Pathology

Transplant Rejection and Graft-versus-Host Disease: Immunology, Types, Diagnosis and Emergency Care Study level: Clinical medicine, emergency medicine and pathology | Topic: Immunopathology Core concept: A transplant is recognised as foreign when recipient immune cells detect donor HLA, minor histocompatibility antigens or blood-group antigens. The recipient may attack the graft (graft rejection), or immunocompetent donor lymphocytes may attack recipient tissues (graft-versus-host disease, GVHD). Timing, allorecognition pathway and target organ determine the clinical syndrome. Learning objectives Define autograft, isograft, allograft and xenograft and explain why histocompatibility matters. Describe direct, indirect and semi-direct allorecognition, antibody-mediated injury and the role of innate inflammation. Distinguish hyperacute, accelerated, acute and chronic rejection in solid-organ transplantation. Explain GVHD after allogeneic haematopoietic transplantation and distinguish acute from chronic disease. Recognise organ-specific warning signs, infection mimics and transplant emergencies. Describe the principles, monitoring and major adverse effects of anti-rejection immunosuppression. 1. Transplant terminology Term Definition Relevance Autograft Tissue moved within the same person. No alloimmune rejection; healing and ischemia remain concerns. Isograft/syngeneic graft Between genetically identical individuals, such as identical twins. Very low alloreactivity; GVHD risk is minimal. Allograft Between genetically different members of the same species. Most human solid-organ and donor stem-cell transplants; HLA mismatch drives rejection. Xenograft Between different species. Pre-existing antibodies and innate barriers create major rejection risk. Graft Transplanted tissue or organ. May be kidney, liver, heart, lung, pancreas, cornea, skin or stem cells. Host The recipient of the graft. Host-versus-graft immunity causes ordinary rejection. Donor lymphocyte chimerism Persistence of donor immune cells in the recipient. Required for GVHD, particularly after allogeneic haematopoietic cell transplantation. 2. Antigens and immune activation 2.1 What the recipient recognises Major histocompatibility complex (MHC/HLA): donor HLA class I and II molecules may be recognised as foreign directly by recipient T cells. Minor histocompatibility antigens: polymorphic peptides derived from otherwise similar proteins are presented by HLA and can activate alloreactive T cells even when major HLA loci are matched. ABO blood-group antigens: preformed anti-A or anti-B antibodies can trigger immediate vascular injury when incompatible organs are transplanted. Endothelial and tissue antigens: antibodies may target donor endothelium, activating complement, coagulation and leukocytes. 2.2 Ischemia–reperfusion as an alarm signal Organ procurement, cold storage and revascularisation produce cellular stress, reactive oxygen species, endothelial activation and release of danger-associated molecular patterns. Complement, innate leukocytes and inflammasomes create a pro-inflammatory environment that lowers the threshold for adaptive alloreactivity. 2.3 Allorecognition pathways Pathway What happens Clinical importance Direct allorecognition Recipient T cells recognise intact donor MHC on donor antigen-presenting cells that migrate from the graft. Strong early response; important in acute cellular rejection. Indirect allorecognition Recipient APCs process donor proteins and present donor peptides on recipient MHC. Persistent response; supports chronic rejection and donor-specific antibody formation. Semi-direct allorecognition Recipient APCs acquire intact donor MHC and display it to recipient T cells. May combine features of direct and indirect activation. Antibody-mediated recognition Preformed or newly produced donor-specific antibodies bind graft endothelium. Hyperacute and acute antibody-mediated rejection; microvascular injury. 3. Mechanisms of graft injury CD8 cytotoxicity: CTLs kill graft parenchymal and endothelial cells by perforin/granzyme and Fas pathways. CD4 cytokine injury: Th1 cells release IFN-gamma and activate macrophages; Th17 cells recruit neutrophils; helper cells provide B-cell support. Antibody/complement injury: donor-specific antibodies activate complement, injure endothelium, recruit neutrophils and promote thrombosis. Delayed-type inflammation: T-cell cytokines cause interstitial infiltrates, oedema and tissue dysfunction. Vascular remodelling: repeated endothelial injury produces intimal thickening, luminal narrowing and chronic ischemia. Innate amplification: NK cells, macrophages, complement, platelets and coagulation pathways intensify the adaptive response. 4. Solid-organ rejection: timing and type Type Typical timing Dominant mechanism Pathology and examples Hyperacute Minutes to hours after reperfusion. Preformed anti-ABO, anti-HLA or endothelial antibodies. Complement activation, diffuse endothelial injury, platelet thrombi, cortical necrosis and immediate graft failure. Accelerated Several days in a previously sensitised recipient. Memory T cells and pre-existing donor-specific antibodies. Rapid vascular and cellular injury; more likely after prior transplant, transfusion or pregnancy. Acute cellular (T-cell-mediated) Usually weeks to months, but can occur any time after immunosuppression is reduced. Recipient T-cell recognition of donor antigens. Interstitial lymphocytes, tubulitis in kidney, bile-duct injury in liver, vascular inflammation and graft dysfunction. Acute antibody-mediated Days to months; may coexist with cellular rejection. New donor-specific antibodies against graft endothelium. Microvascular inflammation, complement deposition (e.g., C4d in selected organs), thrombosis and graft dysfunction. Chronic Months to years. Persistent low-grade T-cell and antibody injury plus nonimmune stressors. Transplant vasculopathy, interstitial fibrosis, tubular atrophy and progressive loss of function. Important: A transplant recipient with deterioration may have rejection, infection, drug toxicity, obstruction, ischemia, recurrence of original disease or nonadherence. Rejection is a diagnosis requiring targeted evaluation, not a synonym for every rise in creatinine or fever. 5. Organ-specific presentation Graft Possible rejection clues Other urgent differentials Kidney Rising creatinine, reduced urine, proteinuria, hypertension, graft tenderness or weight gain. Dehydration, obstruction, renal artery/vein thrombosis, calcineurin toxicity, infection and recurrent disease. Liver Rising AST/ALT, bilirubin, alkaline phosphatase, fever or graft dysfunction. Biliary obstruction, vascular thrombosis, viral infection, drug injury and sepsis. Heart Fatigue, dyspnoea, reduced exercise tolerance, arrhythmia, hypotension or heart failure. Acute coronary syndrome, infection, pulmonary embolism, graft vasculopathy and drug toxicity. Lung Falling FEV1, cough, dyspnoea, hypoxia, fever or new infiltrates. Pneumonia, pulmonary embolism, anastomotic problems and chronic lung allograft dysfunction. Pancreas/islet Hyperglycaemia, recurrent insulin need or abnormal pancreatic enzymes. Pancreatitis, infection, medication effect and metabolic disease. Cornea Pain, photophobia, redness, reduced vision, endothelial rejection line or graft oedema. Infection, raised intraocular pressure, wound problems and trauma. 6. Diagnosis of solid-organ rejection Establish the baseline: organ function, prior rejection, donor-specific antibodies, drug levels and usual vital signs. Assess adherence and exposure: missed doses, vomiting/diarrhoea, new medicines, herbal products and grapefruit can alter immunosuppressant levels. Exclude infection early: fever and graft dysfunction may be bacterial, viral, fungal or opportunistic infection; immunosuppression can blunt signs. Perform organ-specific tests: creatinine/urinalysis, liver tests, echocardiography, spirometry, imaging or graft ultrasound as appropriate. Measure donor-specific antibodies: useful for antibody-mediated rejection but must be interpreted with graft function and biopsy. Biopsy when safe and indicated: histology often distinguishes cellular rejection,

Hypersensitivity Reactions: Gell–Coombs Types I–IV, Mechanisms, Diagnosis and Emergency Care Study level: Clinical medicine, emergency medicine and pathology | Topic: Immunopathology Core concept: Hypersensitivity is an exaggerated or inappropriate immune response that causes tissue injury. The classic Gell–Coombs system groups reactions by mechanism: Type I IgE and mast cells, Type II antibodies against fixed cell or matrix antigens, Type III circulating immune complexes, and Type IV sensitised T cells. Real diseases may combine mechanisms, and anaphylaxis must be treated clinically without waiting for a laboratory test. Learning objectives Define hypersensitivity and differentiate allergy, autoimmunity, drug intolerance and ordinary toxicity. Compare the immune effector, timing, tissue injury and examples of types I–IV. Explain sensitisation, elicitation, mast-cell mediators, complement, immune complexes and T-cell injury. Recognise anaphylaxis, severe cutaneous drug reactions, serum sickness, haemolysis and other emergencies. Use a history-led diagnostic approach and select appropriate tests without over-interpreting positive results. Outline acute treatment, prevention, documentation and referral principles. 