Pluripotent hematopoetic stem cells

1.Erthryoid progenitor cells- RBC’s, platelets, megakaryocytes

2.Myeloid Progenitor cells

Leukocytes-

2a. Granulocytes (have granules in cytoplasm which are toxic and kill micro-organisms +
they induce inflammation)

1. Neutrophils- most common, a type of phagocyte, they go to the site of infection

first. They can work in anaerobic conditions. They die at the site of infection and
create pus.
2. Eosinophils- scond most common, they protect against intestinal parasites such as
helminth worms. They induce peristalsis of the gut and histamine inflammation.
3. Basophils- very rare, they induce peristalsis of the gut and histamine
inflammaton.

2b. Others

1.Monocytes- these are large phagocytic cells that are mobile throughout the
circulatory system. They are bigger than granulocytes and have an indented nucleus.
They are the progenitors of the macrophage.

2. Macrophage- these are basically monocytes but of the tissues. They live within
tissues and stay there. They are also phagocytic. They are large irregularly shaped
cells with vacuoles that store broken down substances. Macrophage usually detect
microbes first and release cytokines to trigger an innate response. Neutrophils will
respond first.

4. Dendritic cells- These are star shaped and are also in body’s tissues just like
macrophages but they are the messengers. They take a piece of the microbe and
go to lymphoid tissue with adaptive immunity and trigger a start of adaptive
immunity response.

5. Mast cells- These have granules but are not granulocytes. It is resident in all
connective tissue(blood,bone,etc.etc.) It has histamine effects and when it
degranulates, these inflammatory effects occur.

2c. Lymphoid progenitor cells

1. Natural killer cells- Large phagocytes that engulf somatic cells with a corrupt
HLA(viruses change the HLA{human leukocyte antigen which is our somatic
cells’ identity)
2. Small lymphocytes- B and T cells( B- cells are for extracellular immunity while
T-cells are for intracellular immunity) B-cells have immunoglobulins attached to
their cell membranes. T-cells have T cell receptors. 10^12 different types of small
lymphocytes are present throughout the body. Each one has a unique receptor. If
the adaptive immune response is not activated, the small lymphocytes circulate
and are not active.

Normally B and T cells are rarely present in the blood and lymph. They are usually in
lymphoid organs and tissues. Spleen has no connection with the lymphatics. It gets
drainage from blood and gives off to blood. It can act like a lymph node as well as
destroy necrotic cells like RBC’s.

Lymph nodes receive the microbes from the blood and this is where the dendritic
cells are to take a piece of the microbe and to call upon the adaptive immunity. They
take residence in the T-cell areas of the lymph node. Many afferent lymphatics drain
to the lymph node, the macrophage and such clean the lymph and one efferent
lymphatic vessel drains towards the thoracic duct.

The T-cells can bind to the dendritic cells in the lymph node. If this happens, this will
trigger differentiation of just that one type of T-cell. Differentiation of T-cells is 3
way

1. Helper T-cell 1- Stays in the lymph node and triggers the specific B-cell to
differentiate
2. Helper T-cell 2- travels to the infected area and helps the macrophage by
releasing cytokines and triggering a greater inflammatory and immune response.
3. Cytotoxic T-cells- these types will go and attack virally infected cells.

B-cells will differentiate by producing a Plasma cell which then releases many
antibodies. Antibodies are like Ig but free floating. They attack microbes.

GI tract + respiratory tract have most microbes. The oral cavity has the most(It is both
respiratory and GI)

Adaptive Immunity-

TCR are more specific than antibodies. The part of antigen receptor that binds is the
epitope.

Ig’s have a Y shape. They have heavy and light chains and variable and constant
regions. The variable regions are the sites for antigen receptors. They are attached to a
carboxyl group transmembranely. Antibodies lack this transmembrane part so they
aren’t bound, they are free.
TCR’s consist of an alpha and beta chain which also have variable and constant
regions.

The antibodies have the V end which binds to the microbe and the I end which binds
to complements, phagocytes, and inflammatory cells. Two antibodies then allow for a
bridge where the complement or phagocyte can destroy the microbe through.

B-cells and T-cells form through somatic gene recombination. B-cells take it a step
further and can undergo hypermutation where they can bind the pathogen more
tightly to the Ig and these can then become Plasma cells.

Antibodies can bind to full pathogens. When they bind they can call upon
macrophage and complement cells to destroy the microbe. Also they neutralize the
microbe so it cannot grow nor infect somatic cells. T-cells can only bind to short
peptide portions of a pathogen called MHC. Major histocompatibility complex which
is produced by antigen processing.

Antigen presenting cells-

MHC 1- present intracellular antigens

MHC2- present extracellular antigens

Different people have different MHC’s, this results in transplant rejections.

B-cell and T-cell formation is clonal. In bone marrow, the B-cells that bind well to
self MHC’s are set for apoptosis. In the Thymus, the T-cells that interact well with
self MHC’s are saved and then from those, the T-cells that bind to self MHC’s too
well are destroyed. It’s positive and negative control for T-cell clonal selection.

CD4 T helper cell- recognize MHC II peptide molecules and help B cells and
macrophage to get activated

Cytotoxic CD 8 T cell- recognize viral MHC I peptide molecules and destroy them.

Antibodies

IgA-(mainly in fluid + mucosa)

IgD- along with IgM but in small amounts
IgE- binds to mast cells and produces a strong inflammatory response against
parasites. Also can cause allergic reaction.
IgG-(mainly in fluid)- binds and induces opsonization as well as complements to
attach, this triggers a double response from Macrophage,
IgM-(mainly in fluid) first to be distributed, binds and induces complements to attach
and then opsonization occurs because of the complements, not the IgM. The
complements only trigger macrophage.
 Chapter 2

Carbs and proteins are most common antigens that are bound to.

The different immunoglobulin types are because of different isotypes of the heavy
chain. A,D,E,G,M

Differences in light chain = kappa and lambda, most are kappa in humans and no
functional difference is found.

The V regions within the Fab arm make antigen BCR’s like this. The hypervariable
regions (CDR’s) of the light chain and heavy chain join on the N termini end and
make an antigen receptor.

There are different types of epitopes

They all bind to the receptor via non covalent forces

1. Heavy chain gene – located on chromosome 14

2. Light chain kappa (κ) gene – located on chromosome 2
3. Light chain lambda (λ) gene – located chromosome 22

Light V chains have variable segments and joining segments

Heavy V chains have variable, joining, and diversity

Light chains recombine V to J

Heavy chains recombine D to J and then the DJ is recombined to the V.

Everything in between is spliced as exons.

RSS’s direct the recombination of gene segments. It flanks the 3 side of the V segment,
both sides of the D segment, and the 5 side of the J segment.

3’-J-5 X ’3’-D-5x’- X 3’-V-5’

V(D)J recombinase are the enzymes needed for the RSS to be carried out.

RAG-1 and RAG-2 are recombinant genes only made in the lymphocytes
The RAG’s splice at the 7 base paired heptamer which is near the V,J, and D segments.
They excise the 23/12 part and join the V and J for instance. The exons are joined at a
coding joint while the introns are cleaved in a circle at a signal joint.
Then P-nucleotides are added spontaneously. Next, N nucleotides are added by TdT. The
two chains are matched and the unpaired nucleotides are excised by exonuclease. The
two segments are then joined at a coding joint by DNA synthesis and ligation.

Naïve B cell= IgM and IgD, they are the first to be presented and they are presented
simultaneously

Look at notes

Every Ig can be made as an antibody or as an immunoglobulin.

Immunoglobulin= hydrophobic at the carboxyl terminus

Antibody= hydrophilic at the carboxyl terminus

When an antigen binds, somatic hypermutation occurs where rapid point mutations
happen on both Vh and Vl regions. This allows for many different types of antibodies to
be synthesized. Affinity maturation is the process in which these mutations allow for the
steady production of antibodies that have a greater affinity for the antigen.

The IgM is secreted as a circular pentamer and therefore it binds securely to the antigen
but it lacks effector possibilities.

To change from IgM or IgG to another type of Ig, the Ig undergoes isotype class
switching but only during antigen binding with the B-cell. The Ig then binds with a
different C region, this makes a different Ig, for instance IgA or IgE.

Functions of Ig’s

Neutralization- binding to the antigen primarily to make it less harmful to the body’s
cells. For instance, the antibody will bind to a virus and then the virus will no longer be
able to attach to a cell.

Opsonization- they bind to antigens and serve as immune system proteins that make it
more efficient for phagocytes to engulf the pathogen. The Fc provides a receptor for the
phagocytes. Complements can also work as opsonins. If an antibody is attached, the
complements can also attach and lyse the cell without the need of a phagocyte.

IgM is produced in bone marrow, lymph nodes, and spleen. It circulates throughout the
lymphatics and the blood.

When adaptive immunity is first called upon, the IgM’s wil have low affinity, so that’s
why they are set up in a pentamer with 10 receptors. When they bind, complements can
come and react with the IgM’s C region and kill the antigen. Also, when there is a
binding to an antigen, this triggers somatic hypermutation and the IgM can isotype class
switch and possibly become an Ig with effector functions.
IgG is the most abundant in the lymph and blood. It is also synthesized in bone marrow,
spleen, and lymph nodes. It is more flexible and smaller than IgM and when it binds to
antigens, it can directly phagocytose or it can also call upon complements. It is
transferred from mother to child through the placenta during pregnancy.

IgA- Monomeric is made in spleen, bone marrow, and lymph nodes and it secreted into
the bloodstream. Dimeric IgA has a J chain and it is a dimer as the name implies (Y
connected to Y). It is secreted in mucous membranes as well as breastmilk and through
tears. It is in the gut and keeps normal flora in check as well as fighting off dangerous
microbes. It is made in the mucous membranes near the mucous parts of the body.

IgE- It binds to mast cells and produces a severe inflammatory response. It is functional
for peristalsis of the gut as well. IgE is very rare but when it binds to mast cells during
adaptive immune response, the mast cells release stored histamine and other chemicals
that recruit cells of the immune system to a certain destination, this induces
inflammation.

Chapter 3

Immunoglobulins and T cells are similar but the main difference is in their receptors and
to what they bind. T cells bind solely to Major Histocompatibility complexes aka MHC
which are present on human cells while Immunoglobulins bind to epitopes on a wide
variety of molecules like proteins, carbs, and lipids.

The T cell receptor has two chains: the alpha and beta chains. Each chain has a variable
region and a constant region and each chain is made up of 2 domains. The two variable
regions’ put together make one receptor. Each variable region has 3 hypervariable
CDR’s.

Pre-binding, the T-cell receptor undergoes gene rearrangement just like the B cell
receptor but after binding, the T-cell receptor does not experience any changes. The T-
cell alpha chain locus is located on chromosome 14 while the T-cell beta chain locus is
located on chromosome 7. The alpha chain has only one possible C region while the beta
chain has only two possible C regions and they have no known functional difference. The
variable region of the alpha chain of the T cell receptor closely resembles the variable
region of a Light chain of an immunoglobulin in that it has only a V and J gene segment.
The variable region of a Beta chain closely resembles the variable region of the Heavy
chain of the immunoglobulin in that it has a Variable, Diversity, and Joining segment.

In the alpha chain variable region, the V and J genes recombinate. In the beta chain
variable region, first the D and J segments recombinate and then the V segment
recombinates with the D part of the DJ. This recombination happens on the CDR3 of the
variable region. RAG 1 and RAG 2 play the same role in the TCR as in the BCR and P
and N nucleotides are also added. When one of the RAG genes do not work, the child is
born with a condition called Severe Combined Impaired Immunodeficiency Disease
(SCID). The child has impaired immunodeficiency of both the B cell and T cell
recombination. Without a bone marrow transplant, the infant dies early. Another similar
disease is Omenn syndrome in which the RAG genes have partial enzymatic function.
The symptoms are similar.

After the germline DNA is recombined, it is transcripted into an mRNA, then it is spliced
to get rid of introns, and finally it is translated into a T cell receptor protein. The alpha
and beta chain are paired in the Endoplasmic reticulum of the cell. The alpha:beta
complex can not leave the ER and move to the cell’s membrane before it is matched with
CD3 proteins and the (squiggly) chain. These four proteins are transmembrane proteins
needed to bind the a:b complex to the cell’s membrane. The 3 CD3 proteins(gamma,
delta, and epsilon) come from chromosome 11 while the (squiggly) chain comes from
chromosome 1. These 4 proteins are important for signaling from the TCR complex back
to the cell once an antigen has binded. People without functioning CD3 epsilon and CD3
delta proteins have immunodeficiency.

There is a second class of T cell receptor. In this one, the gamma chain resembles the
alpha chain while the delta chain resembles the beta chain. There are a:b TCR’s and
gamma:delta TCR’s, never a mix. The delta chain is located on chromosome 14 between
the Valpha and Jalpha segments. This means when the alpha Variable segment is being
recombinated, the gamma chain is deleted. The gamma chain is located on chromosome
7.

For T-cells to be able to bind on human cell’s, the antigen must be processed into a
peptide chain and presented in a MHC complex on the cell’s surface.

There are 2 classes of T cell: T cells that possess CD4 glycoproteins on their cell
membranes and T cells that possess CD8 glycoproteins on their cell membranes.

CD8 cytotoxic T cells are responsible for killing infected human cells. CD4 helper T
cells’ main function is to help other cells of the immune system to fight an extracellular
pathogen.

There are 2 types of CD4 helper T cells: TH1 cells and TH2 cells. TH1 cells’ main
function is to activate tissue macrophages to phagocytose and kill intracellular pathogens
and to secrete cytokines and other chemicals.
TH2 cells function is to make B cells produce antibodies so that the antibodies can help
fight an extracellular antigen. The AIDS virus binds to the CD4 helper T cell receptor and
enters it. This causes immunodeficiency.

There are 2 types of MHC molecules: MHC I and MHC II.

MHC I presents an antigen peptide of intracellular origin to CD8 cytotoxic T cells while
MHC II presents an antigen peptide of extracellular origin to CD4 helper T cells.
MHC I molecule consists of an alpha complex and B2-microglobulin. The aheavy chain
alpha complex consists of three components (a1, a2, and a3). a1 and a2 form the MHC
binding site while a3 and B2-microglobulin form the part connected to the membrane.

MHC II molecule on the other hand consists of 2 chains: alpha and beta. The a1 and B1
make up the binding site, while the a2 and B2 portion make up the part that is attached to
the membrane.

MHC complexes can process a wide variety peptides. This is known as degenerate
binding specificity. Peptides that bind to MHC I are 8-10 amino acids long while the
peptides that bind to MHC II are 13-25 amino acids long. This is due to the fact that
MHC II has a freer structure than MHC I.

MHC I peptides are processed in the cytosol and delivered to the ER. These antigens are
intracellular. MHC II peptides are from extracellular antigens. They are engulfed and
processed in the cell’s lysosomes and endosomes.

For MHC I: {Mechanism}

The viruses use the ribosomes in the cell’s cytosol to synthesize viral proteins.
Meanwhile, the cell’s protein complex, proteasome, processes the virus proteins into
peptides.

This peptide is then transported from the cytosol to the ER by a protein called TAP. TAP
has 2 structurally related peptide chains, TAP 1 and TAP 2. The peptide transport ability
of TAP depends on the binding and hydrolysis of ATP. The peptides are about 8 amino
acids long and have a hydrophobic carboxy end. The heavy a chain is translocated into
the ER as well and there it is bound to the peptide by chaperone proteins.

Calnexin binds to the heavy alpha chains and retains the partly folded chain in the ER. It
is a calcium dependent lectin. When the B2-microglobulin has binded to the heavy
chains, calnexin is released. Calreticulin then binds to the heavy chain/B2 microglobulin
complex and a second component, tapasin, binds to TAP 1 of TAP. This puts the heavy
chain/B2 microglobulin complex in a position to receive a processed peptide. Most of the
peptides that are presented by TAP miss to bind to the MHC I complex. However, once
the MHC I complex has binded to a peptide, all the chaperones release and a vesicle
carries the MHC I complex through the stacks of the Golgi apparatus and to the cell’s
membrane.

In normal people, the MHC I cannot leave the ER without binding to a peptide but in
Bare lymphocyte syndrome, the TAP protein is non functional and the MHC I is left bare
and transported to the cell’s membrane. Less than 1% of the MHC I’s on human cells
present an antigen peptide so the person is plagued with respiratory infections from early
life. This is due to the fact that CD 8 cytotoxic T cells cannot recognize the infected cells.

When there isn’t an infection, normal human cells also present normal peptides. This
peptide presenting happens constantly and normally it doesn’t produce an immune
response.

For MHC II: {Mechanism}

The macrophages and neutrophils have the capability to phagocytose extracellular

material. They create vesicles called phagosomes which are made up of the plasma
membrane and extracellular material within it. As the vesicles move inwards through the
cell, proton pumps acidify by proton pumps. The vesicles then bind to a lysosome and
produce a phagolysosome. Within the phagolysosomes, enzymes process the material
into a peptide. MHC II complexes are then carried to the vesicle and it binds to the
antigen peptide. This MHC II complex is then carried to the cell’s membrane by outgoing
vesicles.

Mycobacteria like the ones that cause tuberculosis and leprosy. They are intracellular
pathogens that do not enter the cytosol so they are not presented in MHC I but instead
they grow within the vesicular system. However, they block the binding of the lysosome
to the phagosome and therefore they cannot be degraded into a peptide and presented in a
MHC II.

The MHC II molecule is formed in the ribosomes. It is translocated to the ER with the
help of an invariant chain. The invariant chain also blocks the MHC II binding site from
binding to peptides that are present in the ER. The invariant chain also helps the MHC II
bind to an endocytic vesicle. Here, the invariant chain is degraded by proteases like
cathepsin S which leaves only a small part of the invariant chain, called the CLIP, bound
to the antigen binding site of the MHC II complex. A glycoprotein, HLA-DM, then binds
to CLIP and aids in its removal. The MHC II then binds to a peptide within the vesicle
and is subsequently transported to the cell’s membrane.

A T cell receptor must be specific to both the MHC and the peptide it is presenting.

