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IMMU2101!Introductory*Immunology"
Introduction*to*the*Course*• 3"assessment"tasks"aside"from"exam"(all"equal):"
o understanding"an"immunology"research"article"(title"and"abstract"written"assessment,"
comprehension"table)."Read"the"article"many"times!"make"notes."It’s"available"on"
blackboard.""
o Oral"presentation."Nobel"laureate"will"be"assigned"to"you"whom"you"have"to"research"and"
introduce"to"your"audience"(the"public).""
o Practical"assessment."A"pre!prac"quiz"at"the"start"of"every"prac"(5"quizzes"worth"5%"each)."
Theory"of"prac"exam"in"week"13.""
Lecture*1:*What*is*the*immune*system?*
The"Immune"System"A"collection"of"cells,"tissues,"and"molecules"that"mediate"resistance"to"infections"and"eliminates"tumours."
Thus,"immunology"is"the"study"of"the"immune"system"and"its"response"to"invading"pathogens"and"tumours.""
Functions:*
• To"prevent"infections"
• To"eradicate"established"infections"
• To"detect"and"eliminate"tumours"
• To"tolerate"self"
Immunity"Immunity"is"defined"as"resistance"to"diseases"caused"by"bacterial,"viral,"fungal,"parasitic"infections,"as"well"
as"tumour"immunity.""
The"Immune"Response"There"are"2"types"of"defective"immune"responses:"
• Congenital"(primary)"immune"deficiencies"e.g."patients"who"completely"lack"key"cells"and"molecules"
of"the"immune"system"
• Acquired"(secondary)"immune"deficiencies"e.g."HIV"infection"leading"to"the"eradication"of"key"
immune"cells"(CD4"helper"T"cells).""
The"immune"system"can"also"over!react:"
• Asthma"
• Atopic"or"allergic"reactions"
• Autoimmune"diseases"
Where"is"the"immune"system?"Integrated"with"other"systems!"gastrointestinal,"cardiovascular,"respiratory,"nervous,"endocrine,"skin."Many"
immune"cells"migrate"around"the"body,"others,"known"as"resident"cells"reside"in"one"place"for"a"long"period"
of"time"awaiting"pathogens.""
Originate"also"from"common"myeloid"progenitors"in"bone"marrow."
Features*
• Monocytes"in"blood"migrate"into"inflamed"tissues"to"become"macrophages"
• Macrophages"may"be"found"as"resident"cells"in"tissues"(e.g."Kupffer"cells"in"the"liver,"alveolar"
macrophages"in"the"lung)"
• Often"long!lived"with"may"contribute"to"the"symptoms"of"some"diseases"e.g."TB"
Functions*
• Potent"antibacterial"functions"
• Secrete"cytokines"
• Research"shows"that"like"neutrophils,"some"macrophages"may"even"help"tumours"to"evade"the"
immune"system"and"grow""
• Macrophages"also"‘talk’"to"lymphocytes"
B"Lymphocytes"Derived"from"common"lymphoid"progenitors"in"bone"marrow"and"also"undergo"maturation"in"bone"
marrow.""
Features*
• Form"part"of"the"Humoral"Immune"Response"which"is"part"of"the"adaptive"immune"system,"
mediated"by"B"
Function*
• Secrete"antibodies"which"are"proteins"that"bind"to"extracellular"antigens"
o Antigens"are"substances"that"induce"an"immune"response"(such"are"called"immunogenic,"
but"also"may"be"sterile).""
o Types"of"antigens:"proteins,"carbohydrates,"lipids,"chemical"haptens"(a"small"molecule"that"
can"elicit"an"immune"response"only"when"attached"to"a"large"carrier"such"as"a"protein).""
o Antigen!specific"receptors"on"lymphocytes"bind"small"parts"(a"few"a.a."only)"of"these"
molecules."These"are"called"antigenic"determinants"or"epitopes!"antigens"can"be"made"of"
lots"of"different"epitopes"
T"Lymphocytes:"2"types"Derived"from"common"lymphoid"progenitors"in"bone"marrow"and"migrate"to"the"thymus"where"they"under"
go"maturation."
Features*
• Form"part"of"the"Cell!mediated"Immune"(CMI)"Response"
• Express"antigen!specific"receptors"on"their"surface"(lots"of"one"type"of"receptor)."1"lymphocyte"
recognizes"1"type"of"antigen.""