1. Definition and terminology Hypersensitivity is an immune response that is excessive, misdirected or damaging to the host. The inciting antigen may be a harmless environmental allergen, a drug, a microbial antigen, an alloantigen or a self-antigen. Allergy usually refers to clinically important hypersensitivity to an otherwise harmless external substance. Atopy is an inherited tendency to make IgE against common environmental allergens; not every atopic person has severe allergy. Condition Immune status Example Expected protective immunity Proportionate response that controls a pathogen with acceptable tissue injury. Antibody response after vaccination. Hypersensitivity Immune response causes clinically important host damage. Anaphylaxis after peanut or penicillin. Autoimmunity Response is directed at self-antigens. Anti-acetylcholine-receptor antibody in myasthenia. Drug intolerance/toxicity Nonimmune pharmacologic or toxic effect. Gastric irritation from an NSAID without an allergic mechanism. Idiosyncratic reaction Unusual response not explained by predictable pharmacology; mechanism may be immune or nonimmune. Some severe drug eruptions. 2. The four-type framework at a glance Type Main effector Typical onset Principal injury Classic examples I: immediate Allergen-specific IgE, mast cells, basophils; late eosinophilic inflammation. Seconds to minutes; late phase 4–24 hours. Vasodilation, oedema, bronchospasm, mucus, smooth-muscle contraction. Anaphylaxis, allergic rhinitis, urticaria, atopic asthma, food allergy. II: antibody-mediated IgG/IgM against cell-surface or extracellular-matrix antigen. Hours to days; depends on antibody and target. Complement/phagocyte destruction, receptor stimulation or blockade, structural disruption. Autoimmune haemolysis, ITP, Goodpasture syndrome, Graves disease, myasthenia. III: immune-complex Soluble antigen–IgG/IgM complexes, complement and neutrophils. Hours to weeks depending on exposure and clearance. Vasculitis, glomerulonephritis, arthritis and tissue necrosis. Serum sickness, Arthus reaction, SLE, some post-infectious syndromes. IV: delayed/cell-mediated Antigen-specific CD4 T cells, macrophages and/or CD8 cytotoxic T cells. Usually 24–72 hours; chronic forms evolve over weeks. Cytokine inflammation, granulomas or direct cytotoxic cell death. Contact dermatitis, tuberculin reaction, granulomatous disease, coeliac disease, type 1 diabetes. Memory aid: “IgE is immediate; II antibodies attack a fixed target; III complexes circulate and deposit; IV is T-cell delayed.” 3. Type I hypersensitivity: IgE-mediated immediate reaction 3.1 Sensitisation An allergen crosses an epithelial barrier and is taken up by dendritic cells. Antigen is presented to naïve CD4 T cells, which polarise toward a Th2 response under IL-4 and related signals. Th2 cells provide CD40L and cytokines, especially IL-4 and IL-13, to B cells. B cells class-switch to allergen-specific IgE, which binds high-affinity Fc-epsilon-RI receptors on mast cells and basophils. The person is now sensitised; symptoms usually appear on re-exposure, not necessarily the first encounter. 3.2 Elicitation and mediator release On re-exposure, allergen cross-links adjacent IgE molecules on mast cells. Rapid degranulation releases preformed histamine, tryptase and proteases. Newly synthesised leukotrienes, prostaglandin D2, platelet-activating factor and cytokines follow. Histamine causes vasodilation, increased vascular permeability, itching, bronchoconstriction and glandular secretion; leukotrienes produce potent prolonged bronchospasm and mucus. A late phase, driven by eosinophils, Th2 cells and cytokines, causes persistent airway or tissue inflammation. Mediator Major effects Clinical correlate Histamine H1 Itch, flushing, wheal, bronchoconstriction, vasodilation and capillary leak. Urticaria, rhinitis, wheeze and hypotension. Histamine H2 Gastric secretion and some vasodilation/tachycardia. GI symptoms and cardiovascular effects. Leukotrienes C4/D4/E4 Powerful bronchoconstriction, increased vascular permeability and mucus. Asthma and severe anaphylactic bronchospasm. Prostaglandin D2 Bronchoconstriction and vasodilation. Airway symptoms and flushing. Tryptase Protease marker of mast-cell activation. Supports recent anaphylaxis if sampled appropriately; a normal result does not exclude it. PAF and cytokines Platelet activation, vascular leak, leukocyte recruitment and late inflammation. Persistent shock and late-phase disease. 3.3 Clinical forms Anaphylaxis: rapidly developing systemic reaction with airway, breathing, circulation and/or severe gastrointestinal involvement. Urticaria and angioedema: superficial wheals and deeper dermal/submucosal swelling. Bradykinin-mediated angioedema is not IgE-driven and responds poorly to antihistamines. Allergic rhinitis and conjunctivitis: sneezing, nasal itch, watery discharge and conjunctival symptoms. Atopic asthma: reversible bronchoconstriction plus chronic eosinophilic airway inflammation; not every asthma exacerbation is allergic. Food allergy: oral itching, urticaria, vomiting, wheeze or anaphylaxis; reactions can be dose-dependent and exercise/cofactor-amplified. Insect-venom and latex allergy: local reactions may be mild, but systemic reactions can progress rapidly. 4. Anaphylaxis: emergency recognition and management Suspect anaphylaxis clinically when sudden illness follows a likely trigger with airway compromise, bronchospasm, hypoxia, hypotension or severe multisystem symptoms. Skin signs may be absent, especially in severe shock; do not wait for rash or a blood test. 4.1 Red flags Airway: tongue/throat swelling, hoarseness, stridor, inability to swallow secretions. Breathing: wheeze, severe bronchospasm, cyanosis, hypoxia or exhaustion. Circulation: collapse, hypotension, weak pulse, syncope or cardiac arrest. Skin/mucosa: generalised urticaria, flushing, pruritus or angioedema (may be absent). Gastrointestinal: repetitive vomiting, cramping or severe diarrhoea, especially with another system involved. Neurologic: anxiety, confusion, dizziness or loss of consciousness from hypoperfusion. 4.2 Immediate treatment sequence Call for help, remove the trigger if possible, position supine with legs raised; allow a patient with severe breathing difficulty to sit with legs extended. Do not let a shocked patient stand or walk. Give IM adrenaline (epinephrine) into the anterolateral thigh immediately. Common emergency guidance uses adrenaline 1 mg/mL (1:1000): adult 0.5 mg (0.5 mL); child 0.01 mg/kg up to 0.5 mg. Repeat after about 5 minutes if airway, breathing or circulation problems persist, following local protocol and available concentration. Assess airway, breathing,

Autoimmune Diseases: Mechanisms, Classification, Diagnosis and Clinical Emergencies Study level: Clinical medicine, emergency medicine and pathology | Topic: Immunopathology Core idea: Autoimmune disease occurs when immune tolerance to self-antigens is lost and self-reactive lymphocytes or antibodies cause tissue injury. The disease may be organ-specific or systemic, often follows a relapsing-remitting course, and can produce life-threatening renal, neurologic, endocrine, respiratory, haematologic or vascular complications. Learning objectives Define autoimmunity and distinguish harmless autoreactivity from autoimmune disease. Explain central and peripheral self-tolerance and how genetic and environmental factors break tolerance. Describe antibody-mediated, immune-complex and T-cell-mediated tissue injury. Classify autoimmune disorders as organ-specific or systemic and recognise representative diseases. Choose investigations rationally, interpret autoantibodies in clinical context and avoid false-positive diagnoses. Recognise emergency presentations and outline safe, multidisciplinary management principles. 1. Definitions and essential distinctions Autoimmunity is an immune response directed against an antigen belonging to the host. Low-level autoreactive B and T cells are common in healthy people; their presence alone is not disease. Autoimmune disease means clinically important autoimmunity that produces inflammation, loss of function, structural damage or organ failure. Term Meaning Clinical implication Self-tolerance Specific unresponsiveness to the body’s own antigens. Prevents destructive responses against normal tissues. Autoantibody Antibody that binds a self-antigen. May be pathogenic, a disease marker, or an incidental finding. Autoimmune disease Autoimmunity plus demonstrable tissue injury or dysfunction. Requires a clinical syndrome, not an isolated laboratory result. Autoinflammatory disease Predominantly dysregulated innate immunity, often without disease-specific autoantibodies. Do not automatically label every inflammatory syndrome autoimmune. Allergy/hypersensitivity Exaggerated immune response to usually harmless foreign antigen. Different antigen target; hypersensitivity may coexist with autoimmunity. 2. Normal self-tolerance: the protective checkpoints 2.1 Central tolerance Central tolerance develops while lymphocytes mature. In the thymus, immature T cells that bind self-peptide–MHC with high affinity undergo clonal deletion (negative selection). Medullary thymic epithelial cells express tissue-restricted antigens under the AIRE transcription factor, allowing deletion of T cells that could attack endocrine and other peripheral tissues. Some self-reactive thymocytes are diverted into the regulatory T-cell (Treg) lineage. In bone marrow, immature B cells undergo receptor editing, deletion or anergy when their B-cell receptor strongly recognises self. 2.2 Peripheral tolerance Central deletion is incomplete, because not every self-antigen is displayed during lymphocyte development. Peripheral tolerance controls escaped cells through: Anergy: antigen recognition without adequate co-stimulation makes a lymphocyte functionally unresponsive. Deletion: repeated stimulation can trigger apoptosis of autoreactive cells. Suppression by Tregs: FOXP3-positive Tregs release inhibitory cytokines and consume IL-2; CTLA-4 reduces co-stimulation. Inhibitory checkpoints: CTLA-4 and PD-1 pathways dampen T-cell activation. Sequestration: some antigens are normally hidden in immune-privileged sites and are exposed after trauma or inflammation. Ignorance and limited access: a self-reactive clone may remain inactive if antigen concentration, presentation or inflammatory signals are insufficient. Exam chain: defective central deletion supplies autoreactive clones; infection or tissue damage supplies inflammation and co-stimulation; genetic susceptibility shapes the target; chronic immune activation and epitope spreading maintain the disease. 