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The Immune System · Chapter 6 of 7
A brake that is off, a bell that will not stop ringing, a liverA large organ that produces bile, detoxifies blood, and stores nutrients. that answers every ring with a protein that misfolds. This chapter traces the whole pathway — trigger, pyrin inflammasome, caspase-1, IL-1β, the cytokine cascade hour by hour, serositis, resolution, and the serum amyloid A that becomes AA amyloid in the gut and the kidney — names the second gene the case carries and the hypothesis it makes, and finds the two points where colchicine and an IL-1 blocker starve the fire.
The question you will answer
One protein fires too easily. How does that become a fever, a serous membrane on fire, and thirty years later a kidney that leaks — and where can the chain be cut?
Opener · The Brake That Is Off · about 2 minutes
The opener is the same narrated animation you will watch in Scene 1.
Watch the opener first. It sets the question; the chapter answers it.
1
Read the chart
Patient chart · Stina
Jun–Sep 2026 · age 51 · on treatment
Jun 2026
Colchicine 0.6 mg twice daily. Diarrhea for two weeks, then settled.
Six weeks on
Flares further apart and softer; “last Tuesday I noticed it was Tuesday and I felt fine”.
Labs
CRP 3; SAA falling but not yet normal; proteinuria stable, not rising; creatinine stable.
Plan
If SAA stays up or flares persist on full-dose colchicine: IL-1 blockade (anakinra daily or canakinumab monthly). Kidney function and urineThe liquid waste excreted by the kidneys. protein every six months.
Genes
MEFV VUS (heterozygous) + LPIN2 (heterozygous). No guideline. “A study of one.”
Chart clues this module: 1 · Page two · 2 · Two arms · 3 · The organs · 4 · Inflammation · 5 · The clean panel · 6 · this chapter
Before you go on · your prediction
Six weeks of colchicine: flares softer and further apart, CRP normal, SAA still up, proteinuria stable. The drug is working at…
Open the one you lean toward. Nothing is recorded and nothing is revealed — you come back to it at the end.
The fever — colchicine is an antipyretic that masks the flares while the disease runs on
Ask what colchicine does to a microtubule, what a neutrophil needs microtubules for, and where in the pathway that sits. Then ask whether an antipyretic lowers SAA.
The neutrophil and the inflammasome — upstream of IL-1β, which is why SAA is falling, slowly
Ask what makes SAA (which organ, on which signal), how long amyloid takes to form and to stop forming, and why “falling but not normal” at six weeks is the expected shape.
Nothing yet — the kidney is the problem now and only a nephrologist can help
Ask what proteinuria that is stable rather than rising means for a kidney with amyloid in it, and what the single most protective thing for that kidney is.
From Stina’s diary
Jun–Jul 2026 · age 51 · “Autumn crocus” · “The waiting room”
2
The story
Three short movements: the case, the anatomyThe study of the structure of the human body. and physiologyThe study of how the body functions., then the tie back to Stina. Each links to the scene where you’ll see it move.
I · A flower and a doctor willing to read page two
Colchicine is a small white pill from the autumn crocus, the standard treatment for this disease since the 1970s, old and cheap. Six weeks in, the fevers were further apart and softer when they came; one Tuesday she noticed it was Tuesday and she felt fine and could not remember the last attack. Her CRP was 3. Her serum amyloid A was falling but not yet normal, and the protein in her urine had stopped climbing. The good news and the rage come in the same pill; she takes them both with breakfast. If the SAA will not settle on a full dose, the next step is an IL-1 blocker, and the kidney will be checked every six months for the rest of her life. There is no guideline for her pairing of genes. Her doctor calls it a study of one.
