1
|
Sikosana ML, Reeve J, Madill-Thomsen KS, Halloran PF. Using Regression Equations to Enhance Interpretation of Histology Lesions of Kidney Transplant Rejection. Transplantation 2024; 108:445-454. [PMID: 37726883 PMCID: PMC10798587 DOI: 10.1097/tp.0000000000004783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 07/07/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND The Banff system for histologic diagnosis of rejection in kidney transplant biopsies uses guidelines to assess designated features-lesions, donor-specific antibody (DSA), and C4d staining. We explored whether using regression equations to interpret the features as well as current guidelines could establish the relative importance of each feature and improve histologic interpretation. METHODS We developed logistic regression equations using the designated features to predict antibody-mediated rejection (AMR/mixed) and T-cell-mediated rejection (TCMR/mixed) in 1679 indication biopsies from the INTERCOMEX study ( ClinicalTrials.gov NCT01299168). Equations were trained on molecular diagnoses independent of the designated features. RESULTS In regression and random forests, the important features predicting molecular rejection were as follows: for AMR, ptc and g, followed by cg; for TCMR, t > i. V-lesions were relatively unimportant. C4d and DSA were also relatively unimportant for predicting AMR: by AUC, the model excluding them (0.853) was nearly as good as the model including them (0.860). Including time posttransplant slightly but significantly improved all models. By AUC, regression predicted molecular AMR and TCMR better than Banff histologic diagnoses. More importantly, in biopsies called "no rejection" by Banff guidelines, regression equations based on histology features identified histologic and molecular rejection-related changes in some biopsies and improved survival predictions. Thus, regression can screen for missed rejection. CONCLUSIONS Using lesion-based regression equations in addition to Banff histology guidelines defines the relative important of histology features for identifying rejection, allows screening for potential missed diagnoses, and permits early estimates of AMR when C4d and DSA are not available.
Collapse
Affiliation(s)
- Majid L.N. Sikosana
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
| | | | - Philip F. Halloran
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
The Molecular Microscope Diagnostic System: Assessment of Rejection and Injury in Heart Transplant Biopsies. Transplantation 2023; 107:27-44. [PMID: 36508644 DOI: 10.1097/tp.0000000000004323] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review describes the development of the Molecular Microscope Diagnostic System (MMDx) for heart transplant endomyocardial biopsies (EMBs). MMDx-Heart uses microarrays to measure biopsy-based gene expression and ensembles of machine learning algorithms to interpret the results and compare each new biopsy to a large reference set of earlier biopsies. MMDx assesses T cell-mediated rejection (TCMR), antibody-mediated rejection (AMR), recent parenchymal injury, and atrophy-fibrosis, continually "learning" from new biopsies. Rejection-associated transcripts mapped in kidney transplants and experimental systems were used to identify TCMR, AMR, and recent injury-induced inflammation. Rejection and injury emerged as gradients of intensity, rather than binary classes. AMR was one-third donor-specific antibody (DSA)-negative, and many EMBs first considered to have no rejection displayed minor AMR-like changes, with increased probability of DSA positivity and subtle inflammation. Rejection-associated transcript-based algorithms now classify EMBs as "Normal," "Minor AMR changes," "AMR," "possible AMR," "TCMR," "possible TCMR," and "recent injury." Additionally, MMDx uses injury-associated transcript sets to assess the degree of parenchymal injury and atrophy-fibrosis in every biopsy and study the effect of rejection on the parenchyma. TCMR directly injures the parenchyma whereas AMR usually induces microcirculation stress but relatively little initial parenchymal damage, although slowly inducing parenchymal atrophy-fibrosis. Function (left ventricular ejection fraction) and short-term risk of failure are strongly determined by parenchymal injury. These discoveries can guide molecular diagnostic applications, either as a central MMDx system or adapted to other platforms. MMDx can also help calibrate noninvasive blood-based biomarkers to avoid unnecessary biopsies and monitor response to therapy.
Collapse
|
4
|
Chronic Active T-Cell Mediated Kidney Rejection as a Clinically Significant Type of Allograft Loss? Diagnostics (Basel) 2022; 12:diagnostics12123220. [PMID: 36553226 PMCID: PMC9777502 DOI: 10.3390/diagnostics12123220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The purpose of this article is to assess the present knowledge about chronic active (CA) T-cell mediated rejection (TCMR) of a kidney. In the research authors review current Banff diagnostic criteria used in kidney rejection, focus on their possible future evolution, and investigate the role of currently available molecular methods that could be implemented into the diagnostic scheme. Research also points out previously and currently available treatment methods applied to CA TCMR and takes into account possible side effects consequent upon the therapy. Moreover, attention is being paid to the CA TCMR coincidence with other kidney rejection types such as antibody-mediated rejection (ABMR) and its influence on the treatment approach. Authors also mark the possibility of non-HLA antibodies coexistence in patients with CA TCMR and describe its possible resonance on kidney allograft function. Nonetheless, it seems that current knowledge about CA TCMR is not sufficient and requires further investigation.
