Spatiotemporal analysis of human intestinal development at single-cell resolution.
IF: 66.850
Cited by: 203


Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer's patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work.


Spatial Transcriptomics
congenital disease
gene expression
human development
human developmental cell atlas
intestinal crypt
intestinal development
mesenchymal cells
single-cell RNA-sequencing
spatial transcriptomics
stem cells

MeSH terms

Endothelial Cells
Enteric Nervous System
Intestinal Diseases
Intestinal Mucosa
Neovascularization, Physiologic
Single-Cell Analysis
Stem Cells
Time Factors
Transcription Factors


Fawkner-Corbett, David
Antanaviciute, Agne
Parikh, Kaushal
Jagielowicz, Marta
Gerós, Ana Sousa
Gupta, Tarun
Ashley, Neil
Khamis, Doran
Fowler, Darren
Morrissey, Edward
Cunningham, Chris
Johnson, Paul R V
Koohy, Hashem
Simmons, Alison

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