Innate Immunity (part II) and
Antigen Recognition by Adaptive Immunity
Innate Immunity against viruses
• Anti-viral immunity has 2 roles
– Blocking infection (antibodies, complement, etc.)
– Blocking viral replication (interferon, killing infected cells, antinucleic acid mechanisms)
• Many viruses evolve extremely rapidly, great challenge for
innate immunity
• This problem is solved in part by a) targeting molecules that
viruses have a hard time changing (dsRNA especially), and b)
having multiple mechanisms, making it harder for a virus to
evade all of them
• Viruses are amazingly good at evasion of immune defenses, but
often the most lethal viruses are those that are not well
adapted to their host (their goal is to grow and be transmitted
to others, not to kill)
INTERFERON: cytokine critical for defense
against virus infections
1) Virus-infected cell
produces interferon to
act on neighboring cells
infected cell
Interferon-a
2) Uninfected cells
respond to become
refractory to viral
growth (“anti-viral
state”)
type 1 interferon=
interferon a/
type 2 interferon=
interferon 
Induction of interferon by dsRNA in
cytoplasm and RLRs
RLRs
Mda5
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IRF: interferon regulatory-factor
(family of transcription regulators)
Anti-viral effects of interferon a/
Many other responses,
less well understood
Note: PKR and OligoA
synthetase induced in
anti-viral state, but only
have enzymatic activity
following virus infection
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Natural Killer (NK) Cells: innate lymphocytes
that protect against intracellular infections
Abbas and
Lichtman
Fig. 2-10
NK cells are regulated by the balance
between activating and inhibitory receptors
stress-induced
proteins (red)
healthy cell
stressed cell
NK cell has activating
receptors and
inhibitory receptors:
killing believed to
occur if activating
receptors dominate
(relative numbers of
ligands on target cell)
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Summary of Innate Immunity to Viruses
•Interferon (type 1) is absolutely critical for anti-virus immune
defense; it is produced in two ways
•by infected cells via RLRs or similar sensors of DNA for
DNA viruses
•by immune cells via nucleic acid-recognizing TLRs
•Interferon induces anti-viral state, which is fully engaged by
recognition of dsRNA in cytoplasm and inhibits virus replication
(also promotes adaptive immunity)
•Killing of infected cells is also performed by natural killer cells
recognizing stress-induced molecules or loss of MHC class I
molecule expression and by cytotoxic T cells which recognize
virus antigens expressed by infected cells (+MHC I)
Pathogens and Innate Immunity
•Particular pathogens often have evolved ways to
evade at least some elements of innate immunity
•Highly successful pathogens may also have
mechanisms for evading adaptive immunity
•On the pathogen side, molecules the pathogen
uses to evade immunity are among the “virulence
factors” of that pathogen
Part II: antigen recognition
• Antigen recognition molecules: structure
and function
• B cell antigen receptors and T cell antigen
receptors: Role in clonal selection
• Classes of antibodies and their structures
• Monoclonal antibodies and their uses in
medicine (lab tests, therapies)
2 Types of Antigen Recognition
• 1) Antibodies
– Defense against extracellular microbes and viruses
by soluble binding molecules linked to effector
functions
– B cells also make a membrane-bound form of
immunoglobulin that serves as their antigen
receptor
• 2) T cell antigen receptor
– Peptide recognition mechanism for detecting
antigens inside cells that are displayed on cell
surface as peptides bound to MHC molecules
The B cell antigen receptor is
membrane Ig + signaling chains
•Antigen binding to more than one
membrane Ig molecule triggers
signaling reactions; tells B cell that
antigen is present, induces
activation (“clonal selection”)
Iga/Ig •Iga/Ig cytoplasmic domains have
signaling function (ITAM sequence)
Signal transduction
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The TCR also has ligand-binding chains
+ signaling chains
Figure 4-1 Abbas & Lichtman
Antibodies
• = immunoglobulins
• Secreted by B lymphocytes (“plasma cells”)
• Great diversity and specificity: >109 different
antibodies; can distinguish between very similar
molecules
• Block infectivity of viruses, action of toxins
(“neutralization”)
• Tag particles for clearance/destruction (activate
complement, “opsonize”for phagocytosis)
• Protect against re-infection (vaccines)
Antibody Structure
2 identical heavy
chains and
2 identical light chains
Both made of
repeating structural
unit: The Ig domain
Light chain
k or l
Ig domain: 110 amino
acids; globular domain
used in many proteins
Heavy chains
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Antibody Structure
Domains at ends of
heavy chain and light
chain are highly
variable and
responsible for
binding antigen
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Fab, variable
domains in color
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Variability in
antibodies is
clustered in the loops
in the variable
domains of the heavy
and light chains
(green); these regions
are responsible for
binding to antigen
(“hypervariable
regions”;
“complementaritydetermining regions”)
Similarities between Ig and TCR
• Both are composed of Ig domains
• Both have two variable subunits (H + L for Ig; TCR a
and TCR ; there are also “d T cells”)
• Both have great diversity and exquisite specificity
• Both recognize antigen via hypervariable loops at the
ends of the variable domains
• Both couple antigen recognition to lymphocyte
activation (“clonal selection”) via signaling chains with
very similar signaling mechanisms (ITAM sequences)
• (Only Ig is secreted and only Ig has class switching to
change the constant domains)
5 Different Antibody Classes
Heavy chains are named by the greek letter
corresponding to the type of antibody (m, , d, a, e)
All classes can have k or l light chains
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Antibody Classes II: Distinctive features
• IgM
– First antibody produced in immune response: multimeric
structure adds to “avidity” for antigen
– Antigen receptor of naïve B cells
• IgD
– Used primarily as antigen receptor, little secreted
• IgG
– Major antibody of serum and extravascular tissues
– Crosses placenta to provide protection in utero
• IgA
– Major antibody of secretions (mucus, saliva, milk, etc.)