Collapse
|
5
|
Halloran K, Mackova M, Parkes MD, Hirji A, Weinkauf J, Timofte IL, Snell GI, Westall GP, Lischke R, Zajacova A, Havlin J, Hachem R, Kreisel D, Levine D, Kubisa B, Piotrowska M, Juvet S, Keshavjee S, Jaksch P, Klepetko W, Halloran PF. The molecular features of chronic lung allograft dysfunction in lung transplant airway mucosa. J Heart Lung Transplant 2022; 41:1689-1699. [PMID: 36163162 DOI: 10.1016/j.healun.2022.08.014] [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: 04/11/2022] [Revised: 07/22/2022] [Accepted: 08/17/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Many lung transplants fail due to chronic lung allograft dysfunction (CLAD). We recently showed that transbronchial biopsies (TBBs) from CLAD patients manifest severe parenchymal injury and dedifferentiation, distinct from time-dependent changes. The present study explored time-selective and CLAD-selective transcripts in mucosal biopsies from the third bronchial bifurcation (3BMBs), compared to those in TBBs. METHODS We used genome-wide microarray measurements in 324 3BMBs to identify CLAD-selective changes as well as time-dependent changes and develop a CLAD classifier. CLAD-selective transcripts were identified with linear models for microarray data (limma) and were used to build an ensemble of 12 classifiers to predict CLAD. Hazard models and random forests were then used to predict the risk of graft loss using the CLAD classifier, transcript sets associated with rejection, injury, and time. RESULTS T cell-mediated rejection and donor-specific antibody were increased in CLAD 3BMBs but most had no rejection. Like TBBs, 3BMBs showed a time-dependent increase in transcripts expressed in inflammatory cells that was not associated with CLAD or survival. Also like TBBs, the CLAD-selective transcripts in 3BMBs reflected severe parenchymal injury and dedifferentiation, not inflammation or rejection. While 3BMBs and TBBs did not overlap in their top 20 CLAD-selective transcripts, many CLAD-selective transcripts were significantly increased in both for example LOXL1, an enzyme controlling matrix remodeling. In Cox models for one-year survival, the 3BMB CLAD-selective transcripts and CLAD classifier predicted graft loss and correlated with CLAD stage. Many 3BMB CLAD-selective transcripts were also increased by injury in kidney transplants and correlated with decreased kidney survival, including LOXL1. CONCLUSIONS Mucosal and transbronchial biopsies from CLAD patients reveal a diffuse molecular injury and dedifferentiation state that impacts prognosis and correlates with the physiologic disturbances. CLAD state in lung transplants shares features with failing kidney transplants, indicating elements shared by the injury responses of distressed organs.
Collapse
Affiliation(s)
| | | | | | - Alim Hirji
- University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Greg I Snell
- Alfred Hospital Lung Transplant Service, Melbourne, Victoria, Australia
| | - Glen P Westall
- Alfred Hospital Lung Transplant Service, Melbourne, Victoria, Australia
| | | | | | - Jan Havlin
- University Hospital Motol, Prague, Czech Republic
| | - Ramsey Hachem
- Washington University in St Louis, St. Louis, Missouri
| | | | | | | | | | - Stephen Juvet
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | | | | | | |
Collapse
|
6
|
Halloran PF, Madill‐Thomsen KS, Pon S, Sikosana MLN, Böhmig GA, Bromberg J, Einecke G, Eskandary F, Gupta G, Hidalgo LG, Myslak M, Viklicky O, Perkowska‐Ptasinska A. Molecular diagnosis of ABMR with or without donor-specific antibody in kidney transplant biopsies: Differences in timing and intensity but similar mechanisms and outcomes. Am J Transplant 2022; 22:1976-1991. [PMID: 35575435 PMCID: PMC9540308 DOI: 10.1111/ajt.17092] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We studied the clinical, histologic, and molecular features distinguishing DSA-negative from DSA-positive molecularly defined antibody-mediated rejection (mABMR). We analyzed mABMR biopsies with available DSA assessments from the INTERCOMEX study: 148 DSA-negative versus 248 DSA-positive, compared with 864 no rejection (excluding TCMR and Mixed). DSA-positivity varied with mABMR stage: early-stage (EABMR) 56%; fully developed (FABMR) 70%; and late-stage (LABMR) 58%. DSA-negative patients with mABMR were usually sensitized, 60% being HLA antibody-positive. Compared with DSA-positive mABMR, DSA-negative mABMR was more often C4d-negative; earlier by 1.5 years (average 2.4 vs. 3.9 years); and had lower ABMR activity and earlier stage in molecular and histology features. However, the top ABMR-associated transcripts were identical in DSA-negative versus DSA-positive mABMR, for example, NK-associated (e.g., KLRD1 and GZMB) and IFNG-inducible (e.g., PLA1A). Genome-wide class comparison between DSA-negative and DSA-positive mABMR showed no significant differences in transcript expression except those related to lower intensity and earlier time of DSA-negative ABMR. Three-year graft loss in DSA-negative mABMR was the same as DSA-positive mABMR, even after adjusting for ABMR stage. Thus, compared with DSA-positive mABMR, DSA-negative mABMR is on average earlier, less active, and more often C4d-negative but has similar graft loss, and genome-wide analysis suggests that it involves the same mechanisms. SUMMARY SENTENCE: In 398 kidney transplant biopsies with molecular antibody-mediated rejection, the 150 DSA-negative cases are earlier, less intense, and mostly C4d-negative, but use identical molecular mechanisms and have the same risk of graft loss as the 248 DSA-positive cases.
Collapse
Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics CentreEdmontonAlbertaCanada,Department of Medicine, Division of Nephrology and Transplant ImmunologyUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Shane Pon
- Alberta Transplant Applied Genomics CentreEdmontonAlbertaCanada
| | | | - Georg A. Böhmig
- Division of Nephrology and Dialysis, Department of Medicine IIIMedical University of ViennaViennaAustria
| | | | - Gunilla Einecke
- Department of NephrologyHannover Medical SchoolHannoverGermany
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine IIIMedical University of ViennaViennaAustria
| | - Gaurav Gupta
- Division of NephrologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | | | - Marek Myslak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation SPWSZ HospitalPomeranian Medical UniversitySzczecinPoland
| | - Ondrej Viklicky
- Department of Nephrology and Transplant CenterInstitute for Clinical and Experimental MedicinePragueCzech Republic
| | | | | |
Collapse
|
7
|
Halloran PF, Einecke G, Sikosana MLN, Madill-Thomsen K. The Biology and Molecular Basis of Organ Transplant Rejection. Handb Exp Pharmacol 2022; 272:1-26. [PMID: 35091823 DOI: 10.1007/164_2021_557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Allograft rejection is defined as tissue injury in a transplanted allogeneic organ produced by the effector mechanisms of the adaptive alloimmune response. Effector T lymphocytes and IgG alloantibodies cause two different types of rejection that can occur either individually or simultaneously: T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR). In TCMR, cognate effector T cells infiltrate the graft and orchestrate an interstitial inflammatory response in the kidney interstitium in which effector T cells engage antigen-presenting myeloid cells, activating the T cells, antigen-presenting cells, and macrophages. The result is intense expression of IFNG and IFNG-induced molecules, expression of effector T cell molecules and macrophage molecules and checkpoints, and deterioration of parenchymal function. The diagnostic lesions of TCMR follow, i.e. interstitial inflammation, parenchymal deterioration, and intimal arteritis. In ABMR, HLA IgG alloantibodies produced by plasma cells bind to the donor antigens on graft microcirculation, leading to complement activation, margination, and activation of NK cells and neutrophils and monocytes, and endothelial injury, sometimes with intimal arteritis. TCMR becomes infrequent after 5-10 years post-transplant, probably reflecting adaptive mechanisms such as checkpoints, but ABMR can present even decades post-transplant. Some rejection is triggered by inadequate immunosuppression and non-adherence, challenging the clinician to target effective immunosuppression even decades post-transplant.