3. Why tolerance fails: causes and risk factors Factor Mechanism Examples or consequences Genetic susceptibility HLA variants alter which self-peptides are presented; non-HLA genes affect Tregs, cytokines, complement, B-cell signalling and checkpoints. HLA-DR3/DR4 with type 1 diabetes; HLA-DR4 with rheumatoid arthritis; HLA-B27 with spondyloarthritis. Sex and hormones Sex-linked immune regulation and oestrogen effects influence B-cell survival and antibody production. Many systemic autoimmune diseases are more common in women; pregnancy may improve or worsen different conditions. Infections Molecular mimicry, bystander cytokines, tissue injury and activation of previously silent clones. Post-streptococcal rheumatic disease; infection-associated arthritis; viral triggers of flares. Molecular mimicry Microbial epitopes resemble self-epitopes, so cross-reactive T cells or antibodies damage host tissues. Cross-reactivity after infection can initiate autoimmunity in a genetically susceptible person. Bystander activation Local interferons, cytokines and danger signals activate autoreactive cells that were not specific for the organism. Inflamed tissue becomes permissive to autoimmune damage. Epitope spreading Initial injury releases new self-epitopes; the immune response broadens from the original target to additional targets. Progressive, chronic disease despite removal of the initial trigger. Cryptic antigens and tissue damage Trauma, necrosis or altered protein processing exposes previously hidden or modified self-antigens. Autoimmunity after tissue injury or drug-induced alteration of proteins. Drugs and chemicals Drug-protein binding creates neoantigens or alters immune regulation. Drug-induced lupus, autoimmune haemolysis or vasculitis; always review the medication timeline. Microbiome, smoking and ultraviolet light Change barrier integrity, antigen exposure and inflammatory signalling. Smoking increases rheumatoid risk; ultraviolet light can promote lupus flares. Failure of clearance Defective complement or phagocytic clearance leaves apoptotic debris and nuclear antigens available for immune-complex formation. Important in systemic lupus erythematosus. 4. Immunopathogenic mechanisms of tissue damage 4.1 Antibody-mediated disease (often called type II hypersensitivity) Cell destruction: IgG or IgM binds cell-surface antigens and activates complement, phagocytosis or antibody-dependent cellular cytotoxicity. Examples include autoimmune haemolytic anaemia and immune thrombocytopenia. Receptor stimulation: an antibody acts as an agonist. Thyroid-stimulating immunoglobulin activates the TSH receptor in Graves disease. Receptor blockade: an antibody prevents a normal ligand from binding. Anti-acetylcholine-receptor antibodies impair neuromuscular transmission in myasthenia gravis. Structural disruption: antibodies against cell-adhesion proteins produce blistering, as in pemphigus vulgaris. 4.2 Immune-complex disease (type III pattern) Soluble antigen–antibody complexes deposit in small vessels, glomeruli, skin, joints or serosal surfaces. Complement activation generates C3a and C5a, recruits neutrophils and produces vasculitis, glomerulonephritis and arthritis. Systemic lupus erythematosus is the classic example. Low serum complement can indicate active consumption, but normal complement does not exclude disease. 4.3 T-cell-mediated disease (type IV pattern) CD4 T cells release cytokines that activate macrophages and recruit inflammatory cells; CD8 cytotoxic T cells kill target cells directly. Type 1 diabetes destroys pancreatic beta cells, multiple sclerosis targets myelin and autoimmune hepatitis injures hepatocytes through combined T-cell and antibody mechanisms. 4.4 Mixed mechanisms Most autoimmune diseases are not pure textbook categories. A patient may have autoantibodies, immune complexes, T-cell injury, thrombosis and cytokine-driven inflammation at the same time. Mechanism guides the test and treatment but does not replace clinical diagnosis. 5. Classification Pattern Main target Examples Typical clues Organ-specific One organ or a restricted tissue antigen. Type 1 diabetes, Graves disease,

Antibodies (immunoglobulins) are antigen-binding glycoproteins made by B cells and plasma cells. Their variable regions recognise specific epitopes, while constant regions determine what happens next—neutralisation, complement activation, phagocytosis, mucosal transport, mast-cell activation or placental transfer. Antibody structure, class and affinity explain serology, vaccination, allergy, autoimmunity, transfusion reactions and many antibody-based therapies. At a glance An antibody is made of two identical heavy chains and two identical light chains. Fab regions bind antigen; the Fc region recruits effector mechanisms and determines class-specific behaviour. IgM is usually the first secreted class; IgG dominates systemic memory; IgA protects mucosa; IgE mediates allergy and helminth defence; IgD is mainly a B-cell receptor. Affinity is the strength of one binding site; avidity is total multivalent binding strength. Antibody results must be interpreted with timing, symptoms, vaccination history, organ function and confirmatory tests. Learning outcomes The learner should be able to draw and label an immunoglobulin, distinguish variable and constant regions, explain heavy-chain classes and light chains, compare IgM, IgG, IgA, IgE and IgD, describe antibody effector functions, interpret affinity and avidity, and recognise antibody-related disease and treatment complications. 1. Basic immunoglobulin structure A conventional antibody has a Y-shaped structure formed by two identical heavy chains and two identical light chains. Disulphide bonds hold the chains together, and non-covalent forces maintain their folded domains. Region Structure Function Variable region Variable domains of one heavy and one light chain form each binding site Recognises a specific epitope Complementarity-determining regions Hypervariable loops within the variable region Make direct contact with antigen Framework region Conserved scaffold around CDRs Maintains antibody shape Fab Antigen-binding arms Neutralisation and specificity Hinge Flexible segment between arms and Fc in some classes Allows different binding angles and distances Fc Constant heavy-chain region Fc-receptor binding, complement, transport and effector function 2. Light and heavy chains 2.1 Light chains Light chains are either kappa or lambda. One antibody uses only one type; both may be present in a person, but an individual B-cell clone expresses one light-chain type. Excess free light chains can occur in plasma-cell disorders and are measured clinically. 2.2 Heavy chains Heavy-chain constant regions define immunoglobulin class: mu for IgM, delta for IgD, gamma for IgG, alpha for IgA and epsilon for IgE. Class switching changes the heavy-chain constant region while retaining the same antigen-binding variable region. 3. Antigen–antibody binding Binding depends on shape, charge, hydrophobic forces and hydrogen bonds. An epitope is the part of an antigen recognised by an antibody; an antigen may contain many epitopes. Antibodies can recognise linear sequences or conformational structures that disappear when a protein is denatured. 3.1 Affinity and avidity Affinity: strength of one binding site–epitope interaction. Avidity: combined strength of all interactions. IgM has moderate affinity per site but high avidity because it binds multivalently. Affinity maturation in germinal centres selects B cells with stronger binding. 3.2 Cross-reactivity An antibody can bind a similar epitope on a different antigen. Cross-reactivity helps some immune protection but can cause false-positive serology or molecular mimicry in autoimmunity. 4. Immunoglobulin classes Class Typical form/location Major functions Clinical points IgM Surface monomer; secreted pentamer in serum Early response, agglutination and strong classical complement activation Large size limits tissue penetration; high avidity; recent infection interpretation requires caution IgG Monomer; serum and extravascular spaces Neutralisation, opsonisation, complement, ADCC and placental transfer Four subclasses have different Fc functions; dominant long-term systemic antibody IgA Serum monomer; secretory dimer in mucosa and milk Neutralisation and immune exclusion at mucosal surfaces Selective deficiency can cause mucosal infection and transfusion reactions IgE Low free serum level; Fc bound to mast cells/basophils Immediate hypersensitivity and helminth defence Cross-linking causes degranulation and anaphylaxis IgD Surface receptor on naive B cells B-cell activation and antigen sensing Little routine serum diagnostic use 5. IgG subclasses IgG1: abundant; responds well to protein antigens and crosses placenta effectively. IgG2: important for polysaccharide responses. IgG3: strong complement activation and a flexible hinge, but shorter half-life. IgG4: limited complement activation and associated with immune tolerance; abnormal levels occur in selected disease. Subclass levels must be interpreted with age, vaccine response and recurrent infection; an isolated low value is not automatically clinically significant. 