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Structure and Function of the
Major Histocompatibility Complex (MHC)
Encoded Proteins
Main topics:
•
•
•
•
•
•
Antigen recognition of T cells
Structure of ”classical” polymorphic MHC I and MHC II molecules
Antigen binding properties of MHC molecules
Heterogeneity/polymorphism of MHC molecules (in drafts)
Non-classical MHC Ib and MHC-like molecules
Other, non-immunological function of MHC
Most of T cells recognize
protein derived short peptides
as antigenic epitopes by the help of the antigen presenting cells
Peptides could be produced from almost any part of the proteins. They can overlap
with the epitopes recognised by the antibodies, but they can also derive from the
cryptic inner side of the proteins.
protein
T cell epitope
B and T cell epitope
The peptides recognised by the T cells produced by proteolytic cleavage from
antigenic proteins,
therefore the T cell epitopes are considered as neoepitopes
The difficulty of peptide recognition
• Short peptides are hard to recognize because they
could not form stabile ordered structure
• Other proteins could stabilize the antigen derived
peptides in a stretched conformation
(CHAPERON FUNCTION)
• Molecules encoded in the MHC gene region provide
the stabilizing function. MHC encoded molecules
are necessary for the peptide recognition of the T
cells
(review)
Two different type of MHC molecules are responsible for the
presentation of peptides from two different cellular compartments
• Endogenous antigen presenting pathway:
-
peptides from proteins (generally synthesized by the cell himself), which are
localised in the cytosol
molecules are encoded in the MHC I gene region  MHC I molecules
peptides are recognized by cytotoxic CD8+ T cells
(e.g. peptides derived from viral proteins synthesized by the infected cell)
• Exogenous antigen presenting pathway:
-
peptides derived from proteins internalized from the extracellular space,
and localised in the endosome
molecules are encoded in the MHC II gene region  MHC II molecules
peptides are recognized by helper CD4+ T cells
(e.g. peptides derived from antigens engulfed and digested by professional antigen presenting
cells)
The two antigen presentation pathways
differ in several ways
(antigen presentation pathways will be discussed on the next lecture in details)
The synthesis and the structure of the classical MHC I and MHC II
molecules
MHC I
MHC II
GENES:
exons: 1
2
3
4
5
67
8
leader,
signal
n.t.
protein
domains s
α-chain NH -
α1
α2
α3
-COOH
NH2-
-COOH
2
3
4 56
leader,
signal
tm c
2
β2-microglobulin
1
7
n.t.
s
α1
α2
s
β1
β2
NH2NH2-
protein
domains
tm c
-COOH α-chain
-COOH β-chain
tm c
peptide bindig site
formed by MHC protein domains
peptide
α1
α1
α2
β2m α3
Immunoglobulin
- like domains
α2
β1
β2
plasma membrane
-COOH
cytosol
COOH-
-COOH
SIMPLIFIED STRUCTURAL MODEL OF THE MHC MOLECULES’
PEPTIDE BINDING SITES
a nchoring
a mino a cids
a nchoring
a mino a cids
Decapeptide
P4 P5 P6
NH P1 P2
P3
P7 P8P9
Octapeptide
-2
2
-1 P1
P4
P6
11
COOH
NH2
"pockets”
P9 10
"pockets”
NH2
COOH
MHCII
MHCI
•
MHC I has frequently a hydrophobic pocket
for the peptide’s C-terminal hydrophobic
amino acid side chain
•
The anchoring amino acid side chains of
the peptide’s „core” region fit into evenly
distributed binding pockets
•
The peptide’s terminal -NH3+ and
-COO- groups could take part in the
anchoring
•
The ends of the long peptides can extend
from the MHC II open binding groove
•
Peptides with different length could
moderately accommodate in the peptide
Connections between the T cell receptor’s CDR loops
and the MHC-peptide complex
The T cell receptor recognize the composite surface made
by the MHC molecule and the bound peptide!