Collapse
Affiliation(s)
- Philip F Halloran
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, AB, Canada.
| | - Gunilla Einecke
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Majid L N Sikosana
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | | |
Collapse
|
8
|
Ravindranath MH, El Hilali F, Filippone EJ. The Impact of Inflammation on the Immune Responses to Transplantation: Tolerance or Rejection? Front Immunol 2021; 12:667834. [PMID: 34880853 PMCID: PMC8647190 DOI: 10.3389/fimmu.2021.667834] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 10/11/2021] [Indexed: 12/21/2022] Open
Abstract
Transplantation (Tx) remains the optimal therapy for end-stage disease (ESD) of various solid organs. Although alloimmune events remain the leading cause of long-term allograft loss, many patients develop innate and adaptive immune responses leading to graft tolerance. The focus of this review is to provide an overview of selected aspects of the effects of inflammation on this delicate balance following solid organ transplantation. Initially, we discuss the inflammatory mediators detectable in an ESD patient. Then, the specific inflammatory mediators found post-Tx are elucidated. We examine the reciprocal relationship between donor-derived passenger leukocytes (PLs) and those of the recipient, with additional emphasis on extracellular vesicles, specifically exosomes, and we examine their role in determining the balance between tolerance and rejection. The concept of recipient antigen-presenting cell "cross-dressing" by donor exosomes is detailed. Immunological consequences of the changes undergone by cell surface antigens, including HLA molecules in donor and host immune cells activated by proinflammatory cytokines, are examined. Inflammation-mediated donor endothelial cell (EC) activation is discussed along with the effect of donor-recipient EC chimerism. Finally, as an example of a specific inflammatory mediator, a detailed analysis is provided on the dynamic role of Interleukin-6 (IL-6) and its receptor post-Tx, especially given the potential for therapeutic interdiction of this axis with monoclonal antibodies. We aim to provide a holistic as well as a reductionist perspective of the inflammation-impacted immune events that precede and follow Tx. The objective is to differentiate tolerogenic inflammation from that enhancing rejection, for potential therapeutic modifications. (Words 247).
Collapse
Affiliation(s)
- Mepur H. Ravindranath
- Department of Hematology and Oncology, Children’s Hospital, Los Angeles, CA, United States
- Terasaki Foundation Laboratory, Santa Monica, CA, United States
| | | | - Edward J. Filippone
- Division of Nephrology, Department of Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, United States
| |
Collapse
|
9
|
Preka E, Sekar T, Lopez Garcia SC, Shaw O, Kessaris N, Mamode N, Stojanovic J, Sebire NJ, Kim JJ, Marks SD. Outcomes of paediatric kidney transplant recipients using the updated 2013/2017 Banff histopathological classification for antibody-mediated rejection. Pediatr Nephrol 2021; 36:2575-2585. [PMID: 34143297 DOI: 10.1007/s00467-021-05103-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/27/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND After the major changes with regard to acute and chronic ABMR in the Banff classification initiated in 2013, there has been an improvement in diagnosing antibody-mediated rejection (ABMR) in adult studies but no data have been published in the paediatric population. METHODS We assessed 56 paediatric kidney transplant biopsies due to kidney dysfunction in patients with donor-specific antibodies (DSA) in a retrospective single-centre study between January 2006 and March 2012. The results were compared with 2003/2007 Banff classification noting the subsequent 2017 and 2019 modifications do not change the 2013 Banff classification with regard to acute antibody-mediated rejection (apart from the addition of gene transcripts/classifiers that do not affect our analysis). RESULTS Following the 2013 Banff classification, there were seven cases (12.5%) diagnosed with ABMR that would have been misclassified when applying the 2003/2007 classification. Evaluating the histological features of all ABMR-related cases, we report the importance of v- (intimal arteritis) and t- (tubulitis) lesions: absence of v- and t- lesions in the biopsy is related to significantly higher kidney allograft survival (OR 7.3, 95%CI 1.1-48.8, p = 0.03 and OR 5.3, 95%CI 1.2-25.5, p = 0.04 respectively). Moreover, absence of t- lesions was associated with significantly fewer rejection episodes the year after the initial biopsy (OR 5.1, 95%CI 1.4-19.8, p = 0.01). CONCLUSIONS Our study supports that the updated 2013 Banff classification shows superior clinicopathological correlation in identifying ABMR in paediatric kidney transplant recipients. Our results can be extrapolated to the recently updated 2019 Banff classification.
