Immunology

1. The Major Histocompatibility
Complex and Antigen
Presentation

2. • Both T and B cells use surface molecules to
recognize antigen; they accomplish this in very
different ways.
• Antibodies or B-cell receptors can recognize an
antigen alone;
• T-cell receptors only recognize pieces of antigen
that are positioned on the surface of other cells.
• These antigen pieces are held within the binding
groove of a cell surface protein called the major
histocompatibility complex (MHC) molecule,
encoded by a cluster of genes collectively called
the MHC locus.

3. • These fragments are generated inside the cell
following antigen digestion, and the complex of
the antigenic peptide plus MHC molecule then
appears on the cell surface.
• MHC molecules thus act as a cell surface vessel
for holding and displaying fragments of antigen
so that approaching T cells can engage with this
molecular complex via their T-cell receptors.

4. • The fact that the genes in this (MHC) region
encode proteins that determine whether a
tissue transplanted between two individuals
will be accepted or rejected, gave MHC its
name.
• The pioneering work of Benacerraf, Dausset,
and Snell helped to characterize the functions
controlled by the MHC, specifically, organ
transplant fate and the immune responses to
antigen, resulting in the 1980 Nobel Prize in
Medicine and Physiology for the trio.

5. • Follow-up studies by Rolf Zinkernagel and
Peter Doherty illustrated that the proteins
encoded by these genes play a seminal role in
adaptive immunity by showing that T cells
recognize MHC proteins as well as antigen.
• Structural studies done by Don Wiley and
others showed that different MHC proteins
bind and present different antigen fragments.

6. • There are many alleles of most MHC genes,
• the specific alleles one inherits play a
significant role in susceptibility to disease,
including the development of autoimmunity.
• Autoimmunity is the system of immune
responses of an organism against its own
healthy cells and tissues.
• Any disease that results from such an
aberrant immune response is termed
an autoimmune disease.

7. • There are two main classes of MHC
molecules:
– Class I and Class II.
• These two molecules are very similar in their
final quaternary structure, although they
differ in how they create these shapes.
• They also differ
– in terms of which cells express them and
– in the source of the antigens they present to T
cells.

8. • Class I molecules
– are present on all nucleated cells in the body
– specialize in presenting antigens that originate from
the cytosol, such as viral proteins.
• MHC class I molecule presents the antigenic
peptide to CD8+ T cells, which recognize and kill
cells expressing such intracellular antigens.

9. • Class II MHC molecules, in contrast,
– are expressed almost exclusively on a subset of
leukocytes called antigen-presenting cells (APCs)
– specialize in presenting antigens from extracellular
spaces that have been engulfed by these cells,
such as fungi and extracellular bacteria.
• MHC class II molecule presents the antigenic
peptide to CD4+ T cells, once expressed on the
cell surface
• CD4+ T cells then become activated and go on
to stimulate immunity directed primarily
toward destroying extracellular invaders.

10. The Structure and Function of MHC Molecules
• Class I and class II MHC molecules are
membrane-bound glycoproteins that are
closely related in both structure and function
• These function as highly specialized antigen-
presenting molecules with grooves.
• These grooves
– form unusually stable complexes with peptide
ligands, and
– Display them on the cell surface for recognition by
T cells via T-cell receptor (TCR) engagement.

11. • Class III MHC molecules, in contrast,
– are a group of unrelated proteins
– do not share structural similarity or function with
class I and II molecules
– although many of them do participate in other
aspects of the immune response.

12. Class I Molecules Have a Glycoprotein Heavy Chain and
a Small Protein Light Chain
• Two polypeptides assemble to form a single class I
MHC molecule:
– a 45-kilodalton (kDa) α chain and
– a 12-kDa β2-microglobulin molecule.
• The α chain is organized into
– three external domains (α1, α2, and α3), each
approximately 90 amino acids long;
– a transmembrane domain of about 25 hydrophobic
amino acids followed by a short stretch of charged
(hydrophilic) amino acids;
– and a cytoplasmic anchor segment of 30 amino acids.

13. • Its companion, β2-microglobulin,
– is similar in size and organization to the α3
domain.
– does not contain a transmembrane region and
– is non-covalently bound to the MHC class I chain.
• Sequence data reveal strong homology
between the α3 domain of MHC class I, β2-
microglobulin, and the constant-region
domains found in immunoglobulins.

16. • The α1 and α2 domains interact to form a
platform of eight antiparallel β strands spanned
by two long α–helical regions.
• The structure forms a deep groove, or cleft ,
with the long α helices as sides and the β strands
of the sheet as the bottom.
• This peptide-binding groove
– is located on the top surface of the class I MHC
molecule, and
– it is large enough to bind a peptide of 8 to 10 amino
acids.

