5. Innate Immunity

Learning Outcomes: L6-9

• Understand the difference between pathogens and commensals
• Explain what is an antigen
• Appreciated the differences between the innate and adaptive immune system
• Summarise the properties of basic cell types of the immune system: Neutrophils, Macrophages, Dendritic Cells, B Lymphocytes, T Lymphocytes
• Become familiar with structure and function of tissues of the immune system: Lymphatic system, Secondary Lymphoid Tissues (Lymph, Nodes, Spleen), Primary Lymphoid Tissues (Thymus, Bone Marrow)
• distinctive features and functions of primary and secondary immune organs
• the topography of embryonic and post-natal haematopoiesis
• the structure of the thymus
• the structure and function of the spleen
• the structure of the lymphatic system
• the structure of lymph nodes
• the relationship between structure and function of immune organs
• characteristic features of immune cells in pathology specimens

Learning Outcomes:

• the principles underpinning innate immunity
• the principles of inflammation
• the mechanism of phagocytosis
• the basic biology of neutrophils
• the basic biology of macrophages
• the basic biology of dendritic cells
• the basic biology of natural killer cells and other innate lymphoid cells
• The principles underpinning complement activation and function
• How innate immune cells sense pathogen
• The type I interferon cascade and function of IFNb
• The NFkB cascade and function of selected cytokines
• How innate immune cells present antigen
• The significance of negative regulators of innate immunity

What is a...

• ​​​​​​Pathogen
• An organism that causes disease: virus, bacteria, fungi, parasite
• Roles in fermentation, digestion, absorption of nutrients
• Host/Microbe symbiosis (how they interact)
• Commensal= one organism benefits, other unaffected
• Mutalism= both orgainsms benefit
• Parasitism= one organisms benefit at expense of the other
• Microbes can be intracellular/extracellular, pathogenic/not- all need to multiply and spread
• Antigen
• Molecule capable of inducing an immune response
• Not always derived from a microbe (cell antigens), not all microbes have antigens(commensal bacteria do't cause immune response)

Mechanisms in Preventing Disease

• Mucosal barriers (physical barrier)- skin, respiratory tract, intestines
• Innate immune system- specific but not highly
• Immediate- what you loose in specificity, gain in speed
• Recognises foreign pathogens via germ-line encoded receptors (inherited receptors)
• No memory
• Adpative immune system- very specific
• Takes days to develop
• Highly specific requires rearrangement of receptor genes (not inherited),
• Generates memory

Mechanisms in Preventing Disease

• Upon encountering a microbe, a cell tries to:
• Clear the microbe or inhibit its replication- phagocytosis, interferon system
• Process the microbe and present to adaptive immune cells
• Alert and attract other cells that will help clear the infection- upregulation of surface receptors, cytokines, chemokines
• Kill itself
• All cells have the potential to perform these activities (to a certain extent), some cells are specifically made and programmed(armed) to do the first 3= innate immune cells

Microbes and the immune system

• 
• No/short pathology= illness, clearance
• Acute disease= infection that is failed to clear
• Chronic disease/prolonged= failure to clear pathogen and failure to stop by immune system

Lymphoid Tissues

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• Primary and Secondary lymphoid tissue
• Immune cells develop in primary lymphoid organs (Thymus and Bone Marrow)
• Lymphocytes differentiate to express antigen receptors: Thymus= T lymphocytes, BM = B lymphocytes
• ​​​​​​​Immune responses occur in secondary lymphoid tissue (Spleen, LN, Peyer's Patch, Mucosal Associated Lymphoid Tissue (MALT), Gut Associated Lymphoid Tissue (GALT), Nasal Associated Lymphoid Tissue (NALT))

