Bench simulation

Virtual immunology laboratory suite

Immersive laboratory experience across 19 workstations: immunofluorescence microscopy, ELISA automation, complement testing, transplant immunology and specialised assays.

Virtual Immunology Lab Suite is available to premium subscribers and trial users.

LIMS

Immunology LIMS

Advanced laboratory information management for immunology with cross-departmental references and complete validation workflow.

Immunology LIMS System is available to premium subscribers and trial users.

Autoantibody work-up

Autoimmunity analysis

Interactive tools for autoantibody screening, ANA / ENA / ANCA patterns, and clinical interpretation with disease associations.

Antinuclear Antibody (ANA) Patterns

Common immunofluorescence patterns and their clinical significance

Homogeneous

Uniform staining of nucleus; associated with SLE and drug-induced lupus

Speckled

Fine or coarse speckles throughout nucleus; seen in SLE, MCTD, and Sjögren's

Nucleolar

Clumpy staining of nucleoli; associated with systemic sclerosis

Centromere

Discrete speckles; highly specific for limited cutaneous systemic sclerosis (lcSSc)

Laboratory Insight

Pattern recognition should be followed by specific extractable nuclear antigen (ENA) testing to identify the exact autoantibody specificity. The immunofluorescence pattern provides important initial diagnostic clues.

Cellular immunology

Flow cytometry guide

Immunophenotyping, gating strategies and clinical applications of flow cytometry in diagnosis: the depth Band 6+ panels expect.

Flow Cytometry Principles

Core concepts of flow cytometry in clinical immunology

Key Components

Flow cytometry analyses multiple characteristics of individual cells simultaneously by suspending cells in a stream of fluid and passing them through an electronic detection apparatus.

Fluidics System

Creates stream of single cells
Hydrodynamic focusing aligns cells
Ensures cells pass through laser one by one
Controls sample flow rate
Managed through sheath fluid pressure

Optics System

Lasers excite fluorochromes
Optical filters select specific wavelengths
Forward scatter measures cell size
Side scatter assesses cell granularity
Fluorescence detects specific antibody binding

Electronic System

The electronic system converts light signals into electronic signals that can be processed by a computer. The process involves:

Signal detection

Amplification

Analog-to-digital conversion

Data storage

Analysis

Fluorochromes

Commonly used fluorochromes in clinical immunology applications:

FITC
(Green)

PE
(Orange ~575nm)

PerCP
(Tandem Red ~675nm)

APC
(Far Red)

Pacific Blue
(Blue)

PE-Cy7
(Red/IR)

FITC-Alexa
(Green)

BUV
(UV)

PID & SID

Immunodeficiency guide

Reference for primary and secondary immunodeficiencies with diagnostic pathways and laboratory findings.

Primary Immunodeficiency Disorders

Genetic disorders affecting immune system development and function

Classification Approach

Primary immunodeficiencies (PIDs) are classified based on the affected component of the immune system. They result from genetic mutations affecting immune system development or function.

Severe Combined Immunodeficiency (SCID)

Definition

Group of disorders characterised by severe defects in T cell development, with variable B and NK cell defects.

Key Features

Profound lymphopenia (especially T cells)
Recurrent severe infections beginning in early infancy
Failure to thrive
Chronic diarrhoea
Can present with skin rash (maternal T cell engraftment)

Common Subtypes

Phenotype	Genetic Defect	Inheritance
T-B-NK+	RAG1/2, DCLRE1C	AR
T-B-NK-	ADA	AR
T-B+NK-	IL2RG	X-linked
T-B+NK+	IL7R, CD3 chains	AR

Antibody Deficiencies

Common Disorders

X-linked agammaglobulinaemia (BTK deficiency)
Common Variable Immunodeficiency (CVID)
Selective IgA Deficiency
Specific antibody deficiency
Hyper-IgM syndrome

Clinical Presentation

Recurrent sinopulmonary infections
Gastrointestinal infections and disorders
Autoimmunity (especially in CVID)
Increased risk of malignancy
Onset typically after 6 months when maternal antibody wanes

CVID Diagnostic Criteria

Age > 4 years
Low IgG and low IgA and/or IgM
Poor response to vaccines
Exclusion of secondary causes

Phagocytic Disorders

Key Disorders

Chronic Granulomatous Disease (NADPH oxidase defects)
Leukocyte Adhesion Deficiency (CD18, selectin defects)
Chediak-Higashi Syndrome (LYST mutations)

Clinical Features

Recurrent bacterial and fungal infections
Abscesses, pneumonia, osteomyelitis
Poor wound healing
Gingivitis and periodontitis
Granuloma formation (in CGD)

Diagnostic Tests

DHR or NBT test for CGD
Flow cytometry for CD18 expression in LAD
Peripheral blood smear for giant granules in CHS
Genetic testing

Complement Deficiencies

Pathway Defects

Classical pathway (C1q, C2, C4): Autoimmunity, immune complex disease
Alternative pathway (Factor D, properdin): Neisserial infections
Terminal pathway (C5-C9): Recurrent meningococcal infections
Regulatory proteins (C1-INH): Hereditary angioedema

Clinical Associations

SLE-like syndrome (early pathway defects)
Recurrent bacterial infections (especially encapsulated)
Neisserial infections (terminal pathway)
Angioedema (C1-INH deficiency)

Diagnostic Approach

CH50 (classical pathway activity)
AP50 (alternative pathway activity)
Individual complement component quantification
Genetic testing

Reference values

Immunology data visualisation

Interactive charts and graphs showcasing key immunological parameters and antibody patterns.