6. IgA and mucosal protection Plasma cells beneath mucosal epithelium produce dimeric IgA joined by a J chain. The polymeric immunoglobulin receptor transports it across epithelial cells, and the secretory component protects it from proteolysis. Secretory IgA blocks attachment and neutralises toxins with relatively little complement-mediated inflammation. IgA in breast milk supports infant mucosal protection. Selective IgA deficiency can be asymptomatic, but some patients develop recurrent respiratory or gastrointestinal infection, allergy, autoimmunity or reactions to blood products containing IgA. 7. Fc receptors and effector functions Effector mechanism How antibody participates Outcome Neutralisation Fab blocks toxin, viral receptor or microbial attachment Prevents entry or tissue injury Opsonisation IgG Fc is recognised by phagocyte Fc receptors Enhanced phagocytosis and killing Complement activation Antigen-bound IgM/IgG recruits C1 C3b coating, inflammation and membrane attack ADCC NK-cell Fc receptors bind antibody-coated targets Target-cell apoptosis Mast-cell activation IgE Fc binds high-affinity Fc-epsilon receptors Histamine, leukotriene and cytokine release Placental transfer FcRn transports IgG across placenta Temporary neonatal systemic protection 8. Antibody production and class switching B-cell receptor binds antigen. Antigen is internalised and peptide presented on MHC II. T follicular helper cells provide CD40L and cytokines. Activated B cells proliferate in follicles and germinal centres. Somatic hypermutation and selection improve affinity. Class switching selects the Fc function suited to the pathogen and tissue. Plasma cells secrete antibody; memory B cells remain. Class switching is irreversible at the DNA level for an individual B-cell clone but preserves antigen specificity. A defect in CD40–CD40L signalling or activation-induced cytidine deaminase can produce hyper-IgM syndromes. 9. Monoclonal and polyclonal antibodies Polyclonal response: many B-cell clones recognise different epitopes on the same antigen; broad but heterogeneous. Monoclonal antibody: one clone recognises one epitope; highly specific and used in diagnostics and treatment. Human, humanised and chimeric products: differ in immunogenicity and pharmacology; product-specific monitoring is required. Antibody fragments: Fab or single-chain fragments may penetrate

Cellular immunity is the T-lymphocyte-mediated arm of adaptive defence. T cells recognise peptide antigens displayed by major histocompatibility complex (MHC) molecules, then coordinate macrophages, B cells and inflammation or directly kill infected and abnormal cells. Cellular immunity is essential against viruses, intracellular bacteria, fungi, tumours and transplanted tissue, but excessive or misdirected T-cell activity causes delayed hypersensitivity, autoimmunity and tissue damage. At a glance CD4 helper T cells: coordinate immune responses through cytokines and cell contact. CD8 cytotoxic T cells: kill infected, malignant or otherwise abnormal cells presenting antigen on MHC I. Regulatory T cells: suppress excessive responses and maintain self-tolerance. Recognition rule: T-cell receptors recognise peptide plus the correct MHC molecule, not free antigen alone. Clinical failure: severe viral, fungal and opportunistic infection, poor tumour surveillance and impaired vaccine responses. Learning outcomes The learner should be able to describe T-cell development and selection, explain MHC I and II antigen presentation, differentiate CD4 helper subsets, describe CD8 cytotoxic killing, explain T-cell memory and tolerance, and apply cellular-immunity concepts to infection, transplantation, autoimmunity and emergency care. 1. T-cell development and the T-cell receptor 1.1 Development in the thymus T-cell precursors arise in bone marrow and mature in the thymus. T-cell receptor (TCR) genes rearrange to create a diverse repertoire. Positive selection preserves cells that can recognise self-MHC; negative selection removes strongly self-reactive cells. Surviving cells become mainly CD4 or CD8 single-positive T cells and leave as naive lymphocytes. 1.2 TCR–CD3 complex The TCR recognises a peptide–MHC complex. CD3 transmits the activation signal, while CD4 or CD8 stabilises interaction with MHC II or MHC I. Co-stimulatory and cytokine signals determine whether the cell becomes an effector, memory or regulatory T cell. 2. Antigen presentation Feature MHC class I MHC class II Expression Most nucleated cells Professional antigen-presenting cells: dendritic cells, macrophages and B cells Antigen source Intracellular/cytosolic proteins, including viral and tumour proteins Extracellular proteins taken up by endocytosis/phagocytosis Processing Proteasome, TAP transport into endoplasmic reticulum and peptide loading Endosomal processing and loading in vesicular compartments Recognised by CD8 cytotoxic T cells CD4 helper T cells Main outcome Kill infected or abnormal target cell Coordinate macrophages, B cells and inflammation Dendritic cells can cross-present selected extracellular antigens on MHC I to prime CD8 responses. Tumours and viruses may evade by reducing MHC expression or interfering with antigen processing. 3. T-cell activation Naive T cells require three coordinated signals: Signal 1: TCR recognition of peptide–MHC. Signal 2: co-stimulation, especially CD28 binding B7 molecules on an activated antigen-presenting cell. Signal 3: cytokines that direct differentiation. Antigen recognition without adequate co-stimulation can induce anergy or tolerance. Inhibitory checkpoints such as CTLA-4 and PD-1 restrain activation; tumours can exploit these pathways to evade immunity. 4. CD4 helper T-cell subsets Subset Key cytokines/transcriptional drivers Main functions and clinical associations Th1 IFN-gamma; T-bet Activates macrophages and supports intracellular pathogen control; tuberculosis and granulomatous inflammation Th2 IL-4, IL-5, IL-13; GATA-3 Eosinophils, IgE, mucus and helminth defence; allergy and asthma Th17 IL-17, IL-22; ROR-gamma-t Neutrophil recruitment and mucosal barrier defence; fungal infection and autoimmune inflammation T follicular helper IL-21 and other signals; Bcl-6 Germinal-centre B-cell help, class switching and affinity maturation Regulatory T cell IL-10, TGF-beta; FoxP3 Suppresses autoreactive and excessive responses; tolerance and immune homeostasis Subsets are functional tendencies rather than completely isolated categories. Cytokine environments and tissue signals can alter phenotype and plasticity. 5. CD8 cytotoxic T cells 5.1 Activation and differentiation Naive CD8 cells are primed by dendritic cells, often with CD4 help and inflammatory cytokines. They expand into armed cytotoxic T lymphocytes (CTLs) and memory cells. CTLs migrate to infected or tumour tissue and inspect MHC I–peptide complexes. 5.2 Killing mechanisms Perforin–granzyme pathway: perforin facilitates entry of granzymes, which activate target-cell apoptosis. Fas–Fas ligand pathway: Fas engagement activates death-receptor apoptosis. Cytokines: IFN-gamma and TNF can inhibit pathogens and alter local inflammation. After delivering a lethal hit, a CTL can detach and kill another target. This precision limits collateral damage, but widespread infection or excessive CTL activity can destroy essential tissue. 6. Cellular immunity against different threats Threat Dominant cellular response Potential pathology Virus-infected cells CD8 CTLs, NK cells, type I interferons and CD4 help Viral cytopathic injury plus immune-mediated tissue damage Intracellular bacteria Th1 IFN-gamma activation of macrophages Granuloma, caseation and chronic inflammation Fungi Th1/Th17 responses, macrophages and neutrophils Invasive disease in T-cell or neutrophil deficiency Helminths Th2, eosinophils, mast cells and IgE Allergic-type tissue injury and airway inflammation Tumour cells CD8 CTLs, NK cells and helper cytokines Immune escape, checkpoint exploitation and tumour progression Transplanted tissue Direct/indirect alloreactive T cells and antibodies Acute or chronic rejection 7. T-cell memory After antigen clearance, most effector T cells die, while memory cells persist. Central memory cells circulate through lymphoid organs; effector memory cells patrol peripheral tissues; tissue-resident memory cells remain near portals of entry. On re-exposure, memory cells activate more rapidly and require less proliferation. Memory can be protective, but it can also sustain chronic infection, autoimmune disease or transplant rejection. Antigenic variation and immune evasion can reduce protective memory. 8. Delayed-type hypersensitivity Type IV hypersensitivity is T-cell mediated and typically appears 24–72 hours after antigen exposure. Th1 and Th17 cytokines recruit macrophages and neutrophils; CD8 cells may directly kill target cells. Examples include tuberculin skin reactions, contact dermatitis, granulomatous inflammation and some drug eruptions. Severe cutaneous adverse reactions, such as Stevens–Johnson syndrome/toxic epidermal necrolysis, involve immune-mediated epithelial injury and are emergencies requiring immediate drug withdrawal and specialist care. 9. Granulomatous inflammation Persistent intracellular pathogens or foreign material stimulate macrophages and T cells. Th1 cells release IFN-gamma, activating macrophages that form epithelioid cells and multinucleated giant cells. Granulomas contain but may not eradicate the cause. They occur in tuberculosis, some fungal infections, sarcoidosis, Crohn disease and foreign-body reactions. 10. T-cell immunodeficiency 10.1 Causes HIV infection, especially with falling CD4 count. Congenital thymic or combined immunodeficiency. Corticosteroids, chemotherapy, transplant medicines and biologic agents. Severe malnutrition, malignancy, ageing or critical illness. 10.2 Clinical pattern Look for recurrent or severe viral, fungal, protozoal and opportunistic infection; persistent diarrhoea; chronic