Lymphoid Tissues

• Rules of Lymphoid Organs:
• Lymphocytes originate and are initially selected to fit the purpose in the primary lymphoid organs
• Lymphocytes are ultimately armed in secondary lymphoid organs (where response happens)
• Such effective, specific armament of lymphocytes takes place when the adaptive immune responses are initiated, e.g. in response to infection
• The divergent weaponries of lymphocytes, just as those of innate cells, are unleashed in the non-lymphoid target tissues
• Functional adaptive immunity requires orchestrated interactions of different immune cells in specific microenvironments within primary and secondary lymphoid organs.
• Functional immunity requires tightly regulated movement of immune cells between immune organs and non-lymphoid target tissues
• Organized structures of lymphocytes in target tissues and organs are often referred to as tertiary lymphoid organs (TLOs)

Primary Lymphoid Tissue: BM

• Haematopoeisis- occurs in bone marrow
• Process of generation of all blood system from HSC
• Haematopoetic cells develop from a common precursor either a common myeloid progenitor or common lymphoid progenitor
• 

Primary Lymphoid Tissue: BM

• Haematopoesis through life
• Fetal life: occurs in yolk sack- from week 4 of development, liver until shortly before birth, spleen until cartilagenous bone vascularised
• Adult/infact life: occurs in BM in children, in adults occurs in BM of pelvis, sternum, vertebrate, cranial bones (less in long bones due to fat deposition)
• Emergency haematopoeisis: in adult life due to chronic inflammation, also occur in spleen, liver or LN (extramedullary haematopoesis)
• 
• Caption: Potential of different bones to be a source of blood cells during life, some bones maintain ability to host HSCs and some lose it (longer bones)

Primary Lymphoid Tissue: Thymus

• Educating T cells: Consists of epithelial cells that house train lymphocytes so they don't recognise self-antigens
• Immature T cells migrate from BM to thymus where they multiple and mature (only 2% of immature T cells achieve proper education to become mature)
• Reaches its peak size by puberty and decreases after (thymus involution)

Primary Lymphoid Tissue: Thymus

• Thymus Structure:
• Capsule= surrounds the 2 lobes holding them together
• Trabeculae= extensions of capsule into cortex and medulla, establish incomplete thymic lobules where blood vessels and nerves pass
• Cortex= Outer layer containing immature T cells from BM
• Medulla= Inner layer mature T cells and Hassals corpuscles (epithelial structures)
• Thymic evolution: with aging= decrease of size and production of naive T cells, increase in adipose tissue, decrease immune function
• 

Secondary Lymphoid Tissue: Spleen

• Highly organised structure:
• Areas rich in immune cells (white pulp)
• Contains specific lymphoid microenvironments (T and B cell zones)
• Contains (PALS) periarteriolar lymphoid sheath in T cell zone- Proliferating lymphocytes around central arterioles, which are branches of the splenic artery(connects spleen to rest of body)
• Areas rich in RBC (red pulp)
• Filters blood, removed old RBCs and other cells, contains macrophages, carry out extramedullary haematopoesis
• Directs immune responses to antigens in the blood
• Hyposplenism= under developed spleen, predisposes to infection
• Splenomegaly= enlarged spleen, common in chronic inflammatory diseases (malaria)

Secondary Lymphoid Tissue: Lymphatics

• Drainage system involved in fluid balance: returns to the blood excess interstitial fluid, plasma proteins, tumour cells use this pathway for spreading from its primary site metastasis (due to inc flow)
• Lymph capillaries: Originate as closed tubes in almost all tissues (except CNS, epidermis and cartilage)
• Capillary wall is constructed of overlapping endothelial cells that respond to fluid pressure
• Lymph vessels: Carry lymph and cells from peripheral tissues to draining LNs
• Lymph:
• Plasma containing proteins and solutes that filters out of venules+ capillaries due to hydrostatic/oncotic pressure
• Tissue derived pathogens may be in lymph
• Cells carried in lymph: lymphocytes, DCs, macrophages, phagocytes

Secondary Lymphoid Tissue: Lymphatics

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• 2 types of lymphatics based on where they are:
• 1. Superficial Lymphatics: follow superficial veins, connect to primary LNs (axillary, inguinal, cervical), drain into deep lymphatics
• LNs strategically placed near areas that serve as entry points of infection
• Symmetrical-2 of each
• Trunk can be divided into 4 quadrants with different drainage by vertical and horizontal lines through umbilicus

Secondary Lymphoid Tissue: Lymphatics

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• 2. Deep Lymphatics: follow main vessels, connect to LN deeper in organs (oara-aoartic nodes either side of the aorta drain the paired organs, nodes anterior the gut etc (pre-aortic)
• Thoracic duct- longest lymph vessel connecting upper LN network to lower network:
• Lymph from 3/4 of body drains into left brachiocephalic vein via thoracic duct
• Lymph from upper righ quadrant enters to righ brachiocephalic vein

Secondary Lymphoid Tissue: Lymphatics

• Lymph Nodes
• Pea sized immune structures strategically placed around the body
• Central component of host defence: represent meeting place for immune cells and their exposure to antigen
• Structure of LN:
• Medulla: contains lymphatic sinuses, plasma cells, B cells, macrophages
• T cell Paracortex
• B cell follicles:
• Primary follicle= mature, naive B cells
• Secondary follicle= Germinal Center reaction: GCs develop in response to Ag stimulation, site of B cell proliferation, selection, affinity maturation and differentiation (where antigenic responses develop)

Cell Movement to and out of LNs

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• Flow of fluid is directional
• Naïve lymphocytes enter via high endothelial venules and exit via efferent(E=EXIT) lymphatics
• APCs enter via afferent lymphatics(A=arrival), scan for lymphocytes and exit via different lymphatics

Cell Movement to and out of LNs

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• How B and T cells are separated:
• Cell movement caused by membrane receptors pulling cell towards areas rich in their ligand= chemotaxis
• Distinct structural (stroma) cells in LN produce distinct chemokines that attract B or Tcells
• B cell areas- CXCL13 (ligand of CXCR5 receptor on B cells)
• T cell areas- CCL21 and CCL19 (ligands of CCR7 receptor on naive T cells and DCs - DCs APCs attracted to same place as T cell

Cell Movement to and out of LNs

• Chemotaxis: Directed movement of cells or organisms in response to chemicals. The cells are attracted or repelled by substances (chemoattractants), commonly forming gradients
• Chemokines: chemotactic cytokines (secreted soluble proteins)

Similar Structure of Spleen and LN

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• Similarities:
• Entry and exit points
• B cell follicles, T cell zones
• Same ligands
• Organised in a similar way since this structure is very efficient to optimise immune response

Mucosa Associated Lymphoid Tissue

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• Similar organisation to spleen and LNs
• Large organised aggregates of lymphoid tissue in digestive, respiratory and genitourinary tracts
• Peyer's Patch:
• Organised aggregates of lymphoid cells in ileum
• Essential for monitoring bacteria populations, preventing growth of pathogenic bacteria in intestine
• Contain large population of Ab-producing plasma cells (exceeding amount in the spleen, lymph nodes and bone marrow combined)

Pathology- how we study tissues

Innate Immune System Overview

• Antigen non-specific:
• Phagocytic cells (macrophages) detect foreign material and seek to remove
• Aided by low number of receptors that recognise broad molecular patterns (not present in euk)
• Macrophages (first line of defence):
• Induce inflammation through secreting soluble factors (cytokines+chemokines)
• Phagocytic
• Found in all peripheral tissue
• Neutrophils:
• Most common WBC in blood
• Migrate rapidly to site of inflammation
• Phagocytic- ingest and kill bacteria
• Release toxic granules

Innate Immune System Overview

Adaptive Immune System Overview

• Antigen Specific: B and T cells require help from T helper cells to respond
• B and T cells express antigen-specific receptors, both are highly variable, specficity confined to a single clone
• Ab on B cells recognise 3D structures and linear peptides
• T cell receptor (TCR) only recognise linear peptides (ensure dont self attack)
• Clonal Expansion:
• Activation of antigen receptor, B and T cells expand, mature and differentiate into highly specialised cell populations

