6. Innate Immunity 3: Pathogen recognition & induction of innate immunity

What are the main hypotheses of immune recognition?

• Self vs. non-self hypothesis (Medawar)

  • Immune system distinguishes self from non-self (clonal selection).

  • Limit: Doesn’t explain pregnancy, autoimmunity, or cancer.

• Pattern recognition hypothesis (Janeway)

  • Distinguishes infectious non-self (microbes) vs. non-infectious self.

  • Limit: Couldn’t fully explain sterile inflammation (e.g., tissue injury).

• Danger hypothesis (Matzinger)

  • Immune system responds to danger signals, not just self vs. non-self.

  • Explains pregnancy, cancer, and viral infections better.

What do receptors of the immune system do?

Recognize signals from pathogens or tissue damage to initiate immune responses.

Main Idea

• Innate: Receptors have very high degree of sensitivity, but low degree of specificity

• Adaptive: Receptors have very high degree of specificity, but low degree of sensitivity

What types of danger signals does the innate immune system detect?

1. External dangers: PAMPs/DAMPs (Pathogen-Associated Molecular Patterns and Damage/Danger-Associated Molecular Patterns)

2. Internal dangers: DAMPs (Damage/Danger-Associated Molecular Patterns)

• Anything out of normal = danger: Cell injury, misbehaved or tumour cells, DNA in wrong location, too much ATP outside cells

How does the innate immune system recognize thousands of microbial pathogens?

Through a limited number of Pattern Recognition Receptors (PRRs) that detect common PAMPs (Pathogen-Associated Molecule Patterns).

What are common features of PAMPs?

• Produced only by microbial pathogens, but not their mammalian hosts (like bacterial cell wall, bacterial/viral DNA/RNA)

• Essential for microbe survival or pathogenesis

• Conserved/invariant structures shared across classes of pathogens (e.g., LPS in all Gram-negative bacteria but not in mammalian cells).

What are DAMPs and give examples?

Molecules released from stressed or injured cells that trigger inflammation (non-infectious source).

• Ex: HSP (heat shock protein), HMGB (high-mobility group box), DNA, Purine Metabolites (ATP, adenosine, uric acid)

What are the main receptors of the innate immune system?

• Phagocytic receptors: Does not lead to signalling

  • Mannose receptor

  • Scavenger receptors

  • Complement receptors

• PRRs (Pattern Recognition Receptors); recognize PAMPs/DAMPs. Lead to signalling → contribute to induced innate immunity:

  • MBL (Mannose Binding Lectin)

  • TLRs (Toll-like Receptors)

  • NODs (Nucleotide-binding oligomerization domain)

  • NLRs (NOD like receptors)

How does Mannose Binding Lectin (MBL) recognize microbes?

Recognize Pattern:

• MBL has clusters of carbohydrate-recognition domains with fixed orientation.

• Binds mannose & fucose residues with correct spacing (high affinity) = danger signal

• Does not bind if spacing is incorrect = not dangerous

What are Toll-like Receptors (TLRs)?

• A family of Pattern Recognition Receptors (PRRs) in innate immunity.

• Detect PAMPs (pathogen molecules) & DAMPs (damage signals).

• Located on cell surface (proteins, lipoproteins) or endosomes (DNA, RNA).

• Humans have 10 TLRs (TLR1–10); mice have TLR1–9, 11.

• Activation triggers signaling → inflammatory cytokines & type I interferons.

Memorize chart…

Where are TLRs located in cells?

• Cell surface: recognize microbial proteins, lipoproteins, glycoproteins, carbohydrates

• Endosomal: recognize microbial/viral DNA and RNA

What does TLR signaling induce?

• Infectious agent/material

Two main pathways leading to:

1. Cell-Surface: MyD88 pathway → Pro-inflammatory cytokine production (TNF-a, IL6)

2. Endosomal: IRF3 or TRIF pathway → Type 1 interferon production

What do RIG-I, MDA5, and MAVS stand for?

RIG-I: Retinoic acid-inducible gene I (for shorter dsRNA)

MDA5: Melanoma differentiation-associated 5 (for longer dsRNA)

MAVS: Mitochondrial antiviral signaling protein

How do RIG-I and MDA5 detect viral RNA and trigger an immune response?

• Infectious agent/material

1. RNA virus replicates in cytoplasm → makes uncapped RNA with 5’-triphosphate.

2. RIG-I detects short dsRNA; MDA5 detects long dsRNA.

• Mammalian dsRNA doesn’t exist

3. Viral RNA binding → RIG-I/MDA5 interact with MAVS on mitochondria.

4. MAVS dimerizes → signaling cascade.

5. Activates NFkB & IRFs.

6. Produces inflammatory cytokines + type I interferons (IFN-α/β).

How do NOD receptors act as intracellular sensors of bacterial infections?

