The blood & immune cell-specific proteome
Blood & immune cells develop from hematopoietic stem cells (HSCs), which are multipotent cells with the ability to self-renew that can differentiate into all types of blood cells included in the lymphoid and the myeloid lineage. These cells reside in the medullary region of the bone marrow. Mature blood cells and immune cells circulate in the blood, and certain immune cells also reside within different tissues, e.g. liver and placenta.
Transcriptome analysis shows that 78% (n=15730) of all human proteins (n=20162) are detected in blood & immune cells and 3234 of these genes show an elevated expression in any blood & immune cells compared to other cell type groups. In-depth analysis of the elevated genes in blood & immune cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in the following types of blood & immune cells: T-cells, B-cells, plasma cells, NK-cells, granulocytes, monocytes, macrophages, Hofbauer cells, Kupffer cells, dendritic cells, Langerhans cells, erythroid cells and platelets.
The blood & immune cell transcriptome
The scRNA-seq-based blood & immune cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific blood & immune cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
As shown in Table 1, 504 genes are elevated in T-cells compared to other cell types. T-cells or T-lymphocytes are a type of lymphocyte that is a part of the adaptive immune system together with B-cells. An example of a protein with elevated expression is T-cell surface glycoprotein CD8 beta chain (CD8B) which is the beta chain of the cell surface glycoprotein CD8 and is an important molecule mediating cell-cell interactions in the lymphoid tissues. Acting as a coreceptor to the T-cell receptor on the T-cell, it recognizes MHC class I molecules displayed by an antigen-presenting cell. Thymocyte Selection Associated (THEMIS) encodes a protein involved in the late phases of T-cell development. It is necessary for lineage commitment and functions through T-cell antigen receptor signaling.
As shown in Table 1, 348 genes are elevated in B-cells compared to other cell types. B-cells or B-lymphocytes are a type of white blood cell of the lymphocyte subtype, that mature in the bone marrow. They express B-cell receptors on their surface that allow them to bind specific antigens, and function in the humoral immunity component of the adaptive immune system by secreting antibodies. Membrane Spanning 4-Domains A1 (MS4A1) is a group enriched in blood, intestine and lymphoid tissue and expressed on the surface of B-cells during maturation and absent in early pro-B cells and the fully differentiated plasma cells. B-lymphocyte antigen CD19 (CD19) functions as a coreceptor for the B-cell antigen receptor complex (BCR) on B-cells.
As shown in Table 1, 636 genes are elevated in plasma cells compared to other cell types. Plasma cells are a large type of lymphocytes that originate in the lymphoid organs as B-cells, with the function to produce large quantities of antibodies by internalizing antigens through receptor-mediated endocytosis. When the B-cell breaks down the antigen, bits of pieces of the antigen called antigenic peptides are presented on the surface through MHCII molecule, where it can be activated by a T-cell to differentiate into specific cells, in this case a plasma cell. Immunoglobulin heavy constant alpha 2 (IGHA2) is a protein that forms the constant region of the antibody heavy chain, which is one of the two types of polypeptide subunits that constitute an antibody (light chain being the other type).
As shown in Table 1, 527 genes are elevated in NK-cells compared to other cell types. Natural killer cells (NK-cells) are a type of cytotoxic lymphocyte that circulate in the blood. As a critical part of the innate immune system, they patrol the body and, upon contact with virus-infected cells, tumor formation and stressed cells, respond rapidly by releasing cytotoxic granules that destroy the target cell(s). NK-cells recognize abnormal cells through different types of receptor protein complexes, including the protein killer cell lectin like receptor K1 (KLRK1), which functions as an activating and costimulatory receptor upon binding to various cellular stress-inducible ligands displayed at the surface of autologous tumor cells and virus-infected cells.
