The Immune System
The immune system is a diffuse collection of cells and organs that function to protect the body
against antigen, which are foreign molecules that are potentially harmful. The two ‘arms’ of the
immune system are the innate and the adaptive immune systems. These two ‘arms’ have
different properties and functions, and they also have a lot of overlap, which will be covered in
more detail later.
As previously stated, the immune system is not contained in one organ, but is distributed in
various organs and tissues throughout the body. Primary immune organs are defined as places
where B and T lymphocytes develop. This group includes the bone marrow, where
hematopoesis occurs (and thus B and T lymphocytes are born) and B cells mature, and the
thymus, where T cells mature (immature cells are located in the cortex, mature cells in the
medulla). Secondary immune organs are sites where mature, but naive, B and T cells encounter
antigen and develop into effector cells. In the spleen, which filters the blood, T cells are located
in the peri-arteriolar sheathes of the white pulp, while B cells are in the follicles, germinal
centers, and the marginal zones. In the lymph nodes, which filter the lymph, B cells are located
in the follicles, and T cells are located in the parafollicular areas.
The immune system operates by some basic principles. One is that there is an element of
specificity, as in each B and T cell is only activated by binding specific antigen that is not ‘self’.
The immune system is capable of discerning what is ‘self’ and what is ‘non-self’, and thus may
be a threat and should be attacked. Another basic feature is the ‘memory’ of the immune system.
When antigen is encountered for a second time, the immune response is heightened and
quickened compared to the first encounter.
The clonal selection theory can explain some basic properties of the immune system. Many,
many B and T cells, each with a unique and randomly generated antigen receptor, are generated
even before the body encounters antigen. This occurs by a process known as somatic
recombination which will be covered later. When the body does encounter antigen, is has a
randomly generated arsenal of B and T cells with many various receptors, just waiting. If
antigen does happen to match one of the B and T cell receptors, the activated lymphocyte will
expand (a process known as clonal expansion), and thus an army of cells will exist in the body
specific for that certain antigen the next time the body encounters it. This explains how the
immune system has its memory. The concept of MHC restriction ensures that T cells recognize
both non self antigen only when bound to a self MHC molecule
THE INNATE ARM OF THE IMMUNE SYSTEM
The innate immune system can be thought of as the body’s first line of more non-specific
defense, and the adaptive immune system is the more specific defense system involving T and B
lymphocytes. However, even though we are dividing the immune system into two ‘arms’, they
work together in many ways, and there are certain cells (such as gamma-delta T cells and CD5 B
cells) that sort of have innate and adaptive characteristics. There is not really a clear, harsh
division; however, the innate and adaptive do exhibit some different characteristics. The innate
immune system is more nonspecific and more quickly acting than the adaptive and has no
immunological memory. The most basic component of the innate immune system is physical
barriers to pathogens, such as skin and mucous membranes. It also includes chemical barriers
such as stomach acid, lysosyme, mucous secretions, and antimicrobial peptides. If a pathogen
manages to slip by the barriers of the body, the innate immune system orchestrates an
inflammatory response. Phagocytic cells, inflammatory cytokines, and the complement cascade,
are also included in the inflammatory response. Interferons, which are compounds produced by
virally infected cells, and natural killer cells, which kill virally infected and tumor cells, are also
considered part of the innate immune system.
Let’s look at the inflammatory response orchestrated by the innate immune system when a
pathogen successfully gets past our barriers. We can learn about the type of pathogen causing the
infection and how long it has been going on by the certain changes in the white blood cell profile
of a patient
Neutrophils are the first on the scene, especially in a bacterial infection. There are large reserves
of neutrophils in the bone marrow and they can be released as needed. When needed,
neutrophils, and also other WBCs (dependent on the type and time course of infection) are
activated to leave the bone marrow by inflammatory cytokines produced by activated
macrophages, injured tissue, and mast cells. IL-8 specifically recruits neutrophils to tissues.
IL-1, IL-6, and TNF-a are classic inflammatory cytokines released by macrophages, and they
induce fever and promote WBC adhesion in the blood vessels, along with eliciting various
inflammatory effects in a wide range of organs and tissues. When the neutrophils and other
WBCs leave the bloodstream and enter the tissues they do so by a process known as diapedesis,
which is rolling and squeezing through the endothelial cells. Diapedesis is made possible when
cytokines induce expression of adhesion molecules on both the WBC and the vessel cell.
Once the neutrophils are out of the blood vessel and in the tissue, they engulf bacteria and die,
and then they themselves are then cleared by macrophages. If there are a lot of immature
neutrophils, called bands, this indicates that infection has been going on for a long time and the
older neutrophils have already been exhausted. Other changes in the WBC profile can indicate
infection. Monocyte percentage can increase in a more prolonged infection, and eosinophil
percentage increases are typically seen with parasitic infections. If an infection continues, fever
(due in part to bacterial pyrogens, IL-6, IL-1, and TNF-a), anemia (because of increased WBC
production), and other organ changes can be observed.