• Infectious agent/material

1. NOD proteins sit inactive in the cytoplasm.

2. Bacterial ligands bind to NOD proteins.

3. Binding → recruitment of RIPK2.

4. RIPK2 activates TAK1.

5. TAK1 activates NFkB.

6. NFkB triggers inflammatory gene expression → cytokine production.

How do NLRs (NALP3) sense cellular damage and activate inflammation?

• Recognizes internal DAMPs (alarms/damage that’s non-infectious)

1. Cell damage → K⁺ ions leak out.

2. K⁺ efflux causes cytoplasmic proteins to dissociate from NALP3.

3. NALP3 dimerizes (activates).

4. Activated NALP3 recruits PYCARD.

5. PYCARD aggregation → activates caspase-1 (proteolytic activation).

6. Caspase-1 cleaves pro-IL-1 & pro-IL-18 → releases mature IL-1 & IL-18.

7. → Strong inflammatory response (furoptosis).

What is the main difference between innate and adaptive immunity?

Innate: rapid, sensitive, non-specific

• Receptors: PAMPs, PRRs; TLRs

• Very simple but very generous

Adaptive: slower, specific, memory

• Receptors: TCR, BCR

• Very effective, but unique and specific 

  

What happens when PAMPs/DAMPs are recognized by APCs through TLRs and other PRRs?

• Recognition: APCs (esp. dendritic cells, macrophages) detect PAMPs/DAMPs via TLRs/PRRs.

• Signaling → Cytokines: Activation triggers gene expression → cytokine release (IFN-α, IFN-β, IFN-λ, IL-2, IL-12, IL-15).

• Innate Activation: Cytokines activate NK, NKT, γδ T cells → early antiviral/antibacterial defense.

• Antiviral State: Cytokines protect nearby non-infected cells from viral spread.

• APC Maturation: Cytokines + IFN-γ make APCs “professional” → upregulate co-stimulatory molecules for T cell priming (adaptive immunity).

• Three Jobs of Innate Immunity:

  1. Contain infection early.

  2. Mature APCs to bridge to adaptive immunity.

  3. Limit collateral tissue damage (esp. lung/brain).

• Clinical Example: Vaccines (e.g., Shingrix) work better when paired with strong TLR ligands (adjuvants) to boost innate → adaptive response.

What are the key differences between type I and type III interferons in viral infection (e.g., COVID-19)?

• Type I (IFN-α, IFN-β): Antiviral but pro-inflammatory → can worsen disease (e.g., harmful in COVID-19).

• Type III (IFN-λ): Antiviral but anti-inflammatory → protective, shown effective in clinical trials for COVID-19.

• Key Point: Not in textbooks yet — new evidence shows IFN-λ is safer and beneficial, unlike IFN-β.

How does the immune response to viral infection progress over time?

1. Early phase: Virus starts replicating → high virus titer.

2. Innate cytokines rise: IFN-α, IFN-β, TNF-α, IL-12 are produced.

3. NK cells activated: Kill infected cells in the early phase (before T cells).

4. Adaptive phase: T cells arrive later → stronger, targeted killing of infected cells.

5. Result: Virus titer decreases as immune responses clear infection.

What happens during viral infection if the innate immune system is absent?

1. Virus replication → uncontrolled (no early defense).

2. No cytokines produced: IFN-α, IFN-β, TNF-α, IL-12.

3. No NK cell killing of infected cells.

4. T cells still activate, but response is delayed.

5. Outcome → Virus overwhelms before adaptive immunity can control it.

How are PAMPs (TLR ligands) used as potent inducers of the innate immune system?

1. Protective immunity → boost defense against viruses, bacteria, parasites.

2. Cancer therapy → activate APCs, increase CTLs & NK cells.

3. Reduce allergic responses → shift cytokines (↑ TH1, ↓ TH2), fewer eosinophils.

4. Improve vaccines → stronger B cell + APC activation, ↑ cytokines.

Can mucosal delivery of TLR ligands protect against viral challenge?

• Control mice: no TLR ligand → 24 hrs later infected with HSV-2 & Influenza → virus kills mice.

• TLR ligand-treated mice: CpG, Poly I:C, or FimH → 24 hrs later infected with HSV-2 & Influenza → mice survive.

• Conclusion: Mucosal TLR ligands induce protective innate immunity against viral infection.

What are the key take-home messages about innate immune receptors?

• Recognize danger: PAMPs (pathogen) & DAMPs (damage).

• TLRs:

  • Surface → recognize microbial proteins/lipoproteins/glycoproteins

  • Endosomal (inside cell) → recognize microbial DNA/RNA

• RIG-I & MDA5: sense cytoplasmic viral RNA

• NLRs: sense DAMPs

• Signaling outcomes:

  1. Pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) + Type 1 IFNs

  2. ↑ Antigen presentation by APCs