A human stomach cell type transcriptome atlas.
Bulk RNAseq
Cell profiling
Gene enrichment
Stomach
Journal
BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720
Informations de publication
Date de publication:
14 Feb 2024
14 Feb 2024
Historique:
received:
17
05
2023
accepted:
02
01
2024
medline:
15
2
2024
pubmed:
15
2
2024
entrez:
14
2
2024
Statut:
epublish
Résumé
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.
Sections du résumé
BACKGROUND
BACKGROUND
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.
RESULTS
RESULTS
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.
CONCLUSIONS
CONCLUSIONS
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.
Identifiants
pubmed: 38355543
doi: 10.1186/s12915-024-01812-5
pii: 10.1186/s12915-024-01812-5
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
36Subventions
Organisme : Hjärt-Lungfonden
ID : 20170759
Organisme : Hjärt-Lungfonden
ID : 20170537
Organisme : Hjärt-Lungfonden
ID : 20200544
Organisme : Vetenskapsrådet
ID : 2019-01493
Organisme : Stockholms Läns Landsting
ID : SLL 2017-0842
Informations de copyright
© 2024. The Author(s).
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