The stomach cell type enriched transcriptome

The stomach is located in the upper left of the abdomen and is the first digestive organ of the gastrointestinal tract. The main function of the stomach is digestion of food, which is possible due to its acidic milieu and secretion of digestive enzymes, which also provides a barrier against ingested microorganisms. The stomach mucosal lining consists of several specialized epithelial cells including parietal cells, chief cells, enteroendocrine cells, and mucous cells.

1361 genes were predicted to have cell type specificity in the stomach.

  • 11 cell types profiled
  • 78 very highly enriched genes
  • 189 highly enriched genes
  • 1094 moderately enriched genes

Stomach cell type enriched transcriptome: Summary

Genes with predicted cell type specificity within stomach are detailed in Table 1. Identified genes are subdivided into 3 specificity categories, based on the difference between the enrichment score in the corresponding cell type, compared to the other cell types profiled in the tissue (see Methods Summary page for details):

  • Predicted specificity: ´Very high´ - Differential score vs. other profiled cell types within the tissue >0.35
  • Predicted specificity: ´High´ - Differential score vs. other profiled cell types within the tissue >0.25
  • Predicted specificity: ´Moderate´ - Differential score vs. other profiled cell types within the tissue >0.15

Table 1. Number of genes in each specificity category in the stomach cell types.

Cell type Very highHighModerate Total enriched
Parietal cells 1 25 48 74
Chief cells 0 5 51 56
Gastric mucous cells 0 42 337 379
Gastric enteroendocrine cells 0 15 32 47
Mitotic cells (Stomach) 63 57 50 170
Endothelial cells 0 5 79 84
Fibroblasts 0 5 161 166
Macrophages 10 30 115 155
Neutrophils 4 5 12 21
T-cells 0 0 23 23
Plasma cells 0 0 186 186
All cell types 781891094 1361

Figure 1. Bar plot of the number of enriched genes in the cell types of the stomach, divided by specificity category

Stomach cell type enriched transcriptome: Illustrative examples

Parietal cells

Parietal cells are secretory epithelial cells located in the gastric glands of the stomach mucosal lining. Parietal cells are also known as oxyntic or delomorphous cells, and their primary function is the secretion of hydrochloric acid, which aids digestion of foods, Genes classified as having specificity in parietal cells include Cobalamin binding intrinsic factor (CBLIF), which is required for vitamin B12 absorption, Solute Carrier Family 9 Member A3 (SLC9A3), an epithelial brush border Na/H exchanger that uses an inward sodium ion gradient to expel acids from the cell, and Acyl-CoA Synthetase Short Chain Family Member 1 (ACSS1), which catalyzes the synthesis of acetyl-CoA from short-chain fatty acids.

SLC9A3 - Stomach


ACSS1 - Stomach


Chief cells

Gastric chief cells (also known as peptic or gastric zymogenic cells) are secretory epithelial cells located in the mucosal layer of the stomach. Gastric chief cells secrete pepsinogen (which is converted to pepsin by stomach acid) and gastric lipase enzymes, which are important in the digestion of proteins and lipids, respectively. Genes classified as having specificity in chief cells include CCAAT Enhancer Binding Protein Alpha (CEBPA), a transcription factor that can modulate the expression of genes involved in cell cycle regulation, as well as in body weight homeostasis. Also with specificity in chief cells are Pepsinogen A4 (PGA4) and pepsinogen A5 (PGA5), which are protein precursors of the digestive enzyme pepsin, a member of the peptidase A1 family of endopeptidases. The encoded precursor is secreted by gastric chief cells and undergoes autocatalytic cleavage in acidic conditions to form the active enzyme, which functions in the digestion of dietary proteins.

CEBPA - Stomach


PGA4 - Stomach


PGA5 - Stomach


Gastric enteroendocrine cells

Gastric enteroendocrine cells are found within the pyloric glands of the stomach mucosa, and secrete several different gastrointestinal hormones in response to both nervous stimulation or histamine release. Genes classified as having specificity in gastric enteroendocrine cells include Chromogranin A (CHGA), a neuroendocrine secretory protein that is a precursor to several different peptides, including vasostatin, pancreastatin, and parastatin, all of which act as autocrine or paracrine negative modulators of the neuroendocrine system. Also with specificity in enteroendocrine cells is Dipeptidase 1 (DPEP1), which is most well studied in the context of the kidney where it hydrolyzes a wide range of dipeptides, including glutathione and leukotriene D4.

CHGA - Stomach


DPEP1 - Stomach


Gastric mucous cells

Gastric mucous cells line the surface and pits of the stomach. They produce and secrete mucus which protects the stomach from the corrosive gastric acids and enzymes secreted by parietal and chief cells. This protective mucosa protects the stomach from damage and self-digestion. Trefoil factor 1 (TFF1) and Trefoil factor 2 (TFF2) are proteins secreted by mucus cells, and are thought to stabilize the mucus layer and potentially modulate mucus viscosity by binding to glycoproteins. Another gene classified as having specificity in mucus cells is Fer-1 like family member 6 (FER1L6), which currently has unknown functionality.

TFF1 - Stomach


TFF2 - Stomach


FER1L6 - Stomach


Mitotic cells

Mitotic cells are found in many tissues, and are responsible for cell renewal to replace aging, damaged or dying cells. Mitotic cells in the stomach are typically located at the base of the gastric pits, and undergo a limited amount of cell divisions before differentiating into the other epithelial cells of the stomach. Stomach and other gut epithelia have a notably higher rate of cell turnover compared to many other cell types in the body, both due to the highly corrosive environment, as well as the strong mechanical forces within the GI tract. Genes classified as having specificity in stomach mitotic cells include TPX2 microtubule nucleation factor (TPX2), required for the normal assembly of mitotic spindles, Baculoviral IAP repeat containing 5 (BIRC5), also called survivin, an apoptosis inhibitor which also functions to localize the mitotic spindle during mitosis, and DNA topoisomerase II alpha (TOP2A), which is essential for altering the topologic state of DNA during replication.

TPX2 - Stomach


BIRC5 - Stomach


TOP2A - Stomach