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The spleen cell type enriched transcriptomeSpleen cell type enriched transcriptome: SummarySpleen cell type enriched transcriptome: Illustrative examplesRed pulpWhite pulpOther
Tissue cell type methods
The spleen cell type enriched transcriptomeThe spleen is a multifunctional organ that plays crucial roles in the immune system and blood filtration. The spleen is typically divided into red pulp and white pulp, the red pulp contains sinusoids which act as a blood filter, removing old and damaged red blood cells from circulation, whereas the white pulp consists entirely of lymphoid tissue. Additionally, the spleen recycles iron from old red blood cells and serves as a site for the production and storage of monocytes and red blood cells. While not essential for survival, as other organs can take over its functions, the spleen contributes significantly to maintaining overall health and fighting infections. ​ 2822 genes were predicted to have cell type specificity in the spleen. ​ Spleen cell type enriched transcriptome: SummaryGenes with predicted cell type specificity within spleen are detailed in Table 1. Identified genes are subdivided into 3 specificity categories, based on the difference between the enrichment score in the corresponding cell type, compared to the other cell types profiled in the tissue (see Methods Summary page for details):
Spleen cell type enriched transcriptome: Illustrative examplesRed pulpThe red pulp is the primary component of the spleen, making up about 75-80% of its tissue. It consists of a network of splenic cords and venous sinuses filled with blood. The red pulp's main functions include filtering blood to remove old or damaged red blood cells, storing platelets and monocytes, and recycling iron from hemoglobin. Specialized macrophages in the red pulp phagocytose worn-out erythrocytes and pathogens. The unique structure of the red pulp, with its narrow passageways, allows for mechanical filtration of blood cells and the trapping of abnormal or aged cells. Endothelial cellsThe spleen contains endothelial cells from both normal blood vessel, as well as specialised sinusoids that assist in the filtering of blood to remove old and damaged red blood cells, or erythrocytes. Genes classified as having specificity in endothelial cells of the spleen include and the Adhesion G protein-coupled receptor L4 (ADGRL4) and Phosphatidylinositol Transfer Protein, Membrane-Associated 3 (PITPNM3).
ErythrocytesErythrocytes (red blood cells) are biconcave, anucleate cells filled with hemoglobin that primarily function to transport oxygen from the lungs to body tissues and carbon dioxide from tissues back to the lungs. In the spleen, older or damaged erythrocytes are filtered out and phagocytosed by macrophages in the red pulp, while the iron from their hemoglobin is recycled for use in new red blood cell production. Erythrocyte genes Hemoglobin subunit alpha 1 (STAB2), and Bisphosphoglycerate mutase (BPGM) are important in the regulation of hemoglobin oxygen affinity.
MacrophagesMacrophages in the spleen are diverse and play crucial roles in various functions, including blood filtration, immune response, and iron recycling. They are found in different regions of the spleen, with red pulp macrophages primarily involved in removing old or damaged red blood cells and recycling iron, while marginal zone macrophages and marginal metallophilic macrophages in the marginal zone are specialized in capturing blood-borne pathogens and initiating immune responses. Genes classified as having specificity in macrophages of the spleen include CD68 (CD68), and the lyzosomal enzyme Tripeptidyl peptidase 1 (TPP1).
White pulpThe white pulp of the spleen is the primary immunological region, comprising about 20-25% of splenic tissue. It consists of lymphoid follicles containing mainly B cells, surrounded by T cell-rich areas called periarteriolar lymphoid sheaths (PALS). The white pulp plays a crucial role in initiating adaptive immune responses against blood-borne antigens. It is organized around central arterioles and contains specialized antigen-presenting cells that help activate T and B lymphocytes, leading to antibody production and cell-mediated immune responses. T-cellsT cells in the spleen are primarily located in the T cell zone (also called the periarteriolar lymphoid sheath or PALS) that surrounds the main lymphoid follicle and central arteriole. These T cells, including naive and central memory T cells, can migrate between the red pulp and white pulp, guided by chemokine gradients and specialized stromal cells, to participate in immune responses against blood-borne antigens. Genes classified as having specificity in T-cells in the spleen include CD5 (CD5), and the CD3 delta subunit (CD3D).
