Innate immunity

At a glance

1. Innate immunity is inborn and works within minutes to hours, the same way at every encounter. It has no memory. Adaptive immunity takes a week or two to answer a first infection, then remembers.
2. Barriers come first: skin, mucus and cilia, stomach acid, and the lysozyme and defensins in secretions.
3. Innate cells sense a small set of molecular patterns that microbes share (PAMPs) and signs of damage (DAMPs) with pattern recognition receptors, such as the Toll-like receptors.
4. Phagocytes, the neutrophils and macrophages, swallow microbes and kill them in a phagolysosome with oxidants and enzymes. Complement tags microbes (C3b), calls in and inflames (C3a, C5a) and punches holes (C5b to C9).
5. Inflammation brings blood, fluid and white cells to the site: leucocytes roll on selectins, stop on integrins and squeeze between endothelial cells. IL-1, IL-6 and TNF raise the temperature and make the liver release acute-phase proteins such as CRP.
6. NK cells kill virus-infected and tumour cells that have lost their HLA class I; interferons put nearby cells into an antiviral state. Dendritic cells carry what they caught to the lymph node and start adaptive immunity.

01Two kinds of immunity

Innate immunity is the defence we are born with. Its receptors are written in the germline and do not change, so it recognises a microbe the same way the first time and the hundredth, it is ready at once, and it keeps much of its strength into old age. Adaptive immunity, carried by T and B lymphocytes, builds receptors for one antigen each by rearranging genes. On a first encounter it needs one to two weeks to answer; on a second, three to seven days, because it remembers.

The two are not separate armies. Innate immunity holds most infections on its own, and where it cannot, it holds them back until the adaptive response arrives. It also starts and steers that response: a dendritic cell that has met a microbe carries it to the lymph node and tells T cells what kind of threat it is.

for innate defences to act

Minutesto hoursfor innate defences to act

for a first adaptive response

1-2weeksfor a first adaptive response

made by the marrow in health, ten times more in infection

10¹¹neutrophils a daymade by the marrow in health, ten times more in infection

02Barriers

The first line keeps microbes out. The skin is a dry, acidic sheet of dead keratinised cells, shed constantly, with fatty acids in its sebum. The mucous membranes of the gut, airways and urogenital tract are thinner and far larger, and most infections start there. Their mucus traps particles, and in the airways the cilia carry it upward on the mucociliary escalator to be swallowed or coughed out. Acid in the stomach kills most swallowed microbes, urine flushes the urethra, and tears, saliva and airway secretions carry lysozyme, which splits the peptidoglycan of bacterial walls. Epithelial cells and neutrophils make defensins, small cationic peptides that open holes in microbial membranes.

The normal microbiota is a barrier too: the bacteria on the skin and in the gut take the space and food a newcomer would need. Broad-spectrum antibiotics remove it, which is why Clostridioides difficile and Candida can overgrow after a course.

03How innate cells see a microbe

Innate cells do not recognise a particular microbe. They recognise molecules that whole classes of microbes share and our cells lack, the pathogen-associated molecular patterns (PAMPs): the lipopolysaccharide of Gram-negative walls, peptidoglycan, flagellin, double-stranded viral RNA, DNA rich in unmethylated CpG. Molecules released by our own damaged or dying cells, such as ATP, DNA, uric acid crystals and heat shock proteins, are damage-associated molecular patterns (DAMPs). Both are read by a limited set of germline-encoded pattern recognition receptors (PRRs).

The best known are the Toll-like receptors (TLRs). Some sit on the cell surface and watch the outside, others line endosomes and wait for what is swallowed:

A TLR that binds its pattern switches on the transcription factor NF-κB, and the cell makes inflammatory cytokines (TNF, IL-1, IL-6), chemokines; for viral patterns it also switches on the IRF transcription factors, which drive type I interferons. In the cytosol other sensors keep watch: RIG-I finds viral RNA, and the NOD-like receptors find bacterial products and danger signals. Some of them, NLRP3 the best studied, assemble an inflammasome, which activates caspase-1 to cut pro-IL-1β and pro-IL-18 into their active forms. Urate crystals switch it on, which is part of why gout is so inflamed.

04The cells

All of them come from the bone marrow, except many tissue macrophages, microglia among them, which settle in the tissues before birth and renew themselves there.

Tissue macrophages take local names: Kupffer cells in the liver, microglia in the brain, alveolar macrophages in the lung and osteoclasts, their relatives, in bone. A macrophage lives for months and can swallow up to about 100 bacteria; a neutrophil kills 5 to 20 before it dies.

05Phagocytosis

1. 1

   Recognition

   The phagocyte binds the microbe directly, through PRRs and receptors such as the mannose receptor, or through opsonins coating it: complement C3b, IgG and CRP, which its complement and Fc receptors hold.