Almost all cells present MHC I molecules on their cell membranes, except for red blood
cells. Cells that express MHC II molecules on their cell membranes are professional
antigen presenting cells which include: dendritic cells, B cells, and macrophages. These
professional antigen presenting cells phagocytose extracellular antigens and present them
in a MHC II complex. Interferon gamma or IFN-y can induce the expression of MHC II
molecules on the cell membranes of cells that normally do not express this complex. This
allows CD4 T cells to recognize these infected cells.

The major histocompatibility complex loci as well as other antigen presenting molecule
loci’s are located on chromosome 6. MHC are important in transplant rejections.

Normal human MHC complexes are called HLA’s: Human leukocyte antigen complex.
Individual diversity in HLA’s are due to gene families(similar genes) and genetic
polymorphism(multiple differences of the same gene in a population). The different
possibilities of a gene are called alleles and the proteins that they make are called
allotypes. HLA’s are either highly polymorphic, oligomorphic, or monomorphic (number
of possible alleles). If you inherit different forms of the gene from each parent, it is
coined heterozygous. If you inherit the same forms of the gene from each parent, it is
termed homozygous.

There are 6 MHC I HLA’s:

HLA-A- polymorphic and present antigens to CD-8 T cells and give ligands for NK cell
binding

HLA-B- polymorphic and present antigens to CD-8 T cells and give ligands for NK cell
binding

HLA-C- polymorphic and present antigens to CD-8 T cells and give ligands for NK cell
binding

HLA-E- oligomorphic and forms ligand for NK cell

HLA-F- monomorphic and intracellular, function unknown

HLA-G- oligomorphic and forms ligand for NK cell

There are 5 MHC II HLA’s:

HLA-DM- regulates peptide loading for HLA DP, DQ ,and DR in the cell (in the ER)

HLA-DO- regulates peptide loading for HLA DP, DQ ,and DR in the cell

HLA-DP- highly polymorphic and present antigens to CD 4 cells

HLA-DQ- highly polymorphic and present antigens to CD 4 cell

HLA-DR- highly polymorphic and present antigens to CD 4 cells

The HLA genes have 3 components and are located on chromosome 6.

Chromosome 6:
Centromere-----(class III region)-----/-----(class II region)------/-----(class III region)-------

B-2 microglobulin gene of MHC I is located on chromosome 15. The invariant chain is
located on chromosome 5.

MHC II genes are clustered on the class II region of chromosome 6. There are A genes
that encode alpha chains and B genes that encode beta chains. So there is HLA-DMA and
HLA-DMB. When there is a functional and non-functional gene, then they are denoted
by numbers. For instance, HLA-DQA1 and HLA-DQA2. HLA-DQA1 is the functional
gene for the alpha chain of the HLA-DQ.

The particular combo of HLA alleles on chromosome 6 is known as a haplotype. These

alleles undergo meiotic recombination at 2% and therefore even though there aren’t many
different alleles, there are many different recombined haplotypes. Healthy individuals
who are HLA homozygous present 3 MHC I HLA’s (HLA-A, HLA-B, and HLA-C) and
3 MHC II HLA’s (HLA-DP,DQ,and DR). Heterzygous individuals can present up to 6
different MHC I HLA’s and 8 different MHC II HLA’s.

The class II region has the genes for all antigen processing molecules as well as TAP,
tapasin, and proteasome (LMP2 and LMP7).

IFN a, IFN B, and IFN y are cytokines that are produced at sites of inflammation. These
cytokines stimulate the increase in expression of HLA-1 heavy chains, B2-microglobulin,
TAP, and LMP 2 and LMP 7 of the proteasome.

LMP 2 and LMP 7 are only produced in infected cells and replace normal proteasome
produced in healthy cells.

The expression of all the HLA-2’s (except for HLA-DO) and the invariant chain are
stimulated by the cytokine IFN-y. These genes are turned on by MHC class II
transactivator (CIITA) which is stimulated by IFN-y.

MHC restriction means that for a T cell to bind, the specific MHC and specific peptide
must both be compatible to the specific T cell receptor.

It is better to be a heterozygote because you present a greater amount of peptides to the T

cells. This is a better immune response.

Sometimes MHC alleles are favored during infection, this is known as directional
selection.

There is interallelic conversion or segmental which means that recombination occurs for
HLA’s. It’s a point mutation where one part of one HLA is substituted into another HLA.
This occurs within the population as time passes.

Any T-cells that bind to autologous self HLA’s are destroyed. 10% of circulating T cells
may however bind to allogeneic isoforms of the MHC. These are coined alloreactive T
cells. When a transplant occurs, there is a possibility for an alloreaction where the
donor’s alloreactive T cells attack the graft cell’s allogeneic MHC’s.

HLA type is the combo of HLA alleles a person has. People with similar HLA types are
good for organ transfers. Immunosuppresant drugs are given to the organ recipient as
well.
Pregnant women produce alloantibodies because of the different HLA’s of the fetus. This
is not dangerous but if the mother receives a kidney, it results in an untreatable graft
rejection.

Chapter 5

T cells are first produced in the bone marrow and as immature T cells they migrate to the
thymus and these thymocytes are embedded in the thymus stroma. They undergo positive
and negative selection. The T cells that do not bind to MHC complexes of the person are
neglected and die and the ones that bind to strongly to MHC complexes are destroyed.

The thymus is composed of a medulla and outer cortex. The maturing thymocytes move
inward toward the medulla. Progenitor cells also proliferate into dendritic cells as well.
Macrophage are also scattered throughout the thymus. A person with DiGeorge’s
syndrome has no thymus, they have symptoms similar to SCID. The thymus degenerates
with age. This does not impair the T cell immunity because T cells are long lived and/or
self renewing. Progenitor cells enter the thymus’ outer cortex and once they are in contact
with the thymus stromal cells, they begin to proliferate. After about a week, they produce
a T cell specific adhesion molecule, CD2, but no CD4 or CD8. They are double negative
thymocytes at this point. As they mature, they produce CD 44 and CD 25, adhesion
molecules, CD 25 is a component for the IL-2 receptor binding site. CD44 degenerates
and the T cell loci begin to rearrange within time.

The T cell rearrangement is a competitive race. The B chain is rearranging and competing
with the delta and y chains. If the delta and y chains rearrange quicker, the T cell get a
delta:y chain TCR, but more often B chains rearrange first and what happens is that it is
paired with a pTa chain to form a pre T cell receptor and a signal is sent to the cell to
cease all rearrangements. Next the a chain competes with delta and y chains. If delta and
y chains rearrange first, the cell will exhibit that kind of receptor but more often, the a
chain rearranges first and the B:a chain is the TCR. The delta chain gene loci is located in
between the a gene loci on the chromosome 14, so the delta chain gets deleted once the a
chain is rearranged. 98% of thymocytes do not rearrange properly and undergo apoptosis.
Macrophages within the cortex phagocytose them.

The B chain of a TCR has VJD chains while the a chain has only VJ chains. B chains
rearrange first and once they are done, they are matched with a pTa alpha chain surrogate
and the a chain begins to rearrange. Once that is finished, the B:a chain complex is
packaged with CD3 proteins and a (squiggly) chain. These are the transmembrane parts.

If a B chain does not rearrange properly, it has 4 more tries(unlike the one try of the B
cell’s heavy chain). This gives the B chain a 80% success rate. Once successful B chain
rearrangement occurs, it induces the expression of 2 co-receptors, CD4 and CD8.

During proliferation after the B chain has successfully rearranged, the RAG 1 and 2
proteins are suppressed so that the B chains can produce many daughter cells where a
chains will then later be able to rearrange and express differences. a chains can rearrange
like Light chains so they have a high success rate. Even if one a chain gets expressed,
another a chain will still rearrange. The B chain will be paired up with 2 a chains, only
one will be used though.

delta:y chain TCR’s are not specific to the person’s MHC so they do not undergo any
type of positive or negative selection. a:B chain TCR’s however must undergo both.

Within the cortex of the thymus, MHC complexes are presented on the epithelial cells.
The mature T-cell receptors that bind to these MHC complexes within 3-4 days are sent a
signal to proliferate, the ones that cannot bind apoptose and are engulfed by
macrophages.

There are about 120,000 different types of MHC’s produced by a heterozygous person.

Bone marrow transplantation is a common treatment for people with lymphoma,

leukemia, SCID, and other inherited immunodeficiencies. The procedure is tha the host’s
bone marrow is destroyed with chemotherapy or other cytotoxic drugs and the host is
transplanted with a donor’s bone marrow. The T cells then go to the thymus and the ones
that are ok with positive selection proliferate. The antigen presenting cells are derived
from the bone marrow coming from the donor so the donor must have at least one HLA I
and HLA II allotype in common with the recipient

If a T cell binds to a MHC I at the epithelial cells of the cortex of the thymus, then it will
become a single positive thymocyte for CD8 protein. If the T cell binds to a MHC II, it
will become a CD4. People with bare lymphocyte syndromes can have that if there are no
MHC I or MHC II complexes at the epithelial cells. This would result in a person without
either CD8 or CD4 cells.

a chain rearrangement ceases once the positive selection is done.

Negative selection occurs in the thymus if a TCR binds to a dendritic cell or a

macrophage. This means it is too self reactive and it will undergo apoptosis and be
engulfed by a macrophage. This only happens in the thymus. If a T cell is too self
reactive in the periphery, it will bind to an anergic protein and become anergic and die
within time. Naïve T cells that have passed the selection circulate throughout the blood
and lymph. At a secondary lymphoid tissue, it can meet an antigen presenting cell in a
Paracortical area aka T zone. Here if it binds, it will activate and proliferate. It can
proliferate into CD8 T cells or CD4 TH1 or CD4 TH2 cells. The TH1 or TH2 is
determined by the nature of the infection. In normal healthy adults, CD4 helper T cells
out number the CD8 cytotoxic T cells by 2 to 1. People with AIDS have this ratio
reversed because the AIDS virus kills CD 4 T helper cells by exploiting the molecule as
its receptor.

As different types of MHC molecules go up in the thymus epithelial cells, there are more
types of positively selected T cells. But, for each new MHC molecule, there is more
negative selection within the thymus. This is a bad thing. There is a maximum of bout 12
MHC molecules expressed in a human so that there are not too many different kinds of T
cells positively selected.

T cell tumors usually occur at either the early or late stage of T cell development.

Chapter 6

Naïve T cells meet their antigens in secondary lymphoid tissues and that is where they
undergo proliferation. They can proliferate and differentiate into CD 8 cells, TH1, or TH2
cells. TH2 cells remain in the secondary lymphoid tissue while the other two types leave
to the site of infection. Dendritic cells and macrophage are antigen presenting cells.
Macrophages are stationary molecules that can only travel to the secondary lymphoid
tissue passively through blood flow while dendritic cells are far superior because they can
actively travel to 2nd lymphoid organs and present the antigen peptide to a Naïve T cell.
Macrophage have different functions as well like tissue repair and phagocytosis, dendritic
cells however are solely antigen presenting cells. They are both located everywhere in the
body,

For blood infections, T cells are activated at the spleen while for tissue infections, the T
cells are activated at 2nd lymphoid tissues. Response to respiratory infections is in the
tonsils or bronchial associated lymphoid tissue. Response to GI infection is in the Peyer’s
patches, appendix, or other gut associated lymphoid tissue.

Immature dendritic cells are in the tissues while activated dendritic cells are in the 2nd
lymphoid organs. They are different in shape and function. Immature ones are important
for capturing antigens but once they do, they lose this function and their dendrites stem
out so that they can communicate to T cells in the lymphoid tissues. They are only
located in T cell regions or para cortical regions within the lymphoid tissue but
macrophage are in both the cortex and medulla. Macrophage have a second function, they
engulf apoptosed cells that have not successfully passed the selections of adaptive
immunity.

Naïve T cells enter a lymph node through the afferent capillaries. Here, they pass through
an HEV (thin walled high endothelial venule) into the cortex of the lymph node. They
then bind to antigen presenting dendritic cells. If they do not find a match, they leave
through the efferent capillaries. If they do find a match, however, they stay in the
lymphoid tissue attached to the dendritic cell and proliferate and differentiate. This takes
several days and once they are finished, they leave through efferent capillaries.

T cells have adhesive molecules that are important for them to migrate to places and for
them to pass through the HEV.

Passing through HEV:

The T cell possesses L-selectin while the HEV cells have CD34 and GlyCAM-1. They
bind; Once that occurs, the LFA-1 molecule on the T cell binds to ICAM-1 and ICAM-2
of the HEV. There is a conformational change in LFA-1 that is triggered by the binding
of CCR7 of the T cell to CCL21 of the HEV. This reaction allows the T cell to squeeze
through the HEV and into the cortex. CCL21 is important in that its on dendritic cells and
stromal cells.

Once inside the cortex the T cell binds to an antigen presenting cell. The T cell’s LFA-1
binds to the dendritic cells ICAM-1 and ICAM-2 just like with the HEV. However,
dendritic cells also have LFA-1 which binds to the T cell’s ICAM-3. There is also a
binding between CD2 on the T cell and LFA-3 on the antigen presenting cell. Finally the
dendritic cell’s DC-SIGN binds to the T cell’s ICAM-3. When a signal is made that there
is a match, the ICAM’s tighten their hold and the antigen presenting and T cell remain
bound for days while the T cell proliferates and differentiates.

Co stimulatory molecules are however needed for the proper binding of antigen
presenting cells with T cells. The B 7 molecules on the APC(antigen presenting cell) bind
to the CD28 molecule on the T cell. At the same time the TCR binds to the MHC II
complex. Once the proliferation is done, CTLA4 replaces CD28 and binds 20 times
stronger to the B7 molecules. This inhibits proliferation.

Dendritic cells are more effective than macrophages which are more effective than B
cells in antigen presenting. Dendritic cells are found only in the paracortical areas(T cell
areas). Macrophages are found everywhere in the 2nd lymphoid organ and B cells are only
found in the lymphoid follicles.

The B7 molecules are only expressed on antigen presenting cells during infection.
Therefore, a T cell cannot recognize an APC during non infection.

Langerhans’ cells of the skin are immature dendritic cells. When they process an antigen,
they begin their migration to a 2nd lymphoid organ. There they become mature activated
APC’s and start to express B7 molecules and they also secrete CCL 18 which is a
cytokine that attracts T cells towards the APC.

Macrophages in 2nd lymphoid tissues have multiple functions. First they phagocytose
apoptosed cells. They also have innate immune functions in phagocytosing any foreign
material passing from the lymph. This cleans the lymph and makes sure that foreign
material do not enter the blood. Once, they meet a foreign antigen, they begin to express
B7 molecules and then they become APC’s.

Macrophages engulf antigens and break them down in their lysosomes and endosomes.
They then process peptides and present them via a MHC II complex on the cell surface to
Naive CD4 cells. However, some diseases such as Listeria monocytogenes will escape
the vesicles and infect the macrophage. This will then trigger an MHC I molecule to be
presented on the cell’s surface where a naïve CD8 cytotoxic cell will recognize it and
lyse the infected macrophage.
B cells also do not express B7 molecules pre infection. B cells bind to an antigen via its
cell membrane Ig’s. The B cell then endocytoses the antigen and processes it and presents
it via a MHC II complex. This is recognized by a CD4 cell. B cells are non migratory but
if they bind to an antigen within the lymphoid follicles, they might meet a specific CD4
cell to bind to.

Whole micro-organisms are usually better for vaccines than highly purified antiantigenic
macromolecules.

When a TCR binds to an MHCII/peptide complex, the CD3 proteins send signals via
ITAMs to the cytoplasmic tyrosine kinases.

TCR binds to the MHCII/peptide complex, the co-receptor, either CD4 or CD8, also
binds to the APC. On the cytoplasmic tails of the CD8 or CD4, there is an Lck protein
tyrosine kinase molecule which activates a cytoplasmic protein tyrosine kinase, ZAP-70.
The ZAP-70 is then triggered to bind to the transmembrane (squiggly) chain of the TCR
that is incorporated with the CD3 proteins. This is very important for signaling, without
ZAP-70, a proper signal could not be sent to the TCR to fully bind.

A human cell has about 10,000 to 100,000 MHC complexes on its surface. When the
proper co receptors are bound, about 100 MHC’s need to present the specific peptide to
the T cell. Without a proper coreceptor binding, the number of MHC’s that need to
present a specific peptide jumps to 10,000. This is almost impossible to achieve in vivo.

Once a TCR/coreceptor and CD28 bind to the APC, there is a signal to the cell to
stabilize mRNA. Additional transcription factors are also activated and this increases the
production of a cytokine named Interleukin-2 (IL-2). The T cell produces IL-2. The IL-2
is secreted and then binds to an IL-2 receptor which is on the T cell’s membrane. This is
vital for the T cell to proliferate. For immunosuppressant drugs such as cylcosporin,
rapamycin, and tacrolimus, they suppress the IL-2 production or binding to IL-2 receptor.
This prevents the proliferation of T daughter cells.

Human cells do not exhibit costimulatory B7 molecules. So when an autoreactive Naïve

T cell binds to a self MHC, it cannot fully bind its CD28. This makes the cell anergic
because it can never make IL-2 ever again. It will die in the future.

When a Naïve CD4 cell binds to an APC, it can either differentiate into a TH1 or TH2
cell. TH1 cells produce cytokines that are secreted to stimulate macrophage activation,
inflammatory responses, and the production of opsonizing antibodies that enhance the
phagocytosis of pathogens. TH2 cells however produce different cytokines that mainly
stimulate B cell differentiation and production of neutralizing antibodies. In a cell
mediated response, TH1 cells are biased while in a humoral mediated response, TH2 cells
are biased.

Cytokines from either TH1 or TH2 will suppress the proliferation of the other kind of TH
cell. In leprosy, where Mycobacterium leprae exploits the infected cell’s vesicular
system, if a cell mediated response is undertook with the proliferation of TH1 cells, the
person can battle the infection with macrophages and usually will survive, but in some
cases, a humoral mediated response will be undertook by the proliferation of TH2 cells.
Antibodies cannot penetrate the infected cells’ membrane and the infection will progress
fatally. (TH1)Tuberculoid leprosy vs. Lepromatous leprosy(TH2).

