THE IMMUNE SYSTEM

NEW DEVELOPMENTS IN RESEARCH PART 1

WEEK 1
INTRODUCTION TO IMMUNOLOGY

TRANSCRIPT
INTRODUCTION

Hello, I am Masa Miyasaka, welcome to OsakaUx, The Immune System, New Developments in
Research.
Do you know how your own body protects you from viruses and other pathogens?
Would you be surprised to hear that cancer may also be controlled by your immunity?
Every day immunology research aims to understand the mysteries of our bodies and seeks out
the seeds for medical application.
This course introduces wide ranging content in general immunology fields from basic knowledge
to front line research.
In particular, I hope that from this course you gain necessary understanding of the new world
of immunology, the world opened up by the illustrious immunologists of the past, and the
unexplored mysteries that are yet to be explained by experiencing a part of the front line
research currently in progress.
In this lecture series, we will be learning how the immune system works, in particular how the
components of the immune system interact with each other, and how the failure of the immune
system leads to various diseases.
We will also be learning how knowledge of the immune system can be in a clinical setting, and
we will hear about cancer immunotherapy and the therapy of autoimmune diseases including
rheumatoid arthritis.
Now, as the very first speaker of this lecture series, I will give you an overview of immunology
so that you will get a rough idea as to what is the immune system all about, what kind of players
act in this system, and how they interact with each other to fight against pathogens.
INTRODUCTION TO IMMUNOLOGY (VIDEO 1)

Inside our body, we have an amazing protection mechanism called the immune system, which is
designed to defend us against millions of bacteria, viruses, fungi, toxins and parasites.
However, this system is not perfect, and sometimes it fails.
For instance, a germ can sometimes invade successfully, making us sick.
Or, instead of getting rid of pathogens, our immune system may sometimes attack our own body
components by mistake, if this happens in your joints, you may develop rheumatoid arthritis.
Alternatively, our immune system may overreact to certain antigens such as pollens.
If this happens in your respiratory tract, you may develop hay fever, which is one of the most
common type of allergy in developed countries.
One important thing to remember concerning the immune system is that it is a system, but not a
single entity.
As you may realize by listening to my talk, our immune system is actually a collection of
many different organs, special cells, and substances, which collectively help protect you from
infections and other diseases.
So, in order for the immune system to function well, it requires balance and harmony among the
various cell types and humoral factors that comprise the immune system.
First of all, let me remind you what "immunity" means.
This word actually derives from the Latin "immunis", which means exemption from military
service, tax payments and other public services.
But nowadays, immunity means more like exemption or protection from disease.
In other words, immunity is defined as resistance to disease, specifically infectious disease.
Now, let us look at the importance of the immune system.
First of all, the immune system is important because it defends us against infections.
This point becomes clearer if you look at the people who have been born with problems with
their immune system, a condition called "immunodeficiency".
These immunodeficient people can become infected very easily and often die of such infections.
So, this tells us how important it is to have an intact immune system.
Second, the immune system is important, because it works as defense against newly arising
transformed cells, such as malignant tumor cells.
The fact that the immunodeficient patients are also prone to develop various types of tumors
underlines the importance of the immune system.
Third, elimination of non-self, such as newly introduced substances or molecules, or tissue
grafts is another important task of the immune system.
Tissue grafts are normally rejected, because the recipients' immune system attacks them and
finally eliminates them.
However, if the recipient is given immunosuppressive drugs to blunt his/her immune response,
tissue graft rejection is delayed or sometimes completely inhibited, indicating the importance of
the immune system.
Finally, if the immune system works excessively, it leads to tissue injury or inflammation, as you
will see in the case of allergy and autoimmune disease.
This slide shows you an amazing capability of our immune system.
By properly stimulating the immune system using part of pathogens or vaccines, we have been
able to dramatically reduce the incidence of certain infectious diseases in developed countries.
This is particularly the case with childhood diseases, such as measles, rubella, mumps and
polio, which were highly prevalent among children some decades ago.
However, subsequent to the development of specific vaccines against them, these diseases are
declining very rapidly, and you hardly see them among properly vaccinated children.
So, this clearly shows the strength of the immune system.
RECOGNIZING INVADERS PART 1 (VIDEO 2)