Collapse
Affiliation(s)
- Evgenia Preka
- Department of Paediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
- Southampton University Children's Hospital, Tremona Road, Southampton, SO16 6YD, UK.
| | - Thivya Sekar
- Department of Paediatric Pathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sergio C Lopez Garcia
- Department of Paediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Olivia Shaw
- Viapath Clinical Transplantation Laboratory, Guy's Hospital, London, UK
| | - Nicos Kessaris
- Department of Transplantation, Guy's Hospital, London, UK
| | - Nizam Mamode
- Department of Transplantation, Guy's Hospital, London, UK
| | - Jelena Stojanovic
- Department of Paediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neil J Sebire
- Department of Paediatric Pathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Jon Jin Kim
- Department of Paediatric Nephrology, Nottingham University Hospital, Nottingham, UK
| | - Stephen D Marks
- Department of Paediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London Great Ormond Street Institute of Child Health, London, UK
| |
Collapse
|
10
|
Palazzuoli A, Tecson KM, Ronco C, McCullough PA. Nomenclature for Kidney Function from KDIGO: Shortcomings of Terminology Oversimplification. Cardiorenal Med 2021; 11:119-122. [PMID: 34091445 DOI: 10.1159/000516615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
The recent Kidney Disease: Improving Global Outcomes (KDIGO) consensus conference proposed a universal nomenclature calling for "Kidney Disease" (KD) to be applied to every form of kidney dysfunction, regardless of etiology. We recognize that the estimated glomerular filtration rate and urine albumin:creatinine ratio are limited in their application to the broad spectrum of KD. However, there are additional in vitro and advanced diagnostic options that can help identify the underlying cause of KD and inform about prognosis and management. While the overarching benefit of generalizing KD as a medical problem lies with screening and detection, the downsides attributable to a nonexact diagnosis (i.e., unclear prognosis and management strategy) are considerable. Finally, the terms "acute kidney injury" and "worsening renal function" are currently used interchangeably by nephrologists and cardiologists alike, and a universal adoption of one term will likely be a sizeable challenge. To be of greater benefit, we propose KD be used as a starting point and that the etiology and other epigenetic determinants of illness continue to be evaluated and characterized.
Collapse
Affiliation(s)
- Alberto Palazzuoli
- Department of Internal Medicine, Cardiovascular Diseases Unit, Le Scotte Hospital University of Siena, Siena, Italy
| | - Kristen M Tecson
- Baylor Heart and Vascular Institute, Baylor Scott & White Research Institute, Dallas, Texas, USA.,Department of Internal Medicine, Texas A&M University Health Science Center College of Medicine, Dallas, Texas, USA
| | - Claudio Ronco
- Department of Nephrology, San Bortolo Hospital and International Renal Research Institute of Vicenza (IRRIV), Vicenza, Italy
| | - Peter A McCullough
- Department of Internal Medicine, Texas A&M University Health Science Center College of Medicine, Dallas, Texas, USA
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Abstract
IMPORTANCE Clinical decision and immunosuppression dosing in kidney transplantation rely on transplant biopsy tissue histology even though histology has low specificity, sensitivity, and reproducibility for rejection diagnosis. The inclusion of stable allografts in mechanistic and clinical studies is vital to provide a normal, noninjured comparative group for all interrogative studies on understanding allograft injury. OBJECTIVE To refine the definition of a stable allograft as one that is clinically, histologically, and molecularly quiescent using publicly available transcriptomics data. DESIGN, SETTING, AND PARTICIPANTS In this prognostic study, the National Center for Biotechnology Information Gene Expression Omnibus was used to search for microarray gene expression data from kidney transplant tissues, resulting in 38 studies from January 1, 2017, to December 31, 2018. The diagnostic annotations included 510 acute rejection (AR) samples, 1154 histologically stable (hSTA) samples, and 609 normal samples. Raw fluorescence intensity data were downloaded and preprocessed followed by data set merging and batch correction. MAIN OUTCOMES AND MEASURES The primary measure was area under the receiver operating characteristics curve from a set of feature selected genes and cell types for distinguishing AR from normal kidney tissue. RESULTS Within the 28 data sets, the feature selection procedure identified a set of 6 genes (KLF4, CENPJ, KLF2, PPP1R15A, FOSB, TNFAIP3) (area under the curve [AUC], 0.98) and 5 immune cell types (CD4+ T-cell central memory [Tcm], CD4+ T-cell effector memory [Tem], CD8+ Tem, natural killer [NK] cells, and Type 1 T helper [TH1] cells) (AUC, 0.92) that were combined into 1 composite Instability Score (InstaScore) (AUC, 0.99). The InstaScore was applied to the hSTA samples: 626 of 1154 (54%) were found to be immune quiescent and redefined as histologically and molecularly stable (hSTA/mSTA); 528 of 1154 (46%) were found to have molecular evidence of rejection (hSTA/mAR) and should not have been classified as stable allografts. The validation on an independent cohort of 6 months of protocol biopsy samples in December 2019 showed that hSTA/mAR samples had a significant change in graft function (r = 0.52, P < .001) and graft loss at 5-year follow-up (r = 0.17). A drop by 10 mL/min/1.73m2 in estimated glomerular filtration rate was estimated as a threshold in allograft transitioning from hSTA/mSTA to hSTA/mAR. CONCLUSIONS AND RELEVANCE The results of this prognostic study suggest that the InstaScore could provide an important adjunct for comprehensive and highly quantitative phenotyping of protocol kidney transplant biopsy samples and could be integrated into clinical care for accurate estimation of subsequent patient clinical outcomes.
Collapse
Affiliation(s)
- Dmitry Rychkov
- Division of Multi-Organ Transplantation, Department of Surgery, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
| | - Swastika Sur
- Division of Multi-Organ Transplantation, Department of Surgery, University of California, San Francisco
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco
- Department of Pediatrics, University of California, San Francisco
| | - Minnie M. Sarwal
- Division of Multi-Organ Transplantation, Department of Surgery, University of California, San Francisco
| |
Collapse
|
13
|
Madill-Thomsen K, Perkowska-Ptasińska A, Böhmig GA, Eskandary F, Einecke G, Gupta G, Halloran PF. Discrepancy analysis comparing molecular and histology diagnoses in kidney transplant biopsies. Am J Transplant 2020; 20:1341-1350. [PMID: 31846554 DOI: 10.1111/ajt.15752] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 01/25/2023]
Abstract
Discrepancy analysis comparing two diagnostic platforms offers potential insights into both without assuming either is always correct. Having optimized the Molecular Microscope Diagnostic System (MMDx) in renal transplant biopsies, we studied discrepancies within MMDx (reports and sign-out comments) and between MMDx and histology. Interpathologist discrepancies have been documented previously and were not assessed. Discrepancy cases were classified as "clear" (eg, antibody-mediated rejection [ABMR] vs T cell-mediated rejection [TCMR]), "boundary" (eg, ABMR vs possible ABMR), or "mixed" (eg, Mixed vs ABMR). MMDx report scores showed 99% correlations; sign-out interpretations showed 7% variation between observers, all located around boundaries. Histology disagreed with MMDx in 37% of biopsies, including 315 clear discrepancies, all with implications for therapy. Discrepancies were distributed widely in all histology diagnoses but increased in some scenarios; for example, histology TCMR contained 14% MMDx ABMR and 20% MMDx no rejection. MMDx usually gave unambiguous diagnoses in cases with ambiguous histology, for example, borderline and transplant glomerulopathy. Histology lesions or features associated with more frequent discrepancies (eg, tubulitis, arteritis, and polyomavirus nephropathy) were not associated with increased MMDx uncertainty, indicating that MMDx can clarify biopsies with histologic ambiguity. The patterns of histology-MMDx discrepancies highlight specific histology diagnoses in which MMDx assessment should be considered for guiding therapy.
