The blood-specific proteome

The blood transcriptome

The scRNA-seq-based blood transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific blood type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:

• Cell type enriched: At least four-fold higher mRNA level in a certain cell type compared to any other cell type.
• Group enriched: At least four-fold higher average mRNA level in a group of 2-10 cell types compared to any other cell type.
• Cell type enhanced: At least four-fold higher mRNA level in a cell certain cell type compared to the average level in all other cell types.

Table 2. Number of genes in the subdivided distribution categories of gene expression in the analyzed blood types.

Protein expression of genes elevated in blood & immune cells

In-depth analysis of the elevated genes in blood using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different types of blood : B-lymphocytes, T-lymphocytes, granulocytes, monocytes, macrophages, Hofbauer cells, Kupffer cells, erythroid cells and other immune cells.

B-cell - lymphoid system

As shown in Table 1, 255 genes are elevated in B-cells compared to other cell types. B-lymphocytes or B-cells 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. MS4A1 is group enriched in blood, intestine and lymphoid tissue and expressed on the surface of B cells during maturation, however it is absent in early pro-B cells and the fully differentiated plasma cells. CD19 functions as a coreceptor for the B-cell antigen receptor complex (BCR) on B-lymphocytes.

MS4A1
CD19

T-cell - lymphoid system

As shown in Table 1, 380 genes are elevated in T-cells compared to other cell types. T-lymphocytes or T-cells are a type of lymphocyte that is a part of the adaptive immune system together with B-lymphocytes. An example of a protein with elevated expression in T-cells are CD8B 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. The THEMIS gene 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.

CD8B
THEMIS

Granulocytes

As shown in Table 1, 576 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 granulocyte population includes eosinophils, basophils, and the neutrophils which is also the most abundant type. MMP9 is a protein detected in neutrophils and may play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. CEBPE is a transcription factor that is involved in terminal differentiation and functional maturation of committed granulocyte progenitor.

MMP9
CEBPE

Monocytes

As shown in Table 1, 596 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 blood stream until they migrate to tissues and body cavities where they are differentiated to macrophages and dendritic cells. They also possess antimicrobial functions. ITGAM is expressed predominantly on human monocytes but also macrophages, granulocytes, and natural killer cells.

ITGAM

Macrophages

As shown in Table 1, 407 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). MRC1 is a type I membrane receptor that can bind on the surface of viruses, bacteria, and fungi, to mediate phagocytosis. MSR1 encodes a receptor on the macrophage cell surface that has homeostatic function by clearing modified lipids and proteins.

MRC1
MSR1

Hofbauer cells - placenta

As shown in Table 1, 660 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. VSIG4 is a protein that is expressed in Hofbauer cells. It is a phagocytic receptor, strong negative regulator of T-cell proliferation and IL2 production. Potent inhibitor of the alternative complement pathway convertases. Another protein expressed in Hofbauer cells is COLEC12, a scavenger receptor that displays several functions associated with host defense. It promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast.

VSIG4
COLEC12

Kupffer cells - liver

As shown in Table 1, 615 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 that comes 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. MARCO is a protein expressed on macrophages including Kupffer cells that may bind both gram-positive and gram-negative bacterias.

MARCO

Erythroid cells - blood

As shown in Table 1, 0 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.

HBB - rectum(blood)
HBD - kidney (blood)

Other immune cells

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. CD207 molecule (HBBCD207) is a receptor expressed on the surface of Langerhans cells, the dendritic cells of the skin. Thanks to this receptor, Langerhans cells bind and absorb antigens on the surface of infectious agents and present the antigens to T-cells.

CD207 - skin

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).

Mast cells are found in the connective tissue throughout the body, in particular in the skin, respiratory system, gastrointestinal and urinary tracts. They are part of the innate and adaptive immune system and are also involved in maintenance of a healthy vascular system. Mast cells have also been connected to diseases such as allergy and asthma.

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 regulation of immunity and inflammation. A protein expressed on the surface of platelets is glycoprotein IX platelet (GP9CD207), which allows attachment to damaged blood vessels.

GP9 - bone marrow

Blood 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 haematopoiesis: deterministic or stochastic. In the deterministic model, it is suggested that different factors in the haematopoietic 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 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 , including interactive images, is described in the Protein Atlas Histology Dictionary.

Background

Here, the protein-coding genes expressed in blood 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 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.

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