This document summarizes antigen processing and presentation by the two main pathways - cytosolic and endocytic. The cytosolic pathway uses MHC class I to process endogenous proteins from within cells, marking them with ubiquitin and degrading them in proteasomes to generate peptides. These are transported by TAP proteins into the ER for loading onto MHC class I for presentation at the cell surface. The endocytic pathway uses MHC class II and antigen presenting cells to process exogenous proteins from outside the cell via endocytosis, phagocytosis and degradation in lysosomes, aided by invariant chain proteins, to generate peptides that are loaded onto MHC class II for presentation.

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AmjadKhan Afridi
Antigen Processing and Presentation MID
Antigens and “foreignness”
• Antigens (or, more properly, immunogens) have a series of features which confer
immunogenicity.
• One of these features is “foreignness.”
• So, we can infer that – most often – antigens – ultimately – originate externally.
• (There are exceptions, of course. Some cells become transformed by disease [e. g.,
cancer] or by aging. In such instances, the antigens have an internal origin.)
What is the significance of these premises?
They indicate that antigens are processed and presented.
There are two presentation systems…
• Are there two processing systems?
• Yes: CYTOSOLIC and ENDOCYTOTIC
• Does this imply that there are different degrees of foreignness?
• And that there are different cells for different degrees of foreignnness?
Cytosolic:
• Uses MHC-I
• Processes ENDOGENOUS proteins (e. g., viral proteins, proteins from bacteria which
invade cells, parasites,and normal cellular constituents [!])
Cytosolic PROCESSING:
• Proteins are marked by adding ubiquitin (a 76 amino acid polypeptide) in an ATP
dependent manner.
• Fed into a “proteasome”; a “big ball of degradative enzymes.”
• Proteasomes of immune system may become specialized by addition of products from
LMP loci (embedded in MHC-II “region”.)

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• Phenotype of LMP is production of “Low Molecular-mass Peptides.”
• LMP’s are polymorphic.
Cytosolic PROCESSING:
• Proteins are marked by adding ubiquitin (a 76 amino acid polypeptide) in an ATP
dependent manner.
• Fed into a “proteasome”; a “big ball of degradative enzymes.”
• Proteasomes of immune system may become specialized by addition of products from
LMP loci (embedded in MHC-II
“region”.)
• Phenotype of LMP is production
of “Low Molecular-mass
Peptides.”
Cytosolic PRESENTATION:
The peptides (produced by proteasomes)
are introduced into the rough
endoplasmic reticulum through an ATP
dependent process mediated by TAP
(transporter associated with antigen
processing.)
TAP are specified by loci embedded in
MHC-II “region.”
Two additional proteins, calreticulin and
tapasin, allow association of the MHC-I
with the TAP-complex and the loading
of processed Ag.
The MHC-Iprocessed Ag is then
delivered to golgi (for glycosylation) and
then to cell surface.
Cytosolic PRESENTATION:
The peptides produced by proteasomes are
introduced into the rough endoplasmic
reticulum through an ATP dependent
process mediated by TAP
 A chaperone, calnexin, associates with alpha chain.
 The asspciation induces conformational change that allows microglobulin to form
quaternary complex.
 Two additional proteins, calreticulin and tapasin,
 allow association of the MHC-I with the TAP

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 The MHC-I/processed Ag is then delivered to golgi (for glycosylation) and then to cell
surface.
Endocytotic:
• Uses MHC-II
• Processes EXOGENOUS proteins
(viz., foreign antigens.)
• Uses APC’s
(esp., “professional” antigen presenting cells)
• How do the APC’s acquire antigens to process?
Endocytotic PROCESSING:
The antigen is introduced into cell by phagocytosis or endocytosis (receptor mediated or
pinocytotic).
The Ag passes through a series of vesicles that have increasing acidity
early endosomes (pH 6.0-6.5)
late endosomes (pH 5.0-6.0)
and lysosome (pH 4.5-5.0).
Lysosomes contain ~140 acid dependent hydrolases including proteases, nucleases, lipases,
glycosidases, phospholipases, phosphatases...
KEY is the presence of the INVARIANT PROTEIN (Ii)
synthesized with the alpha and beta chains of MHC-II.
The invariant chain exists as a trimer and has attached to it
three sets of alpha/beta chains.
The invariant chain has a series of signals that contribute to the
delivery of the complex from the lumen of the rough
endoplasmic reticulum, through the golgi, and through the
microbodies (early endosome, late endosome, lysosome).
In the lysosome, the bulk of the invariant chain is degraded; a
portion, CLIP (Class II Invariant chain Peptide) remains in the
cleft until displaced by processed antigen.
INVARIANT PROTEIN (Ii) is synthesized with the alpha
and beta chains of MHC-II.
The invariant chain exists as a trimer and has attached to it
three sets of alpha/beta chains.

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Endocytotic PROCESSING:
INVARIANT PROTEIN (Ii) with the alpha and
beta chains of MHC-II.
The invariant chain exists as a trimer and has
attached to it three sets of alpha/beta chains.
The invariant chain signals the delivery of the
complex from the lumen of the rough endoplasmic
reticulum, through the golgi, and through the
microbodies
In the lysosome, the bulk of
the invariant chain is degraded;
a portion, CLIP (Class II
Invariant chain Peptide)
remains in the cleft until
displaced by processed
antigen.
Antigen presenting cells…
Dendritic cells:
 Langerhans cells found in epidermis and mucous membranes.
 Interstitial dendritic cells which populate most organs.
 Interdigitating dendritic cells present in T-cell areas of secondary lymphoid tissue
and the thymic medulla
 Circulating dendritic cells… in the blood… and lymph (known as veiled cells.)

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Cross-talk
What is the consequence?
But not all immunogens are proteins…
There may be specialized systems for presentation of non-peptide antigens.
There are non-protein antigens which do not require presentation.
Instead they stimulate B-cells, directly without T-cell intervention.
Dr. Riaz Muhammad
Notes: Advanced Immunology
Chapter# 1: Antigen Processing & Presentation (1st )
Date: 16th September, 2019
Prepared by Amjad Khan Afridi