Lecture 3 - immune recognition of invading pathogens

What are the two main arms of the vertebrate immune system?

1. Innate immunity – immediate, non-specific, inborn.

2. Acquired immunity – slower, specific, generates memory.

What are the three types of innate barriers in the immune system?

Mechanical (e.g., tight junctions), Chemical (e.g., low pH, defensins), Microbiological (e.g., normal flora).

What is the role of tight junctions in innate immunity?

They seal epithelial tissues, preventing microbial penetration (mechanical barrier).

How does mucociliary clearance defend against pathogens?

Mucus traps microbes; cilia move mucus out of the respiratory tract.

Name three chemical defenses on epithelial surfaces.

Fatty acids (skin), lysozyme (tears, saliva), pepsin (stomach).

What is the function of lysozyme?

It hydrolyzes β-1,4-glycosidic bonds in bacterial peptidoglycan, mainly affecting Gram-positive bacteria.

What are defensins and where are they found?

Antimicrobial peptides in the skin and gut; they insert into microbial membranes and form pores.

What are cryptidins and where are they secreted from?

Defensin-family peptides with bactericidal activity; secreted by Paneth cells in the intestine.

How do normal flora (commensals) contribute to innate immunity?

They compete with pathogens for space and nutrients and may secrete antimicrobial compounds.

Which cytokines are released during inflammation after barrier breach?

IL-1β, IL-6, TNF-α, IL-18.

What is the size range of particles phagocytosed by different macrophages?

Splenic: ~5 µm, Peritoneal: ~10 µm, Alveolar: ~15 µm.

What reactive oxygen species are produced during oxidative burst?

Superoxide (O₂⁻) and hydrogen peroxide (H₂O₂).

What triggers innate immune activation without phagocytosis?

Recognition of PAMPs or DAMPs by PRRs leading to cytokine release and antigen presentation.

What are PAMPs and give two examples.

Pathogen-associated molecular patterns; examples: LPS, viral dsRNA.

What are DAMPs and give two examples.

Damage-associated molecular patterns; examples: extracellular DNA, HMGB1.

What is a key feature of PRRs compared to adaptive receptors?

PRRs are germline-encoded, non-variable, and do not require gene rearrangement.

Name three secreted PRRs.

Lysozyme, Mannose-binding lectin (MBL), Complement proteins (e.g., C3b).

What is the function of collectins in innate immunity?

Bind microbial carbohydrate motifs and enhance phagocytosis.

What are natural antibodies and which cells produce them?

Less variable antibodies produced by B1 B cells; considered part of innate-like immunity.

Give two examples of C-type lectin PRRs.

Mannose receptor, DC-SIGN.

What are scavenger receptors and name two examples.

PRRs recognizing anionic polymers and LDLs; examples: MARCO, CD36.

What are the main complement receptors involved in pathogen recognition?

CR1 (CD35), CR3 (CD11b/CD18).

What cytokine is produced by NK cells upon activation?

Interferon-gamma (IFN-γ).

What do NK cell inhibitory receptors recognize?

MHC class I molecules on healthy cells.

What determines NK cell activation?

Balance between activating and inhibitory receptor signals.

What do NOD-like receptors detect and give two examples.

Cytosolic bacterial peptidoglycans; examples: NOD1, NOD2.

What disease is associated with NOD2 polymorphisms?

Crohn’s disease (Cooney et al., 2010, Nat. Med.).

What does RIG-I detect and name three viruses it recognizes.

Short dsRNA with 5’-triphosphates; SeV, VSV, HCV.

What RNA viruses are recognized by MDA5?

EMCV, Mengo virus, Theiler’s virus (long dsRNA).

What is the function of cGAS in the cGAS-STING pathway?

Detects cytosolic DNA and produces cGAMP, activating STING.

What are the downstream effects of cGAS-STING activation?

Type I interferon (IFN-α) and NF-κB activation.

Which TLRs are expressed on the cell surface and what do they detect?

TLR2 (LTA), TLR4 (LPS).

Which TLRs are found on endosomal membranes?

TLR3 (dsRNA), TLR7/8 (ssRNA), TLR9 (CpG DNA).

What domains are found in TLRs?

LRR (ligand-binding), TIR (signaling).