Collapse
Affiliation(s)
- Katelynn Madill-Thomsen
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gunilla Einecke
- Department of Nephrology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia
| | - Philip F Halloran
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada.,Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
| | | |
Collapse
|
14
|
Trailin A, Hruba P, Viklicky O. Molecular Assessment of Kidney Allografts: Are We Closer to a Daily Routine? Physiol Res 2020; 69:215-226. [PMID: 32199018 DOI: 10.33549/physiolres.934278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Kidney allograft pathology assessment has been traditionally based on clinical and histological criteria. Despite improvements in Banff histological classification, the diagnostics in particular cases is problematic reflecting a complex pathogenesis of graft injuries. With the advent of molecular techniques, polymerase-chain reaction, oligo- and microarray technologies allowed to study molecular phenotypes of graft injuries, especially acute and chronic rejections. Moreover, development of the molecular microscope diagnostic system (MMDx) to assess kidney graft biopsies, represents the first clinical application of a microarray-based method in transplantation. Whether MMDx may replace conventional pathology is the subject of ongoing research, however this platform is particularly useful in complex histological findings and may help clinicians to guide the therapy.
Collapse
Affiliation(s)
- A Trailin
- Department of Nephrology, Transplant Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic.
| | | | | |
Collapse
|
15
|
Sigdel T, Nguyen M, Liberto J, Dobi D, Junger H, Vincenti F, Laszik Z, Sarwal MM. Assessment of 19 Genes and Validation of CRM Gene Panel for Quantitative Transcriptional Analysis of Molecular Rejection and Inflammation in Archival Kidney Transplant Biopsies. Front Med (Lausanne) 2019; 6:213. [PMID: 31632976 PMCID: PMC6781675 DOI: 10.3389/fmed.2019.00213] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023] Open
Abstract
Background: There is an urgent need to develop and implement low cost, high-throughput standardized methods for routine molecular assessment of transplant biopsies. Given the vast archive of formalin-fixed and paraffin-embedded (FFPE) tissue blocks in transplant centers, a reliable protocol for utilizing this tissue bank for clinical validation of target molecules as predictors of graft outcome over time, would be of great value. Methods: We designed and optimized assays to quantify 19 target genes, including previously reported set of tissue common rejection module (tCRM) genes. We interrogated their performance for their clinical utility for detection of graft rejection and inflammation by analyzing gene expression microarrays analysis of 163 renal allograft biopsies, and subsequently validated in 40 independent FFPE archived kidney transplant biopsies at a single center. Results: A QPCR (Fluidigm) and a barcoded oligo-based (NanoString) gene expression platform were compared for evaluation of amplification of gene expression signal for 19 genes from degraded RNA extracted from FFPE biopsy sections by a set protocol. Increased expression of the selected 19 genes, that reflect a combination of specific cellular infiltrates (8/19 genes) and a graft inflammation score (11/19 genes which computes the tCRM score allowed for segregation of kidney transplant biopsies with stable allograft function and normal histology from those with histologically confirmed acute rejection (AR; p = 0.0022, QPCR; p = 0.0036, barcoded assay) and many cases of histological borderline inflammation (BL). Serial biopsy shaves used for gene expression were also processed for in-situ hybridization (ISH) for a subset of genes. ISH confirmed a high degree of correlation of signal amplification and tissue localization. Conclusions: Target gene expression amplification across a custom set of genes can identify AR independent of histology, and quantify inflammation from archival kidney transplant biopsy tissue, providing a new tool for clinical correlation and outcome analysis of kidney allografts, without the need for prospective kidney biopsy biobanking efforts.
Collapse
Affiliation(s)
- Tara Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Mark Nguyen
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Juliane Liberto
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Dejan Dobi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Henrik Junger
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Flavio Vincenti
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Zoltan Laszik
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| |
Collapse
|
16
|
Wang Z, Lyu Z, Pan L, Zeng G, Randhawa P. Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue. BMC Med Genomics 2019; 12:86. [PMID: 31208411 PMCID: PMC6580566 DOI: 10.1186/s12920-019-0538-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND RNA-seq is poised to play a major role in the management of kidney transplant patients. Rigorous definition of housekeeping genes (HKG) is essential for further progress in this field. Using single genes or a limited set HKG is inherently problematic since their expression might be altered by specific diseases in the patients being studied. METHODS To generate a HKG set specific for kidney transplantation, we performed RNA-sequencing from renal allograft biopsies collected in a variety of clinical settings. Various normalization methods were applied to identify transcripts that had a coefficient of variation of expression that was below the 2nd percentile across all samples, and the corresponding genes were designated as housekeeping genes. Comparison with transcriptomic data from the Gene Expression Omnibus (GEO) database, pathway analysis and molecular biological functions were utilized to validate the housekeeping genes set. RESULTS We have developed a bioinformatics solution to this problem by using nine different normalization methods to derive large HKG gene sets from a RNA-seq data set of 47,611 transcripts derived from 30 biopsies. These biopsies were collected in a variety of clinical settings, including normal function, acute rejection, interstitial nephritis, interstitial fibrosis/tubular atrophy and polyomavirus nephropathy. Transcripts with coefficient of variation below the 2nd percentile were designated as HKG, and validated by showing their virtual absence in diseased allograft derived transcriptomic data sets available in the GEO. Pathway analysis indicated a role for these genes in maintenance of cell morphology, pyrimidine metabolism, and intracellular protein signaling. CONCLUSIONS Utilization of these objectively defined HKG data sets will guard against errors resulting from focusing on individual genes like 18S RNA, actin & tubulin, which do not maintain constant expression across the known spectrum of renal allograft pathology.