CD4"T"cells"–"Helper"T"cells"(Th"cells)"
Features*
• Characterized"by"their"surface"expression"of"the"CD4"molecule.""
Functions*
• ‘help’"other"cells"of"the"immune"response"by""
Lecture*2:*Principles*of*Innate*Immunity*In"the"bone"marrow,"hematopoietic"stem"cells"give"rise"to"cells"of"the"innate"and"adaptive"immune"system.""
Hallmarks"of"the"Innate"Immune"System"
Speed*
Neutrophils"are"abundant"in"our"blood"so"the"system"activates"within"minutes!"it"is"early"and"rapid.""
Duration*
It"is"short!lived"as"it"induces"inflammation,"of"which"too"much"is"dangerous.""
Repetitive**
Responds"the"same"way"each"time"a"microbe"is"encountered"
Interactive*
The"innate"and"adaptive"immune"are"not"separate!"their"cells"interact.""
Components"of"Innate"Immunity"
Epithelial*Barriers*
Discussed"previously"
Cells*in*Circulation*and*Tissues*
• Phagocytes"
o Neutrophils"and"macrophages"
o Scavengers"that"ingest"microbes"
• Exocytes"
o Eosinophils,"mast"cells,"basophils"
o Release"active"mediators"from"granules"
Molecules*
• Cytokines"
o Tumour"necrosis"factor"(TNF)"is"a"proinflammatory"cytokine,"interleukin!1"(IL!1)."These"will"
only"affect"a"target"if"cell"expresses"receptor."
• Plasma"proteins"
o Complement"proteins,"mannose!binding"lectin,"C!reactive"protein"
Pattern"Recognition"Receptors"These"specifically"respond"to"patterns"on"the"surface"of"microbes"(not"expressed"on"mammalian"cells,"only"
microbes)."Three"types"of"cells"express"PRRs:"epithelial,"endothelial"and"resident"immune"cells."The"
patterns"they"detect"may"be"one"such"as"a"repeating"pattern"of"carbohydrates.""
PAMPs*
Different"microbes"express"different"microbial"‘patterns’"called"pathogen1associated(molecular(patterns.("
DAMPs*
The"innate"immune"system"also"recognizes"molecules"that"are"released"from"damaged"or"necrotic"cells"
called"damage!associated"molecular"patterns"(DAMPs)."E.g."DNA"is"not"usually"found"outside"of"cell"so"it"
indicates"that"a"nearby"cell"is"damaged.""
The"binding"of"PAMPs"and"DAMPs"to"PRRs"triggers"a"cascade"of"events:"
• Release"of"soluble"mediators"(e.g."cytokines)"
• Recruitment"of"innate"immune"cells"(neutrophils,"monocytes)"
We"can"detect"different"patterns"using"different"detectors"that"can"be"found"in"different"locations!"
extracellular,"cytosolic"or"endosomal.""
TollFlike*receptors*(TLR)*
e.g."TLR!4"binds"lipopolysaccharide"(LPS)"
Nuclear*Oligomerisation*Domain*(NOD)Flike*receptors*(NLR)*
Intracellular"PRR’s;"activate"the"inflammasome.""
Mannose*Binding*Protein*(lectin)*
Binds"multiple"mannose"molecules"in"fungi"and"bacteria.""
The"First"Responders:"Tissue"Resident"Dendritic"Cells""Dendritic"cells"within"tissues"exposed"to"the"environment"express"PRRs."These"cells"are"strategically"located"
to"maximize"chance"of"1st"encounter."They"move"rapidly"along"collagen"fibres.""
Langerhans*cells**
These"are"dendritic"cells"of"the"skin"and"mucosa"and"are"stationary.""
When"PRR"detect"DAMPs"or"PAMPs"it"triggers"a"cascade"of"events.""
"
The"First"Responders:"Mast"Cells""Mast"cells"are"strategically"located"in"line"with"blood"cells."In"this"way"they"can"respond"very"rapidly;"also"
because"they"have"prepackaged"cytokines.""
