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immunity 2: MIT lecture – more on immunity and auto-immunity

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So we’re looking at cell-mediated and auto-immunity in this second lecture. We see an image of listeria, an intracellular bacterium, pushing out the edges of the cell, so that it can move between cells without entering the extracellular space. Listeria is a food-borne bacterium which can cause severe intestinal illness. So think of a host cell with an intracellular pathogen, bacterial or viral, taking advantage of these cells to reproduce and spread. This is not good.

B cells, as described before, have an antigen receptor, initially on the plasma membrane, and sometimes secreted into the intracellular space, while T cells only have the membrane-bound form. In any case these antibodies are directed outwardly. How can a listeria-like infection, within the cells, be dealt with? This involves a process called antigen presentation, in which peptides – short sequences of amino acids – are presented and displayed on the cell surface, so that T cells, in this case, can observe what is happening within the cell. This involves another molecule previously mentioned, the major histocompatibility complex (MHC). There are two classes of MHC. Class 1 has a heavy chain – a long polypeptide – and a light chain. So, two polypeptides encoded by different genes. It has two Ig domains proximal to the plasma membrane – and it’s all inserted into this membrane – an integral membrane protein. Then at the other end, distal to the plasma membrane, is another structure, which, looking at its crystal structure, is a ‘beta sheet with two alpha helices’, shaped somewhat like a cup [a beta sheet is a common secondary structure in proteins, formed by polypeptide strands (beta strands) connected laterally by hydrogen bonds, creating a pleated, twisted, sheet-like structure]. Inside the cup is a peptide which displays some of its amino acids, away from the MHC molecule, for T cells to observe. 

So these Class 1 MHCs are membrane proteins displayed on all nucleated somatic cells, and the peptides held by these MHCs are derived from the cytoplasm within the cell. They are loaded on to the MHC molecule, which is translated (using ribosomes and types of RNA) on the endoplasmic reticulum (ER), and its extracellular domain is initially present in the lumen (internal space) of the ER. Its peptides come from proteins in the cytoplasm. What happens to these proteins – including unfolded proteins and those that might be ubiquitinated [refers to a protein that has had ubiquitin, a small protein, covalently attached to it, often marking the protein for degradation or influencing its function or localisation – thanks AI, and it has of course dawned on me that this MIT course has followed on from earlier biochemistry learnin] – is that they’re processed by the proteasome [a large, cylindrical protein complex that degrades proteins tagged with ubiquitin, a process essential for maintaining cellular homeostasis and regulating various processes like cell cycle and protein quality control], which this lecturer describes as ‘a kind of shredder-like function for protein’, which cuts the proteins into peptides which can then be pumped into the ER lumen via a transporter, TAP…

The transporter associated with antigen processing (TAP) is a heterodimeric protein complex (TAP1 and TAP2) that transports peptides from the cytosol into the endoplasmic reticulum (ER), where they bind to MHC class I molecules, a crucial step in antigen presentation to cytotoxic T cells.
from AI overview

From there they are loaded onto the class 1 MHC molecule. The source of these peptides is from proteins in the cytoplasm, processed by the proteasome. So now that a peptide-MHC complex has been created, it can then be trafficked to the plasma membrane of the cell, where the peptide will be displayed for T cells to observe. The types of T cell that look at these class 1 molecules are known as CD8+ T cells. 

There are also class 2 MHC molecules, which have fundamentally different properties. Both molecules display peptides on the cell surface (antigen presentation), but the structure of MHC class 2 is quite different. Instead of a heavy and light chain, there are two chains of roughly equal size, and they’re encoded by different genes than the class 1 MHC. There are two Ig domains proximal to the plasma membrane, and at the end of the MHC molecule there’s a groove or pocket that holds a peptide (aka a peptide-binding cleft). 

The class 2 MHC is expressed on a more restricted set of cells. They’re expressed specifically on specialised antigen-presenting cells, such as B cells and phagocytic cells [also known as phagocytes, they are specialised cells of the immune system that engulf and destroy foreign substances, pathogens, and cellular debris through a process called phagocytosis].

