UNIVERSITY OF DEBRECEN

FACULTY OF MEDICINE
DEPARTMENT OF IMMUNOLOGY

PÉTER GOGOLÁK – GÁBOR KONCZ

Elementary Immunology
Short textbook for BSc students

Debreceni Egyetemi Kiadó

Debrecen University Press
2017
INDEX
PREFACE............................................................................................................ 5
INTRODUCTION .................................................................................................. 6
What can be recognized by the immune system? ........................................ 6
Signs of biological danger ....................................................................................6
The antigen ..........................................................................................................6
Destroying pathogens and tumour cells ....................................................... 7
THE STRUCTURE AND ORGANIZATION OF THE IMMUNE SYSTEM ........................ 8
Primary lymphoid organs ............................................................................. 8
Secondary lymphoid organs and the lymphatic system: .............................. 9
PROPERTIES AND CELLS OF THE INNATE AND ADAPTIVE IMMUNE RESPONSES .. 13
Phagocytes and other cells of innate immunity .......................................... 15
Cells of the adaptive (acquired) immunity ................................................. 19
Communication between immunocytes: cytokines and cell surface
molecules .................................................................................................... 20
THE INNATE IMMUNE SYSTEM ......................................................................... 22
Recognition of pathogens by the innate immune system: danger signal
sensing receptors, pattern recognition, opsonins ........................................ 22
Elimination of pathogens by the innate immune system............................ 25
The alarm system of the body: the acute inflammation ............................. 27
The function of the complement system .................................................... 30
MHC MOLECULES, ANTIGEN PRESENTATION ................................................... 31
The MHC molecules .................................................................................. 32
MHC I and MHC II .................................................................................... 32
Antigen presentation .................................................................................. 33
MHC I .................................................................................................................33
MHC II ................................................................................................................35
B- AND T CELL RECEPTORS.............................................................................. 37

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 Generation of Lymphocyte diversity.......................................................... 41
Clonal selection of T- and B lymphocytes and development of tolerance. 42
FUNCTIONS OF B CELLS AND EFFECTOR FUNCTIONS MEDIATED BY ANTIBODIES
........................................................................................................................ 45
Antigen presentation by B cells ................................................................. 45
B cell effector functions: the function of antibodies .................................. 46
Neutralization ............................................................................................. 48
Effector mechanisms mediated by the Fc part of the antibodies................ 50
T CELLS ........................................................................................................... 52
T cell subsets and their functions ............................................................... 54
THE IMMUNOLOGICAL MEMORY, PASSIVE AND ACTIVE IMMUNIZATION .......... 57
Characteristics of the memory response..................................................... 58
Immunization ............................................................................................. 59
Passive immunization ........................................................................................60
Active immunization and vaccines ....................................................................60
IMMUNOLOGICAL TOLERANCE......................................................................... 61
COMMUNICATION BETWEEN THE INNATE AND ADAPTIVE IMMUNE SYSTEM ..... 62
THE PROCESS OF IMMUNE RESPONSE ............................................................... 63
Bacteria, viruses and parasites ................................................................... 65
DISORDERS OF IMMUNE SYSTEM...................................................................... 69
Allergic diseases ......................................................................................... 70
Autoimmune diseases ................................................................................. 71
Immune complex diseases .......................................................................... 72
Immunodeficiencies ................................................................................... 74
GLOSSARY....................................................................................................... 75

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Preface
This textbook is primarily intended for BSc students, but it is useful for
everyone who seeks fast basic knowledge in the field of immunology. The
information provided also makes the understanding of the “full-bodied”,
advanced level immunology text books easier. The length of the text is kept
limited and a significant part of it is constituted in the glossary, which contains
the most important terms of the fields of biology and immunology. These terms
are indicated in the text by italic typeface at their first appearances.

5
Introduction
The main function of the immune system is protection of the body against
various pathogens, different biological toxins and even against altered,
dangerous, abnormal cells inside the body. The two chief and clearly distinct
functions of the immune system are recognition of the dangerous and/or
pathogenic structures followed by the elimination/neutralization of these
structures.

What can be recognized by the immune system?

Signs of biological danger
Microbes differ significantly from the cells of our own body. These differences
are manifested in their building materials, physical and chemical structure.
Most of these are completely absent from our cells, while they are
characteristic of various taxonomic groups of microbes or other pathogens
(viruses, bacteria, uni- and multicellular parasites). Typical examples of these
small conserved molecular motifs are double stranded RNA of some viruses,
or lipopolysaccharides (LPS) found in the cell wall of the Gram-negative
bacteria. These materials are collectively referred to as pathogen-associated
molecular patterns, or PAMPs. The immune system can effectively sense the
presence of these chemical structures with relatively few receptors called
pattern-recognition receptors, PRRs, and interprets them as “danger”.
Engagement of PRRs evokes strong activation signals. In addition to the above
mentioned microbe-derived danger signals, injury or abnormal processes in the
body may also act as danger signals resulting in the activation of PRRs. In the
case of cell damage intracellular materials can appear in the extracellular space
(outside of the cell). This presents a danger signal and alarms the immune
system even in the absence of pathogens. These types of danger signaling
molecules are called as damage-associated molecular patterns (DAMPs).
The antigen
The concept of antigen is easily understandable, yet antigen is one of the most
ill-defined terms in immunology. As a general definition, the antigen is an
entity recognized specifically by the B- and T-lymphocytes. The focus of this
definition is on “specificity”. This presumes the presence of highly specific
receptors that can bind to a given material or structure, but fail to recognize
others. These extreme specificities have been demonstrated by experiments in
which some small chemical modifications of an antigen can render an antigen
unrecognizable by the receptor which had been recognized in its original form.
Or it may work the other way around; after chemical modification the altered
antigen can be recognized with high specificity by another receptor which,

6
before the modification, was unresponsive to it. Though in most cases small
changes do not cause such a drastic effect in antigen recognition: modifications
usually result in small changes in the binding affinity of the receptor to its
specific antigen. The immune system can produce a vast variety of highly
specific antigen receptors (in the order of billions). This receptor diversity is
achieved by an elegant and sophisticated molecular genetic mechanism. An
individual cell produces only one type of antigen-specific receptor, so one
lymphocyte is specific to only one type of antigen. Based on these we can
create a simple but seemingly circular definition: The antigen is an entity
recognized by the antigen receptors.
It is important to note, that not only pathogens can be considered as antigens.
Antigen recognition could involve the recognition of the self-derived
materials, but normally these don’t provoke a destructive immune response.
The immune system is normally tolerant to self-antigens. According to the
response following antigen recognition, we can classify immune responses into
immunogenic and tolerogenic immune responses, and antigens into
immunogenic and tolerogenic antigens (as discussed later).
What terms should be used to describe immune recognition?
Lipopolysaccharide, a bacterial cell wall component or a viral double stranded
RNA should be considered as a PAMP, when it is recognized by pattern-
recognition receptors on various cell types. However, these structures are
referred to as antigens when discussed from the point of view of lymphocytes
that recognize them with their antigen-specific receptors, potentially capable
of recognizing minor chemical or structural differences in PAMPs. Generally
the first recognition of the pathogens and other danger signals are mediated by
PRRs, and the fine recognition and distinctions between self, non-self or
modified self-molecules are mediated by lymphocytes with antigen receptors.

Destroying pathogens and tumour cells

The elimination of the pathogens, infected cells and dangerous tumour cells
can be mediated by only a few mechanisms. Defense mechanisms against
extracellular and intracellular pathogens are based on distinctly different
mechanisms. Extracellular pathogens can be directly attacked by the immune
system while elimination of the intracellular pathogens is almost always
mediated by killing of the infected cells. Elimination of tumour cells is similar
to that of cells infected with intracellular pathogens.

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The structure and organization of the immune system
The cells of the immune system can be found almost everywhere throughout
the body. Some of them operate “lonely” residing in various peripheral tissues.
Immune cells can even be found in the epidermis. Others, together with several
other immune cell types assemble into immune tissues with various levels of
complexity. Lots of immune tissue ‘isles’ (follicles, folliculi) can be found in
the mucosal membranes. At several places the immune tissues are organized
into smaller or larger organs called lymphoid organs. The so called primary
lymphoid organs are responsible for the production of the immune cells
(interchangeably called ‘white blood cells’). The secondary lymphoid organs
are sites where cells of the adaptive immune system (the B- and T-
lymphocytes) can first encounter the antigens. The secondary lymphoid organs
provide an appropriate environment for the activation, proliferation, and
differentiation of the lymphocytes.

Primary lymphoid organs

The red bone marrow is located in the spongy bone tissue of various bones. All
the blood cells, so almost all white blood cells (leukocytes) including the
lymphocytes of the immune system derive from the red bone marrow. The
development of these cells starts from stem cells (hematopoietic stem cells).
The stem cells in the red bone marrow initially differentiate into some
specialized immune cell type in response to various/specific cytokines, and
other chemical and local environmental stimuli. Two large developmental
lineages can be defined:
The myeloid lineage gives rise to the macrophages, dendritic cells, mast cells,
and granulocytes. The other developmental pathway, the lymphoid lineage,
provides the precursors of lymphocytes, which finally develop into B cells, T
cells, or NK-cells. (Figure 1.)

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Figure 1. The development of immunocytes in the red bone marrow
The cells of the immune system develop from the haematopoietic stem cell derived myeloid-
and lymphoid precursor cells

The red bone marrow and the thymus are the two primary lymphoid organs in
the body as they are the sites of lymphocyte development. The progenitors of
T-lymphocytes exit the bone marrow and enter the thymus where they
complete their development. There is no active (immunogenic) immune
response in the protected environment of the primary lymphoid organs. In
healthy individuals pathogens are absent in the primary organs because this is
a place where self-materials of the body (the self-antigens) are typically
introduced to the developing lymphocytes. The cells of the adaptive arm of the
immune system can meet the self-antigens here, and can ‘learn’ the antigens
which should be considered as harmless, and thus, must be tolerated. Thanks
to this ‘education’ the lymphocytes that leave the primary lymphoid organs
will tolerate self-antigens present in both the primary lymphoid organs and the
peripheral tissues of the body. You can find more information about these
processes later in the ‘Immunological tolerance’ chapter.

Secondary lymphoid organs and the lymphatic system:

Secondary lymphoid organs are the activation sites of the adaptive arm of the
immune response. Lymphocytes which successfully leave the primary
lymphoid organs are called naïve lymphocytes, because they have not yet

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encountered their specific antigen. naïve lymphocytes migrate into the
secondary lymphoid organs, where they can meet and recognize microbial
antigens. Antigen recognition induces activation of the naïve lymphocytes,
which as a result, will proliferate and differentiate to become fully functional,
‘effector’ lymphocytes.
The blood transports nutrients and oxygen for the cells and tissues of the body.
Some components of the blood plasma are filtered out from the capillaries into
the tissues. This fluid, also known as lymph, contains various metabolic
products of the tissue cells, or in case of an injury, microbes or other foreign
materials from the environment.
Lymph is collected by the lymphatic capillaries. Lymphatic capillaries are
glove-like structures that originate in the tissues with closed ends and unite to
form small lymphatic vessels, and later the lymphatic system. Foreign antigens
are transported by the lymph into a nearby lymph node (also called as the
draining lymph node) which provides a convenient checkpoint for monitoring
antigen content of the lymph. The lymph filtered through the lymph node will
enter into a larger lymphatic vessel. The small, bean shaped lymph nodes are
distributed along the lymphatic vessels. They can form small groups in some
parts of the body, the neck, armpits, groin or the abdomen, in particular. The
continuously migrating cells of the immune system can gather in special, well
defined compartments of the lymph nodes to encounter the accessible antigens,
and to meet and communicate with other cells of the immune system. (Figure
2.)

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Figure 2. The scheme of the lymphatic system and the lymph node.
The lymphatic circulation is a network of lymphatic capillaries, small and larger lymphatic
vessels that collects and transvers lymph into the venal blood. Lymph enters the regional
lymph node via the afferent lymphatic vessels. Lymph exits the lymph node via a single, large
efferent lymphatic vessel and continues its journey further in the lymphatic system. The
lymphocytes can encounter the antigens within the B- and T cell zones of the lymph node.

The secondary lymphoid organs are the places where the lymphocytes meet
their specific antigens the first time. If B- and T-lymphocytes “camping” in
lymph nodes meet the antigen to which they possess a specific antigen
receptor, they recognize it. After binding the antigen, provided other necessary
activation signals are also received, they rapidly go through several cycles of
cell division (proliferation). Thus, at the end of this process the number of
antigen specific lymphocytes is increased many fold. The non-specific

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lymphocytes, which fail to recognize any antigen will exit the secondary
lymphoid organ sooner or later. They leave via the efferent lymphatic vessel,
subsequently enter other secondary lymphoid organs/tissues and eventually,
they will return into the blood circulation. They repeat these cycles until they
find an appropriate antigen. If they fail to meet their specific antigen within a
few days or for some cells for a few weeks they will die by apoptosis.
Antigens not only enter the lymph nodes passively carried by the lymph. They
can also be transported by phagocytic cells patrolling the tissues e.g. tissue
macrophages and dendritic cells. These cells can engulf different antigens and
actively transport them into the local lymph nodes using the lymphatic vessels.
Once they have arrived at the lymph node they present the engulfed and
processed antigens to the assembled T-lymphocytes.
Lymphocytes can use both the lymphoid vessels and the blood vessels for
traveling throughout the body. They generally enter the lymph nodes through
the special kind of post-capillary veins called high endothelial venules, present
in the lymph node. Lymphocytes exit the nodes through the efferent lymphatic
vessel. They use the lymphatic system to travel back into the bloodstream. The
lymphatic and the blood circulation is directly connected at the shoulder-neck
region of the body. By the help of the left and right large main collecting
lymphatic ducts the lymph, together with the travelling cells returns into the
large veins. This way the lymphocytes can visit a large number of lymph nodes
in all parts of the body in a relatively short time in order to find pathogen-
derived antigens.
It is important to note that the naïve lymphocytes usually can’t get access to
the tissues where the pathogens enter the body (skin, mucosa). But after their
efficient activation in the secondary lymphoid organs, they become fully
functional effector lymphocytes which can reach the peripheral tissues.
The spleen is a long flat secondary lymphoid organ located at the upper left
part of the abdomen. Similar to lymph nodes, the spleen has compartments,
where the immune cells can communicate with each other, and can be
activated. The spleen doesn’t have direct (afferent) connection with the
lymphatic vessels, instead it functions as a filter of blood. The assembled
lymphocytes in the spleen can encounter the antigens present in the blood.
Lymphoid tissues (follicles) can be found at several locations in the body.
Significant lymphoid tissues can be found in the wall of the digestive system
and in the airways which are the main gateways of infection by various
pathogens. Such lymphoid tissues are present in the tonsils and in the adenoid
of the upper respiratory tract, in Peyer's patches found within the wall of the
small intestine, or in the appendix of the coecum.

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Multiple cell types may participate directly or indirectly in the immune
response. In addition to cells various body fluids contain components essential
to the coordinated operation of the immune system. Depending on whether the
cellular or the soluble component plays a more prominent role in a particular
response we call it a cellular- or humoral immune response, respectively.