See it move: Scene 1 · The Brake That Is Off · Scene 5 · Two Places to Starve the Fire
II · The pathway, hour by hour
Step one is a trigger — stress, a cold, a period, exertion, cold weather, surgery, or nothing at all — that nudges the innate arm the way it nudges everyone’s. Step two is the sensor. Pyrin, in the neutrophil and the monocyte, normally sits braked by a cellular switch (RhoA) and fires only when a bacterial toxin cuts the brake; the FMF variants loosen the brake so that the nudge is enough. Pyrin assembles with the adapter ASC and the enzyme caspase-1 into the inflammasome; caspase-1 cleaves pro-IL-1β to IL-1β and opens the cell so it pours out. Step three is the cascade: hours 0–2, IL-1β floods the tissue and blood; hours 2–6, it recruits other cellsThe basic structural and functional units of life. to make IL-6 and TNF-α and the signal spreads; hours 6–12, vessels dilate, neutrophils march (Chapter 4), the hypothalamusA small but vital brain region controlling hormones, temperature, and autonomic functions. resets, and the fever spikes. Step four is serositis: IL-1β and its cascade target the serous membranesThin tissues that line body cavities and secrete fluid. — peritoneumThe membrane lining the abdominal cavity and organs., pleuraThe double-layered membrane surrounding the lungs and lining the thoracic cavity., pericardiumThe membrane surrounding the heart., synovium — which inflame, leak an effusion, and turn every movementA fundamental property of life involving motion of the body or its parts. into friction and pain. Step five is the peak at twelve to forty-eight hours: fever to 40, a belly that mimics appendicitis, a chest that stabs with each breath, one hot joint. Step six is resolution at twenty-four to seventy-two hours: inflammasome components run out, IL-10 and regulatory T cells damp the signal, the neutrophils are spent, and the fire burns out for want of fuel. Her second gene adds a hypothesis the case keeps labelled as one: LPIN2, the Majeed gene, encodes lipin-2, whose absence lets the NLRP3 inflammasome and IL-6 run hot; one copy usually does nothing, but a half-expressed LPIN2 beside a half-expressed MEFV may be two atypical diseases amplifying each other — and the reason neither looked textbook enough to be named for forty-nine years. The story’s model, not a published finding.
See it move: Scene 1 · The Brake That Is Off · Scene 2 · Hour Zero to Hour Seventy-Two · Scene 3 · Two Genes, One Fire
III · The slow fuse, and the two cuts
Every flare’s IL-1β and IL-6 reach the liver, and the liver answers with the acute-phase proteinsLarge molecules made of amino acids with various functions in the body.: CRP, which falls when the flare does, and serum amyloid A, which falls more slowly and, when the flares never stop, never quite returns. SAA that stays high for years misfolds, fragments, and stacks into fibrils — AA amyloid — that deposit around the vessels of the gut wall (Chapter 17’s re-stained biopsy), in the mesangium and capillary walls of the glomerulusA network of capillaries in the nephron where blood filtration occurs. (Chapter 19’s Congo red, apple-green under polarizedA resting neuron’s membrane with a more negative charge inside than outside. light), and in the spleen, the liver, the heart. The kidney is where it kills: protein leaks, albuminA plasma protein that helps maintain osmotic pressure and transport substances. falls, ankles swell, and without treatment the filter fails. Before colchicine, up to sixty percent of FMF patients died of that. The chain can be cut at two points. Colchicine binds tubulin, stops microtubules assembling, stops neutrophils crawling and keeps pyrin’s brake on; taken daily — never only during attacks, because it prevents and does not treat — it stops flares in 60–70% and nearly all amyloidosis. For the 5–10% it fails, the second cut is IL-1β itself: anakinra, a daily receptorA structure that detects stimuli. blocker; canakinumab, a monthly antibody against the cytokine; rilonacept. They do not fix the gene; they starve the fire of its signal, and the liver, hearing nothing, stops making the deposit. Monitoring is the kidney, every six months: creatinine, urine protein, and SAA — the number that says whether the fuse is still burning.
See it move: Scene 4 · From SAA to Amyloid · Scene 5 · Two Places to Starve the Fire
3
Watch · explore · think · check
5 scenes. Each one has a short animation or a slide, something to explore, a true/false spot-check of your thinking, and a quick check. Every scene gives you an evidence card for your board.
How to read the scenes
- Animation (dark teal) — a short animated explainer, one idea each
- Slide (dark teal) — a still to study: a micrograph, a diagram or a map
- Explore (purple) — something to push on while you watch
- Game (purple) — a quick challenge
- Think (gold) — reason it out, then spot-check yourself with a few true/false questions; not graded
- Check (gold) — a quick H5P that scores itself
Scene 1 of 5
The Brake That Is Off
Pyrin, ASC, caspase-1, IL-1β.
Animation · in production · 2 min
The Brake That Is Off
A neutrophil in cross-section. Pyrin braked by RhoA; a bacterial toxin cuts the brake in a healthy cell; an FMF variant loosens the brake so an ordinary nudge releases it. Assembly: pyrin + ASC + caspase-1 = the inflammasome; caspase-1 cleaves pro-IL-1β; the cell opens and IL-1β pours out — the bell rings. The smoke-detector-three-rooms-away analogy from the case home. Why a VUS can still be a loose brake.
Prefer the full lecture? Antimicrobial Proteins (original video on the site)
Explore · in production
Set the threshold
A neutrophil with a pyrin brake you can tighten or loosen and a trigger dial (stress, a cold, cold weather, a bacterial toxin). Set the brake to “healthy” and predict which triggers fire the inflammasome; set it to “FMF” and predict again. Then add colchicine and predict what moves. Read the IL-1β output on a meter; nothing is scored.
Think · not graded
A smoke detector that fires on a birthday candle three rooms away is not detecting smoke; it is detecting its own thresholdThe minimum voltage needed to trigger an action potential.. What is the clinical equivalent of lowering a detector’s sensitivity, and which of her two drugs does it — and which one instead unplugs the alarm?
The true/false spot-check for this prompt is in production.
Check · Drag the Words
Assemble the pyrin inflammasome.
This self-scoring check is in production.
Evidence card 1
Add it to your evidence board
The brake is loose; an ordinary nudge rings the bell.
Scene 2 of 5
Hour Zero to Hour Seventy-Two
The cascade, the serositis, the burn-out.
Slide · in production
A Flare on the Clock
The fire burns itself out because it runs out of fuel, not because anything put it out.
Prefer the full lecture? Barriers, Fever and Inflammation (original video on the site)
Game · in production
Build the flare
Six event cards — trigger, IL-1β surge, IL-6/TNF amplification, fever and neutrophil march, serositis peak, burn-out — and a 72-hour ruler. Place each card at the hour you predict, then overlay the case’s own timings. Then pick a membrane (peritoneum, pleura, pericardium, synovium) and predict the symptom and the module of the course that already met it. Last: slide a “colchicine daily” marker in and predict which cards shrink.
Think · not graded
A flare resolves because the cell runs out of inflammasome parts and the neutrophils are spent. What does that predict about the minimum interval between flares, and why might the “every few weeks” rhythm of her whole life be the cell’s refill time rather than any trigger?
The true/false spot-check for this prompt is in production.
Check · Single Choice
Why do FMF attacks stop on their own?
This self-scoring check is in production.
Evidence card 2
Add it to your evidence board
Seventy-two hours, one program, no scar — and no pathogen anywhere on the clock.
Scene 3 of 5
Two Genes, One Fire
MEFV, LPIN2, and a hypothesis labelled as one.
Animation · in production · 1 min 50 s
Two Genes, One Fire
MEFV on chromosome 16 → pyrin; one VUS, one copy — a loose brake. LPIN2 on chromosome 18 → lipin-2; one variant, one copy — in full Majeed syndrome (two copies) lipin-2’s absence lets the NLRP3 inflammasome and IL-6 run hot; one copy usually does nothing. The hypothesis: two half-expressed diseases priming each other — more IL-6, lower threshold — which is why neither looked textbook enough to be named. On screen: “the story’s model, not a published finding”. The old recessive rule for MEFV and the 30–50% of heterozygotes with manifestations.
