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Chancharoenthana W, Traitanon O, Leelahavanichkul A, Tasanarong A. Molecular immune monitoring in kidney transplant rejection: a state-of-the-art review. Front Immunol 2023; 14:1206929. [PMID: 37675106 PMCID: PMC10477600 DOI: 10.3389/fimmu.2023.1206929] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Although current regimens of immunosuppressive drugs are effective in renal transplant recipients, long-term renal allograft outcomes remain suboptimal. For many years, the diagnosis of renal allograft rejection and of several causes of renal allograft dysfunction, such as chronic subclinical inflammation and infection, was mostly based on renal allograft biopsy, which is not only invasive but also possibly performed too late for proper management. In addition, certain allograft dysfunctions are difficult to differentiate from renal histology due to their similar pathogenesis and immune responses. As such, non-invasive assays and biomarkers may be more beneficial than conventional renal biopsy for enhancing graft survival and optimizing immunosuppressive drug regimens during long-term care. This paper discusses recent biomarker candidates, including donor-derived cell-free DNA, transcriptomics, microRNAs, exosomes (or other extracellular vesicles), urine chemokines, and nucleosomes, that show high potential for clinical use in determining the prognosis of long-term outcomes of kidney transplantation, along with their limitations.
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Affiliation(s)
- Wiwat Chancharoenthana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Tropical Immunology and Translational Research Unit (TITRU), Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Opas Traitanon
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Asada Leelahavanichkul
- Center of Excellence on Translational Research in Inflammation and Immunology (CETRII), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Adis Tasanarong
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
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Halloran PF, Reeve J, Madill-Thomsen KS, Demko Z, Prewett A, Gauthier P, Billings P, Lawrence C, Lowe D, Hidalgo LG. Antibody-mediated Rejection Without Detectable Donor-specific Antibody Releases Donor-derived Cell-free DNA: Results From the Trifecta Study. Transplantation 2023; 107:709-719. [PMID: 36190186 PMCID: PMC9946174 DOI: 10.1097/tp.0000000000004324] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Trifecta (ClinicalTrials.gov #NCT04239703) is a prospective trial defining relationships between donor-derived cell-free DNA (dd-cfDNA), donor-specific antibody (DSA), and molecular findings in kidney transplant biopsies. Previous analyses of double results showed dd-cfDNA was strongly associated with rejection-associated molecules in the biopsy. The present study analyzed the triple results in 280 biopsies, focusing on the question of dd-cfDNA levels in DSA-negative antibody-mediated rejection (AMR). METHODS Molecular Microscope Diagnostic System biopsy testing was performed at Alberta Transplant Applied Genomics Centre, dd-cfDNA testing at Natera, Inc, and central HLA antibody testing at One Lambda Inc. Local DSA and histologic diagnoses were assigned per center standard-of-care. RESULTS DSA was frequently negative in both molecular (56%) and histologic (51%) AMR. DSA-negative AMR had slightly less molecular AMR activity and histologic peritubular capillaritis than DSA-positive AMR. However, all AMRs-DSA-positive or -negative-showed elevated %dd-cfDNA. There was no association between dd-cfDNA and DSA in biopsies without rejection. In AMR, %dd-cfDNA ≥1.0 was more frequent (75%) than DSA positivity (44%). In logistic regression, dd-cfDNA percent (area under the curve [AUC] 0.85) or quantity (AUC 0.86) predicted molecular AMR better than DSA (AUC 0.66). However, the best predictions incorporated both dd-cfDNA and DSA, plus time posttransplant (AUC 0.88). CONCLUSIONS DSA-negative AMR has moderately decreased mean molecular and histologic AMR-associated features compared with DSA-positive AMR, though similarly elevated dd-cfDNA levels. In predicting AMR at the time of indication biopsies in this population, dd-cfDNA is superior to DSA, reflecting the prevalence of DSA-negative AMR, but the optimal predictions incorporated both dd-cfDNA and DSA.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Transcriptome Sciences, Inc, Edmonton, AB, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
| | | | | | | | | | | | | | | | - Luis G. Hidalgo
- Division of Transplantation, Department of Surgery, University of Wisconsin, Madison, WI
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Ventura-Aguiar P, Ramirez-Bajo MJ, Rovira J, Bañón-Maneus E, Hierro N, Lazo M, Cuatrecasas M, Garcia-Criado M, Liang N, Swenerton RK, Cofan F, Cucchiari D, Esforzado N, Montagud-Marrahi E, Oppenheimer F, Piñeiro G, Revuelta I, Torregrosa V, Ahmed E, Soboleva K, Kaur N, Zimmermann BG, Al Haj Baddar N, Demko ZP, Escrig C, Tabriziani H, Gauthier P, Billings PR, Amor AJ, Ferrer J, Campistol JM, Diekmann F. Donor-derived Cell-free DNA Shows High Sensitivity for the Diagnosis of Pancreas Graft Rejection in Simultaneous Pancreas-kidney Transplantation. Transplantation 2022; 106:1690-1697. [PMID: 35289777 PMCID: PMC9311279 DOI: 10.1097/tp.0000000000004088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Pancreas graft status in simultaneous pancreas-kidney transplant (SPKTx) is currently assessed by nonspecific biochemical markers, typically amylase or lipase. Identifying a noninvasive biomarker with good sensitivity in detecting early pancreas graft rejection could improve SPKTx management. METHODS Here, we developed a pilot study to explore donor-derived cell-free DNA (dd-cfDNA) performance in predicting biopsy-proven acute rejection (P-BPAR) of the pancreas graft in a cohort of 36 SPKTx recipients with biopsy-matched plasma samples. dd-cfDNA was measured using the Prospera test (Natera, Inc.) and reported both as a fraction of the total cfDNA (fraction; %) and as concentration in the recipient's plasma (quantity; copies/mL). RESULTS In the absence of P-BPAR, dd-cfDNA was significantly higher in samples collected within the first 45 d after SPKTx compared with those measured afterward (median, 1.00% versus 0.30%; median, 128.2 versus 35.3 cp/mL, respectively with both; P = 0.001). In samples obtained beyond day 45, P-BPAR samples presented a significantly higher dd-cfDNA fraction (0.83 versus 0.30%; P = 0.006) and quantity (81.3 versus 35.3 cp/mL; P = 0.001) than stable samples. Incorporating dd-cfDNA quantity along with dd-cfDNA fraction outperformed dd-cfDNA fraction alone to detect active rejection. Notably, when using a quantity cutoff of 70 cp/mL, dd-cfDNA detected P-BPAR with a sensitivity of 85.7% and a specificity of 93.7%, which was more accurate than current biomarkers (area under curve of 0.89 for dd-cfDNA (cp/ml) compared with 0.74 of lipase and 0.46 for amylase). CONCLUSIONS dd-cfDNA measurement through a simple noninvasive blood test could be incorporated into clinical practice to help inform graft management in SPKTx patients.
