The genetics and heterogeneity of MHC Heterogeneity of MHC molecules Mutations Alleles Allele frequency MHC gene region and genes The inheritance of MHC

The genetics and heterogeneity of MHC

• 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

topics, keywords:

Why are so many MHC variants?

• The replication rate of pathogenic microorganisms is faster than human reproduction

• The genes of a pathogen can mutate frequently in a given time and can easily evade the efficient antigen presentation by MHC molecules

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 an appropriate variant in the population which gives efficient protection

Multiple MHC variants Various peptide binding „pockets” Multiple various peptide binding specificity

The beneficence of the MHC polymorphismThe 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

Population threatenedwith extinction

Pathogen that evadesMHC X

MHCXX

v

Multiple variety of MHC

v

vv

vv

v

vv

v

v

v

v

v v v

v

vv

v

vv

v

vv

– vulnerable individualsv

v

Heterogeneous population is protected

hypothetical model

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 allelesMHC 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.

The diversity of the peptid presenting MHC molecules of the 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

• The polymorphic residues (allelic variations) is clustered in the peptide binding siteAllelic variants can reach 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

Fundamental immunology, 6th ed, Philadelphia, 2008, Lippincott Williams & Wilkins

DPB1*01011 TAC GCG CGC TTC GAC AGC GAC GTG GGG GAG TTC CGG GCG GTG ACG GAG CTG GGG CGG CCT GCT GCG GAG TAC TGG AAC AGC CAG AAG GAC ATC CTG GAG GAG DPB1*01012 --- --- --- --- --- --- --- --- --A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*02012 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*02013 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -AC -A- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*0202 CT- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -AG --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*0301 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --C --- --- --- --- --- --- --- C-- --- --- --- DPB1*0401 -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*0402 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*0501 CT- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -AG --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*0601 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --C --- --- --- --- --- --- --- C-- --- --- --- DPB1*0801 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*0901 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --C --- --- --- --- --- --- --- --- --- --- --- DPB1*1001 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*11011 --- --- --- --- --- --- --- --- --A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- C-- --- --- --- DPB1*11012 --- --- --- --- --- --- --- --- --A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- C-- --- --- --- DPB1*1301 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*1401 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --C --- --- --- --- --- --- --- C-- --- --- --- DPB1*1501 --- --- --- --- --- --- --- --- --A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- C-- --- --- --- DPB1*1601 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*1701 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --C --- --- --- --- --- --- --- --- --- --- --- DPB1*1801 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*1901 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -AG --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*20011 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --C --- --- --- --- --- --- --- C-- --- --- --- DPB1*20012 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --C --- --- --- --- --- --- --- C-- --- --- --- DPB1*2101 CT- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -AG --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*2201 CT- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -AG --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*2301 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*2401 -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -AG --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*2501 -T- -T- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -A- -A- --- --- --- --- --- --- --- --- C-- --- --- --- DPB1*26011 --- --- --- --- --- --- --- --- --A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- DPB1*26012 --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---

30 HLA-DPB1 allele sequences between nucleotides 204 and 290 (amino acids 35-68)

Most polymorphisms derive from point mutations

Y-F A-V Silent A-D A-EE-A

I-L

Polymorphic sequences encode amino acids associated with the

peptide binding site

Some polymorphism doesn’t influence the peptide binding specificity of the molecules

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 thedistribution of MHC alleles’frequency in different human geographical populations:

• 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”

• Some HLA allele frequency is in correlation with the occurrence of a specific disease in a population. The correlation could be either positive or negative.

EUR AFR ASIHLA- A1 15.2 5.72 4.48HLA- A2 28.7 18.9 24.6HLA- A3 13.4 8.44 2.64HLA- A28 4.46 9.92 1.76HLA- A36 0.02 1.88 0.01

Frequency (%)Serotypes

HLA alleles

HLA proteins (2015)

The heterogeneity of human MHC alleles and proteins

The numbers of the identified alleles has been increasing year by year

http://hla.alleles.org/

Janeway’s Immunobiology, 8th ed. (Garland Science 2012)

(Human Leukocyte Antigen)

(Histocompatibility-2)

chromosome 6

mouse chromosome 17

3 subregion – according the function of the genes

Leukocytes were used for the identification of the proteins Human Leukocyte Antigen (HLA)

3.8Mbp~225 genes (orf)

on chromosome 6

The MHC sequencing consortiumNature 401, 1999

MAP OF THE HUMAN MHC FROM THE HUMAN GENOME PROJECT

various protein coding genes, non-protein coding genes (e.g. miRNA), pseudogenes

Journal of Human Genetics (2009) 54, 15–39

The MHC gene region is quiet short

http://www.ensembl.org/Homo_sapiens/Location/View?db=otherfeatures;g=2550;r=6:29600000-33400000p q

You can have detailed information about the genes

from databases

The inheritance of HLA

A1A2

A203A210

A3A9

A10A11A19

A23(9)A24(9)A2403

A25(10)A26(10)

A28A29(19)A30(19)A31(19)A32(19)A33(19)A34(10)

A36A43

A66(10)A68(28)A69(28)A74(19)

A80

B5B7

B703B8

B12B13B14B15B16B17B18B21B22B27

B2708B35B37

B38(16)B39(16)B3901B3902

B40B4005

B41B42

B44(12)B45(12)

B46B47B48

B49(21)B50(21)B51(5)B5102B5103B52(5)

B53B54(22)B55(22)B56(22)B57(17)B58(17)

B59B60(40)B61(40)B62(15)B63(15)B64(14)B65(14)

B67B70

B71(70)B72(70)

B73B75(15)B76(15)B77(15)

B78B81B82

Cw1Cw2Cw3Cw4Cw5Cw6Cw7Cw8

Cw9(w3)Cw10(w3)

B: C: A:HLA-

MHC haplotype – the combination of the MHC alleles encoded by one of the diploid chromosome pair

MHC Igének:(izotípusok)

allé

lok

(a p

opul

áció

ban)

THE HAPLOTYPE

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

ACBDP DQ DR

AB CDP DQ DR

AB CDP DQ DR

AB CDP DQ DR

AB CDP DQ DR

possible combinations in the offsprings

parent 1

parent 2 ×

• The MHC region is rather short

• Rare meiotic recombinations (linkage)

• generally the haplotypes are inherited




The genetics and heterogeneity of MHC Ipq

6:

-COOH

α3

α2α1

β2m

exons: 1 2 3 4 5 76 8leader,signal

β2-microglobulin(chromosome 15)

α-chaintm cα1 α2 α3

NH2-

NH2-

-COOH

-COOH

proteindomains

n.t.

pq6:

-COOH

α3

α2α1

β2m

-COOH

α3

α2α1

β2m

cytosol

membrane

HLA-B HLA-C HLA-A

The genetics and heterogeneity of MHC I

**

The heterogeneity of the human MHC I

diploid individualchromosome 6 MHC I region

haplotype(maternal origin)

haplotype(paternal origin)

One individual: generally 6 kind of MHC I molecule

A

A

B

BC

Ccodominant

expression

pq6:

B C AHLA

0

500

1000

1500

2000

2500

3000

3500

4000

45003977

27403192

alleles




The genetics and heterogeneity of MHC II pq6:

Allelic variants of the classical polymorphic MHC II moleculesThe alpha chains are less polymorphic than the beta chains

(Alpha chain should bind the non-polymorphic HLA-DM during the ”peptide editing”)

HLA-DRA is monomorphic in practice. The two proteins are almost identical.

The genetics and heterogeneity of MHC IIDPDQDR

haplotype(of maternal origin)

Intrahaplotype or ”cis” combinations

A BA BA B

p q6:

β2

β1α1

α2

A BA BA B

β2

β1α1

α2 β2

β1α1

α2 β2

β1α1

α2 β2

β1α1

α2 β2

β1α1

α2

haplotype(of paternal origin)

The most favoured and frequent combinations on the cell

HLA-DRA practically monomorphic

DR DRDQ DP DQ DP

DQ

haplotype(of maternal origin)

A B

p q6:

DPDR

A BA B

haplotype(of paternal origin)

β2

β1α1

α2

”cis”HLA-DQ

β2

β1α1

α2

”cis”HLA-DQ

α1

α2 β2

β1

”trans”HLA-DQ

β2

β1α1

α2

”trans”HLA-DQ

The α and β chains of the maternal and paternal haplotype can be combinedAll isotype (DP, DQ , DR) can produce cross haplotype combinations (”trans”)

α and β chains of different alleles can prefer or unfit each other

The genetics and heterogeneity of MHC II

DQ

A B

DR

A B

α1

α2 β2

β1

β2

β1α1

α2

The α and β chains of different MHC II gene isotypes (HLA-DR, HLA-DQ, HLA-DP) can be combined

if they prefer each other.

