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Pettersson L, Westerling S, Talla V, Sendel A, Wennberg L, Olsson R, Hedrum A, Hauzenberger D. Development and performance of a next generation sequencing (NGS) assay for monitoring of dd-cfDNA post solid organ transplantation. Clin Chim Acta 2024; 552:117647. [PMID: 37951377 DOI: 10.1016/j.cca.2023.117647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
The aim of this study was to evaluate the analytical performance of a novel NGS assay, intended for monitoring of donor-derived cell-free DNA (dd-cfDNA), and describe its validity in clinical plasma samples from kidney transplanted patients. Artificial and clinical samples with increasing amounts of patient DNA were evaluated using NGS analysis of indel markers. Monitoring of dd-cfDNA with the NGS assay presented herein demonstrated a sensitivity of ≥0.1% dd-cfDNA and excellent accuracy (R2 0.99) throughout an extensive range of dd-cfDNA (0.1-30%). The precision of the test was determined for two levels (0.1% (LoD) and 1%) of dd-cfDNA. The between run precision (CV%) for the respective level was 16% and 9% and the corresponding result for the within run precision was 19% and 7%. To evaluate performance of the assay in clinical samples, 507 retrospective monitoring samples from 21 patients transplanted either with kidneys from living or deceased donors were analyzed. Monitoring samples were sampled at multiple time points from 24 h up to 90 days post-transplantation. We show that in one patient, increase of dd-cfDNA preceded increase of creatinine caused by acute cellular rejection by several days. In conclusion, the NGS assay displayed a combination of high sensitivity with good accuracy and precision in both artificial and clinical dd-cfDNA samples.
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Affiliation(s)
| | | | - Venkat Talla
- Devyser AB, Instrumentvägen 19, SE-12653 Stockholm, Sweden
| | - Anton Sendel
- Dept. Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Wennberg
- Clinic for Transplantation Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Olsson
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anders Hedrum
- Devyser AB, Instrumentvägen 19, SE-12653 Stockholm, Sweden
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Abstract
Monitoring kidney transplants for rejection conventionally includes serum creatinine, immunosuppressive drug levels, proteinuria, and donor-specific antibody (DSA). Serum creatinine is a late marker of allograft injury, and the predictive ability of DSA regarding risk of rejection is variable. Histological analysis of an allograft biopsy is the standard method for diagnosing rejection but is invasive, inconvenient, and carries risk of complications. There has been a long quest to find a perfect biomarker that noninvasively predicts tissue injury caused by rejection at an early stage, so that diagnosis and treatment could be pursued without delay in order to minimize irreversible damage to the allograft. In this review, we discuss relatively novel research on identifying biomarkers of tissue injury, specifically elaborating on donor-derived cell-free DNA, and its clinical utility.
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Affiliation(s)
- Bhavna Chopra
- Nephrology and Hypertension, Allegheny General Hospital, Pittsburgh, PA 15212, United States
| | - Kalathil K Sureshkumar
- Division of Nephrology, Department of Medicine, Allegheny General Hospital, Allegheny Health Network, Pittsburgh, PA 15212, United State
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Filippone EJ, Gulati R, Farber JL. Noninvasive Assessment of the Alloimmune Response in Kidney Transplantation. Adv Chronic Kidney Dis 2021; 28:548-560. [PMID: 35367023 DOI: 10.1053/j.ackd.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/28/2021] [Accepted: 08/26/2021] [Indexed: 11/11/2022]
Abstract
Transplantation remains the optimal mode of kidney replacement therapy, but unfortunately long-term graft survival after 1 year remains suboptimal. The main mechanism of chronic allograft injury is alloimmune, and current clinical monitoring of kidney transplants includes measuring serum creatinine, proteinuria, and immunosuppressive drug levels. The most important biomarker routinely monitored is human leukocyte antigen (HLA) donor-specific antibodies (DSAs) with the frequency based on underlying immunologic risk. HLA-DSA should be measured if there is graft dysfunction, immunosuppression minimization, or nonadherence. Antibody strength is semiquantitatively estimated as mean fluorescence intensity, with titration studies for equivocal cases and for following response to treatment. Determination of in vitro C1q or C3d positivity or HLA-DSA IgG subclass analysis remains of uncertain significance, but we do not recommend these for routine use. Current evidence does not support routine monitoring of non-HLA antibodies except anti-angiotensin II type 1 receptor antibodies when the phenotype is appropriate. The monitoring of both donor-derived cell-free DNA in blood or gene expression profiling of serum and/or urine may detect subclinical rejection, although mainly as a supplement and not as a replacement for biopsy. The optimal frequency and cost-effectiveness of using these noninvasive assays remain to be determined. We review the available literature and make recommendations.
