The lung cell type enriched transcriptome

The lung is a respiratory organ responsible for gaseous exchange between air and blood. The lung contains many branching airways, or bronchioles, which end in small cup shaped structures called alveoli, where gaseous exchange occurs. These many branching airways give the lung a massive surface area over which gaseous exchange can take place.

2422 genes were predicted to have cell type specificity in the lung.

  • 16 cell types profiled
  • 1059 very highly enriched genes
  • 494 highly enriched genes
  • 869 moderately enriched genes

Lung cell type enriched transcriptome: Summary

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

Cell type Very highHighModerate Total enriched
Respiratory ciliated cells 590 53 37 680
Alveolar cells type 1 43 42 48 133
Alveolar cells type 2 20 122 221 363
Mitotic cells (Lung) 111 26 16 153
NK-cells (Lung) 3 13 40 56
B-cells 4 1 6 11
Endothelial cells 0 9 88 97
Smooth muscle cells 14 13 36 63
Fibroblasts 28 64 165 257
Macrophages 4 51 104 159
Neutrophils 60 52 47 159
Mast cells 10 4 3 17
T-cells 6 29 54 89
Plasma cells 166 15 4 185
All cell types 1059494869 2422

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

Lung cell type enriched transcriptome: Illustrative examples

Respiratory ciliated cells

Ciliated cells are epithelial cells that line the bronchi and bronchioles. Their luminal surface is covered in motile cilia, which beat constantly and serve to move inhaled dust or microbes that are trapped in the sticky mucus coating of the lung towards the esophagus for digestion and disposal. Genes classified as having specificity in ciliated cells include Dynein axonemal intermediate chain 1 (DNAI1), which forms part of the dynein complex of the respiratory cilia, as well as the Armadillo Repeat Containing 3 (ARMC3) gene.

DNAI1 - Lung


ARMC3 - Lung


Mitotic cells

Mitotic cells are found in many tissues, and are responsible for cell renewal to replace aging, damaged or dying cells. In the bronchus, cells at the base of the ciliated epithelial layer divide to replace damaged cells from the epithelial surface, in lung tissue the cell renewal required to heal after injury is thought to involve reprogramming of alveolar type II cells. Genes classified as having specificity in mitotic cells include centromere protein F (CENPF), essential for chromosome segregation during mitosis, as well as the apoptotic inhibitor Survivin (BIRC5).

CENPF - Lung


BIRC5 - Lung


Alveolar type I cells

Alveolar type I cells are thin epithelial cells that line the walls of the alveoli and allow gaseous exchange between the air and the blood. Genes classified as having specificity in type I alveolar cells include Sciellin (SCEL), thought to regulate protein assembly in stratified epithelia, as well as LMO7, thought to be involved in protein-protein interactions.

SCEL - Lung


LMO7 - Lung


Alveolar type II cells

Alveolar type II cells are smaller than type I cells, and are primarily responsible for the secretion of surfactant, a film of phospholipids and proteins that coat the inside of the alveoli, both assisting in gaseous exchange and lowering surface tension, preventing the alveoli from collapsing. Genes classified as having specificity in type II alveolar cells include surfactant protein C (SFTPC),a hydrophobic protein essential for surfactant function, as well as the RAP1 GTPase activating protein RAP1GAP.

SFTPC - Lung


RAP1GAP - Lung