MENU- THE HUMAN PROTEOME
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The germ cell-specific proteomeGerm cells give rise to the gametes in humans, which are cells that can undergo meiosis, as opposed to somatic cells that undergo mitosis. Gametes are diploid germ cells that undergo development into haploid eggs and sperm through oogenesis and spermatogenesis. Transcriptome analysis shows that 77% (n=15083) of all human proteins (n=19670) are detected in germ cells and 4545 of these genes show an elevated expression in any germ cells compared to other cell type groups. The germ cell transcriptomeThe scRNA-seq-based germ cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific germ cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
Protein expression of genes elevated in germ cellsIn-depth analysis of the elevated genes in germ cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different types of germ cells: Spermatogonia, spermatocytes, early spermatids, late spermatids and other germ cells.
Spermatogonia - testisAs shown in Table 1, 657 genes are elevated in germ cells in spermatogonia compared to other cell types. Spermatogonia are diploid cells that form the basal layer of the seminiferous duct and present the initial phase of the spermatogenesis, before meiosis. The spermatogonia undergo asymmetric cell division resulting in two subtypes, type A cells that have stem cell-like properties and maintain the spermatogonia population, and type B spermatogonia that will continue to evolve into primary spermatocytes. Examples of genes expressed in premeiotic spermatogonial cells include testis-specific protein, Y-linked 2 (TSPY2), a transcription factor primarily expressed in the nuclei of spermatogonia, which plays a key role in male sex determination and differentiation by controlling testis development and male germ cell proliferation. Another example is sarcoma antigen 1 (SAGE1), which is a cancer related gene that belongs to the Cancer Testis Antigen (CTA) family, suggested to constitute important targets for immunotherapy.
Spermatocytes - testisAs shown in Table 1, 1185 genes are elevated in germ cells in spermatocytes compared to other cell types. Spermatocytes are derived from type B spermatogonia and can be subdivided into primary spermatocytes that enter the first meiosis, and secondary spermatocytes that enter the second meiosis to produce haploid spermatids. The longest phase of meiosis is prophase I which is subdivided into different stages including preleptotene and pachytene. Several of the testis-specific proteins localized to spermatocytes are involved in testicular differentiation, proliferation and meiosis. Pachytene spermatocytes are easily recognizable by being the only meiotic germ cells observed on testicular histology sections due to the long duration of meiotic prophase I. The structural synaptonemal complex protein (SYCP3) is involved in the recombination and segregation of meiotic chromosomes. The synaptogyrin 4 (SYNGR4) protein is a membranous protein that belongs to the synaptogyrin family and its function is unclear.
Early spermatids - testisAs shown in Table 1, 3158 genes are elevated in germ cells in early spermatids compared to other cell types. Spermatids result from the division of secondary spermatocytes and hence meiosis completion. These cells are divided into early spermatids (round spermatids) and late spermatids (elongated spermatids). Although spermatids are not divided, they undergo a complex process of metamorphosis (called spermiogenesis). Early spermatids are transcriptionally active. One example of an early spermatid protein is the sperm acrosome associated 4 (SPACA4), which is a sperm surface membrane protein that may be involved in sperm-egg plasma membrane adhesion and fusion during fertilization. Another example is the protein product of zona pellucida binding protein (ZPBP), which is believed to play a role in acrosome compaction and sperm morphogenesis. It is one of several proteins that are believed to participate in the merging of sperm and the zona pellucida of the egg cell.
Late spermatids - testisAs shown in Table 1, 2532 genes are elevated in germ cells in late spermatids compared to other cell types. The late spermatid will eventually mature into spermatozoa which will be released in the seminiferous tubule lumen. The DNA will become densely packed and form an acrosome and a mid area with mitochondria. Different from the early spermatids, late spermatids are transcriptionally inert when the acrosome is fully developed because of the tightly packed chromatin. Examples of cell type enriched proteins in late spermatids are spermatogenesis associated 3 (SPATA3) and protein phosphatase 1 regulatory subunit 32 (PPP1R32). However, their function is yet to be studied.
Other germ cellsThe female germ cells, oocytes, are produced in the ovaries, in an anatomical structure called ovarian follicle. Oogenesis is a discontinuous process that starts during fetal life with the development of the primary oocyte. A single layer of granulosa cells surrounds each primary oocyte, arrested in prophase I until puberty. The granulosa cells, in turn, are enclosed in a thin layer of extracellular matrix. These structures are referred to as primordial follicles. At puberty, the primordial follicles eventually develop into primary, secondary and tertiary vesicular follicles. Each month, typically only one developing primary follicle becomes dominant and achieves complete maturation to release the oocyte. Inhibin alpha subunit (INHA) expressed in the ovaries is a protein that negatively regulates follicle stimulating hormone (FSH) in the pituitary gland. Cadherin 11 (CDH11) is another protein expressed in the ovaries as well as in other tissues. Cadherins are a protein family that is related to cell-to-cell adhesion and is important to maintain the structure in connective tissue. Germ cell functionGerm cells are precursor cells to the gametes of the human male and female. These cells are the only cells in the body that undergo meiosis instead of mitosis as compared to other somatic cells. The germ cells will differentiate into egg and sperm cells through spermatogenesis (sperm cell development) and oogenesis (egg cell development). When germ cells differentiate into unfertilized eggs and sperm they will become haploid (half of the genetic code) gametes through meiosis. Haploid cells, when merged, will contribute to genetic differences in the offspring, creating individuals that are genetically different. The histology of organs that contain germ cells, including interactive images, is described in the Protein Atlas Histology Dictionary. BackgroundHere, the protein-coding genes expressed in germ 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 germ cell types. The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 13 different normal tissues, as well as analysis of human peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering and the clusters obtained were gathered at the end, resulting in a total of 192 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 average normalized protein-coding transcripts per million (pTPM) 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 13 organs 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) |
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The Human Protein Atlas
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