Immunology Book

1997 Microbiology 526-032: Immunology 1 By Duy Thai
3rd Year Medicine Page 1 of 3
IMMUNOLOGY 1
• The immune system has evolved to protect against pathogens. Once pathogens are able to enter the body, the internal
temperature of 37°C is perfect to incubate the pathogens. Without an immune system, these pathogens are able to
multiply and cause harmful effects.
• Pathogens can be:
1. Micro-organisms
• Micro-organisms are very small, and hence can enter the body very easily. From largest to smallest,
micro-organisms can be:
• (A normal cell is around 10 - 20 microns)
• Bacteria (1-2 microns)
• Ricketsia (0.1 microns)
• Viruses (0.02 - 0.04 microns)
2. Fungi
3. Helminths (worms)
• Immunity is protection and resistance against foreign organisms.
• There are 2 divisions of the immune response:

1. Innate
2. Adaptive
The innate immune response

• The innate immune response is built in to the body. We are born with it. It cannot learn new things, nor can it be
customised to attack against specific agents. Hence it is also called the non-specific response.
• Some examples of the innate division:
A. Skin & mucous membranes
• Protects our insides from the germ infested outside world
B. Secretions
• Contains enzymes which attack and injure bacteria. e.g. Lysozyme - breaks down bacterial cell
membranes (only useful against G+ bacteria). Since it is an innate response, it breaks down any
bacterial cell membrane (i.e. not specific for any one particular type of bacteria)
C. Low pH in gut
• Prevents bacteria from proliferating (acid fast bacteria can resist it)
D. Mucous
• Traps foreign particles and removes them from the body. The mucous in the respiratory tract is wafted
out by the movement of cilia. If the cilia are defective (e.g. paralysed due to smoking) then the mucous
accumulates and recurrent sinus and pulmonary infections can occur.
E. Excretion
• The above examples are our built in defenses to try and keep micro-organisms out of our internal environment. If they
successfully breach these defenses, more sophisticated methods are available to get rid of them.
Acute phase reactants

• These proteins are found circulating in the blood and increase shortly after an infection. Hence, to see if a person has
been infected by a bacteria or virus even if they do not show any symptoms, a blood analysis is done which would show
elevated levels of these proteins.
A. C reactive protein
• Binds polysaccharide molecules on the surface of bacteria
• By binding to the bacteria, it labels the bacteria as a candidate for complement activation and
phagocytosis by neutrophils and macrophages. This labelling is called opsonisation.
B. Mannose binding protein (MBP)
• Opsonises bacteria by binding to mannose which is common on bacterial cell walls.
C. Complement proteins
• A chain of enzymes and pro-enzymes which, when activated by the above 2 proteins (and other
factors), punches holes in cellular membranes. C’ also opsonises bacteria.
• There are 3 pathways of activation
• Activation is pro-inflammatory – i.e. will lead to inflammation via certain compounds released, C5a,
C3a
• Can work alone, in which case it is part of the innate response or it can work in conjunction with
antibodies as part of the adaptive response (ADCC)
• Micro-organisms are recognised by the body as being foreign by their own molecules which are coated on their surface
(antigens).
• These molecules can be proteins and carbohydrates unique to that micro-organism and act as a fingerprint which the
body uses to identify them as foreign and eliminate them.
• Not all micro-organisms cause disease

• Some bacteria colonise their host but do not cause harm to the host (commensals). Instead, they assist in
normal body functions. Their presence prevents other, more harmful bacteria from inhabiting the same place.
• When the immune system is suppressed, as in a course of antibiotics, these harmless are killed and replaced by
pathogenic bacteria which are antibiotic resistant.
• Innate immunity is not enough. Micro-organisms are not the same and so each will react differently to innate immunity.
Some micro-organisms may not survive, others may find ways of getting around the innate mechanisms. That is why we
have another branch - the adaptive immune response. (* Note that only G- bacteria are susceptible to complement lysis)
The adaptive immune response

• There are 2 branches of the adaptive immune response:
1. Humoral system
• Consists of antibodies
• Found in nearly all body fluids
2. Cellular system
• Consists of lymphocytes (B and T)
• The cells are capable of destroying an organism or other infected cells
• The way the immune system recognises micro-organisms is via their molecular surface.
• An antigen is any molecule which is capable of eliciting an immune response.
• Foreign molecular surfaces are highly antigenic and immunogenic. That means that they have a high capacity to elicit
and immune response.
• Cells of the immune response do not recognise the whole antigen. Instead, they recognise specific topographical features
of the antigen (epitopes).
• An antigen may have many epitopes, each epitope being recognised by one antibody (or cell of the immune response)
specific for that epitope only.
• Epitopes can be:
A. Continuous
• The epitope is made up of a single, continuous polypeptide strand
B. Non-continuous
• The epitope is broken up into separate bits and scattered along a polypeptide chain. The epitope is
formed when the chain is folded, bringing the epitope portions together.
Vaccination
• An individual can become resistant to infection by being exposed to the organism causing the infection. This is a result
of the adaptive response.
• The immune system remembers the encounter and so the next time infection occurs, a specific response is produced
which is quicker, stronger and more effective.
• Mutations of epitopes on the surface of an antigen results in resistance to a specific immune response. That is why some
vaccinations against the flu do not work because a new strain of flu virus (containing different antigens) has evolved to
evade detection.
• No matter how well developed our immune system is, there will always be one micro-organism which will evolve
capabilities of evading attack. i.e there is an interplay between our immune system and the world of infectious diseases.
• The principle of vaccination is isolating the antigenic portion of an organism from the part which causes the harmful
effects and then injecting the antigenic portion, thus stimulating an adaptive immune response which will remember the
antigen. When the real infection occurs, the body is well prepared.
Cells Of The Immune System

• All cells of the immune system are derived from the bone marrow.
• Erythroid line
• Gives rise to RBC
• Lymphoid line
• Gives rise to lymphocytes
• Myeloid line
• Gives rise to:
• Eosinophils
• Basophils
• Mast cells
• Neutrophils
• Macrophages
Neutrophils
• Neutrophils are the first to appear in an acute inflammatory response.
• Also known as polymorphonuclear leukocytes (PMN) due to a lobulated nucleus
• They have a very short lifespan
• Recognise bacteria by opsonisation
• In order for a neutrophil (or macrophage) to get to its target, it must undergo 4 steps:
1. Must get to the micro-organism (activation & extravasation)
• This occurs via chemotaxis.
• Chemotaxis is the process whereby a cell is attracted to a site of inflammation as a result of the
chemicals released at that site. The cell follows the path of increasing concentration. That is, it follows
the chemical trail until it gets to the target, where the chemical concentration is greatest.
2. Adherance to opsonised bacterium via FcR
• The cells have molecular receptors (FcR) on their surface for the constant region of Ig and
complement proteins.
3. Ingestion (phagocytosis)
• The organism is housed in a phagosome
4. Digestion by intracellular enzymes
• The enzymes are found in granules (lysosomes) and released into the phagosome, forming a
phagolysosome
Macrophages
• In the blood a macrophage is called a monocyte.
• In tissues it is known as a macrophage.
• In certain specialised tissues, macrophages have special names and also acquire special local qualities. They
have other roles in addition to their role in the immune response.
• Kupfer cells in the liver
• Microglia in the brain
• Osteoclasts in bone
• Type II alveolar cells in the lungs (alveolar macrophages)
• Unlike neutrophils:
• Macrophages are not activated immediately. They are part of a delayed immune response.
• Macrophages also work more closely with T and B lymphocytes.
IMMUNOLOGY 2
Macrophages (continued from IMMUNOLOGY 1)

• Macrophages are derived from the bone marrow.
• Some of their main functions are:
• Scavengers of the immune system. Their job is to keep tissues clean by phagocytosing bacteria, any foreign
matter, parasites and dead (necrotic) cells.
• In the tissues, they are also able to promote healing by:
• Removing dead cells
• Secreting chemicals
• e.g. Cytokines, interleukins which can attract T cells, increase vascular permeability and
cause fever (especially IL-1).
• Other chemicals, e.g. TNF (also called called cachetin) can increase the catabolic rate of body
tissues, leading to excessive weight loss. Can also provoke inflammation
• Attract fibroblasts and trigger fibroblast differentiation
• Corticosteroids can suppress macrophage function. Sometimes corticosteroids are given to prevent tissue rejection in
transplant patients.
Stages of inflammation (covered in more detail in path)

• During inflammation, blood vessels dilate and there is movement of plasma fluid into the tissues.
• Inflammation is a non-specific reaction, i.e. it occurs in every tissue of the body and is stereotyped.
• Local inflammation produces:
• Heat (due to increased blood flow)
• Pain (due to compression/damage to nerves and hyperalgesics – bradykinin, PGE2, PGI2)
• Swelling/oedema (due to loss of plasma fluid into tissues)
• The increase in blood flow (due to vasoactive chemicals – Histamine, Serotonin, PGI2) is a way of getting immunological
cells towards the site of inflammation quickly.
• Initially, neutrophils migrate out of the circulation and into the tissues, then head towards the site of
inflammation via chemotaxis. However, after neutrophils have done their job, they tend to die.
• Macrophages come next. Macrophages have the advantage of not dying on the job. Hence they come and gobble
up necrotised tissue as well as the dead neutrophils. Then then go back to the regional LN and show their
contents to T cells (see later lectures)
• The next cells to arrive are cells of the specific immune response (it takes them around 7 days to become
activated by macrophages and to get to the site).
• When the T and B cells arrive, the macrophages are able to act as an antigen presenting cell (APC), presenting the
phagocytosed material to T cells. This, along with cytokines released is able to activate the T cells.
• The T cells in turn activate B cells, which divide and differentiate into plasma cells, secreting antibodies against the
antigen.
• Most of the lymphocytes are not found circulating in blood. The usually reside in lymph nodes, bone marrow, spleen and
tissues (e.g. MALT)
Primary lymphoid organs

• Bone Marrow
• T and B lymphocytes originate from the same lymphoid stem cell.
• T cells migrate out into the thymus to mature.
• B cells stay in the bone marrow.
• In the bone marrow, the B cells are undergoing rigorous testing to see which B cells are going to make
antibodies against self. These B cells are deleted. Those that do pass this test migrate out into the
circulation and reside in the secondary lymphoid organs as virgin B cells.
• Thymus
• Once the T cells have migrated to the thymus, they begin their testing. Here, they are tested to see whether they
will react to self HLA molecules and self proteins. If so, they are destroyed. Only those cells which pass are
allowed to enter the circulation to protect the body.
Secondary lymphoid organs

