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.

2397 genes were predicted to have cell type specificity in the lung.

16 cell types profiled
1060 very highly enriched genes
477 highly enriched genes
861 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 high	High	Moderate	Total enriched
Respiratory ciliated cells	593	65	38	696
Alveolar cells type 1	40	42	47	129
Alveolar cells type 2	13	105	230	348
Mitotic cells (Lung)	105	24	13	142
NK-cells (Lung)	3	12	33	48
B-cells (Lung)	4	1	6	11
Fibroblasts	26	57	154	237
Endothelial cells	0	3	68	71
Smooth muscle cells	13	15	50	78
Macrophages	5	54	106	165
Neutrophils	84	43	41	167
Mast cells	10	4	3	17
T-cells	7	31	67	105
Plasma cells	157	21	5	183
All cell types	1060	477	861	2397

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
DNAI1
ARMC3 - Lung
ARMC3

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
CENPF
BIRC5 - Lung
BIRC5

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
SCEL
LMO7 - Lung
LMO7

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
SFTPC
RAP1GAP - Lung
RAP1GAP