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Review
. 2024 Nov 15:3:1474920.
doi: 10.3389/frtra.2024.1474920. eCollection 2024.

A review of cell-free DNA and epigenetics for non-invasive diagnosis in solid organ transplantation

Alizée Sebastian  1   2 , Monique Silvy  2 , Benjamin Coiffard  3 , Martine Reynaud-Gaubert  3 , Frédérique Magdinier  4 , Jacques Chiaroni  1   5 , Christophe Picard  1   5 , Pascal Pedini  1   5
Affiliations
Review

A review of cell-free DNA and epigenetics for non-invasive diagnosis in solid organ transplantation

Alizée Sebastian et al. Front Transplant. .

Abstract

Introduction: Circulating cell-free DNA (cfDNA) is emerging as a non-invasive biomarker in solid organ transplantation (SOT) monitoring and data on its diagnostic potential have been increasing in recent years. This review aims to summarize the main advances in technologies, clinical applications and future perspectives of cfDNA for transplantation, and to approach the contribution of epigenetics to improve the specific detection of rejection.

Methods: Published literature investigating cfDNA as a biomarker for the diagnosis of transplant rejection was systematically reviewed, specifically clinical trials evaluating the test performance of algorithms predicting rejection based on cfDNA fraction. Literature highlighting epigenetic features in transplant rejection was also reviewed to outline the potential contribution of the epigenomic analysis to the needs of rejection-specific diagnosis.

Results: 40 articles were reviewed, and results were extracted and summarized. 16 met the inclusion criteria by evaluating the diagnostic performance of a predictive test for the discrimination of rejection vs. non-rejection patients (2 heart, 3 liver, 4 kidney, and 7 lung transplantations). The recurring conclusion is the kinetics of dd-cfDNA levels, strongly increasing immediately after transplantation and reaching basal levels after days to weeks and remaining stable in non-rejection patients. On the other hand, rejection is characterized by an increase in dd-cfDNA levels, depending on the transplanted organs. In addition, the epigenetic signature can help improve the specificity of the diagnosis of rejection by searching for specific epigenetic features that are by the clinical status of patients.

Conclusion: Cell-free DNA is a promising non-invasive biomarker but still needs standardization of technologies and protocols to be used for diagnostic purposes. Moreover, the lack of specificity of this marker can be compensated by the contribution of epigenetic analysis for which data are growing, although progress is still needed for its use in a clinical context.

Keywords: biomarker; cfDNA; diagnosis; epigenetic; methylation; transplantation.

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Conflict of interest statement

Authors AS and MS are employed by company BeDia Genomics. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
Schematic representation of the principle of bisulfite DNA conversion for the methylation study.
Figure 2
Figure 2
Global representation of characteristics of transcriptionally active (a) or inactive (b) chromatin.
Figure 3
Figure 3
Representation of nucleosome occupancy regarding the expression or repression of genes. TSS, transcription starting site.
See this image and copyright information in PMC

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