User:Kinkreet/Immunology/Development of the Immune System

Primary Lymphoid Organs
The organs in which the lymphocytes are formed and developed (matured and selected) are termed the primary lymphoid organs; the organs where the immune cells encounter antigen and generate a response are called secondary lymphoid organs. Primary lymphoid tissues include the bone marrow and thymus; secondary lymphoid tissues include the lymph nodes, spleen and mucosa-associated lymphoid tissue (MALT) such as the Peyer's patches, tonsils, appendix and BALT.

Haematopoietic Stem Cells (HSC)
The bone marrow is the main site of haematopoiesis in adults (foetal liver in embryo), which produce haematopoietic stem cells (HSCs) that give rise to all the red and white blood cells of the body.

Long term haematopoietic stem cell (LT-HSC) can self-renew indefinitely in the bone marrow; during a cell division, one of the two daughter cells can differentitae to a short-term HSC by gaining a CD34 marker. ST-HSC can self-renew only for a few weeks, and must differentiate into multipotent progenitors (MPPs) by gaining the Flk2 (CD135) marker; at this stage, the MPP has lost its ability to self-renew. MPPs can differentiate into lymphoid-primed multipotent progenitors (CMPP) by activation of the PU.1 transcription factor, or to common myeloid progenitors (CMP) and megakaryocyte-erythroid progenitor cell (MEP) using the GATA-1 transcription factor; these two factors mutually inhibit each other, and so to ensure only one lineage is produced at any one time, as is the case during differentiation, where one cell lineage takes over.

LMPP will continue to differentiate to Granulocyte-Monocyte Progenitor (GMP) if the PU.1 signal continues to persist, or if early B-cell factor (EBF) and Pax5 is present, it will differentiate instead to B cell precursors; in the presence of Notch-1, CMPP will differentiate to earliest thymic progenitors (ETP, or TSP, thymus-settling cell), or to natural killer cells in the presence of E4BP4 and Id2. GMP differentiate to neutrophil precursors with Gfi-1, and to macrophages in the presence of Egr-1,2 and Nab-2. ETP or TSP differentiate to T cell precursors, which further differentiate to CD4+ (with Th-POK), NKT (w. PLZF) and γδT (w. SOX13).

MEP can differentiate to erthyrocyte precursor with EKLF signal, and to megakaryocyte with Fli-1 signal. As each step is regulated, the number of cells of each type can be controlled. The main point is that there are transcription factors that controls the differentiation and production of each lineage, the more differentiated a cell is, the more complex the cocktail of factors required to get to that stage of the differentiation. Knockout mice using miRNA has been useful in elucidating the effect of each transcription factor.

Because there are so many steps in the differentiation, a single dysregulation can lead to detrimental effects. When the body respond to injury, all levels of the haematopoietic tree increase their level of differentiation, and so all must be regulated.

Example: B cell development
PU.1 and Ikaros are trasncriptional factors that lead to the expression of FLT3, and causes the HSC to differentiate into MPP. Flk2/Flt3 along with PU.1 induces the epxression of IL-7R, differentiating MPP to CLP, and upregulates E2A upon cytokine binding. E2A and PU.1 lead to the expression of EBF in specific B-lineage cell, and then EBF lead to the expression of Pax-5, which in turn leads to the expression of CD19, BLNK, and Igα on the cell surface.

Structure of Bone Marrow
The bone marrow exists in the medullary cavities of bones, which is enclosed by the thick wall of compact bone. It is made up of a dense network of medullary vascular sinuses, thin-walled vessels which allows for the passage of haemocytes, surrounded by haemocytes and their progenitors. Because there is such a diverse range of haemocytes in the bone marrow, the different types of haemocytes are thought to be organised differently spatially, to allow for different environments to exist at different regions of the bone marrow. Bone marrow stromal cells create these distinct microenvironments called niches, which maintain blood-cell viability and produce the environmental factors which helps maintain the specific cells. For example, stromal cells interact with B cells through cell adhesion molecules and provide soluble factors. erythroid cells form an 'island' around macrophages to help themselve differentiate. However, the stromal cells are not well characterised between the different environments for all cells.

There has been opposing views as to how the different haematopoietic cells are organised. Some groups has found that progenitors are found mainly at the endosteum, a thin layer of osteogenic cells (including osteoblast, which sustain haematopoesis and maturation of B cells) which line the medullary cavity, or at the sub-endosteal region. They migrate into the center as they mature. However, a different group has found that the progenitors are spread throughout the whole of the bone marrow, and localisation does not occur.

It has been found that plasma cells return to the bone marrow

Thymus
The thymus is a two-lobed organ that lies over the heart and major blood vessels. Each lobe is made up of many lobules, each of which has a outer cortex and an inner medulla, and separated from neighbouring lobules through trabeculae (connective tissues).