Neutrophils and macrophages are just two examples of phagocytic cells, an important
component of innate immunity. These phagocytic cells have evolved to recognize specific
patterns that are indicative of pathogens, called PAMPs (pathogen-associated-molecular-
patterns) through Toll-Like-Receptors (TLRs). Some examples of these PAMPs are
lipopolysaccharide (LPS) in bacterial cell walls, mannose, double stranded RNA, single stranded
DNA, and flagellin. Recognition of these PAMPs promotes engulfing and killing of the
pathogens through the use of a phagolysosome. However, this does not always work, as in the
case of mycobacterium tuberculosis, which can actually live inside of the phagolysosome.
Engulfing of pathogens can promote phagocytic cells to make inflammatory cytokines, such as
IL-1, IL-6 and TNF-a. These cytokines promote inflammation in general, and will cause an
accumulation of fluid, plasma proteins, and WBCs in the tissues.
The complement system is a series of serine proteases that can enhance the inflammatory
response and phagocytosis of pathogens by cells in the innate immune system. It occurs in a
cascade pattern, and has regulatory ‘brakes’ to inactivate the cascade when needed. There are
two main phases of the complement cascade: activation and amplification. There are three
complement pathways, and they are distinguished by their ‘activation’ phase: the classical
pathway, the alternative pathway, and the mannose-lectin pathway. Although they all have
different ways of being activated, they all converge and use the same set of molecules
eventually. Specifically, they all form what is called a C3 convertase. We’ll talk about the
alternative pathway here, and the classical pathway in the section on humoral immunity, because
it needs antibodies to start it off.
The alternative pathway can be activated without any specific antibody. The main effects of this
pathway are opsonization of pathogens by a molecule called C3b, lysis of pathogens by the
membrane attack complex, and the release small proteins that are of mediators of inflammation.
Let’s first talk about how the molecule C3b ends up opsonizing pathogens. The alternative
pathway it begins when a protein called C3 is spontaneously hydrolyzed at a very low rate in the
blood, forming the fragments C3a and C3b. C3b will bind to a protein called factor B. When B
binds C3b, a protease called factor D is now able to cleave B into its fragments, Bb and Ba. Bb
remains associated with C3b to form C3bBb, which is a C3-convertase, meaning it is an enzyme
which will cleave C3 at a much faster rate than its spontaneous hydrolysis. Now, C3b is
hydrophobic, so it is attracted to cell membranes. If it happens to land upon a ‘self’ (human)
cell, there are regulatory proteins which will thwart the cascade and prevent our own cells from
being marked for phagocytosis. CR1 and DAF are two molecules that will prevent the formation
of a C3 convertase on our cell surfaces when C3b is bound. C3 convertase formation can also be
inhibited by factor I, with help from cofactor H, by cleaving C3b into its inactive form, iC3b,
which will not form the C3 convertase. If C3b binds to a pathogen cell membrane, however,
there are none of these regulatory molecules and the C3 convertase will be allowed to form,
stabilized by a molecule called Properdin. If C3bBb, the C3 convertase, is allowed to form, it
will rapidly cleave more molecules of C3, causing more and more C3b to be deposited on the
cell (opsinization) and mark it for phagocytosis. Macrophages have the CR1 (complement
receptor 1) which will allow them to recognize C3b repeats and phagocytose opsonized
pathogen. C3b can also combine with bound antibody promoting antigens to stick to vessel
A second effect of complement cascade is the production of mediators of inflammation. The
small fragments created by cleavage of complement proteins, namely C5a, C4a, and C3a, act as
mediators of inflammation and as anaphylatoxins. C5a is also a potent chemoattractant for
A third effect of the complement cascade is the production of the membrane attack complex
(MAC). So we continue on…after the formation of C3 convertases of C5 convertases can form
as follows: The C5 convertase in the alternative pathway is formed by binding C3b to the C3
convertase C3bBb to make (C3b)2Bb. C5b, produced by the C5 convertase, initiates the
assembly of the membrane attack complex (MAC). C5b binds C6, C7, C8, and multiple C9s.
This complex forms a pore which inserts into the pathogen cell membrane and causes lysis. The
molecules CD59, Protein S, and HRF all prevent the MAC from inserting into host cells. If a
patient is deficient in any component of complement downstream to the C3 convertase, they
usually just are more susceptible to infections by Neisseria species of bacteria. However, if they
are deficient in C3 convertase activity, the complement pathway will be seriously thwarted and
they will have major immunodeficiencies.
ADATPIVE IMMUNE SYSTEM
The adaptive immune response involves B and T lymphocytes. As we’ve said before, it is
intricately entwined with the innate immune response. However, the nature of it is very different.