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Garg N, Mandelbrot DA, Parajuli S, Aziz F, Astor BC, Chandraker A, Djamali A. The clinical value of donor-derived cell-free DNA measurements in kidney transplantation. Transplant Rev (Orlando) 2021; 35:100649. [PMID: 34507254 DOI: 10.1016/j.trre.2021.100649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/21/2022]
Abstract
Early diagnosis is critical to minimizing the damage rejection can do to the transplanted kidney. Donor-derived cell-free DNA (dd-cfDNA) represents non-encapsulated fragmented DNA that is continuously shed into the bloodstream from the allograft undergoing injury, with a half-life of about 30 min. This article reviews the available evidence regarding the diagnostic value of dd-cfDNA in kidney transplantation, as a result of which two assays, Allosure and Prospera, have garnered Medicare approval. We provide information on important scenarios and contexts including antibody-mediated rejection, T-cell mediated rejection, pre-test probability of rejection, timing of the test, repeat transplants, and background cell-free DNA levels to help our understanding of the test characteristics and utility of these assays in clinical practice. Data on multimodality assays including gene expression profiles and serial monitoring of dd-cfDNA in high risk situations are emerging.
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Affiliation(s)
- Neetika Garg
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Didier A Mandelbrot
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Sandesh Parajuli
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Fahad Aziz
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Brad C Astor
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Anil Chandraker
- Transplantation Research Center, Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Arjang Djamali
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Division of Transplant Surgery, University of Wisconsin School of Medicine and Public Health Madison, WI, USA.
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Schütz E, Asendorf T, Beck J, Schauerte V, Mettenmeyer N, Shipkova M, Wieland E, Kabakchiev M, Walson PD, Schwenger V, Oellerich M. Time-Dependent Apparent Increase in dd-cfDNA Percentage in Clinically Stable Patients Between One and Five Years Following Kidney Transplantation. Clin Chem 2021; 66:1290-1299. [PMID: 33001185 DOI: 10.1093/clinchem/hvaa175] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) is reportedly a valuable tool for graft surveillance following kidney transplantation (KTx). Possible changes in dd-cfDNA(%) reference values over time have not been evaluated. For long-term monitoring after KTx, changes in host cfDNA might represent a biasing factor in dd-cfDNA(%) determinations. METHODS Plasma samples were obtained (n = 929) 12-60 months after engraftment in a cross-sectional cohort of 303 clinically stable KTx recipients. Total cfDNA(copies/mL), dd-cfDNA(%), and dd-cfDNA(copies/mL) were determined using droplet-digital PCR. Stability of threshold values in these stable KTx recipients over time was assessed by 80th, 85th, and 90th quantile regression. RESULTS Upper percentiles of total cfDNA showed a significant decline of -1902, -3589, and -4753 cp/mL/log(month) (P = 0.014, <0.001, and 0.017, respectively), resulting in increasing dd-cfDNA(%) percentiles by 0.25, 0.46, and 0.72%/log(month) (P = 0.04, 0.001, and 0.002, respectively), with doubling of the 85th percentile value by 5 years. In contrast, dd-cfDNA(cp/mL) was stable during the observation period (P = 0.52, 0.29, and 0.39). In parallel increasing white blood cell counts and decreasing tacrolimus concentrations over time were observed. After 5 years, the median total cfDNA was still 1.6-fold (P < 0.001) higher in KTx recipients than in healthy controls (n = 135) and 1.4-fold (P < 0.001) higher than patients with other medical conditions (n = 364). CONCLUSIONS The time-dependent decrease of host cfDNA resulted in an apparent increase of dd-cfDNA fraction in stable KTx patients. For long-term surveillance, measurement of absolute dd-cfDNA concentrations appears to be superior to percentages to minimize false positive results.
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Affiliation(s)
| | - Thomas Asendorf
- Department of Medical Statistics, University Medical Center Goettingen, Goettingen, Germany
| | | | - Verena Schauerte
- Central Institute for Clinical Chemistry and Laboratory Medicine, Klinikum Stuttgart, Stuttgart, Germany
| | - Nina Mettenmeyer
- Chronix Biomedical, Goettingen, Germany.,Department of Clinical Pharmacology, University Medical Center Goettingen, Goettingen, Germany
| | - Maria Shipkova
- Central Institute for Clinical Chemistry and Laboratory Medicine, Klinikum Stuttgart, Stuttgart, Germany
| | - Eberhard Wieland
- Central Institute for Clinical Chemistry and Laboratory Medicine, Klinikum Stuttgart, Stuttgart, Germany
| | - Mariana Kabakchiev
- Central Institute for Clinical Chemistry and Laboratory Medicine, Klinikum Stuttgart, Stuttgart, Germany
| | - Philip D Walson
- Department of Clinical Pharmacology, University Medical Center Goettingen, Goettingen, Germany
| | - Vedat Schwenger
- Department of Nephrology, Transplant Center, Klinikum Stuttgart, Stuttgart, Germany
| | - Michael Oellerich
- Department of Clinical Pharmacology, University Medical Center Goettingen, Goettingen, Germany
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Cheng D, Liu F, Xie K, Zeng C, Li X, Ni X, Ge J, Shu L, Zhou Y, Shi H, Liu H, Chen J. Donor-derived cell-free DNA: An independent biomarker in kidney transplant patients with antibody-mediated rejection. Transpl Immunol 2021; 69:101404. [PMID: 33971294 DOI: 10.1016/j.trim.2021.101404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/23/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Antibody-mediated rejection (ABMR) is a major cause of kidney transplant failure which requires donor-specific antibodies (DSA) for a definitive diagnosis. Donor-derived cell-free DNA (ddcfDNA) is an emerging biomarker used to assess kidney allograft injury. However, current data is limited to predict the accuracy of ddcfDNA in ABMR diagnosis. This study was conducted to compare the performance of DSA with plasma ddcfDNA for the diagnosis of ABMR. METHODS In this retrospective single-center observational study, we enrolled 50 kidney transplant recipients who were diagnosed with the suspicion of rejection between June 2018 and May 2019 at the Jinling Hospital. Plasma ddcfDNA was measured by using a novel target region capture sequencing methodology. A total of 37 patients who were tested with DSA and biopsy were divided into four subgroups (ABMR+/DSA+, ABMR+/DSA-, ABMR-/DSA+, ABMR-/DSA-) for the distribution of ddcfDNA (%) by ABMR and DSA. RESULTS The median level of ddcfDNA in biopsy showed that the ABMR group (1.66%, IQR 1.34-3.76%) was significantly higher than the median level (0.63%, IQR 0.43-0.74%) in non-ABMR (p < 0.001). With a ddcfDNA cutoff of 0.96%, the AUC was 0.90 (95%CI, 0.86-0.95), which was associated with a sensitivity of 90.5% (95%CI, 69.6-98.8%) and specificity of 96.6% (95%CI, 82.2-100%), a PPV of 95% (95%CI, 73.4-99.2%) and NPV of 93.3% (95%CI, 78.9-98.1%) were also observed. Among the four subgroups, ddcfDNA had no significant difference in both DSA+ group and DSA-group (p > 0.05). In the diagnosis of ABMR, the specificity, sensitivity, PPV and NPV of DSA were 50%, 74.1%, 41.7%, 80%, respectively. CONCLUSIONS ddcfDNA levels in the blood could highly distinguish (biopsy-supported) ABMR occurrence, irrespective of whether this method is accompanied by DSA or not.
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Affiliation(s)
- Dongrui Cheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Feng Liu
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Kenan Xie
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Caihong Zeng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Xue Li
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Xuefeng Ni
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Jun Ge
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Lipin Shu
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Yang Zhou
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Haifeng Shi
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Haitao Liu
- AlloDx Biotech Co, Ltd, Shanghai, 201100, China
| | - Jinsong Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China.
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Dengu F. Next-generation sequencing methods to detect donor-derived cell-free DNA after transplantation. Transplant Rev (Orlando) 2020; 34:100542. [PMID: 32265093 DOI: 10.1016/j.trre.2020.100542] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/30/2022]
Abstract
Following the initial technical challenge of implanting an organ, maintaining the organ against a vast array of pathologies for years to come, remains a colossal challenge for all clinicians working in transplantation. Drug toxicity, opportunistic infection, primary disease recurrence, and the constant battle against organ rejection are all differentials that are considered when graft dysfunction is observed, promoting a lifetime of laborious surveillance. Cell free DNA (cfDNA) since its discovery in 1948 has made an impactful change in transplantation. A growing body of evidence in transplantation (109 manuscripts from 55 studies) shows the promise of this tool as an early and accurate detection of allograft injury rejection as well the benefit to rule out injury as part of screening and routine monitoring. With next generation sequencing rapidly becoming the standard of care in quantifying DNA, understanding this science in the context of transplantation is critical to ensure studies, outcomes and care is improved.
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Affiliation(s)
- Fungai Dengu
- Nuffield Department of Surgical Sciences, University of Oxford, United Kingdom.
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Hurkmans DP, Verhoeven JGHP, de Leur K, Boer K, Joosse A, Baan CC, von der Thüsen JH, van Schaik RHN, Mathijssen RHJ, van der Veldt AAM, Hesselink DA. Donor-derived cell-free DNA detects kidney transplant rejection during nivolumab treatment. J Immunother Cancer 2019; 7:182. [PMID: 31300068 PMCID: PMC6626432 DOI: 10.1186/s40425-019-0653-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/26/2019] [Indexed: 01/03/2023] Open
Abstract
Background In solid organ transplant (SOT) recipients, transplant rejection during immune checkpoint inhibitor (ICI) treatment for cancer is a clinical problem. Donor-derived cell-free DNA (dd-cfDNA) can be detected in blood and is a sensitive biomarker for diagnosis of acute rejection in SOT recipients. To our best knowledge, this is the first case report of a kidney transplant recipient with advanced cancer treated with ICI who was monitored with dd-cfDNA. Case presentation A 72-year old female with a long-standing renal transplant was diagnosed with advanced melanoma in 2018 and was treated with the anti-PD1 antibody nivolumab. Within 12 days after the first administration of nivolumab, dd-cfDNA ratio increased to 23%, suggesting allograft rejection. Her kidney transplant function deteriorated and acute rejection was confirmed by renal transplant biopsy. As the rejection could not be controlled despite immunosuppressive treatment, a transplant nephrectomy was necessary and haemodialysis was started. Immunological analysis of the renal explant showed infiltration of alloreactive, nivolumab-saturated, PD1+ cytotoxic T cells. After transplant nephrectomy, she experienced nivolumab-related toxicity and rapid disease progression. Conclusion Clinicians prescribing ICIs should be aware that SOT recipients are at risk of transplant rejection as a result of T cell activation. Dd-cfDNA is a sensitive biomarker and should be further studied for early detection of transplant rejection. Immunological analysis of the kidney explant showed marked graft infiltration with alloreactive PD-1+ cytotoxic T cells that were saturated with nivolumab.
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Affiliation(s)
- Daan P Hurkmans
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Jeroen G H P Verhoeven
- Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Rotterdam Transplant Group, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kitty de Leur
- Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Rotterdam Transplant Group, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Karin Boer
- Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Rotterdam Transplant Group, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Arjen Joosse
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carla C Baan
- Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Rotterdam Transplant Group, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dennis A Hesselink
- Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Rotterdam Transplant Group, University Medical Center Rotterdam, Rotterdam, The Netherlands
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