Mixed isotype MHC II heterodimers

DRα DQα DRβDQβ

• It is also possible between (maternal and paternal) haplotypes

• Lots of combinations are unfit (few percent can appear on the cells)

• The expression of mixed isotype dimers can increase if some isotype express only one chain of the pair (e.g. the other is a null-allele)



The extreme heterogeneity of the HLA-DR locus (1.)

The structure of the HLA-DR locus can have large differences between individuals (Even the two haplotypes of an individual can greatly differ from each other.)• The HLA-DR locus encode the monomorphic alpha chain (HLA-DRA)• The HLA-DR locus encode at least one beta chain (HLA-DRB1)

β2

β1α1

α2

This two gene are expressed generally in everyone

a HLA-DRαβ molecule

HLA-DRA gene α-chain HLA-DRB1 geneβ-chain


The extreme heterogeneity of the HLA-DR locus (2.)

The structure of the HLA-DR locus can have large differences between individuals (Even the two haplotypes of an individual can greatly differ from each other.)

• The HLA-DR locus can contain multiple HLA-DRB gene isotypes• The HLA-DRB isotypes can encode additional β protein chains (HLA-DRB3, -DRB4, -DRB5)• Some HLA-DRB isotypes are pseudogenes (Ψ) (HLA-DRB2, -DRB6, -DRB7, -DRB9)• The additional β chains can be combined with the α chain to form other functional HLA-

DR isotypes

The HLA-DR locus of different individuals or haplotypes contains generally the HLA-DRA, HLA-DRB1, plus• one additional protein coding HLA-DRB isotype• and 2-3 HLA-DRB pseudogenes in various combinations

See the examples:

DRA DRB1 DRA DRB3 DRA DRB5DRA DRB4

HLA-DR molecules

http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000204287;r=6:32436594-32591703

ΨDRB9

ΨDRB6

HLA-DRB5 HLA-DRB1

HLA-DRAAn example of a haplotype:

p q6:

Possible DR β encoding isotypes: DRB1, DRB5

HLA-DR locus can encode multiple beta chains

DRA DRB1DRA DRB5

ΨDRB9

ΨDRB2

HLA-DRB3

HLA-DRB1

HLA-DRA

http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000204287;r=CHR_HSCHR6_MHC_COX_CTG1:32386175-32523582

Other haplotype

p q6:



DRA DRB1DRA DRB3

A third haplotype(similar to the previous one)

ΨDRB9

ΨDRB2

HLA-DRB3

HLA-DRB1

HLA-DRA

HLA-DQB1

http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000204287;r=CHR_HSCHR6_MHC_QBL_CTG1:32396557-32596654

p q6:



DRA DRB1DRA DRB3

ΨDRB9

ΨDRB7

HLA-DRB4

HLA-DRB1

HLA-DRAA fourth haplotype

ΨDRB8

http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000204287;r=CHR_HSCHR6_MHC_MANN_CTG1:32474790-32742976

p q6:



DRA DRB1DRA DRB4

A simplified example: individuals with multiple and single HLA-DRB isotypes

DRB1

DRB1DRB5

DRB3maternalhaplotype

paternalhaplotype

DRB1

DRB1

ΨDRB6maternalhaplotype

paternalhaplotype

4 isotype in one person a person with only one isotype

identicalhaplotypes(with identical

alleles)

DRαDRβ

DRαDRβ

DRαDRβ

DRαDRβ

DRαDRβ

ΨDRB6

HLA-DR molecules4 different peptide bindingspecificity

a single peptide bindingspecificity

The HLA-DQ has two alpha and two beta coding isotype

HLA-DQA2

HLA-DQB2

HLA-DQA1

ΨHLA-DQB3HLA-DQB1


These are the α and β chainsof the ”classical” HLA-DQ molecule

These isotypes have shown expressed only by Langerhans cells

http://www.ncbi.nlm.nih.gov/pubmed/8026991

p q6:

Generally the HLA-DQA1/HLA-DQB1 is expressed in the professional APC

• It seems the neighbouring genes (isotypes) which are in the same orientation can use each other’s exons by alternative splicing

• The exons of some pseudogenes can be used this way also

• In the case of MHC I (HLA-A, -B, -C), such an exon exchange involving the second and third exons (alpha1 and alpha2 domains of the MHC I proteins) would increase the variability of the peptide binding site.