!"dilates"blood"vessels"allowing"for"more"blood"3low"to"the"area"(redness)"and"3luid"to"come"in"(swelling)"
!"induces"the"expression"of"adhesion"molecules"on"endothelial"cells"lining"the"blood"vessels"(veins)."Puts"up"a"'sticky"carpet'"to"which"neutrophils"adhere"to."!"attracts"other"innate"immune"cells"(neutrophils"and"monocytes)"
Release"of"in3lammatory"mediators:"histamine"and"cytokines"like"TNF"and"IL!1"
Binding"of"microbial"patterns"to"PRRs"
Naïve"vs"Activated"Lymphocytes"
Naïve*lymphocytes*
• Have"the"capacity"to"engage"with"antigens"but"have"not"yet"encountered"their"antigen"
• Circulate"between"secondary"lymphoid"tissues"
• Are"mature"
Activated*Lymphocytes*
• Mature"lymphocytes"that"have"been"presented"with"their"foreign"antigen"and"been"activated"
• Stop"circulated"between"lymphoid"tissues"
• Migrate"to"peripheral"tissues."Note:"memory"lymphocytes"must"be"mature"and"activated"
B"and"T"cell"Receptors"Antigen"receptors"of"these"cells"recognize"different"structures.""
• B"cell"receptors"(BCR)"bind"native"shapes"on"macromolecules"e.g."whole"proteins,"carbohydrates,"
lipids.""
• T"cell"receptors"(TCR)"bind"foreign"peptides"together"with"host"membrane"proteins"(called"MHC"
molecules).""
Each"B"or"T"lymphocyte"has"multiple"antigen"receptors"(~100"000"receptors"per"cell)."On"any"one"cell,"every*
antigen*receptor*has*the*same*specificity"which"is"encoded"within"the"DNA"of"the"lymphocyte.""
Clonal"Selection"Hypothesis"Proposed"by"Sir"Macfarlane"Burnet."This"explains"how"the"immune"system"can"respond"to"a"large"number"
and"variety"of"antigens."Our"immune"system"must"be"able"to"recognize"all"possible"antigenic"specificities"
encountered."Cells(of(adaptive(immune(system(have(the(ability(to(proliferate.(
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MHC"Class"I"Pathway"Aka"intracellular"or"cytosolic"pathway."Here,"different"proteins"are"sourced"from"the"cytosol"including:""
• Virus"
• tumour"and"normal"self"proteins"which"helps"to"regulate"immune"system!"CD8"cells"should"not"
recognize"these"
• microbial"proteins"that"have"‘escaped’"or"have"been"transported"out"of"phagosome"
"
If"there’s"no"class"I"MHC"molecule"on"the"surface,"you"do"not"generate"CD8"T"cells!"
If"you"have"a"TAP"deficiency,"you"cannot"present"MHC"molecules"on"surface"of"cells,"which"leads"to"BLS!"
Bare"Lymphocyte"Syndrome.""
MHC"Class"II"Pathway""
"
Proteins"are"unfolded"(from"their"2D"and"3D"conformations)"and"tagged"with"ubiquitin"so"it"can"be"
recognized"by"proteasome.""
The"proteasome"(which"is"present"in"every"nucleated"cell)"‘shreds’"the"proteins"into"peptides."This"is"
enhanced"by"inflammatory"cytokines"(TNF,"IL!1)"
Peptides"are"actively"moved"by"TAP"transporter"molecules"into"the"ER,"where"class"I"molecules"are"
being"synthesised"(as"α"chain"and"β2"microglobulin)"
The"newly"formed"Class"I"MHC"molecule"binds"to"TAP"via"Tapasin"
Peptides"are"loaded"into"the"MHC"Class"I"groove."The"peptides"are"small"as"the"groove"is"a"closed"
conformation.""
The"peptide"loaded"MHC"class"I"molecules"then"move"from"ER"to"golgi,"where"they"are"packaged"
into"exocytic"vesicles.""
For"CD8"cells"to"recognize"the"MHC"class"I"molecules,"they"are"presented"on"the"surface.""
In"summary:"CD8"T"cells"can"‘see’"inside"any"nucleated"cell."That"cell"will"only"be"killed"if"it’s"presenting"a"peptide"that"is"
non!self."CD4"T"cells"only"‘help’"a""cell"if"they"recognize"the"peptide"that"you’re"presenting.""
Feature* Class*II*MHC*Pathway* Class*I*MHC*Pathway*
Composition*of*stable*peptideFMHC*complex*
Involves"polymorphic"α"and"β"chains,"peptide.""
