Autoimmune Disease Diagnostics

Autoimmune Disease Diagnostics

Autoimmune diseases arise when the immune system mistakenly attacks the body’s own tissues. Immune repertoire-based diagnostics offer a new paradigm for detecting disease-specific T and B cell signatures, enabling earlier diagnosis and better disease stratification.

The Diagnostic Challenge

Current Limitations

Traditional autoimmune diagnostics rely on:

1. Genetic markers (HLA typing)

   • Identifies predisposition, not disease
   • Most carriers never develop disease

2. Autoantibodies

   • Indirect markers of immune activation
   • May appear late in disease course
   • Some require active disease (e.g., celiac serology needs gluten exposure)

3. Clinical criteria

   • Often subjective
   • May require years of symptom accumulation
   • Leads to diagnostic delays

The Opportunity

T and B cells directly mediate autoimmune pathology. Detecting disease-specific lymphocyte signatures offers:

• Direct measurement of pathogenic immune response
• Earlier detection (before tissue damage)
• Specificity that genetic markers lack
• Independence from disease activity requirements

Disease-Specific T Cell Signatures

The Biological Basis

In autoimmune diseases, T cells that recognize self-antigens:

1. Escape thymic deletion (central tolerance failure)
2. Become activated in the periphery
3. Expand clonally
4. Accumulate in affected tissues
5. Mediate inflammation and tissue damage

These disease-associated T cells often share:

• Common TCR structural features (V gene usage, CDR3 motifs)
• HLA restriction (presented by specific HLA alleles)
• Clonal expansion (detectable frequencies in blood)

Key Discovery: Paired Chain Requirement

Critical insight: Many disease-specific signatures require both TCR chains.

Example from HLA-B27 spondyloarthropathy research:

• A specific TRB CDR3 motif is found in patients
• The same motif is also found in healthy HLA-B27+ carriers
• Only when paired with TRAV21 does the signature distinguish disease
• Single-chain (β-only) sequencing misses this distinction

Disease Examples

HLA-B27-Associated Spondyloarthropathy

The Disease:

• Includes ankylosing spondylitis (AS), reactive arthritis, psoriatic arthritis
• Strong HLA-B27 association (~90% of AS patients are HLA-B27+)
• 7-10 year average diagnostic delay
• Irreversible joint damage accumulates during delay

The Diagnostic Gap:

HLA typing alone has poor positive predictive value.

The T Cell Signature:

Research has identified pathogenic T cells characterized by:

• TRAV21 alpha chain usage
• Specific TRB CDR3 motif (conserved amino acid patterns)
• Expansion in active disease
• Tissue localization in affected joints

Diagnostic Approach:

1. Obtain peripheral blood sample
2. Perform paired TCR sequencing (IMBERA-seq)
3. Quantify TCRs matching pathogenic signature (TRB motif + TRAV21)
4. Compare to established thresholds
5. Report disease probability

Validation: Tetramer staining confirms specificity of signature-positive T cells.

Celiac Disease

The Disease:

• Autoimmune response to dietary gluten
• Affects ~1% of population; 80% undiagnosed
• Intestinal damage, malabsorption, systemic complications

The Diagnostic Gap:

Current serology (anti-TTG, anti-DGP antibodies):

• Requires active gluten consumption
• Fails for patients on gluten-free diet (GFD)
• Many patients self-initiate GFD before diagnosis

The T Cell Signature:

Gluten-specific T cells are well-characterized:

• HLA-DQ2/DQ8 restricted (present deamidated gluten peptides)
• Conserved TCR features: TRAV26-1, TRBV7-2 enrichment
• Specific CDR3 motifs for different gluten epitopes
• Persist in blood even during GFD

Diagnostic Advantage:

• Memory T cells persist regardless of GFD status
• Can diagnose patients already on GFD
• No gluten challenge required

Implementation:

Patient presents with suspected celiac disease
                    ↓
Currently on GFD?
    YES → Standard serology will fail
        → TCR-based test: detects memory T cells
    NO  → Either test may work
        → TCR-based test offers additional specificity

