1
|
Lu H, Sun X, Yang C, Zheng M, Ni B, Han Z, Tao J, Ju X, Tan R, Shen B, Gu M, Wang Z. Iguratimod ameliorates antibody-mediated rejection after renal transplant by modulating the Th17/Treg paradigm. Int Immunopharmacol 2024; 136:112409. [PMID: 38850789 DOI: 10.1016/j.intimp.2024.112409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Iguratimod (IGU) is widely used in clinical practice due to its stable anti-inflammatory effects. Our previous studies have confirmed that the proportion of Th17/Treg balance in patients taking IGU altered significantly. This study aims to explore the role of IGU in antibody-mediated rejection (ABMR) and its potential mechanisms. METHODS We conducted bioinformatics analysis of sequencing data from the GEO database to analyze the abundance of immune cell infiltration in transplanted kidney tissues. In vivo, IGU was intervened in a mice secondary skin transplantation model and a mice kidney transplantation ABMR model, and histological morphology of the grafts were examined by pathological staining, while relevant indicators were determined through qRT-PCR, immunohistochemistry, and enzyme-linked immunosorbent assay, observed T cell differentiation by flow cytometry, and preliminarily assessed the immunosuppressive effect of IGU. In vitro, we established Th17 and Treg cell induction and stimulation differentiation culture systems and added IGU for intervention to explore its effects on their differentiation. RESULTS Through bioinformatics analysis, we found that Th17 and Treg may play important roles in the occurrence and development of ABMR. In vivo, we found that IGU could effectively reduce the damage caused by ABMR to the grafts, alleviate the infiltration of inflammatory cells in the graft tissues, and reduce the deposition of C4d in the grafts. Moreover, it is also found that IGU regulated the differentiation of Th17 and Treg cells in the spleen and peripheral blood and reduced the expression of IL-17A in the grafts and serum. In addition, same changes were observed in the induction and differentiation culture system of Th17 and Treg cells in vitro after the addition of IGU. CONCLUSION IGU can inhibit the progression of ABMR by regulating the differentiation of Th17 and Treg cells, providing novel insights for optimizing clinical immunosuppressive treatment regimens.
Collapse
Affiliation(s)
- Hongcheng Lu
- Department of Urology, Wuxi People's Hospital Affiliated to Nanjing Medical University, 299 Qingyang Road, Wuxi 214023, Jiangsu, People's Republic of China
| | - Xulin Sun
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, 121# Jiangjiayuan Road, Nanjing, Jiangsu, People's Republic of China
| | - Chengcheng Yang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, 121# Jiangjiayuan Road, Nanjing, Jiangsu, People's Republic of China
| | - Ming Zheng
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, 121# Jiangjiayuan Road, Nanjing, Jiangsu, People's Republic of China
| | - Bin Ni
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, 121# Jiangjiayuan Road, Nanjing, Jiangsu, People's Republic of China
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, Jiangsu, People's Republic of China
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, Jiangsu, People's Republic of China
| | - Xiaobin Ju
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, Jiangsu, People's Republic of China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, Jiangsu, People's Republic of China
| | - Baixin Shen
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, 121# Jiangjiayuan Road, Nanjing, Jiangsu, People's Republic of China.
| | - Min Gu
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, 121# Jiangjiayuan Road, Nanjing, Jiangsu, People's Republic of China; Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, Jiangsu, People's Republic of China.
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, Jiangsu, People's Republic of China.
| |
Collapse
|
2
|
Madill-Thomsen K, Halloran P. Precision diagnostics in transplanted organs using microarray-assessed gene expression: concepts and technical methods of the Molecular Microscope® Diagnostic System (MMDx). Clin Sci (Lond) 2024; 138:663-685. [PMID: 38819301 PMCID: PMC11147747 DOI: 10.1042/cs20220530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
There is a major unmet need for improved accuracy and precision in the assessment of transplant rejection and tissue injury. Diagnoses relying on histologic and visual assessments demonstrate significant variation between expert observers (as represented by low kappa values) and have limited ability to assess many biological processes that produce little histologic changes, for example, acute injury. Consensus rules and guidelines for histologic diagnosis are useful but may have errors. Risks of over- or under-treatment can be serious: many therapies for transplant rejection or primary diseases are expensive and carry risk for significant adverse effects. Improved diagnostic methods could alleviate healthcare costs by reducing treatment errors, increase treatment efficacy, and serve as useful endpoints for clinical trials of new agents that can improve outcomes. Molecular diagnostic assessments using microarrays combined with machine learning algorithms for interpretation have shown promise for increasing diagnostic precision via probabilistic assessments, recalibrating standard of care diagnostic methods, clarifying ambiguous cases, and identifying potentially missed cases of rejection. This review describes the development and application of the Molecular Microscope® Diagnostic System (MMDx), and discusses the history and reasoning behind many common methods, statistical practices, and computational decisions employed to ensure that MMDx scores are as accurate and precise as possible. MMDx provides insights on disease processes and highly reproducible results from a comparatively small amount of tissue and constitutes a general approach that is useful in many areas of medicine, including kidney, heart, lung, and liver transplants, with the possibility of extrapolating lessons for understanding native organ disease states.
