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"

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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""

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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"

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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"

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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"