• IgE
– Important for immune defense against helminths; allergy and
asthma
Affinity and Avidity
•Affinity: the strength of binding between a single
binding site and a single ligand
•Avidity: the strength of binding between a molecule and
a complex ligand. If there are multiple binding sites then
the avidity may be increased by increasing the number of
binding sites or by increasing the affinity of those
binding sites
Affinity and Avidity II
•IgM is produced early in an immune response when the
affinity for antigen often is low; as an immune response
continues, antibody affinity is improved, this is combined
by “class switching” to the use of smaller molecules (IgG,
IgE and IgA). The increased affinity compensates for the
decrease in number of binding sites in maintaining the
overall avidity for antigen
Antibody Classes II: Distinctive features
• IgM
– First antibody produced in immune response: multimeric
structure adds to “avidity” for antigen
– Antigen receptor of naïve B cells
• IgD
– Used primarily as antigen receptor, little secreted
• IgG
– Major antibody of serum and lymph
– Crosses placenta to provide protection in utero
• IgA
– Major antibody of secretions (mucus, saliva, milk, etc.)
• IgE
– Important for immune defense against helminths; allergy and
asthma
Antibodies and medicine
• Vaccination works by inducing production of protective
antibodies
• Antibodies from immunized or pooled donors (“IVIG”) can
provide “passive immunity” (used for tetanus, snake bites,
etc.; to treat immunodeficiencies)
• Antibodies are often used to diagnose infectious diseases
(e.g., presence of antibodies in patient’s blood), determine
bloodtype, diagnose type of cancer, etc.
• Increasingly, antibodies are used to treat diseases (cancer,
autoimmune disease, etc.): advantage of monoclonal
antibodies
Monoclonal Antibodies
• Normal antibodies are “polyclonal”, as they are mixtures of
antibodies made by several different clones of B cells
• Monoclonal antibodies: Single antibody (all same H and L chains):
more reliable, consistent; can be produced in unlimited quantities
• Made by fusion of B cells to a transformed cell line of the plasma
cell type and selection for “hybridomas” that produce antibody
with the desired properties
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Use of antibodies in lab tests:
immunoprecipitate-based tests
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(Polyclonal antibodies)
Use of antibodies in lab tests: ELISA
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Enyzyme-linked immunosorbant assay (ELISA): measure levels
of antibody or antigen, depending on assay design (“sandwich
ELISA is shown)
Use of antibodies in lab tests: flow
cytometry
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Flow cytometry: measure the amount of a protein on the
surface (or inside) individual cells; measure the numbers of
particular types of cells in blood (etc.)
Monoclonal antibodies used in medicine
Standardized, unlimited reagents for diagnosis or therapy
(human antibodies or “humanized” antibodies can be made)
The list of monoclonal antibodies FDA-approved for
therapy is increasing by several per year
Names: fully human: -mumab
humanized: -zumab
chimeric:
-ximab
murine:
-omab
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Monoclonal antibodies as therapeutics
A potential problem, as with other protein therapeutics, is
immunogenicity, a fraction of patients make an antibody
against the therapeutic. This can make the therapeutic
ineffective in those individuals.
In general, the more “human” the monoclonal antibody, the
less immunogenicity, but this is not a perfect correlation
(see syllabus for further discussion of this issue).
Anti-TNF therapeutics
TNFR2
Adalimumab (Humira)
etc.
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Infliximab, etc.: anti-TNF monoclonal antibodies (+ 3 others)
Etanercept: fusion between TNF receptor extracellular domain
and Fc part of IgG1, which greatly extends half-life in serum
These agents are used to treat Rheumatoid arthritis, Crohn’s
disease, etc.