Molecular monitoring’s true value focuses on those methods that can be used to help determine early warning signals and help identify patients at higher risk of allograft injury. Tests should be minimally invasive for the patient; the risk should be low and with high diagnostic accuracy – which is the potential of active surveillance. Unfortunately, when a biopsy is needed, this is generally more invasive and tailored for clinically indicated testing rather than to be used as an active surveillance method. However, there are some instances where a biopsy can also be used as an active surveillance method, such as with heart transplants.

 

Molecular advances led to the rise of several post-transplant methods that have flexibility as both active surveillance tools and clinically indicated tests, with increasing sensitivity and specificity1. Earlier rejection detection, improving graft viability, and enhancing patient quality of life remain characteristics of modern monitoring methods. Clinicians will use a thorough approach of both active surveillance and clinically indicated testing with a range of blood draws and invasive biopsies respectively on a need by basis.

 

Overall, whether clinically indicated or active surveillance, many methods are used to complement and augment one another to improve diagnostic and clinical interpretation. The following methods are routinely used for molecular monitoring.


Biomarkers

A biomarker is a measurable substance in the body indicating the progression of a disease, biological process or if treatment is occurring. In the case of HLA monitoring, biomarkers can help track immune system activity related to HLA in terms of transplant rejection or immune response changes.

Ideal Biomarkers Characteristics

  • Minimally invasive
  • Typically for diagnosis severity of rejection
  • Minimize unwarranted biopsies
  • Limitations with biomarkers are that there may be variability in the biomarker levels and limits in specificity and sensitivity2
  • Limitations include separation of rejection from infection or other organ damage.

Types of Biomarkers Tests – Chemokine Testing

  • Help mediate the immune response to the transplant
  • CXCL9 and CXCL10
    • Raised Urinary levels of CXCL9 and CXCL10 are associated with both antibody mediated rejection and t cell mediated rejection.
    • CXCL9 and CXCL10 may be able to differentiate between ABMR and T cell-mediated rejection in early post-transplant period.
    • CXCL9 and CXCL10 levels are investigated as potential biomarkers for Bronchiolitis Obliterans Syndrome (BOS), a form of chronic lung allograft dysfunction after lung transplantation

Types of Biomarkers Tests – dd-cfDNA Testing

  • Reliable biomarker for allograft injury or rejection
  • Able to be detected in the recipient’s blood
  • Unable to differentiate between injury or rejection.

Types of Biomarkers Tests – Chimerism Testing

  • Assesses the success of stem cell or bone marrow transplantation
  • Detect early signs of graft rejection or engraftment failure
  • Detects early signs of cancer recurrence.

Types of Biomarkers Tests - RNA-Based Testing

  • RNA profiles help identify patients at higher risk for rejection, enabling tailored immunosuppressive therapy
  • MicroRNA (miRNA)
    • Small non-coding RNAs that regulate gene expression
    • Specific miRNA profiles can reveal transplant rejection and overall graft health
  • Long Non-Coding RNA (lncRNA)
    • lncRNA expression patterns can reflect immune responses
  • Messenger RNA (mRNA)
    • Changes in mRNA of immune related genes can signal allograft dysfunction and rejection
    • Exosomal mRNA signatures can determine allograft health
      • Kidney transplant monitoring to measure the exosomes excreted in urine (high concentrations of mRNA derived from T cells)

Viral Load

Viral load is the amount of virus present in a person’s blood. In terms of HLA monitoring, measurement of the amount of virus present can be used to determine how well the treatment is working or the state of the patient.

Viral Load Monitoring Characteristics

  • Crucial in transplant recipients due to their immunocompromised state
  • Patients are susceptible to both primary and reactivated viral infections
  • Allows for early detection and tracking of viremia
  • Limitations of viral load monitoring includes the timing of measurement and may not reflect the viral dynamics in a patient along with interpretation challenges, viral loads may not directly correlate with clinical disease
  • Creates a difficult balance between prevention of rejection and prevention of viral infection.

Types of Viral Load Monitoring

  • Cytomegalovirus (CMV) being the most popular
    • Leading cause of morbidity and mortality in transplant recipients
    • CMV can cause direct damage to the allograft3
  • Other viruses such as Epstein-Barr virus (EBV) and BK virus (BKV) are also monitored3
  • Recently monitoring viruses such as TTV have been suggested as a sensitive measure of over- or under-immunosuppression in transplant patients4

Microarray

A microarray is a tool used to test many genes via a small chip that contains probes in a grid pattern. For HLA monitoring, microarray-based platform testing is used to quickly analyze many HLA genes to detect changes or mismatches that could affect transplant compatibility or immune responses.

Microarray-Based Platform Characteristics

  • Require biopsy sample in general to assess allograft health and monitor for rejection
  • A limitation of microarrays is that the test may not detect low frequency profiles effectively5
  • High-throughput technology that uses miniaturized arrays of nucleic acids, proteins, or other biomolecules to analyze samples
    • Kidney Transplant
      • Microarrays can help monitor kidney transplants for rejection and assess the risk of graft failure
    • Lung Transplantation
      • Microarrays can help identify biomarkers associated with chronic lung symptoms
    • Heart Transplantation
      • Microarrays can be used to analyze gene expression in heart biopsies to monitor for rejection and overall allograft health

Single Cell

Single cell technology analyzes at the single cell level for any characteristic changes. In HLA monitoring, this technology identifies how individual cells react to the transplanted issue as opposed to analyzing the average response from all cells together.

