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The genetics and heterogeneity of
the Major Histocompatibility Complex (MHC)
topics, keywords:
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Peter Gogolak,
UD, Dept. of Immunology,
[email protected]
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
hypothetical model
The beneficence of the MHC polymorphism
The outcome of an infection in a population with or without polymorphic MHC
Example: If a single type of MHC (MHC X) was the only in the population
MHC
XX
Multiple variety of MHC
v
– vulnerable individuals
v
v
Pathogen that
evades
MHC X
v
v
v
v
v
v
v
Population threatened
with extinction
v
v
v
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v
v
Heterogeneous population is protected
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
!!!
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
Polymorphic residues of the MHC molecules are located in the
peptide binding site of the molecules
Fundamental immunology, 6th ed, Philadelphia, 2008, Lippincott Williams & Wilkins
• The polymorphic residues (of the alleles) is clustered in the peptide binding site
Allelic variants could have 20 aa differences in the sequence (10% of the total sequence )
• MHC polymorphism influences the peptide binding:
Different allelic variants bind different peptides with different efficiency (motifs!)
→ This has influence on the T cell activation
→ It can explain why different persons mount immune responses with
different efficiency
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
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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
-------------------------------------------------------------
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HLA typing (identification) and nomenclature
Serotyping:
Genotyping:
antibodies or sera with specific
antibodies are used
The sequence of the peptide binding domains’
exones are determined (hybridisation or sequencing)
(fast, cheap)
• the allotype can be exactly determined, small
differences can be shown (even in the non coding
regions  differences in the promoter, enhacer
regions can influence the expression) :
• cross reaction could occure
• the hidden epitopes can’t be
identified
• only the large “allele groups”
can be identified:
HLA-A (3492pc.)
HLA-A (28pc.) HLA-B (62pc.) HLA-C (10pc.)
HLA-B (4358pc.) HLA-C (3111pc.)
A*01:01:01:01
B*07:02:01
C*01:02:01
B*07:02:02
C*01:02:02
A1
B5
Cw1
A*01:01:01:02N
A2
B7
Cw2
A*01:01:01:03
B*07:02:03
C*01:02:03
A203
B703
Cw3
A*01:01:02
B*07:02:04
C*01:02:04
A210
B8
Cw4
A*01:01:03
B*07:02:05
C*01:02:05
B*07:02:06
C*01:02:06
A3
B12
Cw5
A*01:01:04
A9
A10
B13
Cw6
A*01:01:05
B*07:02:07
C*01:02:07
B14
Cw7
A*01:01:06
B*07:02:08
C*01:02:08
A11
B15
Cw8
A*01:01:07
B*07:02:09
C*01:02:09
Cw9(w3)
Cw10(w3)
A*01:01:08
B*07:02:10
C*01:02:10
A*01:01:09
B*07:02:11
C*01:02:11
A*01:01:10
B*07:02:12
C*01:02:12
B*07:02:13
…
…
B*82:03
C*01:02:13
…
…
C*18:09
B*83:01
C*18:10
A19
A23(9)
…
…
A69(28)
B16
B17
…
…
…
A74(19)
B78
A80
B81
A*01:01:11
…
…
A*80:02
B82
A*80:03
The number of the identified
serotypes are much lower
compared to the genotyped
allele number
×
2016.
HLA alleles and proteins identified until 2016
HLA alleles and proteins
source: hla.alleles.org
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The numbers of the identified alleles has been increasing year by year
How a genetically identified allele is named (nomenclature)
×
source: hla.alleles.org
Nomenclature
HLA
HLA-DRB1
HLA-DRB1*13
HLA-DRB1*13:01
HLA-DRB1*13:01:02
Indicates
the HLA region and prefix for an HLA gene
a particular HLA locus i.e. DRB1
a group of alleles that encode the DR13 antigen or sequence homology to
other DRB1*13 alleles
a specific HLA allele
an allele that differs by a synonymous mutation from DRB1*13:01:01
HLA-DRB1*13:01:01:02 an allele which contains a mutation outside the coding region from DRB1*13:01:01:01
HLA-A*24:09N
HLA-A*30:14L
etc.
a 'Null' allele - an allele that is not expressed
an allele encoding a protein with significantly reduced or 'Low' cell surface expression
etc.
MAP OF THE HUMAN MHC
FROM THE HUMAN GENOME PROJECT
3.8Mbp
~225 genes (orf)
on chromosome 6
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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 subunit (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.
p
q
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You can have detailed
information about the genes
from databases
http://www.ensembl.org/Homo_sapiens/Location/View?db=otherfeatures;g=2550;r=6:29600000-33400000
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
Because of the haplotype inheritance, you can find HLA identical children in
families with high offspring numbers
The probability of the presence of HLA identical children in the family
%
Number of the offsprings in the family
HLA Polymorphy
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
Allelic variants of the classical polymorphic MHC II molecules
The alpha chains are less polymorphic than the beta chains
Probably because the alpha chain should bind the non-polymorphic HLA-DM during the ”peptide editing”
HLA-DRA is virtually monomorphic. The two proteins are almost identical,
and the second known variant has low allele frequency
HLA alleles and proteins
(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
…….
Az MHC II genetikája és heterogenitása
The extreme heterogeneity of the HLA-DR locus
The structure of the HLA-DR locus can have large differences between haplotypes, even in the
genome of the same individual:
gene content variation
• HLA-DRA encodes the monomorphic alpha chain
• You can find at least on beta chain encoding gene (usually the HLA-DRB1)
HLA-DRA gene
α-chain
α1
α2
β1
β-chain
HLA-DRB1 gene
β2
This is the general, most frequent combination
in the human population
But the HLA-DRB isotype can have additional subtypes beside the HLA-DRB1 :
The human genome
generally encodes one
HLA-DR alpha chain
(HLA-DRA) and at least
one HLA-DR beta chain
(HLA-DRB1)
Structural variability in the HLA-DR locus:
Gene content variability in 4 different haplotypes
HLA-DRB1
HLA-DRB5
Ψ
1st
haplotype
Ψ
HLA-DRA
Ψ
Different haplotypes could
generally contain other HLADR beta chain encoding
subtypes and beta chain
pseudogenes (Ψ) in different
number.
2nd
haplotype
Ψ
HLA-DRB4
Ψ
3rd
haplotype
Ψ
Ψ
HLA-DRB3
×
Ψ
Ψ
http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000196126;r=6:32437723-32592565
4th
haplotype
A simplified example: individuals with multiple and single HLA-DRB isotypes
a person with different
HLA-DRB subtypes
DRB3
a person with only one isotype
ΨDRB6 DRB1
DRB1
maternal
haplotype
maternal
haplotype
DRB5 DRB1
ΨDRB6 DRB1
paternal
haplotype
paternal
haplotype
identical
haplotypes
(with identical
alleles)
The HLA-DRA is monomorphic:
HLA-DR molecule
combinations:
DRβ
DRα
DRβ
DRα
DRβ
DRα
4 different peptide binding
specificity
DRβ
DRα
DRβ
DRα
a single peptide binding
specificity
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 different groups
or populations in areas hosting 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”
Minor Histocompatibility antigenes
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):
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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)
Lots of updated information about HLA:
http://hla.alleles.org/
http://www.ebi.ac.uk/ipd/imgt/hla/