6 - Ag presentation

pathways of Ag processing

cytosolic

intravesicular

extracellular pathogens + toxins

cytosolic pathogens

degraded in:

peptides bind to:

prsented to:

effected on presenting cell:

degraded in: cytosol

peptides bind to: MHC-1

presented to: CD8

effect on presenting cell: cell death

intravesicular pathogens

degraded in:

peptides bind to:

prsented to:

effected on presenting cell:

degraded in: endocytic vesicles

peptides bind to: MHC-2

presented to: CD4

effect on presenting cell: activation to kill intravesicular bacteria + parasites

extracellular + toxins pathogens

degraded in:

peptides bind to:

prsented to:

effect on presenting cell:

degraded in: endocytic vesicles

peptides bind to: MHC-2

presented to: CD4

effect on presenting cell: activation of B cells to secrete Ig to eliminate extracellular bacteria/toxins

MHC-1

peptide binding domain:

nature of peptide-binding groove:

general size of bound peptides:

peptide binding domain: α1/α2

nature of peptide-binding groove: closed at both ends

general size of bound peptides: 8-10 AAs

MHC-2

peptide binding domain:

nature of peptide-binding groove:

general size of bound peptides:

peptide binding domain: α1/β1

nature of peptide-binding groove: open at both ends

general size of bound peptides: 13-18 AAs

general step of endogenously derived peptide presentation by MHC-1

1. recognizes Ub or damaged proteins

2. Ag processing through immunoproteasome

3. peptide-MHC association by TAP

4. expression on cell surface

immunoprotease function

deegrades cytosolic proteins into small peptide fragments

immunoprotease particle types

19S and 20S

19S regulatory particle

recognizes Ub-proteins, feeds into catalytic core

• on either side of immunoproteasome

20S core particle

cleaves Ub-proteins into peptide fragments

where does TAP shuttle peptides into?

the RER lumen and the peptide loading complex (PLC)

PLC parts

calnexin

calreticulin

ERp57

tapasin

calnexin

stabilizes MHC-1α chain prior to addition of β2m

calreticulin

stabilizes MHC-1α/β2m prior to peptide loading

ERp57

promotes MHC-1 folding and links w/ tapasin

tapasin

forms bridge btw MHC-1 and TAP

PLC function

stabilizes MHC-1 and ensures proper folding and peptide loading

how long are the peptides that immunoproteasomes make?

btw 3-22, 8-12 most common

how long a chain does TAP preferentially transport?

8-16 AAs

ERAAP

edits peptides to 8-10 AAs

• then transported to cell surface

general step of exogenously derived peptide presentation by MHC-2

1. Ag uptake

2. antigen processing through endosome

3. peptide-MHC association via Ii/CLIP

4. expression on cell surface

how are exogenous Ags digested

intravesicular proteases

how are B cells digested exogenously?

BCR crosslinking induces endocytosis

• end up in an endosome

how mononuclear phagocytes digested exogenously

phagocytosis internalizes or cell debris

• end up in a phagosome

what does acidification from Ag processing activate

proteases that degrade cargo into peptides

• lysosomes

Ii/CLIP

stabilize MHC-2 chains prior to Ag loading

Ii/CLIP stabilization general steps

1. new MHC-2 binds to Ii

2. Ii cleaved into CLIP in MIIC

3. CLIP replaced w/ Ag peptide

Ii

first chaperone that new MHC-2 binds to

• prevents premature peptide loading

where is the Ii cleaved into CLIP

in the MHC-2 loading compartment

what cleaves the Ii?

pH-dependent endosomal proteases

when is CLIP replaced with an Ag peptide?

after fusion of MIIC w/ endo/phagolysosome

HLA-DM and HLA-DO

chaperones that regulate peptide loading

HLA-DM mechanism

1. facilitates exchange of CLIP for Ag peptide

2. presentation of Ag peptide

HLA-DO mechanism

1. co-chaperone inhibits HLA-DM

2. display of CLIP on cell surface

types of gene structure of MHC

polymorphism

polygeny

both

polymorphism

multiple unique alleles

polygeny

multiple copies of MHC

• NOT multiple alleles

HLA complex

codes MHC genes

HLA complex

• class 1

loci: A, B, C

MHC isotypes: HLA-A, HLA-B, HLA-C

HLA complex

• class 2

loci: DPα + DPβ, DQα + DQβ, DRα + DRβ

MHC isotypes: HLA-DP, HLA-DQ, HLA-DR

HLA complex

• class 3

non-MHC immune genes

• complement, TNF-family cytokines

gene structure of HLA complex on chromosome 6

—class 2—————-class 3—————-class 1—————

what are the three highly polymorphic MHC-1 isotypes

HLA-A, HLA-B, HLA-C

which MHC-1 isotypes are oligomorphic

HLA-D, HLA-F

which MHC-1 isotypes are monomorphic

HLA-E

MHC-2 polymorphic isotypes

HLA-DP, HLA-DQ— both chains

MHC-2 oligomorphic isotypes

HLA-DM

MHC-2 HLA-DO

monomorphic α and oligomorphic β

MHC-2 HLA-DR

oligomorphic α and highly polymorphic β

which is more polymorphic, MHC-1 or MHC-2

MHC-1 classic

which MHC genes are deemed as “classic”

the most polymorphic in each type

where is the highest variability on MHC molecules

right in the cleft!

• diverse for different peptides

humans who are heterozygous for all 3 classical MHC-1 genes express how many isoforms?

6

humans who are heterozygous for all 6 classical MHC-2 genes express how many isoforms?

12

which chromosome has the MHC/HLA complex

chromosome 6

why is recombination for the HLA complex rare?

the HLA complex is gene-dense

what is caused by the low recombination?

linkage disequilibrium from MHC alleles

linkage disequilibrium

MHC alleles are not independently assorted

• ALWAYS as a set from mat + pat chromosomes

so how are MHC alleles inherited?

in “blocks” known as haplotypes

haplotype

particular combination of MHC alleles found on single chromosome

• PERSIST OVER TIME

strong selective pressures maintain what

that certain allele combinations that work well together

• reinforces persistence of specific haplotypes over time

evolutionary adaptive haplotype

bind distinct, non-overlapping sets provide broader Ag coverage + more advantageous evolutionarily

evolutionarily maladaptive haplotype

redundant specificities cover a smaller total fraction of possible nonself Ags

• host more vulnerable to pathogens

high polymorphism of HLA

promotes broad Ag coverage in outbred populations

inbreeding

leads to homozygosity of MHC alleles

• decreases fitness even when haplotypes are otherwise adaptive

balancing selection

type of natural selection that maintains multiple alleles w/in a population rather than favoring a single one

mechanisms of balancing selection for MHC genes

heterozygote advantage

frequency-dependent selection

pathogen-mediated selection

heterozygote advantage

individuals with 2 different MHC alleles can present a wider variety of Ags, giving them stronger and more flexible immune responses against diverse pathogens

frequency-dependent selection

rare MHC alleles provide a temporary advantage bc pathogens adapt to evade common alleles, causing alleles frequencies to cycle over time and preserving diversity

pathogen-mediated selection

different environments favor different MHC alleles depending on local pathogen pressures, leading to distinct allele patterns across populations

trans-species polymorphism

MHC allelic lineages shared across species

why does trans-species polymorphism occur

balancing selection preserves multiple alleles over millions of years, preventing them from being lost during evolution

what does the presence of shared MHC lineages show

that immune diversity predates human speciation

• maintained by long-term selection pressures from pathogens