First line and induced innate defence

• What are the three types of protection against pathogens?

  1. Barrier: physical barrier, antimicrobial enzymes And peptides, and the complement system
  2. Innate immune system: direct killing, phagocyte recruitment, and acute phase response
  3. Adaptive immune system: expansion of antigen-specific lymphocytes and formation of memory cells
• Describe the cellular effectors in innate immunity

  • Macrophages and monocytes: first cells to respond
  • consist of resident (sensor) and monocyte derived macrophages (effectors)
  • Granulocytes: specialised effector cells
  • Dendritic cells: antigen presentation, trigger T cell response
• Describe PAMPS

  Pathogen Associated Molecular Patterns (PAMPs)

  • Motifs presented by pathogenic organisms
  • Bacterial components
  • LPS, peptidoglycan, And flagelllin
  • Viral ssRNA
  • Viral dsDNA
• Describe DAMPs

  Damage Associated Molecular Patterns (DAMPs)

  • Motifs present in endogenous molecules shielded from the immune system until after injury
  • DNA, heat shock proteins, and ATP
• Describe pattern recognition receptors

  These receptors recognise PAMPs and DAMPs to stimulate cytokine production, phagocytosis, and ROS production. Used in both innate and adaptive immunity:

  • Innate: recognise pre-defined structures, germline encoded
  • Adaptive: formed via random gene rearrangement and recognise random structures

  Consist of both plasma membrane bound receptors (C-type lectins, scavenger receptors, complement receptors, and Fc receptors) and intracellular (RLRs, cGAS, NLRs) and they ingest bound particles, leading to internalisation and destruction.
• Describe C-type lectin receptors

  These receptors are found on dendritic cells.

  • e.g.., dectin-1: binds to beta-1,3-glucans, fungal recognition
  • mannose receptor: binds to mannosylated ligands, fungal, bacterial, viral recognition

  Stimulate the production of pro-inflammatory mediators.
• Describe scavenger receptors

  Class A: I, II and MARCO

  • bind to low density lipoproteins, recognise bacteria

  Class B: CD36

  • bind to long fatty acid chains
• Describe the structure of toll-like receptors

  Family of similar molecules linked to inflammatory cytokine expression found in mammals.

  • Leucine-rich repeats (LRR): determines ligand specificity
  • Toll IL-1 receptor domain (TIR): induces intracellular signalling
  • Transmembrane domain
• Describe signal transduction for TLRs

  TLRs activate transcription factors: NF-kB, AP-1 and IRF. This results in induction of cytokine and interferon expression, which stimulates anti-viral or anti-bacterial responses.

  1. Dimerised TLRs recruit IRAK-1 and IRAK-4, which activate TRAF-6 (E3 ubiquitin ligase)
  2. TRAF-6 and NEMO are polyubiquitinated to create a scaffold for the activation of TAK1.
  3. TAK1 associates with IKK and phosphorylates IKK-beta, which in turn phosphorylates IkB.
  4. IkB is degraded, releasing NFkB into the nucleus to induce expression of cytokine genes
• Describe the function of IRFs

  Interferon regulatory factors are transcriptional regulators that are phosphorylated to induce IFN gene expression

  • IRF3: promotes antibacterial and antiviral innate immunity
  • IRF7: promote antiviral innate immunity
  • IRF9: mediates type I IFN responses
• Describe RIG-I-like receptors

  • RIG-I recognises uncapped ssRNA and binds to MAVs, which results in dimerisation and recruitment of TRAF6 and the NF-kB or IRF signalling pathway.
  • Involved in viral recognition
  • Stimulate cGAS and STING activation
• Describe the cGAS/STING axis

  • STING: stimulates interferon genes and senses cyclic dinucleotides
  • cGAS: cyclic GMP-AMP synthase

  1. dsDNA from viruses activates cGAS from ATP and GTP
  2. cGAMP binds to STING dimer present on the ER membrane and activates its signalling
  3. STING activates TBK1, which phosphorylates IRF3. which enters the nucleus and induces expression of type 1 interferon genes.
• Describe the classes of NLRs

  • NLR-A: acidic trans activating domain (not a PRR)
  • NLR-B: BIR domain
  • NLR-C: CARD domain
  • NLR-P: pyrin domain

  All contain a NACHT domain and many contain a leucine rich repeat region
• Describe NOD signalling

  NOD proteins reside within the cytoplasm in an inactive form and they induce a signalling cascade leading to the ubiquitylation and activation of TAK1 and IKK. IKK degrades IKb and activates NF-kB signalling.

  • NOD1: binds to a ligand present in peptidoglycan
  • NOD2: binds to the ligand MDP in peptidoglycan
• Describe the classical secretion pathway for PRR-induced cytokine transcription and secretion

  Most TLRs and NLRs induce gene transcription of cytokines with a secretion signal. These cytokines are then secreted via the classical pathway through the ER and the golgi.
• Describe the unconventional protein secretion pathway

  This pathway is specific to cytokines IL-1B and Il-18, which require processing before being secreted independent of the ER and Golgi. Instead they are secreted via membrane pores, endosomes, and lysosomes. NF-kB induces the expression of IL-1B and IL-18, which are initially translated in a non-active pro-form and are activated via proteolytic cleavage via caspases.
• Describe the role of the inflammasome in the regulation of IL-1B and IL-18

  These are strong pro-inflammatory cytokines, which need to be tightly regulated in order to prevent excessive release. Therefore, two signals, pathogen and damage, are required to stimulate the formation of the inflammasome, which in turn stimulates the assembly of active caspase, which cleaves the cytokines and activates them.