Primary lymphoid organs Secondary lymphoid organs

 red bone marrow and  spleen, lymph nodes, the different skin-,
thymus gut-, respiratory tract associated lymphoid
 production and initial tissues
differentiation of  induction sites of the adaptive immune
immunocytes response (not exclusive, mainly connected
 the main sites of the with the adaptive immune response)
development of  site of lymphocyte activation and
immunological differentiation of naïve lymphocyte into
tolerance effector cells

Properties and cells of the innate and adaptive immune

responses
The elements of innate immunity appear long before birth, and are
constitutively present in the body. Its components are generated continuously,
their production can only be increased moderately, even when they are needed.
Thus, certain elements of the innate system can be exhausted. Nevertheless,
innate immunity can provide an immediate response because its components
are always present in the body. The innate immune responses are not antigen
specific. It senses various „danger” signals released from microbes or by
damaged tissues. During an immune response the number of innate immune
cells shows only moderate changes. Though infections can induce a small
increase in cell numbers, rather the localization and activation state of the cells
will be changed.
Cells of the innate immune system are constantly renewing to replace old dying
cells ensuring continuous responsiveness of the system. The typical cellular
elements of the innate immunity are granulocytes, dendritic cells,
monocytes/macrophages and NK (natural killer) cells. Its humoral components

13
include the complement system (described later), antimicrobial proteins,
enzymes or peptides.
It has been observed centuries ago that people who survived the ravages of an
epidemic were untouched when faced with that same disease again – they had
become immune to infection. The reason for this is that during the first
(primary) immune response in addition to activated effector B and T cells
memory B and T cells are also formed. During the subsequent exposure to the
same pathogen, thanks to the presence of long-lived antigen specific memory
cells, the immune system is ready to launch a faster, more intensive and thus
much more effective immune response. This kind of antigen specific immune
response – characterized by memory and improved response upon second
exposure - is called acquired or adaptive immune response.
Active adaptive immunity is not yet present in the newborn. However, the
adaptive immune system continuously produces new lymphocytes with diverse
antigen specificity. Only a few of these (naïve) lymphocytes are able to
recognize a particular pathogen, therefore, only a small number of
lymphocytes are available to respond to any given pathogen. When an antigen
enters the body, only a few cells will respond, but they will divide intensively
to produce a large number of effector cells which can successfully fight even
the fast-growing microbes. The immune system shapes its response according
to its actual challenges. The number of effector cells gradually decreases after
they have completed their functions, however, some long-lived memory cells
will survive, providing protection should the same pathogen be detected again.
Activation, proliferation and differentiation of lymphocytes take time,
therefore, relatively longer time (about one or two weeks) is necessary to
achieve the maximal response following exposure to an antigen. However the
immune system can react more quickly the next time it comes into contact with
the same antigen because of the presence of memory cells that have gone
through an initial proliferation and differentiation process. Only a few days (3-
5 days) is sufficient to boost the immune response again.
The cellular components of the adaptive immunity are T and B cells bearing
antigen-specific receptors. Its humoral elements include immunoglobulins or
antibodies produced by plasma cells that differentiate from B cells. Antibodies
can be found almost everywhere in our body.
The immune system consists of a wide range of different cell types including
lymphocytes and also various types of phagocytes. The cells of innate
immunity are able to fight different kinds of invading pathogens while a given
cell of adaptive immunity is designed to recognize only one specific target by
its antigen-specific receptor with high efficiency. For an effective response the

14
immune cells need to communicate with each other. Sometimes a direct cell-
cell contact among the immune cells is required, while at other times cells use
soluble messenger molecules for communication. The freshly generated, so-
called „naïve" lymphocytes – which have not encountered their antigens yet –
are unable to function without previous interaction with other immune cells. In
this case they may become functionally unresponsive after antigen exposure.
This state of the cells is referred to as anergy.
The components of innate immunity are essential for the activation of adaptive
immunity, in return some elements of the adaptive immunity can facilitate
some of the functions of natural/innate immunity. Thus, the two systems work
in concert supporting each other’s functions.
Innate Immunity Adaptive Immunity
 requires several days to
 immediate reaction
develop
properties  not antigen specific
 antigen-specific
 no memory
 has memory
monocytes/macrophages
dendritic cells B cells
cells granulocytes
mast cells T cells
NK cells

Phagocytes and other cells of innate immunity

The cells of the innate immune system include phagocytic cells such as
monocytes/macrophages and the dendritic cells. These large cells are able to
engulf, kill and digest microbes, but they are also involved in the phagocytosis
of other materials, for example dead cells or cell debris. In the case of these
cells phagocytosis is not only the function of the elimination of the engulfed
material. The processing and „presentation” of pathogen-derived ingested
materials to lymphocytes plays an important role in the activation of the
adaptive immune response.
The following section provides an overview of innate immune cells:

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 Monocytes which circulate in the blood are the precursors
of phagocytes. After entering the tissues they differentiate
into macrophages or into dendritic cells. Specialized
macrophages found in various tissues and organs often have
different names. For example, macrophages are referred to
as microglia in the central nervous system, Kupffer cells in
the liver, osteoclast in the bones, alveolar macrophages in
the lung and histiocytes in connective tissues.

The macrophages are perhaps the most ancient cells of the

immune system, with numerous functions.
 During bacterial infections macrophages are one
of the first cell types which recognize the pathogen.
 After detection of pathogens they may be able to
destroy them alone.
 Upon activation, macrophages secrete messenger molecules
(cytokines) which induce local inflammation and recruit other immune
cells to the site of infection.
 As professional antigen-presenting cells (APC), macrophages
participate in the induction of the adaptive immune response.
 In addition to engulfing and elimination of foreign antigens, dead cells
or tissue debris of various sizes, macrophages also play an important
role in the regeneration of damaged tissues, mainly by the secretion of
growth factors.
The name macrophage – as discussed above – does not necessarily refer to a
specific cell type, rather it is a collective name of cells with similar functions.
The functions listed above are often divided among the different subtypes of
the macrophages.

Granulocytes with typical morphological properties are the

effector cells of innate immunity against bacteria and some
eukaryotic parasites. Their cytoplasm contains a large
number of preformed granules with powerful antimicrobial
substances for the elimination of parasites or microbes.
Neutrophil granulocytes are the most abundant members of the granulocyte
family that also represent the most abundant population of circulating white

16
blood cells in the human body. These phagocytes are real „kamikaze cells”
specialized only for the destruction of bacteria/pathogens. In healthy
individuals neutrophils circulate in the blood stream and they are absent from
healthy but not from inflamed tissues. In the case of an injury or pathogen
exposure, a large number of neutrophil granulocytes migrate quickly from the
blood to the sites of infection following chemical signals such as cytokines and
chemokines produced by danger signal-sensing cells (e.g. macrophages). At
the site of infection they engulf the bacteria or release the substances stored in
their granules to eliminate the pathogens. Subsequently, neutrophils die by
programmed cell death in a short time capturing the bacteria in their own
apoptotic bodies. Later, the dead cells and other cell debris are cleaned up by
macrophages.
The main functions of eosinophil and basophil granulocytes are similar to
that of mast cells to be discussed later in this section. By special toxic
substances stored in their granules they provide protection against unicellular
and multicellular eukaryotic parasites that are too large to be taken up by
phagocytosis. Eosinophils and basophils also play a pivotal role in the
development of allergic reactions (described later).

Dendritic cells were named based on their branch-like

projections, similar to the dendrites of neurons. Like
macrophages, they also have various subtypes in
different tissues and organs. During infection, as most
innate cells, dendritic cells detect the pathogens
immediately. However, the main function of dendritic
cells is not the direct elimination of pathogens, rather
to deliver pathogen-derived antigens into the lymph
nodes and present them to various types of T cells. Because of this activity they
are called professional antigen-presenting cells. Immature dendritic cells
localize in the peripheral tissues mainly at the sites of pathogen entry (skin,
gut, and lung). In these tissues their functions are the immediate recognition
and uptake of pathogens. Activation by the recognition of harmful microbes
induce characteristic changes in dendritic cells. They start to migrate into the
draining lymph nodes through lymphatic vessels and they increase the
expression of cell surface molecules essential for the activation of other
immune cells. In the lymph nodes dendritic cells present the antigen in
complex with MHC molecules for T cells (a more detailed description of the
process will be provided in later sections). It is important to note that as the
most effective professional antigen-presenting cells, dendritic cells are able to
activate „naïve” T cells freshly released from the thymus.

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 The natural killer cells (NK cells) are a special class of
lymphocytes. Similar to cytotoxic T cells they take part in
the elimination of infected or malignant cells of the host.
They store pre-formed toxic substances in their granules.
They destroy the target cells by releasing the substances of
these granules or by direct cell-cell interaction. In addition
to the recognition of pathogen-associated molecular patterns and opsonins
(described later), NK cells are specialized for sensing of typical stress-induced
molecules on the surface of infected or tumour cells. However, the healthy host
cells block the function of NK cells through inhibitory NK-cell receptors. Cells
bearing „normal” self-markers are not attacked by NK cells. Furthermore NK
cells are very aggressive toward cells that are missing „normal” self-markers.
Overall, the activation of NK cells is regulated by the balance of inhibitory and
activating signals. (a more detailed description of the process will be provided
in later sections).

Mast cells provide protective immune responses against

parasites. Mast cells unlike the functionally similar
basophil granulocytes, are localized in various tissues,
e.g. in the skin or in the wall of the bronchoalveolar or
gastrointestinal tracts. The mediators of these cells
released from their granules are responsible for the
symptoms of allergic reactions; however, these mediators
had originally evolved for the elimination of multicellular parasites.

Platelets (thrombocytes) are blood circulating fragments derived from

megakaryocytes, their large precursor cells present in the bone marrow. They
also contain granules in their cytoplasm. Platelets play a role in the formation
of thrombus during coagulation. When activated, they gather to form
aggregates at the site of injured endothelium and then release substances of
their granules containing coagulation factors, growth factors acting on various
cell types involved in anti-microbial responses.

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 Professional antigen-presenting
Phagocytes
cells
 Macrophages  Macrophages
 Dendritic cells  Dendritic cells
 Neutrophil granulocytes  B-lymphocytes

Cells of the adaptive (acquired) immunity

The cells of adaptive immunity are the B- and T-lymphocytes (or also called B
and T cells). These cells carry a unique receptor specialized for the recognition
of only one type of antigen. Although the individual cells are able to recognize
only one antigen, the billions of B and T cells together can detect billions of
different structures.
B cells recognize the antigens by their cell surface antigen
receptors. The antigen receptor of the B cell is a cell surface
immunoglobulin. B cells express numerous membrane-
bound cell surface immunoglobulins, so one antigen can be
bound by more receptors at the same time. Following
detection of antigens B cells get activated and differentiate
into plasma cells. Plasma cells, the terminally differentiated form of B cells do
not carry cell surface immunoglobulins, but they produce large amounts of
these proteins in a soluble form which are commonly known as antibodies.
Secreted immunoglobulins enter the surrounding tissue fluids and blood
circulation. Secreted immunoglobulins or antibodies recognize the antigens of
various pathogens and bind to them to mark (called opsonization) or to
inactivate them (called neutralization).
Two main types of T cells are distinguished. The cytotoxic
T cells specialized in the killing of infected or tumour cells
and the helper T cells which play an important role in the
facilitation and regulation of the immune responses. Helper
T cells can enhance cytotoxic T cell responses, help
macrophages to destroy the engulfed microbes and support
antibody production of B cells. The two cell types can be
easily distinguished based on their cell surface molecules. Cytotoxic T cells
express CD8 while helper T cells express CD4 cell surface receptors. Briefly,
they are CD8+ (CD8-positive) or CD4+ (CD4-positive) cells.
As has been repeatedly mentioned, please note that freshly generated so-called
„naïve” T and B lymphocytes derived from the primary lymphoid organs are
not fully functional! Further maturation/activation processes in the secondary

19
 lymphoid organs or tissues are required for „naïve” lymphocytes to
differentiate into functional effector cells.

Communication between immunocytes: cytokines and cell surface

molecules
Immune cells communicate with each other in several ways. (Figure 3.)
 By cell surface molecules and receptors through direct cell-cell
interaction. (The most important cell surface molecules are discussed
in the appropriate chapters.)
 By soluble molecules, which play a pivotal role in the communication
of immune cells. These chemical messengers can be different peptides,
proteins, glycoproteins, which are collectively called cytokines.

Figure 3. Communication in the immune system.

Cells of the immune system exchange information with each other through direct cell-cell
contact or through soluble factors, primarily via secreted cytokines which are sensed by
cytokine-specific receptors on the target cells. (Each cell can express a large number of different
receptors. The number of cell surface cytokine receptors expressed by a given cell may vary
considerably, reaching up to millions/ cell. In the figures of this lecture notes neither the number-
nor the size of receptors are not presented on scale.)

20
Cytokines are hormone-like substances which are effective at very low
concentration. Secreted cytokines can act in an autocrine manner on the cell
that produced them or they can act locally on other cells in a paracrine manner.
However, some cytokines can also have endocrine effects by influencing the
function of distant cells or organs.
Responsiveness of a cells to a given cytokine is determined by the expression
of the cell surface receptor specific to that particular cytokine. A single cell
expresses various cytokine receptors so a given cell is usually affected by
multiple cytokines which could modify (enhancing or inhibiting) each other’s
effect. Of course, a particular cytokine can affect the functions of many
different cell types and can induce different responses in different types of
cells. The functions of each cell will be influenced by the combined effects of
the parallel signals (cytokines, other receptor signals, cell-cell interactions).
Cytokines are classified in many ways, and these groups often overlap with
each other. For example, some cytokines belong to both the group of
lymphokines and the group of monokines as they are produced by both
lymphocytes and monocytes.
Cytokines involved in the communication between white blood cells
(leukocytes) are often referred to as interleukins. Interleukins are distinguished
from each other by numbers. To date, more than 30 kinds of interleukins have
been described. One of them is interleukin-2 (IL-2) which induces the
generation and cell division of T cells. Other cytokines regulate the activation
and differentiation of leukocytes (e.g. IL-12, IL-4, IL-10). The so-called pro-
inflammatory cytokines including for example TNF, IL-12 or IL-6, have
pivotal roles during inflammatory processes.
There are some cytokines which can act as growth factors influencing
maturation and differentiation of various cell types of the immune system. For
example, the granulocyte-macrophage colony-stimulating factor (GM-CSF)
induces the production of granulocytes and monocytes in the bone marrow.
Cytokines inhibiting (interfering with) viral infection are classified as a
separate group called interferons.
Chemokines are cytokines that induce chemotaxis, attracting the appropriate
chemokine receptor bearing cells towards the source of the chemokine. Such
mediators facilitate for example the migration of blood-circulating
lymphocytes and tissue-localized dendritic cells towards the lymph nodes.
Large amounts of chemokines (e.g. CXCL8) and chemotactic factors (e.g.
cleavage products of complement proteins) are produced in the infected or
inflamed tissues which recruit neutrophil granulocytes, monocytes among
other cells to the site of inflammation.

21
The innate immune system
The innate (or natural) immune cells are the monocytes/macrophages, the
dendritic cells, the granulocytes and the NK cells. Humoral components of
innate immunity include antimicrobial substances produced not only by
immune cells: enzymes, antimicrobial peptides (e.g. defensins) can be
produced by the liver or the epithelia. The proteins of the complement system
and their cleaved fragments play a particularly important role.
The ancient mechanisms of innate immunity provide an immediate response.
The most important phases of the response:
 detection of pathogen or danger signal,
 alarming and mobilization of other elements of immune system
(including both the innate and the adaptive components),
 elimination of the pathogen as soon as possible.

