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McNamara ME, Jain SS, Oza K, Muralidaran V, Kiliti AJ, McDeed AP, Patil D, Cui Y, Schmidt MO, Riegel AT, Kroemer AH, Wellstein A. Circulating, cell-free methylated DNA indicates cellular sources of allograft injury after liver transplant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588176. [PMID: 38617373 PMCID: PMC11014558 DOI: 10.1101/2024.04.04.588176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Post-transplant complications reduce allograft and recipient survival. Current approaches for detecting allograft injury non-invasively are limited and do not differentiate between cellular mechanisms. Here, we monitor cellular damages after liver transplants from cell-free DNA (cfDNA) fragments released from dying cells into the circulation. We analyzed 130 blood samples collected from 44 patients at different time points after transplant. Sequence-based methylation of cfDNA fragments were mapped to patterns established to identify cell types in different organs. For liver cell types DNA methylation patterns and multi-omic data integration show distinct enrichment in open chromatin and regulatory regions functionally important for the respective cell types. We find that multi-tissue cellular damages post-transplant recover in patients without allograft injury during the first post-operative week. However, sustained elevation of hepatocyte and biliary epithelial cfDNA beyond the first week indicates early-onset allograft injury. Further, cfDNA composition differentiates amongst causes of allograft injury indicating the potential for non-invasive monitoring and timely intervention.
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Affiliation(s)
- Megan E. McNamara
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Sidharth S. Jain
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Kesha Oza
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
- Department of General Surgery, MedStar Georgetown University Hospital, Washington, DC, USA
| | - Vinona Muralidaran
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - A. Patrick McDeed
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Digvijay Patil
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Yuki Cui
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Marcel O. Schmidt
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Anna T. Riegel
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Alexander H.K. Kroemer
- MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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Cox DR, Lee E, Wong BK, McClure T, Zhang F, Goh SK, Vago A, Jackett L, Fink M, Jones R, Perini MV, Dobrovic A, Testro A, Starkey G, Muralidharan V. Graft-derived cfDNA Monitoring in Plasma and Bile During Normothermic Machine Perfusion in Liver Transplantation Is Feasible and a Potential Tool for Assessing Graft Viability. Transplantation 2024; 108:958-962. [PMID: 37902630 PMCID: PMC10962428 DOI: 10.1097/tp.0000000000004842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/12/2023] [Accepted: 08/09/2023] [Indexed: 10/31/2023]
Abstract
BACKGROUND Ex vivo normothermic machine perfusion (NMP) is an organ preservation technique that enables an extended assessment of graft suitability before liver transplantation (LT). Established monitoring protocols used during NMP vary significantly in their assessment of transplant suitability when applied to the same grafts. Graft-derived cell-free DNA (gdcfDNA) analysis is an emerging tool for monitoring graft health post-transplantation. We investigated the feasibility of monitoring gdcfDNA during NMP for LT in a proof-of-concept, observational study. METHODS Serial plasma and bile samples were collected during NMP for 10 consecutive grafts, at 15 min post-machine reperfusion and then 2-h intervals. Digital polymerase chain reaction was used to quantify gdcfDNA at each time point. RESULTS Five grafts were suitable for LT, there were no cases of primary nonfunction or death in the recipients. gdcfDNA was quantified in all bile and plasma samples (n > 100). In plasma, gdcfDNA concentrations climbed post-machine reperfusion until 4.25 h (median 2.25 h = 15.98 × 10 6 copies/mL, 4.25 h = 40.21 × 10 6 copies/mL). gdcfDNA levels then diverged significantly when comparing the viable and non-viable graft groups (6.25 h, median viable: 117.15 × 10 6 copies/mL versus non-viable: 16.72 × 10 6 copies/mL, P = 0.01). These opposing trends correlated in each graft and in all cases with the viable/non-viable outcome. There was a trend of gradual decline in bile gdcfDNA from viable grafts post-machine reperfusion; discarded grafts showed more variable patterns of release. CONCLUSIONS gdcfDNA analysis during NMP is a feasible and potential tool to inform viability assessment during NMP for LT. Bile gdcfDNA monitoring offers the prospect of an objective means to assess the degree of biliary injury associated with organ procurement.
