Single-Cell Transcriptional Analyses Identify Lineage-Specific Epithelial Responses to Inflammation and Metaplastic Development in the Gastric Corpus

Gastroenterology. 2020 Dec;159(6):2116-2129.e4. doi: 10.1053/j.gastro.2020.08.027. Epub 2020 Aug 21.


Background & aims: Chronic atrophic gastritis can lead to gastric metaplasia and increase risk of gastric adenocarcinoma. Metaplasia is a precancerous lesion associated with an increased risk for carcinogenesis, but the mechanism(s) by which inflammation induces metaplasia are poorly understood. We investigated transcriptional programs in mucous neck cells and chief cells as they progress to metaplasia mice with chronic gastritis.

Methods: We analyzed previously generated single-cell RNA-sequencing (scRNA-seq) data of gastric corpus epithelium to define transcriptomes of individual epithelial cells from healthy BALB/c mice (controls) and TxA23 mice, which have chronically inflamed stomachs with metaplasia. Chronic gastritis was induced in B6 mice by Helicobacter pylori infection. Gastric tissues from mice and human patients were analyzed by immunofluorescence to verify findings at the protein level. Pseudotime trajectory analysis of scRNA-seq data was used to predict differentiation of normal gastric epithelium to metaplastic epithelium in chronically inflamed stomachs.

Results: Analyses of gastric epithelial transcriptomes revealed that gastrokine 3 (Gkn3) mRNA is a specific marker of mouse gastric corpus metaplasia (spasmolytic polypeptide expressing metaplasia, SPEM). Gkn3 mRNA was undetectable in healthy gastric corpus; its expression in chronically inflamed stomachs (from TxA23 mice and mice with Helicobacter pylori infection) identified more metaplastic cells throughout the corpus than previously recognized. Staining of healthy and diseased human gastric tissue samples paralleled these results. Although mucous neck cells and chief cells from healthy stomachs each had distinct transcriptomes, in chronically inflamed stomachs, these cells had distinct transcription patterns that converged upon a pre-metaplastic pattern, which lacked the metaplasia-associated transcripts. Finally, pseudotime trajectory analysis confirmed the convergence of mucous neck cells and chief cells into a pre-metaplastic phenotype that ultimately progressed to metaplasia.

Conclusions: In analyses of tissues from chronically inflamed stomachs of mice and humans, we expanded the definition of gastric metaplasia to include Gkn3 mRNA and GKN3-positive cells in the corpus, allowing a more accurate assessment of SPEM. Under conditions of chronic inflammation, chief cells and mucous neck cells are plastic and converge into a pre-metaplastic cell type that progresses to metaplasia.

Keywords: Atrophy; Gastric Cancer; Immune Response; SPEM.

Publication types

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

MeSH terms

  • Animals
  • Biomarkers / analysis
  • Biomarkers / metabolism
  • Carcinogenesis / genetics
  • Carcinogenesis / immunology
  • Carrier Proteins / analysis
  • Carrier Proteins / metabolism
  • Chief Cells, Gastric / immunology
  • Chief Cells, Gastric / pathology*
  • Disease Models, Animal
  • Female
  • Gastritis, Atrophic / immunology*
  • Gastritis, Atrophic / microbiology
  • Gastritis, Atrophic / pathology
  • Helicobacter Infections / genetics
  • Helicobacter Infections / immunology*
  • Helicobacter Infections / microbiology
  • Helicobacter Infections / pathology
  • Helicobacter pylori / immunology
  • Humans
  • Male
  • Membrane Proteins / analysis
  • Membrane Proteins / metabolism
  • Metaplasia / diagnosis
  • Metaplasia / genetics
  • Metaplasia / immunology
  • Metaplasia / pathology
  • Mice
  • Precancerous Conditions / diagnosis*
  • Precancerous Conditions / genetics
  • Precancerous Conditions / immunology
  • Precancerous Conditions / pathology
  • RNA-Seq
  • Single-Cell Analysis
  • Stomach Neoplasms / pathology
  • Stomach Neoplasms / prevention & control*


  • Biomarkers
  • Carrier Proteins
  • GKN3P protein, human
  • Membrane Proteins
  • gastrokine 3 protein, mouse