Single-Cell Technology Characteristics

  • Offers a detailed way to analyze the gene expression profiles of individual cells within a transplanted organ through cell to cell resolution
  • High Resolution Mapping
  • Limitations of single-cell sequencing include incomplete data and may not capture profiles that are present in a heterogeneous population
  • Emerging technology, currently no FDA approved single cell based test

Types of Single-Cell Technology

  • Single-Cell RNA Sequencing
    • High resolution mapping of immune cells to measure rejection related statuses6

Epigenetic

Epigenetic is the study of how genes are activated without any changes to the DNA sequence. Epigenetic monitoring for HLA looks at the chemical changes that control HLA gene activity, which could be used to determine how transplant tolerance and rejection may occur.

Epigenetic Monitoring Characteristics

  • Emerging as a promising tool to assess graft health7
  • Refer to changes in gene expression that do not involve alterations to the underlying DNA sequence
  • Limitations of epigenetic monitoring includes interpretation challenges due to associating epigenetic changes to direct clinical outcome

Types of Epigenetic Monitoring

  • T Cell Receptor (TCR) Sequencing
    • Track donor-reactive T cells and immune repertoire diversity
  • Methylation Profiling of cfDNA
    • Identify tissue of origin of cfDNA to infer which organ is injured
  • MicroRNA Profiling
    • Detect miRNA signatures associated with graft rejection or tolerance
  • Other viruses such as Epstein-Barr virus (EBV) and BK virus (BKV) are also monitored
  • Splice variants and methylation of key immune genes may affect graft outcome.

Next-Generation Sequencing

Next-Generation Sequencing is a technology that analyzes considerable amounts of reads and the ability to produce large amounts of DNA for analysis. With HLA monitoring, NGS provides detailed information about HLA genes, allowing for detection of variations or immune changes for both transplant matching and rejection monitoring.

Methodology for molecular monitoring - NGS Testing Characteristics

  • NGS is increasingly utilized for post-transplant monitoring
  • NGS offers improved sensitivity and accuracy compared to traditional methods
  • Longer turnaround times are typically a characteristic of NGS against other monitoring platforms, but this is changing due to new advances
  • Incorporated in many methods mentioned
  • Limitation of NGS includes not providing uniform coverage
  • Relatively short reads can result in ambiguity
  • Third generation sequencing may in the future help solve many of the issues with ambiguity and turnaround time

The information provided on this page is intended for educational purposes only. It is not a substitute for professional training, regulatory guidance, or clinical judgment. While every effort has been made to ensure accuracy, methodologies and assays may vary by laboratory and manufacturer. Users are encouraged to consult relevant standards, institutional protocols, and product documentation before implementing any procedures.


References

  1. Rumpler, Marc J., Christopher McCloskey, and Christopher Lawrence. “A New Era in Post-Transplant Monitoring.” Association for Diagnostics & Laboratory Medicine (ADLM), 1 Apr. 2023, https://myadlm.org/cln/articles/2023/april/a-new-era-in-post-transplant-monitoring

  2. Song, Yuan, Wang, Yihui, Wang, Wenyuan, Xie, Yuji, Zhang, Junmin, Liu, Jing, Jin, Qiaofeng, Wu, Wenqian, Li, He, Wang, Jing, Zhang, Li, Yang, Yali, Gao, Tang, Xie, Mingxing. Advancements in noninvasive techniques for transplant rejection: from biomarker detection to molecular imaging, Journal of Translational Medicine, 2025, pp. 1-28, Volume 23, Issue 1, DOI: 10.1186/s12967-024-05964-4
  3. Blazquez-Navarro A, Dang-Heine C, Wittenbrink N, Bauer C, Wolk K, Sabat R, Westhoff TH, Sawitzki B, Reinke P, Thomusch O, Hugo C, Or-Guil M, Babel N. BKV, CMV, and EBV Interactions and their Effect on Graft Function One Year Post-Renal Transplantation: Results from a Large Multi-Centre Study. EBioMedicine. 2018 Aug;34:113-121. doi: 10.1016/j.ebiom.2018.07.017. Epub 2018 Jul 30. PMID: 30072213; PMCID: PMC6116415.
  4. Spezia PG, Carletti F, Novazzi F, Specchiarello E, Genoni A, Drago Ferrante F, Minosse C, Matusali G, Mancini N, Focosi D, Antonelli G, Girardi E, Maggi F. Torquetenovirus Viremia Quantification Using Real-Time PCR Developed on a Fully Automated, Random-Access Platform. Viruses. 2024 Jun 15;16(6):963. doi: 10.3390/v16060963. PMID: 38932255; PMCID: PMC11209079.
  5. Park WD, Stegall MD. A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds. BMC Genomics. 2007 Mar 30;8:88. doi: 10.1186/1471-2164-8-88. PMID: 17397532; PMCID: PMC1852103.
  6. Mou L and Pu Z (2025) The single-cell revolution in transplantation: high-resolution mapping of graft rejection, tolerance, and injury. Front. Immunol. 16:1670683. doi: 10.3389/fimmu.2025.1670683
  7. Velut, Y., Poulet, G., Bersez, T. et al. Epigenetic signatures on plasma cell-free DNA to detect kidney allograft rejection in a non-invasive way: development of a 10-plex digital PCR assay. Biomark Res 13, 118 (2025). https://doi.org/10.1186/s40364-025-00834-7

The information presented on this website is intended solely for educational and general informational purposes. It is not intended  to provide medical advice, constitute clinical guidance, or serve as a substitute for professional judgment in patient care.