CD8 cells, because of their nature, are tougher to stimulate. They can only be stimulated
by a dendritic cell and even so, they need a strong binding to the co stimulatory receptors
which does not always happen. However, when a CD8 cytotoxic cell does bind it
produces a receptor for IL-2 and when it binds well enough, it begins to produce its own
IL-2. Sometimes, it will not bind well enough to the co stimulatory molecules, and CD4
cell that has bound to the same dendritic cell can enhance the dendritic cell’s
costimulatory receptors which will aid the CD8 cell to bind well. Also, the bound CD4
cell will produce IL-2 and secrete them. The CD-8 cell, if close enough to the CD4 cell
will have some of the CD4’s IL-2 bind to its IL-2 receptor which will help the CD-8 cell
proliferate. CD-8 cytotoxic cells can be dangerous to human tissue. For instance, in
respiratory tract, the CD8 cells will destroy endothelial cells but this will leave the
secondary layer exposed for secondary bacterial infection.

After the CD8 or CD4 cells proliferate into Effector cells, the CD8 and most TH1 cells
will leave the lymphoid tissue and enter the circulation while the TH2 cells will remain in
the lymphoid organ.

The Effector T cells do not need a B7-CD28 co-stimulatory binding for them to recognize
their targets. This is useful because not all cells present B7 molecules. Also, when a T
cell becomes an Effector cell, it expresses more adhesive molecules on its cell surface
such as LFA-1 and CD2. This is useful because not all cells have many ICAM-1 and
LFA-3 molecules. So, the higher expression of the LFA-1 and CD2 aid the T effector cell
to bind properly to its target. Also, when a T cell becomes an effector cell, it no longer
expresses L-selectin because it does not further need to enter an HEV into lymphoid
organs. Instead, the effector T cell expresses VLA-4 adhesion molecules. This VLA-4 is
important to bind to inflamed endothelial cells throughout the body.

T cells will “taste test” targets and the interaction will be short lived if the cell does not
possess the specific MHC complex and specific antigen peptide. However, once the
effector T cell does bind to a specific target, there is a conformational change in the LFA-
1 molecule which strengthens the T cell’s lock on the target cell.

Effector T cells have two molecules that carry out their effector functions: cytokines and
cytotoxins. All T cells produce cytokines but of different type while only cytotoxic cells
produce cytotoxins.

Cytokines are small secreted proteins or membrane bound proteins that either have
autocrine functions(changes genetic expression within the cell that produced the
cytokines) or paracrine functions( changes genetic expression within other nearby cells).

Membrane bound cytokine receptors possess a protein kinase on their cytoplasmic tails.
A common one is Janus kinase (JAK) which once the receptor is bound, the JAKs
dimerize and they phosphorylate a family of proteins called STATs. STATS then
dimerize and travel from the cytoplasm to the nucleus. At the nucleus, the STATS trigger
specific genes. Most times, for a signal to work, both membrane bound and secreted
cytokines have to work together so clinically it is tough to induce an artificial cytokine
signal. IL-3 and GM-CSF, however, have been clinically successful. These cytokines
signal for an increase in granulocyte and macrophage production in the Bone Marrow
(myelopoiesis).

In tuberculoid leprosy, which is the milder form because it is a cell mediated response,
the cytokines that are present are IL-2, IFN-y, and TFN-B. However in lepramatous
leprosy, which is a humoral mediated response, the cytokines present are IL-4, IL-5, and
IL-10.

CD-8 cells have lytic granules which contain potent cytotoxins. When a CD-8 cell binds
to a target, it releases its lytic granule on the infected cell’s membrane. The cytotoxins
begin to shrink the cell. As this is happening the CD-8 detaches from the dying cell and
produces more lytic granules. CD-8 cells also produce cytotoxins, one of which is IFN-y.
IFN-y inhibits the replication of virus proteins in the infected cells as well as inducing the
increased presentation of viral peptides in MHC I complexes. It also calls macrophages to
phagocytose dead cell remains.

Cytotoxins shrink the infected cell. This is called apoptosis, it prevents viruses from
escaping the cell as well as halting all cellular replication. Apoptosis is a programmed
cell death from within where the cell’s own nucleases destroy the cellular DNA. Viruses
within apoptosing cells also undergo this.

There are 2 mechanism for inducing apoptosis by CD-8 cells:

1. Perforins and granulysin make holes in the cell membrane of the infected cell.
This allows granzymes to enter which cleave certain cellular proteins. This
triggers nucleases and other cell enzymes to begin destroying the infected cell.
2. FAS ligand on the CD 8 cell binds to FAS on the infected cell and this causes
apoptosis. FAS ligand/ FAS is the main mechanism for inducing apoptosis on
unwanted and autoreactive lymphocytes. If a person is missing the FAS gene, the
person will then develop a condition called Autoimmune lymphoproliferative
syndrome (ALPS).

Macrophages phagocytose microbes and place them in phagosomes. They present the
antigen peptides via MHC II molecules to TH cells that are activated to become TH1
cells. The TH1 cells than cause macrophage activation. Macrophage activation helps
the macrophage fuse lysosomes with phagosomes that have antigens within them. It
also helps the macrophage to produce more lytic substances. With people who have
AIDS, CD4 cell populations drop significantly and antigens flourish within the
macrophage’s phagosome. Such are Pneumocystis carinii and several mycobacteria;
these can cause severe and even fatal diseases. Macrophage activation also causes the
increased expression of MHC II/peptide and B7 molecules which increase the
 macrophage’s antigen presenting abilities. This stimulates more CD4 cells which will
then recruit more macrophages. IFN-y + CD-40 ligand produced by the T cell as well
as TFN-a produced by the macrophage, together, help the activation of macrophages.
CD-8 cells can also produce IFN-y and therefore can also activate macrophages.

Cytokines secreted by TH2 are IL-4, IL-10, IL-13, and TGF-B. These activate B cells
but they also inhibit macrophage activation. Also, when a CD 4 cell loses contact
with a MPC II complex, the cell CD 4 cell will stop making IFN-y. This is another
way to check the macrophage response.

Some organisms thrive within the macrophage’s vesicle system. TH1’s that are
possible in producing macrophage activation are important here. They secrete IFN-y
and CD40 ligand to activate the macrophage to help it destroy the antigen. When the
macrophage is infected and loses the capability of becoming activated, the TH1 cell
can then secrete Fas ligand and TNF which will bind to the macrophage’s Fas ligand
and TNF receptors and cause the macrophage to undergo apoptosis. The bacteria will
get out during apoptosis but it will be re-engulfed by healthy macrophages.

The TH1 cell is important for orchestrating the entire cell mediated immune response.
First TH1’s will secrete IL-3 and GM-CSF to induce the production of macrophages
and neutrophils at the Bone marrow. Also, they will secrete IL-2 which will stimulate
T cell proliferation. They will also secrete TNF-a and lymphotoxin which will cause
endothelial cells to change their adhesion molecules so circulating T cells will bind to
the them. CCL2 will also be secreted which will guide the macrophages to the site of
infection.

When a bacteria resists the macrophage phagocytosis and infects the cells, T cells can
then cause a granuloma which is where the area of blood that has resistant bacteria is
surrounded by T cells. This cuts off oxygen and results in caseation necrosis.

TH2 cells will only stimulate specific B cells in paracortical areas of 2nd lymphoid
tissue. When the TH2 cell recognizes a specific match, it will produce CD40 ligand
which will bind to the B cell’s CD40 and stimulate the B cell. Also, the TH2 cell will
secrete IL-4, IL-5, and IL-6 which will all stimulate the B cells to proliferate and
differentiate.

There must be cognate recognition between the presenting B cell and T cell in order
for an antigen to be presented properly. For instance, in the case of Haemophilus
influenza virus, it is very dangerous in children and produces meningitis because
there is a lack of associated peptide epitopes that could engage TH2 cells. There is a
vaccine in which the immunizing antigen was the bacterial polysaccharide covalently
bound to tetanus toxoid which provides good peptide epitopes on the MHC II for TH2
cells to recognize.

Regulatory or suppressor CD4 T cells can suppress the action of other T cells.
They produce inhibitory molecules such as IL-4, IL-10, TGF-B, and CD25 which is the
a-chain of the IL-2 receptor molecule. Regulatory CD4 molecules can be useful in the
future in suppressing the host’s T cell response to transplanted organs.

Chapter 7

Antibodies are not destructive to pathogens. They just bind tightly to their targets. They
bind to the pathogen and this can lead to many things. First, they neutralize the pathogen
by binding to glycoproteins of the pathogen so that it can’t bind to human cells. Also, this
neutralization affects the pathogen’s ability to replicate. Also, when they bind to a
pathogen with their Fab receptor, they can bind to macrophages with their Fc receptor
and this causes opsonization. Opsonization is aided by a group of proteins that do not
distinguish between antigens. These are complements.

During a primary infection, B cells that are activated without T cell help give an early
defense. The problem is that these B cells haven’t undergone isotypic switching or
affinity maturation. They are primarily the IgM antibodies that the B cell has on its
surface from gene rearrangement. The effectiveness of antibodies does however increase
as the infection takes its course. T cell help to certain B Cells allows for affinity
maturation and isotypic switching which will make more potent antibodies. This however
takes about a week to happen. Also, Memory B cells and high affinity antibodies are the
products of an infection. This allows a reinfection to be fought off with a stronger
secondary response.

Cross-linking of the Ig with an antigen is the first step in the activation of the Naïve B
cell. The transmembrane proteins, Iga and Igb are responsible for communicating with
the cell. The ITAMS of the BCR become phosphorylated by BLK, Fyn, or Lyn and this
allows the Syk tyrosine kinase to bind to the tail of Igb. This results in intracellular
signaling pathways which lead to changes in gene expression within the nucleus. This
alone however, will not activate the B cell. There are additional signals that are needed.
For instance, there needs to be binding of the B cell co receptor. The B cell co receptor is
a complex of 3 proteins: CR2(CD21) which binds to complement components of the
antigen, CD19 which acts as a signaling chain of the receptor, and CD81, the function is
unknown. This B cell co receptor is generally not enough, often the B cell needs signals
from T cell helpers as well. Once the naïve B cell is activated, it proliferates into a larger
Plasma cell which secretes antibodies. The Naïve B cell is small and has a small
cytoplasm while the activated Plasma cell is much larger and has a big cytoplasm which
is full of rough ER which will produce the antibodies.

The fact of whether a B cell needs T cell help or not for activation is based on the
antigen. The antigens that induce activation without the help of TH cells are called
thymus independent antigens or TI antigens. The opposite are called thymus dependent
antigens or TD antigens. The first example is the TI-1 antigen group which are the Gram
negative bacteria which possess a Lipopolysaccharide (LPS) on their surface. This binds
to the B cell’s LPS binding protein and CD14. This will trigger the B cell to proliferate
into a Plasma cell and secrete only IgM antibodies.
The second TI antigen group is the TI-2 group is composed of protein or carbohydrate
epitopes that are present in high density on the microorganism’s surface. They cross link
the Ig and B cell co receptor so much that a need for T cell help is overridden. The typical
bacteria that have TI-2 antigens are those that express polysaccharides on their cell
surfaces. B-1 cells are typically activated and a response usually occurs about 48 hours
after the encounter. B-1 cell populations are fully matured after the age of 5, this is why
infants under that age are not good against polysaccharide antigens. Also, a TI-2 antigen
will not induce isotypic switching or somatic hypermutation. There is also no
development of memory for these types of infections.

TD antigens are brought to the lymph nodes by APC’s. This will cause a T cell in the
paracortical area to be activated. TH2 cells that are activated then encounter Naive B
cells that were roaming around. Through cognate interactions, the TH2 cell activates the
Naïve B cell.

The mechanism:

Ig binds to MHC II of the TH2 cell. CD40L of the TH2 cell binds to the CD40 of the B
cell. This causes the B cell to produce NFkB which causes the B cell to increase its
expression of I-CAM1 which strengthens the TH2 and B cell bond. The T cell then
produces a cytokine IL-4 which causes the B cell to proliferate. Some of the activated B
cells will move to the medullary cords of the lymph node and proliferation will occur
under the help of IL-5 and IL-6 which are produced by TH2 cells. They will primarily
produce a quick response and therefore they will mostly secrete IgM antibodies. Other
activated B lymphoblasts will stay attached to their TH2 cells and move to primary
follicles of the secondary lymphoid organ. Here they become centroblasts which will
undergo affinity maturation. This is now a germinal center of the lymphoid tissue and this
is where B cell division occurs and that is what causes the swelling of lymph nodes
during an infection. This swollen part is the dark zone of the lymph node. Non-dividing
centrocytes leave the dark zone and move to the light zones of the lymph node to interact
with follicular dendritic cells (FDCs). These FDCs are stromal cells of the primary
follicles. They bind to antigens but do not internalize them, instead they just hold on to
them. They don’t have any MHC sites either. The T cells that migrated along with the B
cells also proliferate at the light zone.

The centroblasts that migrated from the dark zones to the light zones are the ones that
undergo somatic hypermutation. They divide into non-dividing centrocytes which present
1 type of hypermutated Ig on its cell surface. This hypermutated Ig can either have more
or less affinity than before. The centrocytes compete with each other at the light zone by
going after a FDC with an antigen on its surface. The FDC has an immune complex on its
surface which consists of complements and antibodies of IgM or IgG. These help bind
the antigen on the FDC surface in what is called an iccosome. Once a centrocyte has
uptaken the iccosome and processed the antigen and presented it on MHC II, it must then
compete with other centrocytes to find a T helper cell within the light zone so it can bind
to the TH cell’s CD40L and TCR with its CD40 and MHC II. Once the centrocyte has
binded to a TH cell, the centrocyte then expresses Bcl-xL protein which inhibits its
apoptosis. This is useful because only the centrocytes possessing the Ig’s with the most
affinity for the antigen will go on to become Plasma cells or Memory B cells while all the
other centrocytes will undergo apoptosis. This process is called affinity maturation. The
TH cell that binds with the centrocyte will also go on to proliferate into a lineage of T
cells. All the centrocytes that undergo apoptosis will get engulfed by macrophages that
are then coined tingible body macrophages. As for any self reactive centrocytes that arise
from somatic hypermutation, they are rendered totally inactive once they show to be
autoreactive.

T cell interactions with activated B cells in the germinal center is important to cause
isotypic switching. Without it, a person could only produce IgM. The T cell secretes
cytokines IL-, IL-5, and IFN-y which are important to signal to the B cell to which
isotype it should switch to. Also, isotypic switching cannot occur without the CD40 of
the B cell binding to the CD40L of the T cell. There is a condition, hyper Ig-M
syndrome, where the person does not have this CD40-CD40L bond and therefore he only
has IgM in his blood. They cannot make any antibodies to thymus dependent antigens,
they have no germinal centers in their secondary lymphoid organs, and they have an
impaired cell mediated immunity as well. They are mostly males because the gene for
this condition is X-linked.

In any immune response, IgM is the first antibody to be produced. It is secreted as a

pentamer in the bone marrow, spleen, and medullary cords of the lymph nodes. It
circulates throughout the blood and the large size of IgM allows it to bind to antigens and
cause agglutination quite nicely but its large size also hinders its ability to leave the blood
and get to damaged tissues. Also, phagocytic cells like macrophages do not carry a Fc
receptor for IgM’s Fc, therefore IgM cannot be bound with these destructive cells to help
in destroying the antigen. However, IgM’s Fc receptors can bind to complements well.

Later in the infection, the smaller IgG is produced and it along with IgM prevent
septicemia. Monomeric IgA is produced and secreted in the lymph nodes or spleen.
Dimeric IgA on the other hand is produced and secreted in secondary lymphoid tissue in
the lamina propria, which is the connective tissue that underlies the basement membrane
of the mucosal membranes. The dimeric IgA is responsible for protecting our mucous
membranes which are in contact with the outside environment. The dimeric IgA is bound
by the cell’s of the mucosa at the poly-Ig receptor. In a movement called transcytosis, the
IgA is transported from the inside outer membrane to the outside outer membrane of the
cell. The poly-Ig receptor , once the IgA is on the outside outer surface of the cell, gets
cut by enzymes to leave only a little secretory piece attached to the IgA. The IgA is held
there along with mucus.

Newborn infants have a weak immune system and through the mother’s milk, dimeric
IgA is given to the baby. This helps in protecting the infant against any pathogens that
look to enter the patient’s body via mucosal membranes. The transported IgA also has
memory from the mother. This is a form of passive transfer of immunity.

IgG is transported from the bloodstream to the tissues via a Brambell receptor on
endothelial cells aka FcRB. Two FcRB’s bind to a Fc region of the IgG and they
transport it across to the tissues of the body. This protects tisses from infections. IgG is
the antibody that has the longest half life of all because it is not in the blood where
degradation pathways occur to degrade other antibodies and cells.

IgG is also given from mother to child when the fetus is still in the womb, this is because
IgG is the only antibody that can cross the placenta and it is done with FcRB aka
Brambell receptors. The infant is at its lowest antibody level from the age of 3 months to
the age of 12 months. This is because the IgG’s received during pregnancy are getting
catabolized and the infant has a weak immune system for the 1st yr of life. It only begins
to produce its own antibodies at the age of 6 months.

Some microbes infect and kill human cells by the use of secreted toxins. Examples are
diphtheria and tetanus. These toxins have a receptor for binding to human cells. The
vaccines for diphtheria and tetanus work on the principle of toxoids. These are
genetically engineered toxins in which the toxicity of the toxin has been removed but the
binding site is left intact. The body then produces antibodies against these toxoids and the
antibodies bind and neutralize the toxoids. This results in memory B cells being produced
and subsequent encounters with tetanus and diphtheria result in the body producing a
secondary response defense to wipe out the infection before damage can be done. The
neutralizing antibodies are highly specific IgG for body tissues and highly specific IgA
for mucosal membranes.

Venom is toxic in nature and no vaccine has been produced. Usually, the human immune
system is too slow to fight off a snake bite but the therapy that has been used is antivenon
which is a form of passive immunity. Highly specific antibodies against the certain
venom that were produced in animals are infused in the patient’s blood and they help
fight the venomous toxins.