Name four TLR adaptor proteins.

MyD88, TRIF, Mal, TRAM.

What transcription factors are activated downstream of TLR signaling?

NF-κB (cytokines), IRF3/7 (type I IFN).

Name two DAMPs that bind TLRs during sterile inflammation.

HMGB1, heat shock proteins.

What is the function of the NLRP3 inflammasome?

Activates caspase-1, leading to IL-1β and IL-18 maturation and pyroptosis.

What is pyroptosis and what triggers it?

Inflammatory cell death triggered by inflammasome activation (e.g., NLRP3).

What does the term "germline-encoded" mean in the context of PRRs?

PRRs are encoded by genes inherited in the germline and do not undergo somatic recombination like BCRs or TCRs; hence, they are non-variable and conserved across individuals.

Why is innate immunity faster than adaptive immunity?

Innate immunity uses pre-formed, germline-encoded receptors that recognize conserved microbial patterns, enabling immediate activation without prior exposure.

How does mannose-binding lectin (MBL) recognize pathogens?

MBL binds to mannose or fructose residues arranged in a specific spatial pattern on microbial surfaces, not typically found on host glycoproteins.

What specific roles do complement fragments C3a, C3b, and C5a play?

• C3a/C5a: Anaphylatoxins – promote inflammation, chemotaxis.

• C3b: Opsonin – tags microbes for phagocytosis.

• C5a: Also a potent chemoattractant for neutrophils.

What are the functions of DC-SIGN and DEC-205?

• DC-SIGN: Recognizes mannose-type carbohydrates on pathogens; important in dendritic cell-mediated recognition.

• DEC-205: Facilitates antigen uptake and presentation by dendritic cells.

What makes B1 B cell-derived natural antibodies part of the innate-like response?

They are polyreactive, of limited diversity (often IgM), and produced without prior antigen exposure.

Why is PRR expression not limited to immune cells?

Many non-immune cells (e.g., epithelial cells, fibroblasts) express PRRs to detect pathogens at barrier sites and initiate local immune responses.

What are the downstream effects of NF-κB activation in innate immune signaling?

Transcription of genes encoding pro-inflammatory cytokines (e.g., IL-1β, IL-6, TNF-α), chemokines, and adhesion molecules.

How does the NLRP3 inflammasome detect both PAMPs and DAMPs?

It integrates signals from diverse stimuli (e.g., ATP, uric acid, microbial components) via ionic flux, ROS, or lysosomal damage pathways.

What makes LPS a potent PAMP and which receptor detects it?

LPS is a major component of Gram-negative bacterial outer membranes; it is recognized by TLR4, often with co-receptor MD-2.

What distinguishes RIG-I and MDA5 in viral RNA recognition?

• RIG-I: Detects short dsRNA or ssRNA with 5′-triphosphates.

• MDA5: Detects long dsRNA. Both are cytosolic sensors.

What role does LGP2 play in RLR signalling?

LGP2 modulates RIG-I and MDA5 signalling — enhancing or suppressing antiviral responses depending on context.

How does STING activation lead to inflammation?

STING activates TBK1 and IRF3/7 to induce type I IFNs and also NF-κB for pro-inflammatory gene expression.

How does the immune system distinguish between host and pathogen nucleic acids?

Host nucleic acids are usually compartmentalized (nucleus/mitochondria), modified (e.g., methylated CpG), or degraded; PRRs detect mislocalized or unmethylated DNA/RNA.

What are the advantages and limitations of PRR-based immunity?

✅ Rapid, broad-spectrum, evolutionarily conserved
❌ No memory, limited to detecting known molecular patterns

Why are endosomal TLRs especially important for viral recognition?

They recognize nucleic acids (e.g., ssRNA, dsRNA, CpG DNA) from viruses internalized via endocytosis, allowing detection of intracellular pathogens.

What is the significance of Medzhitov’s 2010 paper on inflammation?

It reframed inflammation as a response not just to infection but also to sterile damage and loss of homeostasis, expanding our understanding of immune activation.

How do PRRs help initiate adaptive immunity?

PRR activation on APCs (e.g., dendritic cells) leads to upregulation of co-stimulatory molecules (CD80/86) and cytokines required for T cell activation.