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The ciliated cell-specific proteomeThe ciliated cell transcriptomeEpendymal cellsChoroid plexus epithelial cellsRespiratory ciliated cellsRespiratory deuterosomal cellsEpididymal efferent duct ciliated cellsFallopian tube ciliated cellsEndometrial ciliated cellsDeep Visual Proteomics analysis of ciliated cellCiliated cells of the fallopian tubeCiliated cell functionBackgroundRelevant links and publications
Single cell type methods
DVP methods
The ciliated cell-specific proteomeCiliated cells with motile cilia are found in many parts of the body, including the respiratory epithelium lining the bronchi and bronchioles, and in glandular epithelia of reproductive tissues. Ciliated cells facilitate mucociliary transport of cells and particles needed for the clearance of unwanted particles in the respiratory tract and the transport of gametes and the early embryo during reproduction. Transcriptome analysis shows that 67% (n=13603) of all human proteins (n=20162) are detected in ciliated cells and 1800 of these genes show an elevated expression in any ciliated cells compared to other cell type groups. In-depth analysis of the elevated genes in ciliated cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in the following types of ciliated cells: brain, pituitary gland, lung, epididymis, fallopian tube and endometrium. In addition, we utilized proteomic data from a mass spectrometry (MS)-based, cell type–resolved atlas of the human body, generated by Deep Visual Proteomics (DVP), a spatial proteomics platform that combines imaging-guided cell selection with high-resolution protein analysis. Ciliated cells of the fallopian tube was included in this analysis. The fallopian tube cell representation includes both secretory and ciliated cells. Out of a total of 14361 detected proteins in all cell types, 8520 were detected in fallopian tube cells. 1079 proteins showed elevated detection in fallopian tube cells compared to other DVP cell types.
The ciliated cell transcriptomeThe scRNA-seq-based ciliated cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific ciliated cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
As shown in Table 1, 1800 genes show elevated expression in ciliated cells, as a group, compared to other grouped cell types. An example of an important protein with elevated expression in ciliated cells is forkhead box J1 (FOXJ1), which is a nuclear transcription factor required for the production of motile cilia. The expression profile of FOXJ1 is observed in ciliated cells across all tissue types included, confirmed at protein level by immunohistochemical stainings.
Expression profiles are compared across the 154 cell types, in addition to the comparison across the 53 grouped cell types. This results in cell specificity categories based on two datasets, one more detailed across all cell types and one more suitable for the general overview based on the grouped cell types with similar expression profile and functions. Cell types are grouped based on function and biology, to facilitate a better overview and to complement the detailed information based on all cell types. Table 2. Number of genes in the subdivided specificity categories of elevated expression in the different types of ciliated cell types, compared to all other cell types.
Ependymal cellsThe ependymal cells are lining the ventricular system of the brain, it consists of a simple columna ciliated epithelium, with a glial origin of development. Eventhough the ependymal cells are glial cells, their main function involves the apical cilia and ciculation of cerebrospinal fluid (CSF). Ependymal cells create a thin, ciliated layer of neuroepithelial tissue that lines the ventricles of the brain and the central canal of the spinal cord. As shown in Table 2, 1388 genes show elevated expression in ependymal cells compared to other cell types. An example of a protein with elevated expression in ependymal cells is RSPH4A, also detected in the ependymal cells of caudate using immunohistochemistry.
Choroid plexus epithelial cellsChoroid plexus epithelial cells are a specialized type of ependymal cell, but they exhibit unique characteristics. Choroid plexus cells and ependymal cells form adjacent single-cell layers that meet at a transitional zone. Unlike ependymal cells, the choroid plexus is supported by a basal lamina and possesses barrier properties. Ependymal cells play a vital role in producing and circulating cerebrospinal fluid (CSF), which supports the central nervous system. As shown in Table 2, 1299 genes show elevated expression in choroid plexus epithelial cells compared to other cell types. Examples of genes with enriched expression are SLC13A4, KCNJ13 and SLC39A12. The sodium/iodide cotransporter SLC5A5 is highly expressed in choroid plexus epithelial cells, and detected at protein level by immunohistochemistry.
Respiratory ciliated cellsRespiratory ciliated cells line the airways of the respiratory tract and help clear mucus, dust and pathogenes from the lunchs by moving them towards the throat for expulsion. Their coordinated ciliary movements is essential for keeping the airways clean and protecting agains respiratory infections. As shown in Table 2, 729 genes show elevated expression in respiratory ciliated cells, compared to other cell types. ARMC3 is an example of genes with elevated expression in respiratory ciliated cells.
Respiratory deuterosomal cellsRespiratory deuterosomal cells are precursor cells in the respiratory epithelium that generate multiple basal bodies needed for ciliogenesis. They play a key role in the renewal and repair of ciliated cells, especially after airway injury. As shown in Table 2, 203 genes show elevated expression in respiratory deuterosomal cells, compared to other cell types. Cycline O (CCNO) and Cell division cycle 20B (CDC20B) are two examples of genes with enriched expression in deuterosomal cells when comparing to other cell types.