Humoral immunity is the antibody-mediated arm of adaptive immunity. B lymphocytes recognise antigen, receive activation signals, and differentiate into plasma cells that secrete immunoglobulins. Antibodies act mainly in extracellular fluids and mucosal surfaces by neutralising toxins and viruses, opsonising microbes, activating complement and recruiting immune effector cells. Effective humoral defence depends on B-cell tolerance, T-cell help, germinal-centre maturation and long-lived memory. At a glance Main cells: B cells, plasma cells, memory B cells and helper/T-follicular helper cells. Main molecules: immunoglobulins, complement, cytokines and Fc receptors. T-dependent response: strong, class-switched, affinity-matured and memory-forming response to most proteins. T-independent response: rapid response to repetitive polysaccharides/lipids, usually dominated by IgM with weaker memory. Clinical failure: recurrent bacterial infection, poor vaccine protection, absent immunoglobulins or abnormal antibody function. Learning outcomes The learner should be able to describe B-cell development and activation, explain immunoglobulin structure and isotypes, compare T-dependent and T-independent responses, describe antibody effector functions and complement interaction, interpret common serology patterns, and recognise humoral immunodeficiency and emergencies. 1. B-cell development and tolerance 1.1 Development B-cell precursors arise in bone marrow. Immunoglobulin gene rearrangement generates a unique B-cell receptor (BCR) for each clone. Immature B cells that strongly recognise self may be deleted, edited or rendered anergic. Mature naive B cells express surface IgM and IgD and circulate through lymphoid tissues. 1.2 Central and peripheral tolerance Central tolerance: self-reactive immature B cells are deleted, revise their receptor or become unresponsive. Peripheral tolerance: lack of T-cell help, inhibitory receptors, regulatory cells and deletion limit autoreactive clones. Breakdown can produce autoantibodies, immune-complex disease or antibody-mediated tissue injury. 2. Antigen recognition and B-cell activation BCRs bind intact, three-dimensional antigen. A B cell internalises the antigen, processes protein fragments and presents them on MHC II. A T follicular helper cell recognises the peptide–MHC II complex and supplies CD40L–CD40 interaction plus cytokines. This “linked recognition” ensures that T-cell help is directed to the same antigen captured by the B cell. 2.1 T-dependent activation Antigen binds the BCR and is internalised. The B cell presents peptide on MHC II. T follicular helper cells provide co-stimulation and cytokines. Activated B cells proliferate and form extrafollicular plasmablasts or germinal centres. Class switching, somatic hypermutation, affinity maturation and memory formation follow. 2.2 T-independent activation Highly repetitive antigens such as bacterial polysaccharides can cross-link many BCRs and activate B cells with limited T-cell help. The response is rapid but often produces mainly IgM, shorter-lived plasma cells and weaker memory. Conjugate vaccines attach polysaccharide to protein so T-cell help can be recruited, improving infant responses and memory. 3. Germinal-centre reaction Process What happens Clinical value Somatic hypermutation Point mutations are introduced into variable-region genes Creates BCR variants with different affinities Affinity selection Higher-affinity clones capture antigen and receive survival signals Improves antibody binding after infection or vaccination Class-switch recombination Constant region changes from IgM/IgD to IgG, IgA or IgE Changes effector function without changing antigen specificity Memory formation Long-lived B cells and plasma cells are generated Faster response on re-exposure Activation-induced cytidine deaminase is central to somatic hypermutation and class switching. Defects can cause hyper-IgM syndromes, recurrent infection and poor vaccine responses. 4. Immunoglobulin structure An antibody contains two identical heavy chains and two identical light chains joined by disulphide bonds. The variable regions form antigen-binding sites; the constant Fc region determines class and interaction with complement or Fc receptors. A flexible hinge allows some antibodies to bind epitopes at different distances. Fab region: binds antigen. Fc region: recruits complement, phagocytes, NK cells or transport mechanisms. Valency: IgG is usually bivalent; secreted IgA is commonly dimeric; IgM is secreted as a pentamer with high avidity. Affinity: strength of one antigen-binding site; avidity is total binding strength across multiple sites. 5. Immunoglobulin classes Class Structure/distribution Main functions Clinical relevance IgM Monomer on B cells; pentamer in serum First response, strong complement activation, agglutination Early serological marker in some infections; high IgM may indicate recent exposure but is not definitive alone IgG Monomer; most abundant serum class; crosses placenta Neutralisation, opsonisation, complement, ADCC and durable memory Long-term vaccine/previous-exposure antibody; maternal neonatal protection IgA Monomer in serum; secretory dimer at mucosa Mucosal neutralisation and immune exclusion with limited inflammation Deficiency predisposes to mucosal infection and transfusion reactions in selected patients IgE Low serum concentration; binds mast cells and basophils Immediate hypersensitivity and helminth defence Allergy, anaphylaxis and parasitic disease IgD Surface receptor on naive B cells; little secreted serum B-cell activation and mucosal signalling Limited routine diagnostic use 6. Antibody effector functions 6.1 Neutralisation Antibody blocks microbial attachment, entry, toxin binding or viral fusion. Neutralisation is often the main protective function against extracellular toxins and viruses. 6.2 Opsonisation IgG Fc regions and complement fragments coat microbes. Neutrophils and macrophages bind these opsonins through Fc and complement receptors, increasing phagocytosis. Patients lacking antibody or complement are especially vulnerable to encapsulated bacteria. 6.3 Complement activation Antigen-bound IgM or IgG activates the classical pathway. Complement enhances inflammation, opsonisation and membrane attack. Complement regulators protect host cells from accidental injury. 6.4 Antibody-dependent cellular cytotoxicity NK cells and other effector cells bind Fc regions on antibody-coated targets and release cytotoxic mediators. This bridges humoral recognition to cellular killing. 6.5 Agglutination and precipitation Multivalent antibodies cross-link particles or soluble antigens, making them easier to clear. IgM is particularly effective because of its pentameric structure. 7. Mucosal humoral immunity Secretory IgA is produced by plasma cells beneath mucosal epithelium. It is transported across epithelial cells and released with a secretory component that protects it from proteases. IgA neutralises pathogens and toxins without strongly activating complement, reducing collateral tissue injury in the gut, airway and genitourinary tract. Breast milk provides secretory IgA and other factors that support infant mucosal defence. Mucosal vaccination aims to generate local antibody and tissue-resident immune protection where pathogens enter. 8. Antibody kinetics and memory During a primary response, IgM usually appears first, followed by class-switched antibody. On repeat exposure, memory B cells rapidly generate higher-affinity IgG, IgA or IgE depending on the tissue and cytokine environment. Long-lived plasma cells can

Innate and adaptive immunity are complementary arms of host defence. Innate immunity acts within minutes through barriers, pattern-recognition receptors, soluble proteins and rapid effector cells. Adaptive immunity develops more slowly during a first encounter, but it recognises specific antigens, generates antibodies and T-cell responses, and remembers previous exposure. Most effective immune responses require both systems working together. At a glance Feature Innate immunity Adaptive immunity Onset Seconds to hours Days during first exposure Recognition Pattern-recognition receptors detect shared microbial/damage patterns B-cell and T-cell receptors recognise specific antigens Receptor diversity Limited, germline encoded Very large, generated by gene rearrangement Memory Traditionally limited; trained innate responses can occur Long-lived B- and T-cell memory is a defining feature Main effectors Barriers, complement, neutrophils, macrophages, NK cells, inflammation Antibodies, helper T cells, cytotoxic T cells and memory cells Learning outcomes The learner should be able to define innate and adaptive immunity, describe physical and chemical barriers, explain pattern recognition and complement, identify major immune cells, compare humoral and cellular responses, explain antigen presentation and immune memory, and relate dysregulation to infection, sepsis, allergy, autoimmunity and immunodeficiency. 1. The layered organisation of immunity Barrier defence: skin, mucosa, mucus, cilia, secretions, microbiota and mechanical clearance prevent entry. Innate recognition and inflammation: resident cells detect danger, release mediators and recruit effectors. Innate killing: complement, phagocytosis, antimicrobial peptides, oxidative mechanisms and NK-cell cytotoxicity limit spread. Adaptive activation: dendritic cells present antigen and activate lymphocytes in lymphoid organs. Resolution and memory: inflammation contracts, tissue repairs and memory cells remain. 2. Physical and chemical barriers Barrier Protective mechanism Failure consequence Skin Keratin, tight junctions, dryness, acidic lipids and antimicrobial peptides Cellulitis, wound infection and invasive disease after barrier disruption Respiratory mucosa Mucus, ciliary clearance, cough, macrophages and airway peptides Pneumonia and infection when cilia or cough are impaired Gastrointestinal tract Acid, bile, peristalsis, mucus, microbiota and secretory IgA Enteric infection or dysbiosis Urinary/reproductive tract Urine flow, mucosal epithelium, pH and microbiota Urinary and genital infection Eye Tears, blinking, lysozyme and intact cornea Keratitis or conjunctival infection Blood-brain barrier Endothelial tight junctions and specialised transport Neuroinvasion or difficult antimicrobial penetration 3. Innate immune recognition 3.1 PAMPs and DAMPs Pathogen-associated molecular patterns (PAMPs) are conserved microbial structures such as lipopolysaccharide, flagellin, unmethylated nucleic acid or double-stranded viral RNA. Damage-associated molecular patterns (DAMPs) are host molecules released by necrotic or stressed cells. Both can activate inflammation; therefore, sterile trauma and infection may look similar early. 3.2 Pattern-recognition receptors Toll-like receptors: detect extracellular or endosomal microbial components. NOD-like receptors: detect cytosolic bacterial products and cellular stress; some form inflammasomes. RIG-I-like receptors: recognise viral RNA in the cytosol. C-type lectin receptors: detect fungal and other carbohydrate patterns. cGAS–STING pathway: detects cytosolic DNA and induces interferon responses. Receptor activation induces NF-kappa B, interferon-regulatory factors, inflammasomes and cytokine production. Excessive activation causes tissue injury, systemic inflammatory response and shock. 4. Innate immune cells Cell Main functions Important clinical clues Neutrophil Rapid chemotaxis, phagocytosis, granules, reactive oxygen species and extracellular traps Neutropenia causes severe bacterial/fungal infection; excessive activation injures tissue Monocyte/macrophage Phagocytosis, cytokines, antigen presentation, tissue repair and resolution Persistent macrophage activation contributes to chronic inflammation Dendritic cell Captures antigen and primes naive T cells; links innate to adaptive immunity Essential for vaccine and antiviral responses Natural killer cell Kills stressed, infected or tumour cells; produces interferon-gamma Recognises reduced MHC I and antibody-coated targets Mast cell Histamine, lipid mediators and cytokines; barrier defence and allergy Anaphylaxis, urticaria and parasite responses Eosinophil Helminth killing and allergic inflammation Parasitic disease, asthma and drug reactions Basophil Circulating type-2 effector cell and histamine source Allergic and helminth-related responses 5. Innate effector mechanisms 5.1 Phagocytosis Chemotaxis directs cells toward complement fragments, chemokines and microbial products. Adhesion and recognition occur through pattern receptors and opsonins such as IgG and C3b. The pathogen is engulfed into a phagosome. Fusion with lysosomes, acidification, proteases, reactive oxygen and nitrogen species destroy the target. Debris is cleared and antigen may be presented to lymphocytes. 5.2 Complement Pathway Trigger Important products Classical Antibody bound to antigen or selected acute-phase proteins C3b opsonisation, C3a/C5a inflammation and membrane attack complex Lectin Microbial carbohydrates recognised by lectin Same central cascade without pre-existing antibody Alternative Spontaneous C3 activation amplified on unprotected microbial surfaces Rapid opsonisation and lysis C3b coats microbes, C3a and C5a promote inflammation, C5a recruits neutrophils, and the membrane attack complex can lyse susceptible organisms. Complement is controlled by host regulators; uncontrolled activation can damage self-tissue. 5.3 Interferons and antiviral defence Type I interferons induce an antiviral state, increase antigen presentation and activate NK cells. Cytokines coordinate fever, acute-phase responses, leukocyte recruitment and adaptive differentiation. Excessive cytokine release can cause capillary leak, hypotension, organ dysfunction and shock. 6. Adaptive immunity 6.1 B lymphocytes and humoral immunity B cells recognise native antigen through the B-cell receptor. With T-cell help, they proliferate, class-switch, affinity-mature and differentiate into antibody-secreting plasma cells or memory B cells. Antibodies neutralise toxins and viruses, opsonise microbes, activate complement and support antibody-dependent cellular cytotoxicity. 6.2 T lymphocytes and cellular immunity CD4 helper T cells: coordinate immune cells through cytokines and contact signals. CD8 cytotoxic T cells: kill infected, malignant or otherwise abnormal cells presenting antigen on MHC I. Regulatory T cells: limit activation and maintain tolerance. Memory T cells: respond quickly during re-exposure. 6.3 Antigen presentation MHC I on nearly all nucleated cells presents intracellular peptides to CD8 cells. MHC II on professional antigen-presenting cells presents extracellularly derived peptides to CD4 cells. Cross-presentation allows dendritic cells to prime CD8 responses against some extracellular or tumour antigens. 7. Innate–adaptive crosstalk Dendritic cells and cytokines determine the type of T-cell response. Complement fragments enhance B-cell activation and antibody responses. Antibodies coat pathogens so neutrophils, macrophages and NK cells can clear them. Helper T cells activate macrophages and support B-cell class switching. Inflammation creates the vascular and cellular environment needed for adaptive cells to enter tissue. Regulatory mechanisms prevent the response from continuing after the threat has been removed. 8. Innate versus adaptive comparison Domain Innate Adaptive Specificity Shared molecular patterns

A primary immune response occurs when the adaptive immune system first encounters an antigen; a secondary response occurs on later exposure to the same or a related antigen. The secondary response is usually faster, larger, longer-lasting and more effective because antigen-specific memory B and T cells were generated during the first response. Innate immunity responds immediately at both encounters and helps determine the quality of the adaptive response. At a glance Feature Primary response Secondary response Responding cells Naive B and T lymphocytes Memory B/T cells plus newly recruited cells Lag phase Longer—days while clones activate Shorter Magnitude Lower Higher Antibody IgM appears first, then class-switched antibody Usually faster, higher-affinity IgG/IgA/IgE depending on site and response Duration Shorter Longer due to memory and long-lived plasma cells Learning outcomes The learner should be able to describe the stages of a primary adaptive response, explain how memory cells produce a secondary response, distinguish primary and secondary antibody patterns, relate responses to vaccination and serology, identify factors that weaken memory, and apply the concepts to infection, immunisation and emergency care. 1. What starts an immune response? An antigen is a molecule recognised by immune receptors. Pathogen-associated and damage-associated signals activate innate cells, which release cytokines and increase co-stimulatory molecules. Dendritic cells capture antigen in tissues and migrate to lymph nodes, where they present peptide fragments to naive T cells. The adaptive response requires more than antigen recognition. A T cell needs antigen displayed on an appropriate major histocompatibility complex (MHC) molecule plus co-stimulation and cytokine signals. This protects against inappropriate activation and contributes to peripheral tolerance. 2. The primary immune response 2.1 Recognition and antigen presentation Dendritic cells process proteins and present peptides on MHC class II to CD4 T cells and, through cross-presentation, selected antigens on MHC class I to CD8 T cells. Naive lymphocytes circulate through secondary lymphoid organs until their receptors encounter the appropriate antigen. Co-stimulation and cytokines determine whether cells become helper, cytotoxic, regulatory or memory populations. 2.2 Clonal selection and expansion Only the rare B or T cell with a receptor that fits the antigen is selected. It proliferates into a clone. This explains specificity: thousands of different clones exist before infection, but only a small subset responds to each antigen. 2.3 B-cell activation B cells bind native antigen through the B-cell receptor, internalise it and present peptide to helper T cells. CD40–CD40L interaction and cytokines support proliferation and differentiation. Some responses to repetitive polysaccharides can be T-independent and generate weaker memory, especially in young children. 2.4 Germinal-centre reaction Activated B cells enter follicles and form germinal centres. They undergo somatic hypermutation and selection for higher-affinity receptors, then class-switch recombination from IgM to IgG, IgA or IgE according to cytokine and tissue signals. The result is affinity maturation and long-lived plasma or memory B cells. 