17. • The α3 domain and β2-microglobulin are organized into
two β pleated sheets each formed by antiparallel
strands of amino acids, known as the immunoglobulin
fold.
• So class I MHC molecules and β2-microglobulin are
classified as members of the immunoglobulin
superfamily .
• The α3 domain appears to be highly conserved among
class I MHC molecules and contains a sequence that
interacts strongly with the CD8 cell surface molecule
found on TC cells.
• All three molecules (class I α chain, β2-microglobulin,
and a peptide) are essential to the proper folding and
expression of the MHC-peptide complex on the cell
surface.

18. Class II Molecules Have Two Non-Identical
Glycoprotein Chains
• Class II MHC molecules contain two different
polypeptide chains which associate by non
covalent interactions
– a 33-kDa α chain and
– a 28-kDa β chain
• Like class I chains, class II MHC molecules
– are membrane bound glycoproteins that contain
external domains,
– a transmembrane segment, and
– a cytoplasmic anchor segment.
• Each chain in a class II molecule contains two
external domains: α1 and α2 domains in one
chain and β1 and β2 domains in the other.

20. • The membrane-proximal α2 and β2 domains
bear sequence similarity to the
immunoglobulin-fold structure, hence, are
also classified in the immunoglobulin
superfamily.
• The α1 and β1 domains form the peptide-
binding groove for processed antigen .
• Although similar to the peptide-binding
groove of MHC class I, this groove is formed
by the association of two separate chains.

21. • Despite the structural similarity between these
two classes of molecule, the two structures are
encoded quite differentially
• The final quaternary structure is similar and
retains the same overall function: the ability to
bind antigen and present it to T cells.
• The peptide-binding groove of class II molecules,
like that found in class I molecules, is composed
of a floor of eight antiparallel β strands and sides
of antiparallel α helices, where peptides typically
ranging from 13 to 18 amino acids can bind.

22. • The class II molecule lacks the conserved
residues in the class I molecule that bind to
the terminal amino acids of short antigenic
peptides, and therefore forms more of an
open pocket.
• In this way, class I presents more of a socket-
like opening, whereas class II possesses an
open-ended groove.

27. Class I and II Molecules Exhibit Polymorphism in
the Region That Binds to Peptides
• Several hundred different allelic variants of class I
and II MHC molecules have been identified in
humans.
• Any one individual, however, expresses only a
small number of these molecules—up to six
different class I molecules and 12 or more
different class II molecules.
• This limited number of MHC molecules must be
able to present an enormous array of different
antigenic peptides to T cells, permitting the
immune system to respond specifically to a wide
variety of antigenic challenges.

28. • A given MHC molecule can bind numerous
different peptides, and some peptides can
bind to several different MHC molecules.
• Because of this broad specificity, the binding
between a peptide and an MHC molecule is
often referred to as “promiscuous.”
• Thus, peptide binding by class I and II
molecules does not exhibit the fine specificity
characteristic of antigen binding by antibodies
and T-cell receptors.

29. General Organization and Inheritance of the MHC
• MHC molecules must be able to bind a wide variety of
antigens, and they must do so with relatively strong
affinity.
• They meet this challenge using very different strategies.
• MHC molecules have opted for a combination of
peptide binding promiscuity and the expression of
several different MHC molecules on every cell
• Using this clever combined strategy, the immune
system has evolved a way of maximizing the chances
that many different regions, or epitopes, of an antigen
will be recognized.

30. • Every vertebrate species studied to date possesses
the tightly linked cluster of genes that constitute
the MHC.
• MHC gene cluster studies originated when it was
found that the rejection of foreign tissue
transplanted between individuals in a species was
the result of an immune response mounted
against cell surface molecules, now called
histocompatibility antigens.
• In the mid-1930s, Peter Gorer, who was using
inbred strains of mice to identify blood-group
antigens, identified four groups of genes that
encode blood-cell antigens.

31. • He designated these I - IV.
• Work carried out in the 1940s and 1950s by
Gorer and George Snell established that antigens
encoded by the genes in the group designated as
II took part in the rejection of transplanted
tumors and other tissue.
• Snell called these histocompatibility genes; their
current designation as histocompatibility-2 (H-2,
or MHC) genes in the mouse was in reference to
Gorer’s original group II blood-cell antigens.

