MHC - Denzin 4/4/16

Question 1

activation of T cells

Answer 1

T cells activated by interaction of

• MHC on antigen-presenting cells
• TCR on T cells

T cells are of two subtypes

• helper CD4 : help immune system - recog class II MHC
• cytotoxic Cd8 : become activated and kill - recog class I MHC

Question 2

MHC basics

MHC complex in mice and humans

Answer 2

• associated with transplantation rejection, recognition/response to other man-made and natural antigens
• bind peptides (have peptide-binding region)
• MHC antigens divided into 2 types: class I and class II
  
  • Class I : polymorphic alpha chain + non-polymorphic beta chain (beta2 microglobulin) - recognized by CD8 T cells
  • Class II : polmorphic alpha + polymorphic beta chains - recognized by CD4 T cells

mouse MHC : H-2

human MHC : HLA (human leukocte antigens)

Question 3

MHC nomenclature/genes

mice

Answer 3

H-2

chr17 : 3 polymorphic Class I genes → alpha chains K, D, L

chr2 : b2-microglobulin gene (not part of MHC locus)

chr17 : 4 polymorphic Class II genes → 2 alpha + 2 beta (make A and E class II antigens)

• class II region also contains non-polymorphic genes

*MHC locus also contains class III genes (some related to antigen processing, MHC-peptide complex formation; some unrealted to MHC fx)

Question 4

MHC nomenclature/genes

humans

Answer 4

HLA

chr6 : 3 polymorphic Class I genes → A, B, C

chr15 : b2-microglobulin gene (not part of MHC locus)

chr6 : 3 polymorphic Class II genes → DP, DQ, DR

• class II region also contains non-polymorphic genes (DM, DO, LMP, TAP)

*MHC locus also contains class III genes (some related to antigen processing, MHC-peptide complex formation; some unrealted to MHC fx)

**invariant chain is on another chromosome (occupies binding site of MHC II, prevents it from binding peptides in ER until it’s replaced with endocytosed exogenous peptide in the endosome)

Question 5

MHC haplotype

Answer 5

particular combo of MHC alleles on a chromosome

in mice…

• inbred strain: all members have same haplotype (designated by small letter - b, d, k, q)
• congenic strains: endogenous MHC replaced by entire MHC locus from another strain
• recombinant strains: (only) a portion of the endogenous MHC complex is replaced by MHC of another haplotype

in humans…

barring identical twins, each individual is a unique haplotype → nearly infinite number of haplotypes

Question 6

MHC expression

Class I vs Class II

Answer 6

MHC class I antigens : expressed on all nucleated cells in body

• virus-infected cells

MHC class II : normally expressed only on APCs

• system that activates/controls immune response
• however, can be induced on “non-professional” APCs under certain conds

Question 7

what is presented by MHC?

Answer 7

division of labor between class I and class II molecules

class I (any cell) presents endogenous antigens (peptides from proteins synth’d within cell) → CD8

ex. cytosolic pathogens (viruses)
* trigger cell death

class II (macrophages) presents exogenous antigens (peptides from endocytosed proteins) → CD4

ex. intravesicular pathogens, extracellular pathogens/toxins (bacteria, etc)

• trigger activation of CD4 T cells → kill intracellular patho
• trigger activation of B cells → secrete Ig to eliminate extravesicular patho/toxin

Question 8

MHC I molecule structure

Answer 8

heavy alpha chain (alpha 1 + alpha 2 = peptide binding region; also alpha 3)

+

beta2-microglobulin

*generally, ends of the peptide binding region are shut (closed groove) → restricts the length of peptide that can be bound to approx 7-10 a.a.

Question 9

MHC II molecule structure

Answer 9

heterodimer (alpha chain and beta chain)

two alpha subunits + two beta subunits

alpha 1 + beta 1 = peptide binding region

*peptide binding region is an open cleft (open groove) → length of peptide that can be bound approx 12-24 a.a.

Question 10

peptide binding by MHC molecules

Answer 10

MHC molecules have to bind (ideally) every possible antigen that comes through the body → need to be able to bind a huge variety of peptides

• unstable when a peptide is not bound (stable binding prevents peptide exchange at cell surface to avoid messing with function!)

binding to MHC is restricted at only a few anchor residues of peptide being bound (all other residues can vary)

• usually two pockets in peptide binding groove of MHC
• rest of the antigen is available to TCR to bind to

implication: there’s a direct relationship between peptide seq and the MHC I allele that will bind it → motifs (can be used to identify epitopes that will bind MHC)
* strong for MHC I, weaker for MHC II

**MHC alleles are highly polymorphic (likelihood of homozygosity at a locus is unlikely) → capacity to bind v diverse group of molecules

Question 11

MHC I peptide “loading”

Answer 11

specialized for viruses (but also accessed by bacteria)

• viruses synth’d in cytoplasm making proteins are eventually turned over/misfolded → proteins are degraded by proteasome in cytosol into peptides
• peptides are transported into ER via TAP (transporter associated with antigen) → forms pore in ER which allows peptide translocation into ER
• peptide-MHC I complex is assembled with affinity-editing and trimming steps
  
  • TAPASIN: bridge betwen TAP and MHC I, edits peptide repertoire to make sure only high affinity peptides are presented
  • ERAP: trims peptides to correct size
• peptide-MHC complex is presented on cell surface for CD8 activation

Question 12

MHC II peptide “loading”

Answer 12

protein particles on bacteria, viruses, basically anything that can be endocytosed

• protein antigen particles endocytosed into endosome and processed into peptides (endosomal/lysosomal enzymes)
• MHC II molecules are synth’d in cytosol, processed in ER, transported to endosome
  
  • invariant chain binds to MHC II, facilitates transport from ER to endosome; invariant chain is protease-sensitive, so will be degraded quick, buuuut specific portion CLIP (class II assoc invariant chain peptides) remains bound to peptide binding groove to prevent premature peptide binding
• HLA-DM associates with MHC II-CLIP in endosome (along with other resident and specialized proteases) to degrade CLIP
  
  • DM edits peptide repertoire to guarantee high affinity peptide presentation
• peptides becomes associated with MHC II and peptide-MHC complexes are presented on cell surface for CD4 activation

Question 13

antigen presenting cells

Answer 13

• collect proteins (some from disease-producing pathos)
• break proteins down into peptides (approx 8-15 a.a.s)
• present MHC-peptide complexes to T cells, enabling them to respond if req

key: APCs initiate adaptive immune response!

3 “professional” APCs

1. dendritic cell
2. macrophage
3. B cells
   * other cells can also fx as APCs, but do not initiate an immune response bc they don’t deliver MHC signal along with the other mols req to activate T cells (co-stimulation)

Question 14

dendritic cells

Answer 14

• most efficient APC, initiate the most immune responses
• several subtypes (ex. Langerhans cells of skin)
• some can be immunosuppresive

fx: sentinels of immune system that migrate through tissues looking for antigen

• when encountered, phagocytose antigen → migrate to lymph nodes and present antigen to T cells → initiate immune resp

two sites of origin/devpt:

1. myeloid DCs (mDC) : bone marrow

• produce IL12; express TLR2, TLR4
• effective in antigen presentation

2. plasmacytoid DCs (pDC) : lymphoid origin?
   * express TLR7, TLR9, IFN-alpha (imp for viral response)

Question 15

routes of antigen entry

Answer 15

epithelia of skin, gut, resp tract (major route)

• lymph nodes will collect antigens from epithelium and connective tissue

blood-borne pathogens

• APCs in spleen will collect antigens from blood

Question 16

innate immune response and DC response

Answer 16

migrating/surveilling DCs are immature (low levels of class II, other mols needed to activate T cells) - specialize in antigen capture

• high expression of FC receptors, mannose receptors
• low expression of T cell activation mols (costim molecules)
• MHC II mols: relatively low number, low half life [ubiquitin ligase that tags MHC II markers on

TLR ligation leads to maturation of DCs

[binding of antigen delivers the TLR signals → signal migration through lymphatics (and maturation) into lymph → once in lymph node, DC can interact with CD4/CD8 T cells]

mature DCs (lymph nodes/spleen) - specialize in antigen presentation to T cells

• low expression of FC receptors, mannose receptors
• high expression of T cell activation mols (costim molecules)
• MHC II mols: relatively high number, high half life [ubiquitin ligase goes away]