• Also known as the reticuloendothelial system
• Comprised of:
• Spleen
• Lymph nodes
• Specialised lymphatic tissues (e.g. MALT)
Lymph nodes
• Lymph nodes filter lymph obtained from tissues.
• Thus, tissues which have any infection will tend to transmit the organism of infection to the lymph where it travels in the
lymphatic vessels. It will not go very far because the lymphatic vessels eventually connect to a lymph node, which filters
the lymph. Any foreign material contained in the lymph will be prevented from going any further.
• Local macrophages will also transport digested organisms to the lymph nodes to present them to T cells
• The B lymphocytes, after leaving the bone marrow, travel in the circulation and enter the lymph nodes via blood vessels
supplying the node.
• The lymphocyte enters the lymph node via specialised high endothelial venules located in the paracortex.
• In the lymph node, the lymphocytes sit and wait for antigens to be presented to them via the afferent lymph vessles.
• B lymphocytes mainly aggregate in the primary lymphoid follicles
• T lymphocytes mainly aggregate in the paracortical regions
• When antigen is encountered, some lymphocytes leave the lymph node via the efferent lymph vessels. From there, the
lymph passes to other lymph nodes before entering into the thoracic duct. From the thoracic duct, the lymph enters into
the systemic circulation, so that the lymphocytes can alert the whole body for an attack.
• Some (most) of the B cells remain in the lymph node and start to divide. The primary lymphoid follicle becomes a
secondary follicle with a pale germinal center. This is where the B cells are actively dividing.
• Once the B cells have fully differentiated, they produce secretory forms of their antibodies to be secreted into the
circulation.
• This increase in the number of B cells leads to enlargement of the lymph nodes (a clinical sign of either
infection or cancer).
MALT
• Note that MALT has its own local circulation
• If lymphocytes in the gut meet antigen, they migrate out to lymph nodes and then back again to the MALT.
Antibodies
• Also known as immunoglobulins and denoted as Ig or Ab
• The general structure of an immunoglobulin is as so: Antigen binding site
Heavy chain
Light chain Variable Region (Fab)
Constant region (Fc)
• The heavy chains have a hinge region in the middle, allowing the arms of the Ig to be flexible in binding antigen.
• The heavy chains are also connected to the light chains via disulfide bonds.
• The variable region is created by a combination of the heavy and light chain.
• The cleft in between the heavy and light chains forms the antigen binding site.
• The whole antigen does not fit inside the antigen binding site. Instead, surface molecules on the antigen
(epitopes) are what fits into the antigen binding site.
• There is perfect complimentarity between the antigen and the binding site. The antigen makes contact with 3
special portions of the antigen binding site. These portions are called complimentarity determining regions.
There are 3 on the light chain and 3 identical ones on the heavy chain. Together, the CDR grip the epitope
tightly.
• The CDR’s are encoded by separate parts of the variable region genes (more in later lectures)
• The constant region is important in determining the class of the antibody.
Light chain
Antigen
Epitope binding site
CDR’s
Heavy chain
Variable region gene
CDR segments on
variable region gene
Functions of antibody
• When an antibody binds to an antigen, it can:
1. Neutralise the toxin
• Prevents a toxin from doing its job by binding to surface molecules required by the toxin
2. Opsonise the antigen
• Makes the antigen more appetizing to macrophages
3. Activate compliment to punch holes into the bacterial membrane
• On the Fc portion there is a small region which is able to interact with complement molecules to
activate the compliment cascade.
How are antibodies developed (a general overview)

1. B cells develop in the bone marrow. Here, they are creating their heavy chain genes and light chain genes by genetic
rearrangement.
2. Any B cell which makes antibodies towards self proteins are removed. This process is called self tolerance.
3. B cells which do not react to self migrate out into secondary lymphoid tissues (e.g. Lymph nodes)
4. When they encounter antigen, they begin to replicate, divide and differentiate, eventually forming plasma cells which
can secrete the antibodies out into the circulation and tissue fluids. (provided T cell help is present to initiate class
switching)
The 5 classes of antibodies

• Each class has a slighly different purpose.
• One B cell can only produce one type of antibody with the same variable region, but can make antibodies with varying
constant regions on the heavy chain. Hence, one B cell can make all 5 classes of antibodies but they all have the same
variable regions. Another, different B cell can also make all 5 classes, all with the same variable region, but with a
different variable region to the first B cell antibodies.
• Light chain genes come in 2 flavours (λ or κ). During Ig development, one of these is chosen, the other is not. Both
cannot be expressed.
• The 5 classes of Ig are:
• Ig M
• One of the first Ig’s produced during the initial immune response
• Ig M is very good at binding complement (hence it is very good at punching holes in membranes)
• It is secreted in a pentameric form (hence having 10 antigen binding sites)
• Ig D
• The other class which is produced during the initial immune response.
• Unlike Ig M, it will be predominantly membrane bound, whereas Ig M can be secreted during the
secondary immune response.
• Ig G
• Part of the mature (secondary) immune response.
• Is able to cross the placenta, hence the mother is able to confer immunity to the unborn child.
• Most important Ig in the blood
• Many subclasses
• Ig A
• Found at mucosal surfaces
• Is predominantly secreted in a dimeric form (2 Ig’s bound together).
• It has associated with it a special protein which prevents it from being digested by gut enzymes when it is
secreted into the gut lumen.
• Ig E
• Specialised to deal with parasites.
• May be the causes of anaphylaxis, hypersensitivity
IMMUNOLOGY 3
Structure of immunoglobulins
• The Ig is made up of a pair of light chains and a pair of heavy chains.
• The variable region is made up of a portion from the light chain and a part of the heavy chain.
• At the bottom is the Fc region, which determines which class the Ig belongs to (M, D, G, A or E). The Fc region is also
important in that it interacts with the complement proteins to initiate the complement cascade.
• The variable region (antigen binding site) is capable of neutralising a viral attack by coating proteins on the virus which
are required for it to work. e.g. Haemagglutenin is present on the flu virus and interacts with the respiratory epithelium
to enter the cells. When an antibody binds to hemogluteinin, steric obstruction prevents the virus from entering the cell
because the hemogluteinin can no longer interact with the cells.
Classes of Ig's
• There are 5 classes of Igs, each with a particular specialty.
• Ig M
• Ig D
• Ig G
• Ig A
• Ig E
• Macrophages and neutrophils have receptors on their surface (Fc receptors) which recognise the Fc portion of the Ig.
• The Fc receptor is unique for every class and subclass of Ig. e.g. The Fc receptor for IgM only interacts with antibodies
(Ig's) which have an Fc(µ) portion (corresponding to IgM)
• Not every Ig class is represented equally. The majority of circulating Ig is IgG, next is IgA. The rarest is IgE, which
attacks parasites.
• If parasites are so abundant, why is IgE circulating at very low levels? The answer is because the Fcε receptor
binding IgE is very effective and so only small amounts are required to ilicit a response. The IgE Fcε receptor is
found on basophils and mast cells and causes histamine release, an important molecule involved in allergic
reactions.
• If circulating levels of a particular Ig class are very high, it could indicate one of 3 possibilities:
• Infection
• Multiple myeloma
• B cells make too much of a type of Ig, which shuts off the production of other Ig classes.
• B cell lymphoma (EBV)
Clonal selection of B cells by antigen

• This model states that at the beginning of an immune response, there are hundreds of B cells (virgin B cells) making
antibodies. These antibodies are expressed on the membrane of the B cell (they are not circulating free yet)
• When an antigen binds to the right Ig (an Ig which fits the antibody correctly), it selects the B cell which produced that
Ig. Antigen binding specificity is determined by the interaction of the 3 complementarity determining regions (CDR) on
the variable region of the Ig.
• This lucky B cell then starts to divide and proliferate.
• Its daughter cells form plasma cells and memory cells.
• Plasma cells are like specialised factories making only that type of Ig which was specific for the
antigen. The antibodies are no longer bound to the B cell membrane, instead they are secreted and
allowed to circulate freely, so that wherever the antigen is hiding, an antibody will be able to find it
and attack.
• Memory cells lie dormant, waiting for reinfection to occur at a later date. When reinfection by the
same antigen occurs, the memory cells are woken up and can mount a faster and stronger immune
response than during the first infection.
Generation of diversity
• Many theories have been put forth as to how the body can make specific antibodies to fit the countless number of
antigens which could be present.
• The old theories (which are now out of date) are:
• For each antigen which could be made, there is a single gene which encodes for it. If this were the case,
virtually all our genetic make up would be responsible for making antibodies.
• Althernatively, there could be a set number of genes which encode for antibodies, but these genes mutate, so
that many new antibodies can be made.
• What actually happens is that the genes responsible for making up an antibody are capable of rearranging (mix
and match), hence able to make up countless combinations.
• Organisation of an antibody gene: Code for Ig
classes
V J C V J C V D J µ ………
λ κ Heavy chain gene
• There is one lambda and one kappa light chain gene, and one heavy chain gene. Hence, 3 genes in total.
• The body selects either a lambda or kappa (but not both) gene and one heavy chain gene. These genes encode for the
light chain and heavy chain of the Ig molecule respectively.
• The light chain genes have variable regions made up of numberous segments and one constant segment. Between these
2 segments are numerous J (joining) regions.
• The heavy chain gene also has numerous variable regions but differ from light chain genes in that they have more than
one constant region. Each constant region codes for each particular Ig class and subclass. In addition, between the
variable and constant region are D (diversity) regions and J (joining) regions.
The genetic sequence of antibody diversity

• What happens during production is the random rearrangement of the various regions. Although it is a random selection,
the process is very ordered.
• I will use the heavy chain as an example, the light chain is just the same.
1. The D and J regions have multiple segments. One segment from the D region is randomly selected and joined
to one segment of the J region (which is also randomly selected. The other D and J segments are removed.
2. A randomly selected segment from the V region is then joined to the D-J region to form a V-D-J region.
3. The V-D-J region is then placed next to one of the constant region segments, often the µ segment (because it
comes first) to ultimately form an IgM, but can also be placed next to any other segment to form an IgA, D, E
or G.
4. The other constant segments are removed, so that all we have now is one segment from each of the V, D, J and
C regions.
5. Transcription takes place to form a primary transcript. This primary transcript is then modified by splicing of
the introns, to form mRNA.
6. Translation of the mRNA produces the heavy chain protein.
All these processes occur in the bone marrow. When released into the circulation
Virgin B cells no longer have the capability to rearrange genes.
However, they may mutate the genes via somatic mutation
• When the light chain protein has been produced in exactly the same manner (except no D region), the 2 heavy and light
chains are combined to form the Ig molecule.
• There are 4 sources from where the diversity came from

1. There are lots of genes responsible for coding a single Ig (2 light chain genes, 1 heavy chain gene)
2. Combanatorial diversity
• This results from the random mix and match of any V segment with any D which can join to any J
segment (occurs in heavy chain)
• The same thing happens in a light chain gene, except that there is no D region and so any V segment
can join with any D segment.
• In addition, there are 2 types of light chains, lambda and kappa and one of each type can join to any
heavy chain.
3. Junctional diversty
• When D-J rearrangement occurs, there is a sloppiness - errors in nucleotide sequence, which leads to
a change in the amino acids. A change in the primary structure leads to a change in secondary
structure which ultimately leads to a change in protein properites. In terms of Ig's this relates to a
change in the structure of the antigen binding site (and hence its antigen binding properties). This
allows for yet another different antibody to be produced.
• There is also junctional diversity at V-DJ
4. Somatic mutation
• As the antigen concentration falls, all the activated B cells are stuck with nothing to do any more.
Some die (via apoptosis), while a small number remain to add to the memory pool. Yet another small
proportion deliberately mutate their variable region gene. Remember that these cells no longer mix
and match V D and J regions because they are stuck with the choices they have made. The choice was
a good one since the cell was selected by an antigen because it matched the antibody. However, just
because the antibody produced fits the antigen, these cells don't think it is good enough and so mutate
the gene responsible for making that antibody.
• What results is an altered form of the antibody which can either be even better (fine tuning of the
antibody) or worse than the original. If it is better, this B cell will be able to catch very small
concentrations of antigen due to stronger binding. If the antibody is worse, the cell dies. This is
natural selection.
• The mature immune response is better becuase of all the fine tuning to antibodies via somatic mutation and natural
selection. This is known as affinity maturation.
• The first antibody made is IgM and IgD.