α"chain"with"peptide"and"β2!microglobulin"molecule"
Cells*that*express*MHC* Dendritic"cells,"mononuclear"phagocytes,"B"lymphocytes"
All"nucleated"cells"
Responsive*T*cells* CD4"" CD8"Source*of*protein*antigens* Endosomal/lysosomal"proteins!"
internalized.""Cytosolic"proteins"(synthesized"in"the"cell)"
Enzymes*responsible*for*peptide*generation*
Endosomal"and"lysosomal"proteases"
Cytoplasmic"proteasome"
Site*of*peptide*loading*of*MHC* Endocytic"vesicles"that"fuse"with"phagolysosome"in"cytoplasm"
ER"
Molecules*involved*in*transport*of*peptides*and*loading*of*MHC*molecules*
Invariant"chain"DW" TAP"
"
"
Extracellular"antigens"(bacteria,"fungi"etc)"are"recognized"by"pattern"recognition"receptors"(PRRs)."
These"are"internalized"by"phagocytosis"into"phagosomes/endosomes."Note"that"not"all"cells"have"
capacity"to"bring"things"from"outside"in"but"macrophages,"dendritic"cells"and"B"cells"can."
Macrophages"and"dendritic"cells"use"PRR"whereas"B"cells"are"very"specific.""
The"endosome"(aka"phagosome)"will"then"fuse"with"the"lysosome"which"contains"proteolytic"
enzymes"which"degrades"proteins"into"peptides."This"is"now"called"a"phagolysosome.""
At"the"same"time,"the"α"and"β"chains"of"MHC"class"II"molecules"are"being"synthesised"in"the"ER."
However,"as"it’s"an"open"conformation,"it’s"unstable."If"there’s"no"peptide"sitting"in"it,"it"breaks"down.""
The"invariant"chain"(Ii)"with"CLIP"occupies"the"peptide"binding"cleft"in"these"newly"synthesised"class"
II"molecules"to"ensure"no"class"I"peptides"enter"cleft.""
Class"II"molecules"are"the"transported"out"of"the"ER"via"the"Golgi"in"a"exocytic"vesicle."The"exocytic"
vesicle"fuses"with"the"phagolysosome.""
But"CLIP"is"still"in"cleft!"it"must"be"removed"and"replaced"with"foreign"peptide."Enzymes"in"the"
phagolysosome"degrade"invariant"chain"leaving"CLIP."A"protein"called"DM"removes"clip"so"now"
pathogen"peptide"is"in"MHC."
Features*TCR*and*BCR*have*in*common* Unique*Features*to*the*TCR*
• Membrane"bound"(but"TCR"are"never"secreted)"
• Constant"regions"• Variable"regions"(3"hypervariable"regions"in"
each"Variable"domain)"
• Two"chains"(α"and"β"chains)."Each"with"2"Ig"(immunoglobulin)"domains""
• No"heavy"and"light"chains"• Slow"on!rate,"slow"off!rate"
"
What"do"TCRs"do?"• Recognizes"self"MHC!"foreign"peptide"complex."Each"TCR"regonises"as"few"as"1!3"a.a."residues"
which"could"change"specificity"if"they"changed.""
• Immunodominant"epitopes"are"epitopes"that"are"more"likely"to"find"their"way"into"the"groove"of"
MHC"class"I"or"II"molecules!"very"likely"to"stimulate"T"cells"
• The"TCR"recognizes"antigen"but"cannot"transit"signals"to"the"T"cell"
o CD3"and"ζ"proteins"together"with"coreceptors"CD4/CD8""and"the"TCR"make"up"the"TCR"
complex"
• TCR’s"don’t"see"free!floating"peptides,"only"peptides"on"MHC"molecules""
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TCR"complex"• TCR"has"a"short"cytoplasmic"tail,"with"no"signal"transduction"sites"
• TCR"recoginises"peptide!"MHC"antigen"
• Activation"via"signaling"molecule"complex""
o CD3"molecules"(γ,"δ,"ε)"and"zeta"(ζ)"chain"
o Always"associated"with"TCR"in"cell"membrane"
o Provide"activation"signal"transduction"via"ITAM"sequences"
! ITAM:"immunoreceptor"tyrosine!based"activation"motif"
• Phosphorylation"of"ITAM"leads"to"the"activation"of"the"transcription"factors"NFAT,"NFκB"and"AP!1."If"
these"transcription"factors"are"not"turned"on"there’s"no"activation"of"T"cells.""