B-cellsB cells in the spleen are primarily located in the white pulp, specifically in the follicles and marginal zone. Follicular B cells participate mainly in T cell-dependent immune responses, while marginal zone B cells are strategically positioned to capture blood-borne antigens and can promote both T cell-independent and T cell-dependent immune responses. Genes classified as having specificity in B-cells in the spleen include CD22 (CD22), and the signal molecule Phospholipase C gamma 2 (PLCG2).
Plasma cellsPlasma cells are specialised lymphocytes derived from B-cells that actively produce and secrete large quantities of antibodies. Genes classified as having specificity in plasma cells in the spleen include the Joining chain of multimeric IgA and IgM (JCHAIN), and the Marginal zone B and B1 cell specific protein (MZB1).
OtherHematopetic stem cellsHematopoietic stem cells (HSCs) are present in in the spleen, though in lower numbers compared to the bone marrow. During stress conditions like anemia or inflammation, splenic HSCs can expand and contribute to extramedullary hematopoiesis, with the spleen serving as an important site for emergency blood cell production. Genes classified as having specificity in hematopetic stem cells in the spleen include cell adhesion molecule and tumour marker CEA cell adhesion molecule 6 (CEACAM6), and Membrane spanning 4-domains A3 (MS4A3), which binds to and modulates CDK2.
Mitotic cellsMitotic cells in the spleen are primarily found in the white pulp, particularly in germinal centres of lymphoid follicles. These actively dividing cells are mainly B lymphocytes undergoing clonal expansion in response to antigenic stimulation, contributing to the adaptive immune response and antibody production. Genes classified as having specificity in mitotic cells in the spleen include DNA topoisomerase II alpha (TOP2A) and Kinesin family member 11 (KIF11), and Cyclin A2 (CCNA2).
Smooth muscle cellsSmooth muscle cells in the spleen are primarily found in the outer capsule surrounding the spleen, as well as in the walls of blood vessels supplying the spleen with blood. These cells contribute to the contractile ability of the spleen, allowing it to adjust its size and blood content in response to physiological demands, such as during exercise or blood loss. Genes classified as having specificity in smooth muscle cells in the spleen include the filament proteins Calponin 1 (CNN1) and Desmin (DES).
FibroblastsFibroblasts in the spleen play crucial roles in maintaining the organ's structure and supporting immune functions. They are found in different regions of the spleen, with fibroblastic reticular cells (FRCs) predominating in the T-cell zone of the white pulp, fibroblastic dendritic cells (FDCs) in the B-cell follicles, and specialized fibroblasts in the red pulp that form a meshwork supporting blood filtration and cell trafficking. Genes classified as having specificity in fibroblasts in the spleen include Ankyrin 2 (ANK2) and the extracellular protein Fibrillin 1 (FBN1).
NK cellsNK cells are innate immune cells that play a crucial role in the body's defence against viruses, stressed cells, and tumors without requiring specific antigen recognition. They are characterized by their ability to quickly respond to threats, primarily through cytotoxic activity and cytokine production, and are found throughout the body's lymphoid tissues. Genes classified as having specificity in NK-cells in the spleen include Killer cell lectin like receptor C3 (KLRC3) as well as genes without previous known association in NK cells such as Chloride Intracellular Channel 3 (CLIC3).
NeutrophilsNeutrophils in the spleen are found in distinct populations, primarily located in the red pulp and marginal zone. These splenic neutrophils play crucial roles in blood filtration, pathogen clearance, and immune responses. Genes classified as having specificity in neutrophils in the spleen include Colony stimulating factor 3 receptor (CSF3R) and the calcium binding protein Grancalcin (GCA). |
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