An important part of antibody defense is its neutralizing ability. Viruses and bacteria
have receptors for binding to human cell surfaces. For instance, the human influenza
virus binds to human cell oligosaccharides via its influenza hemagglutinin protein. If
antibodies can bind to these receptors on the microbe, they can prevent the microbe from
binding to a human cell.

Antibodies that bind to antigens cannot destroy the antigen. Instead, a phagocytic effector
cell must come and bind to the Fc region of the bound antibody and destroy the antigen.
Neutrophils and Macrophages possess a Fcy receptor which binds to the Fc regions of
bound antibodies. For instance, IgG antibodies will bind to a virus and then a Neutrophil
or Macrophage will come and bind to the Fc regions of the antibodies and in turn it will
phagocytose the antibody covered antigen. The Fcy does not have a high affinity for
antibodies that are freely circulating, instead they only bind to antibodies that are attached
to an antigen. After phagocytosis, the phagosome will be fused with a lysosome in a
phagolysosome and the contents will be destroyed within the phagocytic cell. Some
microbes, like the bacteria Streptococcus pneumoniae, have a defense in which they
cannot be bound to macrophages so antibody coating is a must for the bacteria’s
destruction. Antibody coating helps macrophages and neutrophils bind more easily to
pathogens, this process is called opsonization. Also, some parasites that are too big for
opsonized engulfment are also attacked by macrophages but instead of engulfment, the
phagocytes release lytic material from their lysosomes onto the surface of the parasite.

IgE antibodies are scarce throughout the body. They are produced by isotypic switching
which is triggered by TH2 cells. IgE antibodies bind well to mast cells, basophils, and
eosinophils. They bind to a FceRI receptor on those cells. They even bind without a
presence of an antigen. A mast cell always carries IgE’s on its surface even in the
absence of an allergen or parasite. Mast cells are sentinel cells which are found in
connective tissues beneath mucosa’s and blood vessels, especially those in the dermis.
The cytoplasms of a resting mast cell has granules filled with histamine and other
molecules that contribute to inflammation, these are known as inflammatory mediators.
When 2 IgE’s bind to an antigen, it triggers either the mast cell, eosinophil, or basophil
that it is attached to, to secrete inflammatory mediators. Inflammation causes increased
permeability of the tissue so that cells from the bloodstream and can flow into the
inflamed tissue. This causes swelling, reddening, and pain but it is also beneficial for the
recruitment of cells to the site of infection.

Since IgE’s are already on mast cells, inflammation occurs very fast. It is usually in
response to parasites and since many parasites are very big, (like the biggest
Diphyllobothrium latum, which can reach 9 meters in length in the small intestine and
cause Vitamin B12 deficiency and megaloblastic anemia), IgE has developed a special
response to these organisms. Basically the inflammation in the respiratory and GI tracts
cause peristalsis which expels the parasite from either the anus or the mouth. The
increased bloodflow also helps to expel the parasite. Some parasites can even be attacked
by secreted lytic material from activated Eosinophils that are attached to IgE that are
bound to parasites like Schistoma mansoni, which causes schistosomiasis.

In developing countries, parasitic infections occur but allergic reactions are quite rare.
The opposite is true in the developed world; we have many allergies. This is an
inappropriate mast cell/IgE response to an allergen which isn’t very harmful regularly. If
the allergic response is very severe, it can lead to systemic anaphylaxis which can lead to
death in some cases.

NK cells are usually responsible for acting during innate immunity but they also have a
receptor for Fc regions called FcyRIII or CD16. These can bind to IGg1 and IGg3
antibodies and they can actually attack the antigen via antibody dependent cell mediated
cytotoxicity(aka ADCC).

There is the complement system which is a group of antigen binding proteins that is
produced and secreted from the liver. It consists of 5% of the serum globulin in the blood
and is circulating as an inactive zymogen. As the antigens are not bound covalently to
antibodies, antibodies can sometimes lose their attachment to antigens. Complement
proteins however covalently bind to the pathogen surface and mark it for destruction.
Neutrophils and macrophages recognize complements and attack the cell via
phagocytosis. The complement proteins can also attack on their own by poking holes in
the antigen’s cell surface.

There are 3 ways to activate the complement system:

1. The classical pathway of complement activation: (C1qrs,C4b,C2a,C3b) (C5-C9)

The classical pathway is triggered by the binding of antibodies to an antigen. The best
antibody for complement binding is IgM because it is a pentamer and complement
C1q of C1 needs at least 2 antibodies to be bound to before it can be activated. The
C1 complement has 3 components, C1q,r, and s. The C1q binds first to 2 antibodies
and causes the C1r and C1s to act as serine proteases with enzymatic activity. The
C1s activates the next 2 complement proteins, C4 and C2. The C4 is cleaved into a
C4b and C4a by C1s. The C4b is a thioester that binds covalently to the antigen and
the antibodies attached. The C2 is also cleaved by C1s into a C2a and C2b. The C2a
binds to the C4b molecule and together they form a classical C3 convertase (C4b2a)
which functions to cleave C3 and convert it into its active form. 1000 C3’s are
cleaved into C3b’s and C3a’s; the C3b is an active thioester. It binds to the antigen’s
cell surface and causes complement fixation. It is responsible for calling macrophages
and neutrophils to destroy the antigen and it can also cause the membrane attack
complex to pokes holes within the pathogen’s cell membrane. The C3b binds to the
classical C5 convertase which is consisted of C4b,C2a, and C3b is designated
(C4b2a3b). C5 is then cleaved by this C5 convertase and C5b initiates the formation
of the membrane attack complex. This occurs when C6 and C7 bind to C5b and
expose a hydrophobic part of C7 which inserts into the lipid bilayer. C8 also binds to
C5b and its hydrophobic part is exposed as well and bound to the membrane which
initiates the polymerization of C9. C9 is the component that forms the transmembrane
pores in the pathogen. A deficiency of C5-C9 can lead to a slight susceptibility to
Neisseria which causes gonnorhea and a form of bacterial meningitis. C3a, C4a, and
C5a all are anaphylatoxins. While their b counterparts bind to pathogens, the
anaphylatoxins are responsible in inducing inflammation in the tissues. They also
cause smooth muscle contraction in the tissue as well as acting as chemoattractants to
neutrophils and monocytes. C5a is the most potent anaphylatoxin.

(C4 deficiency is present in 30% of the human population; it is the most common
human immunodeficiency. Lacking C4a causes a susceptibility to systemic lupus
erythematosus while C4b causes a lowered resistance to infections)

2. Lectin pathway of complement activation: This occurs when MBL (mannose

binding lectin) is secreted by hepatocytes in response to IL-1, IL-6, and TNF-a
effects on the body. MBL binds to a mannose part of a carbohydrate on an antigen
surface. The MBL then acts exactly like C1q and initiates the cleavage of C2 and
C4. This leads to complement activation.
3. Alternative pathway of complement activation(probably the earliest activation
pathway evolutionarily): Spontaneous C3 hydrolysis occurs normally at low
levels but is increased during encounters with a pathogen. iC3 from the C3
hydrolysis binds to factor B in the blood and extracellular fluid which causes it to
 be susceptible to cleavage by factor D. iC3Bb is formed which is the alternate
soluble form of C3 convertase. This then cleaves C3 into C3a and C3b. When
C3b attaches to the pathogen’s surface and is bond to by factor B and cleaved by
factor D, it then results in the C3 convertase of the alternative pathway (C3bBb).
C3 convertase cleaves more and more C3 and fix more C3b on the pathogen’s
surface. This allows for opsonization through the CR1 on neutrophils and
macrophages. C3b’s can bind to an already existing C3bBb to form an alternate
C5 convertase (C3b2Bb). This activates C5 which subsequently activates C6-C9
(membrane attack complex) which causes the C9 to create

C3b can play the same role as C4b and it can bind to Bb and form an alternative C3
convertase. It is better at cleaving other C3’s than the classical C3 convertase.

There are 4 types of complement receptors present on immune cells which are
categorized in 2 groups, Group 1: CR1 and CR2 and Group2: CR3 and CR4.

CR1 is located on macrophages and neutrophils and binds to C3b or C4b. They
trigger the phagocyte to engulf the pathogen but this isn’t enough. There needs to
cytokine IFN-y produced by T cells or an Fcy of an antibody bound to the phagocyte.

CR2 aka CD21 is expressed on B cells and follicular dendritic cells. It is a co-receptor
that binds to iC3b, C3d, and C3dg. If this binds, then the bond between a B cell/FDC
with an antigen will be stronger. The Epstein Barr Virus utilizes the CR2 co-receptor
of B cells and infects them.

CR3 and CR4 are B-integrins which bind to iC3b on pathogen surfaces. They are
located on phagocytes and they help phagocytosis to occur. They also function to
attach to adhesion molecules of endothelial cells during inflammation.

Erythrocytes possess CR1 and they can bind to C3b or C4b that is on the pathogen’s
surface. This forms an immune complex on the RBC which then flows to the liver
and spleen where macrophages are and they engulf the immune complexes and leave
the RBC’s to continue circulating. Immune complexes can accumulate in certain
places, one such place is the renal podocytes of glomeruli of kidneys. Glomeruli have
special mesangial cells which are responsible for cleaning out the immune complexes
and repairing kidney tissue but if the deposits become too big, the kidneys can
become diseased and it can lead to kidney failure.

There are complement inhibitors that can inhibit the complement system action. The
first class consists of plasma proteins that disrupt complement enzyme functions. The
2nd class are on human cell surfaces and disrupt the fixation of complements on
human cells.

1. C1 Inhibitor aka C1INH inhibits activated C1r and C1s and therefore inhibits the
classical pathway of complement activation. A lack of C1INH is evident in the
condition, hereditary angioneutoric edema. This condition causes the patient to
 have abnormal amounts of edema in the skin, gut, and airways because of higher
levels of activated C1 in the blood. C2 kinin and bradykinin are the 2 peptides that
cause the edema. The production and stability of the classical C3 convertase is
controlled by a C4-binding protein (C4BP) which competes with C2a and binds to
C4b and renders it susceptible to inactivation by factor I. C3b is likewise
regulated by factor H. When people don’t have factor I, they allow C3 convertase
to be made unchecked and it depletes its amount and they have low levels of C3b
when needed during bacterial infection.
2. The decay accelerating factor (DAF) on cells binds to the C3b or C4b of C3
convertase and renders it inactive. Membrane co-factor protein (MCP) has the
same function but it induces factor I to cleave C4b and C3b and render them
inactive. CR1 on cells which sometimes induces opsonization by binding to C3b
and C4b can also act as a inhibitor by inducing factor I to cleave the 2. CDF aka
protectin is on human cell surfaces which prevent C9 recruitment at human cell
surfaces. DAF,MCP, and CD59 are all linked to cytoplasmic tail and if this is not
produced the patient will have paroxysmal nocturnal hemoglobinuria which is
characterized by episodes of complement mediated lysis of RBCs. Secreted S
protein, clusterin, and factor J all prevent the soluble complex of C5b, C6, and C7
to associate with human cell membranes.

Chapter 8

The immune system consists of 3 levels of defense: physical barrier, innate immunity,
and adaptive immunity.
Most of the pathogens are blocked by the physical barriers or are eliminated by the
innate immunity before any symptoms of disease begin. Also, good bacteria compete
with harmful bacteria, so they help us as well. Once all that fails, adaptive immunity
is called upon and usually at this stage symptoms of disease have already begun.

There are 4 types of pathogens: Bacteria, viruses, fungi, and parasites ( unicellular
protozoa or multicellular worms). Pathogens can either be extracellular or
intracellular. All pathogens however are extracellular at one point or another and can
be attacked by antibodies.

Different pathogens have different characteristics. Some produce symptoms while

some indirectly produce symptoms from the effects of our immune system. Also,
some pathogens like anthrax can be spread over long distances because of its ability
to live in many different types of environments. HIV however cannot be spread over
long distances because it is very sensitive to changes in the environment. For an
infection to occur, usually a large dose of the pathogen must enter the host and
overwhelm the innate immunity. If it does so, the antigens will be presented at
lymphoid tissues to the adaptive immunity. Infection can lead to recovery, death of
the host, or something in between like in the case of herpes.

The physical barrier also has chemical weapons that guard us against pathogens.
Tears and saliva have lyzozymes that degrade bacterial cell walls while hydrolytic
enzymes of the stomach lining create an unfriendly environment for bacteria growth.
All epithelial cells secrete antimicrobial peptides called defensins. a-defensins are
composed of neutrophil peptides and cryptdins made by Paneth cells of the small
intestine. The B-defensins are secreted by the epidermis, respiratory tract, and GI
tract. They work better under lesser ionic strength environments like sweat, tears, and
the lumen of the gut. The gut is also colonized by 500 different commensal species of
harmless bacteria that compete against harmful bacteria. For instance, E. coli in the
gut secretes colicins which prevent other bacteria to colonize the gut. When
antibiotics are taken, this good flora is killed and further infection can insue after
antibiotic treatment is ceased.

One of the first steps of innate immunity is the stimulation of the complement system.
During innate immunity, this stimulation is done by the alternative pathway of
complement activation.
Spontaneous C3 hydrolysis occurs normally at low levels but is increased during
encounters with a pathogen. iC3 from the C3 hydrolysis binds to factor B in the blood
and extracellular fluid which causes it to be susceptible to cleavage by factor D.
iC3Bb is formed which is the alternate soluble form of C3 convertase. This then
cleaves C3 into C3a and C3b. When C3b attaches to the pathogen’s surface and is
bond to by factor B and cleaved by factor D, it then results in the C3 convertase of the
alternative pathway (C3bBb). C3 convertase cleaves more and more C3 and fix more
C3b on the pathogen’s surface. This allows for opsonization through the CR1 on
neutrophils and macrophages. C3b’s can bind to an already existing C3bBb to form
an alternate C5 convertase (C3b2Bb). This activates C5 which subsequently activates
C6-C9 (membrane attack complex) which causes the C9 to create pores in the
pathogen’s cell wall. Properdin, CR1, DAF, factor H, and protein MCP all inhibit the
action of the alternate pathway of complement activation to attack human cells.

Some bacteria like Staphylococcus aureus and Streptococcus pyogens have a lot of
sialic acid on their membranes and therefore they mimic human cells. This causes
factor H to inactivate any complements on the surface of these bacteria. This trick by
these bacteria only works when antibodies are not coating their surfaces.

Besides complements, other plasma proteins inhibit the spread of infection. These are
usually induced during blood vessel damage. For instance, during vessel damage,
clotting occurs which platelets are vital for. During clotting, platelets release a
cascade of molecules from their cytoplasm such as prostaglandins, hydrolytic
enzymes, growth factors, and other factors that are responsible for antimicrobial
defense, wound healing, and inflammation. A second cascade system caused by
damage to the blood vessels is the kinin system which secretes the vasoactive
bradykinin which increases bloodflow.

Many pathogens produce proteases to damage human cells. Some even hijack the
cell’s proteases and use them against the host. Human serum and secretions contain
plasma proteins that inhibit the action of these proteases. 10% of the serum proteins
 are protease inhibitors. They generally work by binding irreversibly to the active site
of the protease that they are specific for. For instance, one is ab a2-macroglobulin
which binds to a protease and first neutralizes it, secondly it envelopes the protease
and together they are destroyed by hepatocytes, fibroblasts, and macrophages.

The first cell that a pathogen encounters in the tissues is the macrophage. These are
mature forms of the circulating monocyte which are long living in a tissue. Some
tissues that have macrophages are the GI connective tissue, respiratory tract lining,
the alveoli of the lungs, and the liver where they are know as Kupffer cells.

Macrophages can engulf pathogens without the help of certain cells. They do this
with the aid of their receptors that are specific for characteristic components of
pathogen surfaces. Such are for bacterial lipopolysaccharides(LPS receptor aka
CD14), lipophosphoglycan receptor, calcium dependent mannose receptor ( binds to
HIV), and more. They can engulf on their own but they engulf more efficiently with
the help of certain molecules. For instance, the C3b binds to the CR1 of the
macrophage and opsonization occurs. Another instance is when C3b is degraded by
factor I into iC3b; it then becomes a ligand for the CR3 and CR4 of the macrophages.
This is also opsonization.

Macrophages also have Toll-like receptors that cause the macrophage to secrete
cytokines. The TLR-4 is important because it binds to LPS that is on Gram negative
bacteria or secreted by them. When a phagocyte engulfs a Gram negative bacteria, it
will secrete its LPS. LPS can bind to TLR-4 directly or it can be brought to it by a
soluble LPS binding protein. TLR-4 dimer and MD-2 then form a complex with LPS
receptor aka CD14 and the LPS. This causes a signal to be sent to the cytoplasm of
the macrophage and induces the macrophage to secrete TNF-a. This is important
because a variant TNF-a is responsible for causing septic shock during sepsis with a
Gram negative bacteria.

There are a total of 10 TLR receptors each with a unique function. For instance,
TLR-3 senses double stranded RNA. All the TLR’s trigger a common pathway of
intracellular signaling which is shared with IL-1. This causes transcription of genes for
inflammatory cytokines. People that have impaired IL-1 receptor associated kinase
(IRAK) complex have an immunodeficiency which suffer from recurrent infections with
pyogenic bacteria and have generally poor inflammatory responses.

When a TLR senses a pathogen, the macrophage is then triggered to secrete a battery
of cytokines and other substances that recruit effector cells, prominently neutrophils,
which rush into the infected area. This causes inflammation which is caused by a
decrease in blood flow, an increase in vessel diameter, and an increase in permeability of
the blood vessel wall. This increases the blood outflow from the circulation into the
inflamed tissue and results in a reddened color. The inflow of cells causes the swelling
and pain.