Collapse
Affiliation(s)
- Katelynn S. Madill-Thomsen
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
| | - Philip F. Halloran
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
3
|
de Nattes T, Beadle J, Roufosse C. Biopsy-based transcriptomics in the diagnosis of kidney transplant rejection. Curr Opin Nephrol Hypertens 2024; 33:273-282. [PMID: 38411022 PMCID: PMC10990030 DOI: 10.1097/mnh.0000000000000974] [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] [Indexed: 02/28/2024]
Abstract
PURPOSE OF REVIEW The last year has seen considerable progress in translational research exploring the clinical utility of biopsy-based transcriptomics of kidney transplant biopsies to enhance the diagnosis of rejection. This review will summarize recent findings with a focus on different platforms, potential clinical applications, and barriers to clinical adoption. RECENT FINDINGS Recent literature has focussed on using biopsy-based transcriptomics to improve diagnosis of rejection, in particular antibody-mediated rejection. Different techniques of gene expression analysis (reverse transcriptase quantitative PCR, microarrays, probe-based techniques) have been used either on separate samples with ideally preserved RNA, or on left over tissue from routine biopsy processing. Despite remarkable consistency in overall patterns of gene expression, there is no consensus on acceptable indications, or whether biopsy-based transcriptomics adds significant value at reasonable cost to current diagnostic practice. SUMMARY Access to biopsy-based transcriptomics will widen as regulatory approvals for platforms and gene expression models develop. Clinicians need more evidence and guidance to inform decisions on how to use precious biopsy samples for biopsy-based transcriptomics, and how to integrate results with standard histology-based diagnosis.
Collapse
Affiliation(s)
- Tristan de Nattes
- Univ Rouen Normandie, INSERM U1234, CHU Rouen, Department of Nephrology, Rouen, France
| | - Jack Beadle
- Centre for Inflammatory Diseases, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Candice Roufosse
- Centre for Inflammatory Diseases, Department of Immunology and Inflammation, Imperial College London, London, UK
| |
Collapse
|
4
|
Kozakowski N. [Update kidney allograft pathology : A better depiction of microvascular inflammation]. PATHOLOGIE (HEIDELBERG, GERMANY) 2024:10.1007/s00292-024-01328-3. [PMID: 38649466 DOI: 10.1007/s00292-024-01328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND The Banff Foundation produces recommendations for classifying various lesions in renal allografts. Experts gather to update the classification every other year based on new scientific and clinical evidence. OBJECTIVES This article presents the most important changes incorporated into the new recommendations after the last Banff conference. MATERIALS AND METHODS The author of this article personally took part in the Banff conference and the subsequent survey, reported on the activities of a Banff working group (peritubular capillaritis) on-site, and contributed to drafting the recently published meeting report. RESULTS Lesions of antibody-mediated kidney allograft rejection (AMR), especially microvascular inflammation, have been part of the diagnostic algorithm for over 20 years. Experts advocated for a simplified AMR algorithm and mindful inclusion of molecular pathological data in the clinicopathological reflection regarding therapeutic decision. A new, more descriptive diagnostic entity-microvascular inflammation, C4d negative and DSA negative-has been introduced into the AMR category to acknowledge this histological constellation and motivate research into this pathophysiologically and immunologically probably different phenotype. CONCLUSIONS The Banff classification provides a structure for diagnosing kidney transplant pathology. Regular updates serve to adapt to ever-growing knowledge about alloimmunity. Particular challenges are capturing the complexity of various immunological scenarios and ensuring an understandable representation of these in a pathology report.
