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Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.

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Elmentaite, Rasa 
Ross, Alexander DB 
Roberts, Kenny 
James, Kylie R 
Ortmann, Daniel 


Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6-10 weeks post-conception. Our analysis reveals the transcriptional profile of cycling epithelial precursor cells; distinct from LGR5-expressing cells. We propose that these cells may contribute to differentiated cell subsets via the generation of LGR5-expressing stem cells and receive signals from surrounding mesenchymal cells. Furthermore, we draw parallels between the transcriptomes of ex vivo tissues and in vitro fetal organoids, revealing the maturation of organoid cultures in a dish. Lastly, we compare scRNA-seq profiles from pediatric Crohn's disease epithelium alongside matched healthy controls to reveal disease-associated changes in the epithelial composition. Contrasting these with the fetal profiles reveals the re-activation of fetal transcription factors in Crohn's disease. Our study provides a resource available at, and underscores the importance of unraveling fetal development in understanding disease.



human fetal gut development, inflammatory bowel disease, intestinal organoids, intestinal stem cells, pediatric Crohn's disease, single-cell RNA sequencing, villus formation, Adolescent, Cells, Cultured, Child, Crohn Disease, Humans, Intestinal Mucosa, RNA-Seq, Receptors, G-Protein-Coupled, Single-Cell Analysis, Transcription Factors, Transcriptome

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Dev Cell

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Elsevier BV
European Commission Horizon 2020 (H2020) Societal Challenges (668294-2 INTENS)
European Research Council (741707)
Medical Research Council (G0701448)
Medical Research Council (MC_PC_12009)
National Centre for the Replacement Refinement and Reduction of Animals in Research (NC/N001540/1)
MRC (MR/T001917/1)
Engineering and Physical Sciences Research Council (TS/H001220/1)
Medical Research Council (MC_PC_17230)