So, our immune system is very effective in getting rid of pathogens or other types of invaders.
Then, how do we recognize such invaders?
What kind of strategies does our immune system exploit to recognize them?
Now, let us study the basic terminology to understand this issue.
First of all, an antigen refers to any substance that provokes an immune response.
This word originally came from ANTIbody GENerator, ANTIGEN, meaning that antigen is the
molecule that can generate antibodies or the molecule that can induce antibody responses in
the body.
Pathogens normally have a number of such antigens on their surface; they are proteins, sugars
or lipids.
In addition, these molecules have a number of determinants or epitopes; an epitope is the part
of an antigen that is recognized by the immune system.
Against these antigenic determinants or epitopes, immune cells have structures necessary for
sensing, and these structures are collectively called sensors.
Basically any type of immune cells has such sensors, and hence, they are able to recognize
molecules or cells invading into our body.
Functionally speaking, our immune system can be subdivided into two.
One is the innate immune system that provides non-specific host defense against invading
pathogens, whereas the other is the adaptive immune system that provides specific and long-
lasting immunity.
The former, the innate system is natural or "innate" to the host, and is ready to respond to
invasion and does not require a period of time for induction.
Once pathogens invade our body by breaching the skin or mucous membrane barriers, the
innate immune system is immediately activated.
As I will describe later, the major cellular components of this system include macrophages,
neutrophils, dendritic cells and natural killer cells.
If the innate immunity could not eliminate pathogens, another immune system, which is called
the adaptive or acquired immune system, is activated, and specific immune responses occur.
This system is highly specific and acquired in nature.
Most importantly, the major players of the adaptive immune system are lymphocytes such as T
cells and B cells, T lymphocytes and B lymphocytes and their products.
The reason why activation of the innate immune system promotes induction of the adaptive
immune system is because activated cellular components of the innate immune system such
as dendritic cells and also cytokines produced by the activated cells act on lymphocytes to
stimulate their proliferation, differentiation, and survival.
This slide shows you what I just mentioned.
Following microbial invasion, the innate immune system, consisting of epithelial barriers,
macrophages, neutrophils, dendritic cells, natural killer cells and so on, and also complement
components that I will explain more later, plays a major role in pathogen elimination.
As you see here, innate immunity starts to act immediately after pathogen invasion and
continues to act for many hours.
When the invading pathogen is not satisfactorily eliminated, adaptive immunity ensues.
B lymphocytes proliferate recognizing the pathogen antigenic determinants and finally produce
antibodies, which block infection and eliminates the pathogen.
When the pathogen invades the cytoplasm, T cells recognize the pathogen with the aid of
dendritic cells.
Here, you see the dendritic cell and this is a T cell.
This leads to the recognition of the pathogen, and finally eradicates the intracellular microbes.
Full-blown adaptive immune responses thus require several days.
Here I show you the major cellular components involved in innate immunity.
Some of them engulf pathogens; Macrophages, neutrophils, dendritic cells.
They are called phagocytes and others act as effector cells, releasing bactericidal proteins or
proteins that can kill microbes, and some act as cytokine producing cells.
Cytokines, such as G-CSF, IL means interleukin, IL-1, IL-6.
They mediate inflammatory and immune reactions, and are principal mediators of
communication between cells of the immune system.
A recent addition to the innate immune system is a group of cells, here, innate lymphoid cells or
ILCs.
We know now that there are, at least, three types of ILCs.
They all secrete cytokines that can activate immune cells including T and B lymphocytes.
So, in this system, you have many different kinds of cells and they secrete bactericidal proteins
and cytokines.
Most ... Quite few of them are called interleukins.
RECOGNIZING INVADERS PART 2 (VIDEO 3)

Let me now tell you about complement proteins.

The complement system is made up of over 25 proteins and protein fragments, which assist the
ability of antibodies and phagocytic cells to clear pathogens from an organism.
They are normally produced by the liver cells and circulate as inactive precursors in the blood.
When infection occurs, microbial products may activate proteases in the system, which cleave
specific proteins to release cytokines, and this amplifies a cascade of further cleavages.
The end-result of this activation cascade is massive amplification of the response and activation
of the membrane attack complex on the surface of the pathogen, which leads to killing of
microbes.
Here I show you an example of complement cascade activation by infection.
In this system, complement proteins are inactive until they are cleaved by a protease, which in
turn, converts the proteins into a protease.
For instance, binding of an antibody to a pathogen triggers the complement activation through
the so-called classical pathway.
And the antibody bound to the pathogen can activate C1, which activates C2 and C4, which
activates C3 and C5, which leads to the sequential activation of C6, C7, C8 and C9, which
finally results in the formation of the membrane-attack complex or MAC on the surface of the
pathogen.
The MAC in turn functions as a channel, allowing the passage of ions and small molecules,
which causes osmotic swelling and killing of the pathogen or infected cells.
Alternatively, when a complement component C3 binds to the microbial cell surface, this
activates a number of other complement proteins in sequence.
This is called an alternative pathway.
Some of the products induce blood vessel dilatation, histamine release from mast cells,
recruitment of phagocytes.
Some of them induce promotional microbial phagocytosis and killing locally, as you see here.
Now, in addition to the classical pathway and the alternative pathway, there is another
complements activation pathway - the lectin pathway.
Upon activation of complement proteins through these pathways, now, inflammatory leukocytes
are recruited to the site of infection, phagocytosis by the activated leukocytes is promoted, and
pathogens are killed at the site of infection.
So, you can see now how important the complement system is as a component of the innate
immune system.
INNATE IMMUNE SYSTEM ACTIVATION (VIDEO 4)