Translocation of NFkB to the macrophage nucleus cause the transcription of various

genes. Such are IL-1, IL-6, CXCL8 (IL-8), IL-12, and TNF-a (tumor necrosis factor-a).
CXCL8 is a chemokine which is a chemoattractant cytokine which attract leukocytes
(neutrophils) to the site of infection. CXCL8 has 2 functions, it first binds to a target
leukocyte and changes the conformation of the leukocyte’s surface adhesive properties so
that the leukocyte can leave the blood and enter the infected tissue. The second function
is to guide the leukocytes to the site of infection. The IL-12 cytokine is an activator of
NK cells. IL-1 and TNF-a stimulate the entry of neutrophils as well as NK cells and other
effector molecules to the infected area by inducing changes in the properties of the
endothelial cells of the local blood vessels. C3a and C5a call upon mast cells to
degranulate and neutrophils to come. The degranulation causes a release of histamine and
helps inflammation. A whole bunch of inflammatory mediators are released at the site of
infection.

In response to TNF-a being made, the endothelial cells of vessels create platelet
activating factor which triggers blood clotting and blockage of vessels so pathogens
cannot go from the tissue to the bloodstream. However, if the microbes do enter the
bloodstream, this will result in LPS to be secreted by Gram negative bacteria and this will
induce a widespread release of TNF-a which will cause dilation of blood vessels and
massive leakage of cells from the bloodstream into the tissues. This can lead to septic
shock where the organs cannot receive enough blood. A symptom of septic shock is a
widespread clotting of capillaries called disseminated vascular coagulation.

Neutrophils, unlike macrophages, are short lived killers that are summoned to come to an
infection site. Neutrophils are a type of granulocyte. They are the most abundant white
blood cell in the human serum and account for 60% of the bone marrow’s cell
production. Neutrophils are normally not in healthy tissue but when there is an infection,
then they become the most common cell in the inflamed tissue. There inflow is the first
step of the inflammatory response and when they die within a few hours, they produce
pus. Pyogenic bacteria are those that cause pus formation.

During infection, inflammatory mediators cause endothelial cells to change their

adhesion molecules. This along with the effect on neutrophils where they are made to
express complementary adhesion molecules facilitates the migration of neutrophils from
the bloodstream to the infected tissue. Neutrophils have receptors for C5a and CXCL8.

Extravasation is the name for the process where neutrophils migrate from the
bloodstream to the tissue. It has 4 steps.

Step 1 is the interaction between leukocytes and blood vessel walls; this causes the
leukocytes to slow down. The interaction occurs between E-selectin/P-selectin of the
endothelial cells which are only expressed during infection and the neutrophil cell
membrane. E-selectin is only expressed a few hours after LPS and TNF-a are sensed by
the endothelial cells.

Step 2 depends on the interaction of LFA-1 and CR3 on the neutrophil and adhesion
molecules on the endothelial cells(ICAM-1 for example). CXCL8 exposure causes the
conformational changes in LFA-1 and CR3. LFA-1 binds tightly to ICAM-1

Step 3 involves diapedesis (neutrophils moving through blood vessel walls to reach the
tissues). This is facilitated by LFA-1 and CR-3.

The 4th and final step is the movement of the neutrophils toward the infected area. This
occurs because the neutrophils follow the source of CXCL8.

Neutrophils act similarly to macrophages in that they possess Fc receptors and receptors
for complement so that they can phagocytose through opsonization. The neutrophils
however have a short lifetime and can attack a wider variety of target cells than what the
macrophage can attack. Almost immediately after a target is engulfed by the neutrophil, a
phagolysosome is formed and in a series of reactions, highly toxic peroxynitrite is formed
to kill the antigen. The general oxidative attack on ingested microbes is accompanied by
a transient increase in O2 in the form of a respiratory burst.

The attack of neutrophils can kill Gram positive, Gram negative, and even some viral
microbes. However, neutrophils cannot replenish their granule weaponry so that they
undergo apoptosis after they attack something. They are engulfed by macrophages once
they are dead. A person with neutrophil deficiency has recurrent infections from the
unchecked normal flora of the body. The toxic lytic weaponry can also diffuse from the
neutrophil and it can be secreted onto a large microbe’s surface. This however can
damage human cells in some instances.

There is a systemic effect of inflammatory cytokines IL-1, IL-6, and TNF-a. This causes
the system to raise its temperature and cause fever. These endogenous pyrogens work on
the hypothalamus to cause it to raise the body’s temperature. Fever is beneficial to the
body because it increases blood flow as well as increasing the adaptive immunity’s
ability for antigen presenting. Viruses and bacteria also do not like a raise in body
temperature.

Another systemic effect of TNF-a, IL-1, and IL-6 causes the hepatocytes of the liver to
secrete soluble acute phase proteins in the acute phase response. 2 of these proteins are C-
reactive protein and mannose binding lectin. C-reactive protein for instance binds to
phosphorylcholine of LPS’s on bacterial cell walls and acts as an opsonin so that C1q can
bind better. This starts off the classical pathway of complement fixation in the absence of
antibodies. Mannose binding lectin (MBL) binds to mannose containing carbohydrates of
bacteria and yeast and is a calcium dependent lectin. MBL has 15-18 binding sites and
when it binds to an antigen, it acts just like C1q and it initiates the cleavage of C4 and
C2. This is the lectin pathway of complement activation. MBL can also act as a receptor
for monocytes which can engulf the pathogen without the help of the complement
system.

People with congenital deficiencies of MBL are susceptible to infection. For instance,
Neisseria meningitidits which is a commensal bacteria in 1% of the normal bacteria will
have a higher risk of going on to cause meningitis in people with MBL deficiencies.
When a cell is infected, it secretes a type I interferon and also expresses a receptor for it.
Since pretty much all cells can get infected, likewise pretty much all can produce type I
interferon. Humans have many different types of type I interferon but IFN-B and IFN-a
are most important. Their gene is on chromosome 9. Once a type I interferon is secreted
from an infected cell it can act paracrinely and autocrinely. When a cell binds to either
IFN-B or IFN-a, it undergoes a process called the interferon response. The major
functions of IFN-B and IFN-a are to induce resistance to viral replication in all cells, to
increase MHC I expression and antigen expression in all cells, and to activate NK cells to
come to infected areas and to kill unrecognized cells. Also, cells that have type I
interferon are better targeted by CD8 cytotoxic cells.

Type I interferon can be important in medicine for the resistance of infection. It can be
used to ameliorate the effects of leukemias, lymphomas, Hepatitis B, C, and Multiple
Sclerosis diseases.

Although most cells can produce and secrete Type I interferon, there are special
leukocytes that account for 1% of the blood’s cells in the serum. These are interferon
producing cells (IPC). They can secrete 1,000 times more interferon than a regular cell
and they do this in the T cell zones of the lymph nodes. The function of IPC’s is not fully
understood but they might be vital in making sure that Professional dendritic cells within
the T cell areas undergo full maturation.

NK cells are a third type of lymphocyte that has cytoplasmic granules and acts during
innate immunity. NK cells have 2 functions, to kill cells and to secrete cytokines. NK
cells are active normally but they increase activity when IFN-y, (IFN-a and IFN-b) type I
interferons, and IL-12 are secreted. The secretion of IL-12 by macrophage causes the NK
cell to release cytokines, primarily IFN-y which goes on to stimulate more macrophages.
This is a positive feedback loop. The macrophages then go on to activate T cells and once
T cells arrive, they secrete IL-10 which inhibits NK cells. When IFN-a and IFN-B are in
the blood, the NK cells are stimulated to produce cytotoxic materials for the killing of
infected cells.

People who have a deficiency with their NK cells have recurrent viral infections; one
good example is herpes.

When any tissue becomes infected, the endothelial cells express stress proteins, MIC-A
and MIC-B. NK cells are then attracted and attack via their NKG2D receptor which is in
a class of NK-cell lectin like receptor. This causes a reaction which causes cytotoxic
granules and cytokines to be released from the NK cell. NK cells also possess killer-cell
immunoglobulin like receptors (KIR). KIR bind to MHC I HLA’s of human cells (HLA-
A, HLA-B, and HLA-C). There are inhibitory KIR which protect human cells from
attacking human cells. NK cells also possess CD94:NKG2A receptors that are also
inhibitory and protect human cells in a similar fashion. There are also activating KIRs
which might aid in activating NK cells. NK cells also possess natural cytotoxicity
receptors which are responsible for mediating the killing of tumor cells.
Some viruses inhibit the infected cell from expressing MHC I complexes. If so, CD8 T
cells will have a lowered function but NK cells will be able to kill these infected cells.

KIRs are the most diverse receptor set in the human genome. They are extremely diverse
in humans and unrelated people usually don’t share KIRs. What is important is that an
NK cell possesses at least one inhibitory receptor for self HLA class I. This keeps NK
cells from attacking self cells but they will mount an attack on another human cell if it
does not possess the same HLA class I proteins.

There is a subpopulation of B and T cells that contribute to innate immunity. They don’t
need to undergo a lengthy period of clonal expansion and differentiation during the
infection. The B-1 lineage of B cells is one type. B-1 cells use a limited amount of V
regions to produce surface IgM which has a general affinity for polysaccharide antigens.
B-1 cells respond quickly to antigens and they are independent of T cell help. They
produce IgM antibodies within 48 hours of infection but there is no isotypic switching
now somatic hypermutation. B-1 cells are characteristically found in the peritoneal cavity
and do not rely on bone marrow for renewal.

y:& T cells are another example of circulating lymphocytes. A specific subclass is

Vy2V&2 T cells. These account for 4% of the T cells in human blood and these respond
quickly to infections by releasing inflammatory cytokines and killing cells. During
infection, these account for 60% of T cells in the blood. They have a specificity for the
stress protein MIC-A but there is a problem because NK cells also bind to MIC-A so
there is competition. y:& T cells can also bind to phosphates and alkylamines. These
ligands are produced during infection as a result of microbial metabolism and breakdown.
These ligands can also be produced during digestion and metabolism. y:& T cells act
more like antibodies than a:B T cells.

There’s a minority subpopulation of B:a T cells that act in innate immunity as well. They
are called NK T cells and they have a restricted TCR repertoire. They bind to lipid
antigens presented by CD1D and they are not restricted to just binding to MHC I
complexes. They undergo positive selection in the thymus where thymocytes present
CD1D. In the intestinal epithelium, CD1D is expressed during infection and it presents
lipid antigens to the NK T cells. NK T cells can also detect MHC I complexes but they
don’t possess CD8 co-receptor, only CD4 or none at all. There function of to release
cytokines like IL-4 and IFN-y to stimulate NK cells, dendritic cells, and macrophages.
They also have the machinery to kill infected cells. CD1D is a lipid presenter protein
which is in the class of CD1. Other CD1 molecules present lipids to CD4 and CD8 T
cells. These are present on monocytes and dendritic cells.
The inflamed environment during infection provides a premium environment for the
actions of the adaptive immunity. The innate immunity develops locally throught the
action of plasma proteins, stimulation of macrophages, recruitment of effector cells, and
inflammation establishment. When the innate immunity fails to destroy an infection,
cytokines, movement of antigens, and other inflammatory mediators facilitate a response
of adaptive immunity that comes from the secondary lymphoid organs. The TH2 cells
and plasma cells remain in the 2nd lymphoid tissue while TH1 and CD8 cytotoxic T cells
migrate to the site of infection.

Infections of the skin and connective tissues are drained to lymph nodes, blood infections
to the spleen, and mucosal infections are dealt with Peyer’s patches and other mucosal
lymphoid tissue.

The first step of producing the adaptive immunity response is the uptake and processing
of antigens by dendritic cells. They migrate to the lymph nodes and are attracted by
chemokines from the stromal cells of the lymph nodes. The dendritic cell matures along
the way to become an APC. Once in the lymph node, they pass through the HEV and
enter the T cell zones as do Naïve T cells which are attracted by CCL18 which is secreted
by APC dendritic cells. Once a Naïve T cell with enough specificity finds the
MHC:antigen peptide complex, it will be signaled to undergo activation (proliferation
and differentiation). The lymph nodes have macrophages as well which engulf most
antigens that pass through the lymph node. Lymph nodes are really good at filtering
lymph as well as catching antigen specific T cells.

In the mucosa of the small intestine, there are Peyer’s patches. On the surface are M cells
which specialize in binding to antigens and through transcytosis they move the antigen
into the Peyer’s patch. Inside, dendritic cells and macrophages are waiting to be activated
and naive T cells come to this T cell area and get activated.

There are 2 types of CD4 T cells: TH1 and TH2. TH1 promote an inflammatory response
with inflammatory effector cells while TH2 promotes the secretion of antibodies. The
decision to which CD4 T cell will turn out during antigen presenting is based on cytokine
environment present during the interaction between an APC and a naïve T cell. If there is
IL-12 and IFN-y, then TH1 cell differentiation is favored. When IL-4 is the dominant
cytokine, then TH2 differentiation is favored.

There is another factor that causes the naïve T cell differentiation to swing either way. If
the peptide that is presented via MHC complex is abundant then a TH1 cell response is
favored while, if the TCR bond to the peptides is not so strong, a TH2 response is
favored.

When one TH cell is favored, the other is usually suppressed. For instance, the secretion
of IL-10 by TH2 cells will inhibit the proliferation of TH1 cells. Likewise, the IFN-y
produced by TH1 cells will inhibit a TH2 response. Most responses involve both TH1
and TH2 however. CD8 cytotoxic cells can also secrete IL-10 and IFN-y and they can
suppress one TH cell and promote the other.
Naïve T cell activation and proliferation takes about 4-5 days. A crucial change in the T
cells surface makeup is this. The T cell loses its L-selectin which is important for
entrance through the HEV. The L-selectin is replaced by VLA-4 which binds to V-CAM1
adhesion molecules of the inflamed tissue.

The pathway of mucosal immune response is as follows: Naïve lymphocytes enter

submucosal lymphoid tissue like Peyer’s patches from the blood. The lymphocytes are
activated in the Peyer’s patches and return to the blood via mesenteric lymph nodes and
the thoracic duct. Then the activated lymphocytes circulate throughout the bloodstream
and enter submucosal lymphoid tissues all over the body.

Clones of antigen specific T cells are proliferated in T cell areas of lymph nodes. Some
become TH2 cells and they remain in the lymph node. Naïve B cells also come to the
lymph nodes where they can pick up an antigen and present a peptide on the MHC II
complex. The activated TH2 cell will respond to this by secreting cytokines which are
necessary for the B cell to undergo differentiation and proliferation. The B cells that are
activated can either become plasma cells and migrate to the medullary cord of the lymph
node or red pulp of the spleen where they secrete first wave antibodies or they can
migrate with their TH2 cell to a primary follicle where they create a germinal center.
They undergo rapid proliferation and somatic hypermutation here. 10% of these
hypermutated B cells will survive and become plasmablasts and migrate to other places.
The plasmablasts that originate in the Peyer’s patches and mesenteric lymph nodes will
start the pathway of mucosal immune response. The plasmablasts originating in the
spleen will migrate to the bone marrow and the plasmablasts originating peripheral lymph
nodes will migrate to the medullary cords.

There is a secondary response that the adaptive immunity can use during the second
encounter with a pathogen. Clones of long lived B and T cells + circulating antibodies are
responsible for this secondary response. The response is so quick and strong that
symptoms rarely begin. The pathogen is usually wiped out in time.

The long lived T and B cells as well as circulating antibodies can provide a defense
against reinfection but these effector cell die off if the pathogen is not encountered for a
while. In that case, our body has memory B and T cells that when confronted with the
same antigen will elicit a fast and strong response that will be sufficient to wipe out the
pathogen before too much damage can be done.

On secondary infection, IgG and IgA are the main antibodies produced. Also, 10-100
times more antigen specific B cells respond during secondary infection compared to the
primary infection. The secondary response also has a higher affinity for the pathogen and
the B cell have more MHC II molecules on their surface. Rarely does a secondary
response fail and memory can last for several years to life.

Since T cells do not undergo somatic hypermutation and isotypic switching, it is tougher
to spot memory T cells. However Naïve T cells predominantly express a CD45RA
isoform which is a tyrosine phosphatase. Memory T cells on the other hand express
CD45RO which sends stronger signals in response to antigen binding than its
counterpart.

CD8 memory T cells can be activated without the help of a CD4 T cell but its more
beneficial with T cell help. Memory T cells also have a shorter induction period than that
of Naïve T cells and there is no cell division involved. Half of all T cells are memory T
cells within the circulation.

Naïve T cells apoptose if they are not stimulated, they continue living by sampling HLA
molecules. This does not occur with memory T cells however. IL-2 inhibits the
proliferation of memory T cells while IL-15 causes proliferation. IL-15 is produced
during the interferon response.

When a secondary response is mounted, naïve lymphocytes are inhibited from being
activated. This rule is used in the prevention of hemolytic anemia of the newborn. When
a Rh- mother has a Rh+ child, the mother can produce antibodies against the child’s
blood and in subsequent pregnancies, the child can be killed by the mother. However, the
prevention occurs when doctors intervene and inject the mother with anti-Rh IgG
antibodies which will inhibit the mother’s immune response.

There is a phenomenon called original antigenic sin in which the body relies on its
memory to fight reinfections. So in the case of mutated strains of HIV, influenza, and
dengue fever, the body will produce an obsolete immune response to an antigen that has
slightly mutated. Influenza therefore can reinfect humans year after year.

Chapter 9

Antibodies are very important for the secondary response against reinfections.
Streptococcus pneumoniae evades the immune system’s memory ability because it has
many different strains, about 90 serotypes. A human cannot mount a secondary response
against a different serotype that it has never encountered before.

Influenza virus is attacked primarily by antibodies that bind to hemagglutinin and

meuraminidase glycoproteins of the viral envelope. The antibodies are made during
primary immune response and the virus is wiped out within a week or 2. Epidemics occur
when many people in the population get influenza. Because influenza virus is a RNA
virus with 8 RNA molecules and RNA is prone to point mutations, the influenza virus
undergoes mutations fairly frequently. This is why reinfection can occur. This type of
evolution causes antigenic drift which is a relatively mild and limited epidemic. This is
because the viruses are similar so the effects aren’t so drastic.