2. 2

   Engulfment

   Receptors bind one after another round the microbe like a zip, and actin pushes the membrane out in arms that close over it. It lands in a vesicle, the phagosome.

3. 3

   Phagolysosome

   Lysosomes and granules fuse with the phagosome. The vacuole acidifies and fills with enzymes: lysozyme, elastase, cathepsins, defensins and lactoferrin, which takes iron away from bacteria.

4. 4

   Respiratory burst

   NADPH oxidase assembles on the phagosome's membrane and makes superoxide, which becomes hydrogen peroxide. In neutrophils myeloperoxidase turns it, with chloride, into hypochlorous acid, bleach. Macrophages also make nitric oxide.

Neutrophils can also throw out their DNA with granule proteins stuck to it, the neutrophil extracellular traps (NETs), which catch and kill microbes outside the cell. Some bacteria escape all this with a polysaccharide capsule that hides their patterns and resists opsonisation, and are cleared only once antibody coats them. Streptococcus pneumoniae, Haemophilus influenzae type b and Neisseria meningitidis are the classic ones, and the spleen matters most against them.

06Complement

Complement is a cascade of plasma proteins, made mostly in the liver, that circulate inactive. Several of them, once switched on, are enzymes that switch on many molecules of the next, so a small trigger ends in a large response. Three pathways start it:

• Classical: C1q binds antibody (IgM, or IgG) on a microbe, and CRP. It is started mostly by antibody that adaptive immunity has made, or by CRP coating the target.
• Lectin: mannose-binding lectin or the ficolins bind the sugars of a microbe's surface, and their proteases switch on C4 and C2, as C1 does.
• Alternative: a little C3 is always being activated on its own in the plasma (tick-over), and the C3b this makes lands on nearby surfaces. On our cells it is broken down at once; on a microbe's surface, which lacks our regulators, it stays and binds factor B, which factor D then cuts.

All three build a C3 convertase, which splits C3 into C3a and C3b at high rate. C3b then joins the convertase to make a C5 convertase, which splits C5. Three things follow:

• Opsonisation: C3b, and its breakdown product iC3b, coat the microbe, and phagocytes hold them with their complement receptors (CR1, CR3). This is complement's most important job.
• Inflammation: the small fragments C3a and C5a, the anaphylatoxins, make mast cells release histamine, and C5a draws neutrophils in.
• Lysis: C5b, with C6, C7, C8 and many C9s, forms the membrane attack complex, a pore in the membrane through which water and ions flood in. It kills Gram-negative bacteria, Neisseria above all; the thick wall of Gram-positive bacteria keeps it out.

Complement also clears immune complexes from the blood, carried on CR1 of red cells to the liver and spleen. Our own cells are kept safe by regulators: C1 inhibitor in the plasma, factor H and factor I, and on our cells' membranes DAF (CD55) and CD59, which blocks the pore.

07Inflammation

Inflammation brings the defenders to the site of infection or injury. Its four classic signs, redness (rubor), heat (calor), swelling (tumor) and pain (dolor), to which a fifth, loss of function, is often added, all follow from what happens in the small vessels. Macrophages and mast cells in the tissue release mediators: histamine from mast cell granules within seconds, then prostaglandins, leukotrienes and platelet-activating factor, while the kinin system makes bradykinin. The arterioles dilate, so more blood flows (redness and heat). The venules leak, so plasma, with its antibodies, complement and fibrinogen, seeps into the tissue (swelling). Bradykinin and prostaglandins sensitise the pain nerves (pain). The fibrin that forms walls the infection off.

White cells leave the blood in the venules of the inflamed tissue, in four steps, each set by its own molecules:

1. 1

   Rolling

   Within minutes, histamine and thrombin bring P-selectin, stored in the endothelial cells, to their surface; over a few hours TNF and IL-1 make them build E-selectin. The selectins catch sugars such as sialyl-Lewis X on the neutrophil loosely, again and again, so it rolls along the wall instead of flowing past.

2. 2

   Activation

   Chemokines such as CXCL8 (IL-8), held on the endothelium's surface, bind the rolling cell's receptors. Within seconds its integrins switch to their high-affinity shape.

3. 3

   Firm adhesion

   The β2 integrins (LFA-1 and Mac-1) bind ICAM-1 on the endothelium, and the cell stops and spreads.

4. 4

   Transmigration

   The neutrophil squeezes between two endothelial cells, through their junctions (PECAM-1, the JAMs), and through the basement membrane (diapedesis). In the tissue it crawls up gradients of CXCL8, C5a, leukotriene B4 and bacterial formyl peptides to the microbes.

