Janeway’s Immunobiology

• Part I. Introduction to immunobiology and innate

immunity.
• Part II. The recognition of antigen
• Part III. The development of mature lymphocyte
receptor repertoires
• Part IV. The adaptive immune response
• Part V. The immune system in health and disease

1
 Phases of Immune responses

• Innate immunity provides the first line of defense. Only if an

infectious organism can breach(突破) these lines of defense
will an adaptive immune response ensue(繼續發生).

2
An immune response occurs in two
phases: antigen recognition and antigen
eradication.

3
The principal characteristics of
innate and adaptive immunity

Memory response

4
 PRINCIPLES OF INNATE IMMUNITY

1-1 Anatomic and chemical barriers are the first defense

against pathogens.

1-2 The immune system is activated by inflammatory

inducers that indicate the presence of pathogens or
tissue damage.

1-3 The myeloid lineage comprises most of the cells of the

innate immune system.

1-4 Sensor cells express pattern recognition receptors that

provide an initial discrimination between self and
nonself.
 PRINCIPLES OF INNATE IMMUNITY

1-5 Sensor cells induce an inflammatory response by

producing mediators such as chemokines and
cytokines.

1-6 Innate lymphocytes and natural killer cells are effector

cells that share similarities with lymphoid lineages of
the adaptive immune system.
 Immune defense involves recognition of
pathogens followed by their destruction

補體

單核球/巨噬細胞 樹突細胞
Innate immune system cells are monocytes/macrophages, dendritic
cells, polymorphonuclear granulocytes (neutrophils, basophils, and
eosinophils), NK cells, mast cells, and platelets. Only some of these
cells are phagocytes.
Granulocytes (顆粒球)
7
PRINCIPLES OF ADAPTIVE IMMUNITY
1. The interaction of antigens with antigen receptors
induces lymphocytes to acquire effector and memory
activity.
2. Antigen-receptor genes are assembled by somatic gene
rearrangements of incomplete receptor gene segments.
3. Bone marrow or the thymus are primary lymphoid
organs and lymphocytes with self-reactive receptors
are eliminated in bone marrow and thymus.
4. Adaptive immune responses are initiated by antigen
and antigen-presenting cells in secondary lymphoid
tissues.
 Selection of
lymphocytes by a
pathogen

Clonal expansion

9
Cells of the Immune System
Immune responses are mediated by a variety of cells, and by the soluble molecules
which they secrete. Although the leucocytes are central to all immune responses,
other cells in the tissues also participate, by signaling to the lymphocytes and
responding to the cytokines released by T cells and macrophages.

granulocytes
natural killer macrophage

中性 酸性 鹼性

Complement is made primarily

by the liver, although there is
dendritic cells some synthesis by macrophages.
10
Cells of the immune system arise from the bone marrow
HSC: 造血幹細胞

CLP CMP

NK: natural killer cells

ILC: innate lymphoid cells

B cells mature in the fetal liver and bone marrow in mammals, whereas T cells mature 11
in the
thymus. The origin of the large granular lymphocytes with NK activity is the bone marrow.
 Lymphoid Tissues and Organs
A. Primary (central ) lymphoid organs
1. Stem cells 
immuno-competent cells
2. Antigen-independent
(扁桃腺及腺樣體or 咽扁桃體)
differentiation
3. Bone marrow, thymus
Lymphocytes mature in the
bone marrow or the thymus.
B. Secondary (peripheral) lymphoid
tissues and organs
1. Immunocompetent cells 
effector cells and memory cells
2. Antigen-dependent differentiation
3. Lymph nodes, spleen, tonsils,
Peyer’s patches, etc.
The peripheral lymphoid organs
are specialized to trap antigen and
allow the initiation of adaptive
immune responses. 12
Effector cell: 具有特化功能的細胞
Naïve T or B cells encounter antigen during their
recirculation through peripheral lymphoid organs
Naïve T cells recirculate through
lymph node, entering through high
endothelial venules (HEV). On
leaving the blood vessel, the T cells
enter the deep cortex of the lymph
node, where they encounter mature
dendritic cells. They leave the lymph
node through the efferent lymphatics
to return to the circulation.

