T cell related (Fleischmann)
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Helper T cells recognize antigenic peptides presented by APCs to their T cell receptors (TCRs).
TCRs are heterodimers.
o αβ dimer TCRs are very specific to Ag (similar to Ig molecules on B cells). Ag is presented by MHC,
adaptive immune response is activated and Ag killed by granulysin & perforin. Membrane bound d/t
transmembrane cytoplasmic tail region. While a T cell can produce 2 of these, it is unlikely that 2
would become self-restricted T cells and leave the thymus.
 α chain (similar to Ig L chain) is encoded by V, J & C gene segments
 β chain (similar to Ig H chain) is encoded by V, D, J & C gene segments = more variability
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Mechanism of TCR rearrangement: pre-T cell has RAG-1 & RAG-2 expressed that will
recognize conserved RSSs  nicks one strand of TCR DNA  DNA loops out  each
rearranged DNA sequence will encode a single type of TCR.
 TCRs have variability because of the different combinations of V, D, J regions that create
different Ag-binding specificities as well alternative joining of D gene sequences. P and N
nucleotide additions also contributes. There is no maturation of affinity here b/c it could be
potentially harmful if a TCR changed then no longer recognized self.
δ dimer TCRs recognize groups of pathogens (similar to Toll receptors of innate immunity – pattern
recognition). Direct interaction w/ Ag. Recognizes regions on M. tuberculosis, other bacteria &
parasites. Part of chronic autoimmune diseases (lupus, MS). Produce cytokines that can recruit αβ
an can present Ag.
CD3 is associated w/ TCR and is composed of 3 dimers (ζζ most imp) that aggregate near the TCR,
include a region, ITAM (immunoreceptor tyrosine-based activation motif) that is important for signal
transduction across the membrane.
CD4 binds to Class II Ag & signal transduction molecule p56Ick that will form a bridge that binds to ζζ.
CD8 binds to Class I Ag, held together by disulfide bond. Both of these co-receptors add to the
binding affinity between TCR & MHC/peptide complex. These T cells are alloreactive to molecules
other than to their cognate MHC (will react to MHCs other than their own d/t genetic differences).
Direct allorecognition occurs when MHCs are recognized as foreign antigens +/- being bound to a
foreign protein. Indirect allorecognition is when an MHC is internalized, processed & presented to
immune system bound to self-MHC.
Other co-receptors that add to binding affinity: CD2B7; LFA-1  ICAM-1; CD28  B7; CD45R 
CD22
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MHC (major histocompatibility) molecules are important for Ag recognition & presentation to the
immune system (at the T Cell Receptor).
There are >100 genes in MHC gene complex divided into Class I, Class II & Class III. Class I & II also have
subclasses of gene loci, giving rise to polymorphism. Polymorphism provides uniqueness and recognition
of non-self. The TCR will only recognize Ag that is bound to their own MHC with cognate Ag = self-MHC
restriction.
o MHC class I presents Ag to CD8+ T cytotoxic cells that will be activated (w/ correct co-stimulatory
molecules & cytokine production) to kill cells expressing the Ag.
 This is on most nucleated cells. When expressed on cell surface, they associate w/ β₂microglobulin (1 peptide). Binding cleft is closed at both ends, binds peptides that are 810 aa in length and anchors them at both ends.
o MHC class II presents Ag to CD4+ T helper cells that will be activated (w/ correct co-stimulatory
molecules & cytokine production) to either activate B cells to mature to Ab-producing plasma cells
OR to activate more CD8+ cytotoxic T cells to kill.
 On APCs. When expressed on cell surface the gene locus encodes 2 peptides, α subunit &
β subunit. Binding cleft is open at both ends, binds peptides 13-22 aas in length and are
anchored along the length of the peptide.
o MHC class III genes aren’t involved in Ag presentation. They include complement proteins &
TNF-α and TNF-β, HSPs
Polymorphism affects ability to make immune response, response to infectious disease & susceptibility to
autoimmune diseases & allergies (ex: if you have HLA-B27, you are more likely to get ankylosing
spondylitis, HLA-DR2  narcolepsy, HLA-A3/B14  hemochromatosis). Most of the differences are seen
in the cleft region (antigenic peptide binding site). There are 6 different MCH I & 12 different MHC II
molecules that arise from different combinations of α and β subunits. Since this is nowhere near the
number of potential Ags that can bind, a weaker association is made when Ag binds to the peptide
binding clefts.
Loci for Class I & II are inherited as a two haplotypes (cassette from each parent) and we have codominant expression of each allele. Recombination is rare between Class I & II because they are so
closely linked.
o Syngeneic: having same gene alleles in your 2 haplotypes as someone else, usually only seen with
identical twins. Congenic: differ only in 1 locus. This is important for transplants.