Recognition of pathogens by the innate immune system: danger

signal sensing receptors, pattern recognition, opsonins
The overall structure as well as composition of macromolecules present on the
surface of microorganisms differ significantly from those found in higher order
organisms. The „aim” of the innate immune cells is to detect characteristic
danger signals and/or molecular structures present in microbial pathogens, but
absent from human cells. These molecules are recognized by immune cells
either in their soluble form or bound to the surface of a pathogen. For example
the essential cell wall components of different bacteria (e.g. polysaccharides,
peptidoglycans and lipopolysaccharides) or flagellin induce strong activation
signals in phagocytes. Similarly, double-stranded RNA present in some viruses
represents a danger signal for various cell types. These molecules indicating
the presence of pathogens are called pathogen-associated molecular patterns
(PAMP). Their presence is clearly a sign of danger, so their appearance has to
be monitored by various types of pattern recognition receptors (PRR)
expressed on different immune cells. The pattern recognition receptors
appeared early on during evolution. They are expressed by all multicellular
organisms from simple worms to the most sophisticated plants. PRRs are
evolutionarily conserved structures as they recognize similarly conserved
target molecules of pathogens.
The function of PRRs is not restricted to the recognition of extracellular
pathogens. Intracellular pathogens living in the cytosol or in the vesicular
system need to be recognized by immunocytes, thus some PRRs need to be
localized in these compartments. Some of these receptors can readily bind to

22
particles in the endosomal compartment, another set of the receptors sense the
pathogens in the cytoplasm. In addition to many immune cells, epithelial cells
localized in various surfaces of the human body can also express pattern
recognition receptors. Almost all types of these receptors are expressed on
different macrophages and dendritic cells. (Figure 4.)
Sometimes self-derived molecules released by necrotic cell death or tissue
damage called danger- or damage-associated molecular patterns (DAMP) can
also serve as danger signals. This involves the “free” form of the genomic DNA
itself, which is enclosed into the nucleus under normal circumstances. Its
appearance in the cytoplasm may suggest that cells were infected by a DNA
virus, or its extracellular localization may indicate damage-induced necrotic
cell death which is an alarm signal for the immune system. Many other
substances originally derived from nucleus or cytosol (e.g. extracellular ATP)
are recognized extracellularly as DAMP by the immune system.
The recognition of pathogens and/or danger signals by the immune system is
mediated by a group of a few dozen receptors only. These receptors are able to
identify essential and conserved structures characteristic of various pathogen
groups. Thus, innate immune cells can detect practically all pathogens by using
these few pattern recognition receptors. However the recognition is not specific
to each pathogen species, because specific (individual) recognition of tens of
thousands of pathogens is impossible by only a few types of receptors. These
receptors, however, provide sufficient information about the type of the
infecting agent, about the site of the infection and about the type and
localization (intra- or extracellular) of the pathogen allowing the induction of
an appropriate anti-microbial immune response.

23
Figure 4. Detection of the pathogens by pattern recognition receptors.
The pattern recognition receptors of the innate immune system recognize structures that are
characteristic of pathogens but not of human cells (e.g. bacterial cell wall components, double-
stranded viral RNA). The pattern recognition receptors localize either on cell surface or inside
the cells allowing the recognition of both extracellular and intracellular pathogens. They do
not distinguish between individual species of microbes, they rather indicate the appearance of
pathogens in the body.

Although innate immune cells are capable of recognizing pathogens in itself,

the response is accelerated and enhanced in the presence of opsonins. Opsonins
produced by the human body bind to pathogens to mark or target them for
destruction. Opsonization facilitates the recognition and phagocytosis of
pathogens by the innate immune cells. In addition to many cell surface
receptors detecting pathogens directly, there are different opsonin receptors
specialized for the recognition of opsonins bound to the surface of pathogens.
The opsonin is forming a bridge between the pathogen and the opsonin
receptor of the phagocytic cell (e.g. Fc receptors or complement receptors).
Various molecules can act as opsonin during the immune response. Such
molecules include antibodies, some complement fragments and the so-called
acute phase proteins synthesized by the liver in response to pro-inflammatory
cytokines. (Figure 5.).

24
Figure 5. Opsonization and pathogen recognition
Opsonization facilitates detection and accelerates phagocytosis of pathogens. The phagocytes
can recognize the microbes by pattern recognition receptors. If the pathogen is coated by
opsonins, the opsonin receptors are sufficient for the indirect detection of pathogens.

Elimination of pathogens by the innate immune system

The extremely fast reproduction rate of pathogens far exceeds that of the
human populations. The number of some bacteria can increase by a hundred
fold within a few hours in ideal circumstances. Therefore, both the immediate
recognition and the early elimination of the invaders are crucial for protecting
the host. The innate immune system represents the first line of defence. It is
responsible both for the quick recognition and the rapid elimination of the
pathogens. In lots of cases a few simple mechanisms can ensure the effective
eradication of the highly variable pathogens:

25
 Phagocytic cells, mainly macrophages and neutrophil granulocytes
engulf the pathogens and subsequently kill them, even at the cost of the
death of the phagocytes themselves.
 Granulocytes and macrophages secrete toxic mediators to kill
microbes, including reactive oxygen species, nitric oxide, or different
degrading enzymes. Multicellular parasites are relatively complex
organisms, often protected by capsule. Mast cells, basophil- and
eosinophil granulocytes are specialized to eliminate these parasites
with their specific destructive enzymes.
 Activation of the complement system may cause the direct lysis of
some pathogens. Alternatively, complement fragments act as opsonins.
 The elimination of intracellular pathogens requires a different strategy.
In this case, microbes are not attacked directly, the infected human cells
need to be killed instead. Among the cells of innate immune system,
NK cells are capable of rapid killing of the infected cells. (Beside NK
cell, the cytotoxic T cells, as part of the adaptive immunity play a major
role in this process, as we will discuss it later.)

26
Figure 6. The elimination of microbes by the cells of innate immune system
Following pathogen recognition, phagocytic cells engulf, kill and intracellularly digest the
microbes. Granulocytes and macrophages secrete toxic mediators. Complement components
lyse pathogens by binding to their surface. NK cells kill infected cells in order to eliminate
intracellular pathogens.

The alarm system of the body: the acute inflammation

Interactions among few cells can be sufficient to initiate the immune response.
Macrophages and dendritic cells play a critical role in this process. These two
cell types are present all over in the human body, especially around the external
and internal surfaces, where pathogens can enter into the tissues. Besides
dendritic cells and macrophages, the cells of the epithelia also contribute to the
alarming process. These few cell types express the entire panel of pattern
recognition receptors. However, their effector functions are markedly different
following the recognition of pathogens. The primary role of dendritic cells is
not the elimination of the pathogens, but to transport the antigens to the lymph
nodes, to present them for T lymphocytes, and thus, alarm and activate the
adaptive immune system. Macrophages on the other hand initiate effector
functions straight away for immediate elimination of the pathogens. Small
number of pathogens can be eliminated by macrophages lining around the
pathogens’ entry site. When a large number of pathogens enter our body

27
macrophages alone cannot cope with the infection. Upon activation of their
pathogen or opsonin sensors they alarm other actors of the innate immune
system, and recruit them into the site of infection by initiating local
inflammation (Figure 7). The extremely fast proliferation of pathogens
demands instant responses. The innate immune system delivers an immediate
immune response, so it plays the main role in the rapid and short-lived (acute)
inflammation. In addition to this „gate-keeper” function dendritic cells and
macrophages are capable and necessary in the activation of the adaptive
immune response. Local inflammation developing around the entry site of
pathogens is absolutely necessary in immune defense against microbes. The
recognition of incoming pathogens by opsonin- or pattern recognition
receptors, activates macrophages resulting in the production of hormone like
molecules –cytokines and chemokines- which recruit and activate other
immune cells. Epithelial cells and mast cells are also able to initiate similar
alarm mechanisms.
The volume of circulating blood increases in inflamed tissues due to
vasodilation (an increase in the diameter of the vessels) and in the meantime,
vessels become permeable (leaky). The chemokines and cytokines produced
by macrophages also activate the cells of the vessel walls, the endothelial layer.
As a result, the expression of several adhesion molecules are induced on the
surface of the endothelial cells around the infected area. Secreted cytokines
also assist the extravasation when phagocytes, such as granulocytes,
monocytes and other cells (e.g. NK cells) migrate into the site of inflammation.
Leaky vessels will allow diffusion of more and more humoral factors,
including those of the complement system and even antibody molecules from
the blood to the infected tissue. Some cytokine-like mediators lower the
sensory-threshold of the nociceptors. As a result, a painful swelling, so-called
oedema develops at the site of infection. Reactions in the inflamed tissue
increase the intensity of lymph flow and thus facilitate the transport of antigens
towards the surrounding lymph nodes initiating the activation of antigen
specific lymphocytes.
The clotting system is also activated to cope with the collateral damage of the
blood vessels and possibly to isolate the pathogens or at least slow down their
spreading. The last phase of inflammation is tissue regeneration. During this
process, special cytokines acting as growth factors potentiate the proliferation
of fibroblasts and/or the process of angiogenesis.

28
Figure 7. Acute inflammation
At the site of infection macrophages recognize the pathogens and subsequently produce
inflammatory cytokines, inducing vasodilation and increased vascular permeability.
Granulocytes, Monocytes, NK cells, complement components can exit from the circulation at
these sites and eliminate the pathogens in the infected tissues.

Inflammatory cytokines (especially TNF, IL-1, IL-6) are produced by the

activated cells, chiefly by macrophages. These cytokines are important at the
site of inflammation, however they also have endocrine effects, acting
throughout the entire human body:
 Induction of fever by acting on the hypothalamus,
 Increased production of acute phase proteins and antimicrobial
molecules by the liver.
 Enhanced production of leukocytes in the bone marrow, to replenish
cells lost during the immune reactions

Various mechanisms of the innate and adaptive immune response create the
anti-viral immune response. Besides cellular components, Type I interferons
play a critical role in innate anti-viral immune responses. Almost all kinds of
cells, (not only the cells of the immune system) are able to produce these

29
cytokines upon viral infection. Infected cells secrete interferons following
recognition of viruses by their pattern recognition receptors. Interferons
transmit autocrine and paracrine effects, inducing anti-viral state inside the
cells, which block the propagation of the viral replication by blocking protein
synthesis or activating the degradation of viral RNA.

The function of the complement system

The complement system itself is able to recognize and eliminate many
pathogens and in the meantime alert further components of the immune
system. It consists of around 30 proteins. Cooperative actions of these proteins
assist and complement the function of antibody molecules. Most of the
complement proteins are present in the blood plasma as inactive proenzymes.
Activation of the first element leads to the activation of the proteolytic cascade
system by a domino effect. Activated complement components process
subsequent proteins of the cascade by limited proteolysis resulting in the
activation of the next component. The different complement components are
cleaved in a regulated, determined sequence. Before the inactivation of an
activated complement factor (enzyme), multiple copies of the next member of
the proteolytic cascade are usually cleaved, which leads to the amplification of
the signal.
The surface of pathogens is able to activate the complement system (either
directly or mediated by the opsonization by antibodies). Certain types of
antibody molecules, related to the adaptive arm of the immune system, are
highly effective opsonins initiating the complement activation.
Several specialized inhibitors block spontaneous, pathogen independent
activation of the complement system in the human body. Some of these
inhibitors are expressed constitutively in the human serum while others on the
surface of cells. The absence of complement inhibitors on the pathogens may
result in complement activation without the specific recognition of pathogens.
The main effector functions of the complement system:
 Mark different microbes (opsonization) and thus help the phagocytic
cells of the innate immune system to recognize, engulf and destroy
opsonized pathogens. In addition, complement factors can bind to
antibody molecules attached to the pathogen surface (antigen-antibody
complexes or immune complexes), consequently further facilitate
phagocytosis.
 Complement driven opsonization is necessary for efficient removal of
soluble immune complexes from the human body (discussed later).

30
  Following activation, the last elements of the complement cascade
creates a pore across the bacterial or cellular membrane. This process
leads to the loss of the transmembrane ion balance, which finally
results in the death of the attacked cells.
 Some of the activated complement components function as a
chemotactic factor and recruit different cells of the immune system to
the site of complement activation. These complement components –
sometimes called as anaphylatoxins – contribute to the process of
inflammation by enhancing vasodilation and increasing the
permeability of blood vessels.

MHC molecules, antigen presentation

T cells and B cells recognize antigens in a very different way. T cells cannot
see the antigen in its native form, only the fragments of the antigens after
partial degradation and processing.

Figure 8. Antigen presentation

T cells recognize peptides in complex with MHC
molecules on the surface of antigen presenting cells. The
peptide and the MHC molecule, as a complex, is
recognized simultaneously by the T cell receptor.

Most of the T cells recognize peptide fragments of protein

antigens. Small peptides in their native form cannot
achieve stable organised conformation. Peptides are
therefore displayed by cell surface molecules of the host
cells which stabilize the structure of peptides by limiting
conformational changes.
These ’peptide display molecules’ are called MHC (Major Histocompatibility
Complex) proteins, and cells that express them are called antigen-presenting
cells. Thus, the main task of the MHC molecules on the surface of an antigen
presenting cell is to present peptides derived from various proteins to T cells.
The antigen-specific receptors of T cells recognize the complex of a peptide
displayed by an appropriate MHC molecule. (Figure 8)

31
The MHC molecules
The MHC molecules (in human also called HLAs – Human Leukocyte
Antigens), are encoded in the Major Histocompatibility Complex gene region.
The MHC gene region encodes most of the proteins that are involved in the
process of antigen presentation.
This region contains the most polymorphic genes (with the highest number of
allelic variations). As a result these genes encode proteins with the greatest
diversity in the human population. Thus, most individuals of the population
possess MHC molecules with slightly different structures but these molecules
have identical function. The different MHC molecules encoded by different
alleles can be recognised as “foreign” when some tissue or organ is
transplanted into an other person, and the immune system will attack, reject
the transpklant. This is why the name of this gene region refers to
histocompatibility.
On the cell surface, a vast number – even millions – of MHC molecules can be
found simultaneously. One MHC molecule has affinity to various peptide
sequences, but one MHC molecule binds only one peptide. All the MHC
molecules on a cell surface together are able to present many different peptides
from various different proteins at the same time to the T cells.
Under normal circumstances only common self-protein derived peptides are
presented by the help of MHC molecules. However, in the case of an infection
microbial peptides can also appear on the cell surface presented by several
MHC molecules among the normal self-peptide presenting ones. Tumour cell-
specific peptide fragments (from altered proteins) can be also presented among
the normal self-peptides this way.
By checking tens of thousands of different peptides bound to MHC molecules
on the surface of the antigen presenting cell, T cells are able to find a few
specific MHC-peptide complexes, which activate them.