Naïve = Virgin

13
Spleen: responsive to
blood-borne antigens

(i) white pulp (白髓, lymphoid tissue)

periarteriolar lymphoid sheath
(PALS): consists of T cell and B cell
areas, T cells are around the central
arteriole, and B cells are in the
lymphoid

(ii) red pulp (紅髓)

plasma cells

(iii) marginal zone (MZ): outer limit

of the white pulp. The marginal zone
contains B cells, macrophages and
dendritic cells.

Aged platelets and RBCs are destroyed in the red pulp by a process called “ hemocatheresis”.
14
血球破壞
(小腸中後段) (大腸多)

15
 Mucosa-associated lymphoid tissue (MALT):
responsive to antigens entering via mucosal surfaces

• The intestinal epithelium (follicle associated epithelium, FAE) is specialized to

allow the transport of pathogens into the lymphoid tissue. This is carried out by
epithelial cells termed M cells, a specialized gut epithelial cells.
(do not produce enzymes or mucin)

• The deep region of the

mucosa contains secondary
follicles with germinal
centers, surrounded by T-
cell areas with dendritic cells
and high endothelial
venules.

16
 Innate immunity
Includes:
• Soluble factors, e.x. complement (補體)
system, antimicrobial proteins, and
interferons (干擾素).

• Immune cells, e.x.macrophages,

neutrophils, dendritic cells, natural killer
(NK)cells, and innate lymphoid cells (ILCs).

參考資料: 1. Peter Parham “ The Immune System”, 4th Edition, Chapter 2-3.
2. “Janeway’s Immunobiology”, 8 th Edition, Chapter 2, page 37-71;
9th Edition, Chapter 3. 17
Phagocytic receptors:
PAMP receptors = PRRs
complement receptors

18
PAMP receptors = Pattern Recognition Receptor (PRR)
Human Toll-like receptors (TLRs)

19
Different TLRs sense infections outside and inside
the cell

20
Sensing LPS by TLR4 activates NF-kB and
inflammatory cytokine synthesis

21
TLR4 activation can lead to the production of
inflammatory cytokines and type I interferons

Nemo deficiency=
X-linked hypohidrotic ectodermal
dysplasia and immunodeficiency,
a disease caused by lack of IKKg
(or NEMO) on X-chromosome.

Patients have impaired NF-kB

activation and susceptible to
bacterial infection.

22
 Important cytokines secreted by macrophages

Cytokine (細胞激素)

IL: interleukin
TNF: tumor necrosis factor

(chemokine
趨化素)

23
 Type I interferons inhibit viral replication
and activate host defenses

•Plasmacytoid dendritic cells are major producer of type I IFNs. 24

 Recognition of viral nucleic acid by RLRs
initiates an inflammatory response
RIG-I-MAVS-IRF3 pathway

RLR: RIG-I-like receptors.

PRRs 分類: TLRs, RLRs, NLRs, CLRs. 25
cGAS is a cytosolic sensor of DNA that signals via
STING to activate type I interferon production
cGAS-STING-IRF3 pathway

cGAS: cyclic GAMP synthase

STING: stimulator of interferon genes 26
 NK receptors distinguish unhealthy
cells from healthy cells
NK cells決定毒殺細
胞的方式之一:

在某些狀況下感染
細胞會表現活化受
體的ligands，使NK
活化執行毒殺!

27
 NK cells react
against cells that Figure 2-50
do not express
MHC class I

方式二

28
Several types of innate lymphoid cells provide
protection in early infection

29
•C3b molecules act
as opsonins; they
bind covalently to
the pathogen and
thereby target if for
destruction by
phagocytes
equipped with
receptors for C3b.

•C3b binds to C3
convertase to form
a C5 convertase
that produces C5a
and C5b (initiates
the late events of
complement
activation).
30
依功能分類補體蛋白:
複習很好用

31
 Figure 2-36

=CD46

32
The importance of these complement regulatory
proteins is underlined by the following diseases:

• C1INH limits the spontaneous activation of C1 in

plasma. C1INH deficiency causes disease hereditary
angioneurotic edema (遺傳性血管性水腫 chronic
spontaneous complement activation leads to extensive
swelling).