• This is because the genes coding for the constant region on the heavy chain which give rise to the M and D
class are closest to the variable region.
• Switching is where the same, refined variable region on the Ig is refined and connected to a class G, A or E
constant region on the heavy chain.
• By looking at the type of Ig circulating, we can see if it is a recent infection. If the circulating Ig are class M or
D then it is a recent infection. If it is IgG, then it is not.
Allelic exclusion
• We have 2 copies of evey gene in our body, one on the maternal chromosome (inherited from mum), and one on the
paternal (inherited from dad). A copy of a gene on a chromosome is called an allele.
• When a heavy chain gene is selected on one chromosome, the other allele is inhibited (prevented from being selected).
This is allelic exclusion.
• The same occurs for the light chains.
• There are 2 light chains, a pair of kappa alleles and a pair of lambda alleles. Kappa light chain genes are the first to
be selected. The other kappa allele is excluded, as well as both lambda alleles (light chain isotope exclusion - don't
need to know this fact - really!). If the selected kappa allele is defective, the other allele is chose; if both are
defective, the lambda allele is chosen.
• If both alleles are defective, the cell dies (apoptosis). The same is said for the heavy chains.
Other cells
• The steps involved in differentiating from a B cell to an active secrtory plasma cell are instructed by molecules released
from a special type of T cell - the T helper cell.
• These cells release cytokines, namely IL4 and IL5 which promote activation, proliferation and differentiation of the B
cells.
IMMUNOLOGY 4
• After the VDJ sections have been arranged, the next step is to combine with one of the constant region genes
V D J µ δ γ ε α
• The first Ig’s synthesised following B cell gene rearrangement are the membrane bound (surface immunoglobulin) forms
of IgM and IgD.
• Why is it the M and D class, rather than the rest? Because these are the first 2 exons of the constant region genes
and hence they are the first ones expressed.
• During gene rearrangement, the other constant region genes are removed, leaving only the µ and δ segments. In
addition, there is another set of genes flanking the µ and δ segments which determine whether the Ig produced
will be membrane bound or secreted.
V D J µ δ
• At this stage, there are 2 choices for the B cell. It can either make a class IgM or a class IgD, but cannot make a
single Ig with 2 classes (i.e. IgMD). It has to choose one or the other, the other being spliced off. Hence, some
transcripts will only contain µ but not δ, producing IgM while other transcripts will only contain δ but not µ,
producing IgD.
• The B cell now expresses the surface IgM and surface IgD, with the majority being IgD. Note that both classes
have the same variable regions and only differ in their constant regions.
• The B cell sits and waits for an antigen to arrive. When there is an antigen which fits the Ig expressed by the B
cell, the B cell becomes activated and divides (clonal selection). Multiple divisions result in the passive B cell to
convert to an active, secretory phenotype (plasma cell). In the plasma cell, the membrane encoding exons are
spliced, leaving the secretory exons. The resulting IgM and IgD formed is now secreted (rather than being
membrane bound)
The immune response

• The first events, when the B cell is rearranging the genes for its Ig’s and producing surface Ig’s, occurs in the bone
marrow.
• After that, the B cells migrate out into the circulation and make their way towards secondary lymphoid tissue
(lymph nodes, spleen or MALT) where they reside, waiting for contact with antigens.
• The second event, when the B cell converts to a secretory plasma cell, occurs in the secondary lymphoid tissue.
• In the primary immune response (1st contact with antigen), small amounts of IgD, M and G are produced. This response
is not very strong.
• Upon a second dose of the antigen, the secondary immune response is initiated. It takes around 14 days to go from a
primary immune response to a secondary immune response. In that time, an infection can wreak havoc in the body.
• What I mean is that the first time the body is infected by an antigen, a primary immune response is initiated
which is very weak. It takes 14 days for the primary immune response to move to a secondary immune response
and during those 14 days, the infection is still active if the primary immune response has not done a good job
(which is the likely case). One the secondary immune response is under way, the infection will have a hard time
trying to survive. The downside is that it takes 14 days to convert from a weak 1°° response to a strong 2°°
response, and in those 14 days, the infection is still active.
• The secondary immune response induces class switching (there is a change in the constant region segments with the same
variable region). Hence,
• IgM/D is converted to IgG
• IgM/D is converted to IgA
• IgM/D is converted to IgE
• The nature of the infection determines what class is required.
• If the infection is at a mucosal surface, then conversion will be predominantly to IgA
• If the infection is due to worms/parasites, conversion will be to IgE
• If the infection is due to bacteria, conversion will be to IgG
B cell activation
• When a surface bound antibody contacts an antigen, it tells the B cell what is happening via signaling molecules
connected to the cytoplasmic tail of the surface Ig.
Antigen Surface Ig
Complement
Cytoplasmic tail
Complement
receptor 2
Signalling molecules (Ig-β/Ig-α)
• Signaling though the surface Ig is not enough to activate B cells unless the signal is very strong. The extra signals are
given by T helper cells and other molecules.
• These other molecules cooperate with the surface Ig to co-stimulate B cells upon encounter with an antigen. E.g.
CD19, complement receptor 2 (CR2). There is amplification of the signal.
T dependent antigens vs T independent antigens

• Sometimes, a B cell can be stimulated without the need for T helper cells or other signaling molecules. The antigen which
stimulates the B cell is called a T independent antigen because it can stimulate the B cell significantly without the need
for T cells.
• These antigens have multiple, repeating epitopes (e.g. repeating sugar structures on bacterial cell walls) which
engage multiple copies of the same surface Ig. In effect, the one antigen is behaving as though it were many and
thus the B cell is stimulated due to summation of all the signals from the Ig’s. (A very strong signal is sent!) e.g.
If there are 5 epitopes which are identical, one B cell will be stimulated by 5 signals because 5 of its surface Ig’s
have been stimulated. Hence, T helpers are not required.
• An antigen which does not stimulate a B cell significantly is known as a T dependent antigen. T helper cells are required
to stimulate the B cell further in order for it to become activated.
• The antigens have multiple, dissimilar epitopes on their surface. Each different epitope can only stimulate one
different B cell which expresses the surface Ig matching it. Hence, if there are 5 different epitopes, 5 different B
cells will be stimulated. Each B cell responds only as if it had contacted one antigen and so only one signal is
sent. T helper cells (and other signaling molecules) are required to boost the signal.
REMEMBER THAT ONE B CELL EXPRESSES SURFACE Ig’S SPECIFIC FOR ONLY ONE ANTIGEN! A B CELL
CANNOT EXPRESS SURFACE Ig’S WITH DIFFERENT VARIABLE REGIONS!!
Advantages and disadvantages of T dependent and T independent antigens

• B cells stimulated by T dependent antigens:
• Switching (producing Ig’s of a class other than M or D) requires signals from T helper cells. Hence T dependent
antigens are able to produce antibodies of different classes.
• Because they need the help of others, they are slow to become activated.
• They are able to mature with high affinity antibodies. Why? Because somatic mutation (the fine tuning of
antibodies produced by a B cell) is instructed via T helper cells as well.
• B cells stimulated by T independent antigens:
• Are activated quickly because they do not need help from others.
• Can only produce lots of IgM, with very little IgG (the antibody of a mature response) because since they don’t
have any T helper cells, they do not receive the signals to switch.
• Also, there is no affinity maturation because the B cell does not receive signals to mutate their variable region
genes (because there are no T helper cells).
• No memory
Initiation of the specific immune response

• The specific immune response begins in the 2° lymphoid tissue. This is where the resting B cells first make contact with
an antigen.
• In the lymph nodes, lymph (containing the antigen) passes through the lymph node and in so doing, allows B cells to
detect the antigen.
• An activated B cell (B cell which is dividing) goes through the following steps:
1. B cell stops making membrane bound Ig’s and start making the secretory form.
2. The B cells are proliferating
3. The B cells are switching
4. The B cells are undergoing somatic mutation
• All the above 4 events are going on simultaneously in the germinal centers of the lymph node.
Microanatomy of the events undergoing in the lymph node:
Antigen
Selects B cell via clonal selection
B cell
Divides and mutates
Mutation can produce Ig’s

which are even more specific, or
maybe not. The Ig is still surface
bound
Follicular Dendritic cells capture any
antigens and acts as a reservoir of
antigens. The antigens are “stuck”
onto the dendrites and B cells are able
to sample these antigens. The dendritic
The B cell expressing the surface cells are also important in maintaining
the life of memory cells (discussed
Ig contacts with a follicular
later).
dendritic cell (an APC) expressing
the Ag
B cells which do not react with the B cells which do respond

Ag (i.e. have mutated into duds) to the Ag divide further
undergo apoptosis
Plasma cell which is Memory cell

producing the secretory
form of the antibody
Antibody released into the Emigration (leave the

circulation to combat the lymph node) to reside in
antigen at other sites other lymph nodes
Somatic mutations
• Recall that the variable regions of an antibody have 3 complimentarity determining regions (CDR’s) which grip the
eptiope. These CDR’s are encoded by special regions on the variable gene segment - so called hypervariable regions. 2
hypervariable regions are on the V segment, the 3rd is made by a combination of the D and J segments.
• Somatic mutations are only confined to the hypervariable regions, and their purpose is to make even better antibodies
than the original one which bound the antigen initially. Sometimes this is not the case and somatic mutation results in an
antibody which is less effective than the original. If this is the case, the B cell which made the dud antibody dies via
apoptosis.
• It is the T cells which instruct the B cells to undergo somatic mutation. Hence, T independent antigens cannot stimulate
somatic mutation.
• With each successive encounter with an antigen, somatic mutation results. This means that if a person is infected with a
particular antigen many, many times, their B cells are so refined (due to so many somatic mutations) that the antibodies to
the particular antigen have extremely high affinity. This means that very minute concentrations of the antigen are
required to be able to bind effectively to an antibody.
• Why does somatic mutation occur?
• Consider an initial infection of an antigen. The concentration of antigen may be 10-7M. An antibody is produced which
can bind to this antigen. The concentration of the antigen thus falls to 10-8M.
• Next, the cell which produced this antibody undergoes somatic mutation. 2 things can happen:
• The mutation results in a dud antibody being formed. This antibody cannot bind to the antigen at a
concentration of 10-8. Apoptosis occurs.
• The mutation results in an antibody which has a higher affinity, being able to bind to antigen at concentrations
of 10-8M
• Even less antigen is now present, say 10-9M
• This B cell now undergoes another mutation.
• The new antibody can bind antigen at concentrations of say 10-7/10-6M. The current level of antigen present is
much less than this. This antibody is thus not good because it can’t compete for the vanishing concentrations of
antigen circulating. Apoptosis occurs.
• Alternatively, the cell produces an antibody which can bind antigen at concentrations of 10-9M. This B cell has
done an excellent job at refining the initial antibody (which could only bind antigen at concentration of 10-7M).
The new antibody can bind very minute concentrations of antigen.
• The progeny of this cell becomes the active ones in the fight against this antigen. Some of the progeny
become memory cells. When all of the antigen is eliminated the plasma cells die off (because there are
no more antigen to stimulate it) and the memory cells remain to provide lasting immunity.
• Notice how the process of natural selection has killed off those cells which are ineffective, and only keeping the best ones.
Memory cells
• Memory cells survive after each antigenic challenge. However, memory cells still need to be exposed to the antigen to be
kept alive, even after the infection has passed and the antigen has been eliminated. How can this be so?
• What happens is that not all of the antigen is really eliminated. Some of the antigens are stuck on the follicular dendritic
cells which lie in the germinal center lymph nodes. The memory cells interact with these dendritic cells and are kept alive
by being exposed to antigen.
• Some infections do not leave behind any antigen. The toxin is not retained in the lymph nodes by the dendritic cells and
so any memory cells against these types of antigens do not survive. Hence there is no lasting immunity towards these
antigens.
• On the other hand, measles leaves heaps of antigens in the lymph nodes and so heaps of memory cells can be nurtured,
leaving life long immunity towards the infection.
Antibody function
• Neutralise
• Toxins
• Viruses
• Some viruses have receptor ligand interaction which allows them to enter cells. Antibodies bind to the
epitopes which may just happen to be what the virus needs to enter the cell. The virus cannot enter the
cell (steric obstruction)
• Opsonise bacteria
• By coating bacteria, the antibodies make them very attractive to macrophages.
• Destroy bacteria by complement mediated lysis. (only Gram neg bacteria are susceptible to this)
• The antibody has a small part on the Fc portion which is able to activate the complement cascade
• The complement cascade can effectively punch holes in the bacterial cell wall
IMMUNOLOGY 5
Bone marrow
Multipotent Myeloid and erythroid

stem cells line
Lymphoid stem cell
Pre B cell Pre T cell NK cell
B cell
Thymus
memory Plasma cell T cells
cytotoxic memory
helper
The cellular arm of the adaptive immunity

