The Major Histocompatibility

Complex

MHC

• The immune system relies on many regulatory mechanisms that govern its ability to respond to infectious agents and neoplastic tissues, but no single scheme is as much a cellular and molecular microcosm of complex biologic systems as that controlled by the Major Histocompatibility Complex (Mhc).

Introduction• The task of displaying cell-associated antigens

for recognition by T cells is performed by specialized proteins that are encoded by genes in a locus called the MHC

• It was discovered as an extended locus containing highly polymorphic genes that determined the outcome of tissue transplants exchanged between individuals

• The physiologic function of MHC molecules is the presentation of peptides to T cells

• In fact, MHC molecules are integral components of the

ligands that most T cells recognize

• The antigen receptor of T cells are actually specific for

complexes of foreign peptide antigens and self MHC

molecules

• A cluster of closely linked genetic loci comprise the

MHC encoding molecules important in immune

functions

• Every vertebrate species examined so far has MHC; in

humans it is called The human leukocyte antigen

(HLA)

The MHC gene region

MHC class I and class II are polygenic

(several loci encoding products with essentially the same function)

a chain

a chain a chain

Class II

b2 microglobulin is not encoded in

MHC

Class I

Identification of Human MHC

• Multiparous women, actively immunized

volunteers, recipients of blood transfusion, and

transplanted patients were sources of anti-HLA

antibodies

• HLA antigens were identified in workshops with

exchange of antisera between researchers

• Initially HLA antigens were identified by

serology and the mixed lymphocyte reaction

(MLR)

Structural Characteristics of MHC

molecules• Each MHC molecule consists of an extracellular

peptide binding cleft, a groove, followed by a pair of Ig- like domain and is anchored to the cell by transmembrane and cytoplasmic domains

• Class I molecules are composed of one polypeptide chain encoded in the MHC and a second, non MHC-encoded chain ( β2 microglobulin), whereas class II molecules are made up of two MHC-encoded polypeptide chains

• The polymorphic amino acid residues of MHC molecules are located in and adjacent to the peptide-binding cleft (a1 and a2 in class I and a1 and β1 in class II. Variation is most in the β chain)

Structure of MHC molecules

• The display of MHC-peptide complexes is

scrutinized by TCRs on T cells and is crucial for

the initiation of adaptive immune responses

• Recently, several genes have been found within

the MHC whose products are important to the

function of MHC class I and II molecules

involved in antigen processing and presentation

• Class III molecules include some of the

elements of serum complement system

Genomic Organization of the MHC

• MHC is located on the short arm of chromosome 6, β2 microglobulin on chromosome 15

• It occupies a large segment of DNA, extending about 3500 kb ( about 4 cetrimorgans) meaning that crossovers within the MHC occur with a frequency of about 4% at each meiosis

• Within the MHC locus are genes that encode several proteins that play critical roles in antigen processing

• One of these proteins, called the transporter associated with antigen processing (TAP), is a heterodimer that transports peptides from the cytosol into the endoplasmic reticulum, where the peptide can associate with the newly synthesized class I molecules

• Other genes in the cluster encode subunits of a cytosolic protease complex, called the proteasome, that degrades cytosolic proteins into peptides that are subsequently presented by class I MHC molecules

• Another pair of genes, called HLA-DMA and HLA-

DMB, encodes a nonpolymorphic heterodimer class II-

like molecule, called HLA-DM that is involved in

peptide binding to class II molecules

• Between the class I and class II gene clusters are

genes that code for several components of the

complement system, for three structurally related

cytokines (TNF, lymphotoxin A, and lymphotoxin B),

and for some heat shock proteins

• The genes that encode these diverse proteins have

been called class III MHC genes

• Between HLA-C and HLA-A are many genes that are called the class I-like molecules because they resemble class I genes but they exhibit little or no polymorphism

• Some of these proteins are class IB, among the class IB molecules is HLA-G and HLA-H

• It also contains many pseudogenes

• There are β2 microglobulin -associated proteins other than MHC class I, these include the neonatal FC receptor and CD1 molecules

A more detailed look at MHC

kb

Class I Molecules

• MHC I class molecules are 45-kDa, single-chain glycoproteins that form a complex with 12-kDa β2 microglobulin

• Co-dominantly expressed genes at each of the three distinct “classical” class I loci, HLA-A, -B, and –C are highly polymorphic with over 100 possible alleles at each locus

• Up to six different class I molecules, two for each locus, are displayed on the surface of each nucleated cell

HLA Classe I

• All MHC class I molecules fold to produce a cleft that holds a peptide of eight to eleven amino acids, although the three dimensional configuration of the cleft are somewhat variable

• Some peptides load into clefts of some MHC class I molecules better than others which has major implications in the nature of the immune response

• In addition, a number of molecules (e.g. HLA-E, F, G, H) are structurally similar to classical MHC class I molecules, but are of much more limited variability and tissue distribution

• The functions of nonclassical MHC class I molecules are not yet fully clear, but in some cases they present carbohydrate as well as peptide fragments to gδ