So what is this process? First, phagocytes are white blood cells. Monocytes, neutrophils and macrophages are phagocytes. From Wikipedia:
Phagocytosis is the process by which a cell uses its plasma membrane to engulf a large particle, giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs phagocytosis is called a phagocyte.
And AI overview:
Endocytosis is a cellular process where a cell engulfs extracellular material, forming an internal vesicle to transport substances into the cell. This process, which includes phagocytosis (cell eating) and pinocytosis (cell drinking), is essential for nutrient uptake, cell signalling, and defence against pathogens.
There’s also another antigen-presenting cell called a dendritic cell:
Dendritic cells (DCs) are crucial immune cells that act as sentinels, capturing antigens and presenting them to T cells to initiate adaptive immune responses, effectively bridging innate and adaptive immunity (from AI overview)
The focus in this lecture will be on the B cells. So class 1 is expressed everywhere, whereas class 2 is expressed specifically on antigen-presenting cells. The source of the peptides and the way they’re generated is also quite different. Peptides for class 2 come from the extracellular space, and are processed by lysosomal proteases.
 
So cells can take in material through endocytosis. An antigen can be endocytosed by the cell, so it’s in a cell vesicle. It can go to the lysosome, where lysosomal proteases can cut up this protein-based antigen into peptides. MHC 2 is translated, like all plasma membrane proteins, in the ER. But in the ER the peptide groove may be blocked – peptides from the cytoplasm cannot interact with class 2, so they’re trafficked to a unique compartment that can combine with the compartment that has the peptides that originated from outside the cell, and then those can be loaded onto the class 2 molecule, so that this can be recognised by T cells. In the case described, not a CD8+ T cell (aka a cytotoxic T lymphocyte (CTL)), but a CD4+ T cell. 
 
So, to review, class 1 MHC is expressed on all nucleated cells, but class 2 is more restricted, expressed specifically on antigen-presenting cells. These two classes are recognised by different T cells – class 1 MHC is recognised by CD8+ cells, class 2 by CD4+ cells. Also the source of the antigens is different in each case – the cytoplasm for class 1, the extracellular space for class 2. So they’re each sampling different pools of proteins. Where the peptide is loaded is also different. For class 1, the endoplasmic reticulum, for class 2, a vesicle compartment resulting from endocytosis of an extracellular antigen. 
 
Now for the T cell receptor (TCR), which has two chains, alpha and beta, into the ectoplasm from the plasma membrane. Each chain or sub-unit has two Ig domains. The receptor recognises antigens through its variable domain, which then binds to the receptor. The TCR interacts or docks with the MHC-peptide complex. For the TCR to do this, it must recognise the specific conformation of the peptide being extended out from the cell. There’s a diversity of TCRs which can discriminate between the different peptides loaded on to MHC. 
 
How does this diversity occur? The same as with antibodies. This rearrangement of gene segments in the variable domain of the antibody is due to recombination at the genomic locus. What does this mean? Good question. 
 
A diagram is shown for the beta chain of the TCR. Like the B cell receptor (BCR), there is a gene rearrangement in the genomic DNA that brings V, D and J segments together to make the variable chain of the T cell receptor. So as with the B cell receptor there’s a gene rearrangement, aka VDJ recombination – not splicing of the transcript [?] but within the genomic DNA. By having this happen in the genomic DNA, an irreversible change occurs. So all subsequent cells derived from the original B or T cell will express the identical B or T cell receptor. An irreversible change to the DNA. But the TCR is not the only way the TCR can interact with antigen-presenting cells. There are other co-receptors on the T cell, CD4 and CD8, expressed on different subsets of T cells. These co-receptors are also required to get an immune response. So if the T cell receptor and the co-receptor both bind to the MHC you get a particular response – both are needed. CD4 cells recognise class 2 of MHC, CD8 recognises class 1. So, two subsets of T cells recognising different MHC complexes. 
 
What should CD8+ T cells do? Where are the peptides coming from that are presented on the class 1 MHCs which will be presented to CD8?  What does it mean if you have a class 1 MHC molecule containing a foreign-looking peptide? These peptides come from the cytosol as foreign elements and ‘need to be dealt with’. You may have, for example, an intracellular parasite taking advantage of the host cell to reproduce itself. If the immune cell has an indication of this sort of problem – for example cancer cells – if you have an oncogenic mutation in the genes, those could be recognised as foreign, and one response might be to do something to the cell to limit expansion of the tumour. Or if it’s an intracellular parasite, you would need to terminate the cell to stop the spread of the virus, say, that the cell is producing. That’s to say – to kill the cell. 
 
So, CD8+ T cells are also known as killer or cytotoxic T cells. So if a CD8+ T cell recognises an MHC class 1 peptide complex then it releases internal material that perforates that cell so that it undergoes cell death. This limits infection by killing the cells that the pathogen is using to replicate itself.  
 
