Major Histocompatibility Complex

Genetic basis of transplant rejection

The MHC was discovered as the genetic locus whose products are responsible for rapid rejection of tissue grafts exchanged between inbred strains of mice. Snell's group linked to a gene on chromosome 17 encoding a blood group antigen called antigen II, and therefore this region was named histocompatibility-2 or simply H-2.

Genomic map of mouse and human MHC

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) MHC-III (Components of complement system)

Antigen recognition by T cells requires peptide antigens and presenting cells that express MHC molecules

Soluble native Ag Cell surface native Ag

Soluble peptides of Ag

No T cell response

No T cell response

No T cell response

Y
Cell surface peptides of Ag No T cell response

Cell surface peptides of Ag presented by cells that express MHC antigens

T cell response

Schematic maps of human and mouse MHCloci

MHC Genes Are Polymorphic

MHC Alleles Are Codominantly Expressed

Both mother and father alleles are expressed

However, Crossover Rate Is Low

0.5% crossover rate Inherited as 2 sets (one from father, one from mother) Haplotype refers to set from mother or father

MHC Products Are Highly Polymorphic

Vary considerably from person to person

Class I MHC Molecule

Comprised of 2 molecules

1 2m

chain (45 kDa), transmembrane 2-microglobulin (12 kDa) Non-covalently associated with each other

Association Of Chain and 2 Is Required For Surface Expression Chain Made Up Of 3 Domains (1, 2 and 3) 2-microglobulin Similar To 3 1 And 2 Form Peptide Binding Cleft
Fits peptide of about 8-10 a/a long

3 Highly Conserved Among MHC I Molecules

Interacts with CD8 (TC) molecule

Structure of MHC class I molecules

1 and 2 domains form two segmented -helices on eight anti-parallel -strands to form an antigen-binding cleft.

Chains

Structures

Properties of the inner faces of the helices and floor of the cleft determine which peptides bind to the MHC molecule

Class II MHC Molecule

Comprised of and chains
1 1
chain and chain associate non-covalently

and chains made up of domains

1 and 2 ( chain) 1 and 2 ( chain)

1and 1 Form Antigen Binding Cleft

Fits peptide of about 13-18 a/a long

CD4 Molecule Binds 2/2 domains

MHC class II molecule structure

Peptide -chain

-chain

Cleft is made of both and chains

MHC-binding peptides
Each human usually expresses: 6 types of MHC class I (A, B, C) and 12 types of MHC class II (DR, DP,DQ)

The number of different T cell antigen receptors is estimated to be

1,000,000,000,000,000
Each of which may potentially recognise a different peptide antigen

How can 18 invariant molecules have the capacity to bind to 1,000,000,000,000,000 different peptides?

Promiscuous

Floppy

Compact
Allows a single type of MHC molecule to bind many different peptides bind peptides with high affinity form stable complexes at the cell surface Export only molecules that have captured a peptide to the cell surface

Cleft geometry

MHC class I

MHC class II
Peptide is held in the cleft by non-covalent forces

Anchor residues in nonameric peptides eluted from Class I MHC molecules

Peptides bound to a particular type of MHC class I molecule have conserved patterns of amino acids

Peptide antigen binding to MHC class II molecules

Negatively charged Hydrophobic

I S N Q L T L D S N T K Y F H K I P D N L F K S D G R I K Y T L N A T K Y G N M T E D H V N H L L Q N A G K F A I R P Y K K S N P I I R T V V F L L L L A Y K V P E T S L S T F D Y I A S G F R Q G G A S Q P P E V T V L T N S P V Y L R E P N V Y G Y T S Y Y F S W A E L T G H G A R T S T Y P T T D Y
Anchor residues are not localised at the N and C termini Ends of the peptide are in extended conformation and may be trimmed Motifs are less clear than in class I-binding peptides Pockets are more permissive

Polymorphism in the MHC affects peptide antigen binding

MHC allele A

MHC allele B

Changes in the pockets, walls and floor of the peptide binding cleft alter peptide MHC interactions and determine which peptides bind. S Y I P S A K I MHC allele A

R G Y V Y Q Q L MHC allele B Products of different MHC alleles bind a different repertoire of peptides

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)]
(122) (239) (323) (440) (62) (80) (89) (108)

1996 1999 2001 2004 2007

Data in our book is from 2007

(111) (207) (395) (559)

(8) (12) (19) (20)

(25) (35) (45) (56)

(16) (20) (20) (25)

(37) (50) (93) (150)

(59) (95) (195) (303)

(2) (3)

DPB, DQB and DRB are the MHC II chain

DPA, DQA and DRA are the MHC II chain

MHC I chain

The number of known alleles at various MHC loci seems to increases over time (why?)

MHC class I

MHC class I and class II are polygenic

(several loci encoding products with essentially the same function)

DP DM LMP/TAP DQ

1 3 4 5

DR

B C

MHC Class II Class III

MHC Class I

Polygeny
CLASS I: 3 types HLA-A, HLA-B, HLA-C (sometimes called class Ia genes) CLASS II: 3 types HLA-DP HLA-DQ HLA-DR. 3 extra DR genes in some individuals can allow 3 extra HLADR molecules Maximum of 9 types of antigen presenting molecule allow interaction with a wide range of peptides

How diverse are MHC molecules in the population?