Generally (but not exclusively):
• CDR3 loops bind to the peptide
• CDR2 loops bind to the MHC molecule
• CDR1 loops bind both the peptide
and the MHC molecule
• The most variable CDR3 loops form contacts
with the most variable part of the MHC-peptide complex (the peptide epitope)
• The other variable loops form contacts mainly with the polymorphic MHC molecules
General properties of the TCRs and the MHC-TCR connections, and
their functional consequences
o The antigen receptors assembled randomly from the gene sequences, so they
can have various different specificity
o T cells “educated” (selected) in the thymus by self MHC molecules. (see next
lectures)
o Significant surface of the TCR connects only with the MHC molecule.
Consequences:
• A self TCR “ignores” (can’t bind) most of the foreign MHC:
 explains MHC restriction
The phenomenon of MHC restriction
other virus
+ ’A’ cells
Virus ’X’
T cells
T
T
T T
T T
Mice ’A’
T
Virus ’X’
+ ’A’ cells
T
T
Mice ’B’
Virus ’X’
Virus ’X’
+ cells of ’B’
+ cells of ’B’
T
T
Virus specific T cells can kill the virus infected cells if they derive from the
same animals, so if they have identical histocompatibility genes
The simplified model of the “MHC restriction”
T cell
T cell
T cell
Peptide: 
MHC:

Binding: 
Peptide: 
MHC:

Binding: 
APC
Peptide: 
MHC:

Binding: 
APC
APC
The TCR could bind to the appropriate MHC molecule
complexed with the appropriate peptide
The TCR recognise the composite surface
General properties of the TCRs and the MHC-TCR connections, and
their functional consequences
o The antigen receptors assembled randomly from the gene sequences, so they
can have various different specificity
o T cells “educated” (selected) in the thymus by self MHC molecules. (see next
lectures)
o Significant surface of the TCR connects only with the MHC molecule.
Consequences:
• A self TCR “ignores” (can’t bind) most of the foreign MHC:
 explains MHC restriction
• Some self TCR can bind strongly to foreign MHC(-peptide) complex:
 explains alloreaction
The rejection is mediated by the genetic (allelic) differences of the
histocompatibility genes:
ALLOREACTION
Beside the beforementioned
polimorphic classical peptide presenting MHC molecules,
there exist non-polimorphic MHC-like molecules:
• MHC class I-like and MHC class II-like molecules
• MHC region encoded molecules and molecules encoded
outside the MHC region
• They have diverse functions
Approx. 5% of the T cells in the body are specific for non-peptide
epitops presented by non-polymorphic MHC-like molecules!
MHC region encoded MHC class Ib proteins
and the MODIFICATION OF THE NK CELL FUNCTIONS
• HLA-G
molecules is expressed on the placental trophoblast cells. They can inhibit the NK
cell activation, protect the MHC I non-expressing placental trophoblast cells from
the damage by interacting an inhibitory NK cell receptor (LILRB1)
Virus infected and tumour cells can express it and exploit its function.
HLA-G have also important role in the development of functional placenta by cytokine producing
NK cells during the pregnancy
You had met them on the previous lectures:
• HLA-E
molecules expressed on most tissues. They can appear on the cell surface by binding
of the signal peptide sequences of HLA-A, B, C proteins and inhibit the NK cell
activation (NKG2A:CD94 lectin like NK inhibitory receptor).
(They can also present some other peptides with limited diversity, and can activate CTL response.)
• MICA, MICB (MHC-class-I-polypeptide-related sequence)(no associated β2 microglobulin)
cellular stress induced proteins (infections could also induce stress response in the cell)
cell surface expression  NK activation and cytotoxicity by the lectin like
activatory receptor NKG2D
Some MHC class Ib proteins
encoded outside the MHC region
• MHC class I –like, non-polymorphic molecules encoded also
outside the MHC region
• MHC I-like structure (β2 microglobulin associated)
• Some of it possess antigen presenting function
• Some do not have immunological function (or not known at least)
MHC class Ib proteins encoded outside the MHC region
CD1 proteins: (CD1a, CD1b, CD1c, CD1e
•
•
•
•
CD1d)
usually expressed by professional APCs
presenting self and microbial lipids (e.g. glycolipids, lipopeptides)
presenting both exogenous and endogenous lipids
antibacterial immunity (e.g. immunity against mycobacteria residing in the phagocytes)
polar headgroup
apolar lipid chain
(lipid anchor)
NATURE REVIEWS IMMUNOLOGY VOLUME 5 | MAY 2005 | 387-
CD1d molecule
with bound α-galactosyl ceramide
The antigen binding of the CD1 molecules
Dirk M Zajonc, Marc A Elsliger, Luc Teyton & Ian A Wilson
NATURE IMMUNOLOGY VOLUME 4 NUMBER 8 AUGUST 2003, p808-
• The hydrophobic lipid chain is located in the narrow, apolar binding groove
• The polar “headgroup” could extend from the CD1 molecule surface
•
The antigenic epitope compose only a small area on the contact surface of the molecule 
Recognizing T cells could show slight general autoreactivity to CD1 expressing cells
MHC I –like molecule,
but MHC II –like, exogenous (endo-lysosomal) antigen presentation
Other MHC class Ib proteins encoded outside the MHC region
MR1 – molecules are expressed on various cell types
(MHC Related-1)
They have polar antigen binding site
They present microbial riboflavin (vitamin B2)
metabolic products and byproducts to mucosa
associated invariant T cells (MAIT)
Corbet AJ et al.: Nature, 2014 vol509, 361-
Many vitamin biosynthetic pathways are unique to bacteria and yeast.
Mammals can only acquire riboflavin, so MAIT cells use these metabolites to
detect microbial infection.
MHC class Ib proteins encoded outside the MHC region
MHC class I –like molecules without direct antigen presenting function
FcRn – neonatal Fc receptor
Transporting IgG (and albumins) to various places of the body. IgG can appear almost in
every compartment of the body including epithelial surfaces, secreted fluids, and the
phoetus (by transplacental transportation). FcRn can salvage the IgG from the
endolysosomal degradation also.  IgG have the highest half life time amongst the
antibody isotypes.
Topics and terms you should know:
•
•
•
•
•
Antigen recognition of T cells
Structure of ”classical” MHC I and
MHC II molecules
Antigen binding properies of MHC
molecules
Non-classical MHC Ib and MHC-like
molecules
Heterogenity/polymorphism of MHC molecules
(next lectures)
Terms:
• peptide, protein
• antigen, epitop
• exon, domain
• molecular chaperon
• effector T cell/naive T cell
• CDR regions of the antigene receptors
• motif (of the bound peptide)
• (polymorphic) MHC I, MHC II molecules
• MHC class Ib
• NK cell activation/inhibition
• CD1 molecule, FcRn, MR1
The Immune System (P. Parham, 4th ed): chapter 5-6 – 5-10 (p120-126), 5-16 – 5-22 (p132-140)
Antigen processing and presentation
•
•
•
•
•
•
Endogenous antigen presentation pathway
Exogenous antigen presentation pathway
Microbial evasion strategies
Cross-presentation
Lipid presentation
Transcriptional regulation of MHC
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
tömör (és kissé elnagyolt) összefoglaló:
Az exogén és endogén eredetű fehérje antigének bemutatása
(exogén út)
(MIIC)
(endogén út)
DM
(TAP)
CD4+
Helper
T
Ii
(ER)
T
CD8+
CTL
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
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
•
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
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 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!
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
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
(a strong affinity peptide can compete with the invariant chain in the ER)
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
•
•
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.
Inflammatory mediators can increase the MHC molecule expression of the cells
• Strong inflammatory environment results the expression of MHC II molecules by nonprofessional 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.
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):
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
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)
The genetics and heterogeneity of
the Major Histocompatibility Complex (MHC)
topics, keywords:
•
•
•
•
•
•
•
•
•
•
Heterogeneity of MHC molecules
Mutations
Alleles
Allele frequency
MHC gene region and genes
The inheritance of MHC
Heterogeneity and expression of MHC class I
Heterogeneity and expression of MHC class II
Mechanisms of heterogeneity
Minor Histocompatibility Antigens
Why are so many MHC variants?