Collapse
Affiliation(s)
- Nicolas Kozakowski
- Klinisches Institut für Pathologie, Medizinische Universität Wien, Währinger Gürtel 18-20, 1090, Wien, Österreich.
| |
Collapse
|
5
|
Bromberg JS, Bunnapradist S, Samaniego-Picota M, Anand S, Stites E, Gauthier P, Demko Z, Prewett A, Armer-Cabral M, Marshall K, Kaur N, Bloom MS, Tabriziani H, Bhorade S, Cooper M. Elevation of Donor-derived Cell-free DNA Before Biopsy-proven Rejection in Kidney Transplant. Transplantation 2024:00007890-990000000-00724. [PMID: 38595232 DOI: 10.1097/tp.0000000000005007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
BACKGROUND Standard-of-care biomarkers for renal allograft rejection are lagging indicators, signaling existing organ injury. This precludes early intervention, when immunological cascades leading to rejection are most susceptible. Donor-derived cell-free DNA (dd-cfDNA) shows promise as an early indicator of rejection, allowing earlier and possibly more effective treatment. This analysis was designed to assess this promise using real-world dd-cfDNA testing evidence. METHODS This retrospective analysis of the prospective, observational ProActive registry study (NCT04091984) assessed dd-cfDNA and serum creatinine levels before biopsy in 424 patients with ≥1 dd-cfDNA test (n = 1013) in the 6 mo before biopsy. RESULTS Of 4667 enrolled patients, 1631 patients had ≥18 mo of follow-up data, of which 424 had a biopsy and were included in this analysis. Twenty-six biopsies showed antibody-mediated rejection (ABMR), 62 showed T cell-mediated rejection, and 336 showed nonrejection; each from a unique patient. dd-cfDNA fractions were significantly elevated 5 mo before ABMR biopsies, and 2 mo before T cell-mediated rejection biopsies, compared with nonrejection biopsies. In contrast, serum creatinine did not discriminate between rejection and nonrejection in advance, or concurrent with biopsy. Among patients with nonrejection biopsies, estimated glomerular filtration rate was significantly lower in cases with ≥2 increased dd-cfDNA results (≥1%), compared with those with 0 or 1 increased dd-cfDNA result. CONCLUSIONS These data indicate that dd-cfDNA is an early indicator of biopsy-proven rejection, especially ABMR, suggesting a greater role for dd-cfDNA in surveillance to identify patients at high risk of ongoing or future rejection, thus requiring closer monitoring, biopsy, or other management changes.
Collapse
Affiliation(s)
- Jonathan S Bromberg
- Department of Surgery, University of Maryland, School of Medicine, Baltimore, MD
| | | | | | | | - Erik Stites
- School of Medicine, University of Colorado Anschutz Medical Campus, Denver, CO
| | | | | | | | | | | | | | | | | | | | - Matthew Cooper
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI
| |
Collapse
|
6
|
Halloran PF, Madill-Thomsen K, Aliabadi-Zuckermann AZ, Cadeiras M, Crespo-Leiro MG, Depasquale EC, Deng M, Gökler J, Hall S, Jamil A, Kim DH, Kobashigawa J, Macdonald P, Melenovsky V, Patel J, Potena L, Shah K, Stehlik J, Zuckermann A. Redefining the molecular rejection states in 3230 heart transplant biopsies: Relationships to parenchymal injury and graft survival. Am J Transplant 2024:S1600-6135(24)00241-7. [PMID: 38527588 DOI: 10.1016/j.ajt.2024.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
The first-generation Molecular Microscope (MMDx) system for heart transplant endomyocardial biopsies used expression of rejection-associated transcripts (RATs) to diagnose not only T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR) but also acute injury. However, the ideal system should detect rejection without being influenced by injury, to permit analysis of the relationship between rejection and parenchymal injury. To achieve this, we developed a new rejection classification in an expanded cohort of 3230 biopsies: 1641 from INTERHEART (ClinicalTrials.gov NCT02670408), plus 1589 service biopsies added to improve the power of the machine learning algorithms. The new system used 6 rejection classifiers instead of RATs and generated 7 rejection archetypes: No rejection, 48%; Minor, 24%; TCMR1, 2.3%; TCMR2, 2.7%; TCMR/mixed, 2.7%; early-stage ABMR, 3.9%; and fully developed ABMR, 16%. Using rejection classifiers eliminated cross-reactions with acute injury, permitting separate assessment of rejection and injury. TCMR was associated with severe-recent injury and late atrophy-fibrosis and rarely had normal parenchyma. ABMR was better tolerated, seldom producing severe injury, but in later biopsies was often associated with atrophy-fibrosis, indicating long-term risk. Graft survival and left ventricular ejection fraction were reduced not only in hearts with TCMR but also in hearts with severe-recent injury and atrophy-fibrosis, even without rejection.