Next, I would like to explain how the innate immune system senses microbes invading our body.
As I told you a while ago, innate immune cells have sensors that detect pathogens, which are
collectively called innate immunity receptors.
These receptors are activated by mainly two types of molecular patterns.
One of them is called pathogen-associated molecular patterns or PAMPs, which are structures
produced by microorganisms but not mammalian cells.
Typical examples are microbial DNAs, RNAs, and cell wall components such as bacterial
lipopolysaccharides.
The other is called damage or danger-associated molecular patterns.
They are endogenous molecules produced by or released from damaged or dying cells.
Examples include high-mobility group box1 (HMGB1) proteins, S100 proteins, uric acid crystals,
and purine metabolites such as extracellular ATP (Adenosine Triphosphate).
Because the innate immunity receptors recognize these structures conserved or shared among
pathogens or damaged cells, they are often called pattern recognition receptors.
So, sensors of the innate system are pattern recognition receptors.
And, these pattern-recognition receptors are expressed ubiquitously.
They include cell surface-associated Toll-like receptors (TLRs) and lectin receptors that
recognize microbial cell surface components, cytoplasmic NOD-like receptors and RIG-like
receptors, and endosome-associated Toll-like receptors that recognize nucleic acids of ingested
microbes.
So, innate immunity receptors are expressed ubiquitously.
Among the pattern recognition receptors, Toll-like receptors or TLRs have been the most studied
so far.
There are at least nine different Toll-like receptors, depending on their localization, and Toll-like
receptors respond to various PAMPs and DAMPs.
For instance, Toll-like receptor-1, -2, -4, -5, and -6 recognize microbial cell wall components,
whereas Toll-like receptor-3, -7, -8, and -9, which are all expressed on the endosomal
membrane, recognize nucleic acids.
These Toll-like receptors all contain a ligand-binding domain composed of leucine-rich motifs
and a cytoplasmic signaling domain or TIR domain.
When microbial components bind to Toll-like receptors via the Toll-like receptor's leucine-rich like
domain, the signals are transmitted intracellularly via the TIR domain, and as a result, various
adaptor proteins are recruited locally, and cytoplasmic transcription factors including NF-B and
interferon-regulatory factors or IRFs are subsequently activated.
IRF activation induces production of type-1 interferons such as interferon alpha and beta, thus
inducing anti-viral states in the cell.
NF-B activation induces expression of certain proinflammatory cytokines and adhesion
molecules, both of which help promote acute inflammation.
NF-B activation also induces expression of costimulatory molecules that are required for
induction of adaptive immunity.
I will tell you more about costimulatory molecules later in this talk.
Among the innate immune receptors, NOD-like receptors or NLRs sense PAMPs and DAMPs in
the cytoplasm.
When NLRs are engaged, it stimulates the formation of the inflammasome complex, which
is a multiprotein complex that mediates activation of caspase-1, and activated caspase-1
proteolytically generates the active form of interleukin-1 or IL-1 from an inactive precursor.
IL-1 is one of the strongest cytokines that can induce inflammation.
So, because IL-1 is, so called, a typical proinflammatory cytokine, this process helps promote
inflammatory responses.
In this slide, one of the NLRs, NLRP-3, is activated by PAMPs or DAMPs, and forms oligomers
with an adaptor protein and an inactive form of caspase-1, which leads to activation of
caspase-1, which in turn activates IL-1.
IL-1 is constitutively produced in inflamed cells as inactive form.
But activated caspase-1 activates IL-1 to induce acute inflammation.
And Toll-like receptor signaling also enhances this process.
So, upon sensing of PAMPs and DAMPs, NLRP-3 oligomerizes with an adaptor protein and
inactive form of caspase-1.
Once recruited, caspase-1 is activated, and cleaves pro-IL-1 (inactive from of IL-1), to generate
biologically active IL-1.
And IL-1 induces acute inflammation and causes fever.
And among these proinflammatory cytokines, you have IL-1, IL-18, TNF (tumor necrosis factor),
and Interleukin-6 and so on.
INNATE IMMUNITY VS. ADAPTIVE IMMUNITY PART 1 (VIDEO 5)

Here I summarize some important properties of the innate immune system, compared with
those of the adaptive immune system.
First, innate immunity receptors recognize PAMPs and DAMPs, and thus their specificity is
broad.
This is also underlined by the fact that the innate immunity receptors are encoded in the
germline and do not mutate as frequently as B-cell receptors and T-cell receptors, both of which
are encoded by genes that undergo gene rearrangements and somatic mutations.
So, basically, all cells have more or less the same innate immunity receptors, whereas, as I
will explain to you later, each lymphocyte expresses a unique receptor, because lymphocytes
respond to antigens on the principle of clonal selection.
Therefore, innate immunity receptors have limited diversity compared with antigen-specific
receptors of the adaptive immune system, while both types of receptors can discriminate self
from non-self molecules.
OK, so much for the innate immune system.
I will now focus on the adaptive immune system that is more specific, more adaptable, and
hence, more potent than the innate immune system.
As you see here, the major cellular components of this system are T and B lymphocytes.
T cells express specific antigen receptors called T-cell receptor, and upon activation, they can
differentiate into several subsets, such as Th1, Th2, Th17, Treg and Tc.
These subsets are diverse in terms of how they are activated and what kind of cytokines they
produce.
On the other hand, B cells express antigen specific receptors called B cell receptors or BCRs
and consist of two major subsets, B1 and B2.
Both subsets have the potential to produce antibodies but of different properties.
Here I show you antigen receptors of T cells and B cells.
They are similar in a sense that they are polypeptides recognizing a specific antigen.
However, they are very different in structure and different in the nature of the antigen they
recognize.
For instance, a T-cell receptor is alpha-beta heterodimer and recognizes only peptides with the
aid of dendritic cells.
As I will explain to you later, a T-cell receptor recognizes so-called peptide-MHC complexes
presented by dendritic cells.
In contrast, a B-cell receptor is tetramer consisting of four polypeptides, namely two heavy
chains and two light chains.
A B-cell receptor can recognize such antigens as proteins and sugars in the absence of dendritic
cells.
This is an important point.
In the adaptive immune system, T cells and B cells have their individual function.
B cells mediate so-called humoral immunity where B cells respond to extracellular microbes by
producing antibodies that can neutralize and eliminate these molecules such as microbes and
microbial toxins.
In contrast, T cells mediate cell-mediated immunity in response to microbes or parasites that are
internalized into or synthesized in cells.
Helper T cells eliminate phagocytosed microbes by secreting cytokines and activating
macrophages, whereas cytotoxic T cells kill infected cells and eliminate reservoirs of infection.
Here I summarize important properties of the adaptive immune responses.
The responses are highly specific, because the responses are mediated by lymphocyte clones
expressing specific antigen receptors.
I will tell you more about clones a little later.
The adaptive immune responses are also highly diverse, which makes the adaptive immune
system to respond to a large variety of antigens successfully.
The adaptive immune responses can also generate memory.
When the adaptive immune system is exposed to the same antigen it has encountered before, it
remembers this and shows a more rapid and more effective response, and this is why vaccines
can confer long-lasting protection against infections.
The adaptive immune responses are self-limited and decline as the infection is eliminated.
The last not least important property of the adaptive immune system is that, although it can
respond to a whole variety of microbes and other foreign antigens, it normally does not react
with self antigens.
As you will hear later in this lecture series, self-reactivity is normally down-regulated so that no
concomitant tissue injury occurs when this system responds to foreign antigens.
INNATE IMMUNITY VS. ADAPTIVE IMMUNITY PART 2 (VIDEO 6)

Now, I will tell you about lymphocyte clones.