Multiple MHC variants  Various peptide binding „pockets” 
 Multiple various peptide binding specificity
• The replication rate of pathogenic microorganisms is faster than human
reproduction
• The genes of a pathogen can mutate frequently: easily evade the efficient
antigen presentation by an MHC molecule
To counteract the flexibility of pathogens
• The MHC has developed many variants
• Some variants could not provide protection from a particular pathogen,
but there should be a variant in the genome or in the population which gives
efficient protection
There are several different MHC molecule variant:
POLYMORPHY
• The peptide binding domains have the greatest polymorphism
• One defined MHC variant can bind various peptides with
different sequences but with similar motif
• Other MHC variants bind peptides which have different motifs
General properties of the MHC molecules:
• A given MHC molecule can bind different peptides
effectively
• A given MHC molecule cannot bind all kinds of peptides
• The peptide binding “pockets” of a given MHC molecule
restricts which peptides would fit in
the set of
all peptides
peptides
presented
by a given
MHC molecule
all peptides
• Efficient antigen presentation needs the presence of
different MHC molecule variants simultaneously
The diversity (polymorphism) of the MHC molecules on the
surface of the antigen presenting cells is achieved by
multiple ways:
peptides
presented
by
different
MHC molecules
The diversity of the peptid presenting MHC molecules of the individual
Polygenic – encoded by multiple genes (evolutionary gene duplications) – ISOTYPES!
human MHC class I molecule isotypes:
Human: HLA-A, HLA-B, HLA-C genes
MHC class II molecule isotypes:
Human: HLA-DP, HLA-DQ, HLA-DR genes
Polymorphic – genes can have various alleles (allotypes)
!!!
MHC genes are the most polymorphic known!
The genes of the peptide presenting ”classical” MHC molecules have several
various alleles in the population. Every isotype can have two alleles in a
given heterozygous individual.
one gene with different alleles
multiple genes, without alleles
multiple genes with different alleles
HLA – Human Leukocyte Antigen
The polymorphy of the HLA-B isotypes in the positions of the pre-matured protein sequences
NH2-
exons:
1
s
2
α1
3
α2
4
5
tm
c
-COOH
6
7
8
α3
source: hla.alleles.org
signal/leader
peptide
•
α1
α2
•
β2m α3
-COOH
•
•
The 2nd and the 3rd exons of the MHC I alpha-chains’ genes are the
most polymorphic.
The 2nd exon of the alpha and beta chains’ genes of the MHC II
could be also polymorphic.
They encodes the peptide binding domains.
Their sequences are determined by the routine genetic HLA typing.
Most polymorphisms derive from point mutations
30 pcs HLA-DPB1 allele sequences between nucleotides 204 and 290 (amino acids 35-68)
Y-F A-V
DPB1*01011
DPB1*01012
DPB1*02012
DPB1*02013
DPB1*0202
DPB1*0301
DPB1*0401
DPB1*0402
DPB1*0501
DPB1*0601
DPB1*0801
DPB1*0901
DPB1*1001
DPB1*11011
DPB1*11012
DPB1*1301
DPB1*1401
DPB1*1501
DPB1*1601
DPB1*1701
DPB1*1801
DPB1*1901
DPB1*20011
DPB1*20012
DPB1*2101
DPB1*2201
DPB1*2301
DPB1*2401
DPB1*2501
DPB1*26011
DPB1*26012
TAC
---T-TCT-T-T-TCT-T-T-T-T-------T---T-T-T-T-T-TCTCT-T-T-T-----
GCG
---T-T-T-T---T-T-T-T-T-T-------T---T-T-T-T-T-T-T-T-T---T-----
CGC
-------------------------------------------------------------
E-A
A-D A-E
Silent
TTC
-------------------------------------------------------------
GAC
-------------------------------------------------------------
AGC
-------------------------------------------------------------
GAC
-------------------------------------------------------------
GTG
-------------------------------------------------------------
GGG
--A
------------------------A
--A
------A
------------------------A
---
GAG
-------------------------------------------------------------
TTC
-------------------------------------------------------------
CGG
-------------------------------------------------------------
GCG
-------------------------------------------------------------
GTG
-------------------------------------------------------------
ACG
