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Morris AB, Bray R, Gebel HM, Cliff Sullivan H. A Primer on Chimerism Analysis: A Straightforward, Thorough Review. Lab Med 2022:6827470. [DOI: 10.1093/labmed/lmac132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Short tandem repeat (STR) analysis to assess chimerism is a critical aspect of routine care particularly in patients facing stem cell transplants but is also relevant in other clinical scenarios. STR analysis provides a means to assess donor and recipient cellular origins in a patient, and, as such, can inform engraftment, rejection, and relapse status in stem cell transplant recipients. In this review of STR testing, the most commonly used method to assess chimerism, its background, procedural details, and clinical utility are discussed.
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Affiliation(s)
- Anna B Morris
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
| | - Robert Bray
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
| | - Howard M Gebel
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
| | - H Cliff Sullivan
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
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2
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Cusick MF, Clark L, Tu T, Goforth J, Zhang X, LaRue B, Gutierrez R, Jindra PT. Performance characteristics of chimerism testing by next generation sequencing. Hum Immunol 2021; 83:61-69. [PMID: 34728094 DOI: 10.1016/j.humimm.2021.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
Chimerism testing provides informative clinical data regarding the status of a biological sample mixture. For years, this testing was achieved by measuring the peaks of informative short tandem repeat (STR) loci using capillary electrophoresis (CE). With the advent of next generation sequencing (NGS) technology, the quantification of the percentage of donor/recipient mixtures is more easily done using sequence reads in large batches of samples run on a single flow cell. In this study, we present data on using a FORENSIC NGS chimerism platform to accurately measure the percentage of donor/recipient mixtures. We were able to detect chimerism to a limit threshold of 1% using both STR and single nucleotide polymorphism (SNP) informative loci. Importantly, a significant correlation was observed between NGS and CE chimerism methods when compared at donor detection ranges from 1% to 10%. Furthermore, 100% accuracy was achieved through proficiency testing over six surveys. Its usefulness was expanded beyond this to help identify suitable donors for solid organ transplant patients using ancestry SNP profiles. In summary, the NGS method provides a sensitive and reliable alternative to traditional CE for chimerism testing of clinical samples.
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Affiliation(s)
- Matthew F Cusick
- Department of Pathology, University of Michigan Medicine, 2800 Plymouth Rd., Building 36, Ann Arbor, MI 48109, USA.
| | - Lauren Clark
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Thuydung Tu
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - John Goforth
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Xiaohai Zhang
- HLA and Immunogenetics, Laboratory, Cedars-Sinai Medical Center, Lab-SSB 197, 8723 Alden D, Los Angeles, CA 90048, USA
| | - Bobby LaRue
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Ryan Gutierrez
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Peter T Jindra
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA.
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3
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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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4
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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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Clinical utility of donor-derived cell-free DNA testing in cardiac transplantation. J Heart Lung Transplant 2021; 40:397-404. [DOI: 10.1016/j.healun.2021.01.1564] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 01/24/2023] Open
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Belkadi A, Thareja G, Dadhania D, Lee JR, Muthukumar T, Snopkowski C, Li C, Halama A, Abdelkader S, Abdulla S, Mahmoud Y, Malek J, Suthanthiran M, Suhre K. Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions. PLoS One 2021; 16:e0249930. [PMID: 33857204 PMCID: PMC8049329 DOI: 10.1371/journal.pone.0249930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/27/2021] [Indexed: 11/19/2022] Open
Abstract
Kidney transplantation is the treatment of choice for patients with end-stage kidney failure, but transplanted allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in kidney transplants is kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from kidney allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human kidney allograft.
