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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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2
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Nel I, Münch C, Shamkeeva S, Heinemann ML, Isermann B, Aktas B. The Challenge to Stabilize, Extract and Analyze Urinary Cell-Free DNA (ucfDNA) during Clinical Routine. Diagnostics (Basel) 2023; 13:3670. [PMID: 38132253 PMCID: PMC10743081 DOI: 10.3390/diagnostics13243670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND The "Liquid Biopsy" has become a powerful tool for cancer research during the last decade. Circulating cell-free DNA (cfDNA) that originates from tumors has emerged as one of the most promising analytes. In contrast to plasma-derived cfDNA, only a few studies have investigated urinary cfDNA. One reason might be rapid degradation and hence inadequate concentrations for downstream analysis. In this study, we examined the stability of cfDNA in urine using different methods of preservation under various storage conditions. METHODOLOGY To mimic patient samples, a pool of healthy male and female urine donors was spiked with a synthetic cfDNA reference standard (fragment size 170 bp) containing the T790M mutation in the EGFR gene. Spiked samples were preserved with three different buffers and with no buffer over four different storage periods (0 h; 4 h; 12 h; 24 h) at room temperature vs. 4 °C. The preservatives used were Urinary Analyte Stabilizer (UAS, Novosanis, Wijnegem, Belgium), Urine Conditioning Buffer (UCB, Zymo, Freiburg, Germany) and a self-prepared buffer called "AlloU". CfDNA was extracted using the QIAamp MinElute ccfDNA Mini Kit (Qiagen, Hilden, Germany). CfDNA concentration was measured using the Qubit™ 4 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Droplet digital PCR (ddPCR) was used for detection and quantification of the T790M mutation. RESULTS Almost no spiked cfDNA was recoverable from samples with no preservation buffer and the T790M variant was not detectable in these samples. These findings indicate that cfDNA was degraded below the detection limit by urinary nucleases. Stabilizing buffers showed varying efficiency in preventing this degradation. The most effective stabilizing buffer under all storage conditions was the UAS, enabling adequate recovery of the T790M variant using ddPCR. CONCLUSION From a technical point of view, stabilizing buffers and adequate storage conditions are a prerequisite for translation of urinary cfDNA diagnostics into clinical routine.
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Affiliation(s)
- Ivonne Nel
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Carolin Münch
- Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Saikal Shamkeeva
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University Hospital, 04103 Leipzig, Germany
| | - Mitja L. Heinemann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University Hospital, 04103 Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University Hospital, 04103 Leipzig, Germany
| | - Bahriye Aktas
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
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Ruppert T, Roth A, Kollmeier J, Mairinger T, Frost N. Cell-free DNA extraction from urine of lung cancer patients and healthy individuals: Evaluation of a simple method using sample volume up-scaling. J Clin Lab Anal 2023; 37:e24984. [PMID: 37991151 PMCID: PMC10749489 DOI: 10.1002/jcla.24984] [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: 09/18/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Urine holds promise as a source for cell-free DNA (cfDNA) analysis of cancer genetics due to its nature as a self-collectable biospecimen available in large quantities. However, pre-analytical variables such as preservation of cfDNA or efficiency of up-scaling specimen volume need to be better explored to increase analysis sensitivity. PATIENTS AND METHODS Initially effects of pH levels on cfDNA stability of urine preserved with EDTA were investigated in three healthy probands. Furthermore, the efficiency of urine volume up-scaling was examined using a simple DNA extraction method and cfDNA in urine of 32 individuals. Quantification was performed by PCR detection of three relevant targets used for EGFR and KRAS gene mutational analysis. RESULTS Only samples preserved with EDTA at alkaline pH levels showed cfDNA stability of up to 10 days at room temperature. Moreover, it was found that increasing the volume up to 100 mL was highly efficient. A similar amount of copies was detected in three different gene sites in all specimens indicating both a good availability and a non-random distribution pattern across genes. Since the median cfDNA copy number was 1642 copies/mL, abundance of cfDNA in this type of liquid biopsy is low. CONCLUSION Predictable sensitivities with different urine volumes on the ground of detectable cfDNA in our study population revealed that up-scaling (>5 mL) is mandatory if the mutation allele frequency is less than 1%.
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Affiliation(s)
- Tilman Ruppert
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Andreas Roth
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Jens Kollmeier
- Department of PneumologyHelios Klinikum Emil von BehringBerlinGermany
| | - Thomas Mairinger
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Nikolaj Frost
- Department of PneumologyCharité ‐ Universitätsmedizin BerlinBerlinGermany
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Jordaens S, Arora A, MacDonald KW, Wood C, Hendrickx JO, Zwaenepoel K, Deben C, Tjalma W, Pauwels P, Beyers K, Vankerckhoven V. UAS™-A Urine Preservative for Oncology Applications. Cancers (Basel) 2023; 15:3119. [PMID: 37370729 DOI: 10.3390/cancers15123119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/26/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Liquid biopsy is a revolutionary tool that is gaining momentum in the field of cancer research. As a body fluid, urine can be used in non-invasive diagnostics for various types of cancer. We investigated the performance of UAS™ as a preservative for urinary analytes. Firstly, the need for urine preservation was investigated using urine samples from healthy volunteers. Secondly, the performance of UAS™ was assessed for cell-free DNA (cfDNA) and host cell integrity during storage at room temperature (RT) and after freeze-thaw cycling. Finally, UAS™ was used in a clinical setting on samples from breast and prostate cancer patients. In the absence of a preservative, urinary cfDNA was degraded, and bacterial overgrowth occurred at RT. In urine samples stored in UAS™, no microbial growth was seen, and cfDNA and cellular integrity were maintained for up to 14 days at RT. After freeze-thaw cycling, the preservation of host cell integrity and cfDNA showed significant improvements when using UAS™ compared to unpreserved urine samples. Additionally, UAS™ was found to be compatible with several commercially available isolation methods.
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Affiliation(s)
- Stephanie Jordaens
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
- Novosanis NV, 2110 Wijnegem, Belgium
| | - Amit Arora
- DNA Genotek Inc., Ottawa, ON K2V 1C2, Canada
| | | | | | | | - Karen Zwaenepoel
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Christophe Deben
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Wiebren Tjalma
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
- Multidisciplinary Breast Clinic, Gynecological Oncology Unit, Department of Obstetrics and Gynecology, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | | | - Vanessa Vankerckhoven
- Novosanis NV, 2110 Wijnegem, Belgium
- Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk, Belgium
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Ju C, Xu X, Zhang J, Chen A, Lian Q, Liu F, Liu H, Cai Y, Zou Y, Yang Y, Zhou Y, He J. Application of plasma donor-derived cell free DNA for lung allograft rejection diagnosis in lung transplant recipients. BMC Pulm Med 2023; 23:37. [PMID: 36703125 PMCID: PMC9881379 DOI: 10.1186/s12890-022-02229-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/07/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) has been applied to monitor acute rejection (AR) in kidney and heart transplantation. This study was aimed to investigate the application of dd-cfDNA levels in the diagnosis of AR and chronic lung allograft dysfunction (CLAD) among the lung transplantation recipients (LTRs). METHODS One hundred and seventy LTRs were enrolled at the First Affiliated Hospital of Guangzhou Medical University between 1 June 2015 and 30 March 2021. Patients were divided into 4 groups: stable group, AR group, infection group and CLAD group. The level of dd-cfDNA was analyzed using target region sequencing and the performance characteristics of dd-cfDNA for diagnosis of AR and CLAD were determined, respectively. RESULTS Kruskal-Wallis test showed that there were some significant differences in the level of dd-cfDNA (%) among the 4 groups, with p < 0.001. Among them, the level of dd-cfDNA (%) was highest (median 2.17, IQR [1.40-3.82]) in AR group, and higher in CLAD group (median 1.07, IQR [0.98-1.31]), but lower in infection group (median 0.71, IQR [0.57-1.07]) and lowest in stable group (median 0.71, IQR [0.61-0.84]). AUC-ROC curve analysis showed that the threshold of dd-cfDNA for AR was 1.17%, with sensitivity being 89.19% and specificity being 86.47%, and the optimal threshold of 0.89% was determined of CLAD, with sensitivity being 95.00% and specificity of 76.99%. CONCLUSIONS Plasma dd-cfDNA could be a useful tool for the assessment of lung allograft rejection, including AR and CLAD, and holds promise as a noninvasive biomarker for "allograft injury" in both acute and chronic rejection following lung transplantation.
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Affiliation(s)
- Chunrong Ju
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
| | - Xin Xu
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
| | - Jianheng Zhang
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
| | - Ao Chen
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
| | - Qiaoyan Lian
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
| | - Feng Liu
- AlloDx (Shanghai) Biotech., Co., Ltd, Shanghai, 201100 China
| | - Haitao Liu
- AlloDx (Shanghai) Biotech., Co., Ltd, Shanghai, 201100 China
| | - Yuhang Cai
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
| | - Yanjun Zou
- AlloDx (Shanghai) Biotech., Co., Ltd, Shanghai, 201100 China
| | - Yalan Yang
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
| | - Yang Zhou
- grid.440785.a0000 0001 0743 511XSchool of Life Sciences, Jiangsu University, Zhenjiang, 212013 China
| | - Jianxing He
- grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000 China
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Zhou Y, Wang Y, Addai FP, Li X, Zhang X, Liu H, Yang G, Zeng F, Jiang T, Liu J. Analysis of cell-free fetal DNA in 16,843 pregnant women from a single center in China using targeted sequencing approach. Placenta 2022; 122:18-22. [DOI: 10.1016/j.placenta.2022.03.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022]
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Chen XT, Qiu J, Wu ZX, Zhang H, Chen T, Yang SC, Zhao GD, He Y, Shen X, Luo JQ, Huang Y, Wang CX, Chen LZ, Wu CL, Huang G. OUP accepted manuscript. Clin Chem 2022; 68:814-825. [PMID: 35587713 DOI: 10.1093/clinchem/hvac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/08/2022] [Indexed: 11/14/2022]
Affiliation(s)
- Xu-Tao Chen
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Jiang Qiu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Zi-Xuan Wu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Hui Zhang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Tong Chen
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Shi-Cong Yang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Guo-Dong Zhao
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Yu He
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Xue Shen
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Jin-Quan Luo
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Yang Huang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Chang-Xi Wang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Li-Zhong Chen
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Cheng-Lin Wu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
| | - Gang Huang
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen University, 58# Zhongshan Rd. 2, Guangzhou, Guangdong Province, China, 510080
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Shen J, Guo L, Lei W, Liu S, Yan P, Liu H, Zhou J, Zhou Q, Liu F, Jiang T, Wang H, Wu J, Chen J, Wang R. Urinary donor-derived cell-free DNA as a non-invasive biomarker for BK polyomavirus-associated nephropathy. J Zhejiang Univ Sci B 2021; 22:917-928. [PMID: 34783222 DOI: 10.1631/jzus.b2100131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BK polyomavirus-associated nephropathy (BKPyVAN) is a common cause of allograft failure. However, differentiation between BKPyVAN and type I T cell-mediated rejection (TCMR) is challenging when simian virus 40 (SV40) staining is negative, because of the similarities in histopathology. This study investigated whether donor-derived cell-free DNA (ddcfDNA) can be used to differentiate BKPyVAN. Target region capture sequencing was applied to detect the ddcfDNAs of 12 recipients with stable graft function, 22 with type I TCMR, 21 with proven BKPyVAN, and 5 with possible PyVAN. We found that urinary ddcfDNA levels were upregulated in recipients with graft injury, whereas plasma ddcfDNA levels were comparable for all groups. The median urinary concentrations and fractions of ddcfDNA in proven BKPyVAN recipients were significantly higher than those in type I TCMR recipients (10.4 vs. 6.1 ng/mL, P<0.001 and 68.4% vs. 55.3%, P=0.013, respectively). Urinary ddcfDNA fractions (not concentrations) were higher in the BKPyVAN-pure subgroup than in the BKPyVAN-rejection-like subgroup (81.30% vs. 56.64%, P=0.025). With a cut-off value of 7.81 ng/mL, urinary ddcfDNA concentrations distinguished proven BKPyVAN from type I TCMR (area under the curve (AUC)=0.848, 95% confidence interval (95% CI): 0.734 to 0.963). These findings suggest that urinary ddcfDNA is a non-invasive biomarker which can reliably differentiate BKPyVAN from type I TCMR.
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Affiliation(s)
- Jia Shen
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Luying Guo
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Wenhua Lei
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Shuaihui Liu
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Pengpeng Yan
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Haitao Liu
- AlloDx (Shanghai) Biotech., Co., Ltd., Shanghai 201100, China
| | - Jingyi Zhou
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Qin Zhou
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Feng Liu
- AlloDx (Shanghai) Biotech., Co., Ltd., Shanghai 201100, China
| | - Tingya Jiang
- AlloDx (Shanghai) Biotech., Co., Ltd., Shanghai 201100, China
| | - Huiping Wang
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Jianyong Wu
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Jianghua Chen
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China.,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China.,Zhejiang University Institute of Nephrology, Hangzhou 310003, China
| | - Rending Wang
- Kidney Disease Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China. .,National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China. .,Key Laboratory of Kidney Disease Prevention and Control Technology of Zhejiang Province, Hangzhou 310003, China. .,Zhejiang University Institute of Nephrology, Hangzhou 310003, China. .,Organ Donation and Coordination Office, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
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9
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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] [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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