• Paroxysmal nocturnal hemoglobinuria (PNH,陣發

性夜間血尿症) is a disease characterized by episodes
of intracellular red blood cell lysis by complement. It
is because both CD59 and DAF fail to function due to
lack of an enzyme involved in the synthesis of GPI tails.

33
34
35
Both heavy chain and light chain have
variable regions and constant regions
•V regions of different
antibodies are for binding to a
(red) wide variety of antigens.

•The C regions of different

antibodies are far less variable
and are the parts with effector
functions.
(blue) N terminus: amino terminus
C terminus: carboxyl terminus

36
There are discrete regions of hypervariability in V domains
HV1=CDR1
HV2=CDR2 FR: framework region
HV3=CDR3

CDR2 CDR3 CDR1 CDR2

CDR1 CDR3

37
•Hypervariable regions form the antigen-binding site.
人類Igs種類及其特性

190
390 390

Fc receptor to IgE

• Serum IgM is a pentamer including 5 IgMs and a J (joining) chain.

38
•sIgA contains two IgAs, a J chain and a secretory component.
Effector mechanisms activated by Igs

調理作用 活化NK 活化mast cells

活化補體
39
Self-MHC restriction:

T cells can only recognize a peptide when

it is presented with a self-MHC molecule
on the membrane of another cell.

40
 Comparison of different antigen-presenting cells
Figure 8-18 part 1 of 2

B7
molecules

II

41
 Structure of MHC class I molecule

MHC class I a chain

•MHC class I molecules consist of 2 polypeptide chains, a larger a chain encoded in

the MHC genetic locus and a non-polymorphic b2-microglobulin (b2m).

•The a1 and a2 domains of MHC class I a chain form peptide binding

sites, they are also sites of polymorphisms (多形性).
42
 The structure of an MHC class II molecule

•MHC class II
molecules consist of
2 two chains, MHC
class II a and b
chains.

•The sites of major polymorphism are located in the peptide binding cleft
formed by the a1 and b1 domain of an MHC class II molecule.

43
 •T cells respond to short contiguous amino acid sequences in proteins. These
sequences were often buried within the native structure of the protein and could
not be recognized directly by T-cell receptor. Antigen must be processed to be
“seen” by T-cell receptor.

•A T-cell receptor recognizes antigen in the form of a complex of a foreign peptide

bound to an MHC molecule.

Differences in the recognition of lysozyme by Igs and T-cell receptor

surface

epitopes for 3 Abs 2 epitopes for T-cell receptor

44
主要在蛋白質表面 主要在蛋白質裡面
(invariant chain blocks
binding of endogenous
antigen)

45
 (chromosome 6)

(chromosome 17)
• HLA-A, HLA-B, and HLA-C gene loci encode class I MHC
molecules.

• HLA-DP, HLA-DQ, HLA-DR gene loci encode class II MHC

molecules.

46
 Human MHC genes are highly
polymorphic

The numbers of HLA alleles assigned by WHO as of Jan. 2010.

The theoretical diversity in class I possible for the human is:

47
893 (HLA-A) x 1431 (HLA-B) x 569 (HLA-C) = 7.27x 108
 Polymorphism and polygeny both contribute to the
diversity of MHC molecules expressed by an individual

• Polygeny:
the presence of
several different
genes with
similar functions.

48
Genetic variation in MHC molecules
affects:
• The ability to make immune
responses

• Susceptibility to infectious
diseases

• Susceptibility to autoimmune
diseases and allergies.
49
 Generation of antibody diversity
• The total number of antibody specificities
available to an individual is known as the
antibody repertoire or immunoglobulin
repertoire.

50
 Ways to generate Antibody Diversity

1. V region is encoded by multiple V, D, and J gene segments.

2. V, D, and J gene segments are combinatorial joining during
development. V(D)J recombination via RAG1/RAG2.
3. Imprecise joining causes diversity at the junction (P-
nucleotide and N-nucleotide additions).
TdT
4. Combinatorial association of heavy chain and light chain.
5. Somatic hypermutation occurs after B cell activation.
AID
51
--V-region genes are constructed from gene segments.
Light chain V region: V, J segments Heavy chain V region: V, D, J segments

52
L, leader sequence; V, variable segment, D, diversity segment; J, joining segment
V(D)J recombination involves both lymphocyte-specific
and ubiquitous DNA-modifying enzymes

• Recombination-Activation Genes: RAG1 and

RAG2 (lymphocyte specific).