2.5 T-cell activation CD4 helper cells: Th1 cells activate macrophages and support intracellular pathogen control; Th2 cells support eosinophils and IgE; Th17 cells recruit neutrophils and strengthen mucosal defence; T follicular helper cells support germinal centres; regulatory T cells limit damage. CD8 cytotoxic cells: recognise peptide on MHC I and kill infected or abnormal cells through perforin/granzyme and death-receptor pathways. 3. Primary response kinetics Phase What happens Clinical/serological meaning Lag Antigen capture, lymphocyte activation and clonal expansion Tests may be negative early; symptoms may precede detectable antibody Log/exponential Rapid proliferation and antibody/cytokine production Antibody titre rises; symptoms may peak Plateau Effector response balances antigen persistence and clearance Clinical improvement may begin Decline Most effector cells die after antigen removal Antibody wanes, but memory cells and long-lived plasma cells remain The exact time course varies by antigen, dose, route, adjuvant, host age and immune status. A negative early antibody test does not always exclude infection. 4. The secondary immune response 4.1 Memory cell activation Memory B and T cells are more numerous, have lower activation thresholds and are distributed through lymphoid and peripheral tissues. On re-exposure, they respond with less delay and can recruit additional innate and adaptive cells. 4.2 Faster and stronger antibody response Memory B cells rapidly become plasma cells. Because many underwent affinity maturation and class switching, the response often contains higher-affinity IgG or mucosal IgA rather than predominantly IgM. Long-lived plasma cells in bone marrow can maintain baseline antibody for years. 4.3 Faster cellular response Memory CD4 and CD8 cells produce cytokines and cytotoxic effects rapidly. Tissue-resident memory cells can respond at the portal of entry before the pathogen disseminates. 4.4 Why secondary protection may fail Antigenic drift or a different strain is poorly recognised. Memory has waned or was never generated adequately. Immunosuppression, malnutrition, extremes of age or severe illness weaken the response. The pathogen evades immunity or establishes a protected reservoir. Antibody prevents severe disease but not all infection or transmission. 5. Tertiary and repeated responses Third and later exposures can produce progressively more mature memory responses, although the pattern depends on antigen variation and immune regulation. Repeated vaccination may broaden or increase antibody titres, but more doses are not automatically better; schedules are based on evidence, age, risk and vaccine characteristics. 6. Primary versus secondary response in serology Pattern Typical interpretation Caution Early IgM then IgG Possible recent primary response IgM can persist, cross-react or be absent; timing and assay matter High-affinity IgG or rising titre Previous exposure, vaccination or secondary response Does not always prove current infection Paired sera with significant rise Evidence of recent infection in selected tests Requires validated timing and laboratory interpretation No detectable antibody No exposure, early window period or impaired response Consider repeat testing, PCR/antigen test or cellular assays as appropriate Serology should be interpreted with symptoms, exposure, vaccination history, local epidemiology and the test’s sensitivity and specificity. Do not diagnose or exclude an emergency solely from antibody status. 7. Vaccination and immune memory Vaccines expose the immune system to a safe antigenic form or genetic instruction so that memory can develop without the full disease. Primary vaccination generates the initial response; booster doses recall memory and may increase antibody

Tumour markers are measurable substances or molecular features associated with cancer. They may be produced by tumour cells, released because of tumour-related tissue injury, or expressed by normal cells in response to a tumour. Markers can support diagnosis, estimate prognosis, select treatment and monitor response, but most are neither sensitive nor specific enough to diagnose cancer alone or to screen the general population. At a glance Circulating markers: proteins, hormones, enzymes, antigens or nucleic acids measured in blood, urine or another body fluid. Tissue markers: proteins or genetic features detected in tumour cells by immunohistochemistry, flow cytometry, cytogenetics or molecular testing. Main uses: treatment selection, monitoring, prognosis, staging support and selected high-risk surveillance. Major limitation: a raised marker may occur in benign disease, and a normal marker does not exclude cancer. Best practice: interpret the result with history, examination, imaging, pathology and serial trends using the same laboratory method where possible. Learning outcomes The learner should be able to define tumour markers, classify circulating and tissue biomarkers, explain their clinical uses and limitations, recognise common markers and associated conditions, interpret trends safely and avoid inappropriate screening or diagnosis based on an isolated result. 1. Definition and classification 1.1 Circulating or fluid markers These are measured in blood, urine, cerebrospinal fluid, pleural fluid or another specimen. Examples include alpha-fetoprotein (AFP), beta-human chorionic gonadotropin (β-hCG), prostate-specific antigen (PSA), carcinoembryonic antigen (CEA) and CA-125. 1.2 Tissue markers These are detected in biopsy or surgical tissue. Immunohistochemistry identifies proteins such as oestrogen receptor, progesterone receptor, HER2, mismatch-repair proteins and PD-L1. Flow cytometry characterises haematological malignancies, while cytogenetics and sequencing detect rearrangements or mutations. 1.3 Molecular biomarkers DNA, RNA, methylation, gene-fusion, copy-number and circulating tumour-DNA features can classify a tumour or identify a target. A biomarker can be diagnostic, prognostic, predictive or a combination. 2. What tumour markers can do Clinical use How the marker helps What it cannot do alone Support diagnosis Raises or lowers suspicion in a compatible clinical picture Usually cannot establish cancer without tissue or definitive disease-specific evidence Risk or surveillance Monitors selected high-risk patients, such as AFP in chronic liver disease pathways Does not replace imaging or specialist follow-up Prognosis Associates with tumour burden, subtype or expected behaviour Cannot determine an individual outcome with certainty Predictive treatment selection Identifies a target or pathway likely to respond to a therapy A marker does not guarantee response; resistance can develop Response monitoring Serial fall may support treatment response; rise may signal progression or relapse Early changes can reflect treatment-related cell death, inflammation or assay variation Recurrence surveillance Trend after definitive treatment may prompt imaging or review Not every recurrence raises a marker and not every rise is recurrence 3. Why isolated results mislead False positive: benign inflammation, pregnancy, liver or kidney disease, smoking, menstruation, prostatitis, assay interference or another cancer raises the marker. False negative: the tumour does not produce the marker, the disease burden is small, the specimen is poorly timed or the assay is insensitive. Biological variation: levels fluctuate with physiology, hydration, organ clearance and tumour kinetics. Analytical variation: different laboratories, platforms and reference ranges are not always interchangeable. Lead-time and overdiagnosis: finding a marker earlier does not automatically improve survival or justify treatment. A marker result should be interpreted as a probability modifier. Ask: “What is the pre-test probability, what benign causes are plausible, and what confirmatory test will change management?” 4. Common circulating tumour markers Marker Common associations Benign/non-cancer causes and cautions Typical clinical use AFP Hepatocellular carcinoma; non-seminomatous germ-cell tumours Pregnancy, chronic hepatitis, cirrhosis and liver injury; some cancers do not raise AFP Surveillance/diagnostic support in selected liver-risk pathways; germ-cell tumour assessment β-hCG Gestational trophoblastic disease; some germ-cell tumours Pregnancy, pituitary hCG, assay interference and rare tumours Diagnosis, staging and response monitoring with imaging and pathology PSA Prostate cancer Benign prostatic enlargement, prostatitis, urinary retention, ejaculation and instrumentation Risk assessment, selected screening after shared decision-making, treatment/recurrence monitoring CEA Colorectal and some pancreatic, gastric, breast and lung cancers Smoking, inflammation, liver disease and benign gastrointestinal disease Baseline and serial monitoring, especially after colorectal cancer treatment CA-125 Epithelial ovarian and related cancers Menstruation, pregnancy, endometriosis, pelvic inflammation, liver disease and effusions Monitoring selected ovarian cancers; not a stand-alone population screening test CA 19-9 Pancreatic and biliary cancers Cholestasis, cholangitis, pancreatitis and Lewis-antigen non-expression Monitoring in a compatible diagnosis; not diagnostic alone CA 15-3/CA 27-29 Breast cancer and some other adenocarcinomas Benign breast/liver disease and other cancers Selected treatment/recurrence monitoring; not general screening Calcitonin Medullary thyroid carcinoma Renal disease, other neuroendocrine conditions and assay variation Diagnosis and surveillance in selected patients/families Thyroglobulin Differentiated thyroid cancer after thyroid tissue removal/ablation Residual benign thyroid tissue and anti-thyroglobulin antibodies Recurrence surveillance with antibody interpretation LDH Lymphoma, leukaemia, germ-cell tumours and high tumour burden Tissue injury, haemolysis, liver disease, infection and muscle injury Prognostic/risk stratification support, not tumour-specific diagnosis 5. Tissue and molecular biomarkers 5.1 Breast and other solid tumours Oestrogen and progesterone receptors: predict potential benefit from endocrine therapy. HER2: overexpression or amplification may support HER2-targeted treatment; test methods and thresholds matter. PD-L1: may inform immunotherapy in selected cancers, but scoring is tumour-specific. Mismatch-repair proteins/microsatellite instability: identify repair deficiency and may predict immunotherapy response or inherited Lynch syndrome risk. 5.2 Haematological malignancy Flow cytometry, immunophenotyping, cytogenetics and molecular tests distinguish leukaemia and lymphoma lineages, classify risk and detect measurable residual disease. Results must be interpreted with blood film, marrow morphology and clinical findings. 