Adaptive Immune System Overview

• DCs: Interphase of Innate and adaptive immunity
• Phagocytic
• Characterised by presence of long dendrite process
• Main function: activation of adaptive response
• Actively survey peripheral tissues, once activated migrate to LN to activate antigen specific naive Tcells
• Lymphatics vessel network:
• Fluid drainage from peripheral tissues, LNs found at drainage points
• If destroyed= Surgically induced lymphodema (associated with breast cancer surgery), elephantiasis(induced by parasitic worms that block draining lymphatic)
• LN= highly organised, B cell follicle- rich in B cells Ab response generated, T cell zone- rich in T cells T cell-DC interactions, T helper response helps make antibodies

Adaptive Immunity Overview

• Steps of adaptive immune response:
• Activation of tissue DCs
• Migration to LN- attracted to same place as T cells due to chemokines
• Activation of antigen specific T helper cells
• Activate B cell- antibody producing cell
• B cell proliferates and produces plasma cells, plasma cell produces Ab

Inflammation

• Occurs as result of infection/ damage(wound)- aim to clear infection and repair(tissue) damage
• Characteristics: Redness, swelling, pain
• A prerequisite for a successful immune response
• Also a potentially harmful process: Components of inflammation that are capable of destroying microbes can also injury bystander normal tissue (if the response is too strong or too long)

Inflammation

• Roles of inflammation in combating infection:
• Deliver effector cells and molecules to site of infection/damage- enhance microbe clearance
• Blood clotting- form physical barrier and prevent spreading of infection to bloodstream
• Enhancement of tissue repair process (resolution of inflammation part of process)
• Three changes to blood vessels during inflammation:
• Increased diameter- dilate, enhance number of cells and molecules reaching site
• Increased adhesion molecules that bind leukocytes- sticky around site of damage
• Increased vascular permeability- allows exit of fluid and proteins into tissue= edema (swelling)
• Extravasation= Attachment of leukocytes to the endothelium followed by their migration through blood vessels to infected tissue

Innate Immune Cells: Myeloid

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• Myeloid lineage innate immune cells
• Neutrophils, macrophages, myeloid DCs
• Derived from common myeloid progenitor (CMP)
• Others cells from the lymphoid lineage are derived from common lymphoid progenitor (CLP)

Innate Immune Cells: Myeloid

• Neutrophils: first at the scene
• Form polymorphonuclear family together with basophil and eosinophils
• Most abundant WBCs = 40-75%
• Recruited to site of infection of injury within minutes
• Predominant cells in pus
• Short lived, quick acting, motile
• Kill pathogens in 3 ways: Phagocytosis, Degranulation, Neutrophil extracellular traps (NET)

Phagocytosis

• Targets (microbes/infected cells) coated in opsonins- protein tag (eg Ab FcR) that enhances phagocytosis
• Requires membrane rearrangement
• Steps:
• Attachment/adhesion and engulfment
• Phagosome formation- invaginations of membrane
• Recruitment of lysosomes
• Phagosome-lysosome fusion
• Microbe killing due to low pH in phagosome and high conc of: ROS, Defensins (antimicrobial peptides), Hydrolytic enz
• 

Degranulation + NETs

• Degranulation
• Once neutrophil is activated-> secrete toxic granules
• Release azurophilic (primary) or specific (secondary) granules- contain proteases, defensins, ROS
• Efficient way of clearing surrounding space in non-highly specific manner
• Neutrophil Extracellular Traps (NETs)
• Usually associated with bacterial infections
• Networks of extracellular fibres primarily composed of DNA and antimicrobial proteins (histones, neutrophil elastase)
• Creates a sticky environment and traps microbes/pathogens- makes them less motile
• Kill them through localised high conc of antimicrobial proteins