CD4+ T cells are quite  different. I will try to get this. They have to do with the MHC class 2 cells, which are B cells that recognise foreign agents. They bind to and internalise those agents, presenting parts of them on the exterior of the cell. The CD4+ T cells would not want to kill those MHC class 2 cells, because they are what is needed to fight the antigen. You have a B cell that can produce antibodies, so you want to help it, to enhance its function. So these CD4+ T cells are also known as helper T cells, as they enhance B cell function in various ways. This association occurs in the lymph nodes, where there are antigen-presenting cells and soluble antigens coming in, as well as B and T cells. These B and T cells are effectively awaiting interactions between distinct immune cell types. When you get a B cell that presents an antigen that’s recognised by a T cell, that cell enhances B cell function in a variety of ways. Firstly it induces a response in the B cell, called affinity maturation. This results from a hypermutation of the variable domain of the antibody, providing more diversity, such that a B cell can be selected with even tighter binding to the antigen. 
 
So affinity maturation creates the transition from weak to tighter binding, a difference between the primary and secondary immune response. Antibodies ‘improve’ due to B and C cell interaction through the affinity maturation process. Also, B cells can produce different types of antibodies (isotypes) – known as isotype switching – and we’re shown a chart titled ‘Ig isotype switching varies the constant domain to elicit varied effector functions’. The chart shows, inter alia, the genomic locus for the heavy chain of an immunoglobulin. There’s a VDJ segment which has undergone recombination, and a string of exons that encode a different isotype for the antibody [In genetics, exons are coding sequences of DNA or RNA that are expressed in the final mRNA product, while introns are non-coding sequences that are removed during RNA splicing].  The first one is mu, which, when it is proximal to VDJ, produces IgM. That’s the initial state of the antibody, which is initially membrane-bound and serves as the B cell receptor. Each of these different constant domains have different effector functions even though they aren’t undergoing variation. They can do different things for the body. As an example, if you had isotype switching, and a recombination event that brought a gamma 2 segment together with VDJ, that would produce isotype IgG, a highly secreted form of the antibody that is effective for bacterial infections. It’s secreted in the blood and can neutralise bacteria and so limit infections.
 
But there are many other possibilities. You could get VDJ together with an alpha, producing an isotype known as IgA, which produces mucosal immunity because it can pass through the epithelial linings. IgE is another antibody type – and the constant domains are constant for each isotype, but they recruit different effector functions. So IgG attacks bacteria by promoting their phagocytosis, while IgE is good at dealing with intestinal worms. So isotype switching allows the immune system to adapt to deal with particular pathogen types.
Another, final way in which T cells enhance this function is to promote the differentiation of B cells, one of which is a memory B cell, which can last for decades in the body, even without antigens. 
 
So if you have a B cell which recognises an antigen – say, a protein – it would internalise that protein via endocytosis and then process it so that peptides from the antigen can be displayed on its surface. If that is recognised by a T cell, this leads to an interaction between the T and B cells, leading to such events as affinity maturation and isotype switching – got that?
 
The variable chain doesn’t change with isotype switching. It’s always able to recognise that antigen, but it is recruiting different effector functions. You can also have differentiation of B cells into plasma cells, which secrete many antibodies to fight infection. 
 
So for a vaccine to be effective you need to engage a T cell response, to have everything happening as above. You can’t just activate the humoral (bodily fluid) side, you need to also activate the cell-mediated side such that they interact, to enhance the immune response.  
The immune system faces a big problem, in that it has to be able to discriminate between self and foreign. If your immune system recognises an antigen that is in fact native to the bodily system, that may result in an auto-immune disease. There’s a balance between tolerating and attacking antigens. We have discussed the B cell receptor, the antibody and the T cell receptor. Our body generates tens of millions of these diverse antigen receptors which recognise different molecules. It does this constitutively, that’s to say, automatically, without the need for any infection. It is just a normal function of T and B cells. It’s also random, in that any combination of V, D and J segments could occur, and they could mutate in various ways, so that you could generate a receptor that recognises a protein native to your body. 
 
