The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Mapping Development of the Human Intestinal Niche at Single-Cell Resolution
Open accessAbstract
SUMMARY The human intestinal stem cell niche supports self-renewal and epithelial function, yet little is known about its development. We used single-cell mRNA sequencing with in situ validation approaches to interrogate human intestinal development from 7–21 weeks post conception, assigning molecular identities and spatial locations to cells and factors that comprise the niche. Smooth muscle cells of the muscularis mucosa, proximal to proliferative crypts, are a source of WNT and RSPONDIN ligands, while EGF is expressed far from crypts in the villus epithelium. Instead, an PDGFRAHI/F3HI/DLL1HI mesenchymal population lines the crypt-villus axis and is the source of the EGF family member NEUREGULIN1 (NRG1). In fetal intestinal enteroid cultures, NRG1, but not EGF, permitted increased cellular diversity via differentiation of secretory lineages. This work highlights complexities of intestinal EGF/ERBB signaling and delineates key niche cells and signals of the developing intestine.
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Cites
UMAP: Uniform Manifold Approximation and Projection
McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826 · cited 2×
“Dimension reduction was performed using principal component analysis (PCA) and then uniform manifold approximation and projection (UMAP) on the top 11–20 principal components (PCs) and 15–30 nearest neighbors for visualization on 2 dimensions (McInnes et al., 2018; Polański et al., 2019).”
SCANPY: large-scale single-cell gene expression data analysis
Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881
Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche
Sato, T., Vries, R. G., Snippert, H. J., van de Wetering, M., Barker, N., Stange, D. E., van Es, J. H., Abo, A., Kujala, P., Peters, P. J., et al. (2009) · Nature · doi:10.1038/nature07935 · Cited by 7,204
Spatial reconstruction of single-cell gene expression data
Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055
Sato, T., Stange, D. E., Ferrante, M., Vries, R. G. J., van Es, J. H., van den Brink, S., van Houdt, W. J., Pronk, A., van Gorp, J., Siersema, P. D., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.07.050 · Cited by 3,753
Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts
Sato, T., van Es, J. H., Snippert, H. J., Stange, D. E., Vries, R. G., van den Born, M., Barker, N., Shroyer, N. F., van de Wetering, M., & Clevers, H. (2011) · Nature · doi:10.1038/nature09637 · Cited by 2,510
A single-cell survey of the small intestinal epithelium
Haber, A. L., Biton, M., Rogel, N., Herbst, R. H., Shekhar, K., Smillie, C., Burgin, G., Delorey, T. M., Howitt, M. R., Katz, Y., et al. (2017) · Nature · doi:10.1038/nature24489 · Cited by 1,750
Designer matrices for intestinal stem cell and organoid culture
Gjorevski, N., Sachs, N., Manfrin, A., Giger, S., Bragina, M. E., Ordóñez-Morán, P., Clevers, H., & Lutolf, M. P. (2016) · Nature · doi:10.1038/nature20168 · Cited by 1,426
Synthetic hydrogels for human intestinal organoid generation and colonic wound repair
Cruz-Acuña, R., Quirós, M., Farkas, A. E., Dedhia, P. H., Huang, S., Siuda, D., García-Hernández, V., Miller, A. J., Spence, J. R., Nusrat, A., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3632 · Cited by 558
Self-citationFujii, M., Matano, M., Toshimitsu, K., Takano, A., Mikami, Y., Nishikori, S., Sugimoto, S., & Sato, T. (2018) · Cell Stem Cell · doi:10.1016/j.stem.2018.11.016 · Cited by 558 · cited 4×
“Efforts have been made to determine more physiological niche factors for in vitro culture systems based on observed in vivo niche cues (Fujii et al., 2018), however niche factors have not been interrogated in the developing human gut using high resolution technologies such as scRNA-seq.”
Influential
Cited by
Fleming, S. J., Chaffin, M. D., Arduini, A., Akkad, A.-D., Banks, E., Marioni, J. C., Philippakis, A. A., Ellinor, P. T., & Babadi, M. (2023) · Nature Methods · doi:10.1038/s41592-023-01943-7 · Cited by 867
Cells of the human intestinal tract mapped across space and time
Elmentaite, R., Kumasaka, N., Roberts, K., Fleming, A., Dann, E., King, H. W., Kleshchevnikov, V., Dabrowska, M., Pritchard, S., Bolt, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03852-1 · Cited by 699
Elmentaite, R., Ross, A. D. B., Roberts, K., James, K. R., Ortmann, D., Gomes, T., Nayak, K., Tuck, L., Pritchard, S., Bayraktar, O. A., et al. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.11.010 · Cited by 316
Burclaff, J., Bliton, R. J., Breau, K. A., Ok, M. T., Gomez-Martinez, I., Ranek, J. S., Bhatt, A. P., Purvis, J. E., Woosley, J. T., & Magness, S. T. (2022) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2022.02.007 · Cited by 242
Impact of the Human Cell Atlas on medicine
Rood, J. E., Maartens, A., Hupalowska, A., Teichmann, S. A., & Regev, A. (2022) · Nature Medicine · doi:10.1038/s41591-022-02104-7 · Cited by 222
Metadata
- Authors
- Holloway, E. M., Czerwinski, M., Tsai, Y.-H., Wu, J. H., Wu, A., Childs, C. J., Walton, K. D., Sweet, C. W., Yu, Q., Glass, I., Treutlein, B., Camp, J. G., & Spence, J. R.
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2021-03
- Volume
- 28
- Issue
- 3
- Pages
- 568-580.e4
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- OpenAlex
- W3109709532
- Cited by
- 182
- References
- 14
- FWCI
- 7.68
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Holloway, E. M., Czerwinski, M., Tsai, Y.-H., Wu, J. H., Wu, A., Childs, C. J., Walton, K. D., Sweet, C. W., Yu, Q., Glass, I., Treutlein, B., Camp, J. G., & Spence, J. R. (2021). Mapping Development of the Human Intestinal Niche at Single-Cell Resolution. Cell Stem Cell. https://doi.org/10.1016/j.stem.2020.11.008
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