Innate Immune Cells: Myeloid

• Macrophages: mature form of monocytes
• Reside in tissue (monocytes are in circulation): eg Microglia = brain, Kuppfer cells= liver, Osteoclasts= bone
• Upon infection: tissue-resident macrophages phagocytose microbes, monocytes are recruited to the infected tissue and mature into macrophages
• Activated through: ​​​​​​​direct interaction with pathogens, factors secreted by T-helper lymphocytes (eg IFNϒ, IL4= cytokines)​​​​​​​
• Function:
• ​​​​​​​Highly pathogenic: engulf and destroy pathogens
• Secrete cytokines that orchestrate inflammatory response
• Present antigens to T lmyphocytes
• Contribute to tissue repair and formation of new blood vessels

Innate Immune Cells: Myeloid

• Myeloid Dendritic Cells: Professional APCs- directly link innate and adaptive
• Long finger- like projections
• Immature DCs migrate from bloodstream to tissues or are tissue-resident
• Phagocytic but not as much as macrophages
• Scan for presence of potential microbe and become activated (mature) upon encounter
• During maturation:
• Become less phagocytic and endocytic
• Proliferate
• Process microbial proteins to small peptides and present to T lymphocytes
• Up-regulate the expression of surface proteins and cytokines for optimal antigen presentation
• Secrete type I interferons: inhibit pathogen replication, induce apoptosis of nearby infected cells, enhance presentation
• Migrate to nearest LN through lymphatics system

Innate Immune Cells: Lymphoid

• Plasmacytoid DCs (pDCs): Subset of DCs derived from CLP that look like plasma cells
• Rare- less than 0.5% of PBMCs
• Antigen sensing/recognition similar to myeloid DCs
• Main function: NOT antigen presentation but production of type I interferons(IFNα and IFNβ), important in antiviral responses

Innate Immune Cells: Lymphoid

• Innate Lymphoid Cells (ILCs):
• Newly discovered family of lymphoid cells that translate cytokine signals into effector cytokines w/out expressing antigen specific receptor (produce cytokines to kill a cell)
• ILCs mirror the phenotypes and functions of T cells:
• Make similar things upon activation but no antigen receptor (do not directly respond to antigen) and no clonal selection upon stimulation
• ILCs respond to signals from infected/injured tissues and produce cytokines
• NK cells -> cytotoxic CD8+ T cells = eg Natural killer cells mirror what CD8+ T cells do
• ILC1 -> CD4+ T helper 1 (TH1) cells
• ILC2 -> CD4+ T helper 2 (TH2) cells
• ILC3 -> CD4+ T helper 17 (TH17) cells
• Next slide- both innate and adaptive cell mirrors

Mirrors

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• CD8 vs NK:
• CD8 cells characterised by ability to make 3 things: Granzymes, Perforin, IFNϒ
• NK cells once activated make the same thing but much earlier and less specific
• ILCs vs T cells
• ILCs sense signal cytokines eg IL12, IL15, IL33 etc
• Translate that signal into an effect
• T cells do this but in a specific and sustained manner

Innate Immune Cells: Lymphoid

• Natural Killer Cells: Type of ILC
• Terminally differentiated cell of lymphoid lineage
• Larger than B and T lymphocytes
• Characterised by cytoplasmic granules containing cytotoxic proteins (granzyme and perforin) that are secreted to kill infected cells
• Also secrete type II IFNϒ cytokine and kill infected cells before cytotoxic T lymphocytes
• 

Innate Immune Cells: Lymphoid

• NK cells become activated in response to:
• Type I interferons (IFNα and IFNβ) secreted by other innate (myeloid) cells (macrophages and DCs)
• Other cytokines produced by an infected tissue (eg IL15)
• Their cytotoxic activity is controlled through inhibitory and activating receptors on their cell membrane
• 2 main functions of NK (mechanisms of clearing infected cells):
• Clearance of 'missing self 'cells
• Antibody-dependent cellular cytotoxicity