There is a hint in the database that suggests the existence of such a mechanism:

Curiosities

Lα1HLA-BHLA-C

α2α3

ex1ex2ex3ex4

A transcript of the HLA-C could use the first two exons of the HLA-B in the case of this haplotype

-COOH

α3

α2α1

β2m

„HLA-B”„HLA-C”

transmembranedomain is missing

The protein could be solubleinstead of a membrane bound one:

HLA-C HLA-B

transcribed region


Mechanisms of the MHC polymorphismsummary

• allelic variances of the populationprincipally: combinations of several thousand alleles,practically: a pair of inherited haplotype combinations of the individual which change rather infrequently by recombinations

• MHC gene/molecule isotypes 2x3 MHC I, 2x3-4 MHC II from the two inherited haplotype

• α- and β-chain combinations of MHC II 6-8 to 10-12 (principally up to 40) MHC II αβ dimer. The intra isotype, intra haplotype α β chains like to combine with each other the best.

• alternative splicing (currently the evidences are based on sequence database data) Alternative splicing could combine peptide binding domains between isotypes (possibly involving the peptide binding domains of the pseudogene isotypes)

Other genes of the MHC regions

• Class I region (Classical polymorphic MHC I molecules)Lots of MHC class Ib molecules: 2 microglobulin-associated, non-polymorphicMHC I–like molecules, with diverse tissue expression, influencing NK cell functions: e.g. HLA-E, HLA-F, HLA-G, MICA, MICB

• Class II region (Classical polymorphic MHC II molecules)Genes involved in the antigen processing, chaperones: HLA-DM/, HLA-DO/, proteasome components (LMP-2 and 7), peptide transporters (TAP-1 and 2)

• Class III regionGenes of some complement proteins: C4 (multiple isotypes), C2 and factor Bcytokines: Tumour Necrosis Factor (TNF) and Lymphotoxin (LT) genes

All three regions contain genes which could be irrelevant in the immunity and contain pseudogenes also:e.g. cytochrome P450 monooxygenase (CYP21A2), RNA helicase (DDX39B), subunit of casein kinase (CSNK2B), heat shock protein HSP-70 (HSPA1A), sialidase (NEU1), etc. etc.

MHC function summary:

Functions of MHC encoded and MHC-like molecules

• Classical polymorphic MHC moleculesendogenic self and non-self peptide antigen presentation: HLA-A, -B, -Cexogenic self and non-self peptide antigen presentation: HLA-DP, -DQ, -DRinhibiting NK cell function: HLA-C, (-A, -B)allogenic immune response against non-self MHC molecules (transplantation)

• Non-classical, non-polymorphic MHC encoded moleculespresentation of non-polymorphic peptide antigens: HLA-E (HLA-F?)participation in the antigen processing: TAP1, -2, HLA-DM, -DO, LMP-2, -7influencing the NK cell function: HLA-E, -F, -G( ), MICA, -B( )other immunological functions: C4, TNF…non immunological functions: HSP-70 (HSPA1A)…

• MHC-like molecules encoded outside the MHC regionpresentation of non-polymorphic, non-peptide antigens: CD1, MR1other immunological functions: FcRn (FCGRT)non immunological function: HFE

- T cell and NK cell selection and differentiation in the primary lymphoid organs- T cell survival on the periphery/memory

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, haplotype

• The inheritance of MHC

• Heterogeneity and expression of MHC class I

• Heterogeneity and expression of MHC class II

• Mechanisms of heterogeneity

• Other proteins of the MHC

various terms (you should know):

• locus• gene• allele• haplotype• isotype (of MHC genes)• alternative splicing• polymorphism• polygeny• homozygote, heterozygote• pseudogene• null allele• allele frequency• exon, domain• MHC, HLA

The Immune System (Parham P): chapter 5-18 – 5-23 (4th ed: p135-147)Basic Immunology (Abbas AK): chapter 3 (4th ed: p55-61)

http://hla.alleles.org/

Lots of information about HLA:

http://www.ebi.ac.uk/ipd/imgt/hla/

Documents

The genetics and heterogeneity of MHC Heterogeneity of MHC molecules Mutations Alleles Allele frequency MHC gene region and genes The inheritance of MHC