T cells

MHC antigen-binding sites

Class II MHC Molecules• Expressed on few cell types: dendritic cells,

macrophages, B-cells, some epithelial cells of the

thymus, and by some activated T-cells

• Class II molecules are encoded by genes within the

DP, DQ, and DR regions of MHC

• Contained within each region are a and β loci (DPa,

DPβ, DQa, DQβ, DRa, and DRβ)

• After synthesis, MHC class II a and β chains associate

only with others encoded within the same region

HLA Class II

• In combination, the 32-to-38 kDa a and 29-to-32 kDa

β chains form a molecular complex that is very similar

to that of the class I complex, with a binding groove

available for holding short peptides

• The ends of the binding grooves of class II molecules

are more open than class I molecules and can

accommodate peptides of 18 to 20 amino acids in

length

• Like class I molecules, Class II molecules are highly

variable, and numerous allelic forms exist for each

locus (except DRa, which appears to be invariant)

• Genetic variation among class II molecules creates a

range of subtly varying binding grooves for which

antigen fragments compete

• An additional form of variation is available to class II

molecules because of their heterodimeric structure

• Termed cis- trans complementation, this diversity

stems from the fact that class IIa and β chains

combine after synthesis

• Thus, a DPa chain derived from a paternal

chromosome may combine with either DPβ chain

derived from a paternal or maternal chromosome

• Therefore, individuals heterozygous for both

DPa and DPβ (a common situation, given the

high level of variation in these genes) can

produce a greater range of class II dimer

combination than if they were homozygous at

DPa or DPβ or at both

• The range of different MHC I and MHC II

molecules expressed can affect the overall

immune capacity of an individual

Class III MHC Molecules

• Class III molecules are a subset of the

components of serum complement and

cytokines

• The C2 and C4 components, as well as the

regulatory factor B (BF) are encoded within the

complex

• The various components of complement are

synthesized by a variety of cells

Expression of MHC molecules

• Class I molecules are constitutively expressed on virtually all nucleated cells, whereas class II molecules are normally expressed on only dendritic cells, B lymphocytes, macrophages, and a few other cell types

• The expression of MHC molecules is increased by cytokines produced during both innate and adaptive immune responses

• IFNα, β, and g increase MHC class I expression

• IFNg increases the expression of MHC class II by macrophages and vascular endothelial cells and IL-4 by B cells

Properties of MHC

• Polymorphism: The most polymorphic genes; large number of alleles in each locus

• Co-dominance of gene expression: both alleles inherited are expressed maximizing the number of MHC molecules available for binding peptides for presentation to T cells

• The set of MHC alleles on each chromosome is called MHC haplotype which are commonly inherited together (more frequently than would be predicted by random assortment, a phenomenon called linkage disequilibrium)

MHC class I and class II are polymorphic [variability at a gene

locus at a frequency higher than predicted by chance (i.e., variability of alleles

in the species)]

The number of known alleles at various MHC

loci seems to increases over time (why?)

(62)

(80)

(89)

(108)

(8)

(12)

(19)

(20)

(25)

(35)

(45)

(56)

(16)

(20)

(20)

(25)

(122)

(239)

(323)

(440)

(111)

(207

)

(395

)

(559

)

1996

1999

2001

2004

2007Data in

our book

is from

2007

(37)

(50)

(93)

(150

)

(59)

(95)

(195

)

(303

)

(2)

(3)

MHC class I

MHC I a chainDPB, DQB and DRB

are the MHC II b

chain

DPA, DQA and DRA

are the MHC II a chain

MHC is

polymorphic and

expression is co-

dominant

What does this mean

for you and your

species?

for example, here is HLA

class I A gene expression

Although there

are thousands of

combinations in

the population*,

there are only 4

combinations

among siblings

414 known HLA-A alleles in humans (previous slide) but a maximum of 2 per person

Ab/r Ay/g

Ab/g Ar/y Ab/y Ar/g

*At A there are 414

known alleles so

there are (414)2 =

171,396 pair

combinations

possible in the

species (although

not all combinations

exist)

Because MHC

loci are

polymorphic,

individuals are

rarely

homozygous at

any of the

(polygenic) MHC

class I and II loci

Lots of

alleles in the

species In an individual,

several non-allelic

genes with essentially

the same function (B,

C and A are all MHC

class I and present

peptides to CTLs)

Ar

Ay

Br Cy Ap

Br Cy Ap

All expressed on

all nucleated cells

(co-dominant)

Major Histocompatibility Complex

• The major function of the molecules encoded by the MHC is to facilitate the display of unique molecular fragments on the surface of cells in an arrangement that permits their recognition by immune effectors such as T-lymphocytes.

Major Histocompatibility Complex

• The MHC molecule

accomplishes its major role in

immune recognition by

satisfying two distinct

molecular functions: the

binding of peptides (or in

some cases nonpeptidic

molecules) and the interaction

with T cells, usually via the αβ

T-cell receptor (TCR).

MHC I• In particular, cell surface MHC class I glycoproteins gather from the cell’s biosynthetic pathway fragments of proteins derived from infecting viruses, intracellular parasites, or self molecules, either normally expressed or dysregulated by tumorigenesis, and then display these molecular fragments at the cell surface.

