Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model

Sci Rep. 2019 Mar 14;9(1):4536. doi: 10.1038/s41598-019-40809-x.


The diverse cellular milieu of the gastric tissue microenvironment plays a critical role in normal tissue homeostasis and tumor development. However, few cell culture model can recapitulate the tissue microenvironment and intercellular signaling in vitro. We used a primary tissue culture system to generate a murine p53 null gastric tissue model containing both epithelium and mesenchymal stroma. To characterize the microenvironment and niche signaling, we used single cell RNA sequencing (scRNA-Seq) to determine the transcriptomes of 4,391 individual cells. Based on specific markers, we identified epithelial cells, fibroblasts and macrophages in initial tissue explants during organoid formation. The majority of macrophages were polarized towards wound healing and tumor promotion M2-type. During the course of time, the organoids maintained both epithelial and fibroblast lineages with the features of immature mouse gastric stomach. We detected a subset of cells in both lineages expressing Lgr5, one of the stem cell markers. We examined the lineage-specific Wnt signaling activation, and identified that Rspo3 was specifically expressed in the fibroblast lineage, providing an endogenous source of the R-spondin to activate Wnt signaling. Our studies demonstrate that this primary tissue culture system enables one to study gastric tissue niche signaling and immune response in vitro.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Lineage
  • Cell Self Renewal
  • Cells, Cultured
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Gastric Mucosa / cytology
  • Gastric Mucosa / metabolism*
  • Gastric Mucosa / pathology
  • Gene Expression Profiling
  • Mice
  • Mice, Knockout
  • Organoids / metabolism*
  • Organoids / pathology
  • Single-Cell Analysis
  • Stem Cell Niche
  • Stem Cells / cytology
  • Stem Cells / metabolism
  • Stomach / cytology
  • Thrombospondins / metabolism
  • Transcriptome*
  • Tumor Suppressor Protein p53 / deficiency
  • Tumor Suppressor Protein p53 / genetics
  • Wnt Signaling Pathway
  • Wnt4 Protein / metabolism


  • R-spondin3 protein, mouse
  • Thrombospondins
  • Trp53 protein, mouse
  • Tumor Suppressor Protein p53
  • Wnt4 Protein
  • Wnt4 protein, mouse