MHC I and MHC II

Two main types of antigen presenting molecules exist. Almost all cells of the
body express MHC class I molecules (red blood cells can be mentioned as an
exception). MHC I molecules bind peptides derived from proteins which are
sliced in the cytosol. This is called as endogenous antigen presentation. Either
the self-proteins of the cell or the proteins of intracellular bacteria, viruses or
the abnormal proteins of the tumour cells can be presented this way to CD8+
cytotoxic T cells.

32
MHC class II molecules show a much more restricted pattern of expression,
being expressed mainly on the surface of the so-called professional antigen
presenting cells. Using MHC II molecules, macrophages and dendritic cells
present extracellular (exogenous) peptides derived from antigens engulfed
from the extracellular space. Self-peptides of the body or foreign microbial
peptides can be presented in complex with MHC II molecules, which can be
recognized by CD4+ helper T cells.
Thus cytotoxic T cells and helper T cells recognize antigens presented by
different types of MHC molecules and the peptides presented by this different
type of MHC molecules are derived from different cellular or tissue
compartments.

Antigen presentation
Based on what we have learned so far, antigen presentation seems to affect the
function of T cells only. In fact, during antigen presentation significant changes
occur in the antigen presenting cells as well. The antigen presenting cell and
the T cell mutually affect each other.
MHC I
With some exceptions (e.g. red blood cells) MHC I molecules are expressed
on all human cells. They display mainly endogenous peptides on the cell
surface for CD8+ cytotoxic effector T cells (Figure 9). Through the presented
peptides, T cells can monitor what kinds of proteins are present inside the cells.
Due to this process T cells could theoretically detect any intracellular
pathogens, thus, antigen presentation by MHC I renders the intracellular space
a subject for immunological
monitoring or immunosurveillance.
The antigen presentation process is

Figure 9. Presentation of intracellular

pathogens on MHC I
MHC I molecules display peptide fragments
which derive from proteins degraded in the
cytoplasm. In case of an infection microbial
peptides derived from intracellular
pathogens are (also) bound to MHC I.
Cytotoxic T cells recognize the MHC-I –
peptide complex and may kill the infected
antigen presenting cell.

33
not selective. It presents peptides from any protein located in the cytosol
(self/non-self), regardless whether it is derived from a pathogen or not. MHC
I molecules can present peptides of the cell’s own proteins, but they can display
peptides derived from intracellular bacteria or in case of a viral infection viral
peptides can be also displayed. Based on the displayed peptides the T cells will
decide whether there is any dangerous modification or infection of the antigen
presenting cell.
MHC I bound peptides are generated in the cytoplasm (cytosol). The large
multi-subunit housekeeping enzyme complex called the proteasome cleaves
proteins into peptide fragments of the correct size to allow complex formation
with MHC I. The degradation of proteins in the cell is a natural process, as all
kinds of cellular proteins are degraded by proteasomes. The generated peptides
are delivered into the endoplasmic reticulum (ER) by a transporter protein
complex. In the ER the freshly synthesized MHC molecules stabilised in
peptide receptive conformation by chaperon proteins, so the transported
peptides can bind to them. Usually 8-10 amino acids long peptides bind to the
peptide-binding groove of MHC I molecules. Once an appropriate peptide has
been bound to MHC I in the ER and the chaperons are dissociated, a
conformational change occurs. The MHC molecule becomes „closed”, unable
to exchange the bound peptide.
In this peptide-bound state, the MHC I molecules can leave the endoplasmic
reticulum and pass through the Golgi-apparatus, finally they appear on the cell
surface. Under normal circumstances „empty” MHC I molecules, without a
bound peptide, cannot be found on the cell surface.
The significance of this strict process is to prevent the binding of extracellular
peptides to MHC I molecules on the cell surface, otherwise healthy cells near
the site of infection could become the targets of cytotoxic effector cells.
When the CD8+ cytotoxic T cells recognize peptides of foreign or harmful
cellular proteins in complex with MHC I molecules, they kill the target cell to
prevent further spreading of the infection or the development of a tumour. MHC
I is expressed on the surface of all nucleated cells, so if any cell becomes infected,
following antigen presentation, they become a target for cytotoxic effector T cells.
In contrast to cytotoxic T cells, natural killer cells (NK cells) isn’t activated by
MHC I bound peptides, but rather the lack of MHC I molecules, which unleash
their activation.
This mechanism can be effective in killing those cells, which lack MHC I
molecules avoiding recognition by the adaptive immune system. For example
certain virus-infected cells express only a very limited number of MHC

34
molecules, thus they become „invisible” to cytotoxic T cells. However NK
cells detect the lack of MHC I and destroy the abnormal cells.
MHC II
The MHC II molecules are expressed by the professional antigen presenting
cells such as dendritic cells, macrophages and B cells. These cells are able to
engulf extracellular antigens and to present them on MHC II molecules to
CD4+ helper T cells. MHC II molecules (unlike MHC I) are specialized to
display antigens derived mainly from exogenous origin (Figure 10).

Figure 10. Peptides derived from

extracellular pathogens are
presented on MHC II molecules
Following engulfment, peptides of
the pathogen appear on the cell
surface in association with MHCII
molecules. The MHCII-peptide
complex is recognized by helper T
cells.

Following phagocytosis or
endocytosis exogenous antigens
get into the endosome. Later the
endosome fuses with lysosomes to
become endolysosomes containing proteolytic enzymes. Peptides generated
here by proteolysis –from exogenous proteins or from engulfed or parasitic
microbes– can form a complex with MHC II molecules.
Similar to MHC I, MHC II molecules are synthesized in the endoplasmic
reticulum. However here they associate with a different set of chaperone
proteins, most importantly with the so-called invariant chain (Ii). The main
functions of the invariant chain is to form a complex with MHC II thus prevent
binding of endogenous peptides into the peptide binding groove of MHC II and
transport of the complex through the Golgi-apparatus in this ‘blocked’ state. In
the endolysosome, proteolytic enzymes degrade the invariant chain, making
the binding site available for peptides derived from extracellular antigens.
Usually 10-20 amino acids long peptides bind to MHC II molecules, however,
since its binding site is ”open at both ends”, longer, overhanging peptides are
also able to fit. After peptide-binding, the MHC II-peptide complex appears on
the cell surface to present antigens to CD4+ helper T cells. In return, activated

35
helper T cells are able to influence the immunological functions of the antigen
presenting cells in several ways:
 Activated effector T-helper cells facilitate the activation and
subsequent antibody production of the antigen presenting B cells, thus
they support the humoral immune response.
 In case of antigen presenting macrophages the effector T-helper cells
further activate them, increasing their efficiency in killing
phagocytosed bacteria “settled in” in their endosomes.

Features of the MHCI and MHC II molecules

MHC I MHC II
Professional antigen
Cells that express MHC All nucleated cells
presenting cells
source self or foreign proteins self or foreign proteins

Bound peptide size 8-10 amino acids 10-20 amino acids

cytoplasmic and nuclear cell-surface and
origin proteins extracellular proteins
Site of peptide generation cytoplasm endolysosome
remains in the ER till the Invariant chain directs it to
MHC transport complex formation specialized vesicles
Site of peptide loading of
ER specialized vesicles
MHC
MHC-peptide complexes reflect the intracellular reflect the extracellular
on the cell surface environment environment

Taken together, activated CD4+ helper T cells increase the activation and
facilitate the function of the antigen presenting cells, while activated CD8+
cytotoxic T cells induce death of the antigen presenting cells.
So far, little has been discussed about the antigen recognition of naïve T cells.
Naïve T cells are activated in the secondary lymphoid organs. T cells that have
not met their specific antigen can be most efficiently activated by dendritic
cells. These professional antigen presenting cells in addition to the MHC
molecules express those cell surface molecules, which provide effective
stimulation for naïve T cells.

36
Activated naïve T cells proliferate and differentiate into effector T cells, which
later will be able to carry out the above mentioned functions of cytotoxic and
helper effector T cells.

B- and T cell receptors

The human population is threatened by a plethora of different microbial
species. Moreover, even a single species can have altered variants with
different pathogenicity. The specific recognition of this enormous variability
requires (at least) an equal number of receptors efficiently recognizing a given
variant of a particular microbe. The B cell receptor, its soluble form the
antibody and the T cell receptor are glycoproteins produced in humans with a
diversity that far exceeds that of the pathogens. One receptor is responsible for
the recognition of a single pathogen, however the billions of receptor variations
together are able to specifically recognize every pathogen.
The antibody (immunoglobulin) is a symmetrical molecule that consists of 4
polypeptide chains in humans, 2 identical shorter so-called light chains and 2
identical longer heavy chains (Figure 11). Each chain contains constant and
variable domains (protein subunits). The light chains consist of a variable and
a constant domain while the heavy chains have one variable domain and –
depending on their type– 3 or 4 constant domains. The heavy and light chains
as well as the two heavy chains are linked by covalent disulphide bonds
(disulphide bridges between the cysteine amino acids). Additional
intramolecular disulphide bridges stabilize the globular structure of each
domain. As a result, a symmetrical Y-shaped structure is created, with 2 arms
containing a light chain and the variable– and the first constant domain of a
heavy chain. The variable domains at the end of the arms form the antigen
binding site. The stem of the Y-shaped structure is built up from the 2 or 3
constant domains of the 2 heavy chains. The constant domains provide stability
for the molecule and they are also responsible for certain effector functions
(Figure 11).

37
 Figure 11 Structure of the
antibody
The antibody molecule
consists of 2 identical heavy
chains and 2 identical light
chains. The terminal variable
domains are responsible for
antigen recognition, while the
constant domains stabilize the
structure of the molecule and
are responsible for the
induction of some effector
functions.

Diversity is characteristic of the variable domains instead of the whole

molecule. Variable domains are responsible for the recognition of the vast
number of different antigens. While the number of variable domains with
different sequences is extremely high, based on the variety of the constant
domains the heavy chains can be divided into 5 major types (IgM, IgD, IgG,
IgA, IgE) and the light chains into 2 types (ĸ and λ). These types are also
known as isotypes.
The antigen binding site of the human immunoglobulin is formed by the
variable domains of a light- and a heavy chain together. Therefore, the heavy
and light chains together and not alone, are able to recognize a given antigen
with high specificity. Since the basic unit of antibody is a symmetrical
molecule (consisting of 2 identical heavy- and 2 identical light chains), it is
capable of creating a dual, two pronged, so-called bivalent interaction with the
specific antigen or bridge together two specific antigens.

38
Figure 12. The cell surface- and soluble forms of the immunoglobulin
The immunoglobulin molecule is expressed on the surface of B cells where it functions as their
antigen recognition receptor. Following antigen binding it transmits activating signals into the
cell through associated signalling molecules. The immunoglobulin is expressed in a soluble
form as well, secreted by plasma cells which had differentiated from activated B cells. The
roles of soluble immunoglobulins are to inactivate pathogens and to facilitate their elimination.

The immunoglobulin molecules are produced in 2 forms during the immune

response:
1. It is highly expressed on the surface of B cells. In this case the heavy
chains contain an additional transmembrane region which anchors the
molecule to the cell membrane. The cell surface-bound
immunoglobulin interacts with other membrane-anchored molecules
which are responsible for signal transduction. The cell surface-bound
immunoglobulin and the associated signaling molecules together are
called B cell receptor (BCR) (Figure 12).
2. The immunoglobulin/antibody can have soluble form as well.
Antibodies are produced by plasma cells differentiated from B cells.
Plasma cells do not express cell surface-bound immunoglobulin
anymore, instead, they produce soluble immunoglobulins continuously
and secrete them into the extracellular space. Structurally, the secreted
antibody molecule is almost identical to the cell surface
immunoglobulin. It recognizes the same antigen as the BCR, only the
transmembrane region is absent, without which it fails to attach to the
cell membrane, or associate with signal transduction molecules.
(Figure 12)

39
The BCR is responsible for both the recognition of antigens and the activation
of antigen specific B cells.
Soluble antibodies facilitate the recognition and contribute to the elimination
of pathogens using other components of the immune system. (described in
more detail at antibody effector functions)

Figure 13. The

structure of the T cell
receptor (TCR)
The T cell receptor
consists of 2
polypeptide chains.
The variable domains
of the TCR recognize
the MHC-peptide
complexes, while the
constant domains
ensure the stability of
the molecule. Only
membrane-bound
forms exist.

The T cell receptor (TCR) is the antigen recognition receptor of the T cells.
Its structure is similar to the immunoglobulin. Its antigen recognition site is
formed by 2 polypeptide chains (the α and β chain in the case of the so-called
αβ T cells or the γ and δ chains in the case of the γδ T cells). Each chain consists
of a constant and a variable domain. Similar to the immunoglobulin, the chains
are linked to each other by covalent bonds and further disulphide bridges
within each chain stabilize the globular structure. The 2 variable domains
together are responsible for the recognition of the antigen in a form of an MHC-
peptide complex, while the constant domains stabilize the structure of the
receptor. The chains are anchored to the cell surface by transmembrane
domains. As part of the receptor complex non-covalently associated signaling
molecules are present. These signaling chains are collectively called the CD3-
complex (Figure 13).
From the point of the structure and function, there are important differences
between the BCR and the TCR. TCR unlike BCR has only 1 antigen binding
site and it does not exist in a soluble form, so the sole function of the TCR is
antigen recognition followed by the activation of the T cell.

40
 Recognition of microbes by receptors of the immune system
cell receptor recognized structure
Pathogen associated
molecular patterns
Innate cells
Pattern recognition (PAMPs),
(e.g. macrophages, receptors (PRR) Danger associated
dendritic cells)
molecular patterns
(DAMPs)
B cell B cell receptor (BCR) almost any structure
T cell T cell receptor (TCR) MHC-peptide complex
Opsonins bound to
Various cell types of
antigens, foreign structures
the immune system Fc- and complement
(antibodies, complement
(especially the innate receptors
components, acute phase
immune cells)
proteins)

Generation of Lymphocyte diversity

One of the major findings of immunology was the clarification of how the
enormous diversity of antigen receptors is produced, using the relatively low
number of genes present in the human genome. In fact, the immune system has
developed highly efficient molecular genetic mechanisms for the generation of
an extremely diverse set of antigen receptors from a limited number of
inherited genes. Without this unique mechanism, recognition of many millions
of different antigens would not be possible. The variable domains of the BCR
and TCR are encoded by gene segments which are often located far away from
each other in the DNA. While conventional genes encode the constant domains
of immunoglobulin chains (heavy- and light) and the TCR chains (α and β),
the variable domains are encoded by gene sequences which are created by the
joining of multiple small gene segments by a random somatic recombination
process. The variable domains of the receptors are combined from 2 or 3 gene
segments. These gene segments are present in many (10-100) variations in the
DNA. During their development lymphocytes start rearranging their original
DNA (so-called germline DNA) to create unique “novel” DNA sequences
originally not present in the germline of the host.

