Immunology

Dr. Jaime De Calisto

 • Exogenous (microbes, food)
An?gen DANGER • Endogenous (cancer)

Immune Response
Innate Acquired
Mediators

Cells Humoral Cells Humoral

• Epithelial Cells • Complement • APCs • An?bodies
• Phagocytes • AMP • LT • Cytokines
• MAC • Cytokines • LB
• Granulocytes
• Monocytes

*TIME, MEDIATORS, SPECIFICITY, MEMORY

 ✅ An?gen

Immune Response

✅ Innate Acquired ✳

Mediators

✅ Cells ✅ Humoral ✳ Cells ✳ Humoral

• Epithelial Cells • Complement • APCs • An?bodies ✅
• Phagocytes • AMP • LT • Cytokines
• MAC • Cytokines • LB
• Granulocytes
• Monocytes
 composed of two identical light chains and two identical a disulfide bridge, and adjacen
heavy chains (Fig. 5-1). Both the light chains and heavy connected by short loops. It is
An?body Structure
chains contain a series of repeating homologous units,
each about 110 amino acid residues in length, that fold
these loops that are the most v
gen recognition, as discussed

A Secreted IgG B Membrane IgM

PARTS Heavy FUNCTIONAntig
bindi
chain Antigen-
binding site N
N V
1. Heavy (H) chains (2) N N
N Hinge VH N An?gen bindingCH1
2. Light (L) chains (2)
3. Variable (V) regions CH1 VL
4. Constant (C) regions Light CL
5. Disulfide bonds chain
C C Fab CH2
6. Hinge region Fc receptor/ region
complement C H2
7. Fc region (FcR/ binding sites Fc
complement binding) region CH3

8. Sugar side chains CH3

Effector - Trigger
CH4

Tail piece C C
Disulfide bond
Ig domain C C

Crystal structure of secreted IgG

C
 in T-independent immune responses tend to be short- tion against the infection. At the same time, activation of
lived. In contrast, class-switched, high-affinity antibody- memory B cells generates a larger burst of antibody that

Effector Func?ons of An?bodies

secreting plasma cells, which are produced in germinal
centers during T-dependent responses to protein antigens,
migrate to the bone marrow and persist at this site, where
●
provides a second and more effective wave of protection.
Many of the effector functions of antibodies are mediated
by the heavy chain constant regions of Ig molecules,
they continue to produce antibodies for years after the and different Ig heavy chain isotypes serve distinct

Neutralization
of microbes
and toxins
Phagocyte
Opsonization and
phagocytosis
of microbes
Fcγ receptor
Antibodies
B cell NK cell Antibody-
dependent cellular
cytotoxicity

Microbe Phagocytosis of
microbes opsonized
with complement
C3b fragments (e.g., C3b)
receptor

Inflammation
Complement
activation Lysis of microbes

FIGURE 13-1 Effector functions of antibodies. Antibodies against microbes (and their toxins,
 An?gen

Immune Response

Innate Acquired
Mediators

Cells Humoral Cells Humoral

• Epithelial Cells • Complement • APCs • An?bodies
• Phagocytes • AMP • LT • Cytokines
• MAC • Cytokines • LB
• Granulocytes
• Monocytes
No Presentation -> No Response
Antigen Presentation: APC & T Cells
Antigen Presentation
• In order to generate immunity, adaptive immune cells DEPEND on
a phenomenon known as ANTIGEN PRESENTATION.

• T CELLS CANNOT RECOGNIZE antigens UNLESS they are

“presented” on a specific MHC context.

• NO PRESENTATION means NO ACTIVATION: cell proliferation &

differentiation/effector capabilities.

• *Unlike T cells, B cells CAN in fact recognize antigens by

themselves. So B cells can be independent of other immune cells
during the activation step, but not during differentiation and
acquisition of their effector properties.
Antigen voyage

Tertiary Tissue/Organ

Epithelial Barriers
&
Antigen Presenting Cells

Lymphatics Blood

Lymph Nodes Spleen

Antigen Presenting Cells (APCs)
Antigen Presenting Cells (APCs)

• APCs are cells that can mediate an immune response by

DISPLAYING ANTIGENS on their cell surface.

• They usually have the capacity to CAPTURE, PROCESS, and

PRESENT ANTIGENS to other immune cells.

• Epithelial Cells, B cells, macrophages, and dendritic cells.

