Cells of the human intestinal tract mapped across space and time.
Rasa Elmentaite,Natsuhiko Kumasaka,Kenny Roberts,Aaron M. 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 Lisgo,Matilda Katan,Steven Leonard,Thomas R. W. Oliver,Thomas R. W. Oliver,C. Elizabeth Hook,Komal Nayak,Lia S. Campos,Cecilia Domínguez Conde,Emily Stephenson,Justin Engelbert,Rachel A. Botting,Krzysztof Polanski,Stijn van Dongen,Minal Patel,Michael D Morgan,Michael D Morgan,John C. Marioni,John C. Marioni,John C. Marioni,Omer Ali Bayraktar,Kerstin B Meyer,Xiaoling He,Roger A. Barker,Holm H. Uhlig,Holm H. Uhlig,Krishnaa T. Mahbubani,Kourosh Saeb-Parsy,Matthias Zilbauer,Menna R. Clatworthy,Menna R. Clatworthy,Muzlifah Haniffa,Muzlifah Haniffa,Kylie R. James,Kylie R. James,Sarah A. Teichmann,Sarah A. Teichmann +51 more
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TLDR
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 as discussed by the authors, using single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions of the developing and up to 11 distinct anatomical regions in the healthy human gut.Abstract:
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. Cells from embryonic, fetal, paediatric and adult human intestinal tissue are analysed at different locations along the intestinal tract to construct a single-cell atlas of the developing and adult human intestinal tract, encompassing all cell lineages.read more
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Cell2location maps fine-grained cell types in spatial transcriptomics
Vitalii Kleshchevnikov,Artem Shmatko,Emma Dann,Alexander Aivazidis,Hamish W King,Tong Li,Rasa Elmentaite,Artem Lomakin,Veronika R. Kedlian,Adam Gayoso,Mika Sarkin Jain,Jun Sung Park,Lauma Ramona,Elizabeth Tuck,Anna Arutyunyan,Roser Vento-Tormo,Moritz Gerstung,Louisa K. James,Oliver Stegle,Omer Ali Bayraktar +19 more
Journal ArticleDOI
Cross-tissue immune cell analysis reveals tissue-specific features in humans
Cecilia Domínguez Conde,L. Jarvis,Dan Rainbow,Steven B. Wells,Tomás Gomes,S Howlett,Ondrej Suchanek,Krzysztof Polanski,H. King,Lira Mamanova,Ni Huang,Peter A. Szabo,Laura Richardson,Liam Bolt,Eirini S. Fasouli,K. Mahbubani,M. Julieta Del Prete,Liz Tuck,Nathan Richoz,Zewen K. Tuong,Lia S. Campos,Hani S Mousa,Edward Needham,Sophie Pritchard,T. Li,Rasa Elmentaite,J. Park,Esfandiar Rahmani,David K. Menon,O. Bayraktar,L. James,K. Meyer,Nir Yosef,Menna R. Clatworthy,Peter J. Sims,Donna L. Farber,Kourosh Saeb-Parsy,J. Jones,Sarah A. Teichmann +38 more
TL;DR: An immune cell atlas of human innate and adaptive immune cells across lymphoid, mucosal, and exocrine sites reveals tissue-specific compositions and features, and reveals insights into how the immune system adapts to function effectively in different organ contexts.
Journal ArticleDOI
Mapping the developing human immune system across organs
Chenqu Suo,Emma Dann,Issac Goh,Laura Jardine,Vitalii Kleshchevnikov,Jong-Eun Park,Rachel A. Botting,Emily Stephenson,Justin Engelbert,Zewen K. Tuong,Krzysztof Polanski,Nadav Yayon,Chuan Xu,Ondrej Suchanek,Rasa Elmentaite,Cecilia Conde,Peng He,Sophie Pritchard,Mohiuddin Miah,Corina Moldovan,Alexander S. Steemers,M. Julieta Del Prete,John C. Marioni,Menna R. Clatworthy,Muzlifah Haniffa,Sarah A. Teichmann +25 more
TL;DR: A comprehensive single-cell RNA sequencing atlas of human developing immune system is performed together with antigen-receptor sequencing and spatial transcriptomics to reconstruct the developing human immune system and identifies, characterised and functionally validated the properties of human prenatal B1 cells and the origin of unconventional T cells.
Journal ArticleDOI
A roadmap for the Human Developmental Cell Atlas
Muzlifah Haniffa,Muzlifah Haniffa,Deanne Taylor,Deanne Taylor,Sten Linnarsson,Bruce J. Aronow,Gary D. Bader,Roger A. Barker,Pablo G. Camara,J. Gray Camp,Alain Chédotal,Andrew J. Copp,Heather C. Etchevers,Paolo Giacobini,Berthold Göttgens,Guoji Guo,Ania Hupalowska,Kylie R. James,Emily Kirby,Arnold R. Kriegstein,Joakim Lundeberg,John C. Marioni,Kerstin B. Meyer,Kathy K. Niakan,Kathy K. Niakan,Mats Nilsson,Bayanne Olabi,Dana Pe'er,Aviv Regev,Aviv Regev,Aviv Regev,Jennifer Rood,Orit Rozenblatt-Rosen,Orit Rozenblatt-Rosen,Rahul Satija,Sarah A. Teichmann,Sarah A. Teichmann,Barbara Treutlein,Roser Vento-Tormo,Simone Webb +39 more
TL;DR: The Human Developmental Cell Atlas (HDCA) project as discussed by the authors aims to create a comprehensive reference map of cells during development by mapping and modelling human development using state-of-the-art technologies.
Journal ArticleDOI
The emerging landscape of spatial profiling technologies
TL;DR: It is envisioned that spatial methods will map entire organs and enable next-generation pathology, among many transformative applications, in the developing landscape of in situ spatial genome, transcriptome and proteome technologies.
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