Immunology: Chapter 3 — Barriers and innate recognition

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3.1 Barriers #

3.1.1 Skin and mucosa #

Most microbes never meet a lymphocyte. Intact skin is dry, keratinised, slightly acidic, continuously shed, and occupied by commensals. A cut, a burn, or a catheter removes that exclusion. Mucosae use mucus and, in the airway, cilia. The stomach adds acid. Tears, saliva, and urine flush surfaces.

3.1.2 Soluble antimicrobial molecules #

Lysozyme, in tears, saliva, and neutrophil granules, cuts the β-1,4 bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan, so a susceptible wall can no longer resist turgor. The Gram-negative outer membrane hides that substrate until something else disturbs it. Defensins and cathelicidins are short cationic peptides, made by epithelia and by phagocyte granules, that insert into microbial membranes. Mannose-binding lectin binds microbial carbohydrates and starts the lectin route of complement.

3.2 Pattern recognition #

3.2.1 PAMPs, DAMPs, and PRRs #

Janeway argued in 1989 that adaptive immunity needs a sign of infection as well as a shape. Pattern-recognition receptors read pathogen-associated molecular patterns: conserved microbial structures absent from healthy host cells, such as lipopolysaccharide, lipoproteins, flagellin, double-stranded RNA, and unmethylated CpG DNA. Commensals make many of the same molecules. Damage-associated molecular patterns are host molecules misplaced by injury, including extracellular ATP, uric-acid crystals, HMGB1, and DNA outside the nucleus, which is why sterile injury also inflames. A given innate cell displays a fixed set of these receptors. There is no rearrangement and no affinity maturation. The output is inflammatory cytokines, type I interferon, or both, and maturation of dendritic cells.

3.2.2 Toll-like receptors #

Toll, a Drosophila gene, was shown by Hoffmann and colleagues to be required for antifungal defence. Beutler and colleagues showed that mouse TLR4 is required for the response to lipopolysaccharide, and Medzhitov and Janeway showed that a human Toll-like receptor can drive NF-κB. At the surface, TLR4 with MD-2 and CD14 binds lipopolysaccharide, TLR2 with TLR1 or TLR6 binds bacterial lipoproteins, and TLR5 binds flagellin. In endosomes, TLR3 binds double-stranded RNA, TLR7 and TLR8 bind single-stranded RNA, and TLR9 binds unmethylated CpG DNA. Most TLRs use the adaptor MyD88 and, through kinases that Cell Biology treats generically, activate NF-κB, producing TNF, IL-1, IL-6, and chemokines. TLR3 uses TRIF; TLR4 uses MyD88 at the surface and TRIF after internalisation. TRIF activates IRF3 and type I interferon. Plasmacytoid dendritic cells, rich in TLR7 and TLR9, are a major circulating source of that interferon.

3.2.3 NOD-like receptors and the inflammasome #

NOD1 and NOD2 recognise peptidoglycan fragments in the cytosol and activate NF-κB. The NLRP3 inflammasome is different: it responds to diverse insults, including ATP through P2X7, uric-acid crystals, and alum, that often share a fall in cytosolic potassium. NLRP3 oligomerises with ASC and procaspase-1. Caspase-1 cleaves pro-IL-1β and pro-IL-18, and cleaves gasdermin D, whose N-terminal fragment pores the membrane, releases IL-1β, and can kill the cell by pyroptosis. Active IL-1β therefore needs two signals. A Toll-like receptor transcribes the precursors through NF-κB, and the inflammasome cuts them. IL-1β has no signal peptide; the pore is its exit.

3.2.4 cGAS–STING #

Cytosolic DNA is abnormal in a cell whose own DNA belongs in the nucleus and the mitochondria. cGAS binds that DNA and makes 2′3′-cyclic GMP–AMP (cGAMP). cGAMP binds STING on the endoplasmic reticulum. STING engages TBK1, TBK1 phosphorylates IRF3, and IRF3 drives type I interferon, with NF-κB activated as well. The pathway reports DNA viruses, bacteria that expose DNA in the cytosol, and host DNA that has escaped a damaged nucleus. TLR9 reads endosomal DNA; cGAS reads cytosolic DNA.

3.3 Key terms, summary, and self-check #

Key terms. PAMP; DAMP; PRR; TLR4; TLR3; TLR7; TLR9; MyD88; TRIF; NF-κB; type I interferon; inflammasome; NLRP3; caspase-1; gasdermin D; cGAS; STING; lysozyme.

Summary. Epithelia, acid, mucus, lysozyme, and antimicrobial peptides act before any clone responds. TLR4 reads lipopolysaccharide and, via MyD88, drives inflammatory cytokines; nucleic-acid TLRs drive type I interferon through TRIF or related IRF pathways. NLRP3 and caspase-1 mature IL-1β only after a second signal and release it through gasdermin pores. cGAS makes cGAMP from cytosolic DNA, and STING turns that into interferon.

Self-check.

1. What bond does lysozyme cut, and why does that kill a susceptible bacterium?

2. Pair TLR4, TLR3, TLR7/8, and TLR9 with their ligands. Which adaptor biases TLR3 toward type I interferon?

3. Why is a Toll-like-receptor signal not enough, by itself, to secrete active IL-1β?

4. What second messenger does cGAS synthesise, and which protein binds it?

5. Give one PAMP and one DAMP. Why can inflammation occur with no microbe present?