Antigenic drift isn’t so dangerous because we have partial immunity to these influenza
strains but every 10-15 yrs, antigenic shift occurs. This is when a part of the human
influenza virus is combined with RNA from an avian influenza virus. Since these viruses
are drastically different than the previous ones, many people get infected and this is a
pandemic. Many more people die from these pandemics and the new hybrid virus
replaces the old strains because it is competitively stronger against humans.

In parasites like the African trypanosomes, there is gene rearrangement for their variable
surface glycoproteins (VSGs). These trypanosomes are in insects and through bites are
transmitted to humans and they live in extracellular spaces. They cause sleeping sickness.
There are more than a 1000 genes that encode for the VSGs and only 1 VSG is present on
each trypanosome but there are always variants. For instance, one type of VSG will be
dominant in most of the population of trypanosomes but the immune response will only
clear those. The other variant types will survive and the cycle will repeat itself. Because
of the chronic cycle of antigen clearance, immune complexes and inflammation
accumulate throughout the body. Neurological damage occurs as a result and therefore
the person gets sleeping sickness. Other diseases that can use gene rearrangement of
surface antigens to evade complete clearance are malaria, Neisseria gonnorhea,
Salmonella typhimurium, and more.

Some viruses hide from the immune system. They enter a state of latency where they do
not replicate within a cell and they do not allow the cell to produce enough antigen
peptides for MHC I. They also do not cause disease at these instances. Such viruses are
the Herpes viruses. For instance in the Herpes simplex virus which causes cold sores,
they first infect epithelial cells and then get wiped out there but they remain dormant in
sensory neurons. When a trigger occurs, the Herpes virus then travels back down the
neuron and reinfects the epithelial cells. Immune responses by CD8 T cells and
antibodies causes a cold sore to again occur. This cycle repeats itself throughout life.
Neurons are a good place for dormancy because neuronal cells do not have much MHC
molecules to present antigens with.

Another type of Herpes is the Herpes zoster virus which remains dormant in a dorsal root
ganglion after chickenpox. During a time of immunosuppression or stress, the virus can
sneak out and reinfect the epithelia. This causes red blisters and extreme pain and is
called shingles. This usually doesn’t occur but if it does, maybe once in a lifetime.

A third type of Herpes is the Epstein Barr virus (EBV). Many children are exposed to this
and it produces a mild cold disease. Adolescents or adults who encounter this for the first
time, however, get mononucleoisis. The EBV infects B cells by binding to the CR2 of the
B cell receptor complex. EBV specific T cells are produced in response and CD8 T cells
after a while destroy the virus. The virus however remains dormant in some B cells and
all the viral proteins are shut off except EBNA-1. EBNA-1 cannot be broken down by
proteasomes so it cannot be presented in MHC I. Reactivation of mononucleosis is rare
unless the patient is immunosuppressed.

Mycobacterium tuberculosis gets phagocytosed by it commandeers the phagosome and

prevents the lysosome from binding. Tuberculosis flourishes within the vesicular system.
Listeria monocytogenes escapes the lysosome and lives in the cytosol but it get processed
in MHC I and CD8 T cells destroy the infected cells. Toxoplasma gondii, the cause of
toxoplasmosis, creates its own vesicle and no other vesicles can bind to it within the cell.
Treponema pallidum, the cause of syphilis, evades antibodies by coating itself with
human proteins.

Viruses are best at escaping the immune system’s grasps. They have several techniques:
preventing antigen peptide processing and presentation in MHC I, preventing
inflammation, capture of cellular genes that encode for cytokines which will divert the
immune response, and synthesis of proteins that inhibit complement fixation.
Some pathogens like staphylococci produce toxins like staphylococcal enterotoxins and
toxic shock syndrome toxin-1. These toxins bind to MHC II molecules without the need
of peptide breakdown within the cell. Therefore T cells are attracted and a response will
be made but against a false antigen. 2-20% of the T cell repertoire can be used against
these superantigens and huge amounts of IL-1, IL-2, and TNF-a will be produced which
will causes systemic shock in the patient.

Some infections induce a strong immune response that is actually detrimental to the
patient. As in the case of respiratory syncytial virus (RSV), which causes wheezy
bronchiolitis caused by TH2 cells. This causes 4500 infants to die in developed countries
each year. A vaccine only made things worse because upon reinfection, the immune
response was even stronger and even more detrimental. Another example of the immune
system causing harm is in the case of Schistoma mansoni, which is a parasite. These
blood flukes lay eggs in the hepatic portal veins and within the portal circulation, a strong
TH2 response is mounted against the eggs. This causes chronic inflammation, hepatic
fibrosis, and eventual liver failure.

Throughout the population, certain people have inherited immunodeficiencies. Most

domnant immunodeficiencies lead to death so most that survive are recessive
immunodeficiencies. Also in the case of X-linked immunodeficiencies, men are much
more susceptible because they carry an XY opposed to the female’s XX. A common
immunodeficiency is one where IFN-y is mutated and signaling to the cell does not
occur. People with this deficiency will be infected with tuberculosis even when the
innocuous strain is given via vaccine.

X-linked agammaglobulinemia (XLA) occurs when a person does not present the
correct signaling molecule, Bruton’s tyrosine kinase, BTK. This causes pre B cells to not
be able to proliferate. B cells are stuck in pre B cell stage and no germinal centers are
present anywhere. These people cannot produce antibodies. These people are susceptible
to extracellular bacteria which possess polysaccharide capsules. They are also prone to
enteroviruses. They get bronchioectasis which is a condition where the proteases of
pathogens and phagocytes cause inflammation in the bronchioles and the bronchioles lose
their elasticity. The treatment for this deficiency is passive immunity in the form of
monthly infections of gamma globulin.

X-linked Hyper IgM syndrome is a syndrome that is more often found in males where
no isotypic switching can occur so IgM is in high amounts. The person has a deficiency
in the T cell’s CD40L which normally binds to CD40 and induces isotypic switching.
Therefore these patients are susceptible to pyogenic bacteria and gamma globulin must be
given monthly to these patients. Germinal centers are not present because of no isotypic
switching. Another problem is that T cells cannot communicate properly with
macrophages via CD40L. Macrophages normally produce GM-CSF when their CD40
binds to normal CD40L which induces inflammation in localized areas. Without this,
patients cannot have inflammatory effects and they suffer from neutropenia which is low
levels of neutrophils within the blood. People experience sores and blisters in the mouth
and throat as a result. Doctors administrate GM-CSF via IV when needed.

Defects in complement system is an immunodeficiency. There are several; a person can

be missing the membrance attack complex C5-C9 which makes them susceptible to
Neisseria. Also, a person can have problems in activating C3 which causes susceptibility
to a wide range of diseases. Also, if a person has a deficiency with C1-C4 complements,
the person cannot produce C3b and C4b which are vital for binding to CR1 on RBC’s so
that the RBC can carry the immune complex to get destroyed in the spleen or liver. This
causes tissue damage because of deposition of immune complexes and the increased
phagocytes that clean up the immune complexes.

Any deficiency in the proteins that control complement activation will lead to an
unchecked amount of complement activation and depletion. In hereditary angioneurotic
edema, C1INH is missing and the inhibition of C1 cannot occur. There are high levels of
C2a which is a vasoactive fragment. This leads to tissue edema and epiglottal swelling
and suffocation.

Leukocyte adhesion deficiency is when mutations encoding CD18, the common B-

subunit for CR2, CR4, and LFA1 occurs. Innate phagocytes lack integrins that allow
them to have adhesion properties. They cannot exit the bloodstream and move to infected
sites. The patients have leukocytes that also cannot phagocytose pathogens covered with
opsonins and even though they have normal B and T cell response, these people suffer
from persisten infections from pyogenic bacteria.

In chronic granulomatous disease, the person has a defect in that the lysosomes of
phagocytes do not produce the superoxide radical O2-. This is because they have a defect
in one of the four proteins in the NADPH oxidase system. People with this disease suffer
from chronic infections with granulomas present in the blood. The therapy is IFN-y.

Chediak-Higashi syndrome is similar but the phagosome cannot bind to a lysosome for
some reason and the pathogen cannot be destroyed within phagocytes.

DiGeorge’s syndrome is where the thymus never develops. There is no to little T cell
function and a person is susceptible to many infections.

Patients who lack IFN-y and IL-12 have a problem in that they can get diseases from
otherwise harmless bacteria. Without IFN-y secreted by NK cells, CD4, and CD8 cells
will cause a lack of signaling for the killing of a pathogen. Also IL-12 is secreted by
infected NK cells which cause them to secrete IFN-y. Without this, problems ensue.
Somatic gene therapy is the therapy in which hematopoetic cells from bone marrow are
taken and the genes that are missing or defected are replaced. The new immunocompetent
cells are then reinfused into the patient. This technique is in its early stages.

HIV has 2 strains: HIV-1 which is more potent than HIV-2. HIV is an RNA virus which
produces a DNA intermediate via reverse transcriptase. The proviruses created then
hijack the cell’s machinery to make viral proteins and RNA genomes. HIV infects cells
that have CD4 surface protein which are TH cells, macrophages, and dendritic cells. The
gp41 of the HIV binds to the CD4 and the gp120 of the HIV must bind to a co-receptor,
in TH cells this is CXCR4.

Refer to slides for HIV info

Chapter 10

In developed countries, 10-40% of the population experiences allergic reactions which

are adaptive immunity responses against harmless allergens.

Type I hypersensitivity is usually through inhaled plant allergens. IgE’s which are
attached to mast cells bind to antigens and cause the mast cells to secrete granular
inflammatory mediators that cause allergic reactions like runny noses or breathing
difficulties.

IgE antibodies are to blame here. They are present in tissues and they have an Fc region
which has high affinity to FceRI receptors on mast cells, basophils, and eosinophils. This
binding occurs during the first exposure to the antigen and causes sensitization. On
subsequent encounters, the IgE will bind to the allergen and cause the mast cells to
degranulate. Mast cell activation is quick; there is no need for proliferation or high
specificity.

The IgE mediated activation of mast cells, eosinophils, and basophils is useful against
parasitic infections but the developed world lacks these and so people become
hypersensitive to allergens.

Mast cells are resident in mucosa and epithelial tissues. They are everywhere except the
retina and the CNS. They release inflammatory mediators like histamine, TNF-a, heparin,
and other similar molecules. Mast cells leave the bone marrow and go to tissues and and
settle near small blood vessels. Their CD117 interacts with stem cell factor and causes
maturation and formation of granules within the cytoplasm. There are 2 types of mast
cell: mucosal and connective tissue mast cells, the mucosal mast cells rely on T cells for
activation.

Histamine has 3 receptors that it can bind to, H1 on smooth muscle cells and endothelial
cells of vessels. This bond causes the vessels to increase permeability which causes
inflammation while it causes smooth muscle to constrict which can cause airway
constriction. It also causes the epithelial lining of mucosa to secrete more mucus.
TNF-a causes an increase in expression of adhesion molecules by endothelial cells.

Upon activation, mast cells produce more IL-4, leukotrienes, prostaglandins and TNF-a.
The leukotrienes have similar functions to histamine but they are more than a 100 times
more potent. Leukotrienes account for all the inflammation, mucus secretion, and
constriction in the later stages of allergic reaction.
PGD2 is an important prostaglandin that the mast cell secretes. It work to increase blood
vessel permeability which causes increased inflammation as well as being a
chemoattractant for neutrophils. Aspirin prevents the effect of PGD2 by binding to
prostaglandin synthase. The cells that are called upon through chemoattraction are
eosinophils, basophils, neutrophils, and TH2 cells.

Eosinophils are produced in bone marrow and they are usually in low numbers
throughout the body. The ones that are, are resident in connective tissues of the
respiratory, GI, and urogenital tracts. The eosinophils have granules which secrete highly
toxic molecules and inflammatory mediators that can damage both pathogen and host.
Eosinophils first release these toxic molecules and slowly later they produce and secrete
leukotrienes, prostaglandins, and cytokines that are vital for inflammation.

Normally the number of eosinophils is low in the blood but upon infection, TH2 cells
secrete IL-5 which induces the bone marrow to produce more eosinophils. Activated T
cells, endothelial cells, and monocytes produce a chemokine CCL11 which binds to the
eosinophil’s CCR3. This causes the eosinophils to approach infected areas.

Eosinophils also do not exhibit FCeRI normally. Only upon an inflammatory response do
they express this FCeRI for the binding of IgE. They then release granular materials.
Also, once activated, the eosinophils express more Fcy receptors and CR’s on their
surface so that IgG and complement bound to antigens can be engulfed.

Certain T cell lymphomas causes the T cell to produce huge amounts of IL-5 which will
cause the bone marrow to produce more eosinophils. This condition is hypereosinophilia
which can cause damage to the endocardium of the heart and neuropathy of the nerves.
Eosinophils are the culprits of airway damage from chronic asthma.

Basophils are granulocytes that have similarities to both mast cells and eosinophils. They
secrete inflammatory mediators and they are normally in low concentrations in normal
blood. There is a recripocal regulation between eosinophils and basophils, when one is
produced, the other is suppressed. The basophils also have FceRI for binding to IgE’s
with antigens.

Under conditions when there is low doses of antigen, plus IL-4 secreted during CD4 T
cell activation into TH2 cells, the isotype IgE is stimulated for production.

Most allergens are small soluble proteins that are dry airborne materials coming from
animals or plants. These allergens are inhaled and they are trapped by the mucus of the
mucosal membranes. The antigenic proteins are carried by APC’s and processed along
the way and presented on a MHC II complex. They are presented to CD4 T cells that will
become TH2 cells. This causes a response that has an increased production of IgE
antibodies along with binding of these IgE to mast cells. The cystein protease derived
from D. pteronyssimus causes more than 20% of the allergic reactions in the developed
world.
Atopy is the genetic predisposition to allergic reactions. Caucasians have a higher
incidence rate. The chromosomes that code for this atopy is on chromosome 5 and 11.

A mutated chromosome 11 would code the B subunit of FcERI incorrectly. The region on
chromosome 5 encodes for many cytokines. For instance, a mutated IL-4 would cause for
isotypic switching in the favor of IgE. This is seen in atopic people. Certain HLA II
allotypes also have a predisposition for atopy.

To test if a person is allergic to something, the doctor will inject a person into the skin
with a small quantity of the suspected allergen. If there is an allergy, the person will have
a sudden wheal and flare which is swelling and redness at the site of injection. This is due
to histamine released by degranulation of mast cells. This is an immediate reaction. A lat
phase reaction also occurs where the person, 6-8 hours after the immediate reaction
subsides, has a more widespread inflammatory response. This is due to leukotrienes,
chemokines, and cytokines produced by mast cells.

To test asthma, the doctor will measure a person’s breathing capacity with and without
the allergen inhaled. There is an immediate response and a late phase response 6 hours
later as well. The late response of asthma can be dangerous because of its higher potency.
Eosinophils and TH2 cells are recruited to the site.

Allergic reactions vary based on which tissue the allergen enters.

Systemic anaphylaxis is caused by allergens in the blood. Mast cell degranulation

throughout the bloodstream causes the smooth muscles to constrict and the blood vessels
to become more permeable. The diffusion of fluid from the blood to the tissues can cause
anaphylactic shock. Things that can cause such reactions are insect bites, peanuts, brazil
nuts, allergies to penicillin and related antibiotics. Anaphylaxis causes death by
suffocation because of the constriction of bronchioles and swelling of the epiglottis. The
treatment is an epinephrine shot which will cause the tight junctions between the
endothelial cells of vessels to close. Also it will cause the respiratory tract to dilate and
the heart to be stimulated.

Allergic rhinitis(runny nose and sneezing) is caused by inhaled allergens. The allergens
will cross the mucous membrane of the nasal passages and activate the mucosal mast
cells beneath the nasal epithelium. The degranulation will cause swelling of the nasal
cavity along with irritation and a mucus discharge rich in eosinophils. It can also go to
the throat and ears.

An allergic reaction within the eyes is allergic conjunctivitis It causes redness, tears, and
inflammation. Both allergic conjunctivitis and allergic rhinitis are short lived and usually
harmless.

Allergic asthma is more serious. Allergic reaction in the lower respiratory tract cause
chronic shortness of breath and trouble breathing. The degranulation of the submucosal
mast cells causes inflammation, constriction of bronchioles, and bronchial fluid and
mucus buildup. This causes air to get trapped within the lungs and it is tougher to breathe.
If not treated, some people can die from asthma. Even when there are no allergens
around, chronic asthma ensues. There could be mucus plugs in the bronchiole system.
Also a generalized hypersensitivity develops where cigarette smoke and sulfur dioxide
can cause trouble breathing. TH2 responses are damaging and if an infection occurs, the
TH2 cells can damage the tissues. Therefore chronic asthma is listed as a hypersensitivity
type IV.

When an allergic reaction is on the skin, urticaria develops which is the same reaction as
wheal and flares. When the allergen gets deeper to the subcutaneous tissue, angioedema
occurs which is a more diffuse swelling. Urticaria and angioedema can be caused by
ingested allergens carried to the skin or by insect bites. Some atopic children have a more
prolonged allergic response in the skin called eczema. It is unknown why though.

The broken down proteins from digested food can cause an allergic reaction. The allergen
will pass across the epithelial wall of the gut and bind to IgE on mucosal mast cells
associated to the GI tract. The mast cells will release histamine and the local blood
vessels will become more permeable and blood will enter the gut lumen. At the same
time, the stomach smooth muscle will have harsh contractions which will expel the
chyme either through the anus or through the oral cavity. The person will have a loss of
food, diarrhea, vomiting, and weakness. Urticaria and angioedema will also occur and
both GI and skin allergic reactions can occur from both ingested allergens and injected
allergens.

In the developing world, parasite infections are more common especially with helminth
worms. A stimulation of CD4 TH2 cells will cause IgE isotypic switching and a great
number of IgE antibodies as well as eosinophils and mast cells throughout the body. Of
the IgE’s produced, many are not antigen specific so there is much competition between
antigen specific and non antigen specific IgE’s. The parasite can then escape. Also, in
parasitic infections, T cell responses can be suppressed by IL-10, TGF-B, and nitric
oxide. These people however do not develop many allergies. People in the developed
world however do because their immune system has not had enough practice against
proper infections. This could be due to the hygiene theory of the modern world.