Collapse
Affiliation(s)
- Zijie Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 China
| | - Zili Lyu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Ling Pan
- Department of Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Gang Zeng
- Department of Pathology, University of Pittsburgh Medical Center, E737 UPMC-Montefiore Hospital, 3459 Fifth Ave, Pittsburgh, PA 15213 USA
| | - Parmjeet Randhawa
- Department of Pathology, University of Pittsburgh Medical Center, E737 UPMC-Montefiore Hospital, 3459 Fifth Ave, Pittsburgh, PA 15213 USA
| |
Collapse
|
17
|
Bestard O, Grinyó J. Refinement of humoral rejection effector mechanisms to identify specific pathogenic histological lesions with different graft outcomes. Am J Transplant 2019; 19:952-953. [PMID: 30411840 DOI: 10.1111/ajt.15171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Oriol Bestard
- Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, IDIBELL, Barcelona University, Barcelona, Spain
| | - Josep Grinyó
- Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, IDIBELL, Barcelona University, Barcelona, Spain
| |
Collapse
|
18
|
Luque S, Lúcia M, Melilli E, Lefaucheur C, Crespo M, Loupy A, Bernal-Casas D, Gomà M, Jarque M, Crespo E, Montero N, Manonelles A, Cruzado JM, Gil-Vernet S, Grinyó JM, Bestard O. Value of monitoring circulating donor-reactive memory B cells to characterize antibody-mediated rejection after kidney transplantation. Am J Transplant 2019; 19:368-380. [PMID: 30085394 DOI: 10.1111/ajt.15055] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/06/2018] [Accepted: 07/29/2018] [Indexed: 01/25/2023]
Abstract
Antibody-mediated rejection (ABMR) is defined by specific histopathological lesions and evidence of circulating donor-specific antibodies (DSA). Although DSA are not always detectable, monitoring donor-reactive memory B cells (mBC) could identify patients at risk of developing ABMR. Peripheral donor-reactive mBC using a novel HLA B cell ELISpot assay, serum DSA, and numbers of different B cell subsets were assessed in 175 consecutive kidney transplants undergoing either for-cause or 6- and 24-month surveillance biopsies for their association with main histological lesions of ABMR and impact on allograft outcome. In 85 incident for-cause biopsies, high frequencies of donor-reactive mBC were detected in all 16 (100%) acute ABMR/DSA+ and most chronic ABMR, with or without DSA (24/30[80%] and 21/29[72.4%], respectively). In a longitudinal cohort of 90 nonsensitized patients, a progressively higher expansion of donor-reactive mBC than de novo DSA was observed at 6 and 24 months (8.8% vs 7.7% and 15.5% vs 11.1%, respectively) and accurately identified patients with ongoing subclinical ABMR (area under the curve = 0.917 and area under the curve = 0.809, respectively). An unsupervised hierarchical cluster analysis revealed a strong association between donor-reactive mBC with main fundamental allograft lesions associated with ABMR and conferred a significant deleterious impact on graft outcome. Monitoring donor-reactive mBC may be useful to further characterize humoral rejection after kidney transplantation.
Collapse
Affiliation(s)
- Sergi Luque
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain
| | - Marc Lúcia
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain
| | - Edoardo Melilli
- Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Carmen Lefaucheur
- Paris Translational Research Center for Organ Transplantation, Institut National de la Santé et de la Recherche Médicale, UMR-S970, Paris, France
| | - Marta Crespo
- Kidney Transplant Unit, Nephrology Department, Hospital del Mar, Barcelona, Spain
| | - Alex Loupy
- Paris Translational Research Center for Organ Transplantation, Institut National de la Santé et de la Recherche Médicale, UMR-S970, Paris, France
| | - David Bernal-Casas
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain.,Department of Genetics, Microbiology and Statistics, Section of Statistics, University of Barcelona, Barcelona, Spain
| | - Montse Gomà
- Pathology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Marta Jarque
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain
| | - Elena Crespo
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain
| | - Núria Montero
- Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Anna Manonelles
- Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Josep M Cruzado
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain.,Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Salvador Gil-Vernet
- Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Josep M Grinyó
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain.,Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Oriol Bestard
- Experimental Nephrology Laboratory, IDIBELL, Barcelona, Spain.,Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| |
Collapse
|
19
|
Barner M, DeKoning J, Kashi Z, Halloran P. Recent Advancements in the Assessment of Renal Transplant Dysfunction with an Emphasis on Microarray Molecular Diagnostics. Clin Lab Med 2018; 38:623-635. [PMID: 30420057 DOI: 10.1016/j.cll.2018.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conventional assessment of renal transplant rejection and injury through use of histology, C4d staining, and HLA antibody testing, has been the standard approach to transplant management. By many measures, these methods of conventional assessment may be considered flawed, particularly with the subjective nature of histologic diagnoses. The Alberta Transplant Applied Genomics Center has developed the Molecular Microscope diagnostic system, which uses microarrays to measure gene expression. These data are analyzed using classifiers (weighted equations) that compare the tested biopsy to a proprietary reference set of biopsies to provide objective measures of the status of the renal transplant.
