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Fernando E, Sanathkumar HT, Ramanathan A, Srinivasaprasad ND, Thirumalvalavan K, Annadurai P, Sujith S. Donor-Derived Cell-Free DNA and Active Rejection in Renal Allografts. Indian J Nephrol 2023; 33:247-253. [PMID: 37781552 PMCID: PMC10503575 DOI: 10.4103/ijn.ijn_152_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 10/03/2023] Open
Abstract
Background Renal allograft rejection contributes to significant morbidity and graft loss. In this setting, early detection of rejection is of paramount importance, which currently relies on histopathology. A reliable non-invasive marker to predict rejection would make surveillance and decision-making easier. Donor-derived cell-free DNA (dd-Cf-DNA) has recently been reported as an emerging tool to predict rejection noninvasively. The utility of cell-free DNA in clinical practice has so far not been studied in an Indian setting. As it offers direct clinical application, we have chosen to investigate this biomarker as a tool to predict rejection. Materials and Methods A pilot study with convenient sample size was designed, as this is the first of its kind study so far reported from India. Patients being evaluated with a graft biopsy for graft dysfunction were included. Patients with stable graft function, defined as creatinine within 10% of their best creatinine and no proteinuria for the preceding 12 months, were also included. Ten milliliters of whole blood from each of the recipients was collected in DNA isolation tubes. Two milliliters of donor blood was also obtained in ethylenediaminetetraacetic acid (EDTA) tubes. All recipients also provided a buccal swab. Total cell-free DNA was extracted from 2 ml of recipient plasma using circulating DNA isolation kit. Upon identification of the donor-specific DNA marker for each of the patients from the paired donor sample, presence of the cell-free DNA fraction in the recipient's plasma was detected and quantified. Renal biopsy reports and clinical details were also recorded. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were analyzed. Receiver operating characteristic (ROC) curve analysis was also performed. Results A total of 31 patients were recruited. Twenty patients underwent graft biopsies for graft dysfunction, of which 12 patients had features of active rejection and eight had nonrejection causes of graft dysfunction. Eleven patients with stable graft were included in the study. In our study, dd-Cf-DNA performed best in predicting antibody-mediated rejection (ABMR) and higher grades of T-cell-mediated rejection (TCMR) (1B). It did not detect TCMR 1A accurately. It serves as a good marker to rule out rejection. It gave a NPV of 100% for TCMR 1B or ABMR, 100% for ABMR alone, and 81% for any rejection. dd-Cf-DNA percentages outperform absolute concentrations in their discriminatory ability. Conclusion We have demonstrated the diagnostic accuracy of dd-Cf-DNA in predicting active rejection of the renal allograft. It performs well in ABMR and higher grades of TCMR. This is the first of its kind study reported from India, to the best of our knowledge. This tool serves as a good rule out test for ABMR and higher grades of TCMR. It performs poorly in TCMR 1A.
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Affiliation(s)
- Edwin Fernando
- Department of Nephrology Government Stanley Medical College and Hospital Chennai, Tamil Nadu, India
| | | | - Aravind Ramanathan
- Department of Nephrology Government Stanley Medical College and Hospital Chennai, Tamil Nadu, India
| | - ND Srinivasaprasad
- Department of Nephrology Government Stanley Medical College and Hospital Chennai, Tamil Nadu, India
| | - K Thirumalvalavan
- Department of Nephrology Government Stanley Medical College and Hospital Chennai, Tamil Nadu, India
| | - Poongodi Annadurai
- Department of Nephrology Government Stanley Medical College and Hospital Chennai, Tamil Nadu, India
| | - S Sujith
- Department of Nephrology Government Stanley Medical College and Hospital Chennai, Tamil Nadu, India
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Jimenez-Coll V, Llorente S, Boix F, Alfaro R, Galián JA, Martinez-Banaclocha H, Botella C, Moya-Quiles MR, Muro-Pérez M, Minguela A, Legaz I, Muro M. Monitoring of Serological, Cellular and Genomic Biomarkers in Transplantation, Computational Prediction Models and Role of Cell-Free DNA in Transplant Outcome. Int J Mol Sci 2023; 24:ijms24043908. [PMID: 36835314 PMCID: PMC9963702 DOI: 10.3390/ijms24043908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023] Open
Abstract
The process and evolution of an organ transplant procedure has evolved in terms of the prevention of immunological rejection with the improvement in the determination of immune response genes. These techniques include considering more important genes, more polymorphism detection, more refinement of the response motifs, as well as the analysis of epitopes and eplets, its capacity to fix complement, the PIRCHE algorithm and post-transplant monitoring with promising new biomarkers that surpass the classic serum markers such as creatine and other similar parameters of renal function. Among these new biomarkers, we analyze new serological, urine, cellular, genomic and transcriptomic biomarkers and computational prediction, with particular attention to the analysis of donor free circulating DNA as an optimal marker of kidney damage.
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Affiliation(s)
- Víctor Jimenez-Coll
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Santiago Llorente
- Nephrology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Francisco Boix
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Rafael Alfaro
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - José Antonio Galián
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Helios Martinez-Banaclocha
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Carmen Botella
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - María R. Moya-Quiles
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Manuel Muro-Pérez
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Alfredo Minguela
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain
- Correspondence: (I.L.); (M.M.); Tel.: +34-699986674 (M.M.); Fax: +34-868834307 (M.M.)
| | - Manuel Muro
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
- Correspondence: (I.L.); (M.M.); Tel.: +34-699986674 (M.M.); Fax: +34-868834307 (M.M.)
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Johnson AC, Silva JAF, Kim SC, Larsen CP. Progress in kidney transplantation: The role for systems immunology. Front Med (Lausanne) 2022; 9:1070385. [PMID: 36590970 PMCID: PMC9800623 DOI: 10.3389/fmed.2022.1070385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
The development of systems biology represents an immense breakthrough in our ability to perform translational research and deliver personalized and precision medicine. A multidisciplinary approach in combination with use of novel techniques allows for the extraction and analysis of vast quantities of data even from the volume and source limited samples that can be obtained from human subjects. Continued advances in microfluidics, scalability and affordability of sequencing technologies, and development of data analysis tools have made the application of a multi-omics, or systems, approach more accessible for use outside of specialized centers. The study of alloimmune and protective immune responses after solid organ transplant offers innumerable opportunities for a multi-omics approach, however, transplant immunology labs are only just beginning to adopt the systems methodology. In this review, we focus on advances in biological techniques and how they are improving our understanding of the immune system and its interactions, highlighting potential applications in transplant immunology. First, we describe the techniques that are available, with emphasis on major advances that allow for increased scalability. Then, we review initial applications in the field of transplantation with a focus on topics that are nearing clinical integration. Finally, we examine major barriers to adapting these methods and discuss potential future developments.
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Assessment of dd-cfDNA Levels in Clinically Stable Lung Allograft Recipients Beyond the Initial 2 y Posttransplant. Transplant Direct 2022; 8:e1411. [PMID: 36406896 PMCID: PMC9671749 DOI: 10.1097/txd.0000000000001411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 01/24/2023] Open
Abstract
UNLABELLED Donor-derived cell-free DNA (dd-cfDNA) is a useful biomarker for the diagnosis of acute allograft injury within the first 1 to 2 y after lung transplant, but its utility for diagnosing chronic lung allograft dysfunction (CLAD) has not yet been studied. Understanding baseline dd-cfDNA kinetics beyond the initial 2 y posttransplant is a necessary first step in determining the utility of dd-cfDNA as a CLAD biomarker. We seek to establish baseline dd-cfDNA% levels in clinically stable lung allograft recipients who are >2 y posttransplant. METHODS We performed a prospective, single-center, observational study to identify plasma dd-cfDNA levels in clinically stable lung allograft recipients >2 y posttransplant. RESULTS Fifty-one subjects were enrolled and ≥3 baseline dd-cfDNA measurements were acquired during a median of 252 d. The median baseline percent dd-cfDNA level in our cohort was 0.45% (interquartile range [IQR], 0.26-0.69). There were statistically significant differences in dd-cfDNA based on posttransplant duration (≤5 y posttransplant median 0.41% [IQR, 0.21-0.64] versus >5 y posttransplant median 0.50% [IQR, 0.33-0.76]; P < 0.02). However, the clinical significance of this small change in dd-cfDNA is uncertain because this magnitude of change is within the biologic test variation of 73%. CONCLUSIONS This study is the first to define levels of dd-cfDNA in clinically stable patients who are >2 y post-lung transplant. These findings lay the groundwork for the study of dd-cfDNA as a possible biomarker for CLAD.
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Zhuo DX, Ginder K, Hardin EA. Markers of Immune Function in Heart Transplantation: Implications for Immunosuppression and Screening for Rejection. Curr Heart Fail Rep 2021; 18:33-40. [PMID: 33400150 DOI: 10.1007/s11897-020-00499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE OF REVIEW Recent developments in high-throughput DNA and RNA sequencing technologies have facilitated the development of noninvasive assays to monitor heart transplant rejection. In this review, we summarize existing assays employed for the surveillance of allograft rejection, as well as promising future directions for such tests in the molecular biology field. RECENT FINDINGS The AlloMap genome expression profiling assay remains the only noninvasive test for rejection surveillance and is incorporated into the International Society of Heart and Lung Transplantation guidelines. Other efforts have focused on messenger RNA (mRNA), microRNA (miRNA), and donor-derived cell-free DNA (dd-cfDNA) as potential viable biomarkers. Mitochondrial pathways in allograft necroptosis and inflammation signaling may represent a novel direction for future research endeavors. Although endomyocardial biopsy remains the gold standard, several converging areas of molecular biology could soon yield successful alternative methods of heart transplant rejection monitoring, with the distinct advantage of avoiding procedural complications.
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Affiliation(s)
- David X Zhuo
- Fellow, Advanced Heart Failure and Transplant Cardiology, Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9047, USA
| | - Katie Ginder
- Nurse Practitioner, Advanced Heart Failure, Transplant, LVAD, Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E Ashley Hardin
- Internal Medicine, Advanced Heart Failure and Transplant Cardiology, Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, 5959 Harry Hines Boulevard, Ste #HP.8.110, Dallas, TX, 75390-9047, USA.
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Hall D, Li A, Cooke R. Biophysics of human anatomy and physiology-a Special Issue in honor of Prof. Cristobal dos Remedios on the occasion of his 80 th birthday. Biophys Rev 2020; 12:731-739. [PMID: 32729063 PMCID: PMC7390459 DOI: 10.1007/s12551-020-00745-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
In 2001, Cristobal dos Remedios was made Professor of Anatomy (now emeritus) within Australia’s highest-ranked university (University of Sydney). For the majority of his career, he has examined the biomechanics and biophysics of human muscle contraction. To coincide with the occasion of his 80th birthday, this Special Issue has commissioned a collection of review articles from experts exploring biophysical subjects within the general areas of human anatomy and physiology. After introducing the scope and contents of the Issue, we provide a short scientific biography, placing his scientific achievements within the context of the course of his life’s developments.
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Affiliation(s)
- Damien Hall
- Department of Life Sciences and Applied Chemistry, Nagoya Institute of Technology, Gokiso Showa, Nagoya, Aichi, 466-8555, Japan.
| | - Amy Li
- Department of Pharmacy & Biomedical Sciences, La Trobe University, Bendigo, VIC, 3552, Australia
| | - Roger Cooke
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94158, USA
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