IF
each individual had 6 types of MHC the alleles of each MHC type were randomly distributed in the population any of the 1,200 alleles could be present with any other allele ~6 x 1015 unique combinations In reality MHC alleles are NOT randomly distributed in the population Alleles segregate with lineage and race (Linkage disequilibrium) Frequency (%) Group of alleles HLA-A1 HLA- A2 HLA- A3 HLA- A28 HLA- A36 CAU AFR ASI 4.48 24.63 2.64 1.76 0.01

15.18 5.72 28.65 18.88 13.38 8.44 4.46 0.02 9.92 1.88

Most polymorphisms are point mutations

Recombination, point mutation & gene conversion
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 ------------------------------------------------------------TTC ------------------------------------------------------------GAC ------------------------------------------------------------AGC ------------------------------------------------------------GAC -------------------------------------------------------------

Silent
GTG ------------------------------------------------------------GGG --A ------------------------A --A ------A ------------------------A --GAG ------------------------------------------------------------TTC ------------------------------------------------------------CGG ------------------------------------------------------------GCG ------------------------------------------------------------GTG ------------------------------------------------------------ACG ------------------------------------------------------------GAG ------------------------------------------------------------CTG ------------------------------------------------------------GGG ------------------------------------------------------------CGG -------------------------------------------------------------

E-A A-D A-E

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 ------------------------------------------------------------TGG ------------------------------------------------------------AAC ------------------------------------------------------------AGC ------------------------------------------------------------CAG ------------------------------------------------------------AAG ------------------------------------------------------------GAC -------------------------------------------------------------

I-L
ATC --------C-------C-------C-C---C-C---------C-C---------C-----CTG ------------------------------------------------------------GAG ------------------------------------------------------------GAG -------------------------------------------------------------

Non-classical MHC genes

Self-peptides (Formylated methionine) derived from subunit of NADH dehrogenase

MHC-Linked Diseases
Defects in MHC gene expression lead to immunodeficiencies (MHC molecules are required for both T cell development and activation) Some MHC alleles are associated with susceptibility or resistance to autoimmune diseases

MHC-Linked Immunodeficiencies
Bare Lymphocyte Syndromes lead to loss of MHC molecule expression:
Defects in TAP genes prevent MHC Class I protein surface expression (even though MHC proteins are normal), so no CD8+ T cells - surprisingly mild immunodeficiency (respiratory and skin infections)

Defects in TFs controlling Class II gene expression (CIITA, RFXANK, RFX5, RFXAP) block CD4+ T cell development - result in SCID (severe combined immunodeficiency)

TYPING METHODS
SEROLOGY used to be the gold standard.
Now being superceded by molecular techniques as they become more robust and time efficient

CELLULAR rarely used now. Orginally used for

Class II typing

MOLECULAR fast becoming the method of choice. Many laboratories test of choice.

SEROLOGY
Complement Dependent Cytotoxicity (CDC) Viable peripheral blood lymphocytes
Viable lymphocytes are incubated with HLA specific antibodies. If the specific antigen is present on the cell the antibody is bound. Rabbit serum as a source of complement is added, incubate. If antibody is bound to the HLA antigen on the cell surface it activates the complement which damages the cell membrane making it permeable to vital stains.

Nomenclature
HLA-A identifies HLA A locus HLA-A1 serologically defined antigen HLA-A* asterisk denotes HLA alleles defined by molecular methods HLA-A*01 2 digit resolution denotes a group of alleles corresponds usually to serological group low resolution HLA-A*0101 4 digit resolution sequence variation between alleles results in amino acid substitutions HLA-A010101 6 digit resolution non coding variation: sequence changes synonymous no amino acid substitution

 HLA-A01010101 8 digit resolution sequence variation occurs within the introns or 5 / 3 extremities of the gene HLA-A01010102N Null allele Alphabetical suffix N Null allele L Low level expression A Aberrant expression C Molecule present in cytoplasm only S Secreted molecule present only as soluble form

Cellular typing
Not / Rarely used by laboratories these days. Requires panels of homozygous typing cells. Cell culture method therefore takes a long time. Labour intensive involves use of radioisotopes.

T cell recognition of a peptide-MHC complex

Major Histocompatibility Complex MHC

In mice the MHC is called H-2
Rapid graft rejection between strains segregated with Antigen-2, encoded as part of the MHC haplotype
(A set of linked genes inherited as a unit)

In humans the MHC is called the Human Leukocyte Antigen system HLA
Only monozygous twins are identical at the HLA locus The human population is extensively out bred MHC genetics in humans is extremely complex

Inbred mice identical at H-2 did not reject skin grafts from each other MHC genetics in mice is simplified by inbred strains

Major Histocompatibility Complex (MHC)

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) MHC-III (Components of complement system)

Replacement substitutions occur at a higher frequency than silent substitution

Suggests that selective pressures may operate on MHC polymorphism Evolution of pathogens to evade MHC-mediated antigen presentation 60% of individuals in south east China & Papua New Guinea express HLA-A11

HLA-A11 binds an important peptide of Epstein Barr Virus Many EBV isolates from these areas have mutated this peptide so that it can not bind to HLA-A11 MHC molecules

Evolution of the MHC to eliminate pathogens In west Africa where malaria is endemic HLA-B53 is commonly associated with recovery from a potentially lethal form of malaria

MHC directs the response of T cells to foreign antigens

MHC antigens PRESENT foreign antigens to T cells

YY YY

Ag

Blocking anti-MHC antibody

Anti

response

No anti

response

YY YY Y

T TT T T

Ag

HLA - Typing