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Häuser F, Mittler J, Hantal MS, Greulich L, Hermanns M, Shrestha A, Kriege O, Falter T, Immel UD, Herold S, Schuch B, Lackner KJ, Rossmann H, Radsak M. One fits all: a highly sensitive combined ddPCR/pyrosequencing system for the quantification of microchimerism after hematopoietic and solid organ transplantation. Clin Chem Lab Med 2023; 61:1994-2001. [PMID: 37167203 DOI: 10.1515/cclm-2023-0198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
OBJECTIVES A combined digital droplet PCR (ddPCR)/pyrosequencing assay system was developed that demonstrated advantages applicable to multiple qualitative and quantitative molecular genetic diagnostic applications. Data for characterizing this combined approach for hematologic stem cell transplantation (HSCT) and allele quantification from graft-derived cell-free (cf) DNA in solid organ transplantation (SOT) is presented. METHODS ddPCR and pyrosequencing assays targeting 32 SNPs/markers were established. ddPCR results from 72 gDNAs of 55 patients after allogeneic HSCT and 107 plasma-cfDNAs of 25 liver transplant recipients were compared with established methods/markers, i.e. short-tandem-repeat PCR and ALT, respectively. RESULTS The ddPCR results were in good agreement with the established marker. The limit of detection was 0.02 % minor allele fraction. The relationship between ddPCR and STR-PCR was linear with R2=0.98 allowing to transfer previously established clinical STR-PCR cut-offs to ddPCR; 50-fold higher sensitivity and a variation coefficient of <2 % enable the use of low DNA concentrations (e.g. pre-sorted cells). ddPCR detected liver allograft injury at least as sensitive as ALT suggesting that ddPCR is a reliable method to monitor the transplant integrity, especially when other biomarkers are lacking (e.g. kidney). CONCLUSIONS Combining pyrosequencing for genotyping and ddPCR for minor allele quantification enhances sensitivity and precision for the patient after HSCT and SOT. The assay is designed for maximum flexibility. It is expected to be suitable for other applications (sample tracking, prenatal diagnostics, etc.).
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Affiliation(s)
- Friederike Häuser
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Jens Mittler
- Department of General, Visceral, and Transplant Surgery, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Misra Simge Hantal
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Lilli Greulich
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Martina Hermanns
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Annette Shrestha
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Oliver Kriege
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Tanja Falter
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Uta D Immel
- Institute of Legal Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Stephanie Herold
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Brigitte Schuch
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Karl J Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Markus Radsak
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
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2
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Li Y, Liang B. Circulating donor-derived cell-free DNA as a marker for rejection after lung transplantation. Front Immunol 2023; 14:1263389. [PMID: 37885888 PMCID: PMC10598712 DOI: 10.3389/fimmu.2023.1263389] [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: 07/19/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Objective Recently, circulating donor-derive cell free DNA (dd-cfDNA) has gained growing attention in the field of solid organ transplantation. The aim of the study was to analyze circulating dd-cfDNA levels in graft rejection, ACR and AMR separately for each rejection type compared with non-rejection, and assessed the diagnostic potential of dd-cfDNA levels in predicting graft rejection after lung transplantation. Methods A systematic search for relevant articles was conducted on Medline, Web of Science, China National Knowledge Infrastructure (CNKI), and Wanfang databases without restriction of languages. The search date ended on June 1, 2023. STATA software was used to analyze the difference between graft rejection, ACR, AMR and stable controls, and evaluate the diagnostic performance of circulating dd-cfDNA in detecting graft rejection. Results The results indicated that circulating dd-cfDNA levels in graft rejection, ACR, and AMR were significantly higher than non-rejection (graft rejection: SMD=1.78, 95% CI: 1.31-2.25, I2 = 88.6%, P< 0.001; ACR: SMD=1.03, 95% CI: 0.47-1.59, I2 = 89.0%, P < 0.001; AMR: SMD= 1.78, 95% CI: 1.20-2.35, I2 = 89.8%, P < 0.001). Circulating dd-cfDNA levels distinguished graft rejection from non-rejection with a pooled sensitivity of 0.87 (95% CI: 0.80-0.92) and a pooled specificity of 0.82 (95% CI: 0.76-0.86). The corresponding SROC yield an AUROC of 0.90 (95% CI: 0.87-0.93). Conclusion Circulating dd-cfDNA could be used as a non-invasive biomarker to distinguish the patients with graft rejection from normal stable controls. Systematic Review Registration https://www.crd.york.ac.uk/prospero/, identifier CRD42023440467.
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Affiliation(s)
- Yunhui Li
- Department of Laboratory Medical Center, General Hospital of Northern Theater Command, Shenyang, China
| | - Bin Liang
- Bioinformatics of Department, Key laboratory of Cell Biology, School of Life Sciences, China Medical University, Shenyang, China
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3
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Kueng N, Arcioni S, Sandberg F, Kuhn C, Banz V, Largiadèr CR, Sidler D, Amstutz U. Comparison of methods for donor-derived cell-free DNA quantification in plasma and urine from solid organ transplant recipients. Front Genet 2023; 14:1089830. [PMID: 36777723 PMCID: PMC9916053 DOI: 10.3389/fgene.2023.1089830] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/12/2023] [Indexed: 01/28/2023] Open
Abstract
In allograft monitoring of solid organ transplant recipients, liquid biopsy has emerged as a novel approach using quantification of donor-derived cell-free DNA (dd-cfDNA) in plasma. Despite early clinical implementation and analytical validation of techniques, direct comparisons of dd-cfDNA quantification methods are lacking. Furthermore, data on dd-cfDNA in urine is scarce and high-throughput sequencing-based methods so far have not leveraged unique molecular identifiers (UMIs) for absolute dd-cfDNA quantification. Different dd-cfDNA quantification approaches were compared in urine and plasma of kidney and liver recipients: A) Droplet digital PCR (ddPCR) using allele-specific detection of seven common HLA-DRB1 alleles and the Y chromosome; B) high-throughput sequencing (HTS) using a custom QIAseq DNA panel targeting 121 common polymorphisms; and C) a commercial dd-cfDNA quantification method (AlloSeq® cfDNA, CareDx). Dd-cfDNA was quantified as %dd-cfDNA, and for ddPCR and HTS using UMIs additionally as donor copies. In addition, relative and absolute dd-cfDNA levels in urine and plasma were compared in clinically stable recipients. The HTS method presented here showed a strong correlation of the %dd-cfDNA with ddPCR (R 2 = 0.98) and AlloSeq® cfDNA (R 2 = 0.99) displaying only minimal to no proportional bias. Absolute dd-cfDNA copies also correlated strongly (τ = 0.78) between HTS with UMI and ddPCR albeit with substantial proportional bias (slope: 0.25; 95%-CI: 0.19-0.26). Among 30 stable kidney transplant recipients, the median %dd-cfDNA in urine was 39.5% (interquartile range, IQR: 21.8-58.5%) with 36.6 copies/μmol urinary creatinine (IQR: 18.4-109) and 0.19% (IQR: 0.01-0.43%) with 5.0 copies/ml (IQR: 1.8-12.9) in plasma without any correlation between body fluids. The median %dd-cfDNA in plasma from eight stable liver recipients was 2.2% (IQR: 0.72-4.1%) with 120 copies/ml (IQR: 85.0-138) while the median dd-cfDNA copies/ml was below 0.1 in urine. This first head-to-head comparison of methods for absolute and relative quantification of dd-cfDNA in urine and plasma supports a method-independent %dd-cfDNA cutoff and indicates the suitability of the presented HTS method for absolute dd-cfDNA quantification using UMIs. To evaluate the utility of dd-cfDNA in urine for allograft surveillance, absolute levels instead of relative amounts will most likely be required given the extensive variability of %dd-cfDNA in stable kidney recipients.
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Affiliation(s)
- Nicholas Kueng
- Department of Clinical Chemistry, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Séverine Arcioni
- Department of Clinical Chemistry, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland,Division of Medical Genetics, Central Institute of Hospitals, Valais Hospital, Sion, Switzerland
| | - Fanny Sandberg
- Department of Clinical Chemistry, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Christian Kuhn
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Vanessa Banz
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Carlo R. Largiadèr
- Department of Clinical Chemistry, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Daniel Sidler
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Ursula Amstutz
- Department of Clinical Chemistry, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland,*Correspondence: Ursula Amstutz,
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4
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Pedini P, Coiffard B, Cherouat N, Casas S, Fina F, Boutonnet A, Baudey JB, Aho P, Basire A, Simon S, Frassati C, Chiaroni J, Reynaud-Gaubert M, Picard C. Clinical relevance of cell-free DNA quantification and qualification during the first month after lung transplantation. Front Immunol 2023; 14:1183949. [PMID: 37180126 PMCID: PMC10174290 DOI: 10.3389/fimmu.2023.1183949] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 05/15/2023] Open
Abstract
Background Many studies have reported the relevance of donor-derived cfDNA (dd-cfDNA) after lung transplantation (LTx) to diagnose and monitor acute rejection (AR) or chronic rejection or infection (INF). However, the analysis of cfDNA fragment size has not been studied. The aim of this study was to determine the clinical relevance of dd-cfDNA and cfDNA size profiles in events (AR and INF) during the first month after LTx. Methods This prospective, single-center study includes 62 LTx recipients at the Marseille Nord Hospital, France. Total cfDNA quantification was performed by fluorimetry and digital PCR, dd-cfDNA by NGS (AlloSeq cfDNA-CareDX®), and the size profile by BIABooster (Adelis®). A bronchoalveolar lavage and transbronchial biopsies at D30 established the following groups: not-injured and injured graft (AR, INF, or AR+INF). Results Quantification of total cfDNA was not correlated with the patient's status at D30. The percentage of dd-cfDNA was significantly higher for injured graft patients at D30 (p=0.0004). A threshold of 1.72% of dd-cfDNA correctly classified the not-injured graft patients (negative predictive value of 91.4%). Among recipients with dd-cfDNA >1.72%, the quantification of small sizes (80-120bp) >3.70% identified the INF with high performance (specificity and positive predictive value of 100%). Conclusion With the aim of considering cfDNA as a polyvalent non-invasive biomarker in transplantation, an algorithm combining the quantification of dd-cfDNA and small sizes of DNA may significantly classify the different types of allograft injuries.
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Affiliation(s)
- Pascal Pedini
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
- ADES UMR, Aix Marseille Univ, Marseille, France
- *Correspondence: Pascal Pedini,
| | - Benjamin Coiffard
- Aix-Marseille University, Lung Transplant Department, APHM, Marseille, France
| | - Nicem Cherouat
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
| | - Sylvia Casas
- Medical Direction, CareDx, Brisbane, CA, United States
| | | | | | | | - Printil Aho
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
| | - Agnes Basire
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
| | - Sophie Simon
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
| | - Coralie Frassati
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
| | - Jacques Chiaroni
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
- ADES UMR, Aix Marseille Univ, Marseille, France
| | | | - Christophe Picard
- Immunogenetics Laboratory, Etablissement Français du Sang, Marseille, France
- ADES UMR, Aix Marseille Univ, Marseille, France
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5
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Sorbini M, Togliatto G, Mioli F, Simonato E, Marro M, Cappuccio M, Arruga F, Caorsi C, Mansouri M, Magistroni P, Gambella A, Delsedime L, Papotti MG, Solidoro P, Albera C, Boffini M, Rinaldi M, Amoroso A, Vaisitti T, Deaglio S. Validation of a Simple, Rapid, and Cost-Effective Method for Acute Rejection Monitoring in Lung Transplant Recipients. Transpl Int 2022; 35:10546. [PMID: 35755857 PMCID: PMC9221674 DOI: 10.3389/ti.2022.10546] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/19/2022] [Indexed: 11/24/2022]
Abstract
Despite advances in immunosuppression therapy, acute rejection remains the leading cause of graft dysfunction in lung transplant recipients. Donor-derived cell-free DNA is increasingly being considered as a valuable biomarker of acute rejection in several solid organ transplants. We present a technically improved molecular method based on digital PCR that targets the mismatch between the recipient and donor at the HLA-DRB1 locus. Blood samples collected sequentially post-transplantation from a cohort of lung recipients were used to obtain proof-of-principle for the validity of the assay, correlating results with transbronchial biopsies and lung capacity tests. The results revealed an increase in dd-cfDNA during the first 2 weeks after transplantation related to ischemia-reperfusion injury (6.36 ± 5.36%, p < 0.0001). In the absence of complications, donor DNA levels stabilized, while increasing again during acute rejection episodes (7.81 ± 12.7%, p < 0.0001). Respiratory tract infections were also involved in the release of dd-cfDNA (9.14 ± 15.59%, p = 0.0004), with a positive correlation with C-reactive protein levels. Overall, the dd-cfDNA percentages were inversely correlated with the lung function values measured by spirometry. These results confirm the value of dd-cfDNA determination during post-transplant follow-up to monitor acute rejection in lung recipients, achieved using a rapid and inexpensive approach based on the HLA mismatch between donor and recipient.
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Affiliation(s)
- Monica Sorbini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Fiorenza Mioli
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Erika Simonato
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Matteo Marro
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | | | - Francesca Arruga
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Cristiana Caorsi
- Immunogenetics and Transplant Biology Service, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Morteza Mansouri
- Immunogenetics and Transplant Biology Service, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Paola Magistroni
- Immunogenetics and Transplant Biology Service, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | | | - Luisa Delsedime
- Pathology Unit, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Mauro Giulio Papotti
- Pathology Unit, Città Della Salute e Della Scienza University Hospital, Turin, Italy.,Department of Oncology, University of Turin, Turin, Italy
| | - Paolo Solidoro
- Lung Transplantation and Advanced Airways Management, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Carlo Albera
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Massimo Boffini
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Mauro Rinaldi
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy.,Immunogenetics and Transplant Biology Service, Città Della Salute e Della Scienza University Hospital, Turin, Italy
| | - Tiziana Vaisitti
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, Turin, Italy.,Immunogenetics and Transplant Biology Service, Città Della Salute e Della Scienza University Hospital, Turin, Italy
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6
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Cell-free DNA in lung transplantation: research tool or clinical workhorse? Curr Opin Organ Transplant 2022; 27:177-183. [PMID: 35649108 DOI: 10.1097/mot.0000000000000979] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW Recent evidence indicates that plasma donor-derived cell-free DNA (dd-cfDNA) is a sensitive biomarker for the detection of underlying allograft injury, including rejection and infection. In this review, we will cover the latest evidence revolving around dd-cfDNA in lung transplantation and its role in both advancing mechanistic insight into disease states in lung transplant recipients as well as its potential clinical utility. RECENT FINDINGS Plasma dd-cfDNA increases in the setting of allograft injury, including in primary graft dysfunction, acute cellular rejection, antibody-mediated rejection and infection. Dd-cfDNA has demonstrated good performance characteristics for the detection of various allograft injury states, most notably with a high negative-predictive value for detection of acute rejection. Elevated levels of dd-cfDNA in the early posttransplant period, reflecting molecular evidence of lung allograft injury, are associated with increased risk of chronic lung allograft dysfunction and death. SUMMARY As a quantitative, molecular biomarker of lung allograft injury, dd-cfDNA holds great promise in clinical and research settings for advancing methods of posttransplant surveillance monitoring, diagnosis of allograft injury states, monitoring adequacy of immunosuppression, risk stratification and unlocking pathophysiological mechanisms of various disease.
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7
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Edwards RL, Menteer J, Lestz RM, Baxter-Lowe LA. Cell-free DNA as a solid-organ transplant biomarker: technologies and approaches. Biomark Med 2022; 16:401-415. [PMID: 35195028 DOI: 10.2217/bmm-2021-0968] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
High-quality biomarkers that detect emergent graft damage and/or rejection after solid-organ transplantation offer new opportunities to improve post-transplant monitoring, allow early therapeutic intervention and facilitate personalized patient management. Donor-derived cell-free DNA (DD-cfDNA) is a particularly exciting minimally invasive biomarker because it has the potential to be quantitative, time-sensitive and cost-effective. Increased DD-cfDNA has been associated with graft damage and rejection episodes. Efforts are underway to further improve sensitivity and specificity. This review summarizes the procedures used to process and detect DD-cfDNA, measurement of DD-cfDNA in clinical transplantation, approaches for improving sensitivity and specificity and long-term prospects as a transplant biomarker to supplement traditional organ monitoring and invasive biopsies.
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Affiliation(s)
- Rebecca L Edwards
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jondavid Menteer
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Cardiology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Rachel M Lestz
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Nephrology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Lee Ann Baxter-Lowe
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
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8
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Keller M, Sun J, Mutebi C, Shah P, Levine D, Aryal S, Iacono A, Timofte I, Mathew J, Varghese A, Giner C, Agbor-Enoh S. Donor-derived cell-free DNA as a composite marker of acute lung allograft dysfunction in clinical care. J Heart Lung Transplant 2021; 41:458-466. [DOI: 10.1016/j.healun.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022] Open
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9
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Jerič Kokelj B, Štalekar M, Vencken S, Dobnik D, Kogovšek P, Stanonik M, Arnol M, Ravnikar M. Feasibility of Droplet Digital PCR Analysis of Plasma Cell-Free DNA From Kidney Transplant Patients. Front Med (Lausanne) 2021; 8:748668. [PMID: 34692738 PMCID: PMC8531215 DOI: 10.3389/fmed.2021.748668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/03/2022] Open
Abstract
Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patients' plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA.
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Affiliation(s)
- Barbara Jerič Kokelj
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Štalekar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Miha Arnol
- Department of Nephrology, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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10
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Donor-Derived Cell-Free DNA to Diagnose Graft Rejection Post-Transplant: Past, Present and Future. TRANSPLANTOLOGY 2021. [DOI: 10.3390/transplantology2030034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Donor-derived cell-free DNA (dd-cfDNA) is a non-invasive biomarker that is more sensitive and specific towards diagnosing any graft injury or rejection. Due to its applicability over all transplanted organs irrespective of age, sex, race, ethnicity, and the non-requirement of a donor sample, it emerges as a new gold standard for graft health and rejection monitoring. Published research articles describing the role and efficiency of dd-cfDNA were identified and scrutinized to acquire a brief understanding of the history, evolution, emergence, role, efficiency, and applicability of dd-cfDNA in the field of transplantation. The dd-cfDNA can be quantified using quantitative PCR, next-generation sequencing, and droplet digital PCR, and there is a commendatory outcome in terms of diagnosing graft injury and monitoring graft health. The increased levels of dd-cfDNA can diagnose the rejection prior to any other presently used biochemistry or immunological assay methods. Biopsies are performed when these tests show any signs of injury and/or rejection. Therefore, by the time these tests predict and show any unusual or improper activity of the graft, the graft is already damaged by almost 50%. This review elucidates the evolution, physiology, techniques, limitations, and prospects of dd-cfDNA as a biomarker for post-transplant graft damage and rejection.
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11
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Diagnostic Accuracy of Donor-derived Cell-free DNA in Renal-allograft Rejection: A Meta-analysis. Transplantation 2021; 105:1303-1310. [PMID: 32890130 DOI: 10.1097/tp.0000000000003443] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) is a potential noninvasive molecular marker of graft rejection after kidney transplant, whose diagnostic accuracy remains controversial. METHODS We performed a systematic review and metaanalysis to evaluate the diagnostic accuracy of dd-cfDNA. Relevant literature was searched from online databases, and the data on the diagnostic accuracy of discriminating main rejection episodes (MRE) and antibody-mediated rejection (AMR) were merged, respectively. RESULTS Nine studies were included in the metaanalysis, of which 6 were focused on the diagnostic accuracy of dd-cfDNA for MRE, whose pooled sensitivity, specificity, area under the receiver operating characteristics curve, diagnostic odds ratio, overall positive likelihood ratio, and negative likelihood ratio with 95% confidence intervals were 0.70 (0.57-0.81), 0.78 (0.70-0.84), 0.81 (0.77-0.84), 8.18 (5.11-13.09), 3.15 (2.47-4.02), and 0.39 (0.27-0.55), respectively. Five tests were focused on discriminating AMR, whose pooled indicators were 0.84 (0.75-0.90), 0.80 (0.74-0.84), 0.89 (0.86-0.91), 20.48 (10.76-38.99), 4.13(3.21-5.33), and 0.20(0.12-0.33), respectively. CONCLUSIONS Donor-derived cell-free DNA can be a helpful marker for the diagnosis of AMR among those recipients suspected of renal dysfunction. Its diagnostic accuracy on the MRE remains uncertain, which requires further prospective, large-scale, multicenter, and common population research.
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12
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Renaud-Picard B, Koutsokera A, Cabanero M, Martinu T. Acute Rejection in the Modern Lung Transplant Era. Semin Respir Crit Care Med 2021; 42:411-427. [PMID: 34030203 DOI: 10.1055/s-0041-1729542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Acute cellular rejection (ACR) remains a common complication after lung transplantation. Mortality directly related to ACR is low and most patients respond to first-line immunosuppressive treatment. However, a subset of patients may develop refractory or recurrent ACR leading to an accelerated lung function decline and ultimately chronic lung allograft dysfunction. Infectious complications associated with the intensification of immunosuppression can also negatively impact long-term survival. In this review, we summarize the most recent evidence on the mechanisms, risk factors, diagnosis, treatment, and prognosis of ACR. We specifically focus on novel, promising biomarkers which are under investigation for their potential to improve the diagnostic performance of transbronchial biopsies. Finally, for each topic, we highlight current gaps in knowledge and areas for future research.
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Affiliation(s)
- Benjamin Renaud-Picard
- Division of Respirology and Toronto Lung Transplant Program, University of Toronto and University Health Network, Toronto, Canada
| | - Angela Koutsokera
- Division of Pulmonology, Lung Transplant Program, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Michael Cabanero
- Department of Pathology, Toronto General Hospital, University Health Network, Toronto, Canada
| | - Tereza Martinu
- Division of Respirology and Toronto Lung Transplant Program, University of Toronto and University Health Network, Toronto, Canada
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13
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Sorbini M, Togliatto GM, Simonato E, Boffini M, Cappuccio M, Gambella A, Arruga F, Mora N, Marro M, Caorsi C, Mansouri M, Magistroni P, Delsedime L, Papotti MG, Amoroso A, Rinaldi M, Vaisitti T, Deaglio S. HLA-DRB1 mismatch-based identification of donor-derived cell free DNA (dd-cfDNA) as a marker of rejection in heart transplant recipients: A single-institution pilot study. J Heart Lung Transplant 2021; 40:794-804. [PMID: 34134912 DOI: 10.1016/j.healun.2021.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/12/2021] [Accepted: 05/07/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) is considered a reliable marker of organ damage with potential applications in the follow-up of transplant recipients. METHODS In this work we present an assay based on the donor-recipient HLA-mismatch (human leukocyte antigen) at the HLA-DRB1 locus to monitor rejection by quantifying the percentage of dd-cfDNA using a droplet digital PCR (polymerase chain reaction) technique. A panel of probes targeting the HLA-DRB1 locus and covering >85% genetic variability was validated and used to assess dd-cfDNA levels in a prospective cohort of 19 adult heart transplant recipients (mean age 50.9±14.8 years). The assay was carried out on a total of 232 liquid biopsies collected at the same time as endomyocardial biopsy (EMB) during routine post-transplant follow-up. RESULTS Results show a significant increase of dd-cfDNA related to ischemia-reperfusion injury (2.22±2.09%) and to acute cellular rejection (1.71±3.10%) compared to stable conditions (0.43±1.04%, p < 0.0001). On the contrary, no increase was observed during infections or vascular complications, underlining the potential role of this biomarker for rejection monitoring. With a cut-off of 0.11%, the test showed 70.8% specificity (95% CI, 58.17% - 81.40%) and 64.2% sensitivity (95% CI, 49.80% - 76.86%) in discriminating acute rejection from no rejection. CONCLUSIONS These data demonstrate that this HLA mismatch-based droplet digital PCR method is effective for monitoring rejection in heart transplant recipients. Compared to next generation sequencing approaches, it is far more flexible, less expensive and provides faster results.
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Affiliation(s)
- Monica Sorbini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Erika Simonato
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città della Salute e della Scienza University Hospital of Torino, Torino, Italy
| | - Massimo Boffini
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città della Salute e della Scienza University Hospital of Torino, Torino, Italy.
| | | | | | - Francesca Arruga
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Nicola Mora
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Matteo Marro
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città della Salute e della Scienza University Hospital of Torino, Torino, Italy
| | - Cristiana Caorsi
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Morteza Mansouri
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Paola Magistroni
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Luisa Delsedime
- Department of Oncology, University of Turin and Pathology Unit, Città della Salute e della Scienza Hospital, Turin, Italy
| | - Mauro Giulio Papotti
- Department of Oncology, University of Turin and Pathology Unit, Città della Salute e della Scienza Hospital, Turin, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy; Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Mauro Rinaldi
- Cardiac Surgery Division, Surgical Sciences Department, Heart and Lung Transplant Center, Città della Salute e della Scienza University Hospital of Torino, Torino, Italy
| | - Tiziana Vaisitti
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, Turin, Italy; Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
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14
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Jang MK, Tunc I, Berry GJ, Marboe C, Kong H, Keller MB, Shah PD, Timofte I, Brown AW, Ponor IL, Mutebi C, Philogene MC, Yu K, Iacono A, Orens JB, Nathan SD, Agbor-Enoh S. Donor-derived cell-free DNA accurately detects acute rejection in lung transplant patients, a multicenter cohort study. J Heart Lung Transplant 2021; 40:822-830. [PMID: 34130911 DOI: 10.1016/j.healun.2021.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Acute rejection, which includes antibody-mediated rejection and acute cellular rejection, is a risk factor for lung allograft loss. Lung transplant patients often undergo surveillance transbronchial biopsies to detect and treat acute rejection before irreversible chronic rejection develops. Limitations of this approach include its invasiveness and high interobserver variability. We tested the performance of percent donor-derived cell-free DNA (%ddcfDNA), a non-invasive blood test, to detect acute rejection. METHODS This multicenter cohort study monitored 148 lung transplant subjects over a median of 19.6 months. We collected serial plasma samples contemporaneously with TBBx to measure %ddcfDNA. Clinical data was collected to adjudicate for acute rejection. The primary analysis consisted of computing the area-under-the-receiver-operating-characteristic-curve of %ddcfDNA to detect acute rejection. Secondary analysis determined %ddcfDNA rule-out thresholds for acute rejection. RESULTS ddcfDNA levels were high after transplant surgery and decayed logarithmically. With acute rejection, ddcfDNA levels rose six-fold higher than controls. ddcfDNA levels also correlated with severity of lung function decline and histological grading of rejection. %ddcfDNA area-under-the-receiver-operating-characteristic-curve for acute rejection, AMR, and ACR were 0.89, 0.93, and 0.83, respectively. ddcfDNA levels of <0.5% and <1.0% showed a negative predictive value of 96% and 90% for acute rejection, respectively. Histopathology detected one-third of episodes with ddcfDNA levels ≥1.0%, even though >90% of these events were coincident to clinical complications missed by histopathology. CONCLUSIONS This study demonstrates that %ddcfDNA reliably detects acute rejection and other clinical complications potentially missed by histopathology, lending support to its use as a non-invasive marker of allograft injury.
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Affiliation(s)
- Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland
| | - Ilker Tunc
- Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland
| | - Gerald J Berry
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Stanford University School of Medicine, Palo Alto, California
| | - Charles Marboe
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Department of Pathology, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland
| | - Michael B Keller
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, 1830 East Monument Street, Baltimore, Maryland
| | - Pali D Shah
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, 1830 East Monument Street, Baltimore, Maryland
| | - Irina Timofte
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; University of Maryland Medical Center, Baltimore, Maryland
| | - Anne W Brown
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Inova Fairfax Hospital, Fairfax, Virginia
| | - Ileana L Ponor
- Department of Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland
| | - Cedric Mutebi
- Immunogenetics Core Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Mary C Philogene
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; National Cancer Institute, Rockville, Maryland
| | - Kai Yu
- National Cancer Institute, Rockville, Maryland
| | - Aldo Iacono
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; University of Maryland Medical Center, Baltimore, Maryland
| | - Jonathan B Orens
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Stanford University School of Medicine, Palo Alto, California
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Inova Fairfax Hospital, Fairfax, Virginia
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, 1830 East Monument Street, Baltimore, Maryland.
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15
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Martuszewski A, Paluszkiewicz P, Król M, Banasik M, Kepinska M. Donor-Derived Cell-Free DNA in Kidney Transplantation as a Potential Rejection Biomarker: A Systematic Literature Review. J Clin Med 2021; 10:jcm10020193. [PMID: 33430458 PMCID: PMC7827757 DOI: 10.3390/jcm10020193] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
Kidney transplantation (KTx) is the best treatment method for end-stage kidney disease. KTx improves the patient's quality of life and prolongs their survival time; however, not all patients benefit fully from the transplantation procedure. For some patients, a problem is the premature loss of graft function due to immunological or non-immunological factors. Circulating cell-free DNA (cfDNA) is degraded deoxyribonucleic acid fragments that are released into the blood and other body fluids. Donor-derived cell-free DNA (dd-cfDNA) is cfDNA that is exogenous to the patient and comes from a transplanted organ. As opposed to an invasive biopsy, dd-cfDNA can be detected by a non-invasive analysis of a sample. The increase in dd-cfDNA concentration occurs even before the creatinine level starts rising, which may enable early diagnosis of transplant injury and adequate treatment to avoid premature graft loss. In this paper, we summarise the latest promising results related to cfDNA in transplant patients.
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Affiliation(s)
- Adrian Martuszewski
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (A.M.); (P.P.); (M.B.)
| | - Patrycja Paluszkiewicz
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (A.M.); (P.P.); (M.B.)
| | - Magdalena Król
- Students Scientific Association, Department of Biomedical and Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Mirosław Banasik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (A.M.); (P.P.); (M.B.)
| | - Marta Kepinska
- Department of Biomedical and Environmental Analyses, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
- Correspondence: ; Tel.: +48-71-784-0171
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16
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Pedini P, Graiet H, Laget L, Filosa L, Chatron J, Cherouat N, Chiaroni J, Hubert L, Frassati C, Picard C. Qualitative and quantitative comparison of cell-free DNA and cell-free fetal DNA isolation by four (semi-)automated extraction methods: impact in two clinical applications: chimerism quantification and noninvasive prenatal diagnosis. J Transl Med 2021; 19:15. [PMID: 33407582 PMCID: PMC7788686 DOI: 10.1186/s12967-020-02671-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-invasive molecular analysis of cell-free DNA (cfDNA) became a sensitive biomarker for monitoring organ transplantation or for detection of fetal DNA (cffDNA) in noninvasive prenatal test. In this study, we compared the efficiencies of four (semi)-automated cfDNA isolation instruments using their respective isolation kit: MagNA Pure 24 (Roche®), IDEAL (IDSolution®), LABTurbo 24 (Taigen®) and Chemagic 360 (Perkin Elmer®). The cfDNA was isolated from 5 plasma samples and the Rhesus D (RhD)-cffDNA from 5 maternal plasmas. The cfDNA were quantified by digital droplet PCR (ddPCR), BIABooster system and QUBIT fluorometer. The cfDNA fragment size profiles were assessed by BIABooster system. Chimerism were quantified by home-made ddPCR and Devyser NGS kit. RhD-cffDNA in maternal plasma were detected between weeks 14 and 24 of amenorrhea using free DNA Fetal RHD Kit® (Biorad®). RESULTS Statistical tests have shown differences in DNA yield depending on the isolation procedure and quantification method used. Magna Pure isolates smaller cfDNA fragment size than other extraction methods (90% ± 9% vs. 74% ± 8%; p = 0.009). Chimerism was only reliable from LABTurbo 24 extractions using the NGS but not with ddPCR whatever extraction methods. RhD-cffDNA were detected by all isolation methods, although IDEAL and LABTurbo 24 systems seemed more efficient. CONCLUSIONS This comparative study showed a dependency of cfDNA yield depending on isolation procedure and quantification method used. In total, these results suggest that the choice of pre-analytical isolation systems needs to be carefully validated in routine clinical practice.
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Affiliation(s)
- Pascal Pedini
- Department of Histocompatibility, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France.
| | - Hajer Graiet
- Department of Histocompatibility, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
| | - Laurine Laget
- Department of Immunohematology, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
| | - Lugdivine Filosa
- Department of Immunohematology, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
| | - Jade Chatron
- Department of Histocompatibility, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
| | - Nicem Cherouat
- Department of Histocompatibility, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
| | - Jacques Chiaroni
- Department of Immunohematology, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
- UMR 7268, ADÉS Aix-Marseille Université/EFS, CNRS, 27 Bd Jean Moulin, 13385, Marseille Cedex 05, France
| | - Lucas Hubert
- Department of Histocompatibility, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
| | - Coralie Frassati
- Department of Histocompatibility, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
| | - Christophe Picard
- Department of Histocompatibility, Établissement Français du Sang PACA-Corse, 149 Bd Baille, 13005, Marseille, France
- UMR 7268, ADÉS Aix-Marseille Université/EFS, CNRS, 27 Bd Jean Moulin, 13385, Marseille Cedex 05, France
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17
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Keller M, Agbor-Enoh S. Donor-Derived Cell-Free DNA for Acute Rejection Monitoring in Heart and Lung Transplantation. CURRENT TRANSPLANTATION REPORTS 2021; 8:351-358. [PMID: 34754720 PMCID: PMC8570240 DOI: 10.1007/s40472-021-00349-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Acute allograft rejection is a common cause of morbidity and mortality in heart and lung transplantation. Unfortunately, the current monitoring gold standard-biopsy plus histopathology-has several limitations. Plasma donor-derived cell-free DNA (dd-cfDNA) has emerged as a potentially valuable biomarker for rejection that addresses some of the limitations of biopsy. This review covers the current state of the evidence and future directions for the use of dd-cfDNA in the monitoring of acute rejection. RECENT FINDINGS The results of several observational cohort studies demonstrate that levels of dd-cfDNA increase in the setting of acute cellular rejection and antibody-mediated rejection in both heart and lung transplant recipients. dd-cfDNA demonstrates acceptable performance characteristics, but low specificity for the detection of underlying injury from rejection or infection. In particular, the high negative predictive value of the test in both heart and lung transplant patients provides the potential for its use as a screening tool for the monitoring of allograft health rather than tissue biopsy alone. SUMMARY Existing evidence shows that dd-cfDNA is a safe, convenient, and reliable method of acute rejection monitoring in heart and lung transplant recipients. Further studies are required to validate threshold values for clinical use and determine its role in the diagnosis of alternative forms of allograft injury.
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Affiliation(s)
- Michael Keller
- grid.94365.3d0000 0001 2297 5165Laborarory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institute of Health, Bethesda, MD USA ,grid.94365.3d0000 0001 2297 5165Department of Critical Care Medicine, National Institute of Health, Bethesda, MD USA ,grid.411935.b0000 0001 2192 2723Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, MD USA
| | - Sean Agbor-Enoh
- grid.94365.3d0000 0001 2297 5165Laborarory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institute of Health, Bethesda, MD USA ,grid.411935.b0000 0001 2192 2723Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, MD USA ,grid.279885.90000 0001 2293 4638Lasker Clinical Research Tenure Track, Laboratory of Applied Precision Omics, Division of Intramural Research, NHLBI, 10 Center Dr, Rm 7D5, Baltimore, USA
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18
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Del Real A, Perez-Campo FM, Perez-Nuñez MI, Sañudo C, Santurtun A, Garcia-Ibarbia C, Garcia-Unzueta MT, Fraga MF, Fernandez AF, Valero MC, Laguna E, Riancho JA. Methylation of the Sclerostin (SOST) Gene in Serum Free DNA: A New Bone Biomarker? Genet Test Mol Biomarkers 2020; 25:42-47. [PMID: 33372860 DOI: 10.1089/gtmb.2020.0172] [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: 11/13/2022] Open
Abstract
Introduction: Cell-free DNA (cfDNA) methylation is an important molecular biomarker, which provides information about the regulation of gene expression in the tissue of origin. There is an inverse correlation between SOST gene methylation and expression levels. Methods: We analyzed SOST promoter methylation in cfDNA from serum, and compared it with DNA from blood and bone cells from patients undergoing hip replacement surgery. We also measured cfDNA methylation in 28 osteoporotic patients at baseline and after 6 months of antiosteoporotic therapy (alendronate, teriparatide, or denosumab). Results: SOST gene promoter methylation levels in serum cfDNA were very similar to those of bone-derived DNA (79% ± 12% and 82% ± 7%, respectively), but lower than methylation levels in blood cell DNA (87% ± 10%). Furthermore, there was a positive correlation between an individual's SOST DNA methylation values in serum and bone. No differences in either serum sclerostin levels or SOST methylation were found after 6-months of therapy with antiosteoporotic drugs. Conclusions: Our results suggest that serum cfDNA does not originate from blood cells, but rather from bone. However, since we did not confirm changes in this marker after therapy with bone-active drugs, further studies examining the correlation between bone changes of SOST expression and SOST methylation in cfDNA are needed to confirm its potential role as a bone biomarker.
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Affiliation(s)
- Alvaro Del Real
- Department of Internal Medicine, Hospital Universitario Marqués de Valdecilla-IDIVAL, University of Cantabria, Santander, Spain
| | - Flor M Perez-Campo
- Department of Molecular Biology, University of Cantabria-IDIVAL, Santander, Spain
| | | | - Carolina Sañudo
- Department of Internal Medicine, Hospital Universitario Marqués de Valdecilla-IDIVAL, University of Cantabria, Santander, Spain
| | - Ana Santurtun
- Unit of Legal Medicine, Department of Physiology and Pharmacology, University of Cantabria, Santander, Spain
| | - Carmen Garcia-Ibarbia
- Department of Internal Medicine, Hospital Universitario Marqués de Valdecilla-IDIVAL, University of Cantabria, Santander, Spain
| | - M Teresa Garcia-Unzueta
- Service of Clinical Biochemistry, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Asturias, Spain
| | - Agustin F Fernandez
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA. Fundación para la Investigación Biosanitaria de Asturias (FINBA), Asturias, Spain
| | - Maria Carmen Valero
- Department of Internal Medicine, Hospital Universitario Marqués de Valdecilla-IDIVAL, University of Cantabria, Santander, Spain
| | - Esther Laguna
- Department of Molecular Biology, University of Cantabria-IDIVAL, Santander, Spain
| | - José A Riancho
- Department of Internal Medicine, Hospital Universitario Marqués de Valdecilla-IDIVAL, University of Cantabria, Santander, Spain
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Waterhouse M, Pennisi S, Pfeifer D, Deuter M, von Bubnoff N, Scherer F, Strüssmann T, Wehr C, Duyster J, Bertz H, Finke J, Duque-Afonso J. Colon and liver tissue damage detection using methylated SESN3 and PTK2B genes in circulating cell-free DNA in patients with acute graft-versus-host disease. Bone Marrow Transplant 2020; 56:327-333. [PMID: 33082554 PMCID: PMC8376639 DOI: 10.1038/s41409-020-01090-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/01/2020] [Accepted: 10/08/2020] [Indexed: 11/24/2022]
Abstract
Cell-free DNA (cfDNA) has been investigated in acute graft-versus-host disease (aGvHD) following allogeneic cell transplantation (HSCT). Identifying the tissue of origin of cfDNA in patients with aGvHD is relevant particularly when a biopsy is not feasible. We investigate the cfDNA tissue of origin in patients with aGvHD using methylated gene biomarkers. Patients with liver, colon, or skin aGvHD (n = 28) were analyzed. Liver- and colon-derived cfDNA was measured using a colon- (SESN3) and liver (PTK2B)-specific methylation marker with digital droplet PCR. A statistically significant difference (p < 0.001) in PTK2B and SESN3 concentration was observed between patients with colon or liver GvHD and the control group. For SESN3 and PTK2B the area under the curve in the receiver-operating characteristic (ROC) space was 0.952 (95% CI, 0.888–1 p < 0.001) and 0.971 (95% CI, 0.964–1 p < 0.001), respectively. Thresholds to differentiate aGvHD from non-aGvHD in colon were 0 (sensitivity: 0.905; specificity: 0.989) and liver 1.5 (sensitivity: 0.928; specificity: 0.910). Clinical improvement of liver or colon aGvHD resulted in PTK2B and SESN3 reduced concentration. Whereas, in those patients without improvement the PTK2B and SESN3 level remained stable or increased. The PTK2B liver-specific marker and the SESN3 colon-specific marker and their longitudinal analysis might improve aGvHD detection.
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Affiliation(s)
- Miguel Waterhouse
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany.
| | - Sandra Pennisi
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Max Deuter
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Nikolas von Bubnoff
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany.,Department of Hematology and Oncology, Medical Center, University of Schleswig Holstein, Lübeck, Germany
| | - Florian Scherer
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Tim Strüssmann
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Claudia Wehr
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Justus Duyster
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Hartmut Bertz
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Jürgen Finke
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany
| | - Jesus Duque-Afonso
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg, Germany.
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Preka E, Ellershaw D, Chandler N, Ahlfors H, Spencer H, Chitty LS, Fenton MJ, Marks SD. Cell-Free DNA in Pediatric Solid Organ Transplantation Using a New Detection Method of Separating Donor-Derived from Recipient Cell-Free DNA. Clin Chem 2020; 66:1300-1309. [PMID: 32882007 DOI: 10.1093/clinchem/hvaa173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/06/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND The use of cell-free DNA (cfDNA) as a noninvasive biomarker to detect allograft damage is expanding rapidly. However, quantifying the low fraction of donor-derived cfDNA (ddcfDNA) is challenging and requires a highly sensitive technique. ddcfDNA detection through unique donor single nucleotide polymorphisms (SNPs) is a recent new approach, however there are limited data in pediatric solid organ transplant (SOT) recipients. METHODS We developed an assay using a combination of 61 SNPs to quantify the ddcfDNA accurately using a custom R script to model for both the patient and donor genotypes requiring only a single sample from the allograft recipient. Performance of the assay was validated using genomic DNA (gDNA), cfDNA and donor samples where available. RESULTS The R "genotype-free" method gave results comparable to when using the known donor genotype. applicable to both related and unrelated pairs and can reliably measure ddcfDNA (limit of blank, below 0.12%; limit of detection, above 0.25%; limit of quantification 0.5% resulting in 84% accuracy). 159 pediatric SOT recipients (kidney, heart, and lung) were tested without the need for donor genotyping. Serial sampling was obtained from 82 patients. CONCLUSION We have developed and validated a new assay to measure the fraction of ddcfDNA in the plasma of pediatric SOT recipients. Our method can be applicable in any donor-recipient pair without the need for donor genotyping and can provide results in 48 h at a low cost. Additional prospective studies are required to demonstrate its clinical validity in a large cohort of pediatric SOT recipients.
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Affiliation(s)
- Evgenia Preka
- Department of Paediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Paediatric Nephrology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Drew Ellershaw
- London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Natalie Chandler
- London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Helena Ahlfors
- London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Helen Spencer
- Cardiothoracic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust and Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health
| | - Matthew J Fenton
- Cardiothoracic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stephen D Marks
- Department of Paediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,University College London Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
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21
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Relja B, Land WG. Damage-associated molecular patterns in trauma. Eur J Trauma Emerg Surg 2020; 46:751-775. [PMID: 31612270 PMCID: PMC7427761 DOI: 10.1007/s00068-019-01235-w] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022]
Abstract
In 1994, the "danger model" argued that adaptive immune responses are driven rather by molecules released upon tissue damage than by the recognition of "strange" molecules. Thus, an alternative to the "self versus non-self recognition model" has been provided. The model, which suggests that the immune system discriminates dangerous from safe molecules, has established the basis for the future designation of damage-associated molecular patterns (DAMPs), a term that was coined by Walter G. Land, Seong, and Matzinger. The pathological importance of DAMPs is barely somewhere else evident as in the posttraumatic or post-surgical inflammation and regeneration. Since DAMPs have been identified to trigger specific immune responses and inflammation, which is not necessarily detrimental but also regenerative, it still remains difficult to describe their "friend or foe" role in the posttraumatic immunogenicity and healing process. DAMPs can be used as biomarkers to indicate and/or to monitor a disease or injury severity, but they also may serve as clinically applicable parameters for optimized indication of the timing for, i.e., secondary surgeries. While experimental studies allow the detection of these biomarkers on different levels including cellular, tissue, and circulatory milieu, this is not always easily transferable to the human situation. Thus, in this review, we focus on the recent literature dealing with the pathophysiological importance of DAMPs after traumatic injury. Since dysregulated inflammation in traumatized patients always implies disturbed resolution of inflammation, so-called model of suppressing/inhibiting inducible DAMPs (SAMPs) will be very briefly introduced. Thus, an update on this topic in the field of trauma will be provided.
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Affiliation(s)
- Borna Relja
- Experimental Radiology, Department of Radiology and Nuclear Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany.
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Frankfurt, Goethe University Frankfurt am Main, 60590, Frankfurt, Germany.
| | - Walter Gottlieb Land
- Molecular ImmunoRheumatology, INSERM UMR_S1109, Laboratory of Excellence Transplantex, University of Strasbourg, Strasbourg, France
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22
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Peng X, Li HD, Wu FX, Wang J. Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics. Brief Bioinform 2020; 22:5840077. [PMID: 32427285 DOI: 10.1093/bib/bbaa060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/16/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
Advances in sequencing technologies facilitate personalized disease-risk profiling and clinical diagnosis. In recent years, some great progress has been made in noninvasive diagnoses based on cell-free DNAs (cfDNAs). It exploits the fact that dead cells release DNA fragments into the circulation, and some DNA fragments carry information that indicates their tissues-of-origin (TOOs). Based on the signals used for identifying the TOOs of cfDNAs, the existing methods can be classified into three categories: cfDNA mutation-based methods, methylation pattern-based methods and cfDNA fragmentation pattern-based methods. In cfDNA mutation-based methods, the SNP information or the detected mutations in driven genes of certain diseases are employed to identify the TOOs of cfDNAs. Methylation pattern-based methods are developed to identify the TOOs of cfDNAs based on the tissue-specific methylation patterns. In cfDNA fragmentation pattern-based methods, cfDNA fragmentation patterns, such as nucleosome positioning or preferred end coordinates of cfDNAs, are used to predict the TOOs of cfDNAs. In this paper, the strategies and challenges in each category are reviewed. Furthermore, the representative applications based on the TOOs of cfDNAs, including noninvasive prenatal testing, noninvasive cancer screening, transplantation rejection monitoring and parasitic infection detection, are also reviewed. Moreover, the challenges and future work in identifying the TOOs of cfDNAs are discussed. Our research provides a comprehensive picture of the development and challenges in identifying the TOOs of cfDNAs, which may benefit bioinformatics researchers to develop new methods to improve the identification of the TOOs of cfDNAs.
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Abstract
Introduction: Lung transplantation remains an important treatment for patients with end stage lung disease. Chronic lung allograft dysfunction (CLAD) remains the greatest limiting factor for long term survival. As the diagnosis of CLAD is based on pulmonary function tests, significant lung injury is required before a diagnosis is feasible, likely when irreversible damage has already occurred. Therefore, research is ongoing for early CLAD recognition, with biomarkers making up a substantial amount of this research.Areas covered: The purpose of this review is to describe available biomarkers, focusing on those which aid in predicting CLAD and distinguishing between different CLAD phenotypes. We describe biomarkers presenting in bronchial alveolar lavage (BAL) as well as circulating in peripheral blood, both of which offer an appealing alternative to lung biopsy.Expert opinion: Development of CLAD involves complex, multiple immune and nonimmune mechanisms. Therefore, evaluation of potential CLAD biomarkers serves a dual purpose: clinically, the goal remains early detection and identification of patients at increased risk. Simultaneously, biomarkers offer insight into the different mechanisms involved in the pathophysiology of CLAD, leading to the development of possible interventions. The ultimate goal is the development of both preventive and early intervention strategies for CLAD to improve the overall survival of our lung transplant recipients.
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Affiliation(s)
- Osnat Shtraichman
- Division of Pulmonary, Allergy & Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Pulmonary institute, Rabin Medical Center, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv, Israel
| | - Joshua M Diamond
- Division of Pulmonary, Allergy & Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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24
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Bery AI, Hachem RR. Antibody-mediated rejection after lung transplantation. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:411. [PMID: 32355855 PMCID: PMC7186640 DOI: 10.21037/atm.2019.11.86] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antibody-mediated rejection (AMR) has been identified as a significant form of acute allograft dysfunction in lung transplantation. The development of consensus diagnostic criteria has created a uniform definition of AMR; however, significant limitations of these criteria have been identified. Treatment modalities for AMR have been adapted from other areas of medicine and data on the effectiveness of these therapies in AMR are limited. AMR is often refractory to these therapies, and graft failure and death are common. AMR is associated with increased rates of chronic lung allograft dysfunction (CLAD) and poor long-term survival. In this review, we discuss the history of AMR and describe known mechanisms, application of the consensus diagnostic criteria, data for current treatment strategies, and long-term outcomes. In addition, we highlight current gaps in knowledge, ongoing research, and future directions to address these gaps. Promising diagnostic techniques are actively being investigated that may allow for early detection and treatment of AMR. We conclude that further investigation is required to identify and define chronic and subclinical AMR, and head-to-head comparisons of currently used treatment protocols are necessary to identify an optimal treatment approach. Gaps in knowledge regarding the epidemiology, mechanisms, diagnosis, and treatment of AMR continue to exist and future research should focus on these aspects.
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Affiliation(s)
- Amit I Bery
- Division of Pulmonary & Critical Care, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ramsey R Hachem
- Division of Pulmonary & Critical Care, Washington University School of Medicine, Saint Louis, MO, USA
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25
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Greer M, Werlein C, Jonigk D. Surveillance for acute cellular rejection after lung transplantation. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:410. [PMID: 32355854 PMCID: PMC7186718 DOI: 10.21037/atm.2020.02.127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Acute cellular rejection (ACR) is a common complication following lung transplantation (LTx), affecting almost a third of recipients in the first year. Established, comprehensive diagnostic criteria exist but they necessitate allograft biopsies which in turn increases clinical risk and can pose certain logistical and economic problems in service delivery. Undermining these challenges further, are known problems with inter-observer interpretation of biopsies and uncertainty as to the long-term implications of milder or indeed asymptomatic episodes. Increased risk of chronic lung allograft dysfunction (CLAD) has long been considered the most significant consequence of ACR. Consensus is lacking as to whether this applies to mild ACR, with contradictory evidence available. Given these issues, research into alternative, minimal or non-invasive biomarkers represents the main focus of research in ACR. A number of potential markers have been proposed, but none to date have demonstrated adequate sensitivity and specificity to allow translation from bench to bedside.
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Affiliation(s)
- Mark Greer
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | | | - Danny Jonigk
- Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany.,Institute for Pathology, Hannover Medical School, Hannover, Germany
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26
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Dauber EM, Kollmann D, Kozakowski N, Rasoul-Rockenschaub S, Soliman T, Berlakovich GA, Mayr WR. Quantitative PCR of INDELs to measure donor-derived cell-free DNA-a potential method to detect acute rejection in kidney transplantation: a pilot study. Transpl Int 2019; 33:298-309. [PMID: 31710731 PMCID: PMC7065216 DOI: 10.1111/tri.13554] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/24/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
The quantification of donor‐derived cell‐free DNA (ddcfDNA) in recipient's plasma is a novel, but technically challenging noninvasive method to assist the diagnosis of acute rejection (AR). A quantitative real‐time PCR (qPCR) approach targeting insertion/deletion polymorphisms (INDEL) was adapted to measure ddcfNA in plasma samples from 29 kidney transplant recipients obtained at time of clinically indicated biopsies (eight patients with a histologically verified AR, nine with borderline rejection and 12 without evidence of rejection). Measured ddcfDNA levels of smaller INDEL amplicon targets differed significantly (P = 0.016, Kruskal–Wallis H test) between recipients with biopsy‐proven AR (median 5.24%; range 1.00–9.03), patients without (1.50%; 0.41–6.50) and patients with borderline AR (1.91%; 0.58–5.38). Similarly, pairwise testing by Mann–Whitney U‐tests revealed significant differences between recipients with AR and without AR (P = 0.012) as well as patients with AR and borderline histology (P = 0.015). Receiver operating characteristic (ROC) analysis revealed an area under the ROC curve for discriminating AR and non‐AR biopsies of 0.84 (95% CI: 0.66–1.00). The determined cutoff value of 2.7% ddcfDNA showed a sensitivity of 0.88 (95% CI: 0.63–1.00) and specificity of 0.81 (95% CI: 0.64–0.98). INDEL qPCR represents a novel method to quantify ddcfDNA on standard qPCR instruments within 6–8 h with high sensitivity and specificity to detect AR.
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Affiliation(s)
- Eva-Maria Dauber
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Wien, Austria
| | - Dagmar Kollmann
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | | | | | - Thomas Soliman
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | - Gabriela A Berlakovich
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | - Wolfgang R Mayr
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Wien, Austria
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27
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Bieńkowski M, Pęksa R, Popęda M, Kołaczkowska M, Frankiewicz A, Żaczek AJ, Gruchała M, Biernat W, Siondalski P. Liquid biopsy for minimally invasive heart transplant monitoring: a pilot study. J Clin Pathol 2019; 73:507-510. [PMID: 31806731 DOI: 10.1136/jclinpath-2019-205926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/21/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Heart transplantation allows for a long-term management of patients with end-stage heart failure. After the surgery, organ rejection is monitored with endomyocardial biopsy, which is an invasive, but not always informative procedure. Therefore, there is a pressing need for a new, safe, yet reliable, diagnostic method. Here, we present a pilot study confronting liquid biopsy based on donor-specific cell-free DNA with the protocol endomyocardial biopsy. METHODS The study was performed on 21 blood samples matched with endomyocardial biopsy (graded according to acute cellular rejection scale) from nine patients after heart transplantation. Genotyping was performed on genomic DNA from donors and recipients for 10 single-nucleotide polymorphisms (SNPs). Cell-free DNA isolated from plasma was analysed with digital droplet PCR to detect donor-specific alleles. RESULTS From 21 analysed endomyocardial biopsies, 4 were graded as 0R and 17 as 1R. Liquid biopsy was successfully performed in each sample for all informative SNPs (median of 3 per patient). We observed a high homogeneity of the results between SNPs in each sample (interclass correlation coefficient of >0.9). CONCLUSIONS There is a undeniable need for an alternative, non-invasive diagnostic procedure of early transplant rejection and investigation of donor-derived cell-free DNA seems to be the promising choice. The very high sensitivity is particularly enticing to consider liquid biopsy as a potential screening tool. Its minimal invasiveness may allow for more frequent examination and, thus, tighter monitoring. The reliable assessment of its clinical utility requires an adequately powered and properly designed multicentre study.
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Affiliation(s)
- Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Marta Popęda
- Laboratory of Cell Biology, Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Magdalena Kołaczkowska
- Department of Cardiac & Vascular Surgery, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Anna Frankiewicz
- 1st Department of Cardiology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Anna J Żaczek
- Laboratory of Cell Biology, Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Marcin Gruchała
- 1st Department of Cardiology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Piotr Siondalski
- Department of Cardiac & Vascular Surgery, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
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28
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Zhou Y, Yang G, Liu H, Chen Y, Li X, Ge J, Wang X, Niu H, Dong W, Jiang T, Shi H, Peng L, Liu L. A Noninvasive and Donor-independent Method Simultaneously Monitors Rejection and Infection in Patients With Organ Transplant. Transplant Proc 2019; 51:1699-1705. [PMID: 31399160 DOI: 10.1016/j.transproceed.2019.04.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/17/2019] [Accepted: 04/05/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND Rejection and infection are 2 major complications affecting the health and survival of patients receiving an allograft organ transplantation. We describe a diagnostic assay that simultaneously monitors for rejection and infection in recipients of kidney transplant by sequencing of cell-free DNA (cfDNA) in plasma. METHODS By using cfDNA in plasma, we established a noninvasive method that simultaneously monitors rejection and infection in patients with a history of organ transplant. A total of 6200 single-nucleotide polymorphisms were captured by liquid hybridization and sequenced by next-generation sequencing. The donor-derived cfDNA (ddcfDNA) level was calculated based on maximum likelihood estimation, without relying on the donor's genotype. We also analyzed the nonhuman cfDNA to test for infections in the patients' plasma. RESULTS Artificial ddcfDNA levels quantified by a donor-dependent and donor-independent algorithm were significantly correlated, with the multivariate coefficient of determination, or R2 value, of 0.999. This technique was applied on 30 patients (32 samples) after kidney transplantation, and a significant difference was observed on the ddcfdNA levels between nonrejection and rejection. Furthermore, 1 BK virus infection and 1 cytomegalovirus infection were revealed by this method, and the enrichment efficiency of the viral sequences was 114 and 489 times, respectively, which are consistent with clinical results. CONCLUSION This method can be used to simultaneously monitor for acute rejection as well as a broad spectrum of infections for patients of allograft organ transplant because it provides comprehensive information for clinicians to optimize immunosuppression therapy.
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Affiliation(s)
- Yang Zhou
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gongda Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Haitao Liu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yawen Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiaofeng Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jun Ge
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China; AlloDx Biotech Co, Ltd, Suzhou, China
| | - Xiaochen Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | | | | | | | - Haifeng Shi
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Longkai Peng
- Department of Urological Organ Transplantation, Center of Organ Transplantation, Second Xiangya Hospital, Central South University, Changsha, China
| | - Lei Liu
- Department of Urological Organ Transplantation, Center of Organ Transplantation, Second Xiangya Hospital, Central South University, Changsha, China.
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29
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Andrikovics H, Őrfi Z, Meggyesi N, Bors A, Varga L, Kövy P, Vilimszky Z, Kolics F, Gopcsa L, Reményi P, Tordai A. Current Trends in Applications of Circulatory Microchimerism Detection in Transplantation. Int J Mol Sci 2019; 20:E4450. [PMID: 31509957 PMCID: PMC6769866 DOI: 10.3390/ijms20184450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023] Open
Abstract
Primarily due to recent advances of detection techniques, microchimerism (the proportion of minor variant population is below 1%) has recently gained increasing attention in the field of transplantation. Availability of polymorphic markers, such as deletion insertion or single nucleotide polymorphisms along with a vast array of high sensitivity detection techniques, allow the accurate detection of small quantities of donor- or recipient-related materials. This diagnostic information can improve monitoring of allograft injuries in solid organ transplantations (SOT) as well as facilitate early detection of relapse in allogeneic hematopoietic stem cell transplantation (allo-HSCT). In the present review, genetic marker and detection platform options applicable for microchimerism detection are discussed. Furthermore, current results of relevant clinical studies in the context of microchimerism and SOT or allo-HSCT respectively are also summarized.
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Affiliation(s)
- Hajnalka Andrikovics
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
- Department of Pathophysiology, Semmelweis University, 1089 Budapest, Hungary
| | - Zoltán Őrfi
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Nóra Meggyesi
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - András Bors
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Lívia Varga
- School of PhD Studies, Semmelweis University, 1085 Budapest, Hungary
- Hungarian National Blood Transfusion Service, 1113 Budapest, Hungary
| | - Petra Kövy
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
- School of PhD Studies, Semmelweis University, 1085 Budapest, Hungary
| | - Zsófia Vilimszky
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Fanni Kolics
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - László Gopcsa
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Péter Reményi
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Attila Tordai
- Department of Pathophysiology, Semmelweis University, 1089 Budapest, Hungary.
- Department of Transfusion Medicine, Semmelweis University, 1089 Budapest, Hungary.
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30
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Donor-specific Cell-free DNA as a Biomarker in Solid Organ Transplantation. A Systematic Review. Transplantation 2019; 103:273-283. [PMID: 30308576 DOI: 10.1097/tp.0000000000002482] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND There is increasing interest in the use of noninvasive biomarkers to reduce the risks posed by invasive biopsy for monitoring of solid organ transplants (SOTs). One such promising marker is the presence of donor-derived cell-free DNA (dd-cfDNA) in the urine or blood of transplant recipients. METHODS We systematically reviewed the published literature investigating the use of cfDNA in monitoring of graft health after SOT. Electronic databases were searched for studies relating cfDNA fraction or levels to clinical outcomes, and data including measures of diagnostic test accuracy were extracted. Narrative analysis was performed. RESULTS Ninety-five articles from 47 studies met the inclusion criteria (18 kidneys, 7 livers, 11 hearts, 1 kidney-pancreas, 5 lungs, and 5 multiorgans). The majority were retrospective and prospective cohort studies, with 19 reporting diagnostic test accuracy data. Multiple techniques for measuring dd-cfDNA were reported, including many not requiring a donor sample. dd-cfDNA falls rapidly within 2 weeks, with baseline levels varying by organ type. Levels are elevated in the presence of allograft injury, including acute rejection and infection, and return to baseline after successful treatment. Elevation of cfDNA levels is seen in advance of clinically apparent organ injury. Discriminatory power was greatest for higher grades of T cell-mediated and antibody-mediated acute rejection, with high negative predictive values. CONCLUSIONS Cell-free DNA is a promising biomarker for monitoring the health of SOTs. Future studies will need to define how it can be used in routine clinical practice and determine clinical benefit with routine prospective monitoring.
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31
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Zhu X, Liu B, Su S, Wang B, Bai Y, Huang H, Liu X, Cheng X, Wang X, Zhu L, Yang W, Gao N, Jing G, Guo Y. A "quasi" confocal droplet reader based on laser-induced fluorescence (LIF) cytometry for highly-sensitive and contamination-free detection. Talanta 2019; 206:120200. [PMID: 31514845 DOI: 10.1016/j.talanta.2019.120200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 01/23/2023]
Abstract
Highly-sensitive and contamination-free droplet digital PCR (ddPCR) is an enabling technology and widely needed for accurate quantification of nucleic acid in clinical applications. In this paper, a novel droplet reader was developed by combining a "quasi" confocal laser-induced fluorescence (LIF) cytometry with a delicate microfluidic chip design. The droplets with a size of 90 μm was illuminated at an out-of-focus position by two aligned laser beams to generate maximum fluorescent signal. Additionally, the lateral offset position of the microfluidic chip should be precisely tuned so that the bandwidth of the FAM and VIC channels were configured at the matching sizes. Then, PMT gain voltages and pneumatic pressures were optimized for better droplet detection efficiencies. An aerosol adsorption experiment was performed to demonstrate that there was no aerosol contamination, and detected copy numbers of both mutants and wild types scaled linearly with the expected input copy numbers (r2>0.998) with a LoB of 0.0 copies and LoD of 3.0 copies. The results demonstrated that this droplet reader with the delicate chip is a convenient, highly-sensitive and contamination-free to detect fluorescence signals inside droplets after ddPCR, which is highly promising for broad applications of ddPCR in clinical diagnosis.
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Affiliation(s)
- Xiurui Zhu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | - Baoxia Liu
- TargetingOne Corporation, Beijing, China
| | - Shisheng Su
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | - Bo Wang
- TargetingOne Corporation, Beijing, China
| | - Yu Bai
- TargetingOne Corporation, Beijing, China
| | | | | | - Xin Cheng
- TargetingOne Corporation, Beijing, China
| | | | - Lingxiang Zhu
- TargetingOne Corporation, Beijing, China; National Research Institute for Family Planning, Beijing, China
| | - Wenjun Yang
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China; TargetingOne Corporation, Beijing, China
| | - Na Gao
- TargetingOne Corporation, Beijing, China
| | - Gaoshan Jing
- Department of Precision Instrument, School of Mechanical Engineering, State Key Laboratory of Precision Measurement Technology and Instruments, Tsinghua University, Beijing, China.
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China.
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Tissot A, Danger R, Claustre J, Magnan A, Brouard S. Early Identification of Chronic Lung Allograft Dysfunction: The Need of Biomarkers. Front Immunol 2019; 10:1681. [PMID: 31379869 PMCID: PMC6650588 DOI: 10.3389/fimmu.2019.01681] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/04/2019] [Indexed: 01/12/2023] Open
Abstract
A growing number of patients with end-stage lung disease have benefited from lung transplantation (LT). Improvements in organ procurement, surgical techniques and intensive care management have greatly increased short-term graft survival. However, long-term outcomes remain limited, mainly due to the onset of chronic lung allograft dysfunction (CLAD), whose diagnosis is based on permanent loss of lung function after the development of irreversible lung lesions. CLAD is associated with high mortality and morbidity, and its exact physiopathology is still only partially understood. Many researchers and clinicians have searched for CLAD biomarkers to improve diagnosis, to refine the phenotypes associated with differential prognosis and to identify early biological processes that lead to CLAD to enable an early intervention that could modify the inevitable degradation of respiratory function. Donor-specific antibodies are currently the only biomarkers used in routine clinical practice, and their significance for accurately predicting CLAD is still debated. We describe here significant studies that have highlighted potential candidates for reliable and non-invasive biomarkers of CLAD in the fields of imaging and functional monitoring, humoral immunity, cell-mediated immunity, allograft injury, airway remodeling and gene expression. Such biomarkers would improve CLAD prediction and allow differential LT management regarding CLAD risk.
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Affiliation(s)
- Adrien Tissot
- Centre de Recherche en Transplantation et Immunologie (CRTI), INSERM, Université de Nantes, Nantes, France.,Service de Pneumologie, Institut du Thorax, CHU Nantes, Nantes, France
| | - Richard Danger
- Centre de Recherche en Transplantation et Immunologie (CRTI), INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Johanna Claustre
- Centre de Recherche en Transplantation et Immunologie (CRTI), INSERM, Université de Nantes, Nantes, France.,Service Hospitalo-Universitaire de Pneumologie - Physiologie, CHU Grenoble Alpes, Grenoble, France
| | - Antoine Magnan
- Centre de Recherche en Transplantation et Immunologie (CRTI), INSERM, Université de Nantes, Nantes, France.,Service de Pneumologie, Institut du Thorax, CHU Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,UMR S 1087 CNRS UMR 6291, Institut du Thorax, CHU Nantes, Université de Nantes, Nantes, France
| | - Sophie Brouard
- Centre de Recherche en Transplantation et Immunologie (CRTI), INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
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Goh SK, Do H, Testro A, Pavlovic J, Vago A, Lokan J, Jones RM, Christophi C, Dobrovic A, Muralidharan V. The Measurement of Donor-Specific Cell-Free DNA Identifies Recipients With Biopsy-Proven Acute Rejection Requiring Treatment After Liver Transplantation. Transplant Direct 2019; 5:e462. [PMID: 31334336 PMCID: PMC6616138 DOI: 10.1097/txd.0000000000000902] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/15/2019] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Assessment of donor-specific cell-free DNA (dscfDNA) in the recipient is emerging as a noninvasive biomarker of organ rejection after transplantation. We previously developed a digital polymerase chain reaction (PCR)-based approach that readily measures dscfDNA within clinically relevant turnaround times. Using this approach, we characterized the dynamics and evaluated the clinical utility of dscfDNA after liver transplantation (LT). METHODS Deletion/insertion polymorphisms were used to distinguish donor-specific DNA from recipient-specific DNA. Posttransplant dscfDNA was measured in the plasma of the recipients. In the longitudinal cohort, dscfDNA was serially measured at days 3, 7, 14, 28, and 42 in 20 recipients. In the cross-sectional cohort, dscfDNA was measured in 4 clinically stable recipients (>1-y posttransplant) and 16 recipients (>1-mo posttransplant) who were undergoing liver biopsies. RESULTS Recipients who underwent LT without complications demonstrated an exponential decline in dscfDNA. Median levels at days 3, 7, 14, 28, and 42 were 1936, 1015, 247, 90, and 66 copies/mL, respectively. dscfDNA was higher in recipients with treated biopsy-proven acute rejection (tBPAR) when compared to those without. The area under the receiver operator characteristic curve of dscfDNA was higher than that of routine liver function tests for tBPAR (dscfDNA: 98.8% with 95% confidence interval, 95.8%-100%; alanine aminotransferase: 85.7%; alkaline phosphatase: 66.4%; gamma-glutamyl transferase: 80.1%; and bilirubin: 35.4%). CONCLUSIONS dscfDNA as measured by probe-free droplet digital PCR methodology was reflective of organ health after LT. Our findings demonstrate the potential utility of dscfDNA as a diagnostic tool of tBPAR.
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Affiliation(s)
- Su Kah Goh
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
| | - Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Adam Testro
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Julie Pavlovic
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Angela Vago
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
| | - Julie Lokan
- Department of Anatomical Pathology, Austin Health, Heidelberg, VIC, Australia
| | - Robert M. Jones
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Hepato-Pancreato-Biliary & Transplant Surgery Unit, Austin Health, Heidelberg, VIC, Australia
| | - Christopher Christophi
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Hepato-Pancreato-Biliary & Transplant Surgery Unit, Austin Health, Heidelberg, VIC, Australia
| | - Alexander Dobrovic
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Hepato-Pancreato-Biliary & Transplant Surgery Unit, Austin Health, Heidelberg, VIC, Australia
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34
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Snell G, Hiho S, Levvey B, Sullivan L, Westall G. Consequences of donor-derived passengers (pathogens, cells, biological molecules and proteins) on clinical outcomes. J Heart Lung Transplant 2019; 38:902-906. [PMID: 31307786 DOI: 10.1016/j.healun.2019.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/15/2019] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
It is recognized that donor factors contribute to lung transplant outcomes. Recent observations and studies have started to elucidate potential mechanisms behind explaining these observations. This perspective piece summarizes evolving lung transplant literature on the subject, focusing on donor "passenger" organisms, cells, hormones, and proteins transferred to the recipient. Many extrinsic and intrinsic donor features or properties have important consequences for subsequent allograft function in the recipient. Potentially, a better understanding of these features may provide useful novel therapeutic targets to enhance allograft outcomes.
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Affiliation(s)
- Gregory Snell
- Lung Transplant Service, Alfred Hospital and Monash University, Melbourne, Victoria, Australia.
| | - Steven Hiho
- Lung Transplant Service, Alfred Hospital and Monash University, Melbourne, Victoria, Australia; Victorian Transplantation and Immunogenetics Service, Australian Red Cross Blood Service, Melbourne, Victoria, Australia
| | - Bronwyn Levvey
- Lung Transplant Service, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - Lucy Sullivan
- Lung Transplant Service, Alfred Hospital and Monash University, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Glen Westall
- Lung Transplant Service, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
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35
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Weigt SS, Shino MY, Wang X. Molecular diagnostics for lung transplant rejection: An information pipeline or a pipe dream? J Heart Lung Transplant 2019; 38:514-515. [DOI: 10.1016/j.healun.2019.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 11/26/2022] Open
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Abstract
After more than 6 decades of clinical practice, the transplant community continues to research noninvasive biomarkers of solid organ injury to help improve patient care. In this review, we discuss the clinical usefulness of selective biomarkers and how they are processed at the laboratory. In addition, we organize these biomarkers based on specific aims and introduce innovative markers currently under investigation.
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Affiliation(s)
- John Choi
- Transplantation Research Center, Renal Division, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Albana Bano
- Transplantation Research Center, Renal Division, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Jamil Azzi
- Transplantation Research Center, Renal Division, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA.
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37
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Yang JYC, Verleden SE, Zarinsefat A, Vanaudenaerde BM, Vos R, Verleden GM, Sarwal RD, Sigdel TK, Liberto JM, Damm I, Watson D, Sarwal MM. Cell-Free DNA and CXCL10 Derived from Bronchoalveolar Lavage Predict Lung Transplant Survival. J Clin Med 2019; 8:jcm8020241. [PMID: 30781765 PMCID: PMC6406976 DOI: 10.3390/jcm8020241] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
Standard methods for detecting chronic lung allograft dysfunction (CLAD) and rejection have poor sensitivity and specificity and have conventionally required bronchoscopies and biopsies. Plasma cell-free DNA (cfDNA) has been shown to be increased in various types of allograft injury in transplant recipients and CXCL10 has been reported to be increased in the lung tissue of patients undergoing CLAD. This study used a novel cfDNA and CXCL10 assay to evaluate the noninvasive assessment of CLAD phenotype and prediction of survival from bronchoalveolar lavage (BAL) fluid. A total of 60 BAL samples (20 with bronchiolitis obliterans (BOS), 20 with restrictive allograft syndrome (RAS), and 20 with stable allografts (STA)) were collected from 60 unique lung transplant patients; cfDNA and CXCL10 were measured by the ELISA-based KIT assay. Median cfDNA was significantly higher in BOS patients (6739 genomic equivalents (GE)/mL) versus STA (2920 GE/mL) and RAS (4174 GE/mL) (p < 0.01 all comparisons). Likelihood ratio tests revealed a significant association of overall survival with cfDNA (p = 0.0083), CXCL10 (p = 0.0146), and the interaction of cfDNA and CXCL10 (p = 0.023) based on multivariate Cox proportional hazards regression. Dichotomizing patients based on the median cfDNA level controlled for the mean level of CXCL10 revealed an over two-fold longer median overall survival time in patients with low levels of cfDNA. The KIT assay could predict allograft survival with superior performance compared with traditional biomarkers. These data support the pursuit of larger prospective studies to evaluate the predictive performance of cfDNA and CXCL10 prior to lung allograft failure.
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Affiliation(s)
- Joshua Y C Yang
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- KIT Bio, 2000 University Avenue, Palo Alto, CA 94303, USA.
| | - Stijn E Verleden
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Arya Zarinsefat
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Bart M Vanaudenaerde
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Robin Vos
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Geert M Verleden
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Reuben D Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Tara K Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Juliane M Liberto
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Izabella Damm
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Drew Watson
- KIT Bio, 2000 University Avenue, Palo Alto, CA 94303, USA.
| | - Minnie M Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- KIT Bio, 2000 University Avenue, Palo Alto, CA 94303, USA.
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38
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The detection of donor-derived cell-free DNA may serve as a biomarker for the early detection of chronic lung allograft dysfunction. EBioMedicine 2019; 40:13-14. [PMID: 30737085 PMCID: PMC6413678 DOI: 10.1016/j.ebiom.2019.01.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/22/2019] [Indexed: 01/08/2023] Open
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39
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Characteristics, properties, and potential applications of circulating cell-free dna in clinical diagnostics: a focus on transplantation. J Immunol Methods 2018; 463:27-38. [DOI: 10.1016/j.jim.2018.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022]
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40
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Young KA, Dilling DF. The Future of Lung Transplantation. Chest 2018; 155:465-473. [PMID: 30171860 DOI: 10.1016/j.chest.2018.08.1036] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/10/2018] [Accepted: 08/15/2018] [Indexed: 12/17/2022] Open
Abstract
The field of lung transplant has made significant advances over the last several decades. Despite these advances, morbidity and mortality remain high when compared with other solid organ transplants. As the field moves forward, the speed by which progress can be made will in part be determined by our ability to overcome several stumbling blocks, including donor shortage, proper selection of candidates, primary graft dysfunction, and chronic lung allograft dysfunction. The advances and developments surrounding these factors will have a significant impact on shaping the field within the coming years. In this review, we look at the current climate (ripe for expanding the donor pool), new technology (ex vivo lung perfusion and bioengineered lungs), cutting-edge innovation (novel biomarkers and new ways to treat infected donors), and evidence-based medicine to discuss current trends and predict future developments for what we hope is a bright future for the field of lung transplantation.
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Affiliation(s)
- Katherine A Young
- Department of Pulmonary and Critical Care, Loyola University Medical Center, Maywood, IL
| | - Daniel F Dilling
- Department of Pulmonary and Critical Care, Loyola University Medical Center, Maywood, IL.
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41
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Yadav DK, Bai X, Yadav RK, Singh A, Li G, Ma T, Chen W, Liang T. Liquid biopsy in pancreatic cancer: the beginning of a new era. Oncotarget 2018; 9:26900-26933. [PMID: 29928492 PMCID: PMC6003564 DOI: 10.18632/oncotarget.24809] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/25/2018] [Indexed: 12/21/2022] Open
Abstract
With dismal survival rate pancreatic cancer remains one of the most aggressive and devastating malignancy. Predominantly, due to the absence of a dependable methodology for early identification and limited therapeutic options for advanced disease. However, it takes over 17 years to develop pancreatic cancer from initiation of mutation to metastatic cancer; therefore, if diagnosed early; it may increase overall survival dramatically, thus, providing a window of opportunity for early detection. Recently, genomic expression analysis defined 4 subtypes of pancreatic cancer based on mutated genes. Hence, we need simple and standard, minimally invasive test that can monitor those altered genes or their associated pathways in time for the success of precision medicine, and liquid biopsy seems to be one answer to all these questions. Again, liquid biopsy has an ability to pair with genomic tests. Additionally, liquid biopsy based development of circulating tumor cells derived xenografts, 3D organoids system, real-time monitoring of genetic mutations by circulating tumor DNA and exosome as the targeted drug delivery vehicle holds lots of potential for the treatment and cure of pancreatic cancer. At present, diagnosis of pancreatic cancer is frantically done on the premise of CA19-9 and radiological features only, which doesn't give a picture of genetic mutations and epigenetic alteration involved. In this manner, the current diagnostic paradigm for pancreatic cancer diagnosis experiences low diagnostic accuracy. This review article discusses the current state of liquid biopsy in pancreatic cancer as diagnostic and therapeutic tools and future perspectives of research in the light of circulating tumor cells, circulating tumor DNA and exosomes.
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Affiliation(s)
- Dipesh Kumar Yadav
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Rajesh Kumar Yadav
- Department of Pharmacology, Gandaki Medical College, Tribhuwan University, Institute of Medicine, Pokhara 33700, Nepal
| | - Alina Singh
- Department of Surgery, Bir Hospital, National Academy of Medical Science, Kanti Path, Kathmandu 44600, Nepal
| | - Guogang Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Tao Ma
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Wei Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
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Eppensteiner J, Davis RP, Barbas AS, Kwun J, Lee J. Immunothrombotic Activity of Damage-Associated Molecular Patterns and Extracellular Vesicles in Secondary Organ Failure Induced by Trauma and Sterile Insults. Front Immunol 2018; 9:190. [PMID: 29472928 PMCID: PMC5810426 DOI: 10.3389/fimmu.2018.00190] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/22/2018] [Indexed: 12/17/2022] Open
Abstract
Despite significant improvements in injury prevention and emergency response, injury-related death and morbidity continues to increase in the US and worldwide. Patients with trauma, invasive operations, anti-cancer treatment, and organ transplantation produce a host of danger signals and high levels of pro-inflammatory and pro-thrombotic mediators, such as damage-associated molecular patterns (DAMPs) and extracellular vesicles (EVs). DAMPs (e.g., nucleic acids, histone, high-mobility group box 1 protein, and S100) are molecules released from injured, stressed, or activated cells that act as endogenous ligands of innate immune receptors, whereas EVs (e.g., microparticle and exosome) are membranous vesicles budding off from plasma membranes and act as messengers between cells. DAMPs and EVs can stimulate multiple innate immune signaling pathways and coagulation cascades, and uncontrolled DAMP and EV production causes systemic inflammatory and thrombotic complications and secondary organ failure (SOF). Thus, DAMPs and EVs represent potential therapeutic targets and diagnostic biomarkers for SOF. High plasma levels of DAMPs and EVs have been positively correlated with mortality and morbidity of patients or animals with trauma or surgical insults. Blocking or neutralizing DAMPs using antibodies or small molecules has been demonstrated to ameliorate sepsis and SOF in animal models. Furthermore, a membrane immobilized with nucleic acid-binding polymers captured and removed multiple DAMPs and EVs from extracellular fluids, thereby preventing the onset of DAMP- and EV-induced inflammatory and thrombotic complications in vitro and in vivo. In this review, we will summarize the current state of knowledge of DAMPs, EVs, and SOF and discuss potential therapeutics and preventive intervention for organ failure secondary to trauma, surgery, anti-cancer therapy, and allogeneic transplantation.
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Affiliation(s)
| | | | - Andrew S Barbas
- Department of Surgery, Duke University, Durham, NC, United States
| | - Jean Kwun
- Department of Surgery, Duke University, Durham, NC, United States
| | - Jaewoo Lee
- Department of Surgery, Duke University, Durham, NC, United States
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Cell-free DNA characteristics and chimerism analysis in patients after allogeneic cell transplantation. Clin Biochem 2017; 52:137-141. [PMID: 29180242 DOI: 10.1016/j.clinbiochem.2017.11.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 11/20/2022]
Abstract
Cell-free DNA (cfDNA) isolated from plasma or serum has received increasing interest for diagnostic applications in pregnancy, solid tumors and solid organ transplantation. The reported clinical usefulness of cfDNA obtained from plasma or serum in patients undergoing allogeneic cell transplantation (alloHSCT) is scarce. OBJECTIVE To analyze the potential clinical utility of cfDNA chimerism analysis after alloHSCT. DESIGN AND METHODS A total of 196 samples obtained from 110 patients were investigated for their chimeric status both in peripheral blood and plasma using standard PCR for microsatellite amplification. Plasma DNA size distribution was analyzed using capillary electrophoresis. RESULTS The mean cfDNA concentration in the transplanted patients was 469ng/ml (range: 50-10,700ng/ml). The size range of almost 80% of the analyzed fragments was between 80 and 200bp. In 41 out of the 110 patients included in the study a mixture of donor and recipient plasma cfDNA was detected. There was a statistically significant difference in the percentage of plasma mixed chimerism between the patients without transplant related complications and the patients with either GvHD (p<0.05) or relapse (p<0.01). In those patients who showed improvement of GvHD also displayed a decrease in the observable percentage of recipient cfDNA during GvHD treatment. In patients without improvement or even with worsening of acute GvHD, stable or increasing levels of recipient cfDNA were detected. CONCLUSIONS cfDNA in combination with peripheral blood and bone marrow cell chimerism analysis might improve its utility in the clinic in particular in those patients with clinical complications after alloHSCT.
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44
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Macías M, Alegre E, Díaz-Lagares A, Patiño A, Pérez-Gracia JL, Sanmamed M, López-López R, Varo N, González A. Liquid Biopsy: From Basic Research to Clinical Practice. Adv Clin Chem 2017; 83:73-119. [PMID: 29304904 DOI: 10.1016/bs.acc.2017.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the molecular analysis in biological fluids of nucleic acids, subcellular structures, especially exosomes, and, in the context of cancer, circulating tumor cells. In the last 10 years, there has been an intensive research in liquid biopsy to achieve a less invasive and more precise personalized medicine. Molecular assessment of these circulating biomarkers can complement or even surrogate tissue biopsy. Because of this research, liquid biopsy has been introduced in clinical practice, especially in oncology, prenatal screening, and transplantation. Here we review the biology, methodological approaches, and clinical applications of the main biomarkers involved in liquid biopsy.
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Affiliation(s)
| | - Estibaliz Alegre
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Angel Díaz-Lagares
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Ana Patiño
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Jose L Pérez-Gracia
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Miguel Sanmamed
- Yale University School of Medicine, New Haven, CT, United States
| | - Rafael López-López
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Nerea Varo
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Alvaro González
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain.
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