Collapse
Affiliation(s)
- Philip F Halloran
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | | | | | - Martin Cadeiras
- Ronald Reagan UCLA Medical Center, Los Angeles, California, USA
| | - Marisa G Crespo-Leiro
- Advanced Heart Failure and Heart Transplant Unit, Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | | | - Mario Deng
- Ronald Reagan UCLA Medical Center, Los Angeles, California, USA
| | - Johannes Gökler
- Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria
| | | | - Aayla Jamil
- Baylor Scott & White Health, Dallas, Texas, USA
| | - Daniel H Kim
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Jon Kobashigawa
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Peter Macdonald
- The Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Vojtech Melenovsky
- Department of Cardiology, Institute for Clinical and Experimental Medicine (IKEM), Prague, Czech Republic
| | - Jignesh Patel
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Luciano Potena
- Heart Failure and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Keyur Shah
- Department of Cardiology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Josef Stehlik
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Andreas Zuckermann
- Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
7
|
Halloran PF, Madill-Thomsen K, Mackova M, Aliabadi-Zuckermann AZ, Cadeiras M, Crespo-Leiro MG, Depasquale EC, Deng M, Gökler J, Hall SA, Kim DH, Kobashigawa J, Macdonald P, Potena L, Shah K, Stehlik J, Zuckermann A, Reeve J. Molecular states associated with dysfunction and graft loss in heart transplants. J Heart Lung Transplant 2024; 43:508-518. [PMID: 38042442 DOI: 10.1016/j.healun.2023.11.013] [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: 07/07/2023] [Revised: 10/23/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND We explored the changes in gene expression correlating with dysfunction and graft failure in endomyocardial biopsies. METHODS Genome-wide microarrays (19,462 genes) were used to define mRNA changes correlating with dysfunction (left ventricular ejection fraction [LVEF] ≤ 55) and risk of graft loss within 3 years postbiopsy. LVEF data was available for 1,013 biopsies and survival data for 779 patients (74 losses). Molecular classifiers were built for predicting dysfunction (LVEF ≤ 55) and postbiopsy 3-year survival. RESULTS Dysfunction is correlated with dedifferentiation-decreased expression of normal heart transcripts, for example, solute carriers, along with increased expression of inflammation genes. Many genes with reduced expression in dysfunction were matrix genes such as fibulin 1 and decorin. Gene ontology (GO) categories suggested matrix remodeling and inflammation, not rejection. Genes associated with the risk of failure postbiopsy overlapped dysfunction genes but also included genes affecting microcirculation, for example, arginase 2, which reduces NO production, and endothelin 1. GO terms also reflected increased glycolysis and response to hypoxia, but decreased VEGF and angiogenesis pathways. T cell-mediated rejection was associated with reduced survival and antibody-mediated rejection with relatively good survival, but the main determinants of survival were features of parenchymal injury. Both dysfunction and graft loss were correlated with increased biopsy expression of BNP (gene NPPB). Survival probability classifiers divided hearts into risk quintiles, with actuarial 3-year postbiopsy survival >95% for the highest versus 50% for the lowest. CONCLUSIONS Dysfunction in transplanted hearts reflects dedifferentiation, decreased matrix genes, injury, and inflammation. The risk of short-term loss includes these changes but is also associated with microcirculation abnormalities, glycolysis, and response to hypoxia.