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Affiliation(s)
- Daniel R.A. Cox
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC, Australia
- Hepatopancreatobiliary and Liver Transplant Surgery Unit, Austin Health, Melbourne, VIC, Australia
- Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin), University of Melbourne, Melbourne, VIC, Australia
| | - Eunice Lee
- Hepatopancreatobiliary and Liver Transplant Surgery Unit, Austin Health, Melbourne, VIC, Australia
| | - Boris K.L. Wong
- Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin), University of Melbourne, Melbourne, VIC, Australia
| | - Tess McClure
- Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin), University of Melbourne, Melbourne, VIC, Australia
- Liver Transplant Unit, Austin Health, Melbourne, VIC, Australia
| | - Fan Zhang
- Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin), University of Melbourne, Melbourne, VIC, Australia
| | - Su Kah Goh
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC, Australia
| | - Angela Vago
- Liver Transplant Unit, Austin Health, Melbourne, VIC, Australia
| | - Louise Jackett
- Department of Anatomical Pathology, Austin Health, Melbourne, VIC, Australia
| | - Michael Fink
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC, Australia
- Hepatopancreatobiliary and Liver Transplant Surgery Unit, Austin Health, Melbourne, VIC, Australia
| | - Robert Jones
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC, Australia
- Hepatopancreatobiliary and Liver Transplant Surgery Unit, Austin Health, Melbourne, VIC, Australia
- Liver Transplant Unit, Austin Health, Melbourne, VIC, Australia
| | - Marcos V. Perini
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC, Australia
- Hepatopancreatobiliary and Liver Transplant Surgery Unit, Austin Health, Melbourne, VIC, Australia
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin), University of Melbourne, Melbourne, VIC, Australia
| | - Adam Testro
- Liver Transplant Unit, Austin Health, Melbourne, VIC, Australia
| | - Graham Starkey
- Hepatopancreatobiliary and Liver Transplant Surgery Unit, Austin Health, Melbourne, VIC, Australia
- Liver Transplant Unit, Austin Health, Melbourne, VIC, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC, Australia
- Hepatopancreatobiliary and Liver Transplant Surgery Unit, Austin Health, Melbourne, VIC, Australia
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3
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Lee WS, Lockhart PJ. Utility of droplet digital polymerase chain reaction for studying somatic mosaicism: brain malformations and beyond. Neural Regen Res 2023; 18:2389-2390. [PMID: 37282462 PMCID: PMC10360090 DOI: 10.4103/1673-5374.371356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Affiliation(s)
- Wei Shern Lee
- Bruce Lefroy Centre, Murdoch Children's Research Institute; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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Berenguer M, de Martin E, Hessheimer AJ, Levitsky J, Maluf DG, Mas VR, Selzner N, Hernàndez-Èvole H, Lutu A, Wahid N, Zubair H. European Society for Organ Transplantation Consensus Statement on Biomarkers in Liver Transplantation. Transpl Int 2023; 36:11358. [PMID: 37711401 PMCID: PMC10498996 DOI: 10.3389/ti.2023.11358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/25/2023] [Indexed: 09/16/2023]
Abstract
Currently, one-year survival following liver transplantation (LT) exceeds 90% in large international registries, and LT is considered definitive treatment for patients with end-stage liver disease and liver cancer. Recurrence of disease, including hepatocellular carcinoma (HCC), significantly hampers post-LT outcomes. An optimal approach to immunosuppression (IS), including safe weaning, may benefit patients by mitigating the effect on recurrent diseases, as well as reducing adverse events associated with over-/under-IS, including chronic kidney disease (CKD). Prediction of these outcome measures-disease recurrence, CKD, and immune status-has long been based on relatively inaccurate clinical models. To address the utility of new biomarkers in predicting these outcomes in the post-LT setting, the European Society of Organ Transplantation (ESOT) and International Liver Transplant Society (ILTS) convened a working group of experts to review literature pertaining to primary disease recurrence, development of CKD, and safe weaning of IS. Summaries of evidence were presented to the group of panelists and juries to develop guidelines, which were discussed and voted in-person at the Consensus Conference in Prague November 2022. The consensus findings and recommendations of the Liver Working Group on new biomarkers in LT, clinical applicability, and future needs are presented in this article.
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Affiliation(s)
- Marina Berenguer
- Hepatology and Liver Transplantation Unit, Hospital Universitario la Fe - IIS La Fe Valencia, CiberEHD and University of Valencia, Valencia, Spain
| | - Eleonora de Martin
- AP-HP Hôpital Paul Brousse, Centre Hépato-Biliaire, Inserm UMR-S 1193, Université Paris-Saclay, Villejuif, France
| | - Amelia J. Hessheimer
- General & Digestive Surgery, Hospital Universitario La Paz, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Josh Levitsky
- Division of Gastroenterology and Hepatology, Department of Medicine, Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Daniel G. Maluf
- Program in Transplantation, Department of Surgery, University of Maryland Medical Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Valeria R. Mas
- Surgical Sciences Research in Transplantation, Chief Surgical Sciences Division, Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nazia Selzner
- Ajmera Transplant Center, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | | | - Alina Lutu
- AP-HP Hôpital Paul Brousse, Centre Hépato-Biliaire, Inserm UMR-S 1193, Université Paris-Saclay, Villejuif, France
| | - Nabeel Wahid
- Division of Gastroenterology and Hepatology, Department of Medicine, Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Haseeb Zubair
- Surgical Sciences Division, University of Maryland School of Medicine, Baltimore, MD, United States
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Cox DRA, McClure T, Zhang F, Wong BKL, Testro A, Goh SK, Muralidharan V, Dobrovic A. Graft-Derived Cell-Free DNA Quantification following Liver Transplantation Using Tissue-Specific DNA Methylation and Donor-Specific Genotyping Techniques: An Orthogonal Comparison Study. EPIGENOMES 2023; 7:11. [PMID: 37367181 DOI: 10.3390/epigenomes7020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/07/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Background: Graft-derived cell-free DNA (gdcfDNA) analysis has shown promise as a non-invasive tool for monitoring organ health following solid organ transplantation. A number of gdcfDNA analysis techniques have been described; however, the majority rely on sequencing or prior genotyping to detect donor-recipient mis-matched genetic polymorphisms. Differentially methylated regions of DNA can be used to identify the tissue-of-origin of cell-free DNA (cfDNA) fragments. In this study, we aimed to directly compare the performance of gdcfDNA monitoring using graft-specific DNA methylation analysis and donor-recipient genotyping techniques in a pilot cohort of clinical samples from patients post-liver transplantation. Results: 7 patients were recruited prior to LT, 3 developed early, biopsy-proven TCMR in the first 6 weeks post-LT. gdcfDNA was successfully quantified in all samples using both approaches. There was a high level of technical correlation between results using the two techniques (Spearman testing, rs = 0.87, p < 0.0001). gdcfDNA levels quantified using the genotyping approach were significantly greater across all timepoints in comparison to the tissue-specific DNA methylation-based approach: e.g., day 1 post-LT median 31,350 copies/mL (IQR 6731-64,058) vs. 4133 copies/mL (IQR 1100-8422), respectively. Qualitative trends in gdcfDNA levels for each patient were concordant between the two assays. Acute TCMR was preceded by significant elevations in gdcfDNA as quantified by both techniques. Elevations in gdcfDNA, using both techniques, were suggestive of TCMR in this pilot study with a 6- and 3-day lead-time prior to histological diagnosis in patients 1 and 2. Conclusions: Both the graft-specific methylation and genotyping techniques successfully quantified gdcfDNA in patients post-LT with statistically significant concordance. A direct comparison of these two techniques is not only important from a technical perspective for orthogonal validation, but significantly adds weight to the evidence that gdcfDNA monitoring reflects the underlying biology. Both techniques identified LT recipients who developed acute TCMR, with several days lead-time in comparison to conventional diagnostic workflows. Whilst the two assays performed comparably, gdcfDNA monitoring based on graft-specific DNA methylation patterns in cfDNA offers major practical advantages over the donor-recipient genotyping, and hence enhances the potential to translate this emerging technology into clinical practice.
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Affiliation(s)
- Daniel R A Cox
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC 3084, Australia
- HPB & Liver Transplant Surgery Unit, Department of Surgery, Austin Health, Melbourne, VIC 3084, Australia
- BEACON Biomarkers Laboratory, University of Melbourne, Melbourne, VIC 3084, Australia
| | - Tess McClure
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC 3084, Australia
- BEACON Biomarkers Laboratory, University of Melbourne, Melbourne, VIC 3084, Australia
- Liver Transplant Unit, Department of Gastroenterology & Hepatology, Austin Health, Melbourne, VIC 3084, Australia
| | - Fan Zhang
- BEACON Biomarkers Laboratory, University of Melbourne, Melbourne, VIC 3084, Australia
| | - Boris Ka Leong Wong
- BEACON Biomarkers Laboratory, University of Melbourne, Melbourne, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
| | - Adam Testro
- Liver Transplant Unit, Department of Gastroenterology & Hepatology, Austin Health, Melbourne, VIC 3084, Australia
| | - Su Kah Goh
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC 3084, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC 3084, Australia
- HPB & Liver Transplant Surgery Unit, Department of Surgery, Austin Health, Melbourne, VIC 3084, Australia
- BEACON Biomarkers Laboratory, University of Melbourne, Melbourne, VIC 3084, Australia
| | - Alexander Dobrovic
- Department of Surgery (Austin Precinct), University of Melbourne, Melbourne, VIC 3084, Australia
- BEACON Biomarkers Laboratory, University of Melbourne, Melbourne, VIC 3084, Australia
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6
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Cox DR, Wong BKL, Lee E, Testro A, Muralidharan V, Dobrovic A, Goh SK. Evaluating DNA recovery efficiency following bisulphite modification from plasma samples submitted for cell-free DNA methylation analysis. Epigenetics 2022; 17:1956-1960. [PMID: 35763697 DOI: 10.1080/15592294.2022.2091821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The detection of methylated templates in cell-free DNA (cfDNA) is increasingly recognized as a valuable, non-invasive tool for diagnosis, monitoring and prognostication in a range of medical contexts. The importance of controlling pre-analytical conditions in laboratory workflows prior to cfDNA quantification is well-established. Significant variations in the recovery of DNA following processes such as cfDNA extraction and sodium bisulphite modification may confound downstream analysis, particularly when accurate quantification of templates is required. Given the wealth of potential applications for this emerging molecular technology, attention has turned to the requirement to recognize and minimize pre-analytical variables prior to cfDNA methylation analysis. We recently described the development of an approach using an exogenous DNA construct to evaluate the recovery efficiency of cfDNA following the extraction and bisulphite modification steps (CEREBIS). Here, we report our experience in the practical application of this technique in 107 consecutive patient plasma samples submitted for quantitative cfDNA methylation analysis. The mean recovery of cfDNA (as estimated using cerebis), following extraction and bisulphite modification, was 37% ± 7%. Nine (8.4%) of the 107 samples were found to be outside of control limits, where the recovery of cerebis indicated significant differences in the efficiency of the pre-analytical processing of these samples. Recognition of these out-of-control samples precluded subsequent molecular analysis. Implementation of data-driven quality control measures, such as the one described, has the potential to improve the quality of liquid biopsy methylation analysis, interpretation and reporting.
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Affiliation(s)
- Daniel Ra Cox
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
| | - Boris Ka Leong Wong
- Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia
| | - Eunice Lee
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
| | - Adam Testro
- Liver Transplant Unit, Austin Health, Heidelberg, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
| | - Alexander Dobrovic
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia
| | - Su Kah Goh
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
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