41
The variable domains of the heavy chain of the BCR and the β-chain of the
TCR are randomly assembled from three gene segments, while the light chain
and the α-chain variable regions are assembled from 2 segments. Random
recombination of gene segments provides the basis of the so-called
combinatorial diversity, which allows generation of over a million different
receptor specificities for both T- and B cells. The diversity is further increased
by several orders of magnitude due to inaccurate joining of the gene segments
during gene rearrangement (some nucleotides are deleted and additional
nucleotides are randomly added at the junctions points using appropriate DNA
modification/repair enzymes). As a result the base sequence is altered, new
sequences appear which again, were not present in the germline sequence. The
junctional and combinatorial diversity together are able to generate around 1014
different B cell receptors and 1018 different T cell receptors.
Taken together, these recombination and repair processes create a new
randomly generated gene sequence, which encodes the variable domain of the
antigen recognition receptor in that particular lymphocyte. Importantly, the
constant domains are not subject to the above assembly mechanisms, therefore
not polymorphic among individual lymphocytes of the host.
Once the recombination process has been completed expression of the newly
assembled gene is initiated. Only the rearranged gene sequence can be
transcribed and translated into a protein from the mature mRNA. Following a
productive rearrangement (that leads to the synthesis of structurally intact
chains of the receptor), further rearrangements are blocked in that particular
cell.
The diversity of the antigen receptors randomly assembled by the above
described mechanism is further increased by the fact that both the TCR and the
BCR are formed as heterodimers randomly chosen from the pool of available
diverse polypeptides: from the heavy and light chains in B cells and from the
α and β (or γ and δ) chains in T cells. The binding site of the receptors is formed
by both polypeptide chains which together determine receptor specificity.

Clonal selection of T- and B lymphocytes and development of

tolerance
10 million-1 billion B and T cells are generated and mature daily in the bone
marrow and in the thymus, replacing the dying cells in the peripheral tissues.
Lymphocytes recognize the antigen with their cell surface-expressed B cell
receptors or T cell receptors. The antigen recognition receptors (BCR or TCR)
are unique with different specificity and each lymphocyte expresses only one
type of antigen recognition receptor of the same specificity. Thus one cell is

42
specialized for the recognition of only one antigen. Overall, lymphocytes
produced on a daily basis represent ~107 – 109 different antigen specificities.
As a result, our lymphocytes together are able to recognize millions of different
antigens at any time. (In contrast with this, the innate immune system uses only
a few dozen different receptors for recognition of highly conserved pathogen-
associated structures.)
Lymphocytes develop in the primary lymphoid organs in the absence of
foreign antigens. As the specificity of the antigen recognition receptors is
generated by a completely random process, in addition to pathogen-specific
receptors, many self-reactive receptors are also produced. In the special
environment of the primary lymphoid organs, those lymphocytes that
recognize self-structures with high “intensity” (have high affinity receptors for
self-proteins) die or become inactivated in the early stage of their development.
This process, called the development of central tolerance, ensures that the
vast majority of strongly self-reactive, potentially autoreactive lymphocytes
are not allowed to leave the primary lymphoid organs.
Mature lymphocytes that have completed their developmental program leave
the primary lymphoid organs and through the blood circulation, regularly enter
the secondary lymphoid organs in search for their specific antigen from the
periphery. If they do not encounter their specific antigen, they continue their
circulation in the blood and lymph to monitor the antigen repertoire of other
secondary lymphoid organs.
Since each lymphocyte is specialized for one particular antigen, the majority
of them will never find their specific antigen.
Those newly developed lymphocytes, for which specific antigen is not present
in the body, spend only a few weeks in the circulation, then die by apoptosis,
because in the absence of their specific antigen they are not needed. This also
provides space for newly developing lymphocytes with different specificity.

43
Figure 14 Clonal expansion of lymphocytes
From the large amount of different B cells those recognizing the pathogen start to proliferate
and form a clone (clonal proliferation/clonal expansion). Non-specific B cells re-enter the
circulation to “find” their specific antigen in the body. Without activation signals generated by
antigen binding B cells die by apoptosis in a few weeks. Different pathogens activate a
different set of specific B cells. Clonal proliferation is characteristic of B- and T cells only.

However, in the presence of pathogens, pathogen-specific lymphocytes present

in the regional secondary lymphoid tissues become activated. Their frequency
can range from 1:1000 to 1:100000.
Remarkably, it is the collection of pathogen-derived antigens that “selects” the
antigen-specific lymphocytes from the available repertoire. The recognition of
antigen leads to the activation and proliferation of the specific lymphocyte.
The resulting progeny cells have identical specificity providing this way the
large number of antigen-specific cells required to control even a massive
infection. (Figure 14).
After elimination of the pathogen, its antigens disappear from the body, thus a
large number of pathogen specific effector lymphocytes is not needed
anymore. At the final stage of the immune response these unnecessary effector
cells die by apoptosis.
However some of the specific B and T cells differentiate into memory cells or
long-lived effector cells, to ensure a quicker and more efficient immune
response in case of reinfection.

44
In the case of B cells the strength/ affinity of the antigen binding usually
improves during the clonal proliferation due to point mutations introduced into
the coding region of the antigen recognition receptor. Cells expressing these
slightly modified receptors must bind the antigen to survive. Lymphocyte
clones with BCR mutations resulting in binding to the antigen with higher
affinity will win the competition for the available antigen, thus survive and
proliferate. As a result, at the end of this selection process B cells recognizing
the same pathogen, with higher affinity will be produced. This process called
“affinity maturation” requires the contribution of helper T cells.

Functions of B cells and effector functions mediated by

antibodies
Antigen presentation by B cells
Similar to dendritic cells and macrophages B cells are professional antigen
presenting cells. The recognition of antigen by BCR induces not only
activation, division and differentiation of the B cell, it also induces endocytosis
of the bound antigen. The BCR-bound antigens can be efficiently internalized
by B cells by the process of receptor-mediated endocytosis. Internalized
antigens are processed and presented on the surface of B cells as peptide-MHC
II complexes (as previously described in the concerning MHC II molecules).
By this mechanism the protein antigens recognized by B cells can “be seen”
by T cells as well. Under these circumstances, chances are good that the B cell
and the T cell will recognize the same antigen, but not necessarily the same
part (epitope) of the antigen. Antigen presentation by MHC II leads to the
activation of helper T cells. The activated T cell can produce cytokines that
facilitate activation and differentiation of B cells. During cellular contact T-
and B cells mutually activate each other via cell surface receptors. Please note
that in this process a positive feedback loop is created in which two
lymphocytes (a T-and a B cell) with the same antigen specificity mutually
support (as well as control) each other’s function (Figure 15.).

45
Figure 15. B and T cells may respond to the same pathogen by amplifying each other’s
response.
Recognition by the BCR triggers internalization of the antigen by receptor –mediated
endocytosis. Following processing antigen-derived peptides are presented to helper T cells.
In turn, helper T cells produce cytokines that help activation and differentiation of B cells.

B cell effector functions: the function of antibodies

Antibody molecules can protect against microbes or other dangerous materials
in two ways. First, they may directly block the binding of the pathogen or toxin
to their cell surface receptors (neutralization) and second, indirectly, by
marking them for destruction through mechanisms to be discussed later in
detail.
The B cells’ characteristic molecules are the immunoglobulins. The
immunoglobulin expressed on the cell surface (BCR) is responsible for
recognition of the antigen, initiation of B cell activation, however the

46
immunoglobulin produced by plasma cells (antibody) mediates the humoral
part of the B cell immune response.
B cells usually encounter antigens in the secondary lymphoid organs, which
provide suitable environment for B cell proliferation. The antigens to be
recognized by B cells enter the lymphoid tissues via the blood- or lymphatic
vessels or even bound to cell surface proteins. B cells do not require the
antigens to be presented by MHC molecules. Antigens can be recognized by B
cells in their original form bound to the surface of cells.
In response to activation by their specific antigen B cells undergo clonal
expansion. A majority of the numerous identical daughter cells of the original
B cell will differentiate into plasma cells, specialized to produce large amounts
of antigen-specific antibody. It should be noted that although plasma cells do
not express the BCR, the specificity of antibodies secreted by the plasma cells
is identical to that of the original B cell. By clonal expansion, a few activated
B cells may generate thousands of plasma cells, each of which is capable of
producing billions of antibody molecules. As a result the number of antibody
molecules produced in response to an infection far exceeds the number of
pathogens. Different B cells recognize different parts (epitopes) of the same
antigen. In case of complex pathogens (e.g. bacteria) several B cells with
diverse but pathogen-specific BCRs are activated. The antibodies produced by
plasma cells can be carried by blood to all tissues and recognize pathogens far
away from the site of production in any tissues of the host (Figure 16.).

47
Figure 16. B cell differentiation into plasma cells.
Upon meeting with antigen, the antigen specific B cells go through clonal expansion,
differentiate into plasma cells (or into memory cells). The plasma cells due to lacking BCR
cannot recognize antigens, however they produce large amounts of antibodies. The antibodies
produced by plasma cells recognize the same antigen as their progenitor B cell initially
activated by the antigen.

Recognition of antigen, clonal expansion, differentiation and antibody

production are time consuming, thus an efficient B cell response requires 7-14
days to develop following the first exposure to the antigen.
Every B cell has a unique BCR with a single specificity, thus, protection of the
host is provided by a set of B cell clones selected from a vast repertoire of
unique B cells by the actual pathogen.

Neutralization
Plasma cells in the body continuously produce surprisingly large amounts,
approximately 1018 antibody molecules per day. Their antibody production
increases in response to infection. Antibodies produced by plasma cells can
exert their effect in several ways:

48
The variable domains are responsible for binding of the antigen with high
affinity. In case of an infection pathogens become covered with specific
antibodies, some of which physically block pathogen cell surface molecules
required for binding to cell surface receptors of the host. Similarly, antibodies
binding to the active parts of various animal or microbial toxins (venomous
snakes, spiders, tetanus), inhibit their toxicity.
This kind of steric inhibitory effect is called neutralization, and antibodies
delivering this effect, are called neutralizing antibodies (Figure 17.).

Figure 17. Neutralization of pathogens by neutralizing antibodies

Immunoglobulin molecules, produced by plasma cells, bound to pathogens or different toxins
may inhibit their effects. They can block binding of pathogens (e.g. viruses) to the cell surface,
thus preventing infection of the cell.

Antibodies produced by the mother’s immune system can be transported

through the placenta or into the breast milk. These antibodies protect the new
born from infections for several months after birth, until the child’s own B cell
repertoire is fully developed. This maternal protection mechanism is also based
mainly on neutralizing antibodies. Large amounts of neutralizing antibodies
are produced on a daily basis by the immune system of the intestines, these
antibodies are transported into the lumen, where they neutralize the dangerous
materials taken up together with food. Some life-saving medical treatments
utilize the direct neutralizing effects of antibodies. For example: upon a snake
bite, antibodies neutralizing different toxins of the snake venom are given to
the patient. (See the part about passive immunization!)

49
While neutralization is based primarily on the variable region of the antibody,
other effector functions are dependent on the constant regions of the antibody
molecule, more precisely on the Fc region.
The Fc region of the antibody (the “stem” of the Y- or fork-shaped antibody
formed by the constant domains of the heavy chains) is recognized by various
cell surface receptors, called Fc-receptors, expressed on several types of
immunocytes. With these receptors, immune cells can recognize antibody
molecules. Antibodies form a bridge between the opsonized pathogen and the
immunocyte. The variable domain of the antibody binds to the pathogen, while
the Fc region binds to the Fc receptor expressed on the immunocyte.
Unlike the variable domains of the antibodies the constant domains are more
or less identical. (The different isotypes are recognized by distinct Fc
receptors). Thus phagocytes and NK cells don’t need to produce a diverse set
of unique receptors for the recognition of millions of pathogens, they “smartly”
recognize the Fc region of opsonizing antibodies attached to any pathogen.
Importantly, most Fc-receptors are not activated by free antibodies. Efficient
activation of phagocytes or NK cells via their Fc-receptors requires immune
complexes. Thus we can say that these receptors are responsible for the
recognition of opsonized antigens.

Effector mechanisms mediated by the Fc part of the antibodies

 Opsonization by immunoglobulins enhances receptor mediated
phagocytosis of pathogens via cell surface expressed Fc-receptors.
(Figure 18.)
 NK cells also express Fc receptors. With these receptors, they are able
to bind cells opsonized by immunoglobulins. This interaction may
trigger their cytotoxic function. This process is called antibody
dependent cellular cytotoxicity (ADCC). (Figure 18.)
 The Fc region of many immunoglobulin isotypes contains complement
binding sites. Such antibodies bound to the pathogen can activate the
complement system. (Figure 18.).
 Fc-receptors recognizing the heavy chains of IgE, play a key role in the
induction of allergic reactions, by activating mast cells and basophil
granulocytes. (As described later!)

50
Figure 18. Antibody mediated effector functions
In addition to neutralization, binding of antibodies to pathogens (opsonization) may facilitate
phagocytosis of the pathogen, may activate the complement system and the NK cells as well.

Immunoglobulins – based on the structure of their heavy chain – are classified

into five major classes, called isotypes: IgM, IgD, IgG, IgE and IgA. However,
in response to adequate stimuli (with the contribution of helper T cells) the B
cell can change the isotype of the produced antibody by a process called
isotype switching or class switching. The cells of the immune system have
different Fc-receptors on their surface that recognize and bind specific
antibody isotypes. Importantly, different types of Fc receptors deliver distinct
effector functions. As a result, by changing the isotype (but not the specificity)
of the produced antibodies, the formed immune complexes or the opsonized
pathogens will bind to a different set of Fc-receptors, thus the effector
functions induced by them usually change.

51
There are some special Fc receptors in the body, which are responsible for the
transport of antibody molecules. Such Fc-receptors transport IgG from the
mother to the fetus, or IgA across epithelial cells or into the breast milk.
It’s important to emphasize that during isotype switching, not the specificity,
but the effector functions of the antibody are altered. As binding specificity
remains the same, neutralizing function of an antibody is not influenced by
isotype switching.
Effector functions of the main antibody isotypes:
 Immunoglobulin G, or IgG is the „swiss army knife” of antibodies.
This isotype can efficiently opsonize pathogens and facilitate the
process of phagocytosis. Some subtypes effectively activate the
complement system as well as the killing function/capacity of NK cells.
This isotype is present at the highest concentration in plasma, and has
the longest half-life. Special Fc receptors transport IgG, from the
mother’s circulation into the fetus across the placenta.
 IgM Many species of bacteria opsonized by IgM can be destroyed
efficiently by the complement system. This type of immunoglobulin
can be found on the surface of naïve B cells where they function as
antigen binding receptors. Unlike IgG, this immunoglobulin is not able
to facilitate the phagocytosis of bacteria directly (only by activating the
complement system). IgM can be transported by Fc receptors, but not
from the mother to the fetus.
 IgA It appears in body fluids including tear, saliva, intestinal fluids,
mainly to protect cells of the mucosal epithelium. Transport of IgA
mediated by specific Fc receptors is considered the most efficient
among antibodies.
 IgE its natural function is protection against parasites, however this
immunoglobulin isotype is responsible for the symptoms of allergic
reactions.
 IgD This isotype is present primarily as an antigen-specific receptor on
the surface of newly formed B cells. Similar to IgM, IgD plays a role
in B cell activation.

T cells
T-lymphocytes express a cell surface antigen receptor called T Cell Receptor
(TCR) which resembles an antigen-binding arm of an antibody.

52
The antigen-specific activation of T cells requires direct contact between the T
cell and an antigen presenting cell as it requires the interaction of the TCR and
MHC molecules. In contrast to B cells, the majority of T cells exclusively
recognize protein-derived peptide epitopes in complex with the
histocompatibility complex (MHC) proteins.

Differences in antigen recognition by B and T cells.

B cell T cell
proteins
carbohydrates
lipids peptide derived from
recognized
proteins (8-20 amino-
substances DNA acids)
steroids
artificial substances etc.

native/intact antigen processed and presented

type of
by an APC as MHC
recognition tissue derived or humoral peptide complexes

The two main populations of T cells contribute to the immune response

differently. Helper T-lymphocytes have more of a regulatory role in the
immune response while cytotoxic T-lymphocytes are professional killer cells
designed for killing of infected- or tumour-cells directly.
Completing their development in the thymus both naïve CD4+ (“helper”) and
naïve CD8+ T (“cytotoxic”) cells enter the circulation. Leaving the blood, they
migrate into secondary lymphoid organs and screen the local antigen-repertoire
on the surface of dendritic cells available at the time of their surveillance. A
continuous recirculation of T cells between various secondary lymphoid
organs is maintained until circulating T cells meet their specific antigen that
induces their activation, followed by clonal expansion and differentiation into
effector T cells. Clonal proliferation of T cells, like that of B cells rapidly
generates a large population of cells (a T cell clone) with antigen specificity
identical to that of their progenitor cell. Those T cells that fail to find their
specific antigen are destined to die by apoptosis within a few weeks.
In most cases antigens for naïve T cells are transported into the lymph node by
dendritic cells. Dendritic cells dispersed in tissues sense pathogens using their

53
pattern recognition receptors. Upon recognition they engulf microbes and
migrate into the regional lymph node. Meanwhile, processing of the pathogen-
derived antigen is completed and peptide fragments are presented on MHC.
Thus, initial activation of T cells occurs in a special environment, the lymph
node, where clonal expansion of antigen-specific T cells occurs. Those T cells
that have gone through clonal expansion and differentiation exit the lymph
nodes. Once in the periphery, they are able to deliver a proper response upon
the second activation by the same antigen present at the site of infection.
In the periphery, cytotoxic T cells (Tc) recognize their specific peptide
fragment (antigen) presented by any nucleated cell expressing MHC I
molecules. Notably, these antigen presenting cells recognized by Tc are
usually infected or tumour cells.
Helper T-lymphocytes (Th cells) can only be activated by professional antigen
presenting cells expressing cell surface MHC II molecules in peripheral tissues
and also in peripheral lymphoid tissues.

Figure 19. The main populations of T cells: helper and cytotoxic T-lymphocytes

T cell subsets and their functions

Helper T cells or Th cells are not directly involved killing of pathogens, they
rather coordinate the immune response by communicating with other
immunocytes. Exogenous proteins processed to peptides by professional APCs
and presented to CD4 co-receptor expressing Th cells via cell surface MHC II
molecules. Antigen-specific activation of Th-cells via the TCR induces

54
cytokine production and expression of novel cell surface molecules on the T-
lymphocyte by which they coordinate the immune response. (Figure 19.)
We can distinguish some major helper T cell types, type 1 (Th1), type 2 (Th2)
type 17 (Th17) and follicular helper T cells. Th1 cells are essential
components of the immune response against intracellular pathogens.
Cytokines secreted by Th1 cells are involved in the recruitment if phagocytes
to the site of infection and enhance the antimicrobial (killing) activity of
macrophages, the killing functions of NK- and cytotoxic T cells.
Th2 cells on the other hand help the immune response essential for the
elimination of parasites and helmiths. By their cytokine secretion they facilitate
the control of parasites by mast cells, basophil- and eosinophil granulocytes.
In addition, macrophages activated by the same cytokines play an essential role
in tissue re-building (repairing tissue damage) once the pathogens had been
cleared.
Another, important subpopulation of Th cells is the Th17 subset, partaking in
immune responses against extracellular pathogens, bacteria or fungi in
particular. They potentiate inflammatory responses by recruiting neutrophils
and monocytes to the site of infection. Th17-cells can be found in large
numbers near the epithelial barriers.
While Th1, Th2 and Th17 cells migrate and function to the peripheral tissues,
follicular helper T cells facilitate the activation and differentiation of B cells
in the secondary lymphatic organs. Their function is essential for the process
of isotype switching of antibody molecules. This cell type was identified
recently, before that, their function was assigned to classical Th1 or Th2 cells.
T-helper subsets can develop from the common naïve Th precursor (a Th0 cell)
in secondary lymphoid organs. Their differentiation is predominantly
regulated by the APC of the local secondary lymphoid tissues, however,
cytokines in their environment have also profound regulatory functions. For
example, secreted cytokines by the Th1 and Th2 subsets mutually inhibit each
other’s differentiation (Figure 20.).

55
Figure 20. Differentiation of naïve helper T cells
Interaction with the APC, together with their cytokine secretion will determine the “fate” of
the differentiating naïve T-helper cell. Various T cell subsets differentiating from the activated
Th0 cells coordinate distinct immune cell functions. Th1 cells secrete cytokines mainly to
enhance the immune response against intracellular pathogens, while Th2 support anti-parasite
immunity. Cytokines produced by different T-helper subpopulations inhibit each other’s
function.

Cytotoxic T cells (killer cells, CTL, CD8+ T cell) recognize and kill
“estranged”, virus-infected or tumour cells present in our body. Under
physiological conditions our cells continuously synthesize and degrade cellular
proteins. Peptides derived from these degraded proteins are transported to the
cell surface and displayed in complex with MHC I molecules. The same
mechanism operates for the presentation of viral- and tumour-associated
proteins.

56
Unlike Th cells, CTLs recognize antigen fragments in complex with MHC I
molecules expressed by all nucleated cells, thus synthesis of foreign or mutant-
self proteins in any cells can be readily detected and eliminated by CTLs.
(Figure 19.)
Although the mechanism of recognition and activation of NK cells and CTLs
are different, the mechanisms of killing the target cells are similar. Both cell
types make contact with the infected- or tumour-cell directly and releases the
content of their intracellular granules containing cytotoxic substances to the
site of cell-cell contact. Some of these cytotoxic substances like perforin
molecules will form pores within the target cell membrane leading to
disruption of the transmembrane ion balance which alone may be sufficient to
cause the death of the target cell.
Granzymes also released by these granules enter the target cell via perforin-
induced pores and trigger apoptosis. Additionally, effector CTL expresses
molecules on the surface which induce apoptosis in the target cell.
Various subsets of regulatory T cells produce inhibitory cytokines that
suppress immune responses against self-antigens.

The immunological memory, passive and active

immunization
The appearance of the adaptive immune system during evolution allowed the
specific recognition of unique antigens which is essential for the development
of the immunological memory. In case of repeated exposure to the same
pathogen the organism responds faster and more effectively compared to the
first exposure. Memory response is characteristic only of B and T cells. The
mechanism of pathogen recognition by innate cells does not allow the
development of an effective, highly-specific memory response.
During clonal proliferation and differentiation, some antigen-specific B and T
lymphocytes in the secondary lymphoid tissues differentiate into memory
cells. The memory cells and their precursors have the same antigen receptor
specificity therefore they recognize the same antigen. Following elimination
of the pathogen, the majority of antigen specific B and T cells becomes
unnecessary and die by apoptosis. However, a relatively large number of
lymphocytes survive and become memory cells. After elimination of the
pathogen, memory cells may survive and preserve their antigen specificity for
decades, even in the absence of their specific antigen. B cells can differentiate
into long-lived plasma cells and may produce antibodies throughout the entire
lifetime of an individual.

57
Characteristics of the memory response
 Upon second exposure (with the same pathogen), antibodies produced
by long-lived plasma cells act immediately to neutralize and opsonize
the pathogen
 The frequency of specific lymphocytes upon antigen re-exposure
within the long-lived memory T or B cell repertoire is much higher than
in the repertoire of naïve lymphocytes.
 Activation of B as well as T memory cells is simpler, thus faster than
that of naïve cells.

Figure 21. The response of memory B cells.

After the specific recognition of the pathogen B cells go through clonal expansion and
differentiate to plasma cells or memory B cells. Following successful eradication of a pathogen
the majority of the plasma cells die, however, some of the antigen specific long-lived plasma
cells and memory B cells survive. Re-infection with the same pathogen induces the activation
of already existing memory cells. In this population, frequency of antigen-specific B cells is
higher than in naïve B cell populations. In addition, they are already differentiated B cells that
have gone through a germinal center reaction, which warrants a faster, more robust and more
effective B cell response. The amount, the specificity and the affinity of the secreted antibodies
are also higher.

58
Antigen-specific effector cells, which develop from memory cells in peripheral
tissues or in secondary lymphoid organs complete their proliferation and
differentiation more rapidly.
Compared to the first encounter (primary immune response), the memory
response reaches its peak three-times faster (within 3-5 days).
 During a memory response not only the number of responding B cells
but the amount of antibodies produced is higher compared to the
primary immune response (Figure 21.)
 Both the affinity and the specificity of antibodies produced during the
memory response are enhanced (affinity maturation) and often their
isotype is switched. In a primary response IgM-type antibodies are
dominant, while repeated infections with the same pathogen increases
the amount of other isotypes (IgG, IgA, IgE)
The differentiation of long-lived plasma cells, affinity maturation as well as
isotype switching of B cells requires the contribution of Th cells.
With ageing the production of naïve lymphocytes decreases. Thus, in elderly
people the immune response is based on memory lymphocytes. Senior people
may be sensitive to infections with pathogens yet unknown to them, however
they can readily maintain protection against microbes they have encountered
long time ago.

The B cell mediated primary and secondary immune response

primary response memory response
Intensity lower high
Antibody isotype mainly IgM (IgM) IgG, IgA, IgE
Antibody affinity low affinity high affinity
Time interval of a
7-14 days 3-5 days
max. response

Immunization
The beneficial features of the memory immune response are utilized when
artificial immunization is used to develop protection against pathogens. Using
passive immunization, antigen-specific antibodies are injected or transfused
into to body. By active immunization both cellular and humoral antigen-

59
specific memory response are induced artificially that usually prevent the
appearance of the disease following exposure to pathogen.
Passive immunization
Immunity can be transferred from one person to another. Antigen specific
antibodies or antibody-enriched serum (antiserum) can be transfused to a
person we aim to protect. These antibodies act immediately, neutralize and
opsonize the antigen.
The application of antiserum or purified antibody is warranted in all cases
when fast and efficient protection is needed immediately (when the antigen has
entered the body). For example, serum containing neutralizing antibodies are
used in cases when venom of poisonous snakes or a toxin of arthropods enter
the victim’s body.
The protection time of passive immunization is limited by the half-life of the
antibody (usually some days to some weeks depending on the subtype).
Newborns are protected from many pathogens by antibodies produced by their
mother. Until birth, IgG antibodies are transcytozed from the maternal to the
fetal blood via the placenta by special Fc receptors. After birth these antibodies
provide temporary protection distributed in the body of the newborn. The
baby’s digestive and respiratory tract are protected by the maternal IgA
supplied by breast feeding.
Active immunization and vaccines
An immune response can be induced by either infection or active
immunization. Vaccines may contain live attenuated or inactivated
pathogenic microbes, purified or artificially synthetized immunogenic
components/subunits of microbes. Attenuated pathogens lose some of their
virulence factors essential for fast proliferation and dissemination. This blocks
their ability to induce serious disease, but allows the development of protective
immunity by the host. Vaccines containing small parts or purified recombinant
proteins of microbes called subunit vaccines are usually less efficient and
require the use of adjuvants. The pathogen-derived antigens are recognized by
the adaptive immune system and a memory response is generated, but most
vaccines will induce transient, mild symptoms only, if any.
Vaccines prepare the immune system for a future infection. During vaccination
the immune system completes all the steps of the relatively slow primary
response, therefore a future response to an infection with the pathogenic
microbe will show the characteristic of a rapid and robust secondary (memory)
response that clears the infection quickly. Vaccination may completely block
or dampen the symptoms of infections. Taken together, vaccination against a

60
microbe mimics the infection with the pathogen, induces a memory response
which enables the host to eliminate the same pathogen and prevent a
potentially fatal disease.
Active immunization with most vaccines is a slow process. It takes weeks or
sometimes months to develop effective protection and sometimes repeated
vaccination is required. Thus, an immediate response is not provided, but
depending on the type of the vaccine it may protect the body against the
targeted microbe for decades or even for life. Good examples of this are
vaccines given to children at an early age.
The efficacy of a vaccine, just like the imunogenicity of antigens in general,
may differ significantly from one person to another. Immunodeficient
individuals may remain unprotected to some or to all pathogens despite the
most sophisticated vaccination schemes. However, when the majority of
individuals within a large human population are vaccinated, these unprotected
individuals of the group are also protected. This phenomenon is called the
“herd immunity”, a kind of “social immunity”.

Active and passive immunization.

Active Passive
inactivated/attenuated
immune serum or
Type of substance pathogen, or pathogen
purified antibody
subunit
the host develops an
immune response exogenous, neutralizing
Mechanism
antibody is provided
memory cells produced
Development of
slow immediate
protection
Duration of
long: years or lifetime some weeks or months
protection

Immunological tolerance
B and T cells of a healthy individual will fail to launch a destructive immune
response to antigens present in self-tissues. This is a result of an active, antigen
specific unresponsiveness as a result of two main mechanisms called central-
and peripheral tolerance.

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Central tolerance is established during lymphocyte development in the
primary lymphoid organs, for B cells in the bonne marrow and in the thymus
for T cells. Antigen receptors of lymphocyte progenitors are exposed to self-
antigens during their development. Those cells carrying receptors that bind to
self-antigens with high affinity are considered potentially autoreactive and die
by apoptosis. Thus, most self-reactive, potentially dangerous autoimmune cells
prone to cause tissue damage in various organs are eliminated at an early stage
of lymphocyte development. This process generating central tolerance is
referred to as negative selection or clonal deletion of autoimmune
lymphocytes. Even though there are mechanisms inducing the ectopic
expression of self-antigens in the primary lymphoid organs, some developing
lymphocytes fail “to get acquainted” with all self-antigens. Thus central
tolerance is considered an efficient but “leaky” mechanism.
Autoimmunity caused by the relatively few self–reactive cells can be
controlled by various peripheral tolerance mechanisms.
1. As described above, naïve T-lymphocytes acquire activation signals
exclusively from activated, mature dendritic cells (DCs) immigrating
from the site of infection to the lymph node. DCs exposed to danger
signals or pathogen associated molecular patterns elevate the cell
surface expression of co-stimulatory molecules which are required for
the proper activation of naïve T cells. The “maverick” autoreactive T-
lymphocytes escaping clonal deletion in the primary lymphoid organs,
will first encounter their specific self-antigen presented by non-
professional APC, or non-activated APC in the absence of co-
stimulation. In the absence of co-stimulation these T-lymphocytes
enter into a state functional unresponsiveness called anergy.
2. Peripheral tolerance of B cells is maintained mainly by the absence of
autoreactive T cells. B-lymphocytes recognizing and presenting self-
antigens fail to find helper T-lymphocytes which are specific for the
same autoantigen. In the absence of T cell mediated costimulatory
signals activation of autoreactive B cells is inhibited.
3. Peripheral tolerance is maintained in part by the aforementioned
regulator T-lymphocytes (Treg) which keep autoreactive lymphocytes
supressed.