Prefer the full lecture? Antigens (original video on the site)
Explore · in production
One copy, two copies
Two gene sliders — MEFV (0, 1, 2 variant copies) and LPIN2 (0, 1, 2) — and an inflammasome threshold readout with a “textbook?” flag. Predict the phenotype for each combination (nothing / atypical / classic FMF / Majeed) before the model answers; find the one cell of the grid that has no guideline. Then write, in one sentence, what evidence would move the two-gene model from hypothesis to finding.
Think · not graded
A hypothesis that explains everything should worry you. What single observation would falsify the two-gene model for her — and what would you accept as the strongest evidence for it, short of a second patient?
The true/false spot-check for this prompt is in production.
Check · Multiple Choice
What is the status of the “two genes amplifying each other” model in this case?
This self-scoring check is in production.
Evidence card 3
Add it to your evidence board
Two half-expressed genes may explain forty-nine years without a name — and the case says “may”.
Scene 4 of 5
From SAA to Amyloid
The liver answers every ring.
Slide · in production
The Slow Fuse: IL-1β → IL-6 → SAA → AA Amyloid
CRP tells you about this week. SAA tells you about the last thirty years.
Prefer the full lecture? Antimicrobial Proteins (original video on the site)
Explore · in production
Thirty years of SAA
A thirty-year trace with a flare-frequency dial and an SAA line that integrates. Set her untreated rhythm and predict when the cumulative deposit crosses the proteinuria line; then move “diagnosis” to 1990, 2017 and 2026 and predict the difference in deposit at each. Nothing is scored; the model’s answer appears after yours, with the Clue #17 and #19 slides at the organs it reaches.
Think · not graded
Her 2017 panel listed MEFV; her first “little protein” was 2024. Using the SAA model, estimate what nine years of daily colchicine from 2017 would have done to the kidney that was biopsied in 2026 — and say which number in her chart is the one that measures that cost.
The true/false spot-check for this prompt is in production.
Check · Fill in the Blanks
Complete the amyloid pathway.
This self-scoring check is in production.
Evidence card 4
Add it to your evidence board
SAA is the integral of every flare; the kidney is where the sum is written.
Scene 5 of 5
Two Places to Starve the Fire
Colchicine at the cell; IL-1 blockade at the signal.
Animation · in production · 2 min
Two Places to Starve the Fire
Colchicine — tubulin binding, no microtubules: neutrophils cannot crawl, pyrin’s RhoA brake stays on, less IL-1β; daily, not during attacks; 60–70% attack-free, 95% improved, amyloidosis nearly abolished; diarrhea as the common cost. IL-1 blockade for the 5–10% colchicine-resistant: anakinra (daily receptor antagonist), canakinumab (monthly anti-IL-1β antibody), rilonacept; CLUSTER trial. What neither does (the gene). Monitoring: creatinine and urine protein every 6–12 months; SAA and CRP in flares. The missed-dose rule.
Prefer the full lecture? Innate Cells (original video on the site)
Game · in production
Cut the chain
The whole pathway as a chain of eight links — trigger, pyrin, inflammasome, IL-1β, IL-6/TNF, neutrophil march, liver SAA, amyloid. Six drug cards: colchicine, anakinra, canakinumab, ibuprofen, prednisone, an antibiotic. Predict which link each card cuts (or none) and what happens downstream; then run a year of each on the SAA integrator. Last: a patient takes colchicine only during attacks — predict the chart at five years.
Think · not graded
Colchicine does not touch the gene, the fever directly, or the amyloid already laid down. Explain, link by link, why it is nonetheless the most protective thing her kidney can be given — and what “falling but not normal” SAA at six weeks tells you to do next.
The true/false spot-check for this prompt is in production.
Check · Mixed Quiz
Treatment in five questions.
This self-scoring check is in production.
Evidence card 5
Add it to your evidence board
Cut the chain at the cell or at the signal; the liver, hearing nothing, stops making the deposit.
