Transplant Immune Monitoring

Transplant Immune Monitoring

Organ transplantation saves lives, but requires lifelong management of the recipient’s immune response. Immune repertoire monitoring offers a powerful approach to assess rejection risk, track immune reconstitution, and potentially identify tolerance—moving beyond reactive diagnosis toward predictive, personalized transplant care.

The Transplant Immune Challenge

Allorecognition

When a patient receives a transplanted organ, their immune system recognizes the donor tissue as foreign:

• Direct allorecognition: Recipient T cells recognize intact donor MHC molecules
• Indirect allorecognition: Recipient T cells recognize processed donor peptides on self-MHC
• Semi-direct pathway: Transfer of donor MHC to recipient APCs

These pathways activate alloreactive T cells—T cells whose receptors recognize donor antigens—driving rejection.

Clinical Challenges

Immune Repertoire in Transplantation

Alloreactive T Cell Signatures

Alloreactive T cells are not random—they often share recognizable features:

Characteristics:

• Expanded clones in graft tissue during rejection
• Specific V gene usage patterns associated with certain HLA mismatches
• CDR3 motifs that correlate with donor-reactivity
• Persistence in blood before and during rejection episodes

The Opportunity:

If we can identify and track alloreactive clones, we can:

1. Detect rejection earlier (rising clone frequency)
2. Assess baseline risk (alloreactive repertoire size)
3. Monitor immunosuppression efficacy (clone suppression)
4. Identify tolerance (absence of alloreactive response)

Why Paired Chain Analysis Matters

Alloreactive T cells are defined by their TCR specificity. Single-chain (β-only) analysis has limitations:

Example: A TRB CDR3 sequence appears in both a rejecting patient and stable controls. With paired chain analysis, we discover:

• In the rejecting patient: paired with TRAV specific for donor HLA
• In stable controls: paired with different TRAV, recognizing viral antigen

Only paired analysis distinguishes these functionally distinct cells.

Applications by Transplant Type

Solid Organ Transplantation

Kidney Transplantation

The largest solid organ transplant population (~25,000/year in US)

Current Monitoring:

• Serum creatinine (late, non-specific)
• Donor-specific antibodies (DSA)
• Protocol and for-cause biopsies

Repertoire-Based Monitoring:

Pre-Transplant:
├── Characterize recipient repertoire
├── Identify potential alloreactive signatures
└── Risk stratification

Post-Transplant Surveillance:
├── Track alloreactive clone frequencies
├── Detect expansion before clinical rejection
├── Monitor response to rejection treatment
└── Assess immune reconstitution

Clinical Scenarios:

Liver Transplantation

• Relatively tolerogenic organ
• ~20% may develop “operational tolerance”
• Repertoire monitoring could identify tolerance candidates

Heart Transplantation

• Rejection has severe consequences
• Endomyocardial biopsy is invasive
• Blood-based repertoire monitoring particularly valuable

Lung Transplantation

• Highest rejection rates
• Chronic rejection (CLAD) major problem
• Bronchoalveolar lavage (BAL) repertoire informative

Hematopoietic Stem Cell Transplantation (HSCT)

HSCT involves replacing the recipient’s immune system with donor-derived cells, creating unique monitoring needs.

Immune Reconstitution

After HSCT, the immune system rebuilds over months to years:

Early Phase (0-3 months):

• Innate immunity recovers first
• T cells initially from graft (donor memory)
• Very limited repertoire diversity

Intermediate Phase (3-12 months):

• Thymic output begins (if thymus functional)
• Repertoire diversity slowly increases
• Naive T cells appear

Late Phase (>12 months):

• Continued diversification
• May never reach normal diversity, especially in adults

Repertoire Metrics for Reconstitution:

Graft-versus-Host Disease (GVHD)

In GVHD, donor T cells attack recipient tissues:

Acute GVHD:

• Skin, liver, GI tract involvement
• Donor T cells reactive to recipient alloantigens
• Repertoire shows oligoclonal expansions

Chronic GVHD:

• More autoimmune-like features
• Fibrotic manifestations
• Repertoire perturbations persist

Monitoring Applications:

• Identify GVHD-associated clones
• Track response to therapy
• Distinguish GVHD from infection

Graft-versus-Leukemia (GVL)

