Cells of the human intestinal tract mapped across space and time

Rasa Elmentaite, Natsuhiko Kumasaka, Kenny Roberts, Aaron Fleming, Emma Dann, Hamish W King, Vitalii Kleshchevnikov, Monika Dabrowska, Sophie Pritchard, Liam Bolt, Sara F Vieira, Lira Mamanova, Ni Huang, Francesca Perrone, Issac Goh Kai'En, Steven N Lisgo, Matilda Katan, Steven Leonard, Thomas R W Oliver, C Elizabeth HookKomal Nayak, Lia S Campos, Cecilia Domínguez Conde, Emily Stephenson, Justin Engelbert, Rachel A Botting, Krzysztof Polanski, Stijn van Dongen, Minal Patel, Michael D Morgan, John C Marioni, Omer Ali Bayraktar, Kerstin B Meyer, Xiaoling He, Roger A Barker, Holm H Uhlig, Krishnaa T Mahbubani, Kourosh Saeb-Parsy, Matthias Zilbauer, Menna R Clatworthy, Muzlifah Haniffa, Kylie R James, Sarah A Teichmann

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The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.

Original languageEnglish
Pages (from-to)250-255
Number of pages6
Issue number7875
Publication statusPublished - 8 Sept 2021

Bibliographical note

We acknowledge support from the Wellcome Sanger Cytometry Core Facility, Cellular Genetics Informatics team, Cellular Generation and Phenotyping (CGaP) and Core DNA Pipelines. This work was financially supported by the Wellcome Trust (W1T20694, S.A.T.; 203151/Z/16/Z, R. A. Barker.); the European Research Council (646794, ThDefine, S.A.T.); an MRC New Investigator Research Grant (MR/T001917/1, M.Z.); and a project grant from the Great Ormond Street Hospital Children’s Charity, Sparks (V4519, M.Z.). The human embryonic and fetal material was provided by the Joint MRC/Wellcome (MR/R006237/1) Human Developmental Biology Resource (https://www.hdbr.org/). K.R.J. holds a Non-Stipendiary Junior Research Fellowship from Christ’s College, University of Cambridge. M.R.C. is supported by a Medical Research Council Human Cell Atlas Research Grant (MR/S035842/1) and a Wellcome Trust Investigator Award (220268/Z/20/Z). H.W.K. is funded by a Sir Henry Wellcome Fellowship (213555/Z/18/Z). A.F. is funded by a Wellcome PhD Studentship (102163/B/13/Z). K.T.M. is funded by an award from the Chan Zuckerberg Initiative. H.H.U. is supported by the Oxford Biomedical Research Centre (BRC) and the The Leona M. and Harry B. Helmsley Charitable Trust. We thank A. Chakravarti and S. Chatterjee for their contribution to the analysis of the enteric nervous system. We also thank R. Lindeboom and C. Talavera-Lopez for support with epithelium and Visium analysis, respectively; C. Tudor, T. Li and O. Tarkowska for image processing and infrastructure support; A. Wilbrey-Clark and T. Porter for support with Visium library preparation; A. Ross and J. Park for access to and handling of fetal tissue; A. Hunter for assistance in protocol development; D. Fitzpatrick for discussion on developmental intestinal disorders; and J. Eliasova for the graphical images. We thank the tissue donors and their families, and the Cambridge Biorepository for Translational Medicine and Human Developmental Biology Resource, for access to human tissue. This publication is part of the Human Cell Atlas: https://www.humancellatlas.org/publications.

Data Availability Statement

The expression data for fetal and adult regions is available on an interactive website: https://www.gutcellatlas.org/. Raw sequencing data are available at ArrayExpress (https://www.ebi.ac.uk/arrayexpress) with accession numbers E-MTAB-9543, E-MTAB-9536, E-MTAB-9532, E-MTAB-9533 and E-MTAB-10386. Previously published first trimester and paediatric data are available at ArrayExpress (E-MTAB-8901)1. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. Source data are provided with this paper.

Code availability
Processed single-cell RNA sequencing objects are available for online visualization and download at https://www.gutcellatlas.org/. The code generated during this study is available at Github: https://github.com/Teichlab/SpaceTimeGut, https://github.com/vitkl/fetal_gut_mapping/, https://github.com/natsuhiko/PHM


  • Adult
  • Aging
  • Animals
  • Child
  • Crohn Disease/pathology
  • Datasets as Topic
  • Enteric Nervous System/anatomy & histology
  • Epithelial Cells/cytology
  • Female
  • Fetus/anatomy & histology
  • Health
  • Humans
  • Intestines/cytology
  • Lymph Nodes/cytology
  • Mice
  • Mice, Inbred C57BL
  • Organogenesis
  • Receptors, IgG/metabolism
  • Signal Transduction
  • Spatio-Temporal Analysis
  • Time Factors


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