There are several diseases caused by auto-immunity. Diseases caused by ‘self-recognising’ antibodies include Myasthenia gravis (muscle weakness), in which individuals generate an antibody against a receptor for a neurotransmitter (acetylcholine). This neurotransmitter is largely involved in sending signals from a motor neuron to a muscle, so antibodies that inhibit this receptor will cause muscle weakness. Self antibodies can also result in diabetes. Individuals can develop antibodies that recognise and inhibit the insulin receptor, leading to insulin resistance and diabetes (Diabetes mellitus). Diseases caused by ‘self recognising’ T cells include multiple sclerosis. The myelin sheath around axons increases the speed of their action potential. If T cells attack the myelin sheath, the electrical signalling process is disrupted, and this is the cause of MS.  Type 1 diabetes (Diabetes mellitus) can also involve T cells. If they attack and destroy the islet cells of the pancreas, the body’s capacity to produce insulin is disrupted. 
 
So the immune system needs to have a way of distinguishing between self and non-self. It needs to have different responses for self versus foreign recognition. For self-recognition, there needs to be a negative selection against that cell, and for foreign recognition, positive selection. Negative selection is mediated by apoptosis [A type of cell death in which a series of molecular steps in a cell lead to its death. This is one method the body uses to get rid of unneeded or abnormal cells]. Positive selection might be activation and also proliferation of the cell type. As shown in the image, entitled ‘Cell division can lead to a clonal population of cells all of which express same antibody’, a cell that recognises a foreign antigen would be activated, undergoing a monoclonal expansion, with the resulting cells expressing the same antibody, recognising the same antigen. So we know what to do with self versus foreign, but how do we distinguish between them? There are several mechanisms. First, the B and C cells in the lymphoid organs, where they mature and undergo genomic rearrangements, are largely protected from foreign agents, so there are only ‘self antigens’ in those generative lymphoid organs. They are the bone marrow for B cells and the thymus for T cells. If a B or T cell’s receptor engages with something tightly during development, this is a signal for the immune system to kill or ‘delete’ that cell. So, upon self-recognition, there will be apoptosis and deletion of the cell. The second way for the body to make the distinction is that it responds better to antigens when there is also a response from the innate immune system – call it a ‘coincidence detector’, strongly indicating a foreign antigen. Otherwise it might be a ‘self antigen’. This is important for vaccine development, as in most vaccines, in addition to having an antigen that’s a part of the infectious agent there’s also an adjuvant – something to activate the innate immune system to respond. This is important because if you only have the antigen the response would be much less robust. You need both systems to respond together if possible. 
 
So in the year of this lecture (2018), the Nobel Prize in physiology or medicine was awarded for work which involved another mechanism which prevents auto-immunity and down-regulates the activity of particular T cells. We have only talked about activation of T cells, with the T cell receptors CD4 and CD8, but there are also inhibiting receptors on the surface of T cells, two of which are CTLA4 and PD1. They keep the immune system in check. It’s about signalling and its activation. Once a signal is sent there is often a negative feedback, causing signal termination. So that you don’t just have a continuous constitutive activation (inflammation and immune response). So this takes us back to the Prize-winning work afore-mentioned, in which the researchers explored the possibilities of signal termination for cancer treatment. Some cancer cells can express the ligand [a molecule that binds to another (usually larger) molecule] for these inhibitory receptors, so that they can prevent the immune system from recognising the tumour. This is basically creating an inhibitor blockade, but this would be a tricky treatment/solution, as it can lead to auto-immune disease. 
 
That’s it for lecture two. I will likely return to this fascinating topic via other lectures/videos in the near future. 

References

Immunology 2 – Memory, T cells & Autoimmunity, MIT OpenCourseWare, YouTube video

the stuff in square brackets is from AI Overview

https://en.wikipedia.org/wiki/Phagocytosis

Written by stewart henderson

April 13, 2025 at 6:58 pm

Posted in B cells, bacteria, biochemistry, immune system, T cells, vaccination

Tagged with , , , , ,

the immune system 1: introducing the adaptive immune system – MIT lecture

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Just something to start with…

It was in 1796 that Edward Jenner created the first vaccine, using material from a cowpox sore on a milkmaid’s hand and injecting it under the skin of an eight-year-old boy. I’ve not been able to ascertain whether Jenner injected the material directly into the boy’s bloodstream. In any case this has been regarded as the world’s first vaccination, a term coined by Jenner (from vacca, Latin for cow). Variolation, using smallpox scabs inhaled by the patient, had been practised in Asia for centuries before Jenner, and was promoted in Britain by Mary Wortley Monagu earlier in the 18th century. Variolation was certainly effective, and for some time there was a dispute about the best treatment. In any case, what was being brought into action by both treatments was the adaptive immune system.

So now to MIT’s introduction to immunology course, presented by Adam Martin. He mentions, in his first lecture, that there are many levels of immunity, and goes on to describe two, innate and adaptive immunity. Innate immunity is ‘the first line of defence’, and acts immediately. Neutrophils, which are white blood cells, are part of this innate system, which is quite static and unchanging, involving a constant surveillance. Adaptive immunity is also known as acquired immunity – and its acquisition takes time.

The adaptive immune system is more specific than the innate. That’s why we need regular flu vaccinations, because flu viruses can evolve quite rapidly. These vaccinations are designed to combat or provide immunity to new strains of the virus.

There are two branches of adaptive immunity: humoral immunity, which is protein-mediated (the proteins are called antibodies). This type of immunity is called humoral because these antibodies are secreted into bodily fluids or humors (blood, mostly). The types of cells that produce these proteins, these antibodies (Ab), are called B cells, which are matured in the bone marrow. The other branch is cell-mediated immunity, which involves T cells, which are matured in the thymus gland, near the top of the lungs.

So far so simple, but next we’re shown a scarily complex chart showing the derivation of all these cells from hematopoietic stem cells – most of these cells comprising the innate system, but also the T and B lymphocytes of the adaptive system (and they’re called lymphocytes because they’re the primary cells found in the lymph). So, it’s important that we can trace the ‘tree’ back to its ‘roots’, the progenitor cells.

Both the humoral and cell-mediated immune system cells have antigen receptors, which recognise specific antigens (Ag). An antigen is any substance that creates/generates an immune response.

Antibodies – goodies; antigens – baddies.

So, the B cell antigen receptor is also called an antibody, and an immunoglobulin (Ig). Structurally, antibodies are proteins with a lipid bilayer, which represents the plasma membrane. Outside of this membrane is the exoplasm, and inside is the cytoplasm. (I’m a little confused here – this sounds like the description of a cell, not a protein). Anyway we’re describing a B cell, and the antibody (protein) can have a trans-membrane domain spanning the plasma membrane, and an exterior Ig domain. These domains are modular folds (polypeptide chains) that are separate from the rest of the protein, and are inserted into the cell membrane, with an N-terminus exterior to the cell and a C terminus within the cell. Each antibody protein has two long polypeptides, the identical ‘heavy chains’ of the molecule. They also have smaller ‘light chains’, and it’s all laterally symmetric. The external tips of these antibodies are what recognises and binds to the antigen.

Now to the T cell receptor (TCR). It’s very different, and simpler, structurally. It has two chains, alpha and beta, and fewer immunoglobulin repeats. The tip of this double chain interacts with the antigen.

The B cell’s receptor, or antibody, has different forms. Some antibodies have transmembrane domains and are anchored in the plasma membrane, but other forms lack the transmembrane domain and instead of being an integral membrane protein, they’re secreted into the blood. The membrane-bound form comes first, but as an infection progresses, the secreted form becomes dominant. The T cell receptor only has the membrane-bound form.

There are many different antibodies, and each given antibody will recognise a different antigenic structure. They can recognise small molecules, proteins, DNA, carbohydrates, lipids, etc. But apparently that’s the B cell’s antibodies. The T cell receptor is more restricted, recognising peptides – short sequences of amino acids – which are presented by the MHC complex (classes 1 and 2). More of that later.

Properties of the immune system. First, specificity – they can finely discriminate between molecules. This is of course essential to avoid the prospect of auto-immune diseases. So, how are such levels of specificity achieved? Well, it’s complex.

Looking at B cell antibodies again, with their heavy and light chains. There are different domains on the heavy chain that are either variable or (more or less) constant. And the same goes for the light chain, with the same lateral symmetry described above. So, looking at the amino acid sequence of the variable part of the antibody (protein) molecule, looking at its structure from N to C terminus …. (?)

By convention, peptide sequences are written N-terminus to C-terminus, left to right (in LTR writing systems) – [from Wikipedia, N-terminus]

Imagine taking these antibodies from the variable region of the chain and aligning them (their amino acid sequence) from N to C. Each is a different antibody (or heavy chain polypeptide) produced by a unique B cell. Then we consider the residue number… 

The amino acid residue number refers to the spot in the linear chain where that particular amino acid is found. For example, the number 20 means that amino acid is 20th in the chain.

.. and how much each amino acid residue varies along the sequence. ‘So if we were to align antibody gene stretches like this’, and check out the variation, we could graph it as in the diagram:

The Y axis being the amount of variation, and the X axis is the residue number along the polypeptide sequence. So you see from this graphic that there are three regions of hyper-variability. These regions are also called complementarity-determining regions (CDRs). Apparently there are always three of them?

So what are these regions? We’re shown a crystal structure of one of them (both heavy chain and light chain), with an antigen attached, as well as a ribbon diagram with its CDR, which contacts the antigen. We’re next shown an Ig fold with three loops extending from it, which can bind to external particles. These IG loops vary in amino acid sequence and each tiny variation will affect the binding ability, or affinity to an antigen. So the key here is the CDR.

Each B cell expresses a unique antibody protein, with unique specificity, due to its unique sequence at the CDR region. To get more of a particular antibody, the cell that expresses it can be clonally expanded, creating monoclonal antibodies. Each of those B cells will have an antibody, or antigen receptor, with that same specificity.

So that’s the generation of specificity, but the generation of diversity is also vital for enhancing the immune system. How is this diversity achieved? There are millions of B cells that have unique antibodies, and there aren’t a million genes producing those cells – we have about 30,000 genes. The answer is somatic ‘reshuffling’ or recombination. We have a single heavy chain gene, and two light chain genes, for antibodies. They’re made up of multiple gene segments. Specifically, the parts that make up the variable domain are composed of gene segments that are shuffled during the development of the B cell to give rise to a diversity of proteins.

So we’re next shown a graphic headed, no doubt importantly, ‘the immunoglobulin gene contains multiple V, D and J segments – one of each needs to be brought together to form a functional antibody gene’. The graphic, which I won’t reproduce here, shows the human Ig heavy chain locus on the right. On the left is a variable (V) gene segment, containing 45 variable genes. There’s a diversity (D) segment next to it, containing 23 more of these genes, and then there are 6 joining (J) segments. All of these are distinct regions of the gene, the exon that encodes this variable region of the antibody.

So there are multiple V, D and J segments.To generate a functional antibody, one V has to be brought together with one D, which then has to be brought together with one J to create the heavy chain. So the next graphic has the heading ‘Rearrangement of genomic DNA is needed to put together a gene that encodes an immunglobulin’. It indicates that, for the light chain, only V and J gene segments are required, whereas the heavy chain also requires the D segments. Most of the cells in our body, and also in the germline at the earliest stage of development, have this arrangement. But during lymphocyte development a recombination event occurs which brings the two (V and J), or three (V, D and J) gene segments together. So, recombination at the heavy and light chain genes for the antibody.

This is all quite different from the recombination that occurs during meiosis and the formation of the gametes. That recombination occurs between homologous chromosomes, while this type brings together and deletes segments along one chromosome to bring these V and J segments together (intra-chromosomal recombination) to create an antibody protein. It’s called VDJ recombination, and is specific to lymphocytes, because during the development of B and T cells there is an induction of recombinases that mediate this recombination [?] In this case a recombination mediated by ‘recombination-activating genes 1 and 2’, aka RAG1 and RAG2.  All this is lymphocyte-specific, and these recombinases mediate this rearrangement, bringing unique V, D and J segments together. The diversity derives from the fact that each segment has a unique sequence, coding for a unique amino acid sequence, and a distinct protein.

But the body derives further diversity from another process. When these segments are shuffled there is imprecision – nucleotides can be added or subtracted (deleted) when these segments are joined. This generates more amino acid diversity, called junctional imprecision. So we have imprecise recombination, leading to the insertion or deletion of nucleotides [the basic structural units of nucleic acids – RNA & DNA – consisting of a nucleoside and a phosphate group]. If there is a multiple of three nucleotides either inserted or deleted, the result is a functional antibody. A multiple of three is required, to avoid a ‘frameshift mutation’, because ‘a cell reads a gene’s code in groups of three bases when making a protein’. That’s the system upon which it operates – if you inserted/deleted a single nucleotide along the line you wouldn’t get a functional protein.

Another important thing – which happens not as a consequence of this recombination process, but of activating the T cell, which is that in addition to these variations, there’s also somatic hypermutation  – an elevated mutation rate at the Ig locus, which increases further the diversity of the amino acid at these variable antibody regions. This is also known as affinity maturation, as it increases the affinity of the antibody for its antigen. Note that this is T cell-mediated.