4
Your evidence board
Every scene gave you an evidence card, and the chart adds more. Sort each card into the column it supports: The drug is working upstream of the signal, slowly, Neither on its own, or The drug is masking the fever while the disease runs on. Some cards can honestly go in more than one place — that’s allowed, and the feedback tells you which cards decide the case.
Evidence board · drag and drop · in production
The sorting board for this chapter’s cards is being built. Until it arrives, sort your evidence cards on paper into the three columns above.
5
Your verdict
Time to decide. Look back at your bet, then build your verdict from statements that hold up — no writing needed.
Look back at your prediction
Six weeks of colchicine, CRP normal, SAA still up, proteinuria stable — the drug is working at…
Find the one you chose at the top. Does the evidence support it, refute it, or revise it?
- The fever — colchicine is an antipyretic that masks the flares while the disease runs on
- The neutrophil and the inflammasome — upstream of IL-1β, which is why SAA is falling, slowly
- Nothing yet — the kidney is the problem now and only a nephrologist can help
Build your verdict · no writing
Choose the statement that holds in each set. The ones you keep become your argument.
This activity is in production.
6
The finding
Finding · the pathway, and where it is cut
Pyrin to Amyloid, and Two Cuts
A loose pyrin brake in neutrophils and monocytes; an inflammasome that fires on an ordinary nudge; IL-1β, then IL-6 and TNF-α, hour by hour to a fever and a serous membrane on fire; burn-out by seventy-two hours with no scar; a liver that answers every flare with serum amyloid A; thirty years of SAA stacked into AA amyloid around her gut vessels and in her glomeruli. Second gene, one copy, a hypothesis labelled as one. Six weeks of colchicine: flares softer, CRP 3, SAA falling, proteinuria stable — the chain cut at the cell, with IL-1 blockade waiting at the signal. Chart entry: one pathway from a variant of uncertain significance to a Congo-red kidney, and two drugs that starve it. The last chapter lays every clue on that pathway.
Next · Chapter 7
One Connected Story
Twenty-one clues on one board, one mechanism behind every one of them, the sentence that separates autoinflammatory from autoimmune — and Chart Clue #22.
Reliable information on rare diseases
NORD · NIH GARD · Orphanet · MedlinePlus Genetics: FMF · FMF & AID Global Association · Autoinflammatory Alliance · Global Genes · Amyloidosis Foundation
Stina has one rare disease. In the United States, about 1 in 10 people live with one of the more than 7,000 known rare diseases. These organizations are where patients, families and clinicians go for trustworthy information.
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← Familial Mediterranean Fever — case home
All pages for Module 22 — The Immune System — Capstone
22.0 Module Overview
22.1 The Lab Result That Names Everything
22.2 Two Arms of Defense
22.3 The Cells and the Lymphatic Organs
22.4 The Inflammatory Response
22.5 Antibodies, Adaptive Immunity and Memory
22.6 From Pyrin to Amyloid
22.7 One Connected Story
22.8 Conclusion and Assessment
22.9 Evidence Behind the Case
All Modules
- Anatomical Language, Membranes & Homeostasis
- Just Enough Chemistry
- The Cell & Its Transport
- Making Cells & Proteins
- The Integumentary System
- The Skeletal System
- The Muscular System
- Nervous Tissue & the Senses
- The Spinal Cord
- The Brain & the Blood–Brain Barrier
- The Autonomic Nervous System
- Special Senses (in developmentThe process of growth and differentiation.)
- The Endocrine System
- Blood
- The Heart
- Blood Vessels
- The Digestive System
- The Respiratory System
- The Urinary System
- Fluids, Electrolytes & Acid–Base Balance
- The Reproductive System
- The Immune System
List of terms
- liver
- urine
- anatomy
- physiology
- cells
- hypothalamus
- serous membranes
- peritoneum
- pleura
- pericardium
- movement
- proteins
- glomerulus
- polarized
- albumin
- receptor
- threshold
- development