We have within our body many clones of lymphocytes that are specific for different antigens.
What I mean by clone here is a population of lymphocytes expressing identical antigen receptors
and hence identical specificities; here I show you three different clones for example.
These clones are derived from a single precursor cell.
They have the ability to respond to a specific antigen and proliferate subsequently.
For instance, when a B cell clone specific for antigen X encounters this the antigen X, it gets
activated and differentiates into the cells that can produce a specific antibody against X, that is,
anti-X antibody.
Similarly, when a B cell clone specific for antigen Y encounters the antigen Y, it gets activated
and differentiates into the cells that can produce specific antibody against Y, that is, anti-Y
antibody.
However, B cell clones with irrelevant specificities do not get activated and produce no antibody.
Basically, T cells also respond to antigen in an identical manner, except that they require antigen
presentation by dendritic cells, as I will describe later.
So, lymphocytes respond to antigens at the clonal level.
A particular antigen selects the clone to be activated.
So, this concept is called the clonal selection theory, which was initially put forward in the 1950s
and eventually yielded several Nobel Prize winners.
In the case of B cells, after some rounds of cell division, the antigen-responding cells, which
are called plasma cells, produce antibodies and antibodies produce membrane-bound antigen
receptors they are secreted as antibody molecules from plasma cells.
And this concept: a specific clone is selected for proliferation by antigen, is called clonal
selection theory.
Here I show you the way how the adaptive immune system responds to antigens.
The lymphocytes that are seeing antigens for the first time are called nave cells.
They are immunologically inexperienced, but upon encounter with a specific antigen, for
instance, antigen X, they mount a so-called primary response in which activated B cells secrete
antibodies specifically reactive against antigen X.
This response declines with time, but when the same antigen X comes in for the second time,
memory B cells are now activated, developing a much stronger and much more long-lasting
response, which is called the secondary response, or secondary immune response.
When a different antigen comes in, it evokes only the primary response, showing the specificity
of the adaptive immune response.
The way T cells respond to antigens is very similar to this, but T cells produce cytokines but not
antibodies.
Now, let us look at the issue of where lymphocytes are produced, where they mature, and where
they respond in the body.
All lymphocytes are derived from stem cells.
These stem cells reside in the bone marrow.
Subsequently, B cells are produced and mature in the bone marrow, whereas T cells are
produced and mature in the thymus.
The bone marrow and the thymus are thus the places where these cells are produced, and
hence, they are called primary lymphoid organs.
From these organs, only mature cells leave and enter the circulation, and continue to circulate
throughout the body.
These are nave T and B cells you find in the blood and lymphoid organs.
They may encounter specific antigens in the secondary lymphoid tissues, such as the lymph
nodes, spleen, and other peripheral lymphoid tissues, and they respond there.
If lymphocytes see antigens in the secondary lymphoid tissues, one may wonder how antigens
get into these tissues.
Microbes enter the body usually by crossing the epithelial barriers, such as those in the skin, the
gastrointestinal tract, or the respiratory tract.
Dendritic cells are abundant in these areas and capture the invading microbes and their
products.
They sense the pathogen-associated molecular patterns or PAMPs of the microbes and become
activated to produce proinflammatory cytokines.
They then lose adhesiveness to the tissue and move into the lymphatic vessels or blood
vessels.
Antigens that evaded uptake by dendritic cells also move into the lymphatic vessels and blood
vessels.
Thus, the microbes and their products are transported into the peripheral lymphoid tissues and
are subsequently recognized by T cells and B cells.
So, in the case of lymphoid antigens, antigens are delivered into lymphatics, finally a lymph
node captures these antigens and T cells respond there.
In the case of blood-borne antigens, the spleen captures antigen and immune response takes
place there.
So, antigen that enter the lymphatic vessels, are transported into lymph nodes.
Whereas those that enter the blood vessels, are transported to the spleen.
So, microbial antigens are displayed in peripheral lymphoid tissues for T cell recognition.
Upon encounters with antigens, nave lymphocytes differentiate into effector cells and memory
cells.
Here, you see nave cells, effector cells and memory cells.
B cells can recognize native antigens in the absence of dendritic cells and differentiate into
plasma cells to secrete antibodies or into memory cells that can respond to the same antigen
more rapidly and more vigorously upon a second encounter.
In contrast, T cells recognize antigens only with the aid of dendritic cells; and this step is called
antigen presentation, because dendritic cells process the internalized antigen and present it as
antigenic peptides to T cells.
T cells then proliferate and differentiate into cytokine-secreting effector cells or memory cells.
Nave cells, effector cells, and memory cells have the following properties.
Nave cells are quiescent, meaning not cycling or dividing, and live for weeks to months.
They have no effector function and migrate mainly to lymph nodes.
In contrast, effector cells are usually cycling and live only for days.
Activated B cells secrete antibodies, whereas helper T cells secrete cytokines, and cytotoxic T
cells can kill microbe-infected cells.
On the other hand, memory cells are quiescent, live long, but have no effector function,
migrating through the lymph nodes and bone marrow.
HOW DO T CELLS RECOGNIZE ANTIGEN - PART 1 (VIDEO 7)

Now, let us move on to the subject of antigen recognition by T cells.

How do T cells recognize antigens and how is it different from antigen recognition by B cells?
As you see here, T cells require dendritic cells for antigen recognition.
When microbes are coming into the tissue, they are captured by dendritic cells, they are
degraded into peptides in endocytic vesicles and transported to the cell surface.
This is antigen uptake and degradation by dendritic cells.
The microbial products enter the cleft of major histocompatibility complex or MHC molecules
and displayed as peptides to T cells.
This is antigen presentation.
When a T cell has an appropriate T-cell receptor that can recognize the peptide, the T cell
makes a conjugate with the antigen-displaying dendritic cells.
However, this alone is not sufficient for T cells to recognize an antigen successfully.
At the same time, costimulatory molecules that are expressed by dendritic cells and T cells must
bind to each other.
So, when both T-cell receptor-peptide-MHC interactions and costimulatory molecule interactions
take place, T cells can recognize antigens successfully, and as a result, they become activated.
Let us look at this issue a bit more closely.
The binding of MHC-peptide complex with T-cell receptor alone provides only one of the signals
required for T cell activation.
When antigen-presenting dendritic cells are unstimulated, they are lacking in costimulatory
molecule expression, although T cells always express costimulatory molecules such as CD28.
In the absence of costimulatory molecules binding between dendritic cells and T cells, binding
of MHC-peptide complex with T-cell receptor alone can provide only signal 1, which alone is not
sufficient for T cell activation.
So, no effective T cell responses occur.
However, when dendritic cells have been activated by microbes and/or by their products
sufficiently, they show increased expression of costimulatory molecules, such as B7, now B7 is
appearing on the surface of dendritic cells, which can provide strong binding between dendritic
cells and T cells.
The activated dendritic cells can also stimulate T cells by secreting cytokines, thus providing
another signal, which is called signal 2, that is essential for proper T cell activation.
So, T-cell receptor-MHC-peptide interactions provide only signal 1, whereas interactions among
costimulatory molecules provide signal 2 to T cells.
In order for a T cell to respond to an antigen properly, signal 1, which is antigen-specific, and
signal 2, which is not antigen-specific are both required.
So, T cell activation requires not only T cell receptor ligation with antigen, but also costimulation.
Costimulation is absolutely essential for T cell recognition.
HOW DO T CELLS RECOGNIZE ANTIGEN - PART 2 ( VIDEO 8)

