Innate Immunity Receptors – Detailed Study Notes

Learning Objectives

• Identify, compare, and contrast receptor location & function across innate immune cells.
• Define and explain significance of:
  • Pathogen-associated molecular patterns (PAMPs)
  • Damage-associated molecular patterns (DAMPs)
  • Pattern-recognition receptors (PRRs)
• Recognize soluble PRRs (pentraxins, collectins, ficolins) and membrane/cytosolic PRR families (TLRs, NLRs, RLRs, CLRs, CDSs).
• Map each PRR family to its: structure, cellular/sub-cellular localization, and ligands.
• Classify PAMPs & DAMPs recognized by each PRR; relate to innate immune path-ways.

Big Picture: Where We Are & What We Already Know

• Previously mastered
  • Natural physical barriers
  • Core principles of innate vs. adaptive immunity
  • Immune cell lineages & hematopoiesis
  • Primary & secondary lymphoid organs (BM, thymus, LN, spleen, MALT/GALT/BALT/NALT, tonsils)
• Today’s focus = molecular recognition that triggers innate responses.

Innate Immunity – Core Functions

• Always present and immediately reactive; oldest branch of immunity.
• Two working modes
  1. Direct microbe removal (phagocytosis, degranulation)
  2. Indirect orchestration (cytokine / chemokine secretion → recruits & activates new cells → bridges to adaptive arm)

PAMPs & DAMPs: Definition + Exemplars

• PAMPs = conserved microbial molecules never found on healthy host cells.
  • Nucleic acids: ssRNA (viruses), dsRNA (viruses), unmethylated CpG DNA (bacteria/viruses)
  • Proteins: pilin, flagellin
  • Cell-wall lipids: LPS (Gram-), lipoteichoic acid (Gram+)
  • Carbohydrates: mannan, β-glucans (fungi)
• DAMPs = host-derived signals from stressed, injured, or dying cells.
  • Stress proteins: heat-shock proteins (HSPs)
  • Crystals: monosodium urate (gout)
  • ECM fragments: proteoglycan peptides
  • Mitochondrial components: formylated peptides, ATP
  • Nuclear components: HMGB1, histones, cytoplasmic $\text{dsDNA}$

Pattern-Recognition Receptors (PRRs) – General Rules

• Germline-encoded (no somatic recombination) → limited but sufficient diversity.
• Non-clonal expression: all cells of same lineage carry identical repertoire.
• Self/non-self discrimination: healthy self tissues either lack relevant ligands or display inhibitory signals.
• No classical memory; however PRR expression levels can be modulated (trained immunity concept).
• Located everywhere a pathogen or danger molecule might appear:
  1. Secreted/soluble in plasma & mucus
  2. Cell-surface (plasma membrane)
  3. Endosomal membranes (sense internalized microbes)
  4. Free in cytosol

Recognition Contexts

• Fluid-phase/soluble → circulating microbes, apoptotic bodies
• Cell-associated → outer molecules of invaders or damaged cells
• Cytosolic-endosomal → pathogens captured in phagosomes/endosomes
• Cytosolic-free → intracellular microbes or leaked PAMP/DAMP molecules

I. Soluble PRRs

Collectins (e.g., Mannose-Binding Lectin – MBL)

• Structure: collagen-like stalk + C-type carbohydrate recognition domain (CRD)
• Binds mannose/fucose on fungi, bacteria, apoptotic cells → activates lectin complement pathway → opsonization & cytokine production.

Complement Components (C1q, C3, etc.)

• Bind microbial surfaces or PRR-coated targets → opsonization, lysis, or enhanced phagocytosis via complement receptors (CR1, CR3…)

Pentraxins (C-reactive protein – CRP, Serum amyloid P – SAP, PTX3)

• Cyclic multimers that bind phosphocholine/phosphatidylethanolamine on microbes & dead cells; recruit C1q → classical complement activation.

Ficolins

• Fibrinogen-like carbohydrate binding domain; recognize $N\text{-acetylglucosamine}$ & lipoteichoic acid (Gram+) → activate complement.

II. Cell-Surface PRRs

C-type Lectin Receptors (CLRs)

• Calcium-dependent CRD motif; examples: Dectin-1/2, Mannose Receptor, DC-SIGN.
• Specialised for fungal β-glucans; signal for phagocytosis and tailored cytokine release (e.g., IL-23 → Th17 responses).
• Clinical link: Dectin-1 mutations → recurrent candidiasis.

N-formyl-Met-Leu-Phe Receptors (fMLP-R / FPR family)

• Detect bacterial peptides starting with $N!f!Met$ → induce neutrophil chemotaxis & ROS burst.

Scavenger Receptors (SR-A, CD36, others)

• Broad ligand range: oxidised LDL, diacylglycerides, apoptotic cells; roles in homeostasis, atherosclerosis, pathogen clearance.

Toll-Like Receptors (TLRs) – Plasma-membrane subset

• TLR1/2/6 hetero- or homo-dimers → bacterial lipoproteins, lipoteichoic acid, lipoarabinomannan (mycobacteria).
• TLR4 (+ co-receptors MD-2, CD14) → LPS (Gram-), some viral glycoproteins, HSPs.
• TLR5 → bacterial flagellin.