While the innate immune response is quick acting, the adaptive takes longer. The innate immune
system has no ‘memory’ while the adaptive does. The innate immune response is nonspecific,
and the adaptive is very specific. As stated, the adaptive immune response refers to the actions
of B and T lymphocytes. Let’s first look at how they develop in the body.
B AND T CELL DEVELOPMENT – The transition from progenitor cell to naïve B/T cell
B and T cells are remarkable cells in that each one carries a unique receptor for a specific
antigen. The receptors on the B and T cells are very similar. They are both heterodimer
molecules, with the B cell having a heavy and light chain, and the T cell having an alpha and
beta chain. Both the B and T cell receptors are made up of a series of immunoglobulin protein
domains. Both receptors have a constant region, and a variable region, which binds antigen.
However, the B cell receptor (which is actually a membrane bound antibody molecule,
antibodies are secreted B cell receptors) binds to conformational epitopes, that is surface
patterns, of antigen, while the T cell receptor binds to a short linear peptide from antigen bound
to an MHC molecule. (More on MHC later).
B cells are born and develop in the bone marrow, in a specialized environment with help from
stromal cells. T cells are also born in the bone marrow, but they develop in the thymus. The
stages of lymphocyte development are marked by what type of immunoglobulin receptors they
You may be wondering how the body can possibly have a B/T cell that binds to the millions of
different antigens out there with the limited size of our genome. The answer lies in the process
of somatic recombination. With somatic recombination, a single progenitor cell is able to give
rise to a large number of daughter cells with a unique antigen receptor. To have this happen,
mini-genes (termed V D and J) are rearranged to form the mature antigen receptor gene. This
process occurs before the cell has ever encountered antigen, and it only happens in B and T cells.
The first step in somatic recombination (and B/T cell development) is the rearrangement of the D
and J mini-genes on the heavy chain (B cells) or beta chain (T cells). Next, the V mini gene is
rearranged on the heavy chain or beta chain locus, forming the mature heavy/beta chain for the
B/T cell receptor, with intervening DNA spliced out. Proteins called RAG1 and RAG2 assist
with recombination of the mini-genes, and a protein called Tdt fills in the gaps created by
recombination with new nucleotides. The area of the receptor with the most variability is called
the CDR3 region, and is located at the junction between the V and D mini-genes on the heavy
This whole time the heavy/beta chain has been rearranging, it has been paired with a ‘stand in’
light/alpha chain. Once a heavy/beta chain has been successfully rearranged it signals the cell to
inhibit additional heavy chain locus rearrangement on the other chromosome. (If, after 2 tries of
rearranging a heavy chain, the cell is still unsuccessful, it dies). This is allelic exclusion, and it
ensures that a single B or T cell will only express one type of receptor. Once the heavy/beta
chain has been made, we have ourselves a pre-B or pre-T cell and cell division is triggered. Now
the light/alpha chain can rearrange. This only involves a V and J mini-gene rearrangement (no
D). The cell now has it’s successfully rearranged heavy/beta chain with a rearranged light/alpha
chain. If this binds very strongly to self-antigen, a process called receptor editing takes place.
The cell has arrested development and the light chain locus on the other chromosome undergoes
rearrangement to give it another try. If, after this second rearrangement, the receptor still binds
very strongly to self antigen, the B/T cell dies by apoptosis. This is negative selection.
An additional note about T cell development. T cells can eventually become one of two types of
effector cells: CD4 or CD8 cells. CD4 and CD8 are co-receptors, and are expressed on the
mature cell in addition to a T cell receptor. When the T cell is before the Pre-T cell receptor
stage (when it will have a successfully rearranged beta chain and a ‘fake’ stand in beta chain), it
is termed ‘double negative’, because it expresses neither the CD4 nor the CD8 co-receptor on it’s
surface. Once the beta chain has been successfully rearranged, Pre-T cell receptor signaling
causes the cell to become ‘double positive’, that is it expresses both the CD4 and CD8 co-
receptors. Once the alpha chain has been successfully made, the T cell can have 3 fates. It can
die from neglect if it does not bind to any MHC molecules on the cells in the thymus, it can die
from negative selection if it binds to MHC with self peptide with a very high affinity, or it can
live because of positive selection if it binds to MHC with self peptide with low affinity. If it is
positively selected for, whether it binds to MHC class I or class II will influence whether CD4 or
CD8 sticks around as the co-receptor (the other one is down-regulated). If it binds MHC-I, it
will become a CD8+ T cell, and if it binds to MHC-II, it will become a CD4+ T cell. Positive
selection ensures that T cells are MHC restricted, that is they will only recognize antigen in the
context of it being bound to an MHC molecule. The end product of all of this is a naïve CD4 or
CD8 T cell that goes out to the periphery. The end product of B cell development is a naïve B
cell that goes out to the periphery.