Collapse
Affiliation(s)
- Meagan Barner
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA
| | - Jenefer DeKoning
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA
| | - Zahra Kashi
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA.
| | - Phillip Halloran
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Alberta Transplant Applied Genomics Center, 250 Heritage Medical Research Centre, Edmonton, Alberta T6G 2S2, Canada; Transcriptome Sciences Inc, Edmonton, Alberta, Canada
| |
Collapse
|
20
|
Sarhan M, von Mässenhausen A, Hugo C, Oberbauer R, Linkermann A. Immunological consequences of kidney cell death. Cell Death Dis 2018; 9:114. [PMID: 29371597 PMCID: PMC5833784 DOI: 10.1038/s41419-017-0057-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Death of renal cells is central to the pathophysiology of acute tubular necrosis, autoimmunity, necrotizing glomerulonephritis, cystic kidney disease, urosepsis, delayed graft function and transplant rejection. By means of regulated necrosis, immunogenic damage-associated molecular patterns (DAMPs) and highly reactive organelles such as lysosomes, peroxisomes and mitochondria are released from the dying cells, thereby causing an overwhelming immunologic response. The rupture of the plasma membrane exhibits the "point of no return" for the immunogenicity of regulated cell death, explaining why apoptosis, a highly organized cell death subroutine with long-lasting plasma membrane integrity, elicits hardly any immune response. Ferroptosis, an iron-dependent necrotic type cell death, results in the release of DAMPs and large amounts of lipid peroxides. In contrast, anti-inflammatory cytokines are actively released from cells that die by necroptosis, limiting the DAMP-induced immune response to a surrounding microenvironment, whereas at the same time, inflammasome-associated caspases drive maturation of intracellularly expressed interleukin-1β (IL-1β). In a distinct setting, additionally interleukin-18 (IL-18) is expressed during pyroptosis, initiated by gasdermin-mediated plasma membrane rupture. As all of these pathways are druggable, we provide an overview of regulated necrosis in kidney diseases with a focus on immunogenicity and potential therapeutic interventions.
Collapse
Affiliation(s)
- Maysa Sarhan
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Anne von Mässenhausen
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Christian Hugo
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany.
| |
Collapse
|
21
|
Halloran PF, Reeve J, Akalin E, Aubert O, Bohmig GA, Brennan D, Bromberg J, Einecke G, Eskandary F, Gosset C, Duong Van Huyen JP, Gupta G, Lefaucheur C, Malone A, Mannon RB, Seron D, Sellares J, Weir M, Loupy A. Real Time Central Assessment of Kidney Transplant Indication Biopsies by Microarrays: The INTERCOMEX Study. Am J Transplant 2017; 17:2851-2862. [PMID: 28449409 DOI: 10.1111/ajt.14329] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 01/25/2023]
Abstract
The authors conducted a prospective trial to assess the feasibility of real time central molecular assessment of kidney transplant biopsy samples from 10 North American or European centers. Biopsy samples taken 1 day to 34 years posttransplantation were stabilized in RNAlater, sent via courier overnight at ambient temperature to the central laboratory, and processed (29 h workflow) using microarrays to assess T cell- and antibody-mediated rejection (TCMR and ABMR, respectively). Of 538 biopsy samples submitted, 519 (96%) were sufficient for microarray analysis (average length, 3 mm). Automated reports were generated without knowledge of histology and HLA antibody, with diagnoses assigned based on Molecular Microscope Diagnostic System (MMDx) classifier algorithms and signed out by one observer. Agreement between MMDx and histology (balanced accuracy) was 77% for TCMR, 77% for ABMR, and 76% for no rejection. A classification tree derived to provide automated sign-outs predicted the observer sign-outs with >90% accuracy. In 451 biopsy samples where feedback was obtained, clinicians indicated that MMDx more frequently agreed with clinical judgment (87%) than did histology (80%) (p = 0.0042). In 81% of feedback forms, clinicians reported that MMDx increased confidence in management compared with conventional assessment alone. The authors conclude that real time central molecular assessment is feasible and offers a useful new dimension in biopsy interpretation. ClinicalTrials.gov NCT#01299168.
Collapse
Affiliation(s)
- P F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada.,Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - J Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
| | - E Akalin
- Montefiore Medical Center, Bronx, NY
| | - O Aubert
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France
| | - G A Bohmig
- Medizinische Universität Wien, Vienna, Austria
| | - D Brennan
- Washington University at St. Louis, St. Louis, MO
| | - J Bromberg
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - G Einecke
- Medizinische Hochschule Hannover, Hannover, Germany
| | - F Eskandary
- Medizinische Universität Wien, Vienna, Austria
| | - C Gosset
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France.,Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - J-P Duong Van Huyen
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France
| | - G Gupta
- Virginia Commonwealth University, Richmond, VA
| | - C Lefaucheur
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France.,Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - A Malone
- Washington University at St. Louis, St. Louis, MO
| | - R B Mannon
- University of Alabama at Birmingham, Birmingham, AL
| | - D Seron
- Hospital Universitari Vall D'Hebron, Barcelona, Spain
| | - J Sellares
- Hospital Universitari Vall D'Hebron, Barcelona, Spain
| | - M Weir
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - A Loupy
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France.,Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| |
Collapse
|
22
|
Wang Z, Yang H, Guo M, Han Z, Tao J, Chen H, Ge Y, Wang K, Tan R, Wei JF, Gu M. Impact of complement component 3/4/5 single nucleotide polymorphisms on renal transplant recipients with antibody-mediated rejection. Oncotarget 2017; 8:94539-94553. [PMID: 29212248 PMCID: PMC5706894 DOI: 10.18632/oncotarget.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/24/2017] [Indexed: 01/29/2023] Open
Abstract
Antibody-mediated rejection (ABMR) is an important risk of allograft dysfunction in kidney transplantation. The complement system is considered to be associated with the generation of alloreative antibodies and donor-specific antibodies. However, the association of complement single nucleotide polymorphisms (SNPs) with ABMR still remained unclear. Blood samples of 199 renal transplant recipients containing 68 with ABMR and 131 with stable graft function were collected, and analyzed by next-generation sequencing with an established gene panel. High quality readout was obtained in 18 C3 SNPs, 9 C4 SNPs and 22 C5 SNPs. Concerning C3 gene polymorphisms, after being adjusted with age, sex and immunosuppressive protocols, rs10411506 and rs2230205 were found to be statistically associated with ABMR in dominant model (rs10411506: OR=2.73, 95% CIs: 1.16, 6.68, P=0.028; rs2230205: OR=2.52, 95% CIs: 1.07, 5.92, P=0.034); rs10411506, rs2230205 and rs2230201 were found different in HET model (rs10411506: OR=3.05, 95% CIs: 1.22, 7.64, P=0.017; rs2230205: OR=2.90, 95% CIs: 1.20, 7.00, P=0.018; rs2230201: OR=2.41, 95% CIs: 1.03, 5.64, P=0.042). The linkage analysis showed relatively high linkage disequilibrium among these SNPs. In addition, no significant correlation was found between C4 SNPs, or C5 SNPs, and the development of ABMR. Our study firstly identified the two SNPs (rs10411506 and rs2230205) in C3 gene were statistically correlated with ABMR in kidney transplantation. These findings may have implications for the diagnosis and prevention of ABMR.