Autoantibody Prevalence in Autoimmune Diseases

Illustrative, approximate percentages for teaching only. Reported positivity varies widely by cohort, disease stage and assay.

Key Clinical Insights:

Anti-dsDNA or anti-Sm antibodies score 6 points (counted once) in the 2019 EULAR/ACR classification criteria for SLE (Aringer et al., 2019), which require an ANA titre of at least 1:80 on HEp-2 cells as the entry criterion
Anti-Sm antibodies are highly specific for SLE but are found in only a minority of patients
Anti-CCP antibodies are more specific than rheumatoid factor for RA: a meta-analysis reported pooled sensitivity of 67% and specificity of 95% (Nishimura et al., Ann Intern Med 2007)
Anti-Ro (SSA) is the predominant autoantibody marker in Sjögren's syndrome
Anti-Scl-70 (anti-topoisomerase I) is associated with the diffuse cutaneous form of systemic sclerosis
Cross-reactivity between diseases reflects shared pathogenic pathways

Foundations

Immunology quick guide

Essential knowledge areas for immunology, from foundational concepts to specialised techniques.

Innate Immunity

The first line of defence against pathogens

Components of Innate Immunity

Innate immunity represents the body's first line of defence against pathogens, characterised by rapid, non-specific responses that do not confer long-lasting protection.

Physical & Chemical Barriers

Epithelial surfaces
Skin and mucous membranes form tight junctions to prevent pathogen entry.
Mucociliary clearance
Mucus entraps pathogens while cilia propel them out of the respiratory tract.
Antimicrobial peptides
Defensins, cathelicidins disrupt microbial membranes. Found in skin, gut, lungs.
Chemical defences
Gastric acid, lysozyme, low pH of skin, vaginal secretions.

Cellular Components

Neutrophils
First cells to migrate to infection sites; phagocytose and destroy pathogens.
Monocytes/Macrophages
Tissue phagocytes; clear debris, present antigens, secrete cytokines.
Dendritic cells
Professional antigen-presenting cells bridging innate and adaptive immunity.
NK cells
Detect and kill virus-infected cells and tumour cells without prior sensitisation.
Mast cells & Basophils
Release histamine and other mediators; important in allergic responses.

Pattern Recognition

Innate immune cells recognise pathogens through Pattern Recognition Receptors (PRRs) that bind to Pathogen-Associated Molecular Patterns (PAMPs), conserved structures present on microbes but not host cells.

Key PRR Families:

Toll-like receptors (TLRs)
Cell surface (TLR1, 2, 4, 5, 6) and endosomal (TLR3, 7, 8, 9) receptors.
NOD-like receptors (NLRs)
Cytoplasmic sensors forming inflammasomes when activated.
RIG-I-like receptors (RLRs)
Detect viral RNA in cytoplasm.
C-type lectin receptors
Recognise carbohydrate structures on pathogens.

Common PAMPs:

Lipopolysaccharide (LPS)
Gram-negative bacterial cell wall component; activates TLR4.
Peptidoglycan
Bacterial cell wall component; activates TLR2.
Flagellin
Bacterial flagella protein; activates TLR5.
Double-stranded RNA
Viral replication intermediate; activates TLR3.
CpG DNA
Unmethylated bacterial DNA motifs; activate TLR9.

Complement System

The complement system is a cascade of plasma proteins that enhance (complement) antibody function and innate immunity through pathogen opsonisation, inflammatory response stimulation, and direct pathogen lysis.

Classical Pathway

Activated by antigen-antibody complexes
C1q binds Fc region of antibodies
Activates C1r and C1s proteases
C4 and C2 cleavage forms C3 convertase
Links adaptive and innate immunity

Alternative Pathway

Activated by microbial surfaces
Spontaneous C3 hydrolysis ("tickover")
Factor B and D form C3 convertase
Properdin stabilises the convertase
Rapid response without antibodies

Lectin Pathway

Initiated by mannose-binding lectin
Recognises carbohydrates on microbes
Activates MASP proteases (like C1r/C1s)
Cleaves C4 and C2
Independent of antibodies

Terminal Pathway Functions:

OpsonisationC3b deposits on pathogen surfaces, enhancing phagocytosis

InflammationC3a, C5a anaphylatoxins recruit leukocytes and induce inflammation

Membrane Attack ComplexC5b-9 forms pores in cell membranes leading to lysis

Clinical Relevance

Defects in innate immunity components typically present with recurrent bacterial infections
Chronic granulomatous disease (NADPH oxidase defects) causes impaired neutrophil killing
Complement deficiencies associate with specific infection patterns and autoimmune diseases
Pattern recognition receptor polymorphisms influence susceptibility to infectious diseases
Excessive innate immune activation contributes to inflammatory and autoimmune conditions

Sources and guidance

This hub's content aligns with the UK's professional and regulatory references for the specialty: