The colon cell type enriched transcriptome

The main function of the colon is to absorb the useful electrolytes, vitamins and water that remain in the intestinal lumen after passing through the rest of the gastrointestinal tract, before excreting the remaining material as feces. In contrast to stomach and small intestine, the mucosal layer of the colon is smooth and lacks villi, but is covered in deep invaginations called colonic crypts. The sigmoid colon is the very last part of the colon, located closest to the rectum and anus.

1918 genes were predicted to have cell type specificity in the colon.

  • 12 cell types profiled
  • 559 very highly enriched genes
  • 622 highly enriched genes
  • 737 moderately enriched genes

Colon cell type enriched transcriptome: Summary

Genes with predicted cell type specificity within colon 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 colon cell types.

Cell type Very highHighModerate Total enriched
Colon enterocytes 180 98 91 369
Colon enteroendocrine cells 133 124 81 338
Enteric glia cells 77 104 59 240
Mitotic cells (Colon) 14 33 38 85
Endothelial cells 5 61 153 219
Smooth muscle cells 94 46 26 166
Fibroblasts 0 5 37 42
Macrophages 26 40 77 143
Neutrophils 7 24 34 65
Mast cells 9 12 8 29
T-cells 2 28 78 108
Plasma cells 12 47 55 114
All cell types 559622737 1918

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

Colon cell type enriched transcriptome: Illustrative examples

Colon enterocytes

The gastrointestinal tract is lined by a simple columnar epithelium of epithelial cells, called enterocytes. The epithelial layer of the colon secretes mucus to protect and lubricate the colon, in addition to regulating the absorption of water and other nutrients from the lumen. Villin 1 (VIL1), a calcium-regulated actin-binding protein that modulates the organization of microvillar actin filaments, and Galectin 4 (LGALS4), a lipid raft and adherens junction stabilizer, are examples of genes classified as having specificity in the colon enterocytes.

VIL1 - Colon


LGALS4 - Colon


Colon enteroendocrine cells

Enteroendocrine cells are found scattered throughout the colonic epithelial layer, and secrete a range of different gastrointestinal hormones in response to stimuli from the digested nutrients inside the intestinal lumen as well as neuronal stimulation. There are multiple types of enteroendocrine cells, defined based on their main hormonal product and the secretory granule ultrastructure. The colon contains fewer types of enteroendocrine cells than the small intestine, however they are important for regulation of intestinal motility and proliferation. Genes classified as having specificity in enteroendocrine cells include secretogranin proteins such as SCG3 and SCG5, which regulate the biogenesis of secretory granules, as well as the intermediate filament protein Peripherin (PRPH).

SCG3 - Colon


SCG5 - Colon


PRPH - Colon


Enteric glia cells

Enteric glia cells are located directly below the epithelial cell layer of the gastrointestinal tract. They make up the majority of the enteric nervous system and share several functional and structural aspects with astrocytes in the central nervous system. Enteric glia cells both send and receive signals from nearby enteric neurons and epithelial cells, and are thought to have an important role in maintaining the integrity and homeostasis of the gastrointestinal epithelium. Genes classified as having specificity in enteric glia cells include Cell adhesion molecule 3 (CADM3), which is involved in calcium independent cell-cell adhesions, especially amongst neurons, and Osteonectin (also known as Secreted protein acidic and cysteine rich, SPARC), a calcium binding protein important in regulating interactions between cells and the extracellular matrix.

CADM3 - Colon


SPARC - Colon


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 colon are predominantly located at the base of the colonic crypts, where they undergo limited cell division before differentiating into epithelial cells of the colon. Marker Of Proliferation Ki-67 (MKI67) and Cell Division Cycle 20 (CDC20), are both well known genes involved in cellular proliferation and classified as having specificity in mitotic cells in the colon.

MKI67 - Colon


CDC20 - Colon