4 human fetus; 3D visualization of extraocular muscles, oculomotor nerves and lacrimal gland in a PCW11.3 human fetus; 3D visualization of the external, middle, and inner ear in a PCW7.5 human embryo. Blain et al., 2024 Cell


HuDeCa HuDeCA (Human Developmental Cell Atlas) is a 5-year program initiated by Inserm to build a reference atlas of embryonic and fetal human cell types. The project has been designed from the outset to enable contributions to the Human Cell Atlas (HCA), an ambitious international initiative to map all normal cell states of the body at every human life stages.

Transparent Human Embryo

Transparent Human Embryo The Collection of Immunolabeled Transparent Human Embryos and Fetuses is the most advanced molecular embryology tool. Building upon the pioneering ‘DISCO’ clearing methods developed for rodent embryos, we have shifted gears to another level, where direct knowledge of molecular and cellular ontogenesis may prove critical to improve Human pregnancy.

Team members

  • Alain CHEDOTALProfessor, UCBL, HDR

Selected publications

  1. A tridimensional atlas of the developing human head.
    Blain R, Couly G, Shotar E, Blévinal J, Toupin M, Favre A, Abjaghou A, Inoue M, Hernández-Garzón E, Clarençon F, Chalmel F, Mazaud-Guittot S, Giacobini P, Gitton Y, Chédotal A.
    Cell (2023) — Show abstract
  2. A human embryonic limb cell atlas resolved in space and time.
    Zhang B, He P, Lawrence JEG, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, Li T, Elmentaite R, Fasouli ES, Prete M, He X, Yayon N, Fu Y, Yang H, Liang C, Zhang H, Blain R, Chedotal A, FitzPatrick DR, Firth H, Dean A, Bayraktar OA, Marioni JC, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA.
    Nature (2023) — Show abstract
  3. Yolk sac cell atlas reveals multiorgan functions during human early development.
    Goh I, Botting RA, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Quiroga Londoño M, Mather M, Mende N, Imaz-Rosshandler I, Yang L, Horsfall D, Basurto-Lozada D, Chipampe NJ, Rook V, Lee JTH, Ton ML, Keitley D, Mazin P, Vijayabaskar MS, Hannah R, Gambardella L, Green K, Ballereau S, Inoue M, Tuck E, Lorenzi V, Kwakwa K, Alsinet C, Olabi B, Miah M, Admane C, Popescu DM, Acres M, Dixon D, Ness T, Coulthard R, Lisgo S, Henderson DJ, Dann E, Suo C, Kinston SJ, Park JE, Polanski K, Marioni J, van Dongen S, Meyer KB, de Bruijn M, Palis J, Behjati S, Laurenti E, Wilson NK, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M.
    Science (2023) — Show abstract
  4. Single-cell roadmap of human gonadal development.
    Garcia-Alonso L, Lorenzi V, Mazzeo CI, Alves-Lopes JP, Roberts K, Sancho-Serra C, Engelbert J, Marečková M, Gruhn WH, Botting RA, Li T, Crespo B, van Dongen S, Kiselev VY, Prigmore E, Herbert M, Moffett A, Chédotal A, Bayraktar OA, Surani A, Haniffa M, Vento-Tormo R.
    Nature (2022) — Show abstract
  5. Bilateral visual projections exist in non-teleost bony fish and predate the emergence of tetrapods.
    Vigouroux RJ, Duroure K, Vougny J, Albadri S, Kozulin P, Herrera E, Nguyen-Ba-Charvet K, Braasch I, Suárez R, Del Bene F, Chédotal A.
    Science (2021) — Show abstract
  6. Revisiting the role of Dcc in visual system development with a novel eye clearing method.
    Vigouroux RJ, Cesar Q, Chédotal A, Nguyen-Ba-Charvet KT.
    Elife (2020) — Show abstract
  7. Clearing method for 3-dimensional immunofluorescence of osteoarthritic subchondral human bone reveals peripheral cholinergic nerves.
    Courties A, Belle M, Senay S, Cambon-Binder A, Sautet A, Chédotal A, Berenbaum F, Sellam J.
    Sci Rep (2020) — Show abstract
  8. Decoding human fetal liver haematopoiesis
    Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M.
    Nature (2019) — Show abstract
  9. Tridimensional Visualization and Analysis of Early Human Development
    Belle M, Godefroy D, Couly G, Malone SA, Collier F, Giacobini P, Chédotal A.
    Cell (2017) — Show abstract
  10. Development of the neurons controlling fertility in humans: new insights from 3D imaging and transparent fetal brains.
    Casoni F, Malone SA, Belle M, Luzzati F, Collier F, Allet C, Hrabovszky E, Rasika S, Prevot V, Chédotal A, Giacobini P.
    Development (2016) — Show abstract
  11. Human Cell Atlas Developmental Biological Network. A roadmap for the Human Developmental Cell Atlas
    Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe'er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S
    Nature (2021) — Show abstract
  12. Tissue clearing and its applications in neuroscience
    Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ.
    Nat Rev Neurosci (2020) — Show abstract

Funding & Support

HCL Lyon
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