• DNA modifying proteins in the repair of DNA

double-strand break: Ku, DNA-dependent protein
kinase (DNA-PK), Artemis, DNA ligase IV etc..
(ubiquitous)

53
 Secondary diversification of the antibody repertoire
--The V(D)J recombination of B cells take place in the bone marrow. These
processes are antigen independent. The primary antibody repertoire of B cells
is developed. (V )
H
--The secondary phase of diversification
occurs in activated B cells and is largely
driven by antigen in the peripheral.
There are three mechanisms: (CH)

(1) somatic hypermutation (VH and VL)

(2) gene conversion
(3) class switching

• All depend on AID.

54
Changes in antigen receptor genes during development

55
56
 T cell development in the thymus

Positive
Negative selection

IL-7 and IL-7R-mediate signals are important

in early lymphocyte development 57
At double positive (DP) stage,
thymocytes undergo positive and
negative selection.

• T cells that recognize self-MHC

molecules are positively selected in
the thymus.

•Positive selection takes place in the

cortex and mediated by the cortical
epithelial cells.

58
 Negative selection in the thymus
• T cells specific for self
antigens are removed in the
thymus by negative
selection.

•Tissue-specific proteins are

expressed in the thymus and
participate in negative
selection. Autoimmune
regulator (AIRE) protein
controls the expression of
tissue-specific genes in the
thymus.

• Lack of AIRE causes a disease called autoimmune polyendocrinopathy-

candidiasis-ectodermal dystrophy (APECED).
59
Severe immunodeficiecies associate
with defects in T cell development

• DiGeorge syndrome: Thymic epithelium fails

to develop normally. T cells cannot mature.

• MHC class II deficiency: CD4 T cells cannot

be positively selected and few develop.

• MHC class I deficiency: patients lack CD8 T

cells. Mutations in TAP1 or TAP2 may lead to this
disease.
60
Pre-BCR signal is important for B cell development

Negative selection
achieves self-tolerance

61
There are four possible fates for
self-reactive immature B cells:
• Cell death by apoptosis- clonal deletion

• The production of new receptor by receptor

editing

• Anergy- an anergic cell expresses low level of surface

IgM and remains unresponsive to the antigen

• Ignorance- an ignorant cell has affinity for a self

antigen but does not sense the self antigen because the
antigen is sequestered, is in low concentration, or does
not activate the BCR. Ignorant cells are thought of as the
seeds of autoimmune diseases.
62
63
Immunodeficiencies caused by development defects in T or B

64
 Humoral response
The humoral immune response is characterized
by the production of antibodies by B cells and
results in the destruction of extracellular
microoganisms and prevents the spread of
intracellular infections.

• Antibody is mainly produced by plasma cells,

the terminal differentiated B cells.

65
The Antibodies Protect the Host in 3 Ways

調理作用

66
T-dependent (TD) and T-independent (TI) antigens

67
Where and When do B cells function?

Adaptive immunity

68
2002
Cellular events in germinal
center

Important events
happened in GC:

Affinity maturation
Class switching
Differentiation

69
Somatic hypermutation introduces mutations into the rearranged
Ig variable regions. Selection of high affinity clones by Ags on
FDCs is the basis of affinity maturation.
• Somatic hypermutation is point mutations generated by an enzyme
called activation-induced cytidine deaminase (AID).

70
Rescued centrocytes in the germinal center
undergo class switching

Mature B cells

Activated mature B cells

in the Germinal Center

• Class switching is
achieved by gene
(DNA) recombination.

• Lack of AID causes a

disease called hyper-
IgM syndrome.
71
71
Class switching is mainly regulated by
T cell-derived cytokines

In mice.

72
 Comparison of normal
and hyper-IgM syndrome
lymph nodes

•CD40 (on B)-CD40L (on T)

interaction is also important for
germinal center formation and isotype
switching.

Hyper-IgM syndromes: a group of

genetic diseases in patients with
overproduction of IgM. They are due to
defects in various proteins involved in
class switching as CD40 ligand (CD40L)
and the enzyme AID.

73
74