Innate Immune Cells: Lymphoid

• Missing self :
• Almost every cell in body expresses MHC-I on surface (immune system recognises 'self')
• Many pathogens down-regulate MHC-I expression in infected cells- t​​​​​o escape recognition, avoid clearance by cytotoxic T lymphocytes, also common in cancer cells
• NK cells kill any cells with no/low MHC-I expression (missing-self)
• 

Innate Immune Cells: Lymphoid

• NK cells Antibody-Dependent Cellular Cytotoxicity (ADCC):
• Another way to kill labelled cells
• NK cells carry receptors for the Fc region of Ab
• Microbes/ cells coated with these antibodies trigger NKs to release cytotoxic granules,+ increase phagocytosis
• 

The Complement System

• A system of soluble pattern-recognition receptors and effector molecules that can detect and destroy microbes
• 3 main receptors that activate the cascade:
• C1q(classical pathway)- complement receptor interacts with Ab coated pathogen surface
• Mannose-binding Lectin (MBL) and ficolins (lectin pathway)- Recognises carbohydrates on pathogen surfaces
• C3 (alternative pathway)- Undergoes spontaneous hydrolysis leading to deposition of C3 convertase on pathogen surface, spontaneous activation of cascade through accumulation of C3 protein on pathogen surface

The Complement System

• The complement activation cascade:
• Circulating proteins react with eachother to fight infection- many are inactive precursor proteases(zymogens)
• At site of infection:
• Initiation of complement system through 1 of 3 ways
• Activates complement enzyme (through proteolytic cleavage of its zymogen
• Activated enzyme cleaves it substrate (another complement zymogen), activating it
• Amplification= activation of small number of complement proteins at start of pathway is amplified-> rapid generation of large complement response
• Has to be strongly regulated to prevent uncontrolled complement activation

Complement Components

Function of Complement

• Complement system helps Ab and phagocytes clear microbes form an organism in 3 ways:
• Opsonisation- enhancing phagocytosis, complement molecule bound to Ab makes phagocytosis easier
• Chemotaxis- some complement proteins act as chemoattractants to recruit more phagocytes to site of complement activation
• Pathogen lysis- complement compounds directly damage bacteria by creating pores in bacterial membrane
• There is a limited number of complement molecules that can perform all 3 functions

Complement: C3 Convergence Pathway

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• Activation of C3 is key event in complement activation
• Mediates effector functions, initated by all 3 pathways

Complement: Immune Complex Clearance

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• A. Antigen-antibody complex formed in the circulation
• B. Complement activation-> deposition of C3b on complex
• C. Complement receptor CR1 on erythrocytes binds immune complex through C3b
• D. Erythrocytes go to spleen and liver, phagocytosis physically removes immune complex from erythrocyte surface

Pathogen Recognition by Innate Cells

• Broad Pathogen Associated Molecular Patterns (PAMPs) are recognised by a small number of Pattern Recognition Receptors (PRRs)
• PRRs are inherited (germline encoded), do not change / adaptive immunity receptors are specific and change
• PRRs are less specific than adaptive receptors- specific enough to distinguish gram -ve from gram +ve but not gram +ve from gram +ve

Innate vs Adaptive Receptors

PAMPs

• Found on nearly all surfaces of a pathogen class
• Eg LPS on surface of Gram -ve bacteria
• Eg dsRNA in dsRNA viruses
• PAMPs are structures essential for the microbes survival

PRRs

• A few proteins can be used to sense millions of pathogens
• All cells express SOME PRRs, DCs and macrophages express ALL PRRs
• 4 families of PRRs:
• Toll-like Receptors (TLRs)
• 10 in humans, cover any type of potential pathogen
• Localisation on endosome: TLR3, TLR7, mainly dealing with viruses (have to enter cell because obligate parasites)
• Or localisation on cell membrane: Cell membrane= TLR2 (recognises Gram +ve bacteria- peptidoglycan), TLR4 (recognises Gram -ve bacteria- LPS)
• ​​​​​​​Nucleotide-binding oligomerisation domain (NOD)- like receptors (NLRs)
• C-type lectin receptors (CLRs)
• RIG-1 like receptors (RLRs)