There are 3 strategies in to reduce the affects of allergic reactions. The first is prevention.
People stay away from allergens.
The 2nd is to prevent it pharmacologically. Antihistamine prevents histamine to bind to
HI receptors on endothelial cells. Corticosteroids suppress general leukocyte function and
are administered either topically or systemically depending on urgency. Cromolyn
sodium prevents the degranulation of activated mast cells and other granulocytes and is
inhaled by asthmatics as a prophylactic. Epinephrine is injected and is used to cure
anaphylaxis.
The 3rd strategy is immunological. A person can be desensitized by being given doses of
the allergen in slowly increasing amounts starting with very little at first. The person will
produce a TH2 cell response in all cases but IgG4 is a good antibody response while IgE
is not. These densensitizing shots must be carefully monitored.
A more recent approach is to make a vaccine with peptides from the allergen. The HLA
class II molecules present these to TH2 cells and anergy is induced in vivo. The
injections are safe but not all peptides can be presented by all human HLA II allotypes so
the injections must be specific. Vaccines can be custom made though.

Type II hypersensitivity is caused by occasional side effects from the administration of

certain drugs where hemolytic anemia occurs. Penicillin, quinidine, and methyldopa are
examples of drugs that can cause type II hypersensitivity reactions. In each case,
chemically reactive molecules bind to the surface components of RBC’s and or platelets
and create new epitopes to which the immune system is not tolerant to. The RBC’s are
attached to by C3b complements and this acts as an opsonin and macrophages engulf the
RBC’s and present them to CD 4 T cells. These then proliferate into TH2 cells which
stimulate naïve B cells which then produce antigen specific antibodies of IgM and IgG
isotype. The attachment of antibodies causes the classical pathway of complement
activation which causes the RBC to either be lysed by membrane attack complexes or to
be phagocytosed by macrophages at the level of the spleen.

Type III hypersensitivity is caused by the deposition of immune complexes. IgG readily
binds to antigen specific antigens and it can either be a huge immune complex of many
molecules or it can consist of only 1 antibody to 1 antigen. The big immune complexes
are good at binding to complement and they are easily taken up and removed by
macrophages. The smaller immune complexes however do not pick up complement as
easily and sometimes they get deposited in the blood vessel walls. There the immune
complexes can bind with the Fc receptors to circulating leukocytes and to C3a and C5a.
C5a in particular stimulates mast cells to release histamine which causes inflammation.
This causes an increase in platelets and other blood cells to the blood vessels. The
platelets accumulate around the immune complex depositions and they cause the blood
vessel to rupture which produce hemorrhaging in the skin. Antigens with few epitopes
can induce small immune complexes to form. Also, in the beginning of an immune
reaction, when there are fewer antibodies, the immune complexes are smaller and worse
at binding complement. 2 IgG antibodies are needed to crosslink a complement so later
when there are more antibodies, the immune complexes can form and become larger.

The Arthus reaction can be induced by giving a hypersensitive person, who has IgG
against the antigen, a subcutaneous shot of antigen. The IgG diffuses into the connective
tissue and forms immune complexes. Leukocytes and antibodies cause erythema and hard
swelling to occur. This lasts only for a day though.

Serum sickness can occur any time a person is injected with large amounts of foreign
protein. This can occur during injection of antivenom, penicillin(non-allergic),
streptokinase(against myocardial infarction), etc. 8-10 days after the injection, the body’s
immune system can begin to produce antibodies against the foreign protein. For instance,
with horse serum, the body produces antibodies which will bind to the foreign protein
and create many immune complexes with complement throughout the body. Small
immune complexes are then deposited in the tissues and leukocytes with Fc receptors or
complement receptors then bind to the immune complexes and cause damage to the
tissue. Serum sickness causes these symptoms: chills, fever, rash, arthritis, vasculitis, and
sometimes glomerulonephritis. Serum sickness usually passes with time though.

A similar thing can happen to serum sickness can occur when a long term infection
cannot be rid of by the body. Antigens keep being formed along with antibodies. Immune
complexes form and damage tissues like the skin and kidneys. Bacterial endocarditis and
chronic viral hepatitis can cause this.

Farmer’s lung is a condition in which a person is continually exposed to the same

pathogens and the immune response in the respiratory tract is IgG, instead of IgE and this
causes lung damage because the immune complexes get deposited in the alveoli. Farmers
exposed to mold spores and hay dust can get this condition.

Type IV hypersensitivity occurs when antigen specific effector T cells mount an attack 1-
3 days after the exposure of sensitizing antigen. The amount of antigen for these reactions
is 100-1000 times more than needed for the antibody mediated hypersensitivity reactions.
A good example of this is tuberclin test where a person is tested to see if he/she has been
infected with tuberculosis. Those are infected, have immunity, have been vaccinated, or
have resolved an infection will have an inflammatory reaction around the site of the
infection 24-72 hours after injection. The response is by TH1 cells that recognize
mycobacterium tuberculosis peptides presented by MHC II which will stimulate memory
T cells. The activated TH1 cells produce cytokines that will mediate the response. In UK
or Europe, BCG vaccine is given to children. A tuberculosis test is given to check for
previous exposure.

Poison ivy exposure generates type IV hypersensitivity reactions. Pentadecacatechol

penetrates the outer layers of skin and forms bonds to skin cell surface proteins.
Macrophages and Langerhans’ cells present the peptides with MHC II to TH1 cells. The
cytokines produced by the TH1 cells cause the stimulation of macrophages which causes
inflammation. Pentadecacatechol also gets presented by HLA I of normal cells and it
activates CD 8 T cells. The CD8 T cells then have the capability to kill any cells with the
peptide incorporated on its HLA I. The first interaction with poison ivy is a sensitizing
one. Later exposure causes dermatitis. This is contact sensitivity which is called so
because the skin is sensitive to the antigen. Metal with nickel in it can also cause such
reactions.

Chapter 11

Autoimmune diseases are those that cause the immune system to attack the host’s healthy
cells. 5% of the population of the developed world has at least 1 of these diseases. Self-
tolerance is normal but these diseases causes a person to break self tolerance. Such
chronic diseases cause inflammation in the human tissue with leukocytes and
lymphocytes infiltrating the region but without a foreign antigen to be fought.
There can be systemic autoimmunity where the entire body is attacked or it can be organ
or cell specific. This is because the human cells present autoantigens that are attacked by
autoantibodies and autoimmune T cells.

Autoimmunity mechanisms are of 3 classes. They correspond to type II(autoantibodies

targeted for human blood cell antigens), type III(deposition of immune complexes), and
type IV hypersensitivity reactions(effector T cells cause it).

Autoimmune hemolytic anemia is a condition where autoantibodies IgG and IgM are
targeted for components of the RBC cell surface. They activate complement system
classically and this either triggers the membrane attack complex to poke holes in the RBC
or for it to be targeted by phagocytes in the spleen.

White blood cells can also be targeted. Because nucleated cells are less susceptible to
complement mediated lysis, the white blood cells are usually targeted for engulfment by
phagocytes in the spleen. A person with lowered amounts of neutrophils has
neutropenia. Blood cells that are part of an immune complex can still function so a
treatment is splenectomy.

Autoantibodies that attack extracellular matrix is rare but it can occur. In the conditon,
Goodpasture’s syndrome, IgG are targeted to a3 chains of type IV collagen which is
found in the basement membranes throughout the body. In the kidney, the IgG attach to
these cells and it causes kidney dysfunction and eventual kidney failure. Treatment
involves plasma exchange to remove autoantibodies as well as immunosuppressive drugs
to prevent new ones from being produced.

Endocrine glands are prone to attacks by autoimmune lymphocytes. The function of

endocrine glands is to secrete hormones into the blood. These hormones have rare tissue
specific proteins that are not usually expressed in other tissues. Each autoimmune disease
is due to an impaired function of a single type of epithelial cell within an endocrine
gland. This can cause an autoimmune response. This is known as organ specific
autoimmune disease.

The thyroid gland regulates the basal metabolic rate of the body through the secretion of
2 hormones: Tri-iodothyronine and tetra-iodothyroxine (thyroxine). The production of
these 2 iodinated derivatives of amino acid tyrosine is produced elaborately. The
epithelial cells of the thyroid gland make a large glycoprotein called thyroglobulin which
is stored in the spherically arranged follicles of the thyroid cells. When increased cellular
metabolism is required, the pituitary gland secretes thyroid stimulating hormone aka
TSH. This induces the endocytosis of iodinated thyroglobulin and the release of thyroid
hormones by proteolytic degradation of the protein. As the blood levels of thyroid
hormones increase, they inhibit the secretion of TSH from the pituitary gland.

In Graves’ disease, autoantibody production is pronounced and the autoantibodies target

the TSH receptor of the thyroid cells. Because the autoantibodies act as a false ligand to
the TSH receptor, they cause a hyperthyroid condition where the thyroid gland keeps
pumping out thyroid hormones. There is little damage to the thyroid gland. The
symptoms are heat intolerance, weight loss, nervousness, irritability, warm moist skin,
bulging eyes, a stare, and enlargement of the thyroid gland. The autoimmune response in
Graves’ disease is TH2 biased. Treatment is to take drugs to inhibit thyroid function. This
is a short term fix; thyroid gland removal or destruction is necessary and the person is
given daily doses of thyroid hormones orally thereafter.

In Hashimoto’s disease aka chronic thyroiditis, there is a TH1 response and both
autoantibodies and autoimmune T cells are produced. The lymphocytes infiltrate and
attack the thyroid tissue. The damaged thyroid gland has germinal centers and looks like
a secondary lymphoid tissue. Patients have hypothyroidism where they lose all ability to
produce thyroid hormones. Treatment is to take daily thyroid hormones orally.

Pregnant women with autoimmune diseases like Graves’ disease will normally donate
their IgG antibodies to the fetus. This will however cause symptoms to be experienced in
the fetus. They will later go away but if they are too dangerous, intervention may be
necessary. Treatment involves total exchange of blood plasma to remove the
autoantibodies. Since lymphocytes cannot cross from mother to fetus, any T cell
mediated autoimmune disease cannot be transmitted from mother to child.

The diagnosis for Graves’ disease can be done on rat thyroid cells which are injected by
antibodies from the patient. The antibodies should cause the thyroid cells to produce cylic
AMP and DNA in disease cases. Also, in pig thyroid cells, doctors can diagnose whether
there is competition between normal TSH and autoantibodies.

T cells are also very specific to which MHC molecules they will bind to so diagnosis
cannot be made in other animals.

Insulin is produced and secreted by the B cells of the islets of Langerhans, which are
within the exocrine part of the pancreas. Insulin is made in response to heightened levels
of blood glucose like after a meal. Insulin binds to the surface receptors of the body’s
cells to induce the uptake of glucose and to incorporate it into fats and carbohydrates.

Insulin dependent diabetes mellitus aka type I diabetes is the condition in which
antibody and T cell response are made targeting the insulin, glutamic acid, and other
specialized proteins of the B cells. CD8 T cells that are specific for an unknown self
antigen of the B cells attack and destroy the B cells. This process is called insulitis where
the lymphocytes infiltrate the B cells. There are 10x8 B cells in the islets of Langerhans
and they have the capability to produce much more insulin than is usually needed.
However, gradual destruction of B cells will cause symptoms in childhood or adolescents
when the B cells cannot make enough insulin for the blood glucose levels. The usual
treatment is the injection of daily doses of purified animal insulin from pigs or cattle.
Some people, however, respond with type III hypersensitivity to animal proteins. They
produce antibodies against the animal insulin and this causes the deposition of immune
complexes, which causes further tissue damage. In such cases, recombinant human
insulin is used.

Systemic lupus erythematosus (SLE) is a disease where there is an autoimmune

response to an autoantigen that is present almost everywhere in the human body. This is
an example of a systemic autoimmune disease. Circulating IgG are specific to
components of healthy human cells. The binding to human cells causes inflammatory
reactions which causes tissue damage. With damage, this releases soluble autoantigens
which can form immune complexes. These immune complexes can be deposited in blood
vessels, kidneys, joints, and other tissues. This can cause more inflammatory responses
and tissue damage. The person has a chronic battle with periods of intense inflammation
and periods of calm non-inflammation. Many patients eventually die from damage to
vital organs such as the kidneys or brain. A characteristic butterfly rash is sometimes on
the person’s face. This is because of the deposited immune complexes in the skin of the
face.

SLE is a rheumatic disease. Over 90% of the patients have arthritis due to immune
complexes deposited in the joints which cause damage. Rheumatoid arthritis is the
most common rheumatic disease. It plagues mostly women and it involves chronic and
episodic inflammation of the joints due to autoantibodies of IgM, IgE, and IgA origin
being made against the Fc region of IgG antibodies. These autoantibodies specific for
immunoglobulins are called Rheumatoid factor.

In affected joints, T cells, B cells, lymphoblasts, plasma cells, neutrophils, and

macrophages infiltrate and cause damage. The plasma cells make rheumatoid factor.
Leukotrienes and prostaglandins are made by inflammatory cells and cause inflammation.
Neutrophils release lysosomal enzymes which cause tissue damage. CD4 T cells also
activate macrophages which enhance the damage to the tissue. Immune complexes also
occur and they cause further damage. Rheumatoid arthritis is treated with a combo of
physiotherapy and anti-inflammatory and immunosuppressive drugs. Treatment with
antibody against TNF-a can also help.

Multiple sclerosis is an autoimmune disease where the TH1 cells and the IFN-y they
produce causes an autoimmune response against the structural proteins of the myelin
sheath of neurons. Activated macrophages are present in sclerotic plaques and they
release proteases and cytokines which are responsible for the demyelination. Symptoms
arise in the early 20s to early 30s and can be variable in severity. They are motor
weakness, impaired vision, lack of coordination, and spasticity. Death can also occur if
the disease is severe. In 90% of the patients, plasma cells within the sclerotic plaques
secrete IgG into the CSF. Treatment is with regular subcutaneous injection of IFN-B1
which reduces in the incidence of attacks.

Myasthenia gravis is an autoimmune disease where the autoantibodies induce the

endocytosis and destruction of acetylcholine receptors on muscle cells. There is then
lower interactin between neurons and muscle cells. Symptoms are muscle weakness,
droopy eyelids, double vision, impaired ability to breathe from weakened respiratory
muscles, and weakened facial muscles. One treatment is pyridostigmine which inhibits
the action of cholinesterase. This allows more acetylcholine to compete with
autoantibodies for acetycholine receptors on the muscle cells. Another treatment is
immunosuppressive drugs azathioprine.

The autoantibodies in Myasthenia Gravis prevent the function of the acetylcholine

receptor so they are called antagonists. The autoantibodies in Graves’ disease have the
exact opposite effect are called agonists. In diabetes mellitus, either antagonists or
agonists can be made. Antagonists cause B cells to be destroyed and therefore there is a
lack of insulin and hyperglycemia. Agonists cause too much insulin to be made, which
causes hypoglycemia. The person then feels light headed from a lack of glucose to the
brain.

The lymphocytes have a greater chance at being autoimmune than do the leukocytes.
Therefore, there are better mechanisms to prevent autoimmune lymphocytes from
developing. During development, many self reactive clones are deleted. Of the self
reactive antigens that do enter the peripheral blood system, some become anergic, some
remain physically separated from autoantigens they could attack, and others are
suppressed by regulatory T cells. T cells need co-stimulation which is dependent on
infections so autoimmune T cells have a tough time being activated.

In the bone marrow, the B cells that are autoreactive for proteins within the bone marrow
and plasma are deleted but other self reactive B cells can survive that are specific for
other self proteins not present in the bone marrow or plasma. An autoreactive B cell may
become activated and it will migrate to T cell areas of the lymphoid tissues but because
of T cell tolerance, there will not be a T cell that has been activated as well. The B cell
will be neglected and not activated and will eventually undergo apoptosis. Soluble
autoantigens in the circulation will bind to other self reactive B cells and cause them to
become anergic. When B cells undergo somatic hypermutation in the germinal centers,
some become self reactive but are signaled to undergo apoptosis.

Within the thymus, during T cell development, negative selection causes T cells that are
self reactive to MHC molecules of thymic cells to be removed. AIRE (autoimmune
regulator) is a gene that encodes peptides derived from many systemic cells within the
MHC molecules of the thymic cells. Therefore, the thymic cells have MHC molecules
that are a sample of the entire body. Any binding to these will cause a T cell to die. If
there is a defect in AIRE then there is an incomplete negative selection in the thymus and
self reactive T cells can survive. This causes B cell and T cell response to develop against
many peripheral tissues and endocrine glands. This condition is called autoimmune
polyglandular disease. There is a wide range of symptoms.

Even when negative selection is working correctly, some self reactive T cells will enter
the bloodstream. They will bind to MHC complexes of human cells but without infection,
these cells will not present B7 co stimulatory molecules, which need to bind to the T
cell’s CD28. Therefore, the T cell will become anergic. During T cell activation, B7 co-
stimulators are kept in check by soluble and membrane bound CTLA-4 molecules, which
compete with CD28 for B7 binding. The allele for the production of less CTLA-4 causes
an increase in susceptibility to Graves’, Hashimoto’s, and insulin dependent diabetes
diseases. The allele for the production of more CTLA-4 is beneficial in preventing these
organ specific autoimmune diseases.

There are regulatory CD4 T cells which express CD25. They respond to self-antigens
presented by MHC II and then are activated to bind to other autoimmune Naïve T cells
that are specific to the same auto-antigen. These regulatory T cells constitute 1-3% of the
CD4 T cell population. They secrete IL-10, IL-4, and TGF-B which are non-
inflammatory cytokines. The Tr cells also do not express CD28 for binding to B7, instead
they possess CTLA-4 which is vital for their co-stimulation. Tr cells possess a
transcriptional repressor FoxP3 which is specified on chromosome X and no other cell
carries it. A defect in the expression of FoxP3 causes autoimmune diseases to occur
which usually causes death.