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Affiliation(s)
- Aziz Belkadi
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Darshana Dadhania
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - John R. Lee
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Thangamani Muthukumar
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Catherine Snopkowski
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Anna Halama
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Sara Abdelkader
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Silvana Abdulla
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yasmin Mahmoud
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Joel Malek
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Manikkam Suthanthiran
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
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Pattar S, Aleinati M, Iqbal F, Madhu A, Blais S, Wang X, Dallaire F, Wang Y, Isaac D, Fine N, Greenway SC. Identification of cell-free DNA methylation patterns unique to the human left ventricle as a potential indicator of acute cellular rejection. Clin Transplant 2021; 35:e14295. [PMID: 33756005 DOI: 10.1111/ctr.14295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/22/2022]
Abstract
Increased levels of donor-derived cell-free DNA (dd-cfDNA) in recipient plasma have been associated with rejection after transplantation. DNA sequence differences have been used to distinguish between donor and recipient, but epigenetic differences could also potentially identify dd-cfDNA. This pilot study aimed to identify ventricle-specific differentially methylated regions of DNA (DMRs) that could be detected in cfDNA. We identified 24 ventricle-specific DMRs and chose two for further study, one on chromosome 9 and one on chromosome 12. The specificity of both DMRs for the left ventricle was confirmed using genomic DNA from multiple human tissues. Serial matched samples of myocardium (n = 33) and plasma (n = 24) were collected from stable adult heart transplant recipients undergoing routine endomyocardial biopsy for rejection surveillance. Plasma DMR levels increased with biopsy-proven rejection grade for individual patients. Mean cellular apoptosis in biopsy samples increased significantly with rejection severity (2.4%, 4.4% and 10.0% for ACR 0R, 1R, and 2R, respectively) but did not show a consistent relationship with DMR levels. We identified multiple DNA methylation patterns unique to the human ventricle and conclude that epigenetic differences in cfDNA populations represent a promising alternative strategy for the non-invasive detection of rejection.
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Affiliation(s)
- Sabrina Pattar
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mohammad Aleinati
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Fatima Iqbal
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Aiswarya Madhu
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samuel Blais
- Division of Pediatric Cardiology, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Xuemei Wang
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Frederic Dallaire
- Division of Pediatric Cardiology, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Yinong Wang
- Alberta Precision Laboratories and Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Debra Isaac
- Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nowell Fine
- Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Steven C Greenway
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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8
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Deng MC. The evolution of patient-specific precision biomarkers to guide personalized heart-transplant care. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021; 6:51-63. [PMID: 33768160 DOI: 10.1080/23808993.2021.1840273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Introduction In parallel to the clinical maturation of heart transplantation over the last 50 years, rejection testing has been revolutionized within the systems biology paradigm triggered by the Human Genome Project. Areas Covered We have co-developed the first FDA-cleared diagnostic and prognostic leukocyte gene expression profiling biomarker test in transplantation medicine that gained international evidence-based medicine guideline acceptance to rule out moderate/severe acute cellular cardiac allograft rejection without invasive endomyocardial biopsies. This work prompted molecular re-classification of intragraft biology, culminating in the identification of a pattern of intragraft myocyte injury, in addition to acute cellular rejection and antibody-mediated rejection. This insight stimulated research into non-invasive detection of myocardial allograft injury. The addition of a donor-organ specific myocardial injury marker based on donor-derived cell-free DNA further strengthens the non-invasive monitoring concept, combining the clinical use of two complementary non-invasive blood-based measures, host immune activity-related risk of acute rejection as well as cardiac allograft injury. Expert Opinion This novel complementary non-invasive heart transplant monitoring strategy based on leukocyte gene expression profiling and donor-derived cell-free DNA that incorporates longitudinal variability measures provides an exciting novel algorithm of heart transplant allograft monitoring. This algorithm's clinical utility will need to be tested in an appropriately designed randomized clinical trial which is in preparation.