The(recognition(of(antigen(and(MHC(complex(leads(ultimately(to(the(activation(of(transcription(factors.((
Antigen"Receptor"Diversity"• We"come"into"contact"with"many"pathogens"and"foreign"molecules"
• Each"lymphocyte"has"only"one"receptor"with"one"specificity"although"each"cell"may"express"many"
copies"of"this"receptor"on"its"surface"
• Clones"develop"in"primary"lymphoid"tissues!"thymus"and"bone"marrow"before"antigen"encounter"
• Clonal"expansion"produces"genetically"identical"cells!"T"and"B"cell"clones"develop"independently"of"
antigen"(we"don’t"have"enough"DNA"to"encode"for"every"possible"combination"of"receptors)"
Generation"of"Diversity"Somatic"combination"of"gene"segments"enables"the"development"of"receptor"diversity.""
• Stem"cells"in"the"bone"marrow"(as"well"as"early"lymphoid"progenitors)"contain"Ig"and"TCR"genes"in"
the"germline"DNA"
• They"home"to"the"T"cell"zones"where"they"have"the"requisite"molecular"machinery"to"activate"naïve"
T"cells"(MHC"molecules,"co!stimulatory"molecules,"adhesion"molecules,"cytokines).""
T"cell"activation"and"differentiation"• Antigen"recognition"by"TCR"complex"together"with"other"stimuli"leads"to"T"cell"activation."If"only"
recognition"and"no"other"signals,"T"cells"will"be"turned"off.""
• Clonal"expansion"and"differentiation"generates"both"effector"and"memory"T"cells:"
o Effector"T"cells"can"eliminate"antigens"in"secondary"lymphoid"tissues"
o Some"effector"T"cells"migrate"from"secondary"lymphoid"tissue"to"the"main"site"of"infection"
and"eliminate"infections"there"
o Some"effector"T"cells"migrate"from"the"T"cell"zones"towards"the"B"cell"follicles"to"‘help’"B"
cells"produce"higher"affinity"antibodies"
o Effector"T"cells"secrete"cytokines"which"are"responsible"for"mediating"elimination"of"
pathogens"
• Memory"T"cells"are"long!lived"and"functionally"inactive"until"they"contact"their"antigens"again"
• Activation"of"T"cells"is"tightly"controlled"
Control"of"T"cell"activation"• Activation"is"tightly"controlled"by"several"receptors"on"T"cells"binding"to"ligands"on"dendritic"cells"
• T"cell"activation"involves"‘cross!talk’"between"T"cell"and"DC"
• Exchange"of"signals"occurs"at"the"immunological*synapse*(the*following*4*steps)"
1.*Recognition*of*Peptide*and*MHC*
• TCR"recognises"peptide!MHC:"antigen"specificity""
• TCR"recognition"is"MHC!restricted"(Doherty"and"Zinkernagel)"
• TCR"binding"to"peptide!MHC"is"low"affinity"so"two"or"more"TCR"(number"depends"on"peptide)"must"
be"engaged"for"several"minutes"to"commence"activation""
2.*a.*CoFReceptors*
• CD4"co!receptor"on"T"helper"cells"binds"conserved"β2"chain"on"MHC"class"II""
• CD8"co!receptor"on"cytotoxic"T"cells"binds"conversed"α3"chain"on"MHC"class"I"
• Stabilises"low"affinity"binding"of"TCR"to"peptide!MHC"
• Ensures"appropriate"T"cell"type"is"activated"
• Activation"via"signaling"through"TCR"complex"
o CD3"molecules"(γ,"δ,"ε)"+"zeta"(ζ)"chain"
o Always"associated"with"TCR"in"cell"membrane""
o Provide"activation"signal"transduction"via"immunoreceptor"tyrosine!based"activation"motif"
(ITAM)"sequences."This"is"present"in"cytoplasmic"part"of"the"tails"of"their"molecules.""
2.*b.*Adhesion*Molecules*
• Need"T"cells"and"dendritic"cells"to"stick"together"
• LFA!1"(leukocyte"function!associated"antigen!1"alo"called"CD11a)"is"an"integrin"molecule"expressed"
in"the"T"cell"membrane.""
• Adhesion"molecules"increase"binding"affinity"of"TCR"to"peptide!MHC"complex"
• Both"CD8"and"CD4"use"this"adhesion"