We should note here that all of these rearrangements are a prime set up for transforming a cell
into a cancer cell. Somatic recombination may cause an oncogenic mutation, and many
leukemias and lymphomas, such as Burkett’s lymphoma, are associated with it. There are other
diseases that it is relevant to talk about here. Bare lymphocyte syndromes cause patients to have
a complete lack of CD4 T cells if they do not express MHC-II and a complete lack of CD8 T
cells if they do not express MHC-I. AIRE (autoimmune regulator) deficiency can occur when
there is a lack of expression of a certain transcription factor in the thymus. This transcription
factor promotes thymic expression of many peripheral proteins, so many self-reactive T cells that
are normally weeded out via negative selection are allowed to mature. These patients have
various autoimmune conditions.
There is a class of T cells, called gamma-delta T cells that arise in the fetal thymus that have a
fixed antigen receptor. They are prevalent in mucosal areas and may play a role in recognizing
common microbes that we encounter at epithelial barriers. In fact some can recognize antigen
even when it is not bound to an MHC molecule. They can be thought of as kind of a bridge
between adaptive and innate immunity.
We have been referring a lot to the MHC molecule. Here is where we can talk about its nature in
a lot more detail. Basically, the MHC molecule is a protein made up of immunoglobin domains
expressed by all nucleated cells in the body. All nucleated cells express MHC class I molecules
on their surface, and antigen presenting cells express MHC class I along with MHC class II
molecules on their surface. The MHC-I protein is made up of one alpha chain and one beta
portion, which is encoded for on another chromosome that serves to stabilize the molecule. The
MHC-II protein is made up of one alpha chain and one beta chain. Note the similarities between
the MHC proteins and the T and B cell receptors. T cells can only respond to antigen when it is
‘presented’ in the context of an MHC molecule. The two MHC molecules bind to antigen in
different ways. MHC-I binds a 8-10 amino acid peptide tightly. MHC-II binds a 13-18 amino
acid in a more wobbly fashion, with the edges hanging off. Pathogens that are inside the cell,
like viruses, bind to MHC-I and activate CD8+ T cells. Pathogens that are outside the cell, like
bacteria, are engulfed by APCs, are presented in MHC-II, and can activate CD4+ T cells.
The MHC (aka HLA- human leukocyte antigen) is encoded for by multiple genes. MHC-I is
coded for by genes called A, B, and C, and MHC-II is coded for by genes DP, DQ, and DR.
Since MHC-I is made up of only 1 alpha chain (the beta stabilizing molecule is encoded for on
another chromosome) there is only one A, B, and C allele on each chromosome, but since MHC-
II is made up of two chains, there are alpha and beta loci for DP, DQ, and DR on each
chromosome. MHC-I and MHC-II are codominantly expressed on cells in the body. That means
that whatever alleles you get from your parents, you are going to express. Unlike B cell and T
cell receptors, a given MHC molecule is not specific for just one antigen; it has the potential to
MHC molecules do not undergo somatic recombination like B cell and T cell receptors.
Diversity is achieved by the face that the MHC gene loci are the most polymorphic in our
species. That is, there are so many different possibilities for MHC molecules among the human
species, so we are very unlikely to come across a pathogen that NO ONE can recognize and will
wipe us all out. However, although there are many different alleles for MHC gene loci, there is a
linkage disequilibrium, in that the frequency of some alleles is higher or lower than expected.
MHCs, or HLAs are what is typed during ‘tissue typing’ for transplants. The highly
polymorphic nature of the MHC genes is why matches are so rare. There are some MHC alleles
that, if you express them, you seem to be more at risk for certain infections and autoimmune
diseases. Certain viral or bacterial antigens, termed superantigens, can bind to the T-cell
receptor and MHC outside of the peptide groove, nonspecifically, and can activate a large and
uncontrollable number of T cells, causing a dangerously huge immune response.
Now we can talk about how MHC-I and MHC-II actually get their antigen in the groove and are
expressed on the cell surface. MHC-I begins in the ER of the cell, partially folded and stabilized
by the calnexin chaperone. It then binds its stabilizing beta chain. It is then released from
calnexin, and binds to other chaperone proteins including calreticulin as it becomes associated
with the TAP transporter. TAP serves to deliver a peptide to the MHC-I groove that has been
degraded by the large protease called the proteosome. The loaded MHC-I is then released from
TAP and exported to the cell surface. TAP deficiencies result in bare lymphocyte syndrome,
which was discussed earlier. (A TAP deficiency would result in no MHC-I produced, and thus an
absence of CD8+ T cells in the patient).
MHC-II also begins in the ER, where it is stabilized by an invariant chain molecule, which binds
in its peptide groove, blocking peptide binding while the MHC-II is still in the ER. It is
packaged into an endosome, where the invariant chain molecule is cleaved, leaving a short
peptide called CLIP in the peptide groove. Endocytosed antigens are taken into the endosomes
and degraded, but can only get into the MHC’s groove in the presence of HLA-DM, which
causes CLIP to be released. The loaded MHC-II can now be exported to the cell surface.