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Affiliation(s)
- Mario C Deng
- Advanced Heart Failure/Mechanical Support/Heart Transplant, David Geffen School of Medicine at UCLA, Ronald Reagan UCLA Medical Center, 100 Medical Plaza Drive, Suite 630, Los Angeles, CA 90095
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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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10
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McClure T, Goh SK, Cox D, Muralidharan V, Dobrovic A, Testro AG. Donor-specific cell-free DNA as a biomarker in liver transplantation: A review. World J Transplant 2020; 10:307-319. [PMID: 33312892 PMCID: PMC7708879 DOI: 10.5500/wjt.v10.i11.307] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/09/2020] [Accepted: 10/30/2020] [Indexed: 02/05/2023] Open
Abstract
Due to advances in modern medicine, liver transplantation has revolutionised the prognosis of many previously incurable liver diseases. This progress has largely been due to advances in immunosuppressant therapy. However, despite the judicious use of immunosuppression, many liver transplant recipients still experience complications such as rejection, which necessitates diagnosis via invasive liver biopsy. There is a clear need for novel, minimally-invasive tests to optimise immunosuppression and improve patient outcomes. An emerging biomarker in this ''precision medicine'' liver transplantation field is that of donor-specific cell free DNA. In this review, we detail the background and methods of detecting this biomarker, examine its utility in liver transplantation and discuss future research directions that may be most impactful.
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Affiliation(s)
- Tess McClure
- Liver Transplant Unit, Austin Health, Heidelberg 3084, VIC, Australia
| | - Su Kah Goh
- Department of Surgery, Austin Health, Heidelberg 3084, VIC, Australia
| | - Daniel Cox
- Department of Surgery, Austin Health, Heidelberg 3084, VIC, Australia
| | | | - Alexander Dobrovic
- Department of Surgery, The University of Melbourne, Heidelberg 3084, VIC, Australia
| | - Adam G Testro
- Liver Transplant Unit, Austin Health, Heidelberg 3084, VIC, Australia
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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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12
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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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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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14
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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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15
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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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16
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Ng HI, Zhu X, Xuan L, Long Y, Mao Y, Shi Y, Sun L, Liang B, Scaglia F, Choy KW, Zhu Z. Analysis of fragment size distribution of cell-free DNA: A potential non-invasive marker to monitor graft damage in living-related liver transplantation for inborn errors of metabolism. Mol Genet Metab 2019; 127:45-50. [PMID: 31027872 DOI: 10.1016/j.ymgme.2019.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 12/31/2022]
Abstract
Graft-derived-cell-free DNA (Gcf-DNA) in plasma is a promising biomarker to monitor graft-rejection after liver transplantation (LTx). However, current methods of measuring Gcf-DNA have several limitations including high cost, long turnaround-time and the need to request donor's genetic information. In this study, eleven patients diagnosed with different inborn errors of metabolism (IEMs) who required living-related LTx were enrolled in order to establish a potentially useful noninvasive method to monitor graft damage. Circulating cell-free DNA (cfDNA) was extracted from plasma specimens serially collected at specific time points (day 0, day 1, day 7, day 14, day 30, day 60) after LTx. The distribution of Gcf-DNA fragment sizes was measured using sequencing read lengths and quantified by using Y-chromosome capture methodology in seven sex-mismatched recipients. In the analysis of fragment size distribution, we observed Gcf-DNA exhibited smaller fragment sizes than the recipient-cfDNA. Based on this phenomenon, two fragment sizes (105-145 bp, 160-170 bp) of the cfDNA pool were extracted to enrich Gcf-DNA. Accordingly, the ratio of short fragments to long fragments (S/L-Frag) in cfDNA was calculated. A high S/L-Frag ratio pointed towards an early trend of graft injury when compared to two routine liver function enzymes (ALT and AST) and Gcf-DNA, and it significantly correlated with ALT (P < 0.0001) and AST (P < 0.0001) during full-blown rejection. In conclusion, we established the Gcf-DNA size profile in patients who have undergone living-related LTx and established a potential biomarker to monitor graft function after LTx.
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Affiliation(s)
- Hoi Ioi Ng
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Xiaofan Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liming Xuan
- Basecare Medical Device Co., Ltd, 218 Xinghu Road, SIP., Suzhou, Jiangsu 215001, China
| | - Yan Long
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Yan Mao
- Basecare Medical Device Co., Ltd, 218 Xinghu Road, SIP., Suzhou, Jiangsu 215001, China
| | - Yu Shi
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Liying Sun
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Bo Liang
- Basecare Medical Device Co., Ltd, 218 Xinghu Road, SIP., Suzhou, Jiangsu 215001, China; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong SAR, China.
| | - Zhijun Zhu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China.
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17
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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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18
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Newell C, Hume S, Greenway SC, Podemski L, Shearer J, Khan A. Plasma-derived cell-free mitochondrial DNA: A novel non-invasive methodology to identify mitochondrial DNA haplogroups in humans. Mol Genet Metab 2018; 125:332-337. [PMID: 30361042 DOI: 10.1016/j.ymgme.2018.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Mitochondrial diseases are a clinically heterogeneous group of diseases caused by mutations in either nuclear or mitochondrial DNA (mtDNA). The diagnosis is challenging and has frequently required a tissue biopsy to obtain a sufficient quantity of mtDNA. Less-invasive sources mtDNA, such as peripheral blood leukocytes, urine sediment, or buccal swab, contain a lower quantity of mtDNA compared to tissue sources which may reduce sensitivity. Cellular apoptosis of tissues and hematopoetic cells releases fragments of DNA and mtDNA into the circulation and these molecules can be extracted from plasma as cell-free DNA (cfDNA). However, entire mtDNA has not been successfully identified from the cell free fraction previously. We hypothesized that the circular nature of mtDNA would prevent its degradation and a higher sensitivity method, such as next generation sequencing, could identify intact cf-mtDNA from human plasma. METHODS Plasma was obtained from patients with mitochondrial disease diagnosed from skeletal muscle biopsy (n = 7) and healthy controls (n = 7) using a specially cfDNA collection tube (Streck Inc.; La Vista, NE). To demonstrate the presence of mtDNA within these samples, we amplified the isolated DNA using custom PCR primers specific to overlapping fragments of mtDNA. cfDNA samples were then sequenced using the Illumina MiSeq sequencing platform. RESULTS We confirmed the presence of mtDNA, demonstrating that the full mitochondrial genome is in fact present within the cell-free plasma fraction of human blood. Sequencing identified the mitochondrial haplogroup matching with the tissue specimen for all patients. CONCLUSION We report the existence of full length mtDNA in cell-free human plasma that was successfully used to perform haplogroup matching. Clinical applications for this work include patient monitoring for heteroplasmy status after mitochondrially-targeted therapies or haplogroup monitoring as a measure of stem cell transplantation.
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Affiliation(s)
- Christopher Newell
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta, Canada.
| | - Stacey Hume
- Department of Medical Genetics, University of Alberta, Alberta, Canada
| | - Steven C Greenway
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Lynn Podemski
- Department of Medical Genetics, University of Alberta, Alberta, Canada
| | - Jane Shearer
- Faculty of Kinesiology, University of Calgary, Alberta, Canada
| | - Aneal Khan
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
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19
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Ng HI, Sun LY, Zhu ZJ. Application of graft-derived cell-free DNA in ornithine transcarbamylase deficiency patient after living donor liver transplantation: Two case reports. Medicine (Baltimore) 2018; 97:e13843. [PMID: 30572553 PMCID: PMC6320025 DOI: 10.1097/md.0000000000013843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RATIONALE Graft-derived-cell-free DNA (Gcf-DNA) in plasma was a promising biomarker to monitor graft-rejection after liver transplantation. However, little is known about the application of Gcf-DNA in living-donor-liver-transplantation (LDLT). PATIENTS CONCERN In this study, 2 patients diagnosed with Ornithine Transcarbamylase Deficiency (OTCD) were enrolled and indicated for LDLT. DIAGNOSES Two patients were genetically diagnosed with OTCD, and they suffered from recurrent and uncontrollable hyper-ammonemia and failed in accepting the normalized OTCD treatments, such as decreasing dietary nitrogen intake and increasing waste-nitrogen excretion. INTERVENTIONS LDLT was performed in the 2 patients uneventfully, and we collected circulating cell-free DNA from plasma in specific postoperative time points (day 1, day 7, day 14, day 30, day 60). Since both of the recipients were sex-mismatch with the donors, we measured Gcf-DNA through the Y-chromosome method and compared it with the routine liver function. OUTCOMES The result showed that Gcf-DNA had the similar discrimination of graft injury trend while compared to routine liver function. The follow-up showed these 2 patients' status is stable. LESSONS Applying Gcf-DNA to monitor graft injury in LDLT is promising, but still long term follow-up and more samples are needed for validation.
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20
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Agbor-Enoh S, Tunc I, De Vlaminck I, Fideli U, Davis A, Cuttin K, Bhatti K, Marishta A, Solomon MA, Jackson A, Graninger G, Harper B, Luikart H, Wylie J, Wang X, Berry G, Marboe C, Khush K, Zhu J, Valantine H. Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation. J Heart Lung Transplant 2017. [PMID: 28624139 DOI: 10.1016/j.healun.2017.05.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Use of new genomic techniques in clinical settings requires that such methods are rigorous and reproducible. Previous studies have shown that quantitation of donor-derived cell-free DNA (%ddcfDNA) by unbiased shotgun sequencing is a sensitive, non-invasive marker of acute rejection after heart transplantation. The primary goal of this study was to assess the reproducibility of %ddcfDNA measurements across technical replicates, manual vs automated platforms, and rejection phenotypes in distinct patient cohorts. METHODS After developing and validating the %ddcfDNA assay, we subjected the method to a rigorous test of its reproducibility. We measured %ddcfDNA in technical replicates performed by 2 independent laboratories and verified the reproducibility of %ddcfDNA patterns of 2 rejection phenotypes: acute cellular rejection and antibody-mediated rejection in distinct patient cohorts. RESULTS We observed strong concordance of technical-replicate %ddcfDNA measurements across 2 independent laboratories (slope = 1.02, R2 > 0.99, p < 10-6), as well as across manual and automated platforms (slope = 0.80, R2 = 0.92, p < 0.001). The %ddcfDNA measurements in distinct heart transplant cohorts had similar baselines and error rates. The %ddcfDNA temporal patterns associated with rejection phenotypes were similar in both patient cohorts; however, the quantity of ddcfDNA was significantly higher in samples with severe vs mild histologic rejection grade (2.73% vs 0.14%, respectively; p < 0.001). CONCLUSIONS The %ddcfDNA assay is precise and reproducible across laboratories and in samples from 2 distinct types of heart transplant rejection. These findings pave the way for larger studies to assess the clinical utility of %ddcfDNA as a marker of acute rejection after heart transplantation.
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Affiliation(s)
- Sean Agbor-Enoh
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Ilker Tunc
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Iwijn De Vlaminck
- Department of Bioengineering, Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Ulgen Fideli
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Andrew Davis
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Karen Cuttin
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Kenneth Bhatti
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Argit Marishta
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Michael A Solomon
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Annette Jackson
- Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Grace Graninger
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Bonnie Harper
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Helen Luikart
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Jennifer Wylie
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Xujing Wang
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Gerald Berry
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Charles Marboe
- Department of Medicine, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Kiran Khush
- Department of Medicine, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Jun Zhu
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Hannah Valantine
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland.
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21
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Schütz E, Fischer A, Beck J, Harden M, Koch M, Wuensch T, Stockmann M, Nashan B, Kollmar O, Matthaei J, Kanzow P, Walson PD, Brockmöller J, Oellerich M. Graft-derived cell-free DNA, a noninvasive early rejection and graft damage marker in liver transplantation: A prospective, observational, multicenter cohort study. PLoS Med 2017; 14:e1002286. [PMID: 28441386 PMCID: PMC5404754 DOI: 10.1371/journal.pmed.1002286] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/17/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Graft-derived cell-free DNA (GcfDNA), which is released into the blood stream by necrotic and apoptotic cells, is a promising noninvasive organ integrity biomarker. In liver transplantation (LTx), neither conventional liver function tests (LTFs) nor immunosuppressive drug monitoring are very effective for rejection monitoring. We therefore hypothesized that the quantitative measurement of donor-derived cell-free DNA (cfDNA) would have independent value for the assessment of graft integrity, including damage from acute rejection. METHODS AND FINDINGS Traditional LFTs were performed and plasma GcfDNA was monitored in 115 adults post-LTx at three German transplant centers as part of a prospective, observational, multicenter cohort trial. GcfDNA percentage (graft cfDNA/total cfDNA) was measured using droplet digital PCR (ddPCR), based on a limited number of predefined single nucleotide polymorphisms, enabling same-day turn-around. The same method was used to quantify blood microchimerism. GcfDNA was increased >50% on day 1 post-LTx, presumably from ischemia/reperfusion damage, but rapidly declined in patients without graft injury within 7 to 10 d to a median <10%, where it remained for the 1-y observation period. Of 115 patients, 107 provided samples that met preestablished criteria. In 31 samples taken from 17 patients during biopsy-proven acute rejection episodes, the percentage of GcfDNA was elevated substantially (median 29.6%, 95% CI 23.6%-41.0%) compared with that in 282 samples from 88 patients during stable periods (median 3.3%, 95% CI 2.9%-3.7%; p < 0.001). Only slightly higher values (median 5.9%, 95% CI 4.4%-10.3%) were found in 68 samples from 17 hepatitis C virus (HCV)-positive, rejection-free patients. LFTs had low overall correlations (r = 0.28-0.62) with GcfDNA and showed greater overlap between patient subgroups, especially between acute rejection and HCV+ patients. Multivariable logistic regression modeling demonstrated that GcfDNA provided additional LFT-independent information on graft integrity. Diagnostic sensitivity and specificity were 90.3% (95% CI 74.2%-98.0%) and 92.9% (95% CI 89.3%-95.6%), respectively, for GcfDNA at a threshold value of 10%. The area under the receiver operator characteristic curve was higher for GcfDNA (97.1%, 95% CI 93.4%-100%) than for same-day conventional LFTs (AST: 95.7%; ALT: 95.2%; γ-GT: 94.5%; bilirubin: 82.6%). An evaluation of microchimerism revealed that the maximum donor DNA in circulating white blood cells was only 0.068%. GcfDNA percentage can be influenced by major changes in host cfDNA (e.g., due to leukopenia or leukocytosis). One limitation of our study is that exact time-matched GcfDNA and LFT samples were not available for all patient visits. CONCLUSIONS In this study, determination of GcfDNA in plasma by ddPCR allowed for earlier and more sensitive discrimination of acute rejection in LTx patients as compared with conventional LFTs. Potential blood microchimerism was quantitatively low and had no significant influence on GcfDNA value. Further research, which should ideally include protocol biopsies, will be needed to establish the practical value of GcfDNA measurements in the management of LTx patients.
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Affiliation(s)
| | - Anna Fischer
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Markus Harden
- Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany
| | - Martina Koch
- Department of Hepatobiliary Surgery and Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tilo Wuensch
- Department of Surgery, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Stockmann
- Department of Surgery, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Björn Nashan
- Department of Hepatobiliary Surgery and Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Otto Kollmar
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Johannes Matthaei
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| | - Philipp Kanzow
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| | - Philip D. Walson
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| | - Jürgen Brockmöller
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| | - Michael Oellerich
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
- * E-mail:
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