Question 17

monocytes and macrophages

Answer 17

APCs

monocytes : immature macrophages : circulate in blood, accumulate at sites of infection

macrophages :

• differentiate and reside in tissues in absence of antigen
• differentiate in response to inflammation (activated by T cell cytokines)

fx of both:

1. phagocytosis (pathogens, debris, senescent cells)
2. antigen presentation
3. cytokine production/signaling (effector cells)

Question 18

major groups of APC and their functions

Answer 18

express both MHC I and MHC II

[antigen uptake → antigen presentation → response]

1. dendritic cells : naive T cell activation (crank up T cells initially) → clonal expansion and diff into effector T cells

2. macrophages : effector T cell activation → T cells in turn activate macrophages, prime them to kill endocytosed stuff

• cell mediated immunity

3. B cells : effector T cell activation → T cell s in turn activate B cells and antibody production (B cells MUST interact with T cells - regulation to make sure both are seeing and responding to the same pathogen)

• humoral immunity

Question 19

exception to class I MHC (endogenous) pathway:

cross presentation of exogenous antigens on MHC I

Answer 19

process by which DCs can ingest viral-infected cells and display viral peptides on MHC I molecules

IMPORTANT: viruses generally don’t infect DCs directly, and DCs initiate most immune responses

• problem: makes it difficult for DCs to get a CD8 adaptive immune response going via class I MHC receptors
• solution: cross presentation! allows for activation of naive CD8 T cells via MHC I receptors

viruses infect every cell of the body

Question 20

self-peptide presentation

Answer 20

majority of MHC I and MHC II molecules are NOT presenting pathogen peptides…presenting self peptides instead!

MHC molecules don’t discriminate between foreign/pathogen and self peptides, BUT peptide is the limiting factor for MHC presentation

• on infection, there is always“empty” MHC I and MHC II waiting to be loaded with peptide

self v nonself discrimination is mediated by T cells → tolerance/autoimmune consequences

Question 21

how do you get diversification of MHC?

Answer 21

MHC is polygenic

MHC is also highly polymorphic (most polymorphic region of human genome)

• MHC II B chain, MHC I beta chain are especially variable
• polymorphisms lie in peptide binding groove → determine peptide binding
• each allele can be diff by as many as 20 a.a.s

Question 22

class 1b genes (non classical)

examples

Answer 22

play roles in recognizing all of the stuff that MHC needs to be able to recognize

examples:

H2-M3 (mouse) binds and presents peptides with N-formylated amino termini

• bacteria! (and self mitochondria)

MIC genes (5 genes, 2 expressed)

• induced in response to cellular stress
• expressed in fibroblasts and epi cells
• recognized by NK cells (gamma-delta T cells, CD8 T cells)

HLA G

• expressed on fetal-derived placental cells that migrate into uterine wall → class I negative, but not killed by NK cells
• HLA-G provides protection!

HLA E

• binds signal sequence peptides from other class I mols → prevents killing by NK cells
• if only HLA E is present, then NK cells kill them

Question 23

goal of MHC presentation is to activate T cells and immune responses

• contingent on binding and presenting pathogen peptides
• problem: each MHC molecule can only bind a small subset of peptides, which means it can only activate T cells to respond to a small subset of pathogens
• need diversity in TCR-ligand repertoire….get it via diversification of MHC-peptide binding repertoire!

Answer 23

1. many diff alleles with many diff peptide binding specificities

• MHC I : HLA-A, -B, -C
• MHC II : HLA-DR, -DP, -DQ

2. multiple MHC pathways can bind and present a diverse set of antigens

• peptides - MHC I, MHC II
• carbs - MHC II (on slide), MHC I (on lecture audio)
• lipids - CD1 (not MHC coded, class I type molecule)

3. different MHC molecules survey various cellular compartments to display as diverse a set of MHC on cell surface

• class I tends to hit cytosol
• class II tends to get endo/lysosome

4. cross presentation pathway
   * linkely essential for viral immunity (lets exogenous peptide be displayed on MHC I to activate CD8 antiviral response)