As shown in Table 1, 364 genes are elevated in granulocytes compared to other cell types. Granulocytes, also known as polymorphonuclear leukocyte (PML), are the major type of white blood cells and part of the innate immune system against bacterial infection. They are characterized by their high content of granules in the cytoplasm and have a nucleus that is lobe-shaped or segmented into two or more connected lobes. The blood granulocyte population includes eosinophils, basophils and neutrophils, the latter being the most abundant type, while mast cells are tissue resident granulocytes found in most parts of the body near mucosal tissues. Membrane spanning 4-domains A2 (MS4A2) is a subunit of a membrane receptor in basophils and mast cells that binds to the FC region of IgE antibodies in order to enable the degranulation response where enzymes and other pro-inflammatory mediators are released to fight infection. One such enzyme is tryptase alpha/beta 1 (TPSAB1), a neutral protease involved in the activation of connective tissue cells.
As shown in Table 1, 882 genes are elevated in monocytes compared to other cell types. Monocytes compose 2-10% of all white blood cells in the human body. The proliferation takes place in the bone marrow and then circulates the bloodstream until they migrate to tissues and body cavities where they are differentiated into macrophages and dendritic cells. They also possess antimicrobial functions. Spi-1 proto-oncogene (SPI1) is a transcription factor that activates gene expression during myeloid and B-lymphoid cell development. Ficolin-1 (FCN1) is a member of the complement system and binds pathogen associated molecular patterns on microbes.
As shown in Table 1, 503 genes are elevated in macrophages compared to other cell types. Macrophages belong to a group of white blood cells called phagocytes, which is a type of cells specialized in phagocytosis, a process that protects the body by ingesting cellular debris, dead cells or pathogens. Mature macrophages are found throughout the body in most tissues, they do not travel far and are rarely seen in the bloodstream, instead they are guarding locally and waiting to be activated. Macrophage polarization is a process where they adopt different functions depending on the signals received from the environment and the two major states are the M1(pro-inflammatory) and the M2(anti-inflammatory). Macrophage mannose receptor 1 (MRC1) is a type I membrane receptor that can bind on the surface of viruses, bacteria, and fungi, to mediate phagocytosis. Macrophage scavenger receptor 1 (MSR1) encodes a receptor on the macrophage cell surface that has a homeostatic function by clearing modified lipids and proteins.
As shown in Table 1, 526 genes are elevated in Hofbauer cells compared to other cell types. Hofbauer cells are fetal macrophages that can be found in the villous stroma at all stages of gestation. The term is used for any fetal derived macrophages in the placental villous core, amnion and chorionic lavae. They have several proposed functions including preventing vertical transmission, i.e transmission from the mother to the fetus, being pro-angiogenic and playing a role in placental morphogenesis. V-set immunoglobulin-domain-containing 4 (VSIG4) is a protein that is expressed in Hofbauer cells. It is a phagocytic receptor, a strong negative regulator of T-cell proliferation and IL2 production, and a potent inhibitor of the alternative complement pathway convertases. Another protein expressed in Hofbauer cells is CD68, a transmembrane glycoprotein that is highly expressed by human monocytes and tissue macrophages.
As shown in Table 1, 465 genes are elevated in Kupffer cells compared to other cell types. Kupffer cells are part of the innate immune defense in the liver, they are specialized macrophages lining the liver sinusoidal endothelial walls and filter the blood from microbial debris and particles which enter through the hepatic portal vein. Kupffer cells make up to 80-90% of all macrophages in the body and their function and structures differ depending on if they reside in the centrilobular or periportal region. Macrophage receptor with collagenous structure (MARCO) is a protein expressed on macrophages including Kupffer cells that may bind both gram-positive and gram-negative bacterias. CD209, is a C-type lectin receptor that binds to pathogen associated molecular patterns on various microorganisms and this binding activates phagocytosis.