-------------------------------------------------------------
GAG
-------------------------------------------------------------
CTG
-------------------------------------------------------------
GGG
-------------------------------------------------------------
CGG
-------------------------------------------------------------
CCT
-------------------------------------------------------------
GCT
---A-AC
-AG
-A---A-AG
-A-A-A-A-------A---A-A-A-AG
-A-A-AG
-AG
---AG
-A-----
GCG
---A-A---A---A---A-A-A-A-------A---A-A-A---A-A---------A-----
GAG
----------C
--------C
----C
----------C
------C
------C
--C
---------------
TAC
-------------------------------------------------------------
I-L
TGG
-------------------------------------------------------------
AAC
-------------------------------------------------------------
AGC
-------------------------------------------------------------
CAG
-------------------------------------------------------------
AAG
-------------------------------------------------------------
Some polymorphism doesn’t influence the peptide binding specificity of the
molecules
(but mutations in the non-coding promoter/enhancer regions can influence the expression)
GAC
-------------------------------------------------------------
ATC
--------C-------C-------C-C---C-C---------C-C---------C------
CTG
-------------------------------------------------------------
GAG
-------------------------------------------------------------
GAG
-------------------------------------------------------------
MAP OF THE HUMAN MHC
FROM THE HUMAN GENOME PROJECT
3.8Mbp
~225 genes (orf)
on chromosome 6
×
The MHC sequencing consortium
Nature 401, 1999
Large gene density!
Various protein coding genes, non-protein coding genes (e.g. miRNA), and pseudogenes
Properties of the human MHC gene region
Located on the short arm (p) of the chromosome 6:
telomere
class I
centromere
class III
class II
divided to 3 subregion depending on the function of the genes:
• Class I region: classical polymorphic, endogenous peptide presenting
molecules (class Ia). Lots of non-polymorphic MHC I-like class Ib molecules: HLA-E,
HLA-F, HLA-G, MICA, MICB molecules (NK cell regulation).
• Class II region: classical polymorphic, exogenous peptide presenting
molecules. Proteins of the antigen processing: chaperones HLA-DM/, HLADO/, proteasome subunits: LMP2 (PSMB9), LMP7 (PSMB8), peptide
transporter subunits (TAP1 and TAP2) genes.
• Class III region:
!!!
Some complement proteins: C4 (polygenic), C2 and factor B, Pro-inflammatory
cytokines: Tumor Necrosis Factor (TNF), Limphotoxin (LT) genes
All three region contain other genes which could be irrelevant in the immunity and
pseudogenes also:
pl. cytochrome P450 monooxigenase enzyme (CYP21A2), RNA helicase (DDX39B), casein kinase subunit
(CSNK2B), heat shock protein HSP-70 (HSPA1A), sialidase/neuraminidase (NEU1), etc. etc. etc.
q
p
(mirrored orientation compared to the previous ones)
Leukocytes were used for the identification of the proteins  Human Leukocyte Antigen (HLA)
chromosome 6
(Human Leukocyte Antigen)
3 subregion – according the function of the genes
mouse chromosome 17
(Histocompatibility-2)
×
Janeway’s Immunobiology, 8th ed. (Garland Science 2012)
The inheritance of the HLA
THE HAPLOTYPE
MHC I
genes:
(isotypes)
MHC haplotype – the combination of
the MHC alleles encoded by one of the
diploid chromosome pair
B5
B7
B703
B8
B12
B13
B14
B15
B16
B17
B18
B21
B22
B27
B2708
B35
B37
B38(16)
B39(16)
B3901
B3902
B40
B4005
B41
B42
B44(12)
allélok (a populációban)
HLA- B:
C:
Cw1
Cw2
Cw3
Cw4
Cw5
Cw6
Cw7
Cw8
Cw9(w3)
Cw10(w3)
A1
A2
A203
A210
A3
A9
A10
A11
A19
A23(9)
A24(9)
A2403
A25(10)
A26(10)
A28
A29(19)
A30(19)
A31(19)
A32(19)
A33(19)
A34(10)
A36
A43
A66(10)
A:
Example of a human MHC I
haplotype pair
One MHC I haplotype of the person:
B14, Cw1, A3
The other MHC I haplotype:
B8, Cw4, A2
The HLA allele names in the example are
the so called ”serotypes”
Inheritence of MHC
• The MHC region is rather short
• Rare meiotic recombinations (linkage)
possible combinations in
the offsprings
DP
DQ DR
B C
• generally the haplotypes are inherited
