IMI 3: The Adaptive Immune System Flashcards
1
Q
Observe the learning outcomes of this session
A
2
Q
What are the two key features of the adaptive immune response?
A
- the immune system changes (adapts) to recognise pathogens specifically
- they memorise their characteristics, allowing the immune system to react much more quickly and specifically in the future
3
Q
The adaptive immune system has both humoral and cell-mediated components
Define humoral and cell-mediated components of adaptive immunity
A
- humoral components of adaptive immunity:
- antibodies that circulate in the blood, perfuse tissues and are secreted onto mucosal surfaces
- cellular components:
- B and T lymphocytes: have the ability to recognise antigens through receptors expressed on their cell surface
4
Q
Where do conventional B and T cells originate from?
Where do these mature lymphocytes then go?
A
- they originate in the primary lymphoid organs (lymphopoiesis)
- T cells: thymus
- B cells: bone marrow
- mature lymphocytes migrate to the secondary lymphoid organs and traffic around the body through blood or lymphatic circulation
- secondary organs include spleen and lymph nodes
5
Q
How much of leukocytes do B and T cells account for in blood?
How much of the cells do they account for in the lymph
A
- They account for 20-40% of leukocytes in blood and 99% of cells in lymph.
6
Q
How do B and T cells become mature?
What do they become?
A
- until encounter with an antigen, both B cells and T cells are naive
- upon the encounter with an antigen, they get activated and can become effector and/or memory cells
7
Q
Give an overview of B cells
- what they make
- naive form and mature form
- roles
A
- B cells make immunoglobulin molecules that bind highly specifically to foreign antigens
- each B cell produces a unique immunoglobulin, with a narrow specificity
- a diversity of immunoglobulin across all B cells of the immune system allows B cells to specifically bind to a wide range of antigens
- Naive B cells express a membrane-bound form of immunoglobulin called the B cell receptor (BCR)
- upon activation, they also produce the immunoglobulin in its secreted form, antibodies
- effector B cells that produce only antibodies but lack a BCR are called plasma cells
- B cells can also act as antigen-presenting cells
- they express phagocytic receptors that similarly to macrophages and dendritic cells, can internalise, process and present antigens on MHC II molecules to T cells
- they can also capture and internalise antigens through the BCR
- this is important because upon presentation, B cells receive signals back from the T cells and from the BCR that allow their differentiation into plasma or memory B cells
8
Q
Give an overview of conventional T cells
- what characterises them
- sub-classifications
A
- Conventional T cells are characterised by the presence of T cell receptor (TCR) and certain co-receptors (CD3 alongside either CD4 or CD8) that define their effector functions.
- The TCR can “recognise” (ie specifically bind) antigens but only when the antigen has been chopped up and is held by a MHC (major histocompatibility complex) molecule. T cells can be sub-classified as:
1. T helper cells (with CD4 on their surface) have important functions in supporting other cells of the adaptive immune system.
2. Cytotoxic T lymphocytes (CTL, with CD8 on their surface) that specialise in killing defective (infected; cancer) host cells. They release cytotoxic granules containing granzyme and perforin that can very effectively kill target cells.
9
Q
What is the adaptive molecule of B cells?
What are its two forms?
A
- the adaptive molecule of B cells is immunoglobulin (Ig)
- it comes in two forms:
1. A transmembrane form that studs, or dots, the surface of the B cell. - This is called the B cell receptor (BCR).
2. A version of the BCR that is missing the transmembrane domain, but has a signal peptide instead, so it is secreted from the cell.
10
Q
What is a soluble Ig?
A
- it is called an antibody
11
Q
What is the immunoglobulin domain?
A
- In discussing the structure of immunoglobulin, we will mention immunoglobulin (the whole BCR or antibody molecule) and Ig domains.
- An Ig domain is a smaller chunk of the immunoglobulin molecule which has a conserved structure held together with an internal disulphide bond.
- The secondary structure of these domains is called the immunoglobulin fold.
- Ig is made up of four polypeptides each made up of 2-5 Ig domains
- This core structural motif is also found in many other proteins: proteins containing this fold (including Ig) are members of the immunoglobulin superfamily.
- In addition to Ig, the immunoglobulin superfamily includes many cell surface molecules you will encounter throughout IMI.
- For instance, this includes MHC molecules; CD4 and CD8; ICAM1; IL-1 receptor (IL-1R); some Fc receptors; inhibitory and stimulatory molecules such as CTLA-4 and CD28.
- Take care not to get confused between immunoglobulin (particularly the B cell receptor) and the immunoglobulin superfamily receptors.
12
Q
What is human Ig formed from?