Communication between the innate and adaptive

immune system
While in invertebrate species only the elements of the innate immune system
are present, the innate and adaptive immune systems not only co-exist in

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humans, rather, they co-operate in total harmony. The innate immune system,
especially macrophages and dendritic cells are essential for initiation of the
adaptive immune response. T cells are unable to function without these antigen
presenting cells. With few exceptions B cells also require the signals coming
from innate immune cells and / or T helper cells.
The cells of the innate immune system do not simply trigger the activation of
T cells. Through their secreted cytokines, costimulatory and adhesion
molecules, they orchestrate the adaptive response. Although activation of the
adaptive immune system comes much later, it is able to augment significantly
the function of innate immune cells.
Cytokines produced by T cells help the activation of macrophages, elimination
of the ingested microbes, maturation of dendritic cells, antigen presentation
and the cytotoxicity of NK cells. Lymphocyte-derived cytokines contribute to
regulation of the action, the maturation and the localization of innate cells. At
the same time cytokines also play a key role in limiting the innate immune
response.
We have already discussed the effect of antibodies produced by B cells. The
antibody molecules opsonize pathogens, facilitate their recognition and
phagocytosis. Opsonization by antibodies also increases the activity of the
complement system and enhances NK cell-mediated killing. Similarly,
antibodies regulate the function of mast cells and granulocytes.
Both the innate and the adaptive immune system have self-control
mechanisms. Cytokines and chemokines produced by macrophages have
autocrine effects regulating macrophage functions. These cytokines are the
main positive and negative regulators of neutrophils in the inflammatory
process, and also of the functional activity of NK cells. Furthermore, they can
increase the production and facilitate the exit of complement proteins from the
blood vessels.
In the case of the adaptive immune system only those B cells can get help from
Th cells which can present appropriate antigen to them. In optimal situation
the B cell and the interacting Th cell recognize the same antigen. In this case,
cytokines produced by the T cells contribute to the activation, affinity
maturation of B cells as well as to generation of memory cells. Antigen
presentation by B cells may facilitate the survival of effector / memory T cells.

The process of immune response

Pathogens may cause mild diseases, like rhinitis induced by rhinoviruses or
debilitating, even fatal diseases, for example the HIV or HBV virus. Our

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immune system consists of multiple, co-operating systems which defend the
body against thousands of pathogens present in our environment. The skin or
the mucosal epithelium lining the airways and gut are the first defense line
against invading pathogens, forming a physical and chemical barrier against
infection. The dry and hard outer layer of the skin is a formidable barrier when
unbroken. Infections occur only when a pathogen crosses these barriers, as in
the case of an injury (e.g. wounds by cuts and burns). Although the
gastrointestinal and respiratory tracts are exposed to a plethora of pathogens
they are protected effectively by multiple mechanisms. Pathogens colonizing
mucosal surfaces enhance secretion of a viscous fluid called mucus. Foreign
agents irritate the respiratory tract triggering cough and sneezing, which
effectively remove these irritants. The acidic environment of the stomach
destroys many pathogens ingested with meals.
The gastrointestinal, respiratory and urogenital tracts are covered by mucosal
epithelium which consists of epithelial cells held together by tight junctions.
These epithelial cells are covered with mucus, containing various oligo- and
polysaccharides. Mucus has a number of protective functions, for example it
may prevent microorganisms from adhering to the epithelium.
Epithelial cells can transport certain antibody isotypes (especially IgA) across
the epithelial cell to the surface of mucosal epithelium using active transport
mechanisms. Therefore, microbes are exposed to antibodies as soon as they
enter our respiratory or digestive system. IgA-mediated protection against
microbes is based primarily on its neutralizing effect.
Invading pathogens are encountered by various immune cells ready for
combat. Macrophages, dendritic cells, effector T cells and B cell are all present
in the subcutaneous or intraepithelial tissues. The invading pathogens are
recognized first by the cells of the innate immune system (eg. macrophages
and dendritic cells), expressing pattern recognition receptors. They
immediately trigger the well-known reactions of the innate immune system
(elimination of pathogens, release of cytokines, recruitment of other
immunocytes) leading to induction of inflammation in the infected tissue.
The increased production and flow of lymph will carry some of the pathogens
into the regional (draining) lymph nodes. Activated dendritic cells also reach
the lymph nodes through the lymph, where they present processed
phagocytosed antigens to the T lymphocytes. Thus B and T lymphocytes,
which recognize the pathogen specific antigens, get activated, proliferate and
differentiate into effector or memory cells.
Depending on the amount and the growth rate of the invading pathogen we can
distinguish between three potential courses of the immune response.

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Small amounts of pathogens are immediately recognized at the site of infection
and are eliminated by macrophages found almost everywhere in our body.
If this mechanism is insufficient for clearing the pathogen more participants of
the innate immune system will be recruited to help macrophages.
If the pathogen survives for an extended period, the adaptive immune system
will also be activated, which finally eliminates the pathogens either by its own
mechanisms, or more often by enhancing the innate response.
If the organism has met the pathogen in the course of an earlier infection, the
effector mechanisms of adaptive immune response can provide immediate
protection. Pathogen-specific antibodies produced by the long-lived plasma
cells neutralize the pathogens and the effector T cells eliminate the infected
cells in a few days, or produce cytokines to enhance the efficiency of the other
participants of immune system. In parallel, memory cells in the lymph nodes
get activated and begin to proliferate rapidly.

Bacteria, viruses and parasites

Hundreds or thousands of viruses, bacteria, fungi, unicellular or multicellular
eukaryotic parasites are able to infect humans. Pathogens use diverse strategies
for infection and to escape immune surveillance. Accordingly, the immune
system uses different strategies to override these mechanisms.

The main strategies of immune system for elimination/neutralization of

extracellular or intracellular pathogens:
innate adaptive
immune system immune system
 phagocytosis
extracellular  production of soluble  antibody production,
pathogens toxic agents neutralization
 complement system
 destroying infected cells
(NK cells)
 intracellular killing and  destroying infected
intracellular cells (cytotoxic T
degradation
pathogens
 release of type I cells)
interferons, intracellular
antiviral mechanisms

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Most pathogenic bacteria and fungi entering the body live in the interstitial
space between cells. These pathogens are called extracellular pathogens.
These are the main targets of antibodies and complement proteins released
from the blood plasma during inflammation. Pathogens opsonized by
antibodies are efficiently recognized by phagocytes, mainly by macrophages
and neutrophil granulocytes, and by the complement system. The complement
system can itself lyse some microbes. As a result, via complement receptors
and Fc-receptors phagocytes are induced to ingest and kill opsonized
pathogens.
Dendritic cells activated by microbes induce high-level expression of
costimulatory receptors and migrate along lymphatic vessels to draining lymph
nodes where they present the pathogen-derived peptides to naïve T
lymphocytes. Pathogens phagocytosed by macrophages are usually killed in
the phagolysosomes. A fraction of microbial peptides not degraded in the
phagolysosomes can be presented on MHC II to the helper T cells. In turn,
effector T-helper cells activated by macrophages using cell-cell contact and
secretion of cytokines (e.g. IFN-γ) will help macrophages to kill the ingested
pathogens or at least prevent their spread (Figure 22).

Figure 22 Elimination of extracellular pathogens

Phagocytes (Mf) recognize pathogens via PRR or pathogens opsonized with antibodies and/or
complement via Fc- and/or complement-receptors. Pathogens bound by these receptors get
ingested and killed in the phagolysosomes by multiple mechanisms (right). Antibodies
produced by plasma cells may neutralize the pathogen and/or activate antibody-mediated
effector functions (middle). (Complement components may directly eliminate pathogens.)
Type 2 cytokine-producing T helper cells augment immune response against extracellular
pathogens primarily (left).

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Viruses and some bacteria are able to invade cells and generate intracellular
infection, therefore their elimination requires an entirely different recognition
and elimination process.
The epitopes of intracellular proteins synthetized in infected cells are presented
at the cell surface through MHC class I molecules. These infected cells are
recognized and eliminated by another group of effector T cells, the cytotoxic
T cells. If intracellular pathogens downregulate expression of MHC class I
molecules, infected cells are recognized and eliminated by NK cells, since the
lack of MHC class I mediated inhibitory signals greatly enhance cytotoxic
activity of NK cells.
Thus, effector functions against intracellular pathogens are not directed to the
pathogen, they are rather focused on destruction of the infected host cells
(Figure 23).
The same effector mechanisms are also characteristic of anti- tumour
responses, as tumour cells as well are aberrant host cells that need to be
eliminated.

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Figure 23 Elimination of intracellular pathogens
Virus-infected cells are recognized via intracellular pattern recognition receptors followed by
production of type I interferons. Concomitantly, MHC class I molecules present antigens of
intracellular pathogens on the cell surface and activate cytotoxic T lymphocytes, which kill the
infected cells (bottom left). In the absence of cell surface MHC I (indicating an aberrant
cellular function) cells become targets for NK cells, which again leads to the elimination of
the cell (right).

Interferons play a key role in anti-viral immunity. IFN-γ is produced mainly

by T helper cells and cytotoxic cells (NK, Tc), and besides their direct antiviral
effect their main function is to promote macrophage functions. In the presence
of IFN-γ macrophages kill engulfed microorganisms more efficiently. In
addition, IFN-γ enhances the expression of MHC class I and II molecules on
the surface of professional antigen presenting cells.

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IFN-α, IFN-β can be produced by almost any cell type following viral
infection. Interferons often have autocrine effects on the cells producing them,
or paracrine effects on neighbouring cells. They interfere with viral replication
by various mechanisms eg. through inhibition of protein synthesis, or increased
expression of MHC class I molecules.
Antibodies may also partake in the defense against viruses. The neutralizing
effect of antibodies prevents viral adhesion to host cells and thereby interferes
with infection.
Viral proteins may also be integrated in the cell membrane of infected cells.
Antibodies recognizing these antigens will bind to them, thus marking the cell
for antibody-dependent cellular cytotoxicity (ADCC). NK cells can kill
infected cells also by ADCC via activation by their Fc receptors.
Some small, unicellular eukaryotic parasite, which exist intracellularly in
some part of their life cycle, such as Plasmodium species, can induce similar
cytotoxic T cell responses. Their extracellular form can be recognized by
antibodies
Elimination of large multicellular extracellular parasites (e.g. flat- and
roundworms) often requires much broader spectrum of immune response
delivered by specialized cells. Mast cells, basophil and eosinophil granulocytes
are involved in inflammation triggered by parasites. These cells release special
toxic agents and degrading enzymes from their vacuoles to destroy the
parasites at the area of infection. In addition to toxic agents many pro-
inflammatory cytokines are also secreted. Some of these increase peristaltic
activity in case of intestinal infection or trigger coughing, sneezing and induce
mucus production in case of a respiratory infection to help removing the
parasites from the body. The parasite-specific IgE antibodies bound to high
affinity Fc receptors of mast cells and basophil granulocytes play important
roles in the activation of these cells and thereby in the immune response against
parasites.

Disorders of immune system

“Too much” as well as “too little” reactivity of the immune system may cause
diseases. The former may lead to the development of the so-called
hypersensitivity reactions while the latter one is called immunodeficiency.
Hyper-reactivity can develop against self-antigens causing autoimmune
diseases. Hypersensitivity reactions specific to either foreign or self-antigens
may cause significant tissue damage to the host.

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Allergic diseases
In some people immune response is triggered by innocuous (harmless) agents
(allergens), such as plant pollen, certain food products (eg. peanut proteins),
animal hair (animal-derived proteins) or house dust (which contains the
excrement components of dust mite). These processes are connected with
abnormal production of allergen-specific IgE antibodies by plasma cells.
The characteristic symptoms of the disease are itching, sneezing, rashes, or in
more serious cases, anaphylactic shock.
This process is triggered by stable, compact, often enzymatically active
antigens. Such antigens are able to cross the epithelium of the respiratory
system or the gastrointestinal tract. T cells contribute to the development of the
disease by promoting the development of antigen-specific, IgE producing B
cells. Antigen-specific IgE antibodies gaining access to all peripheral tissues
bind to the high affinity Fcε receptors (IgE-specific, Fc-epsilon receptors) on
mast cells. From that point, the body is „sensitized” to the antigen. These
sensitized mast cells survive for years.
At the second exposure the allergen will activate many Fcε-receptors via
crosslinking the antigen-specific IgE bound to them. Consequently, mast cells
become activated and release their stored bioactive agents (histamine,
serotonin, various enzymes) which rapidly induce the typical symptoms of
allergy (immediate reaction). This rapid, usually immediate reaction to the
antigen (allergen) is called Type I hypersensitivity reaction (Figure 24).
Later, in the second phase of the reaction, (also called the late response) mast
cells and basophil granulocytes produce additional inflammatory mediators
(late lipid mediators and cytokines).

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Figure 24 Mechanism of allergic response
Expression of high affinity Fcε receptors on mast cells is antigen independent. After
appearance of an allergen specific IgE-type antibodies are produced by plasma cells which
bind to these Fcε receptors whit high affinity. Crosslinking of Fcε receptor-linked antibodies
by the allergen induces activation of the mast cell: the release of granular content and cytokine
production.

The main role of the mast cells, basophil granulocytes and molecules (IgE) are
well known in immune response against parasites. Thus most of the symptoms
of allergic reactions results from effector mechanisms designed to kill or expel
parasites.

Autoimmune diseases
Sometimes regulatory mechanisms maintaining self-tolerance fail, resulting in
increased production of self-reactive antibodies and lymphocytes. As a result,
healthy cells and tissues become targets of the effector mechanisms of immune
response.
Antibodies can be produced against various cell surface receptors this way.
Some of these auto-antibodies may interfere with the normal function of the
receptor by inhibiting the binding of its natural ligand (blocking or antagonistic
antibodies). This is the case in myasthenia gravis, an auto-immune disease, in
which antibodies specific to acetylcholine receptors at the postsynaptic neuro-
muscular junctions inhibit the excitatory effects of the neurotransmitter
acetylcholine causing muscle weakness. Other auto-antibodies can have

71
stimulating effects on receptors (agonistic antibodies). In Graves’ disease (also
known as Basedow-syndrome) auto-antibodies continuously stimulate the
thyroid-stimulating hormone (TSH) receptor, resulting in hyperthyroidism. In
other cases, binding of the auto-antibody to the target cell does not change
cellular functions, but triggers antibody-dependent effector functions
described earlier. In penicillin-sensitive persons antibodies recognize
penicillin covalently coupled to cell surface proteins of red blood cells. Similar
to any other antigens or pathogens, red blood cells opsonized by penicillin-
specific antibodies become targets of phagocytes and the complement system.
Those reactions when antibodies bind to common or modified cell surface
antigens and trigger effector functions causing damage to self-tissues are called
Type II hypersensitivity reactions.
T cells may also cause hypersensitivity or autoimmune disease by a mechanism
called Type IV hypersensitivity. In patients with Type I diabetes mellitus
cytotoxic T lymphocytes kill the insulin producing beta cells of the pancreas.
In gluten-sensitive individuals the modified gliadin peptide derived from the
wheat protein gluten is presented via MHC class II molecules to T cells leading
to their activation that triggers the production of pro-inflammatory cytokines
and thereby inflammation.
Some people are sensitive to chemicals produced by plants (e.g. poison ivy),
others to nickel-containing jewellery. When these materials come into contact
with skin they modify skin proteins. The modified protein presenting cells
become targets of Tc- or Th cells that induce inflammation (contact
dermatitis). These processes –with the antigen presentation– require 48-72
hours to develop, consequently, this type of reaction is often called delayed-
type hypersensitivity.