Collapse
Affiliation(s)
- Zijie Wang
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Haiwei Yang
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Miao Guo
- Research Division of Clinical Pharmacology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Zhijian Han
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Jun Tao
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Hao Chen
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Yuqiu Ge
- School of Public Health, Nanjing Medical University, Nanjing 211166, P.R. China
| | - Ke Wang
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Ruoyun Tan
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Min Gu
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| |
Collapse
|
23
|
Garg N, Samaniego MD, Clark D, Djamali A. Defining the phenotype of antibody-mediated rejection in kidney transplantation: Advances in diagnosis of antibody injury. Transplant Rev (Orlando) 2017; 31:257-267. [PMID: 28882367 DOI: 10.1016/j.trre.2017.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/29/2022]
Abstract
The diagnostic criteria for antibody-mediated rejection (ABMR) are constantly evolving in light of the evidence. Inclusion of C4d-negative ABMR has been one of the major advances in the Banff Classification in recent years. Currently Banff 2015 classification requires evidence of donor specific antibodies (DSA), interaction between DSA and the endothelium, and acute tissue injury (in the form of microvasculature injury (MVI); acute thrombotic microangiopathy; or acute tubular injury in the absence of other apparent cause). In this article we review not only the ABMR phenotypes acknowledged in the most recent Banff classification, but also the phenotypes related to novel pathogenic antibodies (non-HLA DSA, antibody isoforms and subclasses, complement-binding functionality) and molecular diagnostic tools (gene transcripts, metabolites, small proteins, cytokines, and donor-derived cell-free DNA). These novel tools are also being considered for the prognosis and monitoring of treatment response. We propose that improved classification of ABMR based on underlying pathogenic mechanisms and outcomes will be an important step in identifying patient-centered therapies to extend graft survival.
Collapse
Affiliation(s)
- Neetika Garg
- Department of Medicine, Nephrology Division, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States.
| | - Milagros D Samaniego
- Department of Medicine, Nephrology Division, University of Michigan, Ann Arbor, MI 48109, United States
| | - Dana Clark
- Department of Medicine, Nephrology Division, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| | - Arjang Djamali
- Department of Medicine, Nephrology Division, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, United States
| |
Collapse
|
24
|
Reeve J, Böhmig GA, Eskandary F, Einecke G, Lefaucheur C, Loupy A, Halloran PF. Assessing rejection-related disease in kidney transplant biopsies based on archetypal analysis of molecular phenotypes. JCI Insight 2017; 2:94197. [PMID: 28614805 DOI: 10.1172/jci.insight.94197] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/05/2017] [Indexed: 01/15/2023] Open
Abstract
Conventional histologic diagnosis of rejection in kidney transplants has limited repeatability due to its inherent requirement for subjective assessment of lesions, in a rule-based system that does not acknowledge diagnostic uncertainty. Molecular phenotyping affords opportunities for increased precision and improved disease classification to address the limitations of conventional histologic diagnostic systems and quantify levels of uncertainty. Microarray data from 1,208 kidney transplant biopsies were collected prospectively from 13 centers. Cross-validated classifier scores predicting the presence of antibody-mediated rejection (ABMR), T cell-mediated rejection (TCMR), and 5 related histologic lesions were generated using supervised machine learning methods. These scores were used as input for archetypal analysis, an unsupervised method similar to cluster analysis, to examine the distribution of molecular phenotypes related to rejection. Six archetypes were generated: no rejection, TCMR, 3 associated with ABMR (early-stage, fully developed, and late-stage), and mixed rejection (TCMR plus early-stage ABMR). Each biopsy was assigned 6 scores, one for each archetype, representing a probabilistic assessment of that biopsy based on its rejection-related molecular properties. Viewed as clusters, the archetypes were similar to existing histologic Banff categories, but there was 32% disagreement, much of it probably reflecting the "noise" in the current histologic assessment system. Graft survival was lowest for fully developed and late-stage ABMR, and it was better predicted by molecular archetype scores than histologic diagnoses. The results provide a system for precision molecular assessment of biopsies and a new standard for recalibrating conventional diagnostic systems.
Collapse
Affiliation(s)
- Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Alberta, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gunilla Einecke
- Department of Nephrology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Carmen Lefaucheur
- Paris Translational Research Center for Organ Transplantation, INSERM, UMR-S970, Paris, France.,Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alexandre Loupy
- Paris Translational Research Center for Organ Transplantation, INSERM, UMR-S970, Paris, France.,Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Alberta, Canada.,Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | |
Collapse
|
25
|
The Role of Humoral Alloreactivity in Liver Transplantation: Lessons Learned and New Perspectives. J Immunol Res 2017; 2017:3234906. [PMID: 28164136 PMCID: PMC5253491 DOI: 10.1155/2017/3234906] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/19/2016] [Indexed: 12/13/2022] Open
Abstract
More than ten years after the initial description of the humoral theory of transplantation by Dr. Paul I. Terasaki, the significance of humoral alloimmunity in liver transplantation has yet to be clearly defined. The liver allograft has an inherent tolerogenic capacity which confers its resistance to cell-mediated as well as antibody-mediated rejection. Nevertheless, the protection against alloimmunity is not complete, and antibody-mediated tissue injury can occur in the liver graft under specific circumstances. In this article the evidence on the clinicopathologic effects of donor-specific alloantibodies in liver transplantation will be examined and interpreted in parallel with lessons learned from renal transplantation. The unique anatomic and immunologic features of the liver will be reviewed to gain new insights into the complex interactions between humoral immune system and the liver allograft.
Collapse
|