T AND B CELLS ACTIVATION BY ANTIGEN- The transition from naïve to activated B/T cell
B and T cells become activated when antigen (or in the case of T cells, antigen in the context of
MHC) binds to their receptors and a signal is transmitted as a result of that. This signal is
initiated and propagated by tyrosine kinase activity. However, the T and B cell receptor
themselves do not have any intrinsic kinase activity to them, so they must associate themselves
with other molecules that do. The result of T and B cell receptors binding antigen is thus a signal
is initiated, which begins with tyrosine phosphorylation of various proteins, and may involve
second messengers such as calcium (important in B cell activation, resulting from the
phosphorylation of phospholipase C and initiation of the IP3/DAG pathway) and G proteins, and
eventually changes occur within the cell. The signal transduction pathway depends on protein-
protein interactions that recognize certain domains (such as SH2 and SH3) within each other.
Lipid rafts in the plasma membrane help to cluster signaling molecules together so they are more
likely to associate with each other. When cells come together to initiate a signaling cascade it is
termed, an ‘immunological synapse’.
Both the T and B cell are associated with invariant molecules which get their tyrosines
phosphorylated when antigen binds the BCR or TCR. For the T cell, the invariant molecule is
CD3, and for the B cell the invariant molecule is Ig-alpha/Ig-beta. The molecule that
phosphorylates the invariant chain is a Src family kinase. The domain on the invariant chain that
gets phosphorylated after ligand binding is called an ITAM. The Src family kinase that does the
phosphorylating is associated with the co-receptor molecule in the B and T cell. In T cells, the
co-receptor is either CD4 or CD8 and the Src family kinase associated is called Lck. After Lck
phosphorylates the cytoplasmic tail of the CD3 invariant molecule, Zap70 is recruited to
continue on with the signaling cascade. In the B cells, the co-receptor is a complex between
CD19, CD21, and CD20, and the Src family kinase associated is called Lyn. After Lyn
phosphorylates the cytoplasmic tail of the CD3 invariant molecule, Syk is recruited to continue
on with the signaling cascade. Src family kinases are regulated by phosphorylation and
dephosphorylation of tyrosines within certain regions. Csk is a tyrosine kinase that
phosphorylates an inhibitory tyrosine in Src family kinases, and CD45 is a tyrosine phosphatase
that dephosphorylates an inhibitory tyrosine in Src family kinases.
Once the invariant chains in T and B cells are phosphorylated, the signal can be passed on
through second messenger signaling. An example of this is the phospholipase C/IP3/DAG
pathway, which creates an increase in intracellular calcium. This causes calcuneurin to localize
the transcription factor NFAT to the nucleus to influence gene transcription. The drug
Clyclosporin A blocks the calcium signaling pathway by inhibiting calcuneurin. Other second
messenger systems that can be initiated by activation of protein kinase c, or through G protein
All of this has been about what B and T cells when they bind antigen. Naïve B and T cells move
from the blood circulation (where they are unlikely to encounter their one specific antigen) to the
lymph circulation, where antigen is concentrated in the lymph nodes and they have a better
chance of being activated. Lymphocytes enter the lymph nodes from the blood through high
endothelial venules (HEVs). Adhesion molecules, such as the ICAM/LFA-1 pair help to assist
the diapedesis of the cell into the lymph node. If the cell does not encounter anything in the
lymph node that bind to its receptor, it leaves the node through the efferent lymphatics, and will
ultimately re-enter the bloodstream through the thoracic duct.
T cells are activated not by free antigen, as B cells are, but by antigen presenting cells that
display a short peptide in their MHC molecule. For a T cell to be activated by an APC, it
receives 2 signals. The first is the signal through the TCR binding the MHC-peptide on the
APC. The second signal is the CD28 molecule on the T cell binding the B7 molecule on the
APC. Binding of the co stimulatory molecule CD28 on T cells causes IL-2 production by the T
cell and clonal expansion. Cytokines that are around at the time of naïve T cell activation can
determine what kind of effector T cell it will develop into.
For a B cell to be activated, it also receives 2 signals, like the T cell. The first signal is the cross-
linking of the B cell receptor by bound antigen. The second signal for the B cell is through the
co-stimulatory molecule CD40, which binds CD40L on the T cell (specifically the Th2 cell, but
we will get to this later). Other antigen presenting cells have the CD40 molecule, and can also
be activated by T cells (such as macrophages). Thus there is reciprocal action between the B and
T cells (and also between other cells in the immune system…this is one way that the adaptive
and innate immune systems are related to each other!).
A B cell can also receive its second signal in a T-independent way, such as recognizing a PAMP
through the Toll-like receptor. This will cause the B cell to differentiate into a plasma cell and
produce a soluble form of its receptor called IgM. There are two types of T-independent
antigens that are capable of activating B cells. The first, TI-1 antigens, are often microbial
surface marker, like LPS, are also termed mitogens. These TI-1 antigens will cause many
different B cells to become activated and begin production of IgM (polyclonal activation).
However, B cells activated in this way will not undergo isotype switching (which will be covered
later) and germinal center formation. TI-2 antigens usually have repeating domains, such as a
bacterial polysaccharide capsule. However, the name TI-2 may be a misnomer, because some T
cell cytokines may actually be involved for B cell activation by these antigens. IgG as well as
IgM can be produced by plasma cells that were activated in response to TI-2 antigen. IgG is
very important for the opsonization of bacteria, which macrophages can bind with their Fc
receptor and engulf. It is important to note that lack of any co-stimulatory signals in both B and
T cells can result in tolerance.
CD5 B cells and Marginal Zone B cells are important subsets of B cells that often respond to
antigen in a T independent manner. More about these in the section on B cell activation.
HOW T CELLS CARRY OUT THEIR FUNCTION ONCE ACTIVATED- The transition from
activation to effector T cells
Once naïve T cells are activated through the TCR and CD28 in the lymphoid organs, they can
have a few effector functions. CD8+ T cells have a cytotoxic effector function, basically killing
cells infected with pathogen. CD4+ T cells can either act as Th1 or Th2 effector cells. There are
mechanisms in the body that function to down-regulate T cell function to prevent immune over-
As a T cell (or a B cell for that matter) goes through development and activation the molecules
expressed on the surface of a can tell a lot about what stage it is in. For example, a naïve T cell
is likely to express L-selectin on its surface, which will cause it to be attracted to the HEV on the
lymph node so that it can find antigen. On the other hand, an armed effector T cell is likely to
express the adhesion molecule VLA-4 on its surface, which will cause it to be attracted to
vascular endothelium so it can enter infected tissues and carry out its function. Once naïve T
cells have a been activated they can carry out their effector function in a variety of ways,
including cytokine production, the use of cytotoxins, and direct cell to cell contact. This
transition from naïve to an effector T cell takes days, not minutes!
First, let’s talk about the possible effector functions of the CD4+ T cell. A naïve CD4 T cell can
develop into a Th1 cell, which functions to activate macrophages, produce inflammatory
cytokines, lyse cells, and help B cells produce opsonizing antibody. On the other hand, CD4+ T
cells can also develop into a Th2 cell, which functions to help B cells produce antibody, and to
help B cells through the production of cytokines. In a nutshell, Th1 cells will basically help
macrophages with the destruction of engulfed pathogen, and Th2 cells will basically help B cells
with the destruction of extracellular pathogen.
It makes sense then, that whatever pathogens are around will help influence whether a naïve CD4
T cell becomes a Th1 or a Th2 effector T cell. When there are engulfable pathogens, like a virus
or bacteria, dendritic cells produce IL-12, which induces NK cells to produce IFN-gamma.
IL-12 and IFN-gamma will influence naïve T cells to develop into Th1 cells. When there are
pathogens like worms that are not usually engulfed, IL-4 production may be induced from some
cells. This IL-4 will cause a naïve T cell that has just been activated to develop into a Th2 cell.
These cytokines have cross regulatory activity. That is, IL-12 and IFN-gamma do not only
promote Th1 development, but they inhibit Th2 development. IL-4 does not only promote Th2
development, but it inhibits Th1 development. As you would expect, Th1 and Th2 cells secrete a
different profile of cytokines which are related to their effector function.
There is clinical relevance to Th1 and Th2 cells. Cytokines made by Th2 cells such as (IL-4 and
IL-5) can induce many of the symptoms that mediate allergic reactions and asthma. Thl can
sometimes become chronically activated when there is an engulfed pathogen that is hard to get
rid of, such as mycobacterium tuberculosis, which lives inside macrophages once it has been
engulfed. Basically, the Th1 cells continually, through production of inflammatory cytokines
and through the CD40/CD40L interaction, activate more and more T cells and macrophages
which can lead to chronic inflammation.
Another clinical example involving Th1 cells is the delayed type hypersensitivity reaction
commonly seen with poison ivy. Lipid soluble poison ivy antigen can penetrate the skin and
react with proteins, altering them. These altered proteins can be taken up by antigen presenting
cells in the skin (macrophages and Langerhans cells) which present the antigen (derived from the
altered proteins) to T cells in the lymph node. Upon the first exposure, a patient will not usually
notice any symptoms. This stage is T cell priming. Upon subsequent exposure, Th1 cells that
were primed will mediate an inflammatory response in the subcutaneous region. This response
can take a few hours, because it is usually a small area and the Th1 cells that recognize this
antigen are relatively rare. The inflammatory response is mostly caused by Th1 cells carrying
out their effector functions, including inflammatory cytokine release, cytotoxicity via the
FAS/FASL interaction (the expression of the FAS-ligand by T cells can bind with the FAS
receptor on another cell, causing apoptosis of that cell), and production of degradative enzymes.
Now, let’s switch gears and talk about the effector functions of CD8+ T cells. Unlike CD4+ T
cells which can have a ‘choice’ of whether to differentiate into Th1 or Th2 cells, naïve CD8+ T
cells will develop into cytotoxic T cells when activated. Cytotoxic T cells basically carry out
their effector function by killing their target cell, which makes sense when we remember that
they are going to be activated by MHC-I molecules, which are expressed by all nucleated cells of
the body. Since most cells in the body can’t carry out phagocytosis, if they have a pathogen
inside them, it is something that infected them, such as a virus, and they should be killed. There
are a couple of mechanisms of cytotoxicity that these effector cells use. The first is granule
release. Perforin is released first from the cytotoxic T cell, which forms pores in the target cell
membrane, allowing the granzyme granules to enter the target cell. Granzyme is a serine
protease that activates the target cell’s apoptotic pathway. These granules are released at the site
of cell contact. The second cytotoxic mechanism is the interaction of FAS-ligand on the T cell
with FAS on the target cell, also serving to activate the target cell’s apoptotic pathway.
There is an additional subset of effector T cells that are neither Th1, Th2, nor cytotoxic, but they
have a regulatory function. Mainly they serve to down-regulate effector T cell development and
function. They can have direct contact with antigen presenting T cells and T cells to carry out
their regulation, or they can produce cytokines that cause this down regulation. Often, these cells
are CD4+ and CD25+.
Fortunately for us, T cell activation will not be allowed to go on forever in the body. When
antigens are not present anymore, effector T cells that have been activated by that antigen will
die by neglect. If there is antigen that is not being taken care of by the immune system and it is
around for a prolonged period of time, the repeated stimulation of effector T cells can cause
death via binding the T cell’s FAS receptor (by another cell’s FAS-L, or even the same cell’s
FAS-L, because there is so much activation, and thus so much FAS-L going on). If there is a
deficiency in the FAS receptor, a disease called autoimmune lymphoproliferative disease (ALPS)
results. These patients experience lymphadenopathy, lymphocytic infiltrates is organs, and
Also, just as there are positive co-stimulatory molecules that provide a second signal for T cell
activation (such as the B7 molecule, which binds CD28 on the T cell), there are negative co-
stimulatory molecules. A B7 can also bind CTLA-4 on the T cell, causing down-regulation.
PD-1, and some Fc-gamma receptors on the T cell are also molecules expressed on the T cell
important in down-regulation of the immune response.
HUMORAL IMMUNITY –The transition from activation to effector B cells
After B cells have been activated by antigen and a second signal from T cells, they are stimulated
to proliferate and differentiate into plasma cells. Proliferation occurs in germinal centers of the
lymph nodes, sites of intense proliferation of B cells that are surrounded by the Th2 cells that
activated them. In these germinal centers, B cells with better and better antigen affinity are
produced via a process called somatic hypermutation. This process occurs only in B cells in
germinal centers, and involves a high level of mutation in variable regions (V, D, and J mini
genes) of the Ig gene. The B cells with increasingly good antigen binding capabilities are
selected for, and higher and higher affinity B cells for the given antigen are ultimately produced
Ultimately, some B cells from the germinal centers will terminally differentiate into plasma cells.
The Th2 cell induces plasma cell differentiation by CD40L binding and secretion of the
cytokines IL4,5,and 6. Plasma cells are a terminally differentiated cell which no longer divides
or responds to antigen. They no longer express membrane bound Ig (the B cell receptor) or
MHC-II but they secrete Ig. They are larger than B cells, and have more ER, ribosomes, and
golgi, representing their secretory function. Some B cells will terminally differentiate into
memory B cells, which can be re-stimulated by antigen, providing immunological memory.
Antibodies produced by plasma cells can bind Fc receptors on various other cells and cause a
variety of things to happen, including but not limited to: promotion of phagocytosis of opsonized
pathogen, neutralization of toxic pathogens, activation of cell killing through the ADCC
(antibody dependent cellular cytotoxixity), and starting off the classical complement pathway.
We can talk here about the different terminology for antibodies, which are produced by plasma
cells. Two antibodies that are isotypes have different Fc regions, which determines what the
antibody will do after it binds antigen. Two antigens that are idiotypes have different FAb
regions, which means that they bind different antigens. Two antigens that are allotypes are the
same except for the small genetic difference between two people.
Plasma cells can produce antibodies of various isotypes. Different isotypes of antibodies have
different functions. IgM is important in the primary immune response, are typically low affinity,
is involved in complement fixation, and exist in serum as a pentamer. IgG is important in the
secondary immune response, is an important opsonin, is involved in complement fixation, toxin
and viral neutralization, and is able to cross the placenta. IgA is involved in preventing
microbial attachment to mucous membranes, is a dimmer in secretions, and is not involved in
complement fixation. IgE mediates the immediate hypersensitivity reaction when it binds to the
Fc receptors on mast cells and basophils, and it is a main defense against parasitic worms. IgD is
found on naïve B cells and in low levels in the serum.