The beneficial flip side of GVHD—donor T cells attack residual malignancy:

• Same alloreactive principle
• Goal: Preserve GVL while minimizing GVHD
• Repertoire analysis may identify protective clones

IMBERA-seq for Transplant Monitoring

Workflow

Baseline Assessment:

1. Pre-transplant recipient sample
2. Characterize existing repertoire
3. Identify potential alloreactive signatures (if donor HLA known)

Post-Transplant Monitoring:

1. Regular blood sampling (monthly, then quarterly)
2. IMBERA-seq analysis
3. Track key clone populations
4. Correlate with clinical status

Rejection Surveillance:

Sample Collection (peripheral blood)
         ↓
    IMBERA-seq Processing
         ↓
    Paired TCR Identification
         ↓
    Clone Frequency Quantification
         ↓
    Comparison to Baseline
         ↓
    ┌─────────────────────────────────────┐
    │ Stable: Continue current management │
    │ Rising clones: Clinical correlation │
    │ Expanded signature: Consider biopsy │
    └─────────────────────────────────────┘

Advantages for Transplant

Clinical Implementation

Sampling Strategy

Recommended Timepoints:

Integration with Other Biomarkers

Repertoire monitoring complements existing tools:

• dd-cfDNA (donor-derived cell-free DNA): Measures graft injury
• DSA (donor-specific antibodies): Antibody-mediated rejection risk
• Gene expression panels: Molecular phenotyping
• Repertoire sequencing: Direct T cell monitoring

Multi-Modal Approach:

Biomarker Integration:
┌──────────────────────────────────────────────┐
│  dd-cfDNA ↑    +    Alloreactive clones ↑    │
│  ─────────────────────────────────────────   │
│  Strong signal for T cell-mediated rejection │
└──────────────────────────────────────────────┘

┌──────────────────────────────────────────────┐
│  DSA positive  +  Repertoire stable          │
│  ─────────────────────────────────────────   │
│  Antibody-mediated process, not T cell       │
└──────────────────────────────────────────────┘

Toward Tolerance Assessment

Operational Tolerance: Graft acceptance without immunosuppression

Currently, there’s no reliable way to identify tolerant patients. Repertoire analysis may provide insights:

Potential Tolerance Signatures:

• Absence of donor-reactive clone expansion
• Enrichment of regulatory T cell signatures
• Stable, diverse repertoire without alloreactive dominance

Future Application: Carefully selected patients with favorable repertoire profiles might be candidates for immunosuppression minimization trials.

Current State and Future Directions

Available Now

• Research-use repertoire sequencing for transplant studies
• Limited clinical implementation at specialized centers
• Growing evidence base for predictive value

In Development

• Validated rejection prediction algorithms
• Standardized monitoring protocols
• Integration with clinical decision support
• Tolerance biomarker panels

Research Priorities

1. Large prospective studies correlating repertoire with outcomes
2. Identification of rejection-predictive signatures
3. Tolerance biomarker discovery
4. Cost-effectiveness analysis
5. Clinical trial integration

Key Concepts Summary

1. Alloreactive T cells drive rejection; their TCRs can be identified and tracked through repertoire sequencing

2. Paired chain analysis (IMBERA-seq) provides definitive identification of alloreactive clones, surpassing single-chain approaches

3. Applications span solid organ transplant (rejection monitoring) and HSCT (reconstitution, GVHD)

4. Non-invasive monitoring through blood sampling enables frequent assessment without biopsy

5. Future potential includes rejection prediction, tolerance identification, and personalized immunosuppression

Related Articles

• T Cell Receptor Structure — TCR biology relevant to allorecognition
• Immune Repertoire — Diversity and clonality concepts
• IMBERA-seq Technology — Paired chain sequencing platform
• Diversity Metrics — Quantifying repertoire reconstitution

References

1. Morris H, et al. (2015). Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients. Science Translational Medicine, 7(272):272ra10.

2. Zuber J, et al. (2016). Bidirectional intragraft alloreactivity drives the repopulation of human intestinal allografts and correlates with clinical outcome. Science Immunology, 1(4):eaah3732.

3. Kanakry CG, et al. (2016). Origin and evolution of the T cell repertoire after posttransplantation cyclophosphamide. JCI Insight, 1(5):e86252.