Type 1 Diabetes (T1D)

The Disease:

• Autoimmune destruction of pancreatic β cells
• Often diagnosed after significant β cell loss
• Pre-symptomatic detection could enable intervention

The T Cell Signature:

Islet-reactive T cells target:

• Insulin, proinsulin
• GAD65 (glutamic acid decarboxylase)
• IA-2 (insulinoma-associated antigen 2)
• ZnT8 (zinc transporter)

Emerging Applications:

• Pre-symptomatic screening (genetic risk + T cell signature)
• Monitoring disease progression
• Assessing immunotherapy response

Rheumatoid Arthritis (RA)

The Disease:

• Chronic inflammatory arthritis
• Multiple autoantigens implicated
• Current diagnosis based on clinical criteria + anti-CCP/RF

T Cell Involvement:

• Citrullinated peptide-reactive T cells
• HLA-DR4 associated (shared epitope)
• Clonal expansions in synovium

Potential Applications:

• Earlier diagnosis before joint damage
• Stratification for biologic therapy
• Monitoring treatment response

Diagnostic Test Development

From Discovery to Clinical Test

Phase 1: Signature Discovery

• Case-control sequencing studies
• Machine learning to identify discriminating features
• Biological validation (tetramer, functional assays)

Phase 2: Assay Development

• Standardized sample processing
• Reproducible sequencing workflow
• Validated bioinformatics pipeline
• Quality control metrics

Phase 3: Clinical Validation

• Analytical validation (accuracy, precision, reproducibility)
• Clinical validation (sensitivity, specificity in intended population)
• Prospective studies

Phase 4: Implementation

• CLIA laboratory certification
• LDT (Laboratory Developed Test) or FDA clearance
• Clinical utility studies
• Reimbursement strategy

Technical Considerations

Why Paired Chain Sequencing?

Sample Requirements:

• Peripheral blood (20 mL typical)
• PBMC isolation within 24 hours
• Fresh or cryopreserved samples

Turnaround Time:

• Sample processing: 1 day
• Sequencing: 2-3 days
• Analysis: 1 day
• Total: ~1 week

Advantages Over Current Diagnostics

Compared to Genetic Testing

Compared to Autoantibody Testing

Current State and Future Directions

Available Now

• Research-use repertoire sequencing
• Some LDT offerings for clonality assessment
• Clinical trials for autoimmune signatures

In Development

• FDA-cleared autoimmune diagnostic panels
• Multi-disease signature panels
• Point-of-care implementations

Future Possibilities

• Pre-symptomatic screening programs
• Treatment response prediction
• Personalized immunotherapy selection
• Population-level immune monitoring

Key Concepts Summary

1. Autoimmune diseases are mediated by self-reactive lymphocytes that can be detected by repertoire sequencing

2. Disease-specific signatures often require paired α-β chain information—single-chain sequencing may miss critical distinctions

3. TCR-based diagnostics offer advantages over genetic and serologic tests: direct measurement of pathogenic cells, earlier detection, independence from disease activity

4. Clinical translation requires rigorous validation but offers transformative diagnostic potential

5. Celiac disease and HLA-B27 spondyloarthropathy are leading applications with well-characterized T cell signatures

Related Articles

• T Cell Receptor Structure — Understanding TCR biology
• Chain Pairing Methods — Why paired sequencing matters
• MRD Testing — Related hematologic applications
• IMBERA-seq Technology — The enabling technology

References

1. Glanville J, et al. (2017). Identifying specificity groups in the T cell receptor repertoire. Nature, 547:94-98.

2. Han A, et al. (2014). Dietary gluten triggers concomitant activation of CD4+ and CD8+ αβ T cells and γδ T cells in celiac disease. PNAS, 111(38):13887-13892.

3. Furst DE, et al. (2024). T cell receptor signatures in autoimmune disease: from discovery to diagnostics. Nature Reviews Rheumatology, 20:123-136.