parent 1
DP DQ DR
B C
A
DP
B C
A
DQ DR
×
parent 2
DP DQ DR
B C
A
DP
B C
A
DQ DR
haplotype –
allele combination on a haploid chromosome, linked with each other
A
The genetics and heterogeneity of MHC I
(Human Leukocyte Antigen)
(Histocompatibility-2)
Janeway’s Immunobiology, 8th ed. (Garland Science 2012)
6:
q
p
The heterogeneity of the human MHC class I
q
6:
diploid individual
chromosome 6: MHC I region
B
haplotype
C
(maternal origin)
B
haplotype
(paternal origin)
codominant
expression
C
A
4358
3492
3111
B
A
C
HLA
alleles
One individual:
generally 6 kind of MHC I molecule
A
p
The genetics and heterogeneity of MHC II
(Human Leukocyte Antigen)
(Histocompatibility-2)
Janeway’s Immunobiology, 8th ed. (Garland Science 2012)
6:
q
p
(animation)
The genetics and heterogeneity of the MHC II
haplotype
(maternal)
haplotype
(paternal)
DR
DQ
DP
A B
A B
AB
A B
A B
AB
HLA-DRA
virtually
monomorphic
The alpha and the beta chains can be combined freely with each other in the ER.
But not all combination can result stabile products !
Intraisotype combinations
Mixed isotype combinations
They are the “preferred” and frequent combinations
(random examples)
Intrahaplotype combinations
DR DR DQ DQ DP DP
Cross-haplotype
combinations
DQ DQ DP DP
Some αβ combinations are
incompatible – rare combinations
…….
summary
Mechanisms of the MHC polymorphism
• allele variations of the population
Principally: combinations of several thousand alleles,
Practically: a pair of inherited haplotype combinations of the individual which change rather
infrequently by recombinations
The large allele numbers result heterozygosity, and the genes of the homologue chromosomes
expressed codominantly  doubles the number of the HLA isotype variations
• MHC gene/molecule isotypes:
3 polymorphic MHC I isotypes: HLA-A, HLA-B, HLA-C
3 polymorphic gene isotype of the MHC II alpha chains: HLA-DPA1, HLA-DQA1, HLA-DRA (monomorphic)
and beta chains: HLA-DPB1, HLA-DQB1, HLA-DRB1
(some additional coding subtypes of the HLA-DRB: -3, -4, -5)
• α- and β-chain combinations of MHC II
10-12 frequent MHC II αβ combinations (intra isotype combinations)
40 principal combinations by the mixed isotype combinations, but the possibility is very low because
of the frequent incompatibility of the mixed isotype αβ chains
(protein encoding HLA-DQA2 and HLA-DQB2 subtypes are also described)
•
alternative splicing (currently only sequence database data indicate them)
Alternative splicing could combine the exones between isotypes (and possibly involving the exones of
the pseudogene isotypes)
THE CLINICAL CONSEQUENCES OF THE MHC POLYMORPHISM
• The efficiency of the vaccinations could differ between individuals with
different MHC haplotypes
• The frequency of some HLA haplotype correlates with the frequency of
some disease in different human populations. The correlation can be
positive or negative: Some haplotype can protect from the disease and
some haplotype could mediate sensitivity against the disease e.g:
o Autoimmune diseases
o Hypersensitivity disorders
The antigen presenting MHC molecules can have direct role in the
pathogenesis of these diseases or they simply act as indicators which
indicates the presence of other inherited linked alleles in the haplotype:
e.g.: the presence of MHC III encoded inflammation mediator gene alleles
(TNF alleles, complement factor alleles)
Natural selection can change the allele frequency in the populations
of different geographical regions which host endemic pathogens
• Some MHC allele could provide more efficient protection against a
specific pathogen than others
This could be observed in the Serotypes Frequency (%)
EUR AFR ASI
distribution of MHC alleles’
HLA- A1 15.2 5.72 4.48
frequency in different human HLA- A2 28.7 18.9 24.6
geographical populations:
HLA- A3 13.4 8.44 2.64
HLA- A28 4.46
HLA- A36 0.02
9.92
1.88
1.76
0.01
• The allele corresponding the HLA-B53 serotype is strongly associated with the
recovery from the lethal form of malaria. HLA-B53 serotype is very common in
some region where malaria (Plasmodium - parasitic protozoa) is endemic.