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Ags that are products of phagocytosis are expressed on MHC II & Ags that are intracellular protein
products are expressed on MHC I
Antigen-Presenting Cells (APCs) process Ag for presentation to T cells.
o Dendritic cells are the most effective APC b/c they the express MHC II & B7 (required costimulatory molecule). Low levels of MHC II are expressed in peripheral tissue, dendritic cell at
immature phase  mature phase occurs in lymphoid tissue where high levels are expressed.
They present peptides, viral Ags & allergens.
o B cells are next best since they express MHC II but need to be activated (by Ag binding to Ab) in
order to express co-stim molecules. Present soluble Ags, toxins & viruses.
o Macrophages are the slowest b/c need to be activated (by phagocytosis of bacteria & by
cytokines) to express both. Present intracellular & extracellular pathogens.
Antigen processing & presentation
occurs via 2 different pathways
depending on where the Ag came from.
The cytosolic pathway is for Ag
presentation on MHC I of endogenous Ag
while the endocytic pathway is for MHC
II of exogenous Ag brought in by
phagocytosis.
o Some of the endogenous
proteins degraded by the
cytosolic pathway are called
DRiPs, defective ribosomal products that arise from incorrect synthesis. Virus infected cells have
a distinct 20S proteasome induced by IFN- & TNF-α. Degradation of misfolded proteins occurs
through the 20S proteasome while those that are intact are tagged with Ubiquitin go through a
26S proteasome (20S + 19S regulatory component). The 20S has 28 polypeptide subunits in 4
rings – outside 2 are α subunits and inside 2 are 7 kinds of β subunits. Enzymatic cleavage or
proteins happens in central tube. The 20S immunoproteasome has IFN- within the β subunits
which makes it more likely to cleave by hydrophobic aas giving greater binding affinity to TAP.
o TAP is a transporter protein heterocomplex that transports peptides from cyto  RER for
synthesis of MHC I. TAP1 & TAP2 dimerize and allow peptide to move through RER to lumen side
where it can then attach to MHC I. TAP prefers peptides 8-16 aa long, which is
good b/c 9 aa is ideal for Class I binding. ERAP1 (ER aminopeptidase) helps trim
them down. Class I also wants to bind to peptides that have specific aas that are
imp in binding to the peptide cleft (carboxyterminal anchor is hydrophobic as
well as another hydrophobic anchor 2-3 aa away from aminoterminus). If they
are too small or if they can’t be used by MHC, ERAP2 degrades them.
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Assembly of MHC Class I molecule (KNOW all the steps in this diagram!)
α-chain made. Calnexin gets up next
to the α subunit and stabilizes. β₂
microglobulin added & calnexin goes
away. Tapasin is adaptor, binds to
class I Ag & to TAP. Calreticulin
opens groove, allowing for ERp57 to
protect = ‘cap’. Once peptide can
bind, calreticulin goes away.
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TAP deficiency pts can’t express Class I molecules or antigentic peptides, can’t fight bacteria, have
overactive NK cells  necrotizing granulomatous lesions on skin of face & extremities.
o The endocytic pathway processes exogenous antigens that are internalized by phagocytosis from
MOS & dendritic cells & receptor-mediated endocytosis by B cells. Ab bound Ag is internalized in
early endosomes  late endosomes  lysosomes where Ag is degraded to 13-18 aa
oligopeptides which are then bound to MHC class II molecules and transported to surface. During
this time, Ab releases Ag and is recycled to membrane.
 Invariant chain combines with MHC Class II after they are made in the RER. This helps the
class II α and β chains fold, keeps other things from binding in the peptide’s spot, helps
transport from RER  Golgi  cytoplasmic vesicles. During this mvmt, the invariant
chain is slowly degraded until all that is left is CLIP, a small fragment. HLA-DM catalyzes
exchange of CLIP & antigenic peptide that will bind very strongly now. (HLA-DM is
regulated by HLA-DO which is expressed only on B cells and in thymus, is NOT induced by
IFN-, and wont bind to HLA-DM under acidic conditions)
Abnormalities:
o Cross-presentation of exogenous Ag occurs when an APC presents exogenous Ag to Class I
(normally its to Class II), we think at the lumen of the RER. Could allow dendritic cells to
phagocytose viruses & present viral Ags w/ Class I = Tc cells activated to kill virus-infected cells
before the infection spreads.
o Nonpeptide Ags can be presented by CD1. CD1 can present Glycolipids & mycolic acid from the
Mycobacterium species. They present to Tc cells w/ δ TCR and NK cells.
