Week 12: Immune Signalling

• 2 types of immunity

  • innate immunity is a general and rapid response that all organisms have and includes cells like macrophage, neutrophils, and dendritic cells
  • adaptive immunity is a learned and specialized response that have memory for future infections and includes cells like B and T cells

  
• macrophages (innate) are professional phagocytes that engulf bacteria which trigger them to release cytokines/chemokines

  • cytokines increase permeability of blood vessels which allow fluids and proteins to pass into the tissues
  • chemokines recruit and guide other immune cells like neutrophils to the site of infection

  
• macrophages distinguish between bad and good by pathogen associated molecular patterns (PAMP) which are non human molecules that macrophages recognize as foreign (like PG, LPS, flagella) -> PAMP are recognized by pattern recognition receptors (PRR) on macrophages which stimulate it to recruit neutrophils which pick up and break down bacteria

  
• dendritic cells are specialized phagocytes that can still uptake bacteria and break them down, and secrete cytokines/chemokines but they are also antigen presenting cells (APC) which is what connects innate immunity to adaptive

  • APC have PRR that take pathogens -> break down -> present specific parts of a pathogen to a naive T cell which cause it to elicit a response -> cause B cells to make specific antibodies (form memory)

  
• phagocytic cells include macrophages, neutrophils, and dendritic cells which use phagocytosis to engulf foreign particles resulting in pathogen destruction and presentation of degraded pathogen to adaptive immune cells
• all innate immune cells can recognize foreign particles and trigger their destruction and promote inflammation
• granulocytes include mast cells, eosinophils, neutrophils, and others which respond to pathogens by degranulation (exocytosis of vesicles that contain material to promote inflammation)
• innate immune response involves recognizing 1) foreign molecules or 2) molecules indicating damage to cells THEN releasing factors that promote an inflammatory response

  • cytokines can induce a pro (IL1) or anti (IL10) inflammatory response
• pro inflammatory signals lead to

  • vasodilation to promote blood flow -> more immune cells at affected area
  • increase vascular permeability -> leukocytes leave blood vessels and enter tissues
  • increase binding and targeting of certain cells (neutrophils) at infection site
  • increase in cell death at infection site to eliminate damaged/infected cells
• PAMP are different and have different toll like receptors (TLR) for each

  • TLR2 -> polyglucan, porins
  • TLR3 -> dsRNA
  • TLR4 -> LPS, mannan, fibrinogen
  • TLR5 -> flagellin
  • TLR6 -> lipotechoic acid, zymosan
• damage associated molecular patterns (DAMP) are internal cell components found outside the cell that are indicative of damage to the cell -> triggers innate then results in 'sterile' activation of adaptive immune system

  • examples are ATP, Cytochrome C (mitochondria), cardiolipin (mitochondria)

  
• while each PAMP/DAMP recognition by a cellular sensor is unique, most lead to the activation of an NFkB signalling pathway
• TLR can be plasma membrane bound for extracellular antigens or intracellular TLR for antigens inside the cell

  • can also have RLR or NLR

  
• PAMP/DAMP recognized by TLR -> TLR dimerization => extracellular TLR activates MyD88 pathway, intracellular TLR activates TRIF pathway -> each pathway results in IKK complex activation which contains NEMO and alpha/beta subunits -> IKK di auto phosphorylation on beta subunit -> IKK phosphorylates IKB (blocks NLS on NFKB) at 2 places which causes ubiquitination and degradation -> NFKB is liberated from IKB which exposes the nuclear localization signal (NLS) and allows it to act as TF for NFKB target genes which usually signal for synthesis of pro inflammatory cytokines depending on context

  
• if no PAMP/DAMP -> NFKB protein is tightly bound to IKB to keep it inactive since IKB blocks the NLS on NFKB to be a TF
• it was found that TLR sensors and MyD88/NEMO are needed for immune system response by causing knockouts in different TLR forms and MyD88 in transgenic mice and infected them with salmonella (gram negative) to monitor survival

  • most types died quicker than the wild type but MyD88 had the most severe since all the extracellular TLR converge at MyD88 activation so mutating that would make the mice unable to recognize ANY kind of extracellular infection
  • same goes for NEMO (intracellular TLR converge here)

  
• cytokines are small protein hormones that act as local mediators in cell/cell communication between immune cells which signal through autocrine, paracrine, endocrine

  • function -> recruit immune cells to site of infection, induce signal transduction to activate specific genes, fighting infection
  • dysregulation -> advanced inflammation, sepsis (cytokine storm)
  • types of cytokines -> chemokines, interferons, interleukins, lymphokines, TNF
• cytokine receptors activate the JAK/STAT pathway

  • cytokine binds inactive monomeric cytokine receptor -> homodimerization of receptors to activate JAK -> associated protein kinase JAK auto/trans phos the JAK and C terminal tyrosine rich tail -> STAT binds to P~ tyrosine site with SH2 domain and is close to JAK -> JAK phos STAT at another site -> STAT outcompete cytokine receptor for homodimerization of P~ STAT through SH2 domain specificity -> homodimer contains tertiary motif that binds alpha importins -> homodimer enters nucleus to be a TF for cytokine responsive elements

  
• JAK/STAT mutations causing:

  lack of signalling -> susceptible to infection/disease

  too much signalling -> excessive inflammation and excessive growth (cancer)/dysplasia
• inflammasomes are a sensor system that are responsive to intracellular PAMP/DAMP at their N terminal which cause oligomerization -> changes conformation to let C terminal interact with adaptor protein or directly with proeffector to activate it through proteolysis to make an effector which cleaves procytokines to mature cytokines

  
• inflammasome sensors are grouped according to their structural features such as nucleotide binding domain like receptors (NLR)

  • NLRP1 sense lethal toxin
  • NLRP3 sense PAMP/DAMP
  • NLRC4 sense needle, rod, flagellin
  • AIM2 sense dsDNA
  • pyrin sense toxin

  
• the C terminal side of inflammasomes/NLR is the site of the activation of caspase-1 which contains PYD and CARD domains and only homodimerize NOT hetero -> procaspase-1 has PYD and CARD domains that bind to these domains on the inflammasome -> oligomerization of NLR -> cleave procaspase-1 to caspase-1 which gets further cleaved into p20 which is a proeffector that cleaves/proteolyzes targets like

  • Gasdermin D -> N terminal fragment triggers pyroptosis
  • pro-IL1beta -> IL1beta, pro inflammatory cytokine for activation and inflammation

  
• inflammasome activation leads to IL1beta release which signals for more inflammation in other cells

  • IL1beta binds IL1 receptor on immune/tissue cells -> triggers recruitment of adaptor protein MyD88 which leads to activation of IRAK kinase -> IRAK forms complex with TRAF6 and TAK to activate NFKB and MAPK -> more synthesis of pro inflammatory genes

  
• pyroptosis is a unique form of programmed cell death different from classical apoptosis and is activated by Gasdermin D cleavage

  • PAMP/DAMP activates inflammasome -> activate caspase-1 -> activate GasD which forms pores in the cell -> cause pyroptosis which is a controlled mechanism to eject cellular contents (proteins, small molecules, metabolites) into the extracellular space so neighbouring cells detect that something is wrong then recruit immune cells