T cell progenitors enter into the thymus and must undergo, first, positive selection to select the progenitors which can react to antigens, and then negative selection to select out the progenitors which react to self antigens. This selection looks at whether the TCR expressed reacts with antigens (positive) and whether it reacts with self-antigens (negative); cells which expresses low concentrations of TCR can potentially escape negative selection and move into the circulation, which may cause autoimmune diseases. Progenitors enter the lobules at the corticomedullary junction through high endothelial venules (HEVs), and move to the cortex to undergo positive selection, and then move back towards the medulla, undergoing negative selection, and then differentiate into DP and then SP T cells.

The cortex is tightly packed with immature, proliferating thymic lymphocytes (thymocytes) and cortical epithelial cells. The medulla is more loosely packed than the cortex, and contains medullary epithelial cells, Hassall's corpuscle, fully-matured macrophages and dendritic cells, as well as more mature thymocytes. The thymic epithelial cells (nurse, cortical and medullary) are involved in T cell development. The Hassall's corpuscles' functions are not well characterised, the best guess is that they clear out dead cells.

In humans, the thymus is largest (relative) at birth, and largest (absolute) during puberty. After puberty, atrophy begins and continues throughout life; this is known as thymic involution. Involution begins with the cortex, and may disappear completely. Cortical involution is thought to be related to increased corticosteroid production. This is not observed in mouse models, where the thymus maintains its size and remain active throughout the life time of the mouse.

Development in Primary Lymphoid Organs
All cells of the immune system all differentiated from haematopoietic stem cells. Haematopoietic stem cells differentiate into three progenitor cell lineages - common lymphoid progenitor, common myeloid progenitor, and common erythroid megakaryocyte progenitor.

Haematopoietic stem cells can be either long term or short term, and long term HSCs are able to self-renew as well as to produce progenitors. The type of lineage it differentiates to will depend on the cytokine signal it receives.

Common Lymphoid Progenitor
The CLP can differentiate into B cells or NK/T cell precursors. Rearrangement of genes

B cell
Progenitor B cells (CD45R+) undergo Ig-gene rearrangement and selection in the bone marrow to produce B cells very close to full maturation; five million of these nearly-mature B cells are released into circulation every day. B cells will remain in circulation until its receptors bind to an antigen, at which point it will be activated (with help from TH cells) and with co-stimulation, undergo class switching and differentiate into a plasma cell or memory B cell. The transition from B to plasma cell sees a change in morphology from that of a large nucleus, to a smaller nucleus but with more ER and Golgi, in line with the fact that it is specialized in synthesising and secreting antibodies.

NK/T cell precursor
The NK/T cell precursors can differentiate into NK cells or T cells. The NK/T cell precursor differentiate in the bone marrow. Thymocytes are then released into the circulation, it will reach the thymus (or foetal liver), where the process of thymopoiesis (a.k.a. thymic maturation or thymic education) will lead to the maturation of thymocytes into mature T lymphocytes. The naive T cells will then enter into the circulation until it is activated by an APC, then it will differentiate into an effector T cell.

Thymocytes enter the thymus as CD3-4-8- thymocytes. In the thymus, it can rearranges their γ, δ and β TCR genes. If the γ:δ receptor is activated, it will shut off the β chain and commit the cell to the γ:δ+CD3+CD4-8- lineage, which is exported to the periphery. If the pre-TCR:pTα complex is activated, it will suppress the γ and δ chains and commit to the CD3+pTα:β+4+8+large active double-positive (DP) thympcytes through gene rearrangement. The β-chain first undergo V(D)J recombination to produce CD25+ CD44low cytoplasmic β+ thymocyte. The α chain gene then undergo V(D)J recombination. The transcription of CD4 and CD8 induces the transcription of the pre-α chain. α chain recombination completes, rounding off the δ chain, and allowing the α chain to complex with the β chain on the cell surface, becoming CD3+α:β+4+8+small resting double-positive (DP) thympcyte. Through positive and negative selection, about 5% of the DP thymocytes develop into single-positive T cells with either CD4-CD8+ (cytotoxic)or CD4+CD8- (helper) features; only these single-positive T cells will reach the periphery. Most cells develop along the α:β pathway.

The T cell receptors (TCRs) on each T cell is practically unique, and the diversity is generated in a similar fashion to B cells. A TCR consists of an α- and a β-chain, each chain has a variable and a constant region, a hinge, a transmembrane region and a cytoplasmic tail. The transmembrane region of the α-chain is more positive than the β-chain.

All the genes for each chain are on the same chromosome, and are rearranged in the same manner as the V(D)J rearrangement of B cells. The α-chain rearrange like the light chain (without the D segment) and the β-chain rearrange like the heavy chain (with the D segment).

Allelic exclusion is observed in T cells, where when one allele of the β-chain is expressed, the other alleles are inhibited, and so only one type of β-chain is observed in one T cell. Allelic exclusion is not so strictly followed by the α-chain, and so two types of α-chain may be observed in one T cell. The TCR diversity is attributed by all the same mechanisms as B cell antibody diversity, namely V(D)J somatic rearrangement and mutation at junction; but there is no hypermutation and affinity maturation.