• This arm of the immune response is mediated by T cells, which are also bone marrow derived. Macrophages also have a
role as well.
• A summary of B cells:
1. B cells rearrange Ig genes whilst in the bone marrow
2. Ig produced is expressed onto the surface
3. Testing to determine which Ig's react to self molecules
4. Migration to secondary lymphoid tissues where B cells wait for trouble to occur
5. When atigen is encountered, B cells divide and differentiate.
6. Become secretory plasma cells which secrete Ig
7. Class switching occurs
8. Somatic mutations occur to refine the Ig structure
• T cells can be considered as the “conductors of the immune orchestra”
• The cellular arm and the humoral arm of the adaptive immune response work together and support each other.
T cells
• T cells develop and mature in the thymus
• There are many subsets of T cells, only 2 of which will be mentioned here.
• T helper cells
• Help B cells in differentiating, class switching and somatic mutation.
• T killer cells
• Roam around the body and look for infected cells; cells which express non self molecules on their
surface.
• Morphologically, the T helper and T killer cells are indistinguishable. However, they can be distinguised by surface
markers. These markers are known as CD markers.
• T helper cells express CD4, T killer cells express CD8.
• CD markers are a group of cell surface molecules on leukocytes and platelets. Apart from their functional use,
CD markers are also used to differentiate cells types (using monoclonal antibodies).
• There are many types of CD marker molecules. Some of which are below:
Marker Distribution Functiom

CD3 Tcells Part of the T cell receptor complex
CD4 T helpers Interacts with class II MHC, also a HIV receptor
CD8 T cytotoxic Interacts with class I MHC
CD20 B cells
CD25 T cells Marker for the IL-2 receptor, shows activation of a T cell
The T cell receptor

• Like the B cell, T cells express specialised molecules on their surface which enable them to detect baddies. In the case of
the B cell, the surface molecules are surface Ig's which bind to epitopes on the antigen surface.
• The surface molecules on T cells are known as T cell receptors. They are NOT the same as surface Ig's on the B cells.
• T cell receptors are coded by a distinct set of genes separate from the set of genes coding for Ig's.
• They also recognise antigen in a different mechanism.
• The Ig recognises the epitopes on the surface of WHOLE antigen. The T cell receptor, on the other hand recognises
FRAGMENTS of antigen proteins (peptides 8-15aas long). The T cell receptor cannot see nor bind to a whole antigen.
• T cell receptors can only recognise antigen fragments expressed on the surface of other cells.via MHC molecules
• There are some cells of the immune system which are specialised to do this task, while normal cells can't help but do it.
e.g. Virally infected cells express viral proteins on the surface becuase the virus has taken controll of the cells nucleus.
• The specialised cells are known as antigen presenting cells. Some examples of APC's are:
• B cells
• Understandable becasue they need the help of activated T cells to work effectively. Hence
they are capable of expressing antigen protein fragments on their surface to activate T cells
which in turn help the B cell.
• Macrophages
• Once they phagocytose the bacteria/antigen, they break it up into fragments. The
macrophage then expresses these peptide fragments on their surface so that T cells can see
them.
• The T cells are activated and sometimes, they themselves can be activated by T cells in
return.
• Dendritic cells
• Note that these are NOT the same as the follicular dendritic cell, which is only found in the
lymph nodes and presents antigen to B cells.
• They are specialised APC's
• The antigen fragment which is expressed on the cell surface is attached to a special molecule known as the HLA
(Human Leukocyte Antigen)
NORMAL CELLS CARRY MHC I à ATTRACT CD8+ à KILL!!!!

APC CARRY MHC II à ATTRACT CD4+ à T HELP!!!!
Molecular structure of the T cell receptor

• The T cell receptor is coded by genes which are separate from Ig genes (i.e. they have no relationship), however, the
structure of the genes are very similar.
• The T cell receptor is dimeric, composed of alpha and beta subunits (similar to heavy and light chains of Ig).
• The arrangement of the genes is very similar to that of the Ig genes in that they have multiple V, D and J regions. The
only different thing is that there is only one C region.
• The α chain has only V J regions
• The β chain has V D J regions
• Due to the similarity of the gene structure, there is also an opportunity for diversity - i.e. you can have rearrangement of
the V region genes with the D and J regions.
• There is also junctional diversity due to the imprecise joining of the V D and J regions.
• The T cell receptor thus is able to bind SPECIFICALLY with one type of antigen peptide. Each T lymphocyte
expresses a unique T cell receptor which is specific for only one type of antigen peptide fragment! (Just like and
antibody is specific for only one type of whole antigen)
• There is also a second set of T cell receptor genes, coding for gamma and delta subunits. It turns out that the gamma
delta rearrangement occurs before alpha beta rearrangement, but it is sloppy, so the cell scraps the gamma delta and uses
the alpha beta chain genes instead.
• 95% of the T cell receptors are alpha beta
• 5% of them are gamma delta
• The part of the T cell receptor which recognises the peptide is also known as a complimentarity determining region
(CDR) and is encoded in the V region.
T cell
HLA molecule
T cell receptor
Antigen peptide
fragment
• During development, T cells migrate towards the thymus where they undergo tolerance (self recognition testing). Any T
cell expressing a T cell receptor which recognises self proteins are deleted. If this does not occur, you would have
autoimmunity.
HLA Molecules
• The molecules which hold the antigen peptide on cell membranes is called the HLA molecule.
• It is distributed on virtually all cell types.
• HLA molecules are encoded in part of the genome called the Major Histocompatability Complex (MHC)
• HLA's are encoded by 6 loci, divided into 2 classes:
• Class I, contains HLA-A, HLA-B and HLA-C
• Found in all nucleated cell types
• Present peptides to T cytotoxic cells so that it can kill virally infected cells.
• Class I HLA's are found on cells which are forced to express non-self peptides (virally infected cells)
and so it makes sense that they would want to attract cytotoxic cells to kill them. The interaction is
prevented from recruiting the wrong T cell by making use of the co-receptors (CD8) which is only
expressed on cytotoxic T's and interacts with a part of the HLA class I molecule.
• Class II, contains HLA-DP, HLA-DQ, HLA-DR
• Specialised cells (macrophages, B cells and dendritic cells) which, instead of being forced to make
non-self pepetides, actually kill the antigen and presents the peptides to the surface. They do this to
recruit the help of T helper cells (they don't want to be eaten by T cytotoxic cells).
• The CD4 molecule on T helper cells interacts with the HLA type II molecule, thus ensuring that the
right T cell is recruited.
The polymorphism of HLA
Class II HLA Class I HLA molecules between individuals is
isolated on this cleft region
γinterferon induces
CD4 bind here CD8 the increased number
binds β2 microglob of Class I HLA’s. This
β subunit is made in
here excess and secreted,
• Each individual is capable of expressing HLA-A, HLA-B, HLA-C, HLA-DP, HLA-DQ, HLA-DR but each one of these
molecules is different in each individual. e.g. One person has HLA-A1, another HLA-A2, another HLA-A7. Hence,
there is no variation of HLA's within an individual, but there is high polymorphism (variation) within a species. (There
are different alleles of the MHC)
Polymorphism of HLA's
• The polymorphism between individuals is only confined to the cleft region (the region which binds the peptide
fragment).
• Because this region differs in all of us, everyone binds a different shape peptide fragment.
• Because we have 2 chromosomes, we have 2 alleles of the MHC. An MHC gene on one chromosome (e.g. the maternal
one) may be different on the other (paternal) one. (therefore, we have a total of 12 MHC molecules)
• The grooves do not bind all peptides. They are highly selective for which shape peptide is allowed to bind. Note that it is
only fussy about the region on the peptide which binds in the groove. The other region of the peptides can vary and it is
these regions which the T cell receptor interacts with.
• Each individual expresses a specific and unqiue peptide fragment on their HLA's.
• The differences in HLA's between individuals accounts for tissue rejection. Foreign HLA (empty, i.e. not binding any
peptide fragment) molecules on an implanted tissue would resemble self HLA molecules with a non-self peptide
fragment, and hence initiate an immune reaction against the tissue.
IMMUNOLOGY 6
More on the HLA molecules

• HLA’s are present on the surfaces of all cells in the body.
• They capture peptides and show them to the T cell receptor on the surface of T cells.
• They are encoded by a cluster of genes (the Major Histocompatability Complex) on the short arm of chromosome
6.
• There are 6 genes encoding for 3 class I HLA’s and 3 class II HLA’s on each chromosome. Since we have 2
chromosomes, we are capable of making a total of 12 HLA molecules.
Class II HLA Class I HLA

DP DQ DR A B C Maternal chromosome
• 12 HLA molecules in total. Note

that the cell surface really contains
hundreds of HLA’s not just 12 as
depicted here
• As an example, there may be 2
HLA-A but they both differ in their
cleft region, hence they would be
known as HLA-A1 and HLA-A2 for
instance. Each one binds a different
type of peptide fragment.
DP DQ DR A B C Paternal chromosome
• An important point to note:

• The presentation of peptides on HLA molecules occurs all the time (HLA’s are seldom empty - when I
say empty I mean not binding any peptide). i.e. It doesn’t just happen when you have an infection..
• The peptide does not have to be an antigenic peptide. The HLA molecules do not discriminate between
self and non-self peptides. That means that when you do not have an infection, you will be presenting
self peptides (formed from destruction and renewal of intracellular organelles) to the surface. It is up to
the T cell to determine what happens. If it is a self peptide, the T cell will not react, if not, then it will be
activated.
• There is no rearrangement of genes of HLA molecules
• If there is no rearrangement of genes, this means that all cells of the body are limited to a maximum
total of 12 HLA molecules on their surface (6 from the maternal allele, 6 from the paternal allele)
• There is no diversity of HLA molecules. 12 is all we have (compared to the virtually limitless number of
T cell receptors and Ig’s able to be produced).
• How can only 12 molecules act as a set of receptors for all the countless number of antigen peptides?
• Lets take the flu virus as an example:
HLA-A1
HLA-A2 Only the HLA-A1 and HLA-

Flu hemoglutenin protein,
the circles represnent HLA-B7 B8 molecules are able to
peptide fragments which bind the peptide fragments.
are able to be expressed The other allele of the
by some HLA and not HLA-A and HLA-B
others. HLA-B8 molecules are unable to
bind the peptides.
HLA-B8
• If it so happens that none of the 12 HLA molecules are able to select a peptide, then theoretically you would
unable to mount a T cell response due to genetic limitations.
• However, hemoglutenin is not the only flu viral protein available for chopping up into small peptides. There are
many others, for example neurominidase. So, if peptides from the hemoglutenin protein don’t fit any HLA’s,
maybe peptides from the neurominidase protein will. It this doesn’t work, then peptides from other flu viral
proteins are available. The cell keeps on trying until 1 peptide fragment is found which can bind to a HLA and
then a T cell can be altered. If on very rare occasions, no peptide is found, then that person will be unable to
mount a specific immune reaction to the flu virus.
• You can see now that only one peptide fragment of a viral protein is required to be expressed by a HLA in order
for a T cell to detect an infection and mount a response.
• It is due to the diversity of peptide fragments and the fact that only one is required, which allows us to get away
with only 12 HLA molecules capable of expressing many different types of antigen peptides.
T-B collaboration (the role of T helpers)