• HLA-B27 and B57 serotypes have higher allele frequency in the group of ”HIV
controllers”
THE ROLE OF THE MAJOR HISTOCOMPATIBILITY GENE
COMPLEX (MHC) IN THE EFFICIENCY OF THE IMMUNRESPONSE
Immunisation:
Antigen
Antigen
mice strain A
Strong
immunresponse
mice strain B
Weak / Zero
immunresponse
Some MHC (allelic) variants can mediate more effective T cell
based immune response than other MHC variants!
Minor Histocompatibility Antigens
(MiHA, MHA, miHA)
Minor histocompatibility antigenes (MiHA, MHA, miHA)
Antigens which are encoded outside the MHC gene regions , and can induce
rejection in the case of transplantation
Alloantigens (alleles can be recognised as “non self”)
Non polymorphic antigens, sometimes with low allele frequency, so there is low possibility
of the incompatibility between a random donor-recipient pair.
They are called “minor” because they encoded outside the Major
Histocompatibility Complex, but they can mediate severe
rejections in transplantations!
• MiHA incompatibility could induce rejections even in the case of HLA
identity. Their compatibility are also very important in the case of different
tissue/organ transplantations.
• They can induce miscarriage (abortion) or birth disorders in pregnancy
The different groups of the MiHA
The classical (strict) definition :
Any non-MHC encoded antigen, which mediate immunogenic T cell response
in the case of transplantation
MiHa antigens are presented by the host MHC molecules
MHC I – CD8+ cytotoxic T cell response
MHC II – CD4+ helper T cell respone (inflammation)
The type of the MHC can limit the presentation (motif!)
Approximately 50 well described MiHA are known recently (sequence, MHC restriction)
Classical example: H-Y antigen (KDM5D) lysine demethylase enzyme, chromosome Y encoded
 women could rise immune response against them (every new male embryo become more and
more endangered after the previous one in the case of pregnancies)
The slack (loose) definition:
Any non-MHC encoded alloantigen, or antigens produced by non-self enzymes which could
mediate general alloreaction
(It could involve T cell, B cell or antibody mediated immune response)
e.g.: Rh antigens: The presentation of the antigen mediate the IgG production of the B cells.
The pathogenesis are mediated by antibody effector functions.
indirect alloreaction:
AB0 blood group antigens – 3 glycosyltransferase alleles with high allele frequency can
produce different oligosaccharide antigens. The enzymes themselves are not immunogenic. Cross
reactions with the microbial flora of the gut induce the immunisation.
Endothelial cells can express AB0 antigens. It can induce “immediate type” antibody mediated
rejection in mismatched transplantation.
The genetics and heterogeneity of MHC
Themes and topics (to know):
• Heterogeneity of MHC molecules (reasons
and consequences)
• Mutations, alleles, allele frequency
• MHC gene region (Class I, II, III)
• The inheritance of MHC
• Heterogeneity and expression of MHC class I
• Heterogeneity and expression of MHC class II
• Mechanisms of heterogeneity
• Clinical consequences
• Minor Histocompatibility Antigens
various terms (you should know):
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
locus
gene
allele
haplotype
isotype (of MHC genes)
polymorphism
polygeny
homozygote, heterozygote
pseudogene
null allele
allele frequency
exon, domain
alternative splicing
gene content variation
MHC, HLA, MiHA
The Immune System (Parham P): chapter 5-18 – 5-23 (4th ed: p135-147)