TLR Architecture & Signalling Cascade

• Extracellular (or luminal) leucine-rich repeats (LRR) = ligand binding site.
• Cytosolic TIR domain = recruits adaptors MyD88 or TRIF.
• Dimerization after ligand binding → kinase cascade → activation of transcription factors NF-κB, AP-1, IRF3/7.
• Outcome spectrum:
  • Pro-inflammatory cytokines (TNF-α, IL-6)
  • Type I interferons (IFN-α/β) via IRF3/7
  • Up-regulation of co-stimulatory molecules on APCs
  • Endothelial activation → leukocyte extravasation

III. Cytosolic PRRs – Endosomal Anchored

Endosomal TLRs

• TLR3 → viral $dsRNA$ (agonist poly I:C); expressed by DCs, NK, B cells.
• TLR7 (constitutive) / TLR8 (inducible) → viral $ssRNA$; agonists imiquimod, R848.
• TLR9 → unmethylated CpG DNA from bacteria/viruses or apoptotic DNA; agonist CpG ODN.

IV. Cytosolic PRRs – Free-Floating

NOD-Like Receptors (NLRs)

• Tripartite modules: LRR (sensing) – NOD/NACHT (oligomerization) – CARD/PYD (signalling).
• NOD1 → $\gamma$-D-glutamyl-meso-diaminopimelic acid (Gram- cell wall)
• NOD2 → muramyl dipeptide (all bacteria)
• Dysfunctions associated with Crohn’s disease, Blau syndrome.

Inflammasome (NLRP3, NLRP1, NLRC4, etc.)

• Multimeric platform → activates caspase-1 → converts pro-IL-1β / pro-IL-18 to active cytokines → pyroptosis.
• Triggers: bacterial flagellin, crystalline urate, ATP, pore-forming toxins.

RIG-Like Receptors (RLRs)

• RIG-I, MDA5, LGP2 sense cytosolic duplexed RNA (dsRNA or panhandle structures) → MAVS adaptor on mitochondria → IRF3/7 & NF-κB → robust type I IFN output.

Cytosolic DNA Sensors (CDS)

• cGAS detects $dsDNA$ → produces $\text{cGAMP}$ → binds STING (ER adaptor) → TBK1 → IRF3 → type I IFN.
• Other STING-independent sensors exist (DAI, IFI16).

Type I Interferon Axis – Convergent Outcome

• Produced downstream of TLR3/7/8/9, RLRs, CDSs.
• Autocrine/paracrine signalling via IFNAR → $\text{JAK}–\text{STAT}$ → transcription of interferon-stimulated genes (ISGs).
• Antiviral effects: block translation, degrade viral RNA, enhance MHC I expression, activate NK cells & dendritic cells.

Functional Consequences of PRR Engagement

• Phagocytosis & intracellular killing (opsonization via C3b, collectins, pentraxins).
• Cytokine & chemokine secretion → local inflammation, systemic acute-phase response.
• Up-regulation of costimulatory/B7 molecules → primes adaptive immunity.
• Endothelial adhesion molecules ↑ → leukocyte trafficking.
• Programmed cell death pathways (pyroptosis, autophagy).

Synergy & Crosstalk

• A single pathogen often triggers multiple PRRs (e.g., virus → TLR3 + TLR7/8 + RIG-I).
• Signalling pathways converge (IRF3/7, NF-κB) allowing tailored yet efficient responses.

Clinical & Therapeutic Relevance

• Vaccine design
  • PRR ligands used as antigens or as adjuvants (e.g., CpG ODN, imiquimod).
• Immunostimulants
  • Cancer therapy, chronic viral infection; 2011 Nobel awarded for PRR discovery.
• Immunomodulation
  • Blocking overactive PRR pathways in stroke, IBD, psoriasis, Alzheimer’s, gout (e.g., TLR4 antagonists).
• Cardiovascular/Renal
  • Alternatives to ACE inhibitors via PRR pathway modulation.

Notable Numerical Facts & Lists

• Humans: 12 TLR proteins identified.
• Four PRR localisation categories; four soluble PRR sub-groups; four major cell-surface PRR sub-groups.
• Key adaptor proteins: MyD88, TRIF (TLR); MAVS (RLR); ASC (inflammasome); STING (CDS).

Sample Exam-Style Scenario (from slides)

• Goal: induce TLR4-dependent cytokines in lung cells.
• Best source ligand: LPS from Gram-negative $E.\ coli$ (choice correct vs. MTB, M. pneumoniae, Staph, Strep).

Practical Implications for Mutations/Deficiencies

• Dectin-1/2 or CLR defects → candidiasis.
• NOD2 SNPs → Crohn’s disease susceptibility.
• RIG-I or STING pathway mutations → altered antiviral and auto-inflammatory phenotypes.

Wrap-Up: Why PRR Diversity Matters

• Limited gene set → broad pathogen recognition via modular receptors.
• Combination of PRR signals creates pathogen- or damage-specific “cytokine flavours”.
• Rapid, pre-configured response buys time until T & B cell adaptive immunity is mobilised.