• When an antigen binds to a surface Ig on the B cell membrane, certain intracellular signalling cascades are set up
to initiate division and differentiation of B cells. However, this alone is not enough to start this process. (need co-
stimulatory molecules!!!)
• When the antigen and antibody complex is formed, the B cell engulfs the complex via receptor mediated
endocytosis.
• Once the antigen-antibody complex is internalised, it is broken up into peptide fragments inside the B
cell.
• These fragments include self (from the Ig) and non-self (from the antigen) peptides which are expressed
on the surface of the B cell using HLA class II molecules.
• An antigen peptide fragment which binds to a HLA waits to be detected by a T helper cell.
• In a distant place, not too far away, a sleepy T cell roams about lazily, looking for someone to kick it into action.
• On its journey, it encounters a macrophage.
• A macrophage, as you will recall is part of the latter stages of the innate (non-specific) immune
response. It has phagocytosed an antigen complex (which is the same as that of the B cells) and digested
it inside one of its phagocytic vacuoles. It then expresses the peptide fragments of the antigen onto its
surface via the HLA class II molecule. This HLA molecule is identical to the HLA molecule on the B cell
we encountered earlier, and they both express exactly the same peptide fragment.
• The macrophage then presents this antigen fragment to the roaming T cell. The T helper cell knows that
this is its job because the HLA class II molecule only interacts with T cells expressing CD4 (which
happen to be T helper cells).
• The T cell receptor detects specifically the bound peptide fragment and comes out of resting. The T cell
receptor - HLA interaction is not enough to completely wake up the T cell. Certain cytokines are also
released by the macrophage which act as co-stimuli, thus enabling full activation of the T cell.
• The activated T helper cell now goes in search for other macrophages, but more specifically B cells so that it can
help. The B cell that we first encountered, expressing the same peptide fragment as the macrophage which
activated the T cell, finds the T helper cell and the two make intimate contact (rated MA!).
• Upon interacting with the B cell, the T cell releases cytokines (IL-2, IL-4, IL-5) which act on interleukin
receptors on the B cell to set about division and differentiation.
• If there is lots of IL-4 produced, the T helper cell induces IgE to be produced
• If there is lots of TGFβ produced, IgA is induced
• The T helper mainly induces class switching to IgG
• In addition to the cytokines (which serve as a form of co-stimulation), there is another form of co-stimulation.
• On the surface of B cells is a molecule known as CD40. This molecule interacts with a CD40 ligand on
the T cell which provides another signal which acts like a volume switch, amplifying all other signals
going on in the B cell. This ensures that the B cell has enough stimulation to be able to divide and
differentiate properly to mount an effective assault on the antigen.
• The interaction of the T cell receptor with the HLA molecule is known as the specific stimulus
• Any other extra stimulation (via cytokines, CD40) is known as co-stimulation
• The T cell receptor makes contact with both the HLA receptor and the bound peptide fragment. I.e. it is able to
“see” 2 things at once.
• If the peptide is changed, then there will be a different T cell receptor.
• If the HLA molecule is changed, the T cell receptor will also change (and so will the peptide)
Clinical manifestations
• Human Immunodeficiency Virus (HIV)
• The receptor for HIV is the CD4 molecule, which just happens to be on T helper cells.
• If HIV is bound to CD4, then the T helper cell will be unable to interact with class II HLA molecules on
the surface of B cells and macrophages. Hence, there is no activation of the humoral arm of the specific
immune response.
• Severe immuno deficiency results due to the virus attacking the key cell required in initiating an
effective immune response.
• Hyper IgM syndrome
• Some children are born with IgM but cannot switch classes to IgG during the secondary immune
response.
• There is a defect in the CD40 allele
• Hence, when T and B cells come together , there is no augmentation and delivery of cytokines to the B
cell. The B cell is thus unable to switch classes. It can still mount a primary response (secreting IgM) but
cannot mount a secondary response.
T cytotoxic cells
• Instead of helping the cell which expresses the peptide fragment, the T cytotoxic cell kills the target cell.
• This is useful to eliminate intracellular pathogens which have taken residency inside the cells of the body, and are
hence “invisible” to antibodies and B cells and macrophages.
• The cells which are infected by intracellular pathogens express viral protein which are made by the cell. The viral
RNA has managed to insert itself into the host cell DNA and become replicated during transcription.
• The peptide fragment is expressed onto the surface using HLA class I molecule.
• CD8, which is expressed on T cytotoxic cells interacts with the HLA class I molecule, thus ensuring that the
target cell recruits this type of T cell and not a T helper cell.
• When the T cytotoxic cell binds to a cell expressing HLA class I molecules, the 2 cells physically stick together
via adhesion molecules.
• The T cytotoxic cell then releases granules containing perforins and granzymes
• Perforins punch holes into the cell membrane, allowing granzymes to enter
• Granzymes activate intermediates in the signally cascade which the cell uses to undergo apoptosis.
• A summary of apoptosis (which is covered in path)
1. Clumping of nuclear chromatin
2. Blebbing and loss of organelles
3. Nuclear fragmentation
4. Formation of apoptotic bodies
5. Apoptotic bodies are phagocytosed.
IMMUNOLOGY 7
Interaction between T cell receptor and HLA molecules

• The interaction between the T cell receptor and the HLA-peptide complex is probably the most crucial interaction in the
immune system. Without this interaction, regulation of specific immunity would not be possible. No interaction = no
specific immune response.
• T cells recognise foreign antigen peptides in combination with MHC gene products (HLA molecules).
• How was the T cell receptor - HLA interaction discovered?
• A genetically engineered mouse, able to only produce HLA class I molecules, is injected with a virus. Since
only HLA class I molecules are expressed, killer T cells will be activated. The experiment measures the ability
of killer T cells to kill virally infected target cells.
• Say the HLA molecule expressed by this mouse is HLA-A1. When binding self peptides, the T cell recognises
the HLA-A1 and peptide as being self, and so leaves the cell alone.
• When injected with a virus, the viral proteins will be expressed by the HLA-A1. The T cell recognises the
HLA-A1 with the viral peptide to be an altered form of self. The killer T cell then destroys the virally infected
cell.
• The binding of a foreign peptide onto the HLA molecule can be thought of as altered self. The HLA
(binding self peptides or empty) is recognised by the T cell to be self, and so the T cell does not react
to it (this is made sure of during T cell testing in the thymus). If, however, the HLA binds a non self
peptide, the HLA is now recognised as being altered self and so the T cell reacts.
• If that same T cell is injected into another mouse, which has been injected with the same virus, nothing will
happen.
• The injected T cell only reacts to HLA-A1 molecules binding viral peptides which fit the pocket of the
HLA-A1.
• This second mouse will express (as an example) HLA-A2 molecules. The HLA-A molecules differ in
the 2 mice (just like they differ in humans) only in their binding pocket region. Hence, HLA-A1 will
bind one type of viral peptide, while HLA-A2 will bind another type of viral peptide (from the same
viral antigen).
• The T cell cannot “see” the HLA-A2 and peptide. Hence, it does not kill the virus infected cells in the
second mouse.
• This is known as genetic restriction.
Tissue transplantation
• T cells are able to recognise 2 things (co-recognition):
• HLA molecule
• The T cell can only detect self HLA molecules
• Viral peptide
• Depending on the characteristics of the HLA binding pocket, the viral peptide is unique to the HLA
molecule (and hence unique to an individual).
• You cannot take T cells from one person and inject them into another because the T cell is unable to recognise the
foreign HLA molecule. However, if you put tissue from one person (containing foreign HLA molecules) into another
person, the T cells (note the plural) will be able to recognise the foreign HLA molecule. Why? Because in the body, there
are thousands of T cells (just like there are thousands of antibodies), each one being able to bind to a specific peptide-
HLA complex. All T cells in the body can “see” self HLA’s with self peptides and leave them alone.
• You can however, take antibodies from one person and inject them into another because antibodies recognise
whole antigens, which are the same in different people.
• The reason why we have flu pandemics is because we have developed excellent antibodies specific against a certain flu
viral antigen. The same is said for those T cells which can bind to the flu peptide. Each has developed to recognise a
particular strain of flu.
• However, the flu virus is able to mutate itself, producing a new strain. In some people, the new strand of flu virus has
proteins which will not be able to bind to any of the 12 HLA molecules we have available. The flu virus is thus unable to
be presented to a T cell and hence these people are unable to get rid of the virus. These are the people which have severe
and life threatening symptoms to the “common cold”.
• Recall that the T cell receptor is coded by genes which are similar in arrangement to antibody genes, and are also
capable of rearrangement, allowing for a diverse number of T cell receptors. The most variable regions of the T cell
receptor (the CDR) fits exactly over the most variable region of the HLA molecule (the binding pocket). The variation of
the binding pocket in a certain HLA molecule is the same for an individual but different between individuals. Both these
regions is where the peptide makes contact.
Superantigens
• These antigens elicit very powerful immune responses because they do not bind in the binding pocket of the HLA
molecule. Instead, they bind to the side of the beta chain of the HLA molecule and attack directly to the T cell receptor.
• This type of binding causes a huge reaction. It is not the toxin which causes the problems. It is the immune response
towards the toxins which is the problem.
• In doing what it thinks is best for the body, the T cells secrete lots of cytokines which activate macrophages, cause
secretion of fluid into the gut, increases vascular permeability - all leading to a lot of diarrhea.
• Superantigens are often from bacteria, and the conditions causes is called toxic shock syndrome.
Concept of co-stimulation
• The interaction between T cell and antigen peptide bound to HLA is known as the antigen specific stimulus.
• This alone is not enough to activate the T cell.
• There are more levels of interaction which are required for a proper immune response.
1. Adhesion
• Adhesion between the T cell and the target cell occurs via adhesion molecules on the cell surface.
• The T cell must be able to stick to the target cell long enough for any interaction to occur.
2. Co-stimulatory molecules
• These are molecules on the surface of the T cell and target cell which interact with each other to
create a second stimulatory signal (the co-stimulatory stimulus)
• The most important molecule on the T cell is CD28 which needs to bind to its ligand, B7 which is on
the membrane of antigen presenting cells. When the T cell receives this signal, it knows that the APC
is serious and becomes activated, releasing various cytokines.
• Another important co-stimulatory molecule is CD40. This molecule is found on the surface of B cells,
macrophages and the vascular endothelium. It reacts to CD40L (CD40 ligand) which is located on the
T helper cell.
• CD40 - CD40L interaction causes:
• In B cells:
• Causes B cell differentiation
• Formation of the germinal center in lymphoid follicles in the lymph nodes
• Class switching (from IgM to IgG)
• In macrophages:
• The activated T cell in turn activates the macrophage, which produces:
• IL-6/8/12
• NO (this molecule scorches bacteria)
• IL-1beta/TNF-alpa
• Vascular endothelium
• Increases adhesion by producing adhesion molecules:
• VCAM
• ICAM
• E selectin
• If we can interfere with co-stimulatory molecules, we can control transplant rejection and autoimmunity. By interfering,
we can prevent the activation of T cells against tissue transplants.
• The HIV virus may interfere with these molecules (it binds to CD4), thus preventing T cell activation and initiation of
the specific immune response.
• In hyper IgM syndrome, B cells lack the CD40 molecule. The T cells are thus unable to cause class switching, hence
there is only production of IgM, not IgG.
• Why do we need so many molecular interactions? Probably to act as a safety check.
What goes on in the thymus?