Once a B cell has differentiated into a plasma cell, it can not change the isotype of Ig it secretes.
However, during proliferation of B cells in the lymph node germinal centers, isotype switching
can occur. What isotype is switched to depends on what cytokines are in the microenvironment.
Cytokines from Th2 cells induce what type of isotype switching occurs. Il-4 promotes switching
from IgA to IgE. IL-5 stimulates switching to IgA. IFN-gamma promotes switching to IgG.
CD5+ B cells, or B1 cells, are a subset of B cells that have a high level of surface IgM and a low
level of IgD. These, like gamma-delta T cells, can be kind of thought of as cells which exhibit
characteristics of the innate and the adaptive immune systems. These develop in the fetus, and
their receptor undergoes no somatic hypermutation, so they have a limited range of specificities.
They seem to be able to recognize common bacterial antigens, and do not need T cell help to
become activated. Abnormal proliferation of these cells is common in some types of leukemia.
Another notable type of B cells is the marginal zone B cells. These exist in the marginal zone of
the spleen, and are responsible for most T-independent type 2 responses (TI-2). They can also be
good APCs for T cells and function in T dependent reactions.
We talked about complement (the alternative pathway) in the section on innate immunity.
Antibodies from plasma cells can activate another complement pathway, called the classical
pathway. The classical pathway involves nine major protein components, activated in the
following order: C1 (which has parts C1q, C1r, C1s), C4, C2, C3, C5, C6-8, C9. Both the
classical pathway and the alternative pathway form a C3 convertase. The difference is how they
get to the formation of that C3 convertase. (The mannose binding lectin pathway is another way
to generate a C3 convertase.)
The pathway begins with the binding of the C1q protein to the Fc region of IgG or IgM, after it
has bound antigen. It takes at least 2IgGs but only 1 IgM (because it is a pentamer), to start the
pathway. (IgA, IgE, and IgD cannot bind C1q). C1q binding to antibody activates the protease
function of C1r, which activates the protease function of C1s. C1s cleaves C2 and C4 into C2a
(which can be converted to C2 kinin, a BV dilator) and C2b, and C4a and C4b. C4b covalently
binds to a pathogen surface, where it binds C2b, forming C4b2b, which is the classical cascade
C3 convertase. This C3 convertase can cleave C3 into C3a and C3b. C3b joins the C4b2b
molecule to form C4b2b3b, the classical pathway C5 convertase. The rest of the pathway from
this point on is the same as the alternative pathway. C3b and C4b can act as an opsonins (the
CR1 on phagocytes will bind to them). Just like in the alternative cascade, the MAC can form.
C3a, C5a (a potent chemoattractant for neutrophils), and C4a can all act as anaphylatoxins.
Many cells have receptors for components of the complement cascade. CR1 on phagocytes can
bind C3b and C4b opsonins, causing phagocytosis of pathogens. There is also a receptor for
C1q, which promotes phagocytosis of immune complex. CR2 (CD21) is a B cell co-receptor.
Binding of antigen-complement to CD21 increases sensitivity of the B cell to antigen by about
1000 times. Epstein Barr virus uses CD21 to enter B cells, and can occasionally cause a
cancerous transformation. CR3 and CR4 allow monocytes, macrophages, neutrophils, and APCs
to extravate into tissue. Mast cells and smooth muscle have receptors for C3a, C4a, and C5a.
Isohemagglutinins are naturally occurring IgM antibodies that exist prior to antigen exposure.
An example of their relevance is blood type. All RBCs have an H substance, which is different
in people of different genotypes . People with type A blood have antibodies against H substance
type B, type O people have antibodies against H type A and H type B, etc. This is because we
will view whatever H substance we do not have as a non-self antigen. So, it is very important to
get the correct blood type in a transfusion, or a massive immune reaction to the ‘non-self’
antigen can occur.
Another clinical example of the importance of humoral immunity is the Rh antigen and
pregnancy. Rh negative mothers can develop antibodies against Rh antigen if they are carrying
an Rh positive baby. This is potentially dangerous to the baby if not assessed and treated, since
the antibodies in this case are IgG antibodies which can cross the placenta. To prevent fetal
harm, Rhogam is an Rh antibody that is given in very low does prophylactically to the mother. It
is the same molecule that the mother would produce in her immune reaction, and it is given in
low enough doses that it will not harm the baby. This low dose administration of Rhogam
prevents the mother from making a large amount of her own Rh antibody. To test if a mother is
Rh positive or negative, the Coombs test can be done. A sample of the mother’s serum is mixed
with a control Rh positive blood sample. Coagulation indicates the presence of Rh antibodies,
and indicates that the mother is Rh negative.