A human stomach cell type transcriptome atlas

• Published in: BMC biology Vol. 22; no. 1; pp. 36 - 21
• Main Authors: Öling, S, Struck, E, Noreen-Thorsen, M, Zwahlen, M, von Feilitzen, K, Odeberg, J, Pontén, F, Lindskog, C, Uhlén, M, Dusart, P, Butler, L M
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 14.02.2024; BioMed Central; BMC
• Subjects: Analysis; Bulk RNAseq; Care and treatment; Cell profiling; Cells; Correlation analysis; Diagnosis; Digestive enzymes; Enrichment; Epithelial Cells; Fibroblasts; Food processing; Gastric cancer; Gastrointestinal system; Gastrointestinal tract; Gene enrichment; Gene expression; Gene Expression Profiling; Genes; Genetic aspects; Humans; Leukocytes (neutrophilic); Lymphocytes T; Macrophages; Male; Medical examination; Medicin och hälsovetenskap; Microorganisms; Neutrophils; Nutrients; Plasma; Plasma cells; Proteins; RNA sequencing; Stomach; Stomach cancer; Stomach Neoplasms; Transcriptome; Transcriptomes; Sweden; Gene enrichment; Stomach; Bulk RNAseq; Cell profiling
• ISSN: 1741-7007; 1741-7007
• DOI: 10.1186/s12915-024-01812-5

The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases. Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell, and plasma cells, identifying over 1600 cell type-enriched genes. We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.