• In the thymus, T cells mature by rearranging their genes. Each T cell expresses its own unique T cell receptor. This
receptor will potentially bind to a specific peptide fragment.
• Some T cells make T cell receptors which recognise self antigens. These T cells are killed off.
• The ones which get through will provide specific immunity.
• Killer T cells express CD8 which recognises class I HLA

• T helper cells express CD4 which recognises class II HLA
• In the thymus, T cells express both CD8 and CD4. Hence they have the potential to recognise class I HLA (thus
becoming Killer T cells) or class II HLA (becoming T helper cells).
• The choice is made in the thymus before the T cells are released.
• T cells which choose to recognise class II HLA will turn off expression of CD8. They are known as CD8-
,CD4+
• T cells which choose to recognise class I HLA will turn off expression of CD4. They are known as CD4-,CD8+
• T cells which recognise and react to self peptides are killed.
• Other T cells have receptors which don’t recognise anything. These cells die by neglect.
• The thymic stromal cells are the cells in the thymus which are instructing the T cells by presenting all the 12 kinds of
HLA molecules to the T cells.
• T cells which make it out into the circulation are positively selected.
• T cells which are actively killed are negatively selected.
Different types of T helper cells

• There are 2 main types of T helper cells:
• T helper 1
• Secrete mainly INF-γ and IL-1
• T helper 2
• Secrete mainly IL-4
• Both types of T helpers express CD4.
• The T helper precursor does not know whether it wants to be helper 1 or helper 2. The choice depends on the external
environment.
• If there is lots of IFN-γ floating about, the T helper will become a helper 1 (Th1)
• If there is lots of IL4, the cell will become a T helper 2 (Th2).
T helper 1 response
• Respond to bacteria, infection, viruses
• Secrete the cytokines:
• IFN-γ
• Activate macrophages
• IL-2
• Helps killer T cells grow
• In all, is responsible for delayed type hypersensitivity. The target cells are killed by the action of macrophages and killer
T cells.
T helper 2 response
• Respond to worms, environmental allergens (all encountered at mucosal surfaces)
• Secrete the cytokines:
• IL-4
• Stimulate the production of IgE (class switching from IgM to IgE) from activated B cells.
• IL-5
• Activates eosinophils
• Is responsible for allergic reactions
Histological changes in macrophages due to prolonged immune response.

• e.g. TB bacteria. Has a waxy coating which protects it from digestive enzymes. Hence, it is able to enter into
macrophages and live there quite happily surrounded by all these cytotoxic chemicals. Macrophage keeps on trying to
kill it but cannot, resulting in a persistent immune response. The macrophages are continually being stimulated by Th1
secreting INF-gamma. This over stimulation causes the macrophages to fuse together, forming epithelial giant cells.
• e.g. Leprosy, a form of TB in which the macrophages are unable to eliminate the bacteria inside them. The macrophages
are releasing all these cytotoxic chemicals which degrade the surrounding tissues, causing the fingers (to take an
example) to be eaten away.
1997 Microbiology 526-032: Immunology 8 - Immunodeficiencies By Duy Thai
IMMUNOLOGY 8: IMMUNODEFICIENCIES
Summary of T helper responses

• There are 2 types of T helper cells
• T helper 1
• T helper 2
• The decision to become a Th1 cell, producing IL2, IFN gamma, TNF, is determined by the cytokine environment (lots of
IFN-gamma). Th1 cells tend to be involved in cytotoxic reactions by activating T cytotoxic cells and macrophages.
• IFN-γ, induces increased HLA class I expression, which is found on all nucleated cells. T cytotoxic cells
interact with the class I HLA molecule (by binding of CD8 to the CD8 co-receptor).
• IFN-γ also activates macrophages
• IL2 stimulates T cytotoxic cells CD8
• TNF is responsible for fever. It is great for killing off target cells (especially tumor cells).
• Th2 cells are induced by lots of IL-4. They are the more “peaceful” T helper cell, helping the B cell to make better
antibodies. They produce IL4, IL10, IL5
• IL4 and IL10 generally regulate the maturation of B cells. IL4 induces class switching in B cells, especially to
IgE class
• IL5 activates eosinophils
• There are other cytokines released by these cells, and many overlap (their names are unimportant). The following
concepts about cytokines should be rememebered:
• Cytokines tend to bind to a receptor with high affinity. Therefore small concentrations of cytokines can still
have marked effects.
• Cytokine receptors are not exclusive to cells of the immune system. They are widespread and hence the effects
of cytokines can be pleiotrophic.
• Pleiotrophic means that the a cytokine can have lots of actions, and the same cytokine can have
different effects on different cells.
• Cytokines are generally pro-inflammatory.
Mouse story
• There once lived 2 mice, one named BALB/c and the other names C3H. Both mice became infected with the leishmania
virus.
• Mouse BALB/c was found to produce predominantly a Th2 response, producing lots of IL4. However he died. If we
injected anti-IL4, thus forcing the body to rely on a Th1 response and produce IFN-γ, the mouse survived.
• Mouse C3H on the other hand, initially produced a Th1 response, producing lots of IFN-γ. He survived initially. If we
were really mean and injected anti- IFN-γ, thus forcing the mouse to rely on a Th2 response, he would die.
• The moral of the story is this:
• The genetic background of an individual influences the type of immunity they mount. Protective immunity
against leishmania depends mainly on a Th1 response. Thus, people who mount an effective Th1 response will
clear the organism more effectively than people who mount a Th2 response.
• People who mount effective Th2 responses to environmental antigens will find that they are more succeptible to
allergies, as we shall see in the next lecture.
PRIMARY IMMUNODEFICIENCY
Also known as hereditary or congenital immunodeficiency. Manifests mainly in children.
B cell deficiency
• X-linked agammaglobulinaemia
• Because it is X linked, it will occur mainly in boys (because they only one copy of the X chromosome).
• Symptoms occur mainly after 6 months of age and manifest as recurrent bacterial and pyogenic infections.
• A pyogenic infection is a pus forming infection
• There is impaired B cell maturation, hence no peripheral B cells, no lymph nodes, no tonsils. There are however, normal
immature B cells in the bone marrow.
• The defect is in an intracellular signally molecule, B cell tyrosine kinase
IgA deficiency
• Commonest hereditary immunodeficiency in causasians
• There is some problem in the class switching to IgA

• Results in recurrent mucosal infections (chronic sinusitis)
• Often associated with impairment of IgG2, IgG4 subclasses
Hyper IgM syndrome

• Polyclonal IgM but no IgG or IgA
• Due to a failure to switch classes. i.e. the B cells cannot undergo mutations due to a lack of cytokines released
from T cells to induce maturation.
• The defect in not in the B cell, but in the T cell.
• There is an X linked recessive defect in the CD40L signalling molecule on T helper cells which prevents them
from interacting with a CD40 molecule on B cells.
• This defective T-B collaboration results in the failure of T helpers to release their cytokines.
Common variable hypoammaglobulinaemia

• Onset occurs in adults
• Affects all Ig classes equally
• It is variable in severity – some people can only have ½ normal circulating antibodies while others can have even
less.
• Due to a defective T-B collaboration
• Results in recurrent pyogenic infections
• Often associated with autoimmunity
All the immunodeficiencies discuss so far are a result of a primary defect in either a B cell or T cell. All are
characterised by recurrent pyogenic infections. The following conditions are slightly different:
T cell immunodeficiency
• SCID: Severe Combines Immuno Deficiency syndrome
• Combined in that it affects both the cellular and humoral systems of the immune response
• Because it is a syndrome, it means that there is a constellation of symptoms, probably resulting from more than
one disease.
• The cell mediated immunity is extremely poor
• Recurrent viral infections, e.g. rotavirus, a common cause of infantile diarrhoea
• Protozoan infections, e.g. pneumocystis carini, which is normally harmless but if you have a defective
immune system, it is very dangerous (also affects people with AIDs)
• The person is easily overwhelmed by normally innocuous organisms.
• There are no lymphocytes around
• Occurs more in males (since it is X linked)
• More than ½ the causes of SCID cases are due to a genetic defect of the γ chain of interleukin receptors on
lymphocytes.
• All the interleukin receptors have identical γ chains. It is the second chain which distinguishes the
different type of receptors. If we impair the γ chain gene, then all receptors will be affected. Most
importantly the IL2 receptor and IL4 receptor are non functional.
• IL2 receptor is a growth stimulus for T cells
• IL4 receptor stimulates B cell differentiation
• The remaining ½ of causes of SCID are due to an adenosine deaminase (ADA) deficiency.
• ADA is involved in the purine metabolic pathways.
• This pathway is widely distributed in most cells of the body and a ADA deficiency does not seem to
affect most cells to a great extent. However, in lymphocytes, this pathway is of utmost importance. No
ADA causes metabolites to accumulate in the cell, thus killing your lymphocytes.
• This is one of the areas where gene therapy is being attempted. You take a retrovirus containing the
normal ADA gene and infect the children’s bone marrow. The virus then inserts the gene segment into
the host DNA and will allow transcription of the functional ADA enzyme.
Non-lymphoid primary immunodeficiency

• Neutrophil defects
• X linked (again!) so mostly males get it.
• Chronic granulomatous disease of childhood.

• Is due to a failure of the oxidative burst inside neutophils intracellular compartments (NADPH oxidase
defect).
• When neutrophils phagocytose anything, an oxidative burst causes toxic chemicals to be
released inside the neutrophil, thus killing the phagocytosed material.
• You get recurrent pyogenic infections
• Pneumonia
• Dermatitis
• Osteomyelitis
• Abscesses
• Granuloma: a residual, persistent antigen which can’t be eliminated. Therefore you have phagocytes and
epithelioid cells around the lesion which cannot get rid of what they have inside (they are constipated).
• Leukocyte adherence deficiency
• Adhesion molecule defects
• CD11, CD8
• Failure of neutrophils to adhere to endothelial cells and hence they cannot get out of the vasculature and
into the tissues.
• Complement deficiencies
• It is a genetic deficiency which results in a lack of any component of the complement pathway
• Deficiencies manifest as infections but not as severe as B cell deficiencies
• Defects in the components of late complement proteins and of the alternative pathway can result in
Neisseria infections. The neisseria bacteria is particularly vulnerable to the membrane attack complex
(MAC) and so deficiencies in C5, C6, C7, C8, C9 will not be able to form the MAC.
SECONDARY IMMUNODEFICIENCY
Also known as acquired immunodeficiency. Results from extrinsic or environmental factors.
• Impairment of the body’s innate defenses