How many genes do we have to code for human Ig?
A
- human Ig is formed of four polypeptide chains:
- two identical heavy chains
- two identical light chains
- these are connected by disulphide bonds to form the well-known Y shape of the antibody molecule
- our genome contains one heavy chaingene, and two light chain genes (x and lambda)
- but any individual B cell can only ever make an antibody using one heavy and one light chain
- so never a mix of x and lamda
13
Q
Describe the structure of immunoglobulin
A
- in the top part of the Y arms, each Ig has two variable regions
- one from the light chain and one from the heavy chain, called VL and VH, respectively
- these are at the N terminus of the Ig protein
- the variation in amino acids at the ends of the arms enables different Igs to bind to different targets
- this region is called the antigen-binding site
- beyond the variable Ig region is the constant region, called CL and CH
- the light chain has one Ig domain in its constant region
- but the heavy chain constant region has 3 or 4 constant domains, depending on the antibody class
- Three constant Ig domains (CH1- CH3) for IgG, IgA and IgD
- four (CH1- CH4) for IgE and IgM.
14
Q
What is similar and different between the BCR and antibody?
A
- the BCR and antibody share the same structural features in the immunoglobulin, but the BCR has an extra transmembrane region in its C terminus (green in image)
- this keeps the receptor anchored in the B cell’s plasma membrane
- the Ig domains are the extracellular part of the BCR
15
Q
Interpret this diagram to explain how the heavy chain gene is organised to allow both antibody and BCR molecules
A
- The schematic below shows how the heavy chain gene is organised to allow it to make both antibody and BCR molecules.
- Soluble (antibody) and membrane bound (BCR) Ig are transcribed from the same gene, but which mRNA is produced depends on alternative polyadenylation and splicing (which you discussed last year in MCB and this year in GEN).
- The transcript can be either polyadenylated early, to leave out exons encoding the trans-membrane domain (green), or spliced (and polyadenylated later) to omit the secretion signal (pink).
- Can you see how the primary transcript is rearranged – based on different sites of polyadenylation and splicing – to produce the mRNA encoding for either the secreted form or the membrane bound of the Ig?
- Since both transcripts come from the same Ig heavy chain gene, you can tell that for any single B cell the secreted and membrane bound form of Ig must have identical extracellular domains, and therefore bind to the same antigen!
16
Q
What are the three functional regions of Ig?
A
- Fab: two fragments corresponding to the antigen-binding regions, that are the two arms of the Y structure broken off the stem
- Fc (fragment crystallisable): one fragment corresponding to the stem of the Y, formed by the terminal part of the constant region
17
Q
Explain the function of the Fab domain
A
- the Fab domain of the antibody contains the variable region
- it is therefore part of the antibody which binds to the antigen
18
Q
Explain the function of the Fc region
A
- the Fc region is crucial for the effector functions of antibodies by binding to various antibody receptors (Fc receptors)
- this includes:
- opsonisation that allows immune cells to bind and act, such as phagocytosis or degranulation
- complement fixation (via C1q)
- mother-to-baby antibody transfer across the placenta and into breast milk
19
Q
What is the complementarity-determining region (CDR)?
A
- looking at the structure of the IgH variable domain, there are three loops in red that contact the antigen
- this is called the complementarity-determining region (CDR)
- CDR1 and CDR2 loops are the most genetically variable parts of the V segment, while CDR3 arises during VDJ recombination
- it is the diversity of sequence in these loops (and equivalent loops in the variable domain of the light chain) that allows our body’s collection of Ig molecules to bind specifically to such a wide variety of targets
20
Q
Which of the following describes the correct composition of human Ig?
A
- A heterotetramer of two identical light chains and two identical heavy chains all connected by disulphide bonds
21
Q
What are the functions of the constant domains of an Ig heavy chain? Select all that apply.
A
- opsonization
- transfer of Ig across epithelia, mediated by Fc receptors
- You may have realised that the constant domains are not all the same (different antibody classes have different C regions). However, the constant domains (through the Fc region) allow all antibodies (which have widely different specificities) to be treated equivalently by other elements of the immune system. This is why the constant region drives effector functions, whereas the V region drives specificity
22
Q
What are the five distinct major classes of Ig in most higher mammals?
Which of these have additional subclasses?
A
- IgG: additional subclasses
- IgA: additional subclasses
- IgM
- IgD
- IgE
23
Q
How do different classes of Ig differ and are similar?