PRRs

PRR Activation: Kinase Cascade

• 
• Exposure of cell to PAMP
• Kinase signalling cascade (with adaptor proteins)
• Activate TF to translocate to nucleus
• Targets:
• Amplifiers
• Antipathogen molecules/mechanisms
• Messengers to activate adaptive response
• Negative regulators to prevent overwhelming activation, eg. ubiquitin ligases ubiquitinate proteins leading to their degradation

Example: TLR4 Activation at Cell Mem

• 
• TLR4 binds LPS
• Kinase cascase
• Activation of 3 transcription families (IRF3, NF-KB, AP-1)
• Downstream of IR3= transcription of IFN-B (type I interferon)
• NF-kB and AP-1 pathways lead to production of inflammatory regulators
• Positive feedback- IFNB activates more cells that express IFNB
• IFNB also activates second wave of TF (STAT family) that contribute to antipathogen gene expression

TLR4 Activation Depends on Localisation

• TLR4 only TLR localised on both endosome and membrane
• MyD88 and TRIF are important adaptor proteins
• MyD88= early event in activation, essential for any TLR response (except TLR3)
• TRIF= shared between TLR3 and TLR4 (only TLR4 when in endosome)
• 

NF-kB Activation Downstream PRRs

• 
• Induces transcription of:
• Chemokines- attract other adaptive and innate immune cells
• Cytokines- promote inflammation eg IL1B, TNFa, IL6, IL8 (which are induced rapidly/ early)

IRF3 + IRF7 Activation Downstream PRRs

• Induce transcription of IFNβ and IFNα and ISGs
• Secreted type I IFNs bind IFNAR (interferon A receptor)= Positive feedback (production of early IFNs)
• Induces second wave of interferon stimulated genes (ISGs) through the action of other TFs of IRF and STAT
• 

Function of Type I interferons

• Functions in immune response:
• Inhibition of pathogen (virus, parasite) replication through inhibition of protein translation in the infected cell
• Induction of cell-death (apoptosis) of infected and neighbouring cells
• Activation of other innate immune cells (eg natural killer cells)
• Activation of antigen presentation machinery (make DCs and macrophages present antigens to T cells)= initiation of adaptive immunity

Summary: 2 Pathways in Innate Activation

• The type I interferon pathway
• Driven by activation of the IRF family TFs
• Leads to production of IFNβ and other interferon stimulated genes (ISGs)
• The NF-κB pathway
• Driven by the activation of the NF-κB TF
• Leads to the production of cytokines (e.g. IL1b, TNFa, IL6)
• Transcription of several inflammatory cytokines + surface receptors can be activated downstream by either pathway

Antigen Presentation Machinery

• Distinct pathways for intracellular and extracellular antigens:
• Components of both systems (including MHC molecules) are upregulated in response to type I interferons (produced in response to PAMP)
• MHC-I proteins have cargo (peptide): self peptide or microbial (antigenic) peptide
• 

End of Innate Immune Response

• Innate immune gene expression programme induces its own negative regulators in later stage:
• Anti-inflammatory cytokines eg IL10
• Phosphatases- stop signalling cascade eg dephosphorylation of p38 by DUSPs
• Intracellular factors: inhibit inflammatory TFs eg lκB (ubiquitin ligase) prevents NFκB from going to the nucleus
• MicroRNAs: non-coding, suppress translation of inflammatory mRNAs eg suppresion of TRAF6 and IRAK1 by miR-146a
• Prolonged response can lead to tissue damage and disease caused by immune system:
• Eg non-cytopathic viruses (hepatitis virus) that establish chronic infection
• Lead to chronic inflammation, creates long, non-resolving response that will damage liver