Antigen Presentation Phenomenon

APC

T cell antigen
Antigen Presentation Molecules
Dendritic Cell
*accessory molecules
MHC-I
MHC-II
(HLA)
T cell
TCR
CD4
CD8 antigen (peptides)
TCR : antigen : MHC
Major Histocompatibility Complex (MHC) loci

HLA region (humans)

MHC (the rest)

• Encodes cell-surface antigen-presenting, processing, and

accessory molecules.
• Is located in the short arm of chromosome 6.
• Participates in the discrimination of self and non-self
antigens (transplant rejection).
 MHC’s highlight features

1. The MHC repertoire is POLYGENIC (multiple loci, group of genes).

2. MHC genes are highly POLYMORPHIC (high variation within the

population and species).

3. MHC expression is CO-DOMINANT (maternal and paternal co-

expression)
(1) MHC repertoire is POLYGENIC

*oversimplified view of the HLA loci

(2) MHC genes are highly POLYMORPHIC
(2) MHC genes are highly POLYMORPHIC
(3) MHC expression is CO-DOMINANT
8/24/2016 https://upload.wikimedia.org/wikipedia/commons/d/d4/MHC_expression.svg
(3) MHC expression is CO-DOMINANT
Genomic arrangement of the MHC loci
Genomic arrangement of the MHC loci
HUMAN MOUSE FUNCTION
classic non-classic
[MHC-IA] [MHC-IB]
HLA-A HLA-E H2-D
MHC-I HLA-B HLA-F H2-K CD8+
HLA-C HLA-G H2-L

HLA-DP I-A CD4+

MHC-II HLA-DQ I-E
HLA-DR
other
MHC-II HLA-DM H2-(D)M peptide loading
genes HLA-DO H2-(D)O mainly in B cells
MHC-III LOCUS

• Encodes some COMPLEMENT PROTEINS: C2, C4, factor B.

• Encodes some CYTOKINES: TNF-α, TNF-C (LT-β)
MHC structure
MHC-I MHC-II
MHC-I structure
MHC-I
• Formed by two polypeptide chains.
• The α chain (43 kDa) is membrane-
bound.
• The β chain (12 kDa) is, named β-2
microglobuline, is not covalently
linked to the α chain and is
encoded by a “non-MHC” gene.
• The antigen (peptide) interacts with
the α chain only: alpha helix & beta
sheets.
MHC-II structure
MHC-II
• Formed by two polypeptide chains.
• Both α chain (34 kDa) and β chain
(29 kDa) are membrane-bound.
• The antigen (peptide) interacts with
both α and β chains: alpha helix &
beta sheets.
MHC-peptide interaction

MHC-I Peptides of 8-11 residues.

MHC-II Peptides of 10-30 residues.

 MHC-peptide interaction
B
Peptide

Anchor
residue
Pockets in floor of peptide binding of peptide
groove of class II MHC molecule
FIGURE 6-13 Peptide binding to MHC molecules. A, These top
views of the crystal structures of MHC molecules show how peptides
MHC restriction

CD8 MHC-I

naive APC

CD4 MHC-II
*DC, MAC, B-cells, Epithelial Cells
Antigen Presentation Pathways Overview
Antigen Presentation Pathways Overview
MHC-I mediated presentation:
cytosolic antigens
MHC-I
(all nucleated cells)
PROTEASOME
(cytoplasm)
ENDOPLASMIC RETICULUM
(Antigen-MHC association)
CD8+ T Cells
(cytotoxic)
MHC-I presentation pathway
• MHC-I —> CD8+ T cells.
• Antigens present in the cytosol.
• Proteasome, TAP, β2m, MHC-I.
• Exocytic Pathway.
The Proteasome: antigen digestion
• The proteasome is a multi-catalytic proteinase complex formed by 28+ subunits.
• It cleaves proteins after hydrophobic and basic amino acids.
• It requires the prior ubiquitination of the target proteins.
• Poly-ubiquitinated proteins are destined to degradation via proteasome.
• IFN𝛾 induces the expression and replacement of certain subunits to convert the
proteasome into the immuno-proteasome.