Collapse
Affiliation(s)
- Philip F Halloran
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | | | - Martina Mackova
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | | | | | | | | | - Mario Deng
- Ronald Reagan UCLA Medical Center, Los Angeles, California
| | - Johannes Gökler
- Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria
| | | | - Daniel H Kim
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | | | - Peter Macdonald
- The Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Luciano Potena
- Heart Failure and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Keyur Shah
- Department of Cardiology, Virginia Commonwealth University, Richmond, Virginia
| | - Josef Stehlik
- Department of Medicine, University of Utah, Salt Lake City, Utah
| | - Andreas Zuckermann
- Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria
| | - Jeff Reeve
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
8
|
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
|
9
|
Ahuja HK, Azim S, Maluf D, Mas VR. Immune landscape of the kidney allograft in response to rejection. Clin Sci (Lond) 2023; 137:1823-1838. [PMID: 38126208 DOI: 10.1042/cs20230493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Preventing kidney graft dysfunction and rejection is a critical step in addressing the nationwide organ shortage and improving patient outcomes. While kidney transplants (KT) are performed more frequently, the overall number of patients on the waitlist consistently exceeds organ availability. Despite improved short-term outcomes in KT, comparable progress in long-term allograft survival has not been achieved. Major cause of graft loss at 5 years post-KT is chronic allograft dysfunction (CAD) characterized by interstitial fibrosis and tubular atrophy (IFTA). Accordingly, proactive prevention of CAD requires a comprehensive understanding of the immune mechanisms associated with either further dysfunction or impaired repair. Allograft rejection is primed by innate immune cells and carried out by adaptive immune cells. The rejection process is primarily facilitated by antibody-mediated rejection (ABMR) and T cell-mediated rejection (TCMR). It is essential to better elucidate the actions of individual immune cell subclasses (e.g. B memory, Tregs, Macrophage type 1 and 2) throughout the rejection process, rather than limiting our understanding to broad classes of immune cells. Embracing multi-omic approaches may be the solution in acknowledging these intricacies and decoding these enigmatic pathways. A transition alongside advancing technology will better allow organ biology to find its place in this era of precision and personalized medicine.
Collapse
Affiliation(s)
- Harsimar Kaur Ahuja
- Surgical Sciences Division, Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, U.S.A
| | - Shafquat Azim
- Surgical Sciences Division, Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, U.S.A
| | - Daniel Maluf
- Program of Transplantation, School of Medicine, 29S Greene St, University of Maryland, Baltimore, MD 21201, U.S.A
| | - Valeria R Mas
- Surgical Sciences Division, Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, U.S.A
| |
Collapse
|
10
|
Mehlman Y, Valledor AF, Moeller C, Rubinstein G, Lotan D, Rahman S, Oh KT, Bae D, DeFilippis EM, Lin EF, Lee SH, Raikhelkar JK, Fried J, Theodoropoulos K, Colombo PC, Yuzefpolskaya M, Latif F, Clerkin KJ, Sayer GT, Uriel N. The utilization of molecular microscope in management of heart transplant recipients in the era of noninvasive monitoring. Clin Transplant 2023; 37:e15131. [PMID: 37897211 DOI: 10.1111/ctr.15131] [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: 06/01/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 10/29/2023]
Abstract
INTRODUCTION Monitoring for graft rejection is a fundamental tenet of post-transplant follow-up. In heart transplantation (HT) in particular, rejection has been traditionally assessed with endomyocardial biopsy (EMB). EMB has potential complications and noted limitations, including interobserver variability in interpretation. Additional tests, such as basic cardiac biomarkers, cardiac imaging, gene expression profiling (GEP) scores, donor-derived cell-free DNA (dd-cfDNA) and the novel molecular microscope diagnostic system (MMDx) have become critical tools in rejection surveillance beyond standard EMB. METHODS This paper describes an illustrative case followed by a review of MMDx within the context of other noninvasive screening modalities for rejection. CONCLUSIONS We suggest MMDx be used to assist with early detection of rejection in cases of discordance between EMB and other noninvasive studies.
Collapse
Affiliation(s)
- Yonatan Mehlman
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Andrea Fernendez Valledor
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Cathrine Moeller
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Gal Rubinstein
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Dor Lotan
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Salwa Rahman
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Kyung T Oh
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - David Bae
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Ersilia M DeFilippis
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Edward F Lin
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Sun Hi Lee
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Jayant K Raikhelkar
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Justin Fried
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Kleanthis Theodoropoulos
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Paolo C Colombo
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Melana Yuzefpolskaya
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Farhana Latif
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Kevin J Clerkin
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Gabriel T Sayer
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| | - Nir Uriel
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York, USA
| |
Collapse
|
11
|
Mubarak M, Raza A, Rashid R, Shakeel S. Evolution of human kidney allograft pathology diagnostics through 30 years of the Banff classification process. World J Transplant 2023; 13:221-238. [PMID: 37746037 PMCID: PMC10514746 DOI: 10.5500/wjt.v13.i5.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 09/15/2023] Open
Abstract
The second half of the previous century witnessed a tremendous rise in the number of clinical kidney transplants worldwide. This activity was, however, accompanied by many issues and challenges. An accurate diagnosis and appropriate management of causes of graft dysfunction were and still are, a big challenge. Kidney allograft biopsy played a vital role in addressing the above challenge. However, its interpretation was not standardized for many years until, in 1991, the Banff process was started to fill this void. Thereafter, regular Banff meetings took place every 2 years for the past 30 years. Marked changes have taken place in the interpretation of kidney allograft biopsies, diagnosis, and classification of rejection and other non-rejection pathologies from the original Banff 93 classification. This review attempts to summarize those changes for increasing the awareness and understanding of kidney allograft pathology through the eyes of the Banff process. It will interest the transplant surgeons, physicians, pathologists, and allied professionals associated with the care of kidney transplant patients.