Neutrophils arrive first, within hours; monocytes follow over a day or two and become macrophages, which clear the dead neutrophils and debris. If the cause is removed, mediators such as the lipoxins and resolvins end the response and the tissue heals. If it persists, inflammation becomes chronic: macrophages and lymphocytes take over, and fibrosis, or granulomas, follow.

08Fever and the acute-phase response

IL-1, IL-6 and TNF do not stay local. They act on the hypothalamus, where they make prostaglandin E2, which raises the set point of temperature: we shiver and seek warmth until the body reaches the new point, and sweat when it falls again. NSAIDs and paracetamol lower fever by blocking prostaglandin synthesis. The same cytokines, IL-6 above all, make the liver change what it secretes:

• C-reactive protein (CRP) binds phosphocholine on bacteria and dying cells, opsonises them and switches on the classical pathway. Its level rises many times over within hours of an infection or injury and falls quickly when it ends, so CRP is followed to judge infection and its response to treatment.
• Mannose-binding lectin, serum amyloid A, fibrinogen and ferritin rise; hepcidin rises and locks iron away from microbes, which over weeks is the anaemia of inflammation.
• Albumin and transferrin fall.

The extra fibrinogen makes red cells stack and settle faster, which is why the erythrocyte sedimentation rate rises too, more slowly than CRP.

09Defence against viruses

A cell that senses a virus makes type I interferons, IFN-α and IFN-β; plasmacytoid dendritic cells make them in huge amounts. Interferons act on the cell and its neighbours, which make enzymes that stop viral replication: protein kinase R, which halts translation, and the 2′,5′-oligoadenylate synthetase, which switches on RNase L to destroy RNA. They also raise HLA class I, so infected cells show more viral peptides to cytotoxic T cells, and they activate NK cells.

Natural killer cells are large granular lymphocytes, CD56 and CD16 positive and CD3 negative, with no rearranged antigen receptor. Each carries activating and inhibitory receptors, and what it does depends on their balance:

• Missing self. Inhibitory receptors, the KIRs (binding HLA-A, -B and -C) and NKG2A (binding HLA-E, which shows pieces of the others), read the HLA class I that every healthy nucleated cell shows. Viruses and tumours often lower HLA class I to hide from cytotoxic T cells, and the NK cell, no longer held back, kills.
• Induced self. Stressed, infected or cancerous cells show ligands such as MICA, which the activating receptor NKG2D binds.
• Antibody. Through CD16, an Fc receptor, NK cells kill cells coated with IgG, antibody-dependent cell-mediated cytotoxicity.

They kill as cytotoxic T cells do, by releasing perforin, which helps granzymes into the target, where they start apoptosis. They act within hours of a viral infection, days before cytotoxic T cells are ready, and their IFN-γ activates macrophages.

10The bridge to adaptive immunity

An immature dendritic cell in a tissue samples everything round it. When its PRRs meet a microbe it changes within hours: it stops taking things in, breaks what it has caught into peptides, loads them on HLA molecules, raises the co-stimulatory molecules CD80 and CD86, and travels in the lymph to the nearest node. There it is the only cell that can switch on a naive T cell, giving it the peptide (signal 1), co-stimulation (signal 2) and cytokines that decide what kind of helper the T cell becomes (signal 3). Without the innate system's verdict that something is dangerous, an adaptive response does not start.

Check yourselfAnswer, then say how sure you were: a lucky guess still counts as a weak point.

1Which pattern recognition receptor senses the lipopolysaccharide of Gram-negative bacteria?

TLR3TLR4TLR9The B-cell receptor

2A 17-year-old has had meningococcal meningitis twice. A deficiency of which proteins is most likely?

C1q, C2 or C4C1 inhibitorC5 to C9, the membrane attack complexMannose-binding lectin

3A virus stops its host cell from making HLA class I, so cytotoxic T cells can no longer see its peptides. Which cell is now most likely to kill the infected cell?

A natural killer cellA neutrophilA mast cellA plasma cell

4In leucocyte adhesion deficiency type 1, neutrophils roll along inflamed venules but cannot stop and leave them. Which step fails?

Rolling on selectinsFirm adhesion of β2 integrins to ICAM-1Phagocytosis of opsonised bacteriaThe respiratory burst

5Chronic granulomatous disease leaves children with deep abscesses of Staphylococcus aureus and Aspergillus. What is missing?

The NADPH oxidase that makes superoxideMyeloperoxidase, so no hypochlorous acid is madeThe C3 convertasePerforin

6What does C3b do on a bacterium's surface?

It punches a pore in the membrane on its ownIt tags the bacterium for phagocytes and helps build the C5 convertaseIt attracts mast cells from the bloodIt neutralises bacterial toxins