5.3 Actionable genetic biomarkers Specific mutations or fusions may guide targeted therapy in lung, colorectal, melanoma, thyroid, breast and other cancers. A negative result may reflect tumour heterogeneity, inadequate tissue or assay limitations. A tissue biomarker is usually a somatic finding unless germline testing confirms inherited risk. 6. Interpreting a tumour-marker result Confirm the indication: Why was it ordered—symptoms, known cancer, high-risk surveillance or treatment planning? Review pre-test probability: Age, symptoms, examination, imaging, family history, exposures and prior cancer. Check the specimen and method: timing, fasting or pregnancy status where relevant, laboratory reference range and assay platform. Look for

Carcinogenesis is the multistep transformation of a normal cell into a malignant clone. It usually requires accumulated genetic and epigenetic changes, selection of fitter subclones and interaction with the tissue microenvironment. Carcinogens can initiate DNA damage, promote expansion of an already altered clone or support progression toward invasion and metastasis. At a glance Initiation: a permanent genetic or epigenetic alteration occurs in a susceptible cell. Promotion: selective, often non-mutagenic stimuli expand initiated cells; this phase may be partly reversible. Progression: additional alterations create heterogeneity, invasion, metastasis, treatment resistance and clinical cancer. Major targets: oncogenes, tumour-suppressor genes, DNA-repair genes, apoptosis pathways, telomere maintenance and angiogenic/immune pathways. Prevention: reduce tobacco and alcohol exposure, vaccinate against oncogenic infections, protect against UV and occupational carcinogens, maintain healthy weight/activity and use evidence-based screening. Learning outcomes By the end of this page, the learner should be able to explain the stages and molecular basis of carcinogenesis, classify carcinogens, distinguish genotoxic from non-genotoxic mechanisms, describe inherited susceptibility and tumour evolution, link important exposures to cancers, and apply prevention and emergency principles. 1. Definition and the multistep model Carcinogenesis is not a single event. A cell acquires a heritable growth advantage, expands clonally and accumulates further changes. The classic model uses three overlapping conceptual stages: Stage Core event Typical features Initiation Permanent alteration in DNA or stable gene regulation Mutation, chromosomal rearrangement, viral integration or epigenetic reprogramming Promotion Selective expansion of initiated cells Chronic inflammation, hormones, repeated injury or proliferative stimuli; may regress if the stimulus stops early Progression Additional changes produce aggressive subclones High-grade atypia, invasion, angiogenesis, metastasis, immune escape and therapy resistance The stages overlap and are not a mandatory sequence for every tumour. A single exposure can have more than one role, and inherited susceptibility may lower the number of additional steps required. 2. Genetic targets in carcinogenesis 2.1 Oncogenes Proto-oncogenes normally promote controlled growth, survival or angiogenesis. Activation by mutation, amplification, translocation or excessive signalling converts them into oncogenes. Examples include RAS pathway activation, MYC amplification and growth-receptor overexpression. 2.2 Tumour-suppressor genes Tumour suppressors restrain proliferation, repair damage or trigger cell death. Loss of TP53, RB, APC, PTEN or other suppressor pathways removes cellular brakes. Both alleles may need to be lost in a classic “two-hit” pattern, although haploinsufficiency and dominant-negative effects occur. 2.3 DNA-repair genes Defects in mismatch repair, homologous recombination, nucleotide-excision repair or other pathways increase the mutation rate and genomic instability. A repair defect may be inherited or acquired in the tumour. 2.4 Apoptosis and senescence pathways Cancer cells may resist apoptosis, inactivate checkpoints, reactivate telomerase or bypass senescence. They survive conditions that would remove normal damaged cells. 2.5 Non-coding and epigenetic regulation Promoter methylation, histone modification, non-coding RNA and enhancer changes can silence suppressors or activate growth pathways without altering the protein-coding sequence. 3. Genotoxic and non-genotoxic carcinogens Mechanism How it acts Examples Direct genotoxic Directly damages DNA or forms adducts Ionising radiation, some alkylating chemicals Metabolic activation Procarcinogen is converted to a reactive metabolite Polycyclic aromatic hydrocarbons and aflatoxin metabolites Oxidative stress Reactive oxygen species damage DNA, proteins and membranes Chronic inflammation, smoke and some metals Epigenetic Alters methylation, chromatin or regulatory RNA Some chemicals, viral proteins and chronic inflammation Hormonal/proliferative Stimulates cell division, increasing opportunities for replication errors Oestrogenic, androgenic or other endocrine environments Immunosuppressive Reduces immune surveillance of altered cells Transplant immunosuppression, advanced immunodeficiency Carcinogenic hazard and individual risk are different. Hazard means an agent can cause cancer; risk depends on dose, route, duration, timing, susceptibility and co-exposures. 4. Physical carcinogens Ultraviolet radiation UVB can create pyrimidine dimers and other DNA lesions, especially in skin. Repeated sun exposure, tanning devices and childhood burns increase cumulative risk of basal-cell carcinoma, squamous-cell carcinoma and melanoma. Protection includes shade, clothing, sunscreen and avoiding artificial tanning. Ionising radiation X-rays, gamma rays and radioactive particles can create single- and double-strand breaks and chromosomal rearrangements. Risk increases with dose and is influenced by age and tissue. Use diagnostic imaging when clinically justified and apply radiation-safety principles. Other physical factors Chronic thermal injury, foreign-body inflammation and selected occupational exposures may contribute to malignant transformation. A persistent non-healing burn scar or ulcer requires assessment. 5. Chemical carcinogens Exposure Mechanism/associated risk Prevention focus Tobacco smoke Multiple DNA adducts, oxidative stress, chronic inflammation; lung and many other cancers Do not smoke; cessation and smoke-free environments Alcohol Acetaldehyde, oxidative stress and synergy with tobacco Reduce or avoid; counsel at-risk patients Aflatoxin contamination Reactive metabolites can mutate tumour-suppressor pathways Food storage, inspection and hepatitis prevention Asbestos Fibres cause chronic inflammation and mesothelial injury Occupational control, protective equipment and surveillance Benzene Marrow toxicity and chromosomal injury Industrial controls and exposure monitoring Arsenic and some metals Oxidative, epigenetic and DNA-repair effects Safe water, occupational controls and regulation Occupational history should include job tasks, duration, protective equipment, ventilation and co-workers with similar symptoms. Record suspected exposure accurately and refer through occupational-health services. 6. Biological carcinogens Human papillomavirus (HPV) High-risk HPV proteins interfere with p53 and RB pathways and can cause persistent epithelial dysplasia and cervical cancer. HPV is also linked to anal, penile, vulvar, vaginal and oropharyngeal cancers. Vaccination, safer-sex counselling and evidence-based cervical screening reduce risk. Hepatitis B and C viruses Chronic hepatic inflammation, regeneration, fibrosis and viral effects increase hepatocellular carcinoma risk. Hepatitis B vaccination and prevention of blood/sexual transmission are important; chronic infection requires testing and appropriate antiviral care. Epstein–Barr virus EBV contributes to selected lymphomas, nasopharyngeal carcinoma and other malignancies, particularly with immune dysregulation or specific cofactors. Most EBV infections do not cause cancer. Helicobacter pylori Chronic gastric inflammation and mucosal atrophy increase gastric adenocarcinoma and some lymphoid tumour risk. Diagnose and eradicate infection according to local guidance when indicated. Other infection-related pathways HIV-related immunosuppression increases risk of Kaposi sarcoma, lymphomas and infection-associated cancers. Parasites such as schistosomes and liver flukes are associated with selected urinary or biliary cancers in endemic settings. 7. Chronic inflammation and tissue injury Persistent inflammation produces reactive oxygen species, cytokines, growth factors, angiogenesis and repeated cycles of cell death and regeneration. Examples