Poly-ubiquitinated proteins

enzymatic digestion

amino acids
 48/==02/4 &-3=,&33&-$
4% = -/0(3,&= 2 5&6(6
9 EA'9$E,9'# ,E13. 6
TAP1 & TAP2: peptide transport ,64-4= )(3=8&4%=4% =,&3
4% = )(
3==(33== ,/)
4% =, ,2- = &$=
 =
$ -= 02 3 -45&/-= :=
8&5%&-= 5% == 3 = 
• TAP stands for Transporter Associated with Antigen Processing.
2 = 02/6 = &-= 2 30/-3
• TAP1/2 mediates the transport of 8+ amino acid long peptides with hydrophobic C-terminal.
4% = (&7 2:=/!=:5/3/)&=0

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Final step of MHC-I presentation

#.3%D -3$7&!:.3*D ;+&D 8&6&7;5.7&D 5'D 65<&3<-!0D
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ER -> GOLGI -> CELL SURFACE

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MHC-II mediated presentation

MHC-II
(only some cells: DC, MAC, B cells)

PHAGOSOME + LYSOSOME
PHAGOLYSOSOME
EDOPLASMIC RETICULUM
MHC-II + Invariant chain (Ic)
MHC-II + ANTIGEN
CD4+ T Cells
(T HELPER CELLS)
 class I MHC molecules, tapasin, and TAP are part of a larger ER move through the Golgi complex and are transported
peptide-loading complex in the ER that also includes cal- to the cell surface by exocytic vesicles. Once expressed
nexin, calreticulin, and other components that contribute on the cell surface, the peptide–class I complexes may be
to class I MHC assembly and loading. Peptides that enter recognized by peptide antigen–specific CD8+ T cells, with

MHC-II-mediated presentation
the ER through TAP and peptides produced in the ER,
such as signal peptides, are often trimmed to the appro-
priate size for MHC binding by the ER-resident amino-
the CD8 coreceptor playing an essential role by binding
to non-polymorphic regions of the class I molecule. Sev-
eral viruses have evolved mechanisms that interfere with
peptidase (ERAP). The peptide is then able to bind to the class I assembly and peptide loading, emphasizing the
cleft of the adjacent class I molecule. Once class I MHC importance of this pathway for anti-viral immunity (see
molecules are loaded with peptide, they no longer have Chapter 16).
an affinity for tapasin, so the peptide–class I complex is
• Invariant chain (Ii) prevents ER peptides to bind MHC-II.
The Class II MHC Pathway for Processing and
released, and it is able to exit the ER and be transported
to the cell surface. In the absence of bound peptide, many
Presentation of Vesicular ProteinsMHC-Ii towards the
• Ii stabilises the assembly of MHC-II in the ER and directs
of the newly formed α chain–β2-microglobulin dimers are
The generation of class II MHC–associated peptides from
unstable and cannot be transported efficiently from the
Golgi apparatus. endocytosed antigens involves the proteolytic degradation
ER to the Golgi complex. These misfolded empty class
of internalized proteins in endocytic vesicles and the bind-
I MHC complexes are transported into the cytosol and
• In the PHAGOLYSOSOME, hydrolytic enzymes
degraded in the proteasomes. cleaves
ing of peptides to Ii andin leaves
class II MHC molecules vesicles. This a short
sequence of events is illustrated in Figure 6-17, and the
Peptides transported into the ER preferentially bind
peptide bound to MHC-II (CLIP) until the interchange of antigens occurs.
individual steps are described next.
to class I but not class II MHC molecules for two reasons.

Uptake of Processing Biosynthesis and

extracellular of internalized Association of Expression of
transport of processed peptides
proteins into proteins in class II MHC peptide-MHC
vesicular endosomal/ with class II MHC complexes on
molecules molecules in vesicles
compartments lysosomal to endosomes cell surface
of APC vesicles
Protein antigen
Lysosome CLIP