T cells leave the bone marrow with CD44 that directs them to the thymus where they will mature. While
they are maturing they are named thymocytes and undergo positive & negative selection. Notch
protein, expressed by thymic stromal cells, must be present for T cells to mature. 3 week process of
maturation: CD4- CD8-  CD4+ CD8+  CD4+ OR CD8+  mature
o Positive selection allows T cells to survive if they recognize self-MHC molecules. Negative
selection eliminates T cells that over-respond to self (or self + peptide) allowing self-tolerant T
cells to be produced = CENTRAL TOLERANCE. About 2% of thymocytes actually mature.
T cell activation occurs from binding of one TCR w/ Ag. (and in Th cells, also need signal from CD28 on T
cell interacting w/ B7 on APC, this induces CTLA-4 expression which can later be bound by B7 to slow
down). Clonal anergy occurs where there is no costimulatory signal present; T cell is worthless.
o Many genes are activated by Ag binding. Immediate Early Genes w/in 30 min, encode
transcription factors: c-Fos, c-Myc, c-Jun, NFAT & NF-κB. Early genes w/in 1-2 hrs, encode IL-2, IL2R, IL-3, IL-6, IFN-. Late genes 2 days later, encode adhesion molecules.
P56Lck phosphorylates ITAMs on ζ chains, creating docking site for ZAP-70 which phosphorylates
adaptor molecules that activate other enzymes  PLPC activation causes breakdown of PIP₂ to
IP₃ & DAG / GEF is also activated leading to the Ras/ MAP Kinase pathway. Small G proteins
active.
 IP₃ causes rapid release of Ca from ER, opens Ca channels in cell membrane & activates
transcription factor NFAT needed for making IL-2 & IL-4.
 DAG activates PKc which phosphorylates lots of things & activates transcription factor
NF-κB that will help make IL-2.
 Ras/MAP Kinase pathway activates Fos/Jun/AP-1 which activates a number of genes
involved in cell division.
o Superantigens bind to both MHC & TCR but aren’t in antigen groove of MHC and stimulate a nonspecific reaction causing a lot of T cells to be activated and overinduction of cytokines. This can
lead to toxic shock. Staph and strep.
T cells are naïve when they leave the thymus. They circulate: blood  lymph  lymphoid tissues 
blood in 12-24 hours. This circulation is needed to provide adequate exposure possibilities between T cell
and Ag. Primary response is initiated when TCR binds Ag: 24 hrs later T cell  blast cell that divides. IL-2
synthesis is increased by IL-2 mRNA synthesis & stabilization, IL-2 binding to the IL-2 receptor also
activates proliferation  clone of T cells. After proliferation, effector (not memory) T cells undergo
apoptosis either by FasL (2-4 hrs) or MHCAg (8-10 hrs)
o Effector T cells can be induced from naïve T cells or from memory T cells when exposed to Ag,
they are short lived can be either CD4+ Th (Th1 secretes IL-2, IFN-, TNF-β and stimulates cell
mediated immunity; Th2 secretes IL-4, IL-5, IL-6, IL-10 and stimulates humoral (Ab mediated)
immunity) or CD8+ Tc.
o Memory T cells can be induced from naïve T cells or from effector T cells after antigenic activation
& differentiation. Long lived & can be reactivated by re-exposure to Ag to become effector cells
(secondary response). Can be activated by all APCs.
o Regulatory T cells (Tregs) regulate the immune response (CD4+Cd25+FoxP3+ subpopulation)
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Stages of T cell maturation:
--DN1 cells enter thymus. CD44 is needed for
localization to thymus. c-Kit is a receptor for stem
cell factor & needed for initiation of growth in thymic
environment. DN1 cells start to proliferate & express
CD25.
--DN2 cells have turned on synthesis of CD25. Turn
on RAG1 & 2 and start rearranging TCR δ, , β. Cells
that will express TCR δ diverge from other T cells w/
transition from DN2 to DN3 and leave thymus.
--DN3 cells have turned off c-kit & CD44. TCR β is
rearranged & combines w/ pre-Tα chain which will
associate w/ CD3 group of molecules to form preTCR.
--Now, activation signal is transduced across membrane, further proliferation & maturation is induced, further
rearrangement of TCRβ is suppressed, TCRα can be rearranged, progression to CD4+CD8+ T cell is induced. (The
delay of rearranging the TCRα allows increased diversity in T cells).
--DN4 turns off expression of CD25. Expression of CD4 & CD8 is turned on. The double positive cells undergo
rapid proliferation, creating clones w/ same β chain. Then α chain is synthesized. Now that the TCR is functional
the T cell can undergo positive and negative selection. The double positive cell then loses one if its positive
markers & the single positive undergoes further negative selection.