Next, to better understand the molecular mechanism underlying antigen recognition by T cells,
we should understand what the MHC is.
Simply speaking, MHC is the marker of self.
Every cell in our body carries the same set of distinctive surface proteins that distinguish us as
self.
This set of markers is called the major histocompatibility complex or MHC.
There are two major classes of MHC proteins.
One group is called MHC class I proteins, and they are expressed on virtually all nucleated
cells.
The other group is called MHC class II proteins, and they are expressed only on certain types of
cells, namely, antigen presenting cells.
So, let us look at the human MHC, which is called the HLA complex.
Here I show you a schematic of the genes encoding the HLA complex.
There are at least three different genes in the class I locus, and they are called HLA-A, B, and C.
There are also at least several genes in the class II locus.
These genes are all highly polymorphic, and there are more than 1,500 alleles for HLA-A, more
than 2,000 for B, and more than 1,000 alleles for C.
Similarly, there are more than 200 alleles for HLA-DQ, more than 1,000 alleles for HLA-DR, and
more than 150 alleles for HLA-DP.
Given that MHC expression is co-dominant, that means that the alleles inherited from both
parents are expressed equally, every person expresses at least six MHC class I alleles and at
least six MHC class II alleles.
Because these alleles are inherited and expressed virtually in any combination, every individual
is likely to express HLA class I and class II proteins that differ from those of another individual.
So, just like a fingerprint, no two person's set of HLA markers are exactly alike except for
identical twins.
Here you see an exception.
I am actually one of twin brothers.
This is a photograph of myself and my twin brother.
We were 5 or 6 years old at the time.
These 2 photos are more recent ones.
My brother Nobu is a rheumatologist, and myself, Masa, is an immunologist.
Between these two persons, MHC proteins are completely shared.
So, HLA class I and class II proteins that I express are completely identical to those of my
brother.
So, I would assume that antigenic peptides presented by our MHC molecules would also be
almost identical or very similar between these two brothers.
But an interesting thing is that our immune responses are not identical; I am allergic to pollens
but my brother is not.
This is probably because T-cell receptors and B-cell receptors we express are not likely to
be identical; this is because T-cell receptor and B-cell receptor diversities depend mainly on
somatic recombination of the DNA encoded segments in individual cells.
I will come back to this issue a little later.
Here I show you the structure of MHC proteins.
The left shows a 2-Dimentional structure, whereas the right shows a ribbon diagram of MHC
Class I proteins.
Each Class I MHC proteins consist of an alpha chain noncovalently associated with a protein
called beta2 microglobulin, here you see microglobulin and here is an alpha chain.
Similarly, each Class MHC class II molecules consist of two chains, called alpha and beta
chains.
In the case of Class I, the alpha 1 and alpha 2 domains form a peptide-binding groove or cleft
that can accommodate peptides of 8 to 11 amino acids.
Class II molecules also have a peptide binding groove, which is formed by alpha 1 and beta 1
domains, and can accommodate peptides of approximately 15, and they are actually 10 to 30
amino acid residues.
Thus, although Class I and Class II proteins are slightly different in subunit composition, they
are very similar in overall structure, and both can display antigens for recognition by T cells.
So, MHC molecules are membrane proteins that can display peptide antigens for T cell
recognition; Importantly, MHC I proteins are expressed by all nucleated cells, whereas MHC
class II proteins are abundantly expressed in antigen-presenting cells.
They are dendritic cells, macrophages and in some cases, B cells.
Here I show you how peptides, shown in yellow, lie on the peptide-binding groove of MHC
molecules and are available for recognition by T cells.
Each MHC Class I molecule can bind a peptide consisting of nine amino acids, whereas each
Class II molecule can bind a peptide consisting of 10-30 amino acids.
Peptide binding to MHC molecules requires the presence of characteristic residues in the
peptide.
As shown in the bottom panel here, these residues are called anchor residues.
These anchor residues anchor the peptide into the pocket of the binding groove, where they
interact with amino acids of the binding groove.
An important thing here is that each MHC molecule can present only one peptide at a time,
because there is only one binding groove, but that each MHC molecule is capable of presenting
many different peptides.
Then, where do these peptides come from?
These peptides are derived from protein antigens that are inside the host cells.
In the case of MHC Class I molecule, peptides derived from cytosolic proteins bind to its groove,
whereas in the case of MHC Class II molecule, peptides derived from proteins that are taken up
into intracellular vesicles bind to its groove.
Now, let me tell you a little bit more about antigen presentation.
As shown here, when a microbe or microbes enter the cell, microbial proteins are degraded into
peptides and bind to class I MHC in the endoplasmic reticulum or ER, and the MHC peptide
complex is subsequently delivered to the cell surface.
In this case, a T cell subset expressing CD8 recognizes the MHC-peptide complex.
So, the first event is antigen uptake, followed by antigen processing within antigen-presenting
cells.
And because MHC proteins are constitutively produced and enter the endoplasmic reticulum,
the MHC and peptide meet and are delivered to the cell surface, and finally presented to T cells.
This is the MHC class I pathway.
In contrast, when microbes are endocytosed, they enter the endocytic vesicle and are degraded
into peptides in infected cells.
Because class II molecules enter the same vesicles, they bind to these peptides and are
transported to the cell surface.
In this case, a T cell subset expressing CD4 recognizes the MHC-peptide complex.
So, once again, the first event is, here, antigen uptake, followed by antigen processing and
then you have MHC biosynthesis, and peptide-MHC association, and finally these peptides are
presented on cell surfaces to be recognized by T cells.
This is the MHC class II pathway.
HOW DO B CELLS RECOGNIZE ANTIGEN - PART 1 (VIDEO 9)