Immune complex diseases

Immune complexes are antigens opsonized with antibodies (Figure 25).
Antibodies may form large, cross-linked complexes with antigens, which
under normal circumstances are rapidly eliminated from the circulation by
phagocytic cells of the spleen.

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Figure 25 Immune complexes
Immune complexes consist of an antigen, an antigen-specific antibody and usually
complement components as well.

In the presence of large quantities of auto-antigens and their specific auto-

antibodies small immune complexes are formed, which remain in circulation
for an extended period of time. In addition, small immune complexes have
access even to the smallest blood vessels including capillaries of the skin, the
glomeruli of the kidney or they can accumulate in the joints as well. Immune
complexes stuck in small vessels activate the complement system via the
classical pathway at the site of deposition. Also phagocytic cells get activated,
since both the complement fragments and the antibody molecules in immune
complexes act as opsonins. This leads to inflammation and destruction of local
self-tissues. These immune complex-mediated autoimmune diseases include
vasculitis, glomerulonephritis or arthritis. Many pathogens (viral hepatitis,
malaria) or environmental agents may trigger similar diseases (eg. „farmer’s
lung” caused by a mold present on hay). Hypersensitivity reactions induced by
immune complexes are called type III hypersensitivity reactions as well.

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The mechanisms leading to the development of autoimmune diseases are often
not clear. Multiple environmental and genetic factors may be responsible.
Environmental factors may include pathogens, chemicals or even strong
sunlight. Hormones may also play a role since most autoimmune diseases are
more common in women than in men. The presence of certain MHC allotypes
is also associated with a higher risk of autoimmune disease development.

Immunodeficiencies
Immunodeficiency is a state when the immune response to all or to a selected
set of pathogens is insufficient, causing severe, recurrent infections or death.
The so-called primary immunodeficiencies are caused by inherited genetic
defects deleting essential components (cells or regulatory mechanisms) of the
immune system. Acquired immunodeficiencies on the other hand are caused
by environmental factors including toxic chemicals, chemotherapy or
immunosuppressive drugs used at organ transplantations to impede
transplant rejection.
Transient immunodeficiency may develop after viral infections, for example
measles, influenza, Epstein-Barr virus-induced mononucleosis. Some surgical
procedures, malnutrition, smoking and stress, even transfusion with white
blood cell-containing blood may cause temporary immunosuppression.
There are over 200 primary immunodeficiency syndromes. Some babies are
born without functional B cells and thus produce minimal or no antibodies, or
when they have a defect in class switching, they produce only IgM antibodies.
The lack of T cells causes an even more severe immune defect, as in the
absence of T cells most B cell functions are also hampered. Therefore, in the
absence of T cells, a combined, fatal immunodeficiency called severe
combined immunodeficiency or SCID develops.
The acquired immune deficiency syndrome, or AIDS is an immunodeficiency
caused by the human immunodeficiency virus HIV. This retrovirus infects the
T-helper cells and monocyte-derived macrophages bearing CD4 surface
molecules. The virus is integrated, in the form of DNA into the human genome,
where it may remain silent and hidden from the immune system for a long time.
However, sooner or later the virus destroys the infected cell. As the number of
the helper T cells in HIV-positive individuals is reduced, the patients gradually
loose immune competence leading to the appearance of opportunistic
infections (infections with organisms that are normally not pathogenic in
immunocompetent individuals) or to development of cancer. This stage of the
disease is called AIDS, which is fatal if left untreated.

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Glossary
adaptive immunity Acquired / learnt immunity. A highly specific
and efficient immune response, emerging after birth that uses
antigen-specific receptors and antibody molecules. Capable
of developing long-lasting immunological memory.
adjuvant a substance mixed up with an immunogen in order to
generate a more intense immune response
anaphylatoxin Small cleavage products of some complement components,
that can cause intense inflammatory reactions (even
anaphylactic reaction).
anaphylaxis anaphylactic shock/ systemic anaphylaxis Serious, systemic
allergic reaction.
anergy Functional unresponsiveness. Generally, naïve lymphocytes
become anergic, if they react with an antigen without
costimulation.
antibody Glycoproteins produced by B cells. They bind appropriate
antigens with high affinity and specificity.
antigen Those molecules that can be recognized by antigen receptors
and thus any material, that triggers a specific response from
the immune system, either tolerance or a destructive immune
response.
antigenic determinant See epitope!
antigen presenting cell or APC. A cell that processes extracellular
or intracellular material and displays it in a form “visible”
/detectable by T-lymphocytes. T cells can only recognize
antigens that are processed and presented by antigen
presenting cells as a peptide in complex with an MHC
molecule. Nearly every cell in the body expresses MHC I
molecules, thus can be regarded as APC. The professional
antigen presenting cells express both MHC I, and MHC II
molecules.
antigen receptor A receptor expressed by B and T lymphocytes that
recognizes native or processed antigens with high
specificity.
apoptosis Programmed or induced cell death. The „suicide” of the cell.

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autocrine effect An effect of a hormone or other chemical substance acting
on the cell by which the substance was produced.
autoimmunity A self-reactive state of the adaptive immune system, when
adaptive immune cells attack self-structures (self-antigens).
BCR B cell receptor. The antigen receptor complex of the B cell.
B cell See B lymphocyte
B lymphocyte A cell type expressing antigen receptors that resemble an
antibody. Precursors of plasma cells which produce large
amounts of antibody.
CD, CD nomenclature, CD molecules, CD antigens Cluster of
Differentiation. Each cell type or the differentiation state of
a lineage can be identified by the set of these cell-surface
expressed molecules. These molecules were found and
identified using specific antibodies. They are numbered by
an international committee, usually following the order of
their discovery. For example: functionally distinct T cell
populations are the CD8 bearing cytotoxic and the CD4
bearing helper T cells.
cellular immune response Immune response mediated by different
immunocytes (e.g.: cellular cytotoxicity mediated by
cytotoxic T or NK cells, or phagocytosis by macrophages)
chaperon A helper protein that facilitates other protein’s folding,
transport etc.
chemokine Cytokine that induces guided migration (chemotaxis) of
cells.
chemotactic factor Any soluble factor with a chemotactic effect.
They may not be produced directly by cells. For example
complement protein’s cleavage products are like this.
complement receptors Receptors that can recognize some cleaved,
activated, molecules of the complement system.

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complement system Approximately 30 proteins found in the plasma,
classified as part of the innate humoral immune response.
Many of these proteins are proenzymes, others are able to
recognize PAMPs. During their activation these proteins are
able to activate each other in a proteolytic cascade reaction.
Some cleavage products of the complement molecules can
function as opsonins. They can induce inflammation others
are able to destroy the activating pathogens directly.
cross presentation Presentation of exogenous antigen on MHC I
molecules. Dendritic cells are capable of this process.
CTL Cytotoxic T Lymphocyte
cytokine A soluble, hormone like messenger molecule produced by
cells. It can influence the function of cells that express the
cytokine-specific receptor.
cytotoxicity Ability to kill cells. Many cells and humoral elements of the
immune system are able to perform this function. It can be
directed against free or engulfed pathogens. In a diseased
state, it may be used against the organism’s own cells.
DAMP Danger (damage) associated molecular pattern. A molecular
pattern that signals danger or damage.
dendritic cells A group of a phagocytic cells with typical dendritic structure.
They act as professional antigen presenting cells. These cells
have a critical role in activation of naïve T cells.
domain Structural and/ or functional unit of protein molecules.
Domains are frequently encoded by independent exons.
endocrine effect An effect induced far away from the effector cell (usually
delivered by blood circulation to anywhere in the body).
endogenous Originates from within (of an organism, tissue, cell)
epithelial cells Cells separating the body from the environment, linening and
protecting internal, external surfaces of our body (skin,
intestines, respiratory system, urinary tract)
epitope or antigen determinant. The part of the antigen that is in
physical contact with the antigen receptor, or the antibody.
exogenous Originates from outside (of an organism, tissue, cell)
extracellular Something that happens or exists outside the cell.

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Fc region The region of the antibody, that is similar to a fragment
formed during limited enzymatic cleavage of an antibody. It
consists of disulphide linked constant domains of the heavy
chains. Intact immunoglobulins have different effector
functions, thanks to this region, e.g. by Fc receptor binding.
Fc receptor A receptor, that is able to recognize the Fc region of an
antibody. Fc receptors cannot recognize the variable region
of the antibody, only the heavy-chains’ constant domains.
glycoprotein Protein post-translationally modified by covalent attachment
of oligosaccharide chains to the polypeptide chain.
granulocytes A group of polymorphonuclear myeloid cells, with similar
appearance under the light microscope: They have granules
in their cytoplasm and a lobed nucleus. Neutrophil,
eosinophil and basophil granulocytes belong in this group,
based on their granular content.
granzyme A protease produced by cytotoxic cells. In the target cell it
induces cell death by apoptosis. .

hematopoietic stem cell Undifferentiated cell type, with the capacity of

self-renewal. Precursors of all cellular components of the
blood.
HLA Human Leukocyte Antigen, an alternative name for the
human MHC-encoded genes. There are 3 classical human
MHC I molecule coding genes, the HLA-A, HLA-B and
HLA-C genes. The HLA-DP, HLA, DQ and HLA-DR gene
regions are responsible for the coding of the classical human
MHC II molecules.
humoral immune response Immune response delivered by
soluble component of the immune system (e.g. antibodies,
antimicrobial peptides or complement proteins).
immune complex The complex of antigens with
bound antigen specific antibodies which usually includes
bound complement proteins
innate immunity The immunity one is born with. Its activation is based on
recognition of PAMPs and DAMPs, (pathogen- or danger
associated molecular patterns). Also called natural
immunity.

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interleukin Cytokines produced by leukocytes
interferon Cytokines with antiviral activity. They are important in
antiviral immune responses
intracellular Something existing or happening inside the cell.
invariant chain (Ii) The invariant chain participates in the maturation
of the MHC II molecules. Binding to the MHC II molecule
in the endoplasmic reticulum (ER), its main role is to inhibit
binding of endogenous peptides in the ER to the MHC II
isotype (of an antibody) Antibodies can be classified into isotypes or
classes based on differences in their constant domains.
Human antibodies based on their heavy chain’s constant
region can be classified into 5 main groups (IgM, IgD, IgG,
IgA, IgE). Based on their light chains, they are divided into
two groups (kappa and lambda). Different antibody (heavy
chain) isotypes can induce distinct effector functions with
different efficiency. Subclasses are called isotypes as well.
leukocyte White blood cells. Granulocytes, monocytes, macrophages,
dendritic cells, NK cells, mast cells, T and B cells belong
here.
lymphocyte White blood cell group based on simple microscopic
similarities: cells of this group have relatively large nucleus,
and minimal cytoplasm. Leukocytes with different functions
that belong to the lymphoid lineage. The adaptive B-, T
lymphocytes and the innate NK cells belong in this group.
LPS, lipopolysaccharide (also called endotoxin) Oligo- or
polysaccharides covalently coupled to lipid molecules,
taking part in the formation of the outer membrane of gram
negative bacteria.
macrophage Monocyte derived large cells, very effective in phagocytosis
of larger particles. Different types of macrophages play a
role in inflammatory processes and in tissue regeneration.
They can also function as professional antigen presenting
cells.
mast cell A cell type specialized in the destruction of single cells or
multicellular parasites. Compounds stored in its granules are
effective against eukaryotic parasites. They play a key role
in some inflammatory and allergic reactions.

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MHC Major Histocompatibility Complex. A chromosomal region
encoding proteins with important role in antigen
presentation. Some proteins expressed by the MHC locus –
also called shortly MHC molecules– are expressed on the
surface of APCs where they present peptides to the T cells.
monocyte A leucocyte that belongs to the myeloid lineage. They are
larger than lymphocytes with a typical „bean„ shaped
nucleus circulating in blood. They are the precursors of
macrophages.
NK cell Natural Killer cell. An innate lymphocyte that can kill
tumour cells or cells infected with pathogens.
opsonin Molecules used for opsonization. These can be antibodies,
cleaved complement proteins or other antimicrobial proteins
for example acute phase proteins produced by the liver.
opsonization The marking of a pathogen or antigen, so effector
mechanisms of the immune system’s can be delivered more
efficiently. Opsonized structures can be engulfed quicker or
they can activate the complement system.
PAMP Pathogen-associated molecular pattern, for example:
bacterial lipopolysaccharide, flagellin, viral double stranded
RNA.
paracrine effect an effect, influencing cellular functions in the vicinity of the
producing cell.
pathogen Any agent causing a disease. It can be a single-cell or
multicellular organism. Prokaryotic, eukaryotic, or virus.
peptide A polymer of a few amino acids.
perforin A cytotoxic protein produced by killer lymphocytes
(cytotoxic T lymphocytes, NK cells). Its polymerized
product forms a pore within the membrane of the target cell.
plasma cell Antibody producing cells that differentiate from B cells.
primary immune response The adaptive immune system’s that is generated
at the first encounter with an antigen or a pathogen. The
process that leads to activation of naïve lymphocytes.

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primary lymphoid organ Organs where the immune cells develop from
undifferentiated precursors. Two organs should be
mentioned as primary lymphoid organ: the red bone marrow
and the thymus.
proenzyme Or zymogen. An inactive enzyme or enzyme precursor that
must be activated by a biochemical process to perform its
function. In case of some complement, limited proteolysis of
zymogens is required for the activation of the subsequent
component of the cascade.
proliferation serial cell divisions
professional antigen presenting cell. Professional APC.
Antigen presenting cells are able to activate naïve T cells.
Unlike other cells, these cells express MHC II molecules, by
which they can present antigen derived peptides to helper T
cells. Professional APCs are dendritic cells, macrophages
and B cells.
proteasome Large enzyme complex in the cell, with a cylindrical shape.
It’s present in each eukaryotic cell and in some bacteria. It
has role in the breakdown of unnecessary proteins. It
produces peptides those are presented by MHC I molecules.
protein A polymer molecule made of amino acids, many of these
polymers have stable secondary and tertiary structure.
PRR Pattern recognition receptor
secondary lymphoid organ The sites where adaptive immune responses are
initiated. The encounter with antigen, the activation and
differentiation of the naïve cells of adaptive immunity occurs
here.
soluble not solid, or cell surface bound (for example: the antibody is
the soluble form of B cell receptor)
stem cell Undifferentiated cell type that has self- renewing capacity. It
can differentiate into a wide variety of cell types.
T cell See T lymphocyte.
T lymphocyte Lymphocyte that bares TCR antigen receptor. It has multiple
functionally distinct types. Some can destroy infected cells,
others influence the outcome of the immune response, or
makes it more efficient

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TCR T cell receptor. T cell’s antigen receptor complex
TNF tumour necrosis factor. Cytokine, produced by many cell
types of the immune system. It has wide range of effects.
This cytokine has more types, however, unless indicated
otherwise, TNF means TNF-α. It can be produced during
inflammatory processes. It can have cell-activating, or cell-
killing effect
Toxin Poison. Toxins of immunologically distant organisms.
Bacteria, produce toxins that behave as antigens. They can
induce antibody production.
zymogen See proenzyme

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