Collapse
Affiliation(s)
- Muhammed Mubarak
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Amber Raza
- Department of Nephrology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Rahma Rashid
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Shaheera Shakeel
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| |
Collapse
|
12
|
Suo L, Murillo MC, Gallay B, Hod-Dvorai R. Discrepancy Analysis between Histology and Molecular Diagnoses in Kidney Allograft Biopsies: A Single-Center Experience. Int J Mol Sci 2023; 24:13817. [PMID: 37762119 PMCID: PMC10531286 DOI: 10.3390/ijms241813817] [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: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Histology diagnosis is essential for the monitoring and management of kidney transplant patients. Nowadays, the accuracy and reproducibility of histology have been criticized when compared with molecular microscopy diagnostic system (MMDx). Our cohort included 95 renal allograft biopsies with both histology and molecular diagnoses. Discrepancies between histology and molecular diagnosis were assessed for each biopsy. Among the 95 kidney allograft biopsies, a total of 6 cases (6%) showed clear (n = 4) or borderline (n = 2) discrepancies between histology and molecular diagnoses. Four out of the six (67%) were cases with pathologically and clinically confirmed active infections that were diagnosed as mild to moderate T-cell-mediated rejection (TCMR) with MMDx. Two cases showed pathological changes that were not sufficient to make a definitive diagnosis of active rejection via histology, while MMDx results showed antibody-mediated rejection (ABMR). In addition, there were six cases with recurrent or de novo glomerular diseases diagnosed only via histology. All other biopsy results were in an agreement. Our results indicate that histology diagnosis of kidney allograft biopsy is superior to molecular diagnosis in the setting of infections and glomerular diseases; however, MMDx can provide helpful information to confirm the diagnosis of active ABMR.
Collapse
Affiliation(s)
- Liye Suo
- Department of Pathology, The State University of New York Upstate Medical University (SUNY Upstate Medical University), Syracuse, NY 13210, USA;
| | - Martha Caicedo Murillo
- Department of Pathology, The State University of New York Upstate Medical University (SUNY Upstate Medical University), Syracuse, NY 13210, USA;
| | - Brian Gallay
- Division of Nephrology and Transplantation, The State University of New York Upstate Medical University (SUNY Upstate Medical University), Syracuse, NY 13210, USA;
| | - Reut Hod-Dvorai
- Department of Pathology, The State University of New York Upstate Medical University (SUNY Upstate Medical University), Syracuse, NY 13210, USA;
| |
Collapse
|
13
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
14
|
Rizvi A, Faiz S, Thakkar PH, Hussain S, Gamilla-Crudo AN, Kueht M, Mujtaba MA. Kidney Allograft Monitoring by Combining Donor-Derived Cell-Free DNA and Molecular Gene Expression: A Clinical Management Perspective. J Pers Med 2023; 13:1205. [PMID: 37623456 PMCID: PMC10455393 DOI: 10.3390/jpm13081205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Donor-derived cell-free DNA (dd-cfDNA) may safely assess kidney allograft rejection. Molecular Microscope (MMDx®) gene expression may offer increased precision to histology. This single-center retrospective study monitored kidney transplant recipients for rejection at specified time intervals by utilizing creatinine (SCr), proteinuria, donor-specific antibodies (DSAs), and dd-cfDNA. A clinically indicated biopsy sample was sent for histopathology and MMDx®. Patients were categorized into rejection (Rej) and non-rejection (NRej) groups, and further grouped according to antibody-mediated rejection (ABMR) subtypes. Rej and NRej groups included 52 and 37 biopsies, respectively. Median follow-up duration was 506 days. DSAs were positive in 53% and 22% of patients in both groups, respectively (p = 0.01). Among these groups, pre- and post-intervention median SCr, proteinuria, and dd-cfDNA at 1 month, 2 months, and at the last follow-up revealed significant difference for dd-cfDNA (all p = 0.01), however, no difference was found for SCr and proteinuria (p > 0.05). The AUC was 0.80 (95% CI: 0.69-0.91), with an optimal dd-cfDNA criterion of 2.2%. Compared to histology, MMDx® was more likely to diagnose ABMR (79% vs. 100%) with either C4d positivity or negativity and/or DSA positivity or negativity. Hence, a pre- and post-intervention allograft monitoring protocol in combination with dd-cfDNA, MMDx®, and histology has aided in early diagnosis and timely individualized intervention.