So the immunoglobulin gene is not expressed until this recombination occurs. So this recombination leads to the expression of either the heavy chain or the light chain gene. This is because the enhancer is downstream in the gene, so by vanquishing the intervening sequence you bring the promoter within range of the enhancer, and the gene is expressed. It’s really quite romantic.

Remember though that there are two copies of these genes – paternal and maternal, so there’s another feature of this system – allelic exclusion. A B cell expresses only one antibody, so if both alleles are expressing, that wouldn’t be the case. With allelic exclusion, if you get a recombination event that leads to a functional antibody for one of your inherited copies of the gene, it suppresses recombination on the other allele, so you will only get one heavy chain and one light chain gene expressed per B cell.

So these junctions between V, D and J segments are found in the CDR-3 region, and are responsible for the high level of variability at the CDR or hyper-variable 3 region.

So the last feature to describe is ‘memory’, the ability to recall a previously experienced infectious substance. The immune system needs to be able to do this, and this is the principle behind vaccination. A vaccine will inject an attenuated or inactivated foreign agent into your bloodstream so that the immune system will be alerted to that antigen if/when it turns up in the system later.

Several ways in which this ‘remembering’ manifests itself, comparing a primary infection with a secondary infection, the adaptive immune system has very different responses. The primary response is a little delayed, taking between 5 and 10 days, while the secondary response is generally between 1 and 3 days. The magnitude of the response, the concentration of antibodies that are produced, is larger the second time around. And the antibodies themselves have become ‘better’. This can be shown by antibody affinity – how tightly the antibody recognises (and binds to?) the antigen. Antibody affinity (‘tightness’ of recognition) is measured as the dissociation constant for an antibody to a given antigen. The lower the number, the tighter the binding. For the primary infection the antibody affinity is weaker, on the order of 10 to the seventh molar in terms of KD [KD, or KD, is a quantitative measure of antibody affinity – ‘the equilibrium dissociation constant between the antibody and its antigen’], and the secondary infection generates antibodies that are functionally better, less than 10 to the negative eleventh molar (sub-nanomolar), a very tight interaction between two molecules. So, more and better. So from the first infection to the next, a type of B cell – a memory B cell – will express an antibody specific to the previously experienced antigen, because, due to irreversible recombination, this will be encoded in the genome. The memory results from VDJ recombination being irreversible, so those memory B cells will be there even if the antigen is not. These cells can be generated by vaccination.

So ‘effector functions of antibodies’. They can bind to a foreign substance, interfering with its functionality. Neutralisation, for example, which means preventing the antigen from entering cells. Also phagocytosis, recruiting phagocytes to internalise the antigen (e.g. a bacterium), and recruiting killing cells to kill cells.(natural killer cells).

The lecture ends with a story in the fight against breast cancer, a treatment based on a mouse monoclonal antibody. So, we can use antibodies from other species to generate treatments. One example is herceptin, which can be used as a treatment for HER2-positive breast cancer. It’s based on a mouse antibody which recognises the HER2 growth factor receptor, which is over-expressed in about 30% of human breast cancers. Researchers have engineered a human antibody with the mouse sequence at its complementarity-determining region. So you have a human antibody, which won’t be attacked or removed by the human immune system, but will recognise HER2, and recruit immune cells to HER2 positive cells, neutralising and possibly killing them. This is the possible therapeutic aspect of antibodies, whatever their source.

So ends the first lecture.

References

30. Immunology 1 – Diversity, Specificity, & B cells, MIT OpenCourseWare video

https://en.wikipedia.org/wiki/N-terminus#:~:text=the%20C%2Dterminus.-,When%20a%20protein%20is%20translated%20from%20messenger%20RNA%2C%20it%20is,end%20of%20the%20growing%20chain.

https://study.com/academy/lesson/what-is-amino-acid-residue.html#:~:text=The%20amino%20acid%20residue%20number%20refers%20to%20the%20spot%20in,is%2020th%20in%20the%20chain.

https://www.genome.gov/genetics-glossary/Frameshift-Mutation#:~:text=A%20frameshift%20mutation%20in%20a,bases%20when%20making%20a%20protein.

https://www.abcam.co.jp/primary-antibodies/kd-value-a-quantitive-measurement-of-antibody-affinity

Written by stewart henderson

March 26, 2025 at 3:10 pm

Posted in adaptive immunity, B cells, Edward Jenner, immunology, vaccination, variolation

Tagged with , , , ,