So, T cells recognize antigens complexed with MHC molecule.

Then, how do B cells recognize antigens?
The way B cells respond to antigens is much simpler than that of T cells.
As you see in this slide which I showed you before, lymphocytes respond to antigens at the
clonal level.
When antigens bind to a B-cell receptor appropriately, only the B cell clone expressing the B-cell
receptor starts to proliferate, and after several rounds of cell division, the proliferating B cells
differentiate into antibody-secreting plasma cells.
The antibody molecules secreted from the plasma cells have the same antigen-binding site as
the initial B-cell receptor.
So, one can say that antibodies exist in two forms one as membrane-bound antibodies on B
cells, and the other as secreted antibodies.
Membrane-bound antibodies or B-cell receptors are used for antigen recognition and also signal
transduction into B cells, whereas secreted antibodies are also specific to antigens, and can kill
invading microbes and neutralize their products.
So, a specific clone is selected for proliferation by antigens, and eventually produces antibody
molecules in the case of B cells.
In the case of T cells, activated T cells produce cytokines.
In this slide, I show you membrane-bound IgM on the left and secreted IgG on the right.
Both of them are immunoglobulins and have two identical heavy chains and two identical light
chains, with each chain containing a variable region and a constant region.
In this picture, V and C mean variable and constant, respectively.
And, each loop-like structure, you find quite a few of them on the structure of immunoglobulin,
this loop is called the immunoglobulin domain or Ig domain.
On the N-terminus, you see two identical antigen-binding sites consisting of the V regions of the
heavy chain and the light chain.
This is the same with IgG.
The rest of the antibody molecule, this part, the rest of the antibody molecule is required for
structural integrity and effector functions.
The C-terminal end of the heavy chain may be anchored in the cell membrane, as seen with
membrane-bound IgM, or it may have no such anchoring domain so that the antibody is
produced as a secreted protein, as you see with secreted IgG.
As you see in this slide, there are at least five different antibody or immunoglobulin isotypes,
IgG, IgE, IgD, IgA and IgM.
IgM found in plasma is pentameric, five-mers.
And they play an important role for early stage protection against pathogens.
IgG is the major immunoglobulin playing an important role in mid- to late-stage protection
against invading pathogens.
Both IgM and IgD are expressed on nave B cells as membrane-bound.
IgA is mainly found in the mucosa and prevents colonization by pathogens.
IgE binds to allergens or molecules that induce allergy, and triggers histamine release from mast
cells.
So, each isotype has distinct biological properties and effector functions.
It is important to remember that, upon antigen stimulation, IgM is produced first.
Then, how are these different Ig isotypes produced?
Upon activation, B cells differentiate into plasma cells and usually secrete IgM.
However, when helper T cells are activated concurrently, various signals derived from the
activated T cells determine which Ig isotype is to be produced.
For instance, when Interferon-gamma is provided by helper T cells, B cells switch to IgG
subclasses, whereas when IL-4 is provided, B cells switch to IgE.
In the mucosal tissues, locally produced cytokines such as TGF beta and BAFF help switch B
cells to secrete IgA.
So, it is mainly helper T cells and also microenvironment that influence which Ig isotype to be
produced at a given time during the course of immune responses.
This is isotype switching.
These immunoglobulin isotypes have different effector functions as you see in this slide.
IgM promotes complement activation in the classical pathway, IgG subclasses play an important
role in Fc receptor-dependent phagocyte responses; they also activate complements and play
an important role in neonatal immunity, because IgG can cross the placenta.
IgE is important for immune responses against helminths by inducing degranulation in mast
cells.
IgE also causes an immediate type of hypersensitivity by inducing mast cell degranulation.
IgA is important in mucosal immunity; IgA is transported through the intestinal epithelial cells
and displayed in the intestinal lumen; such IgA is important for neutralization of microbes and
microbial toxins.
Therefore, immunoglobulins are essential for protection against pathogens.
HOW DO B CELLS RECOGNIZE ANTIGEN - PART 2 (VIDEO 10)