• Burns, lesions, abrasions, cuts etc… (all cause breakage of the skin)
• Obstruction or impaired drainage of a body tube or viscus
• Smoking causes the cilia in the respiratory tract to become paralysed, hence mucous cannot be swept upwards
to be expelled.
• Cytotoxic drugs which impair marrow replenishment of lymphoid and myeloid precursors
• Chronic illnesses which lead to marrow suppression, e.g. diabetes, hepatitis
• Infiltration of the marrow with myloid or mailignancies (resulting from radiation exposure)
• Nutritional deficiencies
• Immunosuppressants, the best one being corticosteroids which suppress inflammation. Corticosteroids interfere with the
transcription of cytokine genes and regulatory proteins.
• Autoimmune diseases which cause self destruction of immune cells:
• Neutropenia
• Lymphopenia
• Infections with viruses: Human Immuno Deficiency Virus (HIV) which leads to AIDS.
IMMUNOLOGY 10: AUTOIMMUNITY
Immunological tolerance
• Developing B and T cells rearrange their receptor genes to create:
• Functional B cells producing immunoglobulins of different variability.
• The immunoglobulins (in general) are capable of recognising a wide variety of epitopes on intact
antigens, but each specific Ig can only recognise a specific epitope.
• Functional T cells expressing T cell receptors of different variability.
• The TCR (in general) are capable of recognising a wide variety of HLA-peptide combinations, but a
specific TCR can only recognise a specific HLA-peptide combination.
• The site of gene rearrangement occurs in:
• Thymus for T cells
• Bone marrow for B cells
• In the thymus, a universal repertoire of receptors is generated and the body has the problem of trying to silence any
lymphocytes which generate self reactive receptors. This is known as immunological tolerance.
• In the thymus, developing T cells are presented with a whole lot of self peptides to test whether or not they will react.
However, there are many other self peptides which are never presented to these developing T cells. Hence, tolerance to
these antigens can never occur in the thymus because the T cells will not encounter them during their “education”.
• These self antigens which are not present in the thymus are usually organ specific, e.g. insulin peptides found
only in the islets of Langerhans.
• There are a number of mechanisms to stop T cells reacting with self proteins which they have not encountered yet.
• Tolerance can be induced by:
• Deleting those T cells which react to self peptides (while in the thymus).
• Anergy
Anergy
• T cells in the circulation which have receptors which can recognise self peptides expressed on HLA molecules do react
with these peptides but nothing happens - there is immunological ignorance. This is known as anergy.
• Anergy is the paralysis of T cells (induction of tolerance in the periphery rather than the thymus) when they encounter a
self peptide in the periphery. However, this can only occur in a non-inflammatory environment.
• If the T cell recognises a self peptide in a sterile environment, it will undergo anergy. If the self peptide is recognised in
an inflammatory environment, then we will have problems.
• The most likely explanation is that in inflammation, there are lots of chemical signals which signify danger
and the presence of antigens which need to be eliminated. When a self peptide is encountered by a T cell under
these conditions, the T cell provides immunity towards the peptide, rather than tolerance. Autoimmunity
results. This is due to the co-stimulatory signals and molecules which are expressed on activated APCs during
the inflammatory response, which activate the T cell.
Self antigen + sterile environment = anergy

Self antigen + inflammation = reaction and autoimmunity
Organ specific autoimmuninty
Tissue Disease
Islets of Langerhans IDDM
Myelenated nerves Multiple sclerosis
Gastric parietal cells Atrophic gastritis and pernicious anaemia
Thyroid epithelium Hypothyroidism
If there is destruction of the thyroid gland
Hyperthyroidism (Graves disease)
Antibodies produced towards the thyroid
receptors stimulate the thyroid gland
Adrenal glands Adrenal insufficiency
Ovaries Ovarian insufficiency
Pituitary gland Pituitary insufficiency
Skin (dermo-epidermal junction) ?Eczema
Dermatitis herpetiformis
Pemphigus vulgaris
Pemphigoid
Lung (alveoli) Fibrosing alveolitits
Muscle fibres Myositis
Motor nerve endings Myasthemia gravis
Systemic autoimmune disorders

• Features of systemic disorders:
• Often, more than one tissue is affected
• Systemic symptoms
• e.g. fever, weight loss, loss of libido
• Multiple apparent targets
• (DNA, RNA, centromeres)
• Both cellular and humoral autoimmune reactions are activated.
• Systemic lupus erythematosus
• Often seen in young women
• Multiple autoantibodies towards nuclear antigens, including DNA.
• Inflammation affecting "connective tissue", mainly serosal, skin, membranes, synovium.
• Clinically a “mimic” disease in that it is hard to diagnose because it can mimic other conditions.
• Immune complexes can deposit in the vascular basement membranes, especially in the kidney capillaries and
skin capillaries.
• The immune complexes cause complement fixation, leukocyte recruitment, inflammation and
vascular damage.
• An example of a type II hypersensitivity reaction.
• Scleroderma
• Sjogren's syndrome
• Rheumatoid arthritis
• Polysynovitis with many extrarticular manifestations. i.e. besides joints, it can also affect for example the lungs,
eyes.
General lab features

• High levels of gamma globulin in the blood, indicating heaps of antbody production.
• Circulating autoantibodies
• Recognise self antigens
• In rheumatoid arthritis, an antibody sees the Fc portion of another antibody as being antigenic.
• Activated circulating T cells associated with particular HLA alleles. This indicates that the particular type of HLA
molecule is important factor to be considered in autoimmune diseases.
• Autoimmunity may be more common in people with certain HLA types
Specific examples: Insulin dependent diabetes mellitus

• The islets of langerhans in the pancreas contain mainly 3 cell types:
• α cells
• Produce glucagon
• β cells
• Produce insulin
• δ cells
• Produce somatostatin
• A biopsy of the pancreas will show staining of very few beta cells in the islets.
• You also see infiltration of lymphocytes which selectively kill the beta cells. This is a very highly specific killing,
targeting only the beta cell and no others.
• The β cell produces unique targets (only a few) which is recognised by the lymphocytes. The alpha, beta and
delta cells are virtually identical, except for those very few unique targets which are the key to distinguishing
which cells make glucagon, insulin or somatostatin.
• IDDM is polygenic in that the disease involves more than one gene. The most important genetic influence is probably
the HLA type.
• Those individuals who have HLA-DR3 and/or DQ2 alleles are particularly succeptible to having IDDM
because these HLA molecules are particularly good at presenting self peptides from the islets. However, simply
having these HLA molecules does not mean you will develop the disease. As mentioned before, many IDDM is
polygenic.
• Some people may make antibodies to beta cells but do not have the right genes switched on to
convert the autoimmunity to an autoimmune disease.
• Autoimmunity =/ autoimmune disease
• Some people may have HLA-DQ2 with autoantibodies to beta cells but still not develop IDDM because the response
generated is Th2 mediated. Those who develop IDDM have a Th1 mediated response.
• Recall that Th2 cells are good at recruiting B cells. However, B cells produce lots of antibodies which are
innocuous because the antigens are found inside the cell, and since antibodies cannot penetrate into the cell,
they cannot cause much damage,
• Th1 cells recruit cytotoxic cells which are able to detect the peptide fragements presented on the surface by
HLA molecules and hence cause cell damage.
• IDDM is an example of a cell mediated autoimmunity.
Specific examples: Myasthemia gravis

• MG is an example of an antibody (humoral) mediated autoimmunity.
• Antibodies are made to the Ach receptor, therefore Ach released from motor end plates cannot tigger a muscle
contraction.
• Patients with MG present with muscle weakness on activity. A clinical test is to tell the patient to try and close and open
their eyes 20 times. They will tire very easily.
• This disease can be "caught", in that it can be transferred to another patient by injecting the antibodies from a person
who has MG to someone who does not.
• You cannot transfer someone’s T cells who have IDDM and expect to induce IDDM in another person. This is because
the T cell will only recognise HLA molecules from the person it was taken from and not recognise the HLA molecules of
the person it was injected to.
Specific example: Multiple sclerosis

• Myelin basic protein is a protein which is present in the myelin sheath of myelinated nerve fibres.
• This disease is strongly associated with HLA-DR2 alleles.
• It is dependent on a Th1 response to cause the disease.
• Th1 cells recognise the peptide fragment and release IFN-gamma and TNF-alpha which recruit macrophages and T
cytotoxic cells. These cells cause damage to the myelinated nerve fibres.
• If you can find someway to convert a Th1 response to a Th2 response, then people with MS may have a light at the end
of the tunnel.
1997 Microbiology 526-032: Immunology11 - Transplantation By Duy Thai
IMMUNOLOGY 11: TRANSPLANTATION
• The immune system was not designed to reject transplants, since transplantation is an unnatural practice. Rejection only
occurs because the immune system is doing the job it was designed to do.
• Rejection is a form of specific immunity - immunological memory can be induced. e.g. If we transplant a genetically
different tissue and it is rejected, a second transplant of that same tissue will be rejected much more quickly (just like a
secodary immune response - in this case it is known as a second set rejection).
Types of transplants
• Syngeneic
• Genetically identical graft such as from an identical twin or clone (mabye in the future?).
• Autologous
• A graft from the same person to a different location on the same person.
• Allogeneic
• The most common type of transplant.
• A transplant from genetically different people, of the same species
• Xenogeneic
• Transplant from a different species.
• This is the most difficult because humans have natural antibodies (IgM and IgG) towards different species
tissue.
• Heart valves can be replaced with pig heart valves because it has low vasculature and low numbers of HLA
molecules.
The rejection response

• An allogeneic graft is usually rejected 3 - 7 days after it is transplanted.
• Alloreactive T helper cells can activate T cytotoxic cells and macrophages, thus causing graft injury.
• Alloantibodies bind to endothelium of graft tissue and cause complement activation.
• Complement activation damages endothelium and initiates inflammation. Platelets are activated and the graft
blood vessels lose their anti-coagulation properties. Thrombosis formation results, causing occlusion and
necrosis of the graft tissue.
Why and how does rejection occur?

• T cells have a T cell receptor (TCR) which recognises both the HLA molecule and the bound peptide fragment (co-
recognition).
• The response of an individual is custom made to fit their own HLA molecules. This is ensured by the process of
tolerance in the thymus. T cells are presented with all the body's HLA molecules while in the thymus.
• T cells which “see” the body’s HLA (with peptide) and do not react to it are positiveley selected.
• T cells which “see’ the body’s HLA (with peptide) and react to it are negativeley selected.
• T cells which do not “see” anything and are totally ignorant die by neglect.
• Thus T cells which make it out into the body are capable of seeing self HLA molecules bound to self peptides and
leaving them alone. Some problems may arise with T cells which see self HLA bound to self peptides which it did not
encounter while it was in training in the thymus. The favourable outcome to this is anergy, if not, autoimmunity may
result.
• What I am trying to say is that the T cells of our body know our HLA molecules as being self. They also know self HLA
bound to self peptide as being self.
• They are also capable of knowning self HLA bound to foreign peptide as being altered self and mounting an
immune response.
• One T cell recognises one HLA peptide combination. That same T cell cannot recognise another HLA peptide
combination, which may be recognised by another one of our T cells. We have many thousands of T cells each
with their own specific TCR.
• Now, lets consider something:
• A T cell needs to be able to recognise both the HLA and the peptide (co-recognition) in order to make a
descision whether to leave it alone or destroy it.
• If we get one T cell specific for one HLA-peptide combination and change just the HLA molecule,
then the T cell will not recognise the combination, even though it may recognise just the peptide. It
needs both the peptide and the HLA.
• If we keep the same HLA and change the peptide, the T cell will not recognise the combination, even
though it may recognise just the HLA.
• What happens in rejection is something so weird, it is hard to believe!!!!
• This rule I have just told you about does not apply to 1 - 2% of the T cell population. So, say you have 10,000 T
cells. 100 of them will break this rule of just being able to see one specific HLA-peptide combination!
• That means that some of the host T cells are capable of recognising and responding to a foreign HLA molecule
binding a peptide. This foreign HLA was not part of the T cell education. It was only educated to recognise the
12 HLA molecules present from its own body. It is just a matter of luck that some T cells can become
smartarses and recognise a HLA is was not supposed to recognise.
• By recognising this foreign HLA-peptide combination, it has inadvertantly triggered a rejection response.
• Normal: Self HLA + self peptide = recognition but no reaction

• Viral infection: Self HLA + foreign peptide = recognition and immune reaction
• Transplantation: Foreign HLA + foreign/self peptide = no recognition and no reaction except for 1% of the
T cell population, which do recognise and do react, causing rejection.
Summary
• A graft is transplanted.
• Host T cells scrutinize the cells of the graft tissue.
• The host T cells sees thousands of unknown peptides complexed to unknown HLA molecules.
• Most T cells will be unable to recognise these HLA molecules and so go away. If this were in the thymus during T cell
development, these T cells would have died through neglect.
• 1% of T cells will recognise the foreign HLA and peptide (alloreactivity).
• These T cells mount an immune reaction towards the graft. If this were in the thymus during T cell development, these
T cells would have been negatively selected because they recognise and destroy, rather than recognise and leave alone.
• ACCIDENTAL CROSS REACTION!
• What happens is that the the peptides presented by the allogeniec HLA may fit so good to the host TCR that it is strong
enough to cause a reaction. This is known as peptide focused.
• It is also possible that the allogeneic HLA molecule can fit the host TCR much better than the original, thus causing a
reaction (HLA focused).
• Summary: what has occured is that the host TCR has encountered new ligands which have produced much better fits
than the original, therefore they are recognised and reacted to.
Clinical transplantation - comaptibility requirements