Collapse
Affiliation(s)
- Asim Rizvi
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Sara Faiz
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Parin H. Thakkar
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Syed Hussain
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Ann N. Gamilla-Crudo
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Michael Kueht
- Department of Transplant Surgery, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA;
| | - Muhammad A. Mujtaba
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| |
Collapse
|
15
|
van den Broek DAJ, Meziyerh S, Budde K, Lefaucheur C, Cozzi E, Bertrand D, López del Moral C, Dorling A, Emonds MP, Naesens M, de Vries APJ. The Clinical Utility of Post-Transplant Monitoring of Donor-Specific Antibodies in Stable Renal Transplant Recipients: A Consensus Report With Guideline Statements for Clinical Practice. Transpl Int 2023; 36:11321. [PMID: 37560072 PMCID: PMC10408721 DOI: 10.3389/ti.2023.11321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/22/2023] [Indexed: 08/11/2023]
Abstract
Solid phase immunoassays improved the detection and determination of the antigen-specificity of donor-specific antibodies (DSA) to human leukocyte antigens (HLA). The widespread use of SPI in kidney transplantation also introduced new clinical dilemmas, such as whether patients should be monitored for DSA pre- or post-transplantation. Pretransplant screening through SPI has become standard practice and DSA are readily determined in case of suspected rejection. However, DSA monitoring in recipients with stable graft function has not been universally established as standard of care. This may be related to uncertainty regarding the clinical utility of DSA monitoring as a screening tool. This consensus report aims to appraise the clinical utility of DSA monitoring in recipients without overt signs of graft dysfunction, using the Wilson & Junger criteria for assessing the validity of a screening practice. To assess the evidence on DSA monitoring, the European Society for Organ Transplantation (ESOT) convened a dedicated workgroup, comprised of experts in transplantation nephrology and immunology, to review relevant literature. Guidelines and statements were developed during a consensus conference by Delphi methodology that took place in person in November 2022 in Prague. The findings and recommendations of the workgroup on subclinical DSA monitoring are presented in this article.
Collapse
Affiliation(s)
- Dennis A. J. van den Broek
- Division of Nephrology, Department of Medicine, Leiden Transplant Center, Leiden University Medical Center, Leiden University, Leiden, Netherlands
| | - Soufian Meziyerh
- Division of Nephrology, Department of Medicine, Leiden Transplant Center, Leiden University Medical Center, Leiden University, Leiden, Netherlands
| | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Carmen Lefaucheur
- Paris Translational Research Center for Organ Transplantation, Kidney Transplant Department, Saint Louis Hospital, Université de Paris Cité, Paris, France
| | - Emanuele Cozzi
- Department of Cardiac, Thoracic and Vascular Sciences and Public Health, Transplant Immunology Unit, Padua University Hospital, Padua, Italy
| | - Dominique Bertrand
- Department of Nephrology, Transplantation and Hemodialysis, Rouen University Hospital, Rouen, France
| | - Covadonga López del Moral
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
- Valdecilla Biomedical Research Institute (IDIVAL), Santander, Spain
| | - Anthony Dorling
- Department of Inflammation Biology, Centre for Nephrology, Urology and Transplantation, School of Immunology & Microbial Sciences, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Marie-Paule Emonds
- Histocompatibility and Immunogenetics Laboratory (HILA), Belgian Red Cross-Flanders, Mechelen, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Aiko P. J. de Vries
- Division of Nephrology, Department of Medicine, Leiden Transplant Center, Leiden University Medical Center, Leiden University, Leiden, Netherlands
| | | |
Collapse
|
16
|
Madill-Thomsen KS, Böhmig GA, Bromberg J, Einecke G, Eskandary F, Gupta G, Myslak M, Viklicky O, Perkowska-Ptasinska A, Solez K, Halloran PF. Relating Molecular T Cell-mediated Rejection Activity in Kidney Transplant Biopsies to Time and to Histologic Tubulitis and Atrophy-fibrosis. Transplantation 2023; 107:1102-1114. [PMID: 36575574 PMCID: PMC10125115 DOI: 10.1097/tp.0000000000004396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/29/2022] [Accepted: 09/12/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND We studied the variation in molecular T cell-mediated rejection (TCMR) activity in kidney transplant indication biopsies and its relationship with histologic lesions (particularly tubulitis and atrophy-fibrosis) and