A
- These differ in size, charge, carbohydrate content and the way they can assemble
- e.g. IgG, IgA and IgD have three constant doains each heavy chain
- IgE and IgM have four
- they all are the typical Ig structure
- even when a B cell changes the Ig class that it produces, the same V region is used, regardless of which antibody class the cell is producing
24
Q
Describe IgM
- structure
- function
A
- IgM is the first Ig to be expressed on B cells as they mature, so is the first to encounter an antigen.
- It makes up approximately 10% of the antibody in adult serum.
- Soluble IgM subunits form as a pentamer (recently discovered to be rotationally asymmetric - see the cryoEM image on right of the figure) connected by another polypeptide - the J chain.
- The pentamer is held together by disulphide bonds between cysteine residues.
- It therefore possesses 10 potential antigen binding sites providing this subclass with high avidity for antigens, even when the affinity of individual binding sites is low.
25
Q
What is avidity?
A
- Avidity is the overall strength of the binding of an antibody to an antigen with multiple binding sites.
- It is different from affinity which refers to the strength of binding at a single site.
26
Q
Describe IgG
- abundance
- subclasses
- function
A
- IgG is the most abundant Ig in normal human serum
- accounts for 70-75% of the total Ig serum pool of a healthy adult.
- In humans there are 4 subclasses, IgG1, IgG2, IgG3 and IgG4 which have different types of g heavy chains (γ1, γ2, γ3, γ4)
- It is the main antibody class for responding to small pathogens inside the body.
27
Q
Describe IgA
- abundance
- subclasses
- function
A
- IgA makes up 15-20% of serum Ig.
- There are 2 subclasses in humans: IgA1 and IgA2 (α1, α2).
- As with IgM, IgA can contain a J chain that facilitates dimerization.
- IgA dimers are the main Ig in mucosal secretions (e.g. saliva, genitourinary, respiratory or gastrointestinal tracts), so is particularly important against pathogens that infect these locations.
28
Q
Describe IgE
- abundance
- location
- function
A
- IgE makes up less than 1% of plasma Ig, but is found in abundance bound to the surface of basophils and mast cells in all humans.
- IgE is important in the response to parasitic helminth infections, but it also plays a role in allergic diseases such as asthma and hay fever, diseases that are more common in developed countries, where people are rarely exposed to parasites.
29
Q
Describe IgD
- abundance
- location
- function
A
- IgD makes up less than 1% of secreted plasma Ig.
- It is present in membrane bound form alongside IgM on the surface of naïve B cells (fully developed B cells that have never encountered an antigen that their Ig binds to).
- IgD is thought to play a role in the activation of B cells prior to their differentiation into antibody-secreting cells, but its function(s) remain(s) something of a mystery.
32
Q
Describe the structure of the TCR
A
- both TCR chains contain a variable region (V) and constant region (C)
- Each is a single Ig domain.
- Both TCR chains have a C terminal transmembrane domain.
- Just like Ig, the variable region confers the specificity that allows different T cells to recognise the unique characteristics of different antigens: variations in the three CDR loops of the variable Ig domain define which antigen each TCR is able to bind.
43
Q
Describe somatic recombination
A
- The loci where the Ig light and heavy chains, and the TCR chains are encoded contains many many alternate versions of the DNA segments used to make up the variable domain of the Ig and TCR molecules.
- The DNA segments that make up the variable domain are termed the variable (V), joining (J) and (for the IgH and TCR-β chains) diversity (D) regions on their corresponding gene.
- The table below shows the number of V, D and J regions in the main Ig and TCR genes. Don’t worry about the exact numbers - just note the large numbers of V regions in all these genes:- this is because two of the CDR loops are entirely encoded by this region.
44
Q
Use this diagram of the genetic structure of the gene loci encoding the heavy and light chains of the B cell receptors to explain VDJ recombination
A
- The heavy chain Immunoglobulin gene is found on chromosome 14 in humans.
While the lambda and kappa light chain genes are found on chromosome 2.
- The heavy chain gene is comprised of what can be described as 4 distinct regions.
- The variable region (often referred to as the V region), the diversity or D region, the joining or J region, and the constant or C region. - The variable, diversity and joining regions of the heavy chain are comprised of multiple distinct copies.
- In humans there are 40 variable regions, 24 diversity regions and 6 joining regions.
- In a final heavy chain gene only 1 of each is expressed. - The constant region encodes, as its name suggests, the constant domain of the heavy chain, and thus eventually will determine if the final immunoglobulin is an IgD, IgM, IgG, IgA or IgE.
- Like the heavy chain, the light chain genes have variable and joining regions, but not diversity regions.
- For instance in humans the kappa locus has 46 variable regions and 5 joining regions.
The key take home from this is that at germline the immunoglobulin genes provide options, through the process described in the video below the heavy chain of 40 V regions, 24 diversity regions and 6 joining regions are reduced to a single combination of one V, one D and J region, which can be different for each mature B cell.
50
Q
How does the T cells receptor (TCR) generate its diversity?
A
- The T cell receptor (TCR) generates its diversity through VDJ or VJ recombination in essentially the same way as the immunoglobulin genes.
- The TCR genetic locus is shown below.
- Note that due to the layout of the TCRβ gene, the Cβ1 constant region can only be used with the D and J regions that precede it, and the Dβ2 region can only be joined to the J regions that follow it.
51
Q
Describe the TCRs of the unconventional T cell: gamma-delta T cells
A
- The γδ T cells use alternative genes for making their TCR: the alternative chains these genes encode are called TCR-γ and TCR-δ.
- The γδ TCR is unlike the classical αβ T cells in that it is activated in an MHC-independent manner - that is to say they bind to ‘free’ antigens rather than those presented on MHC, making their antigen recognition process conceptually more similar to the BCR than the αβ TCR.
- The γδ TCR genes are rearranged in much the same way as αβ TCR and Ig genes.
- However, these genes are much less diverse, having fewer V, D and J gene segments, as shown in the table below.
- The γδ T cells are most prevalent in the mucosa, and are thought to be important for recognising lipid antigens, but are also significant players in immunotherapy against cancer, (an area you will cover both in CBIO (if you are doing it) and in IMI10). They may also sometimes contribute to autoimmunity, which you will explore in IMI9.
54
Q
What are the main components of T cell receptor complex?
A
- TCR-α
- TCR-β
- CD3
57
Q
How is the process of somatic hypermutation triggered?
A
- The process of somatic hypermutation is triggered only after antigen-BCR binding in the secondary lymphoid organs (spleen, lymph nodes).
- It is in these secondary lymph nodes that most B cells hang out, after maturation (including VDJ recombination) in the bone marrow.
- It is here, in fact, that naïve B cells are thought to encounter many antigens brought by APCs, particularly dendritic cells
- When their BCR recognises an antigen, the B cell is activated and proliferate.
- This leads to the formation of germinal centres (GC), which are anatomically distinct regions within the B cell follicles of the lymphoid tissue (see figure below).
- Here, these activated B cells differentiate into so-called germinal centre B cells.
- It is in these cells that AID becomes active.
- They interact tightly with specialised stromal cells called follicular dendritic cells (FDCs) and CD4+ T cells, to regulate the process of SHM and the concurrent process of affinity maturation.
58
Q
What happens to B cells in different parts of the germinal centre?
A
- Dark zone:
- AID levels are high and your active Ig genes will undergo many mutations
- if your antibody cannot be made (e.g. frameshift or stop codon), you will die
- you may also be triggered to switch antibody class here e.g. IgM to IgG
- Light zone:
- this is where B cells take their new BCR to show to dendritic cells, compete for antigen and show off their processed antigen to T cells
- if they lose the fight to bind antigen, or the antigen they bind is not recognised by the T cell they die
61
Q
What is class switch recombination (CSR)?
A
- As well as developing antibody with a high affinity, the immune system also needs to decide which isotype of antibody is required.
- This is also set in the germinal centre via class switch recombination (CSR).
- According to the signals received by the B cell, the heavy chain may change from one type to another, through genetic recombination.
- A naïve B cell (making IgM and IgD) might receive signals telling it to switch to one of the IgG isotypes (in the body) or an IgA (at mucosal surfaces), or IgE (against multicellular invaders).
- The heavy chain gene contains a sequence of constant regions encoding for the constant domains of the Ig classes.
- In humans this order is shown in blue in the figure below.
- Note that Cµ and Cδ are adjacent, as naive B cells make both IgM and IgD BCRs by alternative splicing.
62
Q
Describe how CSR works
A
- During CSR, a series of enzymes (including our old friend AID) introduce DNA double strand breaks (DSBs) and chop out the intervening DNA, containing unused constant regions and the remaining sequence is then re-joined.
- With the exception of IgD and IgM, only a single BCR class can be expressed at the same time.
- Take a look at the diagram below to see how this process occurs when class switching from IgM to IgG1.
- At the bottom of the panel you will notice that the segment order VDJ-γ1 sequence allows splicing of the mature transcript for the IgG1 heavy chain.
- Precisely how the immune system decides which isotope is needed remains something of a mystery.
- It is undoubtedly shaped by the combination of PAMPs and signals changing the cytokines released by the T cells and APCs (more of this in IMI5), but the details are poorly understood.
65
Q
Match the letter from the image to the process (captial) or effector (lowercase)
A
74
Q
Observe the phases of B cell development
A