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Affiliation(s)
- Pedro Ventura-Aguiar
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Maria Jose Ramirez-Bajo
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Jordi Rovira
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Elisenda Bañón-Maneus
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Natalia Hierro
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Marta Lazo
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Miriam Cuatrecasas
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
| | - M.A. Garcia-Criado
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
| | | | | | - Federic Cofan
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - David Cucchiari
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Nuria Esforzado
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Enrique Montagud-Marrahi
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Federic Oppenheimer
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Gaston Piñeiro
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Ignacio Revuelta
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Vicens Torregrosa
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
| | - Ebad Ahmed
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Karina Soboleva
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Navchetan Kaur
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Bernhard G. Zimmermann
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Nour Al Haj Baddar
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Zachary P. Demko
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Cesar Escrig
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Hossein Tabriziani
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Philippe Gauthier
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Paul R. Billings
- Pathology Department, Center for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Antonio J. Amor
- Radiology Department, Center for Imaging Diagnosis, Hospital Clínic, Barcelona, Spain
| | - Joana Ferrer
- Endocrinology Department, Hospital Clinic, Barcelona, Spain
| | - Josep M. Campistol
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Fritz Diekmann
- Renal Transplant Unit, Nephrology and Kidney Transplant Department, Hospital Clinic, Barcelona, Spain
- Laboratori Experimental de Nefrologia i Trasplantament, Fundacio Clinic - IDIBAPS, Barcelona, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
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Halloran PF, Reeve J, Madill-Thomsen KS, Demko Z, Prewett A, Billings P. The Trifecta Study: Comparing Plasma Levels of Donor-derived Cell-Free DNA with the Molecular Phenotype of Kidney Transplant Biopsies. J Am Soc Nephrol 2022; 33:387-400. [PMID: 35058354 PMCID: PMC8819982 DOI: 10.1681/asn.2021091191] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The relationship between the donor-derived cell-free DNA fraction (dd-cfDNA[%]) in plasma in kidney transplant recipients at time of indication biopsy and gene expression in the biopsied allograft has not been defined. METHODS In the prospective, multicenter Trifecta study, we collected tissue from 300 biopsies from 289 kidney transplant recipients to compare genome-wide gene expression in biopsies with dd-cfDNA(%) in corresponding plasma samples drawn just before biopsy. Rejection was assessed with the microarray-based Molecular Microscope Diagnostic System using automatically assigned rejection archetypes and molecular report sign-outs, and histology assessments that followed Banff guidelines. RESULTS The median time of biopsy post-transplantation was 455 days (5 days to 32 years), with a case mix similar to that of previous studies: 180 (60%) no rejection, 89 (30%) antibody-mediated rejection (ABMR), and 31 (10%) T cell-mediated rejection (TCMR) and mixed. In genome-wide mRNA measurements, all 20 top probe sets correlating with dd-cfDNA(%) were previously annotated for association with ABMR and all types of rejection, either natural killer (NK) cell-expressed (e.g., GNLY, CCL4, TRDC, and S1PR5) or IFN-γ-inducible (e.g., PLA1A, IDO1, CXCL11, and WARS). Among gene set and classifier scores, dd-cfDNA(%) correlated very strongly with ABMR and all types of rejection, reasonably strongly with active TCMR, and weakly with inactive TCMR, kidney injury, and atrophy fibrosis. Active ABMR, mixed, and active TCMR had the highest dd-cfDNA(%), whereas dd-cfDNA(%) was lower in late-stage ABMR and less-active TCMR. By multivariate random forests and logistic regression, molecular rejection variables predicted dd-cfDNA(%) better than histologic variables. CONCLUSIONS The dd-cfDNA(%) at time of indication biopsy strongly correlates with active molecular rejection and has the potential to reduce unnecessary biopsies. CLINICAL TRIAL REGISTRATION NUMBER NCT04239703.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Center, Edmonton, Canada,Department of Medicine, University of Alberta, Edmonton, Canada,Transcriptome Sciences Inc., Edmonton, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Center, Edmonton, Canada
| | - Katelynn S. Madill-Thomsen
- Alberta Transplant Applied Genomics Center, Edmonton, Canada,Transcriptome Sciences Inc., Edmonton, Canada
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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] [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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