Epididymal efferent duct ciliated cellsEpididymal efferent duct ciliated cells is located in the male reproductive tract, they help move sperm and fluid through the efferent ducts of the epididymis. Their ciliary motion assists in sperm concentration and transport. As shown in Table 2, 516 genes show elevated expression in epididymal efferent duct ciliated cells, compared to other cell types. An example of a protein elevated in the epididymal efferent duct ciliated cells is cilia- and flagella-associated protein 53 (CFAP53), required for motile cilium formation.
Fallopian tube ciliated cellsFallopian tube ciliated cells are found in the lining of the oviducts, these cells faciliatet the movement of the egg towards the uterus. Their coordinated movment is vital for successful fertilization and early embryo transport. As shown in Table 2, 655 genes show elevated expression in Fallopian tube ciliated cells, compared to other cell types. An example of a protein elevated in the fallopian tube ciliated cells is the cilia apical structure protein, Sentan (SNTN).
Endometrial ciliated cellsEndometrial ciliated cells are present in the uterine lining, these cells help circulate uterine fluid and may assist in creating a favourable environment fr embryo implantation. Their activity fluctuates with the hormonal changes across the menstrual cycle. As shown in Table 2, 519 genes show elevated expression in Endometrial ciliated cells, compared to other cell types. Radial spoke head component 1 (RSPH1) is an example of genes with elevated expression in ciliated cells, including
Deep Visual Proteomics analysis of ciliated cellProteomic data from a mass spectrometry (MS)-based, cell type–resolved atlas of the human body, generated via Deep Visual Proteomics (DVP), a spatial proteomics platform that combines imaging-guided cell selection with high-resolution protein analysis, is integrated to the Single Cell Type resrouce. This enables exploration of global protein detection profiles with RNA expression profiles. The DVP data includes 13496 detected proteins and covers 27 cell types which is grouped into 24 main cell types used for classification and the RNA comparison. The cell type specificity categories were applied to the protein data. Here, we describe the included ciliated cell and show examples of proteins with elevated detection. Ciliated cells of the fallopian tubeDVP resulted in 1079 proteins classified as elevated in cells of the fallopian tube. In total, 8520 proteins were detected in fallopian tube cells, out of these, 315 were only detected in fallopian tube cells, compared to the other 23 DVP samples. Fallopian tube cells are represented by both secretory and ciliated cells, in the distrubution and specificity categories secretory and ciliated cells are combined by max-value. The two cell types are shown separately on gene summary pages, however due to sampling overlap they were combined in the classifications and RNA comparison. Most of the 451 proteins enriched in fallopian tube cells are related to ciliated proteins. Proteins enriched in the fallopian tube were strongly associated with motile cilium structure and function, including dynein motor proteins (DNAH5, DNAH9) and ciliary assembly factors (AK7, CFAPs, CCDC family proteins). This expression pattern is consistent with the specialized role of fallopian tube ciliated epithelial cells in generating fluid flow that supports fertilization and embryo transport within the reproductive tract. Both ciliated and secretory cell samples from the fallopian tube showed detection of DNAH5 at protein level, where as RNA is specific to ciliated cells. Similarly, secretory cell markers, such as OVGP1, show similar level of detection on protein level although enriched in secretory cells on RNA level. Ciliated cell functionCiliated cells are specialized epithelial cells that possess hair-like structures called silia on their surface. These cilia move in coordinated waves to move fluids, particles, or cells along the epithelial surfaces. They play a crucial role in maintaining the cleanliness and function of various organs by faciliatating transport and preventing blockage or infections. Ciliated cells are found throughtoit the body, particularly in the respiratory tract, reproductive system, and central nervous system. A motile cilia is different from primary cilia, involved in sensory and signaling. The histology of organs that contain ciliated cells, including interactive images, is described in the Protein Atlas Histology Dictionary. BackgroundHere, the protein-coding genes expressed in ciliated 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 ciliated cell types. The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq and snRNA-seq experiments (36 datasets) covering 34 tissues. All datasets (unfiltered read counts of cells) were clustered independenty using leiden clustering, resulting in a total of 1175 different cell type clusters. The clusters were then manually annotated based on a survey of known tissue and cell type-specific markers. The RNA-seq data from each cluster of cells was aggregated to mean normalized protein-coding counts per million (nCPM) for all protein-coding genes. A specificity and distribution classification was performed for both single cell types individually, as well as grouped into 53 main cell type groups. The specificity classification determined the number of elevated genes, while the distribution determined whether genes are detected in one, several or all cell types or cell type groups. It should be noted that since the analysis was limited to datasets representing 34 tissue types, 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) |
The Human Protein Atlas project is funded