As shown in Table 1, 462 genes are elevated in dendritic cells compared to other cell types. Dendritic cells are antigen-presenting cells present in tissues that are in contact with the external environment, e.g. skin, but also in an immature state in the blood, and upon activation they migrate to the lymph nodes to interact with T-cells and B-cells. They act as messengers between the innate and the adaptive immune systems. CD300A is a receptor expressed on the surface of e.g. dendritic cells, monocytes, macrophages and mast cells to name a few. Studies have shown that CD300a inhibits lymphocyte activity. Another example of a protein with elevated expression in dendritic cells is interferon regulatory factor 7 (IRF7), an important transcriptional regulator of type I interferon (IFN)-dependent immune responses and plays a critical role in the immune response against DNA and RNA viruses.
As shown in Table 1, 611 genes are elevated in Langerhans cells compared to other cell types. Langerhans cells are dendritic cells that originate from bone marrow progenitors and have their function in the epidermis of the skin, where they represent as the first line of immunologic defense. Like macrophages, LCs present antigens to lymphocytes through different surface receptors and are able to regulate innate and adaptive responses . One well-known surface receptor is langerin (CD207). Cluster of Differentiation 1a (CD1A) is a transmembrane glycoprotein with structural similarities to MHC class I. CD1A mediates primarily lipid-based antigens to T-cells.
As shown in Table 1, 434 genes are elevated in erythroid cells compared to other cell types. Erythroid cells, also called erythrocytes or red blood cells, acquire oxygen from the inhaled air in the lungs and transport the oxygen to all tissues of the body via the circulatory system. Hemoglobin subunit beta HBB and subunit delta HBD are components of the hemoglobin molecule which is expressed exclusively in erythroid cells and bind oxygen.
Platelets are produced by megakaryocytes in the bone marrow and are released to the circulating blood. Their main role is to initiate blood clot formation in response to blood vessel injury. In addition, they have possible roles in the regulation of immunity and inflammation. A protein expressed on the surface of platelets is platelet glycoprotein IX (GP9), which allows attachment to damaged blood vessels. A protein released from active platelets is platelet factor 4 (PF4), which is involved in platelet aggregation.
Blood & immune cell function
The blood has many important functions including oxygen/carbon dioxide transport, removal of waste, coagulation, and body temperature regulation etc. Blood that accounts for about 7% of the human body weight circulates the body through blood vessels and is synthesized in the hematopoiesis process. The HSCs can give rise to all blood cells including; B-lymphocytes, T-lymphocytes, natural killer cells, granulocytes, monocytes, erythrocytes, and platelets. Studies have suggested two models for hematopoiesis: deterministic or stochastic. In the deterministic model, it is suggested that different factors in the hematopoietic microenvironment decide what the HSCs should differentiate into. In the stochastic model, the HSCs differentiate into the specific blood cells by randomness.
In addition to antibody production in response to contact with antigens, B-cells are also classical antigen-presenting cells and secrete cytokines. Naive B lymphocytes reside in lymph nodes and have not yet been exposed to an antigen. Upon antigen activation they will differentiate to either plasma cells or memory B-cells. Memory B lymphocytes are formed within germinal centers following primary infection, and are important in generating an accelerated and more robust antibody-mediated immune response in the case of re-infection. They are localized in areas of facilitated antigen encounter and compared to naive B-cells they have a higher affinity to the immunizing antigen, a lifespan of decades instead of weeks, and faster and more efficient proliferation and differentiation.
T-cells originate from hematopoietic cells in the bone marrow, which develop into immature thymocytes in the thymus. The thymocytes differentiate into several types of mature T-cells; T-helper cells, cytotoxic T-cells, memory T-cells, regulatory T-cells and natural killer T-cells. During maturation, T-cells undergo β-selection and positive selection in the thymic cortex and negative selection in the thymic medulla.
The histology of organs that contain blood & immune cells, including interactive images, is described in the Protein Atlas Histology Dictionary.
Here, the protein-coding genes expressed in blood & immune 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 blood & immune cell types.
The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 29 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 557 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 29 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)