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The germ cell-specific proteomeThe germ cell transcriptomeSpermatogenic cell typesOocytesDeep Visual Proteomics analysis of germ cellOocytesGerm cell functionBackgroundRelevant links and publications
Single cell type methods
DVP methods
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 67% (n=13603) of all human proteins (n=20162) are detected in germ cells and 4103 of these genes show an elevated expression in any germ cells compared to other cell type groups. In-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 the following types of germ cells: spermatogenic cell types of the testis (undifferentiated spermatogonia, differentiating spermatogonia, early primary spermatocytes, late primary spermatocytes, early spermatids and late spermatids), and oocytes in the ovaries. In addition, we utilized proteomic 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. Oocytes was included in the analysis. Out of a total of 14361 detected proteins in all cell types, 8142 were detected in germ cells, and 951 were classified as elevated in germ cells. Further details on the cell type specific proteome profile, as well as examples of enriched proteins in germ cells, are provided below. 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:
Spermatogenic cell typesSpermatogenic cells represent the developmental stages of sperm formation, progressing from undifferentiated spermatogonia to mature spermatids. This process involves successive differentiation and meiosis, as spermatogonia develop into primary spermatocytes and then spermatids, ensuring the production of haploid sperm capable of fertilization. Table 2. Number of genes in the subdivided specificity categories of elevated expression in the analyzed spermatogenic cell types compared to all other cell types.
Undifferentiated spermatogoniaDiploid primitive germ cells residing on the basement membrane of seminiferous tubules. They undergo asymmetric division to self-renew and produce differentiating (type B) spermatogonia, maintaining the spermatogonial stem cell pool. As shown in the table, 399 genes show elevated expression in undifferentiated spermatogonia compared to other cell types. The majority of genes with elevated expression in is shared with differentiating spermatogonia and early primary spermatocytes, such is the case for MAGEC2.
Differentiating spermatogoniaDiploid germ cells derived from undifferentiated spermatogonia that have committed to the spermatogenic lineage. They proliferate and mature toward the primary spermatocyte stage, marking the transition to meiosis. As shown in the table, 523 genes show elevated expression in differentiating spermatogonia compared to other cell types. An example of proteins with elevated expression in differentiating spermatogonia 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.
Early primary spermatocytesSpermatocytes 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. As shown in the table, 904 genes show elevated expressio in early primary spermatocytes compared to other cell types. 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.
Late primary spermatocytesGerm cells progressing through late prophase I toward the first meiotic division. They will generate haploid secondary spermatocytes. As shown in in the table, 2153 genes are elevated in late primary spermatocytes compared to other cell types. An example of a protein with elevated expression in late primary spermatocytes is A Disintegrin and A Metalloprotease domain 2 (ADAM2), also called fertilin beta, involved in the sperm-egg membrane binding.
Early spermatidsSpermatids 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. 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. As shown in Table 2, 2512 genes are elevated in early spermatids compared to other cell types. 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.
Late spermatidsDifferent from the early spermatids, late spermatids are transcriptionally inert when the acrosome is fully developed because of the tightly packed chromatin. As shown in Table 2, 2821 genes are elevated in late spermatids compared to other cell types. An examples of a cell type enriched protein in late spermatids is spermatogenesis associated 3 (SPATA3)
OocytesThe female germ cells, oocytes, are produced in the ovaries, in an anatomical structure called the 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, called the zona pellucida. 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 into the fallopian tube.
As shown in the table, 934 genes are elevated in Oocytes compared to all other cell types. Examples of cell type enriched proteins in oocytes include folliculogenesis specific bHLH transcription factor (FIGLA) and zona pellucida glycoprotein 3 (ZP3). FIGLA is a transcription factor that plays an important role in the regulation of oocyte-specific genes essential for normal ovarian follicular development, including ZP3, a component of the zona pellucida, a structure that is important for subsequent fertilization by a sperm cell.
Deep Visual Proteomics analysis of germ 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 germ cell and show examples of proteins with elevated detection. OocytesDVP resulted in 951 proteins classified as elevated in Oocytes. In total, 8142 proteins were detected in Oocytes, out of these, 192 were only detected in Oocytes, compared to the other 23 DVP samples. The 279 proteins enriched in oocytes are broadly consistent with a germ cell/oocyte transcriptional and structural program, highlighted by key markers such as FIGLA (oocyte lineage transcription factor), DDX4 (germ cell RNA helicase), and zona pellucida components ZP2/ZP3/ZP4, which are central to oocyte extracellular coat formation and fertilization. Additional enrichment of factors like OOSP2 and chromatin/regulatory proteins (e.g., H1-8, TLE2) supports active oocyte-specific gene regulation and developmental competence. At the same time, the presence of several genes classically associated with testis or broader germline programs (e.g., DAZL, MAGE family members) is not unusual, as many “cancer/testis” or germ cell genes are shared across gametogenic lineages. Overall, the signature still most strongly reflects a germline/oocyte context, with some expected overlap from conserved reproductive and germ cell–associated expression programs. 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 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) |
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