HLA-DM

Endocytic
vesicle Class
Endosome II MHC CD4
Ii
Exocytic
vesicle
Chaperone α
β
CD4+
helper
T cell
Golgi
ER
FIGURE 6-17 The class II MHC pathway of antigen presentation. The stages in the processing of extracellular antigens are described in the text.
CLIP, class II–associated invariant chain peptide; ER, endoplasmic reticulum; Ii, invariant chain.
proteins have been proteolytically degraded into peptides.
The invariant chain is a trimer composed of three 30-kD
subunits, each of which binds one newly synthesized class
II MHC αβ heterodimer in a way that blocks the peptide-
MHC-II mediated presentation
binding cleft and prevents it from accepting peptides. As
a result, class II MHC molecules cannot bind and present
peptides they encounter in the ER, leaving such peptides
to associate with class I molecules (described earlier).
The class II MHC molecules are transported in exocytic
Invariant chain : MHC-II -> Class II-associated invariant chain
vesicles toward the cell surface. During this passage, the
vesicles taking class II MHC molecules out of the ER meet
genic peptides produced from extracellular proteins. This
removal is accomplished by the action of a molecule called
HLA-DM (or H-2M in the mouse), which is encoded
within the MHC, has a structure similar to that of class II
MHC molecules, and colocalizes with class II MHC mol-
ecules in the MIIC endosomal compartment. Unlike class
II MHC molecules, HLA-DM molecules are not polymor-
phic, and they are not expressed on the cell surface. HLA-
DM acts as a peptide exchanger, facilitating the removal
of CLIP and the addition of other peptides to class II MHC
molecules.

Transport of Transport of Expression of

Synthesis of Binding of
class II MHC peptide-Class II peptide-MHC
class II MHC processed peptides
and li MHC complex complex on
in ER to class II MHC
to vesicle to cell surface cell surface
HLA-DM–catalyzed
removal of CLIP HLA-DM

Peptide
antigens
Ii

Class Proteolytic
II MHC degradation of Ii
CLIP

Endosome
(MIIC/CIIV)
ER
FIGURE 6-19 The functions of class II MHC–associated invariant chain and HLA-DM. Class II molecules with bound invariant chain, or CLIP,
are transported into vesicles, where the Ii is degraded and the remaining CLIP is removed by the action of DM. Antigenic peptides generated in the
vesicles are then able to bind to the class II molecules. Another class II–like protein, called HLA-DO, may regulate the DM-catalyzed removal of CLIP
T Cell Receptor: TCR
TCR (αβ)
144 Chapter 7 – Immune Receptors and Signal Transduction

• Expressed only by T lymphocytes and N N

α chain
β chain
NKT cells.
Vβ
Vβ Vα Vα
• Formed by two covalently linked
membrane-bound chains: α and β, or 𝛾
FIG
and δ. sche
of a
antig
• They have Variable (V) and Constant (C) Cβ Cα
Cβ Cα
Vα d
of th
crys
regions. the
Bjork
of T
• They have a hinge region. Copy
Transmembrane
region
• They have a short cytoplasmic tail. Disulfide bond

C C Ig domain
• They are part of the immunoglobulin
Carbohydrate
superfamily. group

TCR chain, like Ig heavy and light chains, is encoded by portion, an

multiple gene segments that are joined together during positively ch
the maturation of T lymphocytes (see Chapter 8). residue (in
The C regions of both α and β chains continue into due (in the
The TCR complex: CD3(𝛾δ𝜀𝛇) & CD4/CD8
Cell Signalling Presentation
Immunological Synapse

APC

T cell synapse
 the maturation of T lymphocytes (see Chapter 8). residue (in the α ch
The C regions of both α and β chains continue into due (in the β chain
short hinge regions, which contain cysteine residues that tively charged resid
TCR-antigen-MHC complex
contribute to a disulfide bond linking the two chains.
Each hinge is followed by a hydrophobic transmembrane
portions of other p
plex and ζ) that are

A B
TCR TCR

Vβ Vα Vα Vβ

F
Peptide M
Peptide
α1 sh
α2 m
α2 α1
ye
o
M
M
ce
1

β2m β2m

MHC α3 α3 MHC
(class I) (class I)
 Immunological Synapse

• Also known as the Supramolecular Adhesion Complex

(SMAC).

• It is the CONTACT SITE between APC and T cells.

 Immunological Synapse: FUNCTIONS

• Starts/Ends molecular signalling.

• Ligand/Receptor interpretation.
• Direct bi-directional secretion of molecules.
• If successful, gives the effector properties to T cells.
Immunological Synapse: STRUCTURE
• Peripheral Supramolecular Activation Complex (pSMAC):
LFA-1, ICAM-1, others (adhesion molecules)

• Central Supramolecular Activation Complex (cSMAC):

MHC-antigen-TCR, CD4, CD8, others
(antigen presentation molecules + accessory molecules)

• Distal Supramolecular Activation Complex (dSMAC):

CD44, CD45, others
Immunological Synapse