32. The MHC Locus Encodes Three Major Classes of
Molecules
• The major histocompatibility complex is a
collection of genes arrayed within a long
continuous stretch of DNA on
• chromosome 6 in humans
• chromosome 17 in mice;
• These regions have been most studied in these
two species
• The MHC is referred to as the
– human leukocyte antigen (HLA) complex in humans
– H-2 complex in mice

33. • The arrangement of genes is somewhat different in the two
species
• In both cases (humans and mice), the MHC genes are
organized into regions encoding three classes of molecules:
– Class I MHC genes encode glycoproteins expressed on the
surface of nearly all nucleated cells; the major function of the
class I gene products is presentation of endogenous peptide
antigens to CD8 T cells.
– Class II MHC genes encode glycoproteins expressed
predominantly on APCs (macrophages, dendritic cells, and B
cells), where they primarily present exogenous antigenic
peptides to CD4 T cells.
– Class III MHC genes encode several different proteins, some
with immune functions, including
• components of the complement system (C4, C2, and factor B) and
• molecules involved in inflammation (inflammatory cytokines, including
the two tumor necrosis factor proteins, TNF- α and TNF-β, also called
lymphotoxin α )

35. Inheritance of MHC

36. • Class I MHC molecules were the first
discovered and are expressed in the widest
range of cell types.
• In mouse, the region encoding Class I MHC
molecules is noncontinuous, interrupted by
the class II and III regions but not in humans
• There are two chains to the MHC class I
molecule: the more variable and antigen-
binding α chain and the common β-2-
microglobulin chain.

37. • The α chain molecules are encoded
–by the K and D regions in mice, with an
additional L region found in some strains,
and
–by the A, B, and C loci in humans.
• β 2-microglobulin is encoded by a gene
outside the MHC.
• Collectively, these are referred to as classical
class I molecules; all posses the functional
capability of presenting protein fragments of
antigen to T cells.

38. • Additional genes or groups of genes within the class I
region of both mouse and human encode nonclassical
class I molecules that are
– expressed only in specific cell types and
– have more specialized functions.
• Some appear to play a role in self/nonself
discrimination. One example is the class I HLA-G
molecule.
• These are present on fetal cells at the maternal-fetal
interface and inhibit rejection by maternal CD8 T cells
by protecting the fetus from identification as foreign,
which may occur when paternally derived antigens
begin to appear on the developing fetus.

39. • Class II MHC molecules are encoded by the
– IA and IE regions in mice
– DP, DQ, and DR regions in humans.
• The terminology is somewhat confusing, since
the D region in mice encodes class I MHC
molecules, whereas DP, DQ, and DR in humans
refers to class II genes and molecules.

40. • The class II region of the MHC locus encodes both the α
chain and the β chain of a particular class II MHC molecule,
and in some cases multiple genes are present for either or
both chains.
• For example, individuals can inherit up to four functional
DR β-chain genes, and all of these are expressed
simultaneously in the cell.
• This allows any DR α -chain gene product to pair with any
DR β chain product.
• Since the antigen-binding groove of class II is formed by a
combination of the α and β chains, this creates several
unique antigen-presenting DR molecules on the cell.

41. • As with the class I loci, additional nonclassical class II
molecules with specialized immune functions are
encoded within this region.
• For instance, human non classical class II genes
designated DM and DO have been identified.
• The DM genes encode a class II–like molecule (HLA-
DM) that
– facilitates the loading of antigenic peptides into class II
MHC molecules.
• Class II DO molecules, expressed only in the thymus
and on mature B cells,
– serve as regulators of class II antigen processing.

42. • Class III MHC region encodes several molecules
that are critical to immune function but have
little in common with class I or II molecules.
• Class III products include
– the complement components C4, C2, and factor B
– several inflammatory cytokines, including the two
tumor necrosis factor proteins (TNF- α and
Lymphotoxin- α [TNF-β]).

43. • Allelic variants of some of these class III MHC
gene products have been linked to certain
diseases.
• For example, polymorphisms within the TNF-α
gene, which encodes a cytokine involved in
many immune processes, have been linked to
– susceptibility to certain infectious diseases and
– some forms of autoimmunity, including Crohn’s
disease and rheumatic arthritis.

45. Expression of MHC Class II Molecules Is
Primarily Restricted to Antigen-Presenting
Cells
• MHC class II molecules are found on a much more
restricted set of cells than class I MHC molecules
• Cells that display peptides associated with class II
MHC molecules and present these peptides to CD4
TH cells, are called antigen-presenting cells
(APCs), and these cells are primarily certain types
of leukocytes.
• APCs are specialized for their ability to alert the
immune system to the presence of an invader and
drive the activation of T cell responses.