Major Histocompatibility Complex (MHC):

A Summary

“A complex of genes encoding cell-surface

molecules that are required for antigen

presentation to T-cells…”

• Fundamentally important:– basis of self / not self distinction– presentation of processed antigen

• MHC-I (on nearly all nucleated cells)

MHC-II (on B-cells, macrophages, dendritic cells)

Major histocompatibility antigens

• MHC loci are highly polymorphic

• Many alternative alleles at a locus

• The loci are closely linked to each other

• A set of alleles is called a HAPLOTYPE

• One inherites a haplotype from mother and

another from father

• The alleles are codominantly expressed

What are the genetic mechanisms?

Nota bene: whatever are the genetic mechanisms, they must account for the huge diversity of “haplotypes”

“Haplotype”: “the set of alleles of linked genes present on one parental chromosome…” synteny

“Synteny”: the association of genes in a distinct region of a chromosome

What are the genetic mechanisms?

• Polygenecity

• Polymorphism

• Co-dominance

• Linkage disequilibrium

What does the “syntenic” organization

of a haplotype look like?

Remember:

polygenecity

polymorphism

co-dominance

Linkage disequilibrium

There are no rearrangements!

What is polygenecity?• Humans have DP, DQ, and DR “regions”

specifying a and b chains of MHC-II.

• Why are these called “regions”?

Inheritance of MHC alleles

Mother Father

A/B C/D

A/C A/D B/C B/D A/R1 R2/C R2/R1

R1=C-D recombination

R2=A-B recombination

Possible children of parents with HLA haplotype A/B and C/D

MHC genes control immune responsiveness

to protein antigens• For almost 20 years after the MHC was discovered, its

only documented role was in graft rejection

• This was a puzzle to immunologists because transplantation is not a normal phenomenon, and there was no obvious reason why a set of genes should be preserved through evolution if the only function of the genes was to control the rejection of foreign tissue grafts

• In the 1960’s and 1970’s, it was discovered that MHC genes are of fundamental importance for all immune responses to protein antigens

• This responsiveness was shown to be inherited

as a dominant trait and the relevant genes were

called immune response (IR) genes and they

were all found to map to the MHC

• We now know that IR genes are in fact MHC

genes that encode MHC molecules which differ

in their ability to bind and display peptides

derived from various protein antigens

Binding of Peptides to MHC

Molecules• For a protein to be immunogenic in an individual, it

must contain peptides that can bind to the MHC

molecules of that individual

• It has become apparent that the binding of peptides to

MHC molecules is fundamentally different from the

binding of antigens to the antigen receptor of B and T

lymphocytes

• MHC molecules show a broad specificity for peptide

binding, and the fine specificity of antigen recognition

resides largely in the antigen receptors of T-cells

• Each class I or class II MHC molecule has a

single peptide-binding cleft that can

accommodate many different peptides

• It is not surprising that a single MHC molecule

can bind multiple peptides because each

individual contains only a few different MHC

molecules (6 for class I and 10-20 for class II

molecules in a heterozygous individual)

• These molecules must be able to present

peptides from the enormous number of protein

antigens that one is likely to encounter

• The peptides that bind to MHC molecules share structural features that promote this interaction

• One of these features is the size (class I accommodate 8-11 amino acids whereas class II can accommodate 10-30 residues long)

• Another factor is the presence of certain amino acid residues that bind certain allelic forms of an MHC-molecule that allows complementarity.

• These residues are distinct from those recognized by TCR

• The association of antigenic peptides and MHC molecules is a saturable, low affinity interaction with a slow on-rate and a very slow off-rate

• Once bound, peptides may remain associated for hours to many days ensuring interactions with antigen-specific T-cells, however, binding is noncovalent

• The MHC molecules of an individual do not discriminate between foreign peptides and peptides derived from self

MHC Supertypes

• Many of the different HLA molecules have similar specificities

• HLA molecules with similar specificities can be grouped together

• Methods to define supertypes

• Structural similarities

• Primary (sequence)

• Tertiary (structure)

• Shared peptide binding motifs

• Identification of cross-reacting peptides

• Ability to generate methods that can predict cross-binding peptides

HLA polymorphism - supertypes

• Each HLA molecule within a supertype binds essentially the same peptides

•Nine major HLA class I supertypes have been defined

• HLA-A1, A2, A3, A24,B7, B27, B44, B58, B62

Supertypes Phenotype frequencies

83 % 86 % 88 % 88 % 86 % 86%

+A1, A24, B44 100 %98 % 100 % 100 % 99 % 99 %

+B27, B58, B62 100 %100 % 100 % 100 % 100 % 100 %

HLA polymorphism - frequencies

MHC: CD Interaction

- The nonpolymorphic Ig-like domains of MHC

molecules contain sites for the T cell molecules

CD4 and CD8 (a3 in class I and β2 in class II)

- A loop in β2 segment of class II molecules is

the binding site for CD4 similar to the binding

site of CD8 to a3 of class I

MHC class I MHC class II