CD3 is a complex made up of 3 dimers: γε (gamma epsilon), δε (delta epsilon) and ζζ or ζη (zeta zeta or zeta eta). CD3 complexes with TCR to form a membrane complex and allows for signal transduction.

Common Myeloid Progenitor
The common myeloid progenitor (CMP) can differentiate into the common granulocyte precursors, which can differentiate into all the granulocytes (neutrophils, eosinophils and basophils). CMP can also differentiate into a yet unknown precursor, which can differentiate into a mass cell or monocyte. Monocyte can then enter into tissues and mature to become macrophages, or it can differentiate into a dendritic cell.

Common Erythroid Megakaryocyte Progenitor
The common erythroid megakaryocyte progenitor can differentiate into megakaryocytes and erythroblasts. Megakaryocytes fragment to give platelets, and erythroblast mature into erythrocytes.

Secondary Lymphoid Organs
Adenoid, tonsil, right and left subclavian veins, lymph nodes, kidney, appendix, spleen. All secondary lymphoid organs share a broadly similar morphology, of having lymphoid follicles. Follicles begins as a network of follicular dendritic cells (FDC, which are not dendritic cells); FDC have complement receptors which allows it to bind to complement opsonized antigens, it also have receptors for the constant region of antibodies, meaning it can present antigens as well as whole pathogens to B cells. The antigens are presented in such a way that allows for the cross-linking of the B cell receptors, which signals for the B cells to proliferate and generate germinal centers.

Lymph Nodes
The lymph nodes are secondary lymphoid organs clustered around the junctions of lymphatic vessels, to filter and trap antigens from the lymph. They have a encapsulated bean-shaped structure, split into three not so distinct sections: medulla (nearest the 'hilum' of the bean), paracortex and cortex. The lymph enters through the afferent lymphatic vessels into the cortex, an area high in B cells. During an infection, the B cells proliferate and its high concentration creates germinal centers. The lymph then passes through the paracortex, an area high in T cells; and finally move to the medulla, an area high in macrophages and plasma cells; finally leaving through the efferent lymphatic vessel. Re-circulating B and T cells can also enter through the blood via high endothelial venules, but leave in the same matter through the efferent lymphatic vessel. However, when a B cell encounters antigen, it will remain in the lymph node and proliferate, generating germinal centers, which eventually release B cells that differentiate into plasma cells and produce antibodies.

Spleen
The spleen can be viewed as two organs merged into one. The red pulp is not really part of the immune system, and its role is simply to filter blood for dead erythrocytes; the white pulp is pretty much a lymph node, and is used to filter out antigens. So whereas lymph nodes are used to filter antigens from lymph, the spleen is used to filter antigens from blood.

Development in the Secondary Lymphoid Organs
After the B and T cells has developed, it moves to secondary (peripheral) lymphoid organs where they are presented with antigens. The peripheral organs also provide the signals for the lymphocytes to sustain themselves. The lymphocytes in the peripheral lymphoid organs drains into the blood circulation via the thoracic duct, which drains into the left subclavian vein (near its junction with the left internal jugular vein); lymphocytes in the blood circulation are pushed out by pressure into the tissue space, and eventually re-enter the peripheral lymphoid organs. This cycle repeats until they encounter an antigen, or die.

At lymph nodes, the naive T and B cells enter the lymph nodes from the blood through the high endothelial venule, and enter from the lymphatics through the afferent lymphatic.

The circulating lymphocytes in the blood must be able to home in back on the lymphatic tissues to continue the cycle from blood to lymphatics, and back to blood. So naive T lymphocytes express L-selectins on their cell surface, these binds to sulfated sialyl-Lewisx on GlyCAM-1 and CD34 (mucin-like vascular addressins) on the surface of HEVs.

To move across the HEV, the naive T lymphocytes first have its L-selectin bind to the mucin-like vascular addressins on the endothelium, while also expressing mucin-like CAM to bind to E-selectins on the endothlial cell; this helps the lymphocyte roll on the inner wall of the HEV. A chemokine receptor on the haematocyte then binds to a specific chemokine released by the endothelial cell, which in turn activate LFA-1, an CD18 integrin which binds tightly to Ig-superfamily CAM (ICAM-1 and ICAM-3) on the surface of HEV. The CD18 family of integrins have share a common β subunit, which allows cells presenting the appropriate ICAM to home in on it. Different tissues uses different integrins to allow different leukocytes to home in on different tissues. Once the lymphocyte is held tightly, it will migrate through between the cells of the HEV and into the periphery phymphathic tissues; this process is known as diapedesis.

T cells must then associate with antigen presenting cells (APCs) to search for antigens. It associates with APCs such as dendritic cells (DCs) using the LFA-1/ICAM-1,2 interaction, as well as CD2/LFA-3 and/or ICAM-3/DC-SIGN interaction. The LFA-1/ICAM-1,2 interaction is weak at first, but upon antigen recognition by the TCR on MHC II, it sends a signal for the conformational change of LFA-1 so that it has a higher affinity to ICAm-1 and ICAM-2.