Next, I would like to briefly explain how antigen receptors or antibody diversity are generated.
Genes for antibodies and T-cell receptors are present in pieces that can be combined in many
different ways in different lymphocytes.
This is called combinatorial diversity, which is the method by which functional antibody genes
are created.
It involves the rearrangement of many gene segments that code for the heavy and light chain
proteins of immunoglobulins or alpha and beta chains of T-cell receptors, and it only occurs in
lymphocytes.
For instance, this shows the germline organization of immunoglobulin heavy chain genes.
There are more than 100 V segments, about 30 D segments, and 6 J segments, and these
three segments are joined together in a random combination.
The very first rearrangement that occurs in lymphocyte DNA joins D and J segments, which is
called D-J joining.
The next rearrangement brings one of the V genes together with the DJ segments jointed
previously, which results in V-D-J joining.
The result is a transcription unit consisting of one V, one D, one J, and one C gene arranged in
this order.
The primary transcript is spliced to yield a messenger RNA consisting of one V, one D, one J,
and one C segment.
This is translated into a polypeptide corresponding to the complete heavy chain.
Given that there are more than 100 V segments, about 30 D segments, and 6 J segments and
that these three segments are joined together in a random combination, this already allows
more than 10,000 combinations at this level.
So, the fundamental principle governing antibody generation is combinatorial diversity, which is
realized by somatic recombination of different gene segments.
So, somatic recombination is the key to create diversity in antigen receptors.
OK.
So, diversity of immunoglobulins and T-cell receptors is produced mainly by random combination
of V, D, and J gene segments.
This somatic recombination occurs not only in the heavy chain but also in the light chain, so the
number of possible combinations goes up to the order of 1 million in the case of immunoglobulin.
Basically the same principle works in the T cell receptor genes, and possible combination arising
on this recombination in this case is the order of 3 million.
Each different combination yields an antigen receptor with a different specificity.
The reason why such recombination occurs only in lymphocytes is because only lymphocytes
express the VDJ recombinase, which is an enzyme required for this recombination.
In addition, this diversity is further increased by adding or deleting nucleotides at the junctions,
which is induced by imprecision of the joining.
This mechanism is called junctional diversity and this is estimated to add up to 10 fold to overall
diversity.
Thus, the total potential repertoire of immunoglobulin is the order of 10 in the case of B cell
receptors, and this is even larger with T-cell receptors.
OK, so this is the very important issue in the generation of antigen receptor diversity.
And, once again, I will repeat that potential repertoire of immunoglobulin is the order of 10, and
this is even larger with T-cell receptors.
Let me describe one more thing about antigen receptors, which is about how they transmit
signals into the cell.
Upon antigen binding, neither a T-cell receptor nor a B-cell receptor can deliver a signal on its
own.
It is the associated invariant chains that can deliver intracellular signals.
In the case of B cells, Ig-alpha chain and Ig-beta chain, these are so-called signaling proteins.
And these signaling proteins are brought into proximity and close to the antigen receptors and
trigger complex signaling cascades in the case of B cells.
Here in the case of T cells, you have CD3 molecule, and together with the function of the T-cell
receptor, this antigen receptor and CD3 signaling, you have effective signal transduction.
Therefore, antigen receptors are non-covalently attached to other invariant molecules the
function of which is to deliver to the inside of the cell the activation signals that are triggered by
the antigen recognition.
Finally, I summarize my talk using two slides which I showed you before.
First, following microbial invasion, the innate immune system plays a major role in pathogen
elimination.
Innate immunity starts to act immediately after pathogen invasion and continues to act for many
hours.
The major cellular constituents would be phagocytes, that is, neutrophils, dendritic cells and
macrophages, you need complements and you also need NK cells.
Subsequently, adaptive immunity follows.
B lymphocytes proliferate recognizing the pathogens antigenic determinants and finally produce
antibodies, which block infection and eliminate the pathogen.
In contrast, T cells recognize the pathogen with the aid of dendritic cells.
They proliferate, and finally eradicate the intracellular microbes.
Full-blown adaptive immune responses thus require several days.
So, please remember that innate immunity provides the initial defense against infections, and
adaptive immunity follows next to provide more specific and long-lasting infections.
OK, so much for the general introduction.
I hope that my lecture helps you build up fundamental knowledge about immunology and will
also help you obtain a good understanding of the rest of the present lecture series.