• Rejection these days is less of a problem due to the great care taken in ensuring that the donor graft tissue is as close a
match as possible to the recipient. This reduces the immunogenicity of the graft tissue, improving transplant survival,
reducing complications and the need for immunosuppresants.
• Red cell cross matching
• The ABO blood grouping is extremenly important (mabye nearly as much as the HLA typing).
• ABO blood group antigens are found on red blood cells and also on the endothelium of graft tissue capillaries.
In the host, preformed antibodies towards these ABO antigens bind and cause endothelial damage.
• There may be other preformed antibodies towards other antigens in the graft tissue (not necessarily
towards ABO antigens). This is more likely if the person has had:
• Blood transfusions
• Multiple pregnancies
• Previous rejection of a graft tissue
• Those people with similar or identical ABO blood grouping are less likely to have antibodies towards the graft
ABO antigens.
• White cell cross matching
• Tests are made to ensure that there are no anti-allogeneic HLA antibodies present in the recipient.
• Minimise HLA allelic differences (tissue typing)
• The closer the HLA molecules, the less likely the recipient T cells will cause an immunological reaction against
the donor HLA molecules because they have already been naturally tolerised.
Rates of rejection
• Hyperacute rejection
• Preformed antibodies to:
• ABO blood group proteins
• HLA molecules
• Xenografts
• The antibodies-antigen complexes activate complement, cause inflammation and platelety aggregation and
thrombosis. Occlusion results, causing ischaemia and necrosis of the tissue
• Acute rejection
• Due to the activation of T cells. Firstly T helper cells which then activate T cytotoxic cells and macrophages
which cause direct cellular damage to the graft tissue
• Chronic rejection
• Take a long time to develop. Mechanisms not really known yet
Clinical considerations in transplantation

• Kidney transplants
• Kidney transplants are usually from living donors (since we can survive with only one kidney) or from the
recently deceased.
• The donors must be ABO compatible, and have the closests HLA matching. Also no anti-HLA present in the
recipient.
• Tissue typing is nationally coordinated.
• Patients are placed on a waiting list and a computer calculates the best possible match from all the
tissue type results nationally.
• Kidney transplants are not critical, since patients can be placed on dialysis machines while waiting.
• Heart/Lung transplants
• These are usually from the recently deceased (we can't live without them).
• Since these organs are critical, patients cannot be on waiting for too long. Often, HLA matching is difficult and
not used as a criteria since other factors tend to be more important, such as size.
• When HLA matching is a problem, and rejection is a real possibility, immunosuppressant drugs are used. The
serious drawback is that any infection developed while immunosuppressed is extremely dangerous because the
body has no way of fighting back.
• Bone marrow transplantation
• ABO blood typing is irrelevant
• Need identical or at most a single mismatch in HLA-A,B,DR,DQ
• From: Allogeneic sibling or family
Unrelated bone marrow donor
Umbilical cord blood donor
* Contains lots of naive, pluripotent stem cells.
* Up to 2 mismatches of HLA molecules
Autologous stem cell (identical HLA)
* Found in peripheral blood
* Bone marrow at other sites
* The stem cells are taken and enriched via growth factors.
• Potential problem: Graft vs Host Disease
• Bone marrow transplants contain a lot more than stem cells. It also contains T cells from the donor.
• It is possible for the T cells from the donor to react with HLA molecules found on normal tissues in
the recipient. Since HLA molecules are found nearly everywhere, there is a global rejecion of the
patient by the transplanted bone marrow.
• This often ocurs as a result of immunosuppression. The patients T cells cannot fight back against the
healthy T cells from the donor bone marrow.
1997 Microbiology 526-032: Immunology12 - Vaccinations By Duy Thai
IMMUNOLOGY 12: VACCINATION
General principles of vaccination

• Protective immunity can be induced by active immunisation.
• “Herd immunity” is a term used to describe the immunisation of a large population, thus preventing disease from
spreading.
• Protectinve immunity can be prolonged or lifelong, depending upon how effective the memory cells have been induced
and maintained.
• e.g. Immunisation to tetnus must be boosted through life, whereas a BCG immunisation only needs to be done
once in a lifetime.
• For immunological memory to be effective, we need the presence of persistent antigen. That means that even
after the infection has passed, some antigens are left behind. In the lymph nodes, follicular dendritic cells have
on their surface bound antigen. So long as the bound antigens are present, the memory cells are protected from
apoptosis.
• If we immunise with a simple antigen, the reservoir of antigen retained in the lymph node by FDCs will
attenuate with time. When there is little antigen left, the memory cells specific for that antigen will die.
• If we immunise with a more structurally similar antigen which is able to replicate, then there will always be
antigen present, and hence we get lifelong immunity.
• Some memory cells may be kept alive by cross reaction with other antigens.
• Vaccines which involve live organisms are generally more effective than vaccines containing inactivated organisms or
purified components of microbrial antigen. However, live organisms as vaccines are far more likely to produce side
effects, since they are capable of making toxins, invading cells and replicating, although to a much lesser extent.
• There are still many diseases out in the community which we still do not have vaccines for - e.g. malaria, HIV, leprosy,
herpes, syphilis.
• New strategies for vaccines are being developed:
• Naked DNA
• Viral DNA is given via a vector which infects cells. The body transcribes these viral proteins.
• Artificial viruses
• Genetically engineered viruses which lack certain genes which make them virulent.
• Virus like particles
• Protein polymers
New horizons for vaccination

• Allergies
• Create immune deviation. By being able to switch from a Th2 dominated response to a Th1 dominated
response, we would be able to minimise the severity of allergic reactions.
• Tumor immunology
• Cytotoxic T cells can eliminate tumors by recognising tumor antigens.
Types of vaccine preparations

• Live attenuated vaccines
• Diminish the virulence of the microorganism while retaining the desired antigen
• Can also be killed vaccines
• An intact, but non-living microorganism. Generally not as effective as the live organism
• People who are immune suppressed or have a serious allergic problem will have heaps of side effects to even a
half dead bacterium. Hence it is important that these types of vaccines are not given to an immunodeficient
child.
• Subunit vaccines
• The antigen is not the actual organism, but antigenic bits of it or toxins made by it.
• e.g. The tetnus toxin is the main problem, not the organism which produces it. The organism can be handled
fine by the immune system, the toxin does the harmful effects.
• The vaccination is an inactivated version of the toxin, known as a toxoid.
• Other subunit vaccines may subcelluar fragments, such as capsular polysaccharides.
1997 Microbiology 526-032: Immunology12 - Vaccinations By Duy Thai
Passive immunotherapy
• We take preformed antibodies made by another human and transfer them by injection to a person at risk, or who have just
contracted the microorganism.
• The antibodies must be given within 48 hours of exposure to the microorganism.
• Typical preparations:
• Hyperimmune anti-hepatitis B globulin
• Given after a needle stick injury, exposure of an open wound or to medical students travelling in
endemic areas.
• Zoster immunoglobulin
• Hyperimmune anti-varicella globulin (i.e. anti herpes zoster)
• Given to immune suppressed individuals (since they can’t make their own antibodies) following
exposure to the virus.
• Also given to pregnant women following exposure.
• The half life of the immunoglobulin is important, since you will need to reinject after the immunoglobulin is cleared. The
typical half life of IgG (the main Ig given) is around 15 - 20 days.
Tumor antigens
• Tumors arise from normal cells with mutated genes. This makes the cells do things that they are not supposed to do.
• Sometimes, there are point mutations or deletions in normal self proteins. These altered self proteins become the targets
for an immunological attack.
• Normal gene products may become upregulated in tumor cells.
• Normal cells may have very low levels of certain proteins being formed, but in tumor cells, these proteins are
suddenly made in excess. At the normal low levels, the immune system ignores these proteins, but when there
are suddenly heaps of them, the immune system sees this as new, foreign peptide and mounts an immune attack.
E.g. MAGE, a melanoma antigen is targeted in melanomas.
• Endogenous proteins specific to a tumor lineage.
• Viral transforming proteins which are involved in changing cells.
Tumor infiltrating lymphocytes

• Microscopically, some tumors have evidence of lymphocyte infiltration.
• These lymphocytes include both CD4+ and CD8+ cells.
• Phenotypically, the lymphocytes are activated, but somehow, the tumor has subverted them so that they cannot work, even
though they are activated.
• In vitro, these lymphocytes are found to proliferate poorly and have poor cytotoxicity.
Tumor evasion of T cell surveillance

• Tumors may secrete suppressive factors, e.g. TGF-β
• Tumor secretion of regulatory cytokines. These may be able to convert a Th1 response to a Th2 response. The tumor flips
the switch so that instead of cytotoxic T cells being activated, we get activation of B cells, producing a whole lot of useless
anitbodies.
• Tumors are also able to turn off their HLA molecules by turning off the genes coding for them. Thus, the tumor cells do
not present antigen peptides and so the T cells cannot “see” them.

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1997 Microbiology 526-032: Immunology 1 By Duy Thai

3rd Year Medicine Page 1 of 3

• Immunity is protection and resistance against foreign organisms.

• There are 2 divisions of the immune response:

The innate immune response

Acute phase reactants

• Not all micro-organisms cause disease

The adaptive immune response

Cells Of The Immune System

Macrophages (continued from IMMUNOLOGY 1)

Stages of inflammation (covered in more detail in path)

Primary lymphoid organs

Secondary lymphoid organs

Light chain Variable Region (Fab)

Constant region (Fc)

Variable region gene

How are antibodies developed (a general overview)

The 5 classes of antibodies

Clonal selection of B cells by antigen

The genetic sequence of antibody diversity

• There are 4 sources from where the diversity came from

• The first antibody made is IgM and IgD.

The immune response

T dependent antigens vs T independent antigens

Advantages and disadvantages of T dependent and T independent antigens

Initiation of the specific immune response

Microanatomy of the events undergoing in the lymph node:

Divides and mutates

Mutation can produce Ig’s

B cells which do not react with the B cells which do respond

Plasma cell which is Memory cell

Antibody released into the Emigration (leave the

Multipotent Myeloid and erythroid

Lymphoid stem cell

Pre B cell Pre T cell NK cell

memory Plasma cell T cells

The cellular arm of the adaptive immunity

Marker Distribution Functiom

The T cell receptor

NORMAL CELLS CARRY MHC I à ATTRACT CD8+ à KILL!!!!

Molecular structure of the T cell receptor

More on the HLA molecules

Class II HLA Class I HLA

• 12 HLA molecules in total. Note

• An important point to note:

• Lets take the flu virus as an example:

HLA-A2 Only the HLA-A1 and HLA-

T-B collaboration (the role of T helpers)

Interaction between T cell receptor and HLA molecules

What goes on in the thymus?

• Killer T cells express CD8 which recognises class I HLA

Different types of T helper cells

Histological changes in macrophages due to prolonged immune response.

Summary of T helper responses

• There is some problem in the class switching to IgA

Hyper IgM syndrome

Common variable hypoammaglobulinaemia

Non-lymphoid primary immunodeficiency

• Chronic granulomatous disease of childhood.

• Impairment of the body’s innate defenses

IMMUNOLOGY 10: AUTOIMMUNITY

Self antigen + sterile environment = anergy

Organ specific autoimmuninty

Systemic autoimmune disorders