The most important genetic factor contributing to susceptibility to autoimmune diseases

is HLA. 50% of sibling pairs will share one HLA haplotype, 25% will share 2, and 25%
will not share any. More autoimmune diseases are associated with HLA II genes than
HLA I genes but one of the strongest is HLA B27 which is strong in association with
ankylosing spondylitis. Linkage disequilibrium is the phenomenon where a specific
combination of HLA’s shows strong correlation to a greater susceptibility to autoimmune
diseases. One of which is the 8.1 haplotype which is characteristic in Caucasians close
living near the North Pole. These associations of HLA and autoimmune diseases are not
written in stone. Most people with a disease associated haplotype will live normal lives.

Autoimmune diseases are more often correlated with HLA II because HLA II presents
peptides to CD4 T cells while HLA I presents to CD8 T cells. The CD4 T cells are more
numerous and cause a immune response and this explains why HLA II is more linked to
autoimmune diseases.

Environmental factors also contribute to autoimmune diseases. For instance, in

Goodpasture’s syndrome, where autoantibodies are made against type IV collagen, only
people who smoke are prone to have autoantibody adhesion in respiratory tract, which
causes pulmonary hemorrhaging. Normally the basement membranes of the respiratory
tract is not accessible but smoking damages the tissue integrity and allows autoanitbodies
to infiltrate.

Since, the anterior chamber of the eye is usually unattainable, when an eye is severely
injured and ruptured, the eye proteins will drain to a lymph node and cause an
immunological response. This can cause blindness in both the healthy and damaged eye.
This is called sympathetic ophthalmia. The damaged eye must be removed quickly and
immunosuppressive treatments must be given.

There is usually oral tolerance in the gut to harmless food proteins and commensal
bacteria so that an unwarranted immune response does not occur. Gut infections usually
cause IgA and TH2 responses. When oral tolerance is broken, diseases can ensue,
In Celiac disease, there is a immune response to gluten proteins of wheat in the gut. CD4
T cells will recognize gluten protein peptides presented by MHC and this will cause
macrophage activation which will cause inflammation in the small intestine. IgG and IgA
stimulation will also occur. Symptoms are diarrhea, anemia, depression, atrophy of
intestinal villi, nutrient malabsorption, and being prone to other diseases. A gluten free
diet is the only treatment. Celiac disease can be labeled as both T cell mediated
autoimmunity and type IV hypersensitivity reaction.

Autoimmune diseases can be the byproduct to a specific response to an infection.

Rheumatic fever is a good example. This is inflammation of heart, kidneys, and joints 2-
3 weeks after a throat infection with Streptococcus pyogenes. The reason for this is
molecular mimicry. They response to S. pyogenes is the production of antibodies that are
specific for cell wall components of the bacteria. These antibodies however also by
chance recognize the self antigens presented on cells at the kidneys, heart, and joints.
Heart failure can ensue. Since T cells are not activated by the autoantibodies, T cell help
never develops and rheumatic fever is transient. T cell activation, therefore, is necessary
for chronic autoimmunity. T cell activation only occurs in the presence of inflammation.

Chlamydia is tied to Reiter’s syndrome and HLA-B27. Salmonella is tied to reactive

arthritis and HLA-B27, etc.

There are 2 mechanisms for the breakdown in T cell tolerance caused by infection.
1. (Non-specific) Anergic or suppressed self reactive T cells within the circulation
can be activated when inflammation occurs from infection.
2. (Specific) There is a cross reactivity by activated T cells. They recognize both
pathogen antigen and human antigen. This is the principle of molecular mimicry.

Another factor is that during inflammation, human cells are stimulated by cytokines
like IFN-y to express more MHC molecules. (MHC II in the case of IFN-y). This can
cause an increased chance in self-reactivity. Co-stimulation is always needed though.
Also, in the course of an infection, dendritic cells are able to present tissue specific
self antigens from dead, apoptotic, and infected cells. They can present this to CD4 T
cells and cause a chronic autoimmune response.

Cryptic epitopes are the self peptides usually not presented in MHC molecules at
sufficient levels. Upon infection, they become expressed and autoimmune responses
can occur.

Intramolecular epitope spreading is the phenomenon where pre-infection, the

autoantibodies are specific for one part of a molecule and but during infection they
change their specific epitope to another part of the molecule. This occurs in
Pemphigus vulgaris and pemphigus foliaceus. This causes blistering of the skin.

Intermolecular epitope spreading is the phenomenon where B cells that bind to one
component of a nucleoprotein particle endocytose the entire particle, and process
peptides from all the parts of the particle’s protein. T cells that are specific for one
peptide derived from the particle can provide help to many different B cells that are
specific for different parts of the nucleoprotein particle. Therefore T cells can activate
B cells that make peptide epitopes from nucleic acids, macromolecules, etc. that the T
cell would not be able to recognize on its own.

In virally infected cells, as in the case of HIV, the virus sometimes causes the cell to
present more self-peptides than viral peptides. This causes the presentation of cryptic
epitopes which can cause autoimmunity.

Apoptotic cells that have been destroyed by NK cells and cytotoxic T cells present
different peptides than when living. This can cause an autoimmune reaction.

Once an infection is over, the autoimmune T cells that have responded to cryptic
epitopes can continue the autoimmune disease.

When the thymus is no longer functional at the age of 60, the T cells become different
in that they are less susceptible to apoptosis. They lack presentation of CD28 and
begin to express KIR which is usually associated with NK cells. Rheumatoid arthritis
occurs in the ages when the thymus is non functional. Patients lack a diversity in
antigen receptors. Also, in their blood and affected joints, they have large expanded
clones of CD4 T cells that lack CD28 and express NK cell receptors, notably
KIR2DS2. They do not need co-stimulation and do not become anergic. Instead they
can be activated by KIR2DS2 and they can produce large amounts of IFN-y.

The incidence of autoimmunity is higher in the developed world. The explanation can
also be attributed to the hygiene theory just like the explanation for the rise in
hypersensitivity reactions.

Chapter 12

The first true viral vaccination was by using cowpox to induce memory for smallpox.
Cowpox and smallpox are similar enough that people can be immune to smallpox
after being exposed to cowpox. These types of vaccinations are rare because a
harmless similar pathogen cannot usually be found.

Another type of viral vaccine is the killed or inactivated virus vaccines. The pathogen
is either destroyed or weakened by formalin or heat or irradiation and this is
introduced into the human body. The body produces memory against the pathogen
and subsequent encounters will have a secondary immune response occur. Examples
are influenza, rabies, and Salk polio vaccines.

Another type of viral vaccine is the live attenuated virus vaccine. This is where a
harmless mutated strain of a virus is introduced and it proliferates throughout the
body but it cannot harm the humans. It is usually produced by growing viruses in
nonhuman hosts. This can also occur naturally because viruses naturally mutate.
Examples are measles, mumps, Sabin polio, and yellow fever vaccines. These are
usually more effective because the virus is alive.

Another type is subunit vaccination. This is where just an antigenic viral component
is presented to the body which the antibodies will recognize. Hepatitis B vaccine is an
example and 80% of people become immunized. The other 20% may have a defect in
their HLA II allotypes.

Bacterial vaccinations

In the case of BCG, a mutated cow strain of mycobacterium tuberculosis is used to

produce immunity. This is an example of a live attenuated bacterial vaccine. Such
types are rare and the USA doesn’t even use BCG.

A second type of bacterial vaccine is the toxoid vaccine. Some bacteria like
diphtheria and tetanus secrete toxins that damage the human tissue. The toxoid
vaccinations work by taking purified toxins and treating them with formalin so that
they lose their harmful toxic nature. However, even though not toxic, it can still be
recognized by our cells. DTP is a toxoid vaccination against diphtheria and tetanus
with whole pertussis bacteria added. The pertussis bacteria causes inflammation at the
site of infection so that the immune response is enhanced against diphtheria and
tetanus.

There are also vaccinations in which encapsulated bacteria are targeted. For instance,
the polysaccharides of the encapsulations are used as antigens. This causes memory
of B cells. Normally encapsulated bacteria cannot be directly bound by complements
of alternate pathway but complements can bind after antibody fixation. This is the
reason for the vaccination. Children do not respond well to these kind of vaccines
because they do not have a good T independent response developed before 18 months
of life. Therefore a conjugate vaccine is used where the polysaccharide is bound to
something like a toxoid which will allow it to be presented to T cell’s. One example
is against H. influenzae.

When a vaccine is given, for a proper immune response to occur, there needs to be
inflammation. Many vaccines do not cause this so adjuvants are added to the mix.
These are molecules that will cause the body to undergo inflammation. Most
adjuvants can be dangerous and few are ok’ed to be used in humans. Freund’s
complete adjuvant is a good experimental one. Alum is legal as is MF59. The B.
pertussis of DTP vaccine also has adjuvant function. ISCOMS can be promising
adjuvants of the future which are immune stimulatory complexes that are lipid
carriers with minimal toxicity. They are loaded with peptides on the cell surface.

Most vaccinations are given by injection or scarification. In the future, techniques are
being tried to make oral vaccines. These are better. Polio has an orally administered
vaccine.

Some live-attenuated virus vaccines can be dangerous. Since, the harmless mutated
pathogen is alive, it is best for producing a proper immune response with memory.
However, the pathogen can become harmful and this is the case in Sabin polio
vaccine. 3 in 1,000,000 are infected with polio after vaccination. There are 3 strains
of attenuated polio used, strain 3 causes the infections usually. The difference
between harmful polio and harmless strain 3 is 10 nucleotide substitutions and this
can revert sometimes. In strain 1, there are 57 substitutions and it is rarer for a
harmful virus to occur. A strategy is to inject the person first with a killed polio
vaccine which will induce some immunity and then give the attenuated vaccine.
Some countries do not use the attenuated vaccine at all like in the USA.

When there is a high incidence of infections, people tend to not worry about the side
effects of the vaccine but when the disease is controlled by the vaccine, people begin
to worry about side effects. As in the case with DTP and whooping cough, the people
worried about the adjuvant pertussis and the inflammation it caused and the side
effects. People stopped taking DTP and whooping cough began to kill children once
again. In Japan, they developed a technique to use parts of pertussis instead of the
whole bacteria. This removes any side effects. There is also a distrust in MMR
vaccine of measles, mumps, and rubella because of rare cases of autism. Measles is
beginning to rise again in the UK where people distrust MMR.

There is a phenomenon called herd immunity. If the entire country is immunized

except the select few, the select few will also be protected because the disease cannot
occur in the immunized and it cannot therefore be transmitted from person to person.
If newborns are not being immunized, there is no such herd immunity.

Vaccines are typically not successful against chronic disease causing pathogens
especially parasites. Research is tough because 30% of the people who encounter
Hepatitis C will fight it off while 70% will suffer from liver damage. Only the sick
seek medical attention so it is hard to study the successes in the immune system.

Genetic engineering can help the future of vaccinations.

HIV vaccinations have been attempted for the last 20 yrs but it hasn’t produced good
results. No person has ever fought off HIV effectively so we don’t know what
immune response can defeat the virus. Therefore, it is tough but a T cell response is
favored because 5% of people who produce a T cell respone rather than antibody
response never catch HIV even though they are frequently exposed.

Transplantation alloreactions occur because of different alloantigens within the

human species. The most important molecule is HLA. When there is an alloreaction
to the transplanted organ from the host’s immune system, this is called transplant
reaction. In bone marrow transplants, however, the host’s bone marrow has been
destroyed by chemotherapy and the transplanted bone marrow is injected into the
patient. There then can occur a Graft vs. Host reaction where the transplanted bone
marrow produces an immune response against the host’s tissues. This is called graft
vs host disease.
An autograft is when skin is transplanted from one part of the body to the other within
the same host. This is done with burn victims. An isograft or syngeneic graft is done
with 2 genetically identical twins and an allograft is done with 2 non genetically
identical people.

Blood transfusions are the most common transplants. RBC’s do not have HLA’s but
they have A,B,O system. There are four possible phenotypes, AB, A, B, or O. If there
is not correct matching, there is a hemolytic reaction analogous to a type II
hypersensitivity reaction. Rhesus factor compatibility must also be matched. A cross
test match is performed to check compatibility.

A,B,O is also present on blood vessels of solid organs. There must be matching as
well in a kidney transplant for instance or else a hyperacute reaction will occur and
the grafted organ will be rejected immediately. This reaction is analogous to type III
hypersensitivity with immune complex deposition causing tissue damage. The vessel
endothelium has HLA I expressed normally and HLA II can be expressed during
infection, inflammation, and trauma. So, it is important that the host does not have
antibodies specific to HLA allotypes. A cross match test is performed where blood
serum from the recipient is assessed for antibodies that are specific to the donor’s
white blood cells. Anti HLA I antibodies react with both T and B cells while anti
HLA II antibodies react with only B cells. Flow cytometry can also be used.

Such antibodies specific to HLA allotypes can occur for several reasons. The most
common is due to previous pregnancy where the mother produces anti HLA
antibodies to the fetus. The fetus though doesn’t get harmed but the mother retains
these anti HLA antibodies in her system. A second way to have anti HLA antibodies
is from a previous transplant. A third way is from blood transfusions. Since there is
no compatibility tests for HLA allotypes in blood transfusions, the platelets and
leukocytes with incompatible HLA allotypes can cause the recepient to produce anti
HLA antibodies. A test checks for PRA, panel reactive antibody where the patient’s
sera is tested against a panel of HLA’s. The higher the PRA, the more difficult to find
a correct match.

Inflammation is present in both the donor’s organ and the patient’s body. This
complicates things. The recepient’s dying organ has produced inflammation so the
body is prepared to detect a transplanted organ and to fight against it. Also, donated
organs are either from dying patient’s which also makes the organ inflamed. The
surgery causes inflammation as well and ischemia to the organ causes blood vessels
and tissue to be damaged so inflammation is also occurring from this. It is optimal if
the donor is alive, healthy, a relative, and near the recepient.

Most organ transplantations will not be a perfect HLA I/HLA II match and the
recipient’s CD4 T cells will react to foreign HLA II while the recepient’s CD 8 T
cells will react to foreign HLA I. This will cause an acute reaction which unlike
hyperacute reactons, need time to develop and reject the organ. This is analogous to
type IV hypersensitivity where the T cell’s attack the tissue. To prevent this, the
patient is given immunosuppressive drugs and anti T cell antibodies.

The direct pathway of allorecognition occurs when the dendritic cells of the inflamed
donor organ are stimulated to migrate to the T cell zones of the 2nd lymphoid tissues.
The T cells then respond to the different HLA allotype of the donor’s dendritic cells
and produce a T cell response. The T cell response against HLA allotypes is actually
stronger than the ones produced against pathogens. The activated CD 4 T cells
activate macrophages to inflame the tissue further while the activated CD8 T cells kill
the transplanted tissue.

The indirect pathway of alloreaction occurs when donor dendritic cells travel to the T
cell zones of 2nd lymphoid tissue and die by apoptosis. The host’s dendritic cells than
engulf the dead cells and process and present the peptide via MHC II. The CD 4 T
cells then recognize the peptide and produce a CD 4 T cell response.

In chronic rejection, naïve B cells respond to allotypic HLA I. The naïve B cells are
activated by TH2 cells that also recognize the HLA allotype through indirect pathway
of T cell activation. Antibodies and CD 4 T cells cause inflammation and tissue
damage and epitope spreading occurs which causes disease progression.

The transfusion effect can also occur and it is excellent for the recepient. It’s when
the indirect pathway of T cell activation gives rise to CD4 T regulatory cells that
suppress alloreactive CD4 and CD8 T cells. This allows the recepient to keep the
organ even if different HLA allotypes are present.

Most transplanted organs are not perfect HLA matches to the recipient’s HLA
allotypes so there is a need for immunosuppressive drugs. There’s 3 kinds. Each is
suppressed in high amounts immediately during and after the operation. The person is
susceptible to infection then because the immune system is suppressed. The drugs are
then lessened in dosage slowly until they are still effective but immunocompetence
returns. The likelihood of cancers rises because the drugs have side effects and also
chronic rejection can form. The 3 types of drugs are
1.Corticosteroids- they are anti-inflammatory. The adrenal cortex normally secretes
the anti-inflammatory steroid, cortisol aka hydrocortisone. The corticosteroid,
prednisone, is a synthetic derivative of cortisol and is 4 times more potent. It is given
in an inactive form(pro-drug) and it is then enzymatically converted into
prednisolone. The steroids act on many cells of the body and they diffuse through the
cell membrane and bind to the steroid receptor complex. This causes Hsp90 to be
released. This allows the steroid/receptor complex to enter the nucleus. There it
induces transcription of about 1% of the cell’s genes. One important anti-
inflammatory function is the inhibition of NFkB which normally causes cytokine
production during immune response. Corticosteroids are used short term and have
several side effects.

2.Cytotoxic drugs- A common one is azathioprine which is a pro drug that gets
converted first into 6-mercaptopurine and then into 6-thioinosinic acid. The principal
function is to stop DNA replication which will cause the cell to apoptose. It prevents
the replication of alloantigen activated lymphocytes but it also damages all other
tissues of the body especially bone marrow, intestinal epithelium, and hair follicles.
This leads to anemia, leucopenia, intestinal damage, hair loss, etc. It is only
administered after transplantation and pregnant mothers shouldn’t take it.
Cyclophosphamide is one of the nitrogen mustard compounds of mustard gas. It is
also a corticosteroid that is used. It causes DNA replication to not occur normally and
cells die. It is a good immunosuppressive but with side effects. Another drug is
Methotrexate.

3. Microbial drugs- Cyclosporin A is one. It prevents the activation of T cells by

disrupting the transduction of signals of the T cell receptor. Cyclosporin A crosses
into the cytosol and binds to cycophilins. This complex then binds to calcineurin
and inhibits it phosphatase ability which inhibits it from activating NFAT. No IL-
2 can be then made and T cell proliferation, differentiation, and activation is shut
down early. Tacrolimus is a similar drug to Cyclosporin A which also inhbits the
activity of calcineurin by forming a complex with FK binding proteins in the
cytosol. NFAT cannot be activated and IL-2 cannot be produced. Rapamycin can
also be used. These drugs have lower side effects than cytotoxic drugs but
nephrotoxicity can still occur.