The lung-specific proteome
The lung is a respiratory organ essential for breathing and responsible for the gaseous exchange between air and blood. The branching airways end in alveoli, which is where the gaseous exchange occurs. The cell types in lung tissue are dominated by pneumocytes, bronchial epithelium, alveolar macrophages, endothelial cells and interstitial cells. Transcriptome analysis shows that 76% (n=15021) of all human proteins (n=19670) are expressed in the lung and 239 of these genes show an elevated expression in lung compared to other tissue types.
The lung transcriptome
Transcriptome analysis of the lung can be visualized with regard to specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the lung compared to other tissues. Elevated expression includes three subcategory types of elevated expression:
Distribution, on the other hand, visualizes how many genes that have, or do not have, detectable levels (NX≥1) of transcribed mRNA molecules in the lung compared to other tissues. As evident in Table 1, all genes elevated in lung are categorized as:
Figure 1. (A) The distribution of all genes across the five categories based on transcript specificity in lung as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in lung as well as in all other tissues.
As shown in Figure 1, 239 genes show some level of elevated expression in the lung compared to other tissues. The three categories of genes with elevated expression in lung compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in lung are defined.
Table 1. Number of genes in the subdivided categories of elevated expression in lung.
Table 2. The 12 genes with the highest level of enriched expression in lung. "Tissue distribution" describes the transcript detection (NX≥1) in lung as well as in all other tissues. "mRNA (tissue)" shows the transcript level in lung as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in lung and the tissue with second highest expression level.
Protein expression of genes elevated in lung
In-depth analysis of the genes elevated in lung, using antibody-based protein profiling, allowed us to visualize the expression patterns of the corresponding proteins within the lung. The analysis showed expression in pneumocytes, ciliated and mucus secreting cells in the respiratory mucosa, as well as in endothelial cells and macrophages.
Proteins specifically expressed in pneumocytes of the lung
Pneumocytes make up the alveolar structure and are essential for normal respiration. Pneumocytes produce surfactant, a lipoprotein complex crucial for the gaseous exchange between air and blood and for lowering surface tension which prevents alveolar collapse. Surfactant is also important for protecting the lungs from infection. Examples of proteins associated with the production and maintenance of pulmonary surfactant include SFTPA1, SFTPC and NAPSA.
Proteins specifically expressed in macrophages of the lung
Airborne microorganisms entering the lungs are digested and destroyed by macrophages, which play an important role in host defense. One example of a protein expressed in macrophages include MRC1, which mediates endocytosis of pathogenic viruses, bacteria and fungi. Other examples include MARCO, a scavenger receptor, part of the innate antimicrobial immune system, and that may bind both Gram-negative and Gram-positive bacteria, and MCEMP1 a protein with unknown function.
Proteins specifically expressed in ciliated cells of the lung
Ciliated cells are found along the bronchi, where they help free the airways from inhaled contaminants. One example of a protein expressed in ciliated cells is SNTN, which is suggested to be a molecular component of the ciliary tip structures, making the distal portion of the cilia more stiff, and thus allowing for better airway clearance.
Proteins specifically expressed in mucus-secreting cells of the lung
Mucus-secreting cells are present in both bronchial epithelium and peribronchial glands. The secreted mucus is important for maintaining a suitable environment for ciliary function and protection against airborne infectious agents and solid particles. One example of a protein expressed in mucus-secreting cells is SCGB1A1, implicated in anti-inflammation and epithelial regeneration after oxidant-induced injury. Defects in SCGB1A1 are associated with asthma.
Proteins specifically expressed in endothelial cells of the lung
Up to 30% of the cells in the lung are endothelial cells, outlining the alveoli and participating in the gaseous exchange. One example of a protein expressed in lung endothelial cells is PRX. PRX encodes a protein suggested to be required for maintenance of peripheral nerve myelin sheath, also playing a role in axon–glial interaction. Distinct expression in lung endothelial cells has previously not been described.
Gene expression shared between lung and other tissues
There are 61 group enriched genes expressed in lung. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including lung, compared to all other tissues.
In order to illustrate the relation of lung tissue to other tissue types, a network plot was generated, displaying the number of genes with shared expression between different tissue types.
Figure 2. An interactive network plot of the lung enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of lung enriched genes and orange nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up to 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.
One example of a group enriched gene in lung and thyroid gland, is NK2 homeobox 1 (NKX2-1). NKX2-1 is a transcription factor suggested to regulate lung surfactant homeostasis and early development of lung structures, while in the thyroid it is involved in regulating the expression of genes important for thyroid hormone production. Mutations in NKX2-1 genes have been associated with breathing difficulty and reduced thyroid gland function (hypothyroidism). Immunohistochemistry shows staining in thyroid glandular cells and respiratory epithelial cells.
The lungs are one of the largest organs in the human body. They are responsible for supplying the circulatory system with oxygen, which will then be transported to all other organs in the body. Inhaled air passes through the nose or mouth via trachea to the bronchi, and further through bronchioli, before finally reaching the alveoli of the lungs. This is where the gaseous exchange occurs; oxygen is exchanged for carbon dioxide which is transported in the opposite direction and exhaled.
The physiological function of the lung is regulated by a complex molecular concert of specialized cell types, such as pneumocytes, macrophages, ciliated cells, mucus-secreting cells and endothelial cells.
The pulmonary alveolus, where the gaseous exchange takes place, is composed of a continuous layer of epithelial cells overlying a thin interstitium. Two morphologically distinct cell types, type I and type II pneumocytes, line the alveoli. Alveolar macrophages are also present on the epithelial surface. The interstitium contains capillaries involved in gaseous exchange, as well as connective tissue and a variety of cells involved in alveolar shape and defense. The trachea, bronchi and bronchioli are air-filled branching tubes that include basal cells, neuroendocrine cells, ciliated cells, serous cells, Clara cells and goblet cells.
Here, the protein-coding genes expressed in lung are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in lung.
Relevant links and publications
Uhlén M et al, 2015. Tissue-based map of the human proteome. Science