46. • Among the various APCs, marked differences in
the level of MHC class II expression have been
observed.
• In some cases, class II expression depends on the
cell’s differentiation stage or level of activation
(such as in macrophages).
• APC activation usually occurs following
interaction with a pathogen and/or via cytokine
signaling, which then induces significant
increases in MHC class II expression.

47. • A variety of cells can function as bonafide APCs.
• Their distinguishing feature is their ability to
express class II MHC molecules and to deliver a
costimulatory, or second activating signal, to T
cells.
• Three cell types are known to have these
characteristics and are thus often referred to as
professional antigen-presenting cells (pAPCs):
– dendritic cells, macrophages, and B lymphocytes.
• These cells differ from one another
– in their mechanisms of antigen uptake,
– in whether they constitutively express class II MHC
molecules, and
– in their costimulatory activity, as follows:

48. – Dendritic cells are generally viewed as the most
effective of the APCs as they constitutively express a
high levels of class II MHC molecules and have inherent
costimulatory activity, they can activate naïve TH cells.
– Macrophages must be activated (e.g., via TLR signaling)
before they express class II MHC molecules or
costimulatory membrane molecules such as CD80/86.
– B cells constitutively express class II MHC molecules and
posses antigen-specific surface receptors, making them
particularly efficient at capturing and presenting their
cognate antigen.
– However, they must be activated by, for example,
antigen, cytokines, or pathogen-associated molecular
patterns (PAMPs), before they express the
costimulatory molecules required for activating naïve TH
cells.

49. • Several other cell types, classified as nonprofessional
APCs, can be induced to express class II MHC
molecules and/or a costimulatory signal under certain
conditions.
• E.g.
– Fibroblasts (skin),
– glial cells(brain),
– pancreatic beta cells,
– thymic epithelial cells,
– thyroid epithelial cells,
– vascular endothelial cells.
• These cells can be deputized for professional antigen
presentation for short periods and in particular
situations, such as during a sustained inflammatory
response.

50. S U M M A R Y
• The major histocompatibility complex (MHC) encodes class I
and II molecules, which function in antigen presentation to T
cells, and class III molecules, which have diverse functions.
• Class I MHC molecules consist of a large glycoprotein α
chain encoded by an MHC gene, and β2-microglobulin, a
protein with a single domain that is encoded elsewhere.
• Class II MHC molecules are composed of two noncovalently
associated glycoproteins, the α and β chains, encoded by
separate MHC genes.
• MHC genes are tightly linked and generally inherited as a
unit from parents; these linked units are called haplotypes.

51. • MHC genes are polymorphic (many alleles exist for
each gene in the population), polygenic (several
different MHC genes exist in an individual), and
codominantly expressed (both maternal and paternal
copies).
• MHC alleles influence the fragments of antigen that are
presented to the immune system, thereby influencing
susceptibility to a number of diseases.
• Class I molecules are expressed on most nucleated
cells; class II molecules are restricted to B cells,
macrophages, and dendritic cells (pAPCs).

52. • In most cases, class I molecules present processed
endogenous antigen to CD8 TC cells and class II
molecules present processed exogenous antigen to CD4
TH cells.
• Endogenous antigens are degraded into peptides within
the cytosol by proteasomes, assemble with class I
molecules in the RER, and are presented on the
membrane to CD8 TC cells. This is the endogenous
processing and presentation pathway.
• Exogenous antigens are internalized and degraded
within the acidic endocytic compartments and
subsequently combine with class II molecules for
presentation to CD4 TH cells. This is the exogenous
processing and presentation pathway.

53. • Peptide binding to class II molecules involves
replacing a fragment of invariant chain in the
binding groove by a process catalyzed by
nonclassical MHC molecule HLA-DM.
• In some cases, exogenous antigens in certain cell
types (mainly DCs) can gain access to class I
presentation pathways in a process called cross-
presentation.
• Presentation of nonpeptide (lipid and lipid-
linked) antigens derived from pathogens involves
the nonclassical class I–like CD1 molecules.

55. • Fibroblasts skin cells within the dermis layer of skin which
are responsible for generating connective tissue and
allowing the skin to recover from injury
• The glial cells surround neurons and provide support for
and insulation between them. Glial cells are the most
abundant cell types in the central nervous system.
• Within the pancreas there are areas that are called the
islets of Langerhans. The beta cells constitute the
predominant type of cell in the islets. The beta cells are
particularly important because they make insulin.
Degeneration of the beta cells is the main cause of type I
(insulin-dependent) diabetes mellitus.