The squamous epithelial cell-specific proteome
Stratified squamous epithelia consist of multiple layers of cells, with superficial layers of squamous (flat) cells and underlying replenishing cells at the basal layer. There are two types of stratified squamous epithelia, keratinized and non-keratinized. The keratinized type is formed by keratinocytes, is dry at the surface and forms the surface of the skin, while the non-keratinized type is kept moist at the surface and found in digestive system tissues and female tissues.
Transcriptome analysis shows that 66% (n=13320) of all human proteins (n=20090) are detected in squamous epithelial cells and 818 of these genes show an elevated expression in any squamous epithelial cells compared to other cell type groups. In-depth analysis of the elevated genes in squamous epithelial cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in the following types of squamous epithelial cells: basal and suprabasal keratinocytes in skin, basal cells and squamous epithelial cells in esophagus, and squamous epithelial cells in other organs.
The squamous epithelial cell transcriptome
The scRNA-seq-based squamous epithelial cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific squamous epithelial cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
Table 1. Number of genes in the subdivided specificity categories of elevated expression in the analyzed squamous epithelial cell types.
As shown in Table 1, 282 genes are elevated in basal keratinocytes compared to other cell types. Basal keratinocytes are stem cells found in the basal layer of the epidermis in skin. They are highly proliferative and responsible for the renewal of keratinocytes. One protein expressed in the basal layer is collagen type XVII alpha 1 chain (COL17A1), which may play a role in hemidesmosome integrity and the attachment of basal keratinocytes to the underlying basement membrane. Another example is keratin 5 (KRT5), a type II cytokeratin which belongs to the keratin family of proteins and is involved in keeping the structural integrity of the basal cells together with keratin 14. Mutations in these types of keratin genes are associated with a complex of diseases termed epidermolysis bullosa simplex.
As shown in Table 1, 392 genes are elevated in suprabasal keratinocytes compared to other cell types. Suprabasal keratinocytes are post-mitotic keratinocytes that reside in the stratum spinosum-layer of the skin epidermis, where they keep differentiating, developing a larger cytoplasm and well-formed bundles of keratin intermediate filaments as they are pushed towards the stratum corneum. Examples of proteins expressed in the stratum spinosum include keratin 10 (KRT10), which plays a role in the establishment of the epidermal barrier on plantar skin, and caspase 14 (CASP14), which is thought to play a role in keratinocyte differentiation and required for cornification.
Basal squamous epithelial cells
As shown in Table 1, 283 genes are elevated in basal squamous epithelial cells compared to other cell types. Basal squamous epithelial cells are stem cells in the basal layer of stratified squamous epithelia, found in proximal digestive tissues such as the esophagus. They are highly proliferative and responsible for the renewal of the layers of squamous epithelial cells above. One protein expressed in the basal layer is calpain small subunit 2 (CAPNS2), which catalyzes the proteolytic breakdown of cytoskeletal structures in order to remodel the shape of the cell, an important process during the differentiation of cuboidal-shaped basal cells into squamous-shaped cells in the superficial epithelial layers. Keratin 15 (KRT15) is an intermediate filament protein that belongs to the keratin family of proteins and is involved in keeping the structural integrity of the basal cells. Mutations in KRT15 are associated with the Kindler syndrome, an autosomal recessive skin disease that leads to very fragile skin that blisters easily.
Squamous epithelial cells
As shown in Table 1, 357 genes are elevated in squamous epithelial cells compared to other cell types. Squamous epithelial cells make up the bulk of cells in stratified squamous epithelia. Multiple layers of these flat cells are found superficial to the basal cell layer, where they are undergoing a differentiation process of cornification on their way towards the luminal surface. Serine peptidase inhibitor Kazal type 5 (SPINK5) and 7(SPINK7), as well as alpha-2-macroglobulin like 1 (A2ML1) encodes proteinase inhibitor proteins with elevated expression in squamous epithelial cells. These proteins have been found to be associated with negative regulation of epithelial defence responses as well as desquamation (shedding of the superficial layers of the epithelium). Cornulin (CRNN) is a rather uncharacterized calcium-binding protein with highly specific cytoplasmic expression in squamous epithelia that has been found to be associated with the immune response and differentiation of squamous epithelial cells.
Other squamous epithelial cells
There are additional squamous epithelial cells in the body that currently lack scRNA-seq data at Human Protein Atlas. Squamous epithelia are also present in digestive tissues and the vaginal tract, parts of the body where there is a need for a barrier that is capable of handling frequent mechanical stress. A variety of keratin intermediate filament proteins are expressed in squamous epithelia to provide structural integrity, including keratin 6A (KRT6A) and 13 (KRT13).
Squamous epithelial cell function
Epithelial cells form sheets of cells, epithelia, that line the outer and inner surfaces of the body and constitute the building blocks for glandular tissues. Hence, epithelial cells are found in many parts of the body, including skin, airways, the digestive tract, glandular tissues and organs, as well as the urinary and reproductive systems. The wide range of functions of epithelial cells can be broadly divided into two main categories, being in charge of the transfer of compounds in or out of the body, as well as being a protective barrier against invading pathogens and physical, chemical or biological abrasion.
To withstand the wear and tear from the environment, the epithelial cells form multilayered (stratified) squamous epithelia that are able to handle consistent abrasion. There are two types of stratified squamous epithelia: the dry keratinized type found in the top layer (epidermis) of skin and the moist non-keratinized type found lining the surface of inner cavities such as the mouth, esophagus and vagina. Squamous epithelia consist of multiple layers of cells, with superficial layers of squamous (flat) cells and underlying replenishing cells. The innermost layer of epithelial cells, in contact with the underlying basal membrane, consists of cuboidal multipotent stem cells, called basal cells. Basal cells divide to renew the entire epithelial lining which is under repeated stress and abrasion from the environment causing the superficial layers to slough off. The daughter cells of basal cells slowly transition into squamous cornified (rigid) dead cells with a high content of keratin filaments as they become increasingly superficially located.
The histology of organs that contain squamous epithelial cells, including interactive images, is described in the Protein Atlas Histology Dictionary.
Here, the protein-coding genes expressed in squamous epithelial cells are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in different squamous epithelial cell types.
The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 25 tissues and peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering, resulting in a total of 444 different cell type clusters. The clusters were then manually annotated based on a survey of known tissue and cell type-specific markers. The scRNA-seq data from each cluster of cells was aggregated to mean normalized protein-coding transcripts per million (nTPM) and the normalized expression value (nTPM) across all protein-coding genes. A specificity and distribution classification was performed to determine the number of genes elevated in these single cell types, and the number of genes detected in one, several or all cell types, respectively.
It should be noted that since the analysis was limited to datasets from 25 tissues and PBMC only, not all human cell types are represented. Furthermore, some cell types are present only in low amounts, or identified only in mixed cell clusters, which may affect the results and bias the cell type specificity.
Relevant links and publications
Uhlén M et al., Tissue-based map of the human proteome. Science (2015)