time posttransplant. METHODS We examined 175 kidney transplant biopsies with molecular TCMR as defined by archetypal analysis in the INTERCOMEX study ( ClinicalTrials.gov #NCT01299168). TCMR activity was defined by a molecular classifier. RESULTS Archetypal analysis identified 2 TCMR classes, TCMR1 and TCMR2: TCMR1 had higher TCMR activity and more antibody-mediated rejection ("mixed") activity and arteritis but little hyalinosis, whereas TCMR2 had less TCMR activity but more atrophy-fibrosis. TCMR1 and TCMR2 had similar levels of molecular injury and tubulitis. Both TCMR1 and TCMR2 biopsies were uncommon after 2 y posttransplant and were rare after 10 y, particularly TCMR1. Within late TCMR biopsies, TCMR classifier activity and activity molecules such as IFNG fell progressively with time, but tubulitis and molecular injury were sustained. Atrophy-fibrosis was increased in TCMR biopsies, even in the first year posttransplant, and rose with time posttransplant. TCMR1 and TCMR2 both reduced graft survival, but in random forests, the strongest determinant of survival after biopsies with TCMR was molecular injury, not TCMR activity. CONCLUSIONS TCMR varies in intensity but is always strongly related to molecular injury and atrophy-fibrosis, which ultimately explains its effect on survival. We hypothesize, based on the reciprocal relationship with hyalinosis, that the TCMR1-TCMR2 gradient reflects calcineurin inhibitor drug underexposure, whereas the time-dependent decline in TCMR activity and frequency after the first year reflects T-cell exhaustion.
Collapse
Affiliation(s)
| | - Georg A. Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Gunilla Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Marek Myslak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation SPWSZ Hospital, Pomeranian Medical University, Szczecin, Poland
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | | | - Kim Solez
- Department of Laboratory Medicine and Pathology, Division of Anatomical Pathology, University of Alberta, Edmonton, Canada
| | - Philip 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
| |
Collapse
|
17
|
Virmani S, Rao A, Menon MC. Allograft tissue under the microscope: only the beginning. Curr Opin Organ Transplant 2023; 28:126-132. [PMID: 36787238 PMCID: PMC10214011 DOI: 10.1097/mot.0000000000001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
PURPOSE OF REVIEW To review novel modalities for interrogating a kidney allograft biopsy to complement the current Banff schema. RECENT FINDINGS Newer approaches of Artificial Intelligence (AI), Machine Learning (ML), digital pathology including Ex Vivo Microscopy, evaluation of the biopsy gene expression using bulk, single cell, and spatial transcriptomics and spatial proteomics are now available for tissue interrogation. SUMMARY Banff Schema of classification of allograft histology has standardized reporting of tissue pathology internationally greatly impacting clinical care and research. Inherent sampling error of biopsies, and lack of automated morphometric analysis with ordinal outputs limit its performance in prognostication of allograft health. Over the last decade, there has been an explosion of newer methods of evaluation of allograft tissue under the microscope. Digital pathology along with the application of AI and ML algorithms could revolutionize histopathological analyses. Novel molecular diagnostics such as spatially resolved single cell transcriptomics are identifying newer mechanisms underlying the pathologic diagnosis to delineate pathways of immunological activation, tissue injury, repair, and regeneration in allograft tissues. While these techniques are the future of tissue analysis, costs and complex logistics currently limit their clinical use.
Collapse
Affiliation(s)
- Sarthak Virmani
- Section of Nephrology, Division of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | | |
Collapse
|
18
|
de Nattes T, Beadle J, Toulza F, Candon E, Ruminy P, François A, Bertrand D, Guerrot D, Drieux F, Roufosse C, Candon S. A Simple Molecular Tool for the Assessment of Kidney Transplant Biopsies. Clin J Am Soc Nephrol 2023; 18:499-509. [PMID: 36723289 PMCID: PMC10103338 DOI: 10.2215/cjn.0000000000000100] [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: 08/26/2022] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
BACKGROUND The Banff Classification for Allograft Pathology recommendations for the diagnosis of kidney transplant rejection includes molecular assessment of the transplant biopsy. However, implementation of molecular tools in clinical practice is still limited, partly due to the required expertise and financial investment. The reverse transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) assay is a simple, rapid, and inexpensive assay that permