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Antigen processing and presentation
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Endogenous antigen presentation pathway
Exogenous antigen presentation pathway
Microbial evasion strategies
Cross-presentation
Lipid presentation
Transcriptional regulation of MHC
(review)
peptide size:
8-10aa
10-20aa
any nucleated cell
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professional APC
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Janeway’s Imunolobiology 8th ed (© 2012 by Garland Science, Taylor & Francis Group, LLC)
(* Naive T cell activation is a topic of another lecture)
Some questions can emerge:
• How could the peptide choose the appropriate MHC
molecule? (MHC I   MHC II)
• Where the peptides are generated?
• Where and how can bind the peptides to the MHC
molecules?
• Is there a possibility that a more fit peptide could
replace the MHC bound peptide on the cell surface?
General properties of the MHC-peptide interaction:
• MHC molecules can be in a receptive, ”open”
conformation until the appropriate peptides bind to them.
• The receptive conformation is maintained by the
chaperones and the biochemical properties (e.g. pH) of
the peptide loading compartment.
• Appropriate peptide can induce the conformational
change of the MHC molecules.
(Appropriate peptide has appropriate binding motif, which allow
effective binding to the MHC molecule  see the previous lecture)
• The bound peptide stabilizes the ”closed” conformation
• ”Closed” MHC molecules can detach from the
chaperones and reach the cell surface
The role of the MHCs’ chaperones
• Stabilizing “empty” MHC molecules
Empty MHC molecules could become denatured, aggregated and rapidly
degraded without chaperones
• Retaining or transporting the MHC molecules in the appropriate peptide
loading compartment
e.g. ER chaperones contain ER retention/targeting signals
• Stabilized empty MHC molecules will bind the best fit peptide
A better fit peptide can displace the weakly bound peptide (competition)
PEPTID EDITING
Endogenous antigen presentation pathway
antigen processing for
MHC class I molecules
ENDOGENOUS Ag PRESENTING PATHWAY
CELLULAR AND MOLECULAR IMMUNOLOGY 8th ed. (Abbas, AK – Lichtman, AH – Pillai, S) (Elsevier, Saunders 2015)
Synthesis and peptide binding of MHC I molecules
Freshly translated
ERAAP can trim the
peptides to fit
Janeway’s Imunolobiology 8th ed
© 2012 by Garland Science, Taylor & Francis Group
The chaperon complexbound MHC molecule is
ready for peptide binding
Through the Golgi-network
The best fit peptide wins the MHC:
PEPTIDE EDITING
The function of the proteasome
• A cell can contain ~30000 proteasomes (1% of the overall protein mass)
• Proteasomes can be found in the cytosol and the nucleus
unfolding
peptides
(Molecular Biology of the Cell 5th ed@ 2008, 2002 by Bruce Alberts, Garland Science)
Proteasomes degrade proteins to peptides
Proteasomal peptide products could be tailored for
MHC I binding
20S subunit of the
constitutive proteasome
protease
subunits
The Immune System 4th ed Parham,P
(© 2015 by Garland Science, Taylor &
Francis Group, LLC)
http://www.rcsb.org/pdb/explore.do?structureId=4R3O
The ”Immune proteasome”
IFN-
• new protease subunits replace the others (LMP2, LMP7, MECL-1)
• produced peptides are more optimized for MHC I binding
protein cleavage preference is changed:
hydrophobic or basic amino acid on the C-terminal of the peptide
TAP complex transports the peptides into the ER
Prefered peptides (for transport):
• 8-16 aa length
• hydrophobic or basic amino acids at
the C-terminal
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top view
side view
Janeway’s Imunolobiology 8th ed (© 2012 by Garland Science, Taylor & Francis Group, LLC)
no proline in the first 3 positions (from the Nterminal)
The preferences of the TAP correspond to
the cleavage specificity of the immune
proteasome and the general binding
preferences of MHC class I molecules
Exogenous antigen presentation pathway
antigen processing for
MHC class II molecules
EXOGENOUS Ag PRESENTING PATHWAY
CELLULAR AND MOLECULAR IMMUNOLOGY 8th ed. (Abbas, AK – Lichtman, AH – Pillai, S) (Elsevier, Saunders 2015)
Newly translated MHC II αβ dimers bind to Ii (invariant chain, CD74)
chaperon
nonameric
complex
Multimerisation
generally turns the low
affinity interactions to
higher avidity
interaction between the
complexes
α-β-Ii
triplex
• A part of the Ii chain can fit into the peptide
binding site of various MHC II molecules
• The bound Ii is blocking the binding site and
prevents the binding of ER resident peptides
• Ii have endosomal localisation signal sequence
Janeway’s Imunolobiology 8th ed
© 2012 by Garland Science, Taylor & Francis Group
MHC II – Ii complexes travel through the
Golgi-apparatus into the endosome
The assembly of the [MHC class II molecule – exogenous peptide] complex
CLIP peptide
peptide editing
Janeway’s Imunolobiology 8th ed
© 2012 by Garland Science, Taylor & Francis Group
CLIP - Class II-associated
invariant chain peptide
proteases: e.g. cathepsins
HLA-DM is a monomorphic
MHC class II-like chaperon, which helps
in the peptide editing
The peptid editing of HLA-DR by the help of HLA-DM in the endo-lysosomal
compartment
cell surface (6)
HLA-DRα
DM detachment
CLIP
best fit
antigenic
peptide
HLA-DRβ
CLIP detachment
starts in the acidic endolysosomal compartment
antigen derived
peptide
DM stabilise the ”empty” DR
Wouter Pos et al.: Cell 2012, 151, 1557–1568
The peptide binding (editing) of the MHC II molecules could take
place in a multivesicular/multilamellar endo-lysosomal vesicle:
named MIIC or CIIV compartment
CIIV – Class II Vesicle or
MIIC – MHC class II Compartment
Immunity, Vol. 22, 221–233, February, 2005, Copyright ©2005 by Elsevier Inc. DOI 10.1016/j.immuni.2005.01.006
Immuno-electron-microscopy, double immunogold labeling
small dots: HLA-DM (10nm nanogold)
larger dots: HLA-DR (15nm nanogold)
The compartment of the MHC II peptide loading is defined
by the presence of HLA-DM
Defficiencies of the antigen processing pathways
• TAP deficiency:
few intra ER peptides  low cell surface MHC I expression
• tapasin deficiency:
altered peptide editing  alteration in the MHC I presented peptide repertoire (altered
peptide set). More ER derived, fewer cytoplasm (protesome) derived peptides.
• B2M (β2 microglobulin) deficiency:
impaired MHC class Ia and class Ib expression (e.g. FcRn, CD1, MR1 !)
• Ii (invariant chain, CD74) deficiency:
alteration in the MHC II presented peptide set (predominant presentation of
endogenous peptides)
- Altered MHC expression or peptide presentation directly influence the development or
the function of the T lymphocytes and NK cells.
- This indirectly influences almost all cells of the immune system and the immune
response.
Pathogens try to interfere with the antigen presentation!
An immune evasion strategy of the Epstein-Barr virus (EBV)
The schematic gene map of the EBV and the targets of the EBV specific CTL response
+
LMP2
± (?)
EBNA-LP
±
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EBNA2 EBNA3A EBNA3B EBNA3C
EBNA1
Jhet C W W W W W W H F Q U P O MS L E Z R K B G D
W WW W W Y
BHRF1
++
BMLF1
BMRF1
++
BZLF1
++
+
LMP1
TXV I
A Nhet
BARF0
++
• “Lytic antigens” and EBNA3 nuclear proteins are the main targets of the
polyclonal CTL response
• The processing of endogenous EBNA1 is ineffective
EBNA1 contains repeated Glycine-Alanine sequences which inhibits the
proteasomal degradation  ineffective antigen presentation
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EBNA1 expression is enough to maintaining the latent viral phase  the virus is
invisible for the CTL immune response in the viral latent phase
Microbes can use different immune evasion strategies
Janeway’s Imunolobiology 8th ed © 2012 by Garland Science, Taylor & Francis Group
MHC ubiquitination
inhibition of the chaperones
inhibition of the TAP function
×
Viral strategies against antigen presentation
Immunoevasins
Janeway’s Imunolobiology 8th ed © 2012 by Garland Science, Taylor & Francis Group
Pathogens try to use various mechanisms to evade the presentation of their antigens
Pathogens try to evade the immune response by disabling the
MHC I expression of the host cells
NK cells possess various inhibitory NK cell receptors which recognise different
MHC class I molecules. Decreased or missing MHC I molecule expression on the
target cells results NK cell activation.
• Absence of polymorphic MHC class I molecules:
- HLA-C alleles are potent NK inhibitors (in most of cases)
- Lots of HLA-A and HLA-B alleles could also inhibit the NK cell activation
with different efficiency
• Absence of HLA-E is an indirect indicator of the missing HLA class I translation:
HLA-E is a potent NK inhibitor (by NKG2A:CD94). HLA-E cannot leave the ER
without binding signal peptides from the classical polymorphic MHC I.
Weak HLA-A, -B, -C translation  weak HLA-E expression.
• activatory signals override the inhibitory signals
• NK cell activation  killing the cells with ”missing self” (see in the previous lectures also)
MHC class II molecules present both exogenous and
endogenous peptides
• If a peptide in the ER is able to bind to an MHC II molecule with high enough affinity, it will
compete the invariant chain. The Ii-MHC II complex is not formed:
- MHC II molecules can’t reach the endolysosomal compartment without the Ii
- MHC II travels to the cell surface with the bound peptide, similarly to the MHC I-peptide
complex
• Self proteins and peptides can reach the endolysosomal system (ERGolgiMIIC). Their
processed peptides can be bound by the MHC II molecules as in the case of the engulfed
antigens.
• Dead self-cells can be engulfed by phagocyte APC-s. Any protein derived peptide in the
endosome can have the opportunity to be presented by the MHC II molecules. Even
cytoplasm derived peptides (from the dead cells) can be presented exogenously by MHC II
molecules this way.
• MHC II molecules can bind (exchange) extracellular peptides on the surface of the APC, and
they can travel back into the endolysosomal system (cell surface CD74 helps)
Is special circumstances the MHC I molecules must present exogenous protein
derived peptides:
Cross-presentation:
Cross-presentation:
exogenous antigen(!)  MHC I molecule(!)
• Naive, antigen specific CD8+ T cells need activation by dendritic cells to mature CTL.
• Lots of viruses are not able to infect DC, so direct MHC I presentation cannot be achieved
• Specialised DC are able to present exogenous antigens by MHC I molecules
Effector CTL
CELLULAR AND MOLECULAR IMMUNOLOGY 8th ed. (Abbas, AK – Lichtman, AH – Pillai, S) (Elsevier, Saunders 2015)
• Endocytosed viral antigens should reach the cytosol to enter the conventional
endogenous antigen presentation pathway
Lipid presentation by CD1 molecules (MHC-like class Ib)
• CD1 synthesis and folding is similar to the conventional MHC I molecules
• Lipid transfer proteins (LTP) in the ER or the endosomal system helps to bind or
exchange the lipids in the binding site of the CD1 molecules: “LIPID EDITING”)
• They can recycle from the cell surface and bind new lipids in the endosomal system
NATURE REVIEWS IMMUNOLOGY
VOLUME 5 | JUNE 2005 | 485-
CD1 molecules can present both endogenous and engulfed exogenous lipids
The IFN-γ mediated transcriptional regulation of
MHC class I and class II molecule expression
and its
receptor chains
and its
receptor chains
BioFactors, 42(4):349–357, 2016
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IFN-γ induced MHC trans activator molecules mediate effective activation of the MHC genes
Pro-inflammatory cytokines, or PRR-s can directly or indirectly increase the MHC expression (NF-kB
pathway or IFN pathway through the trans activators)
The NOD-like trans activators of the MHC genes mediate
the formation of large enhanceosome complexes
(NLRA)
BioFactors, 42(4):349–357, 2016
• The large enhanceosomes can integrate different transcription factors and chromatin
remodelling proteins for effective gene activation
• CITA enhanceosomes increase the expression of the MHC I presentation pathway’s genes:
HLA-A, -B, -C, HLA-E, TAPs, B2M, proteasome subunits, …
• CIITA enhanceosomes bind to the promoter regions of the MHC II presentation pathway’s
genes: HLA-DR, -DP, -DQ, -DM, -DO, Invariant chain (Ii) and could influence the MHC I genes
also in some professional APC-s.
MHC II expression of human
monocyte derived dendritic cells
- before the activation/maturation
- after the activation/maturation
(by TLR7/8 ligands)
The histograms below show the results of a
flow cytometric measurements
~10 fold
difference
Inflammatory mediators can increase the
MHC molecule expression of the cells
• Strong inflammatory environment
results the expression of MHC II
molecules by non-professional antigen
presenting cells also (e.g. endothelia)
• IFN-γ induces MHC II expression of the
IFN-γ receptor expressing cells (e.g.
helper T cells after their activation)
Ectopic expression of MHC II
molecules exacerbate (increase the
severity) of the transplant rejections.
non-activated
activated
ANTIGEN PROCESSING AND PRESENTATION
short incomplet summary
(exogenous Ag.)
(endogenous Ag.)
8-10aa
10-20aa
(CTL)
(helper)
(CIIV/MIIC)
CELLULAR AND MOLECULAR IMMUNOLOGY 8th ed. (Abbas, AK – Lichtman, AH – Pillai, S) (Elsevier, Saunders 2015)
Themes and topics (you should know):
• Endogenous antigen
presentation pathway
• Exogenous antigen
presentation pathway
• Cross-presentation
• Main viral evasion strategies
• Lipid presentation
• Transcriptional regulation of
MHC
various terms (you should know):
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protein, peptide
cellular compartments
MHC I, MHC II molecules
proteasome, immunoproteasome
TAP (1, 2)
chaperon
tapasin
signal sequence/peptide
protein targeting/sorting
Ii (invariant chain), CLIP
HLA-DM
endosome, MIIC/CIIV
peptide editing
cross-presentation
”missing-self” theory
lipid transport proteins (LTP)
“lipid editing” term
NLRC5, CIITA trans activators
CITA, CIITA enhanceosomes as terms
The Immune System (P. Parham, 4th ed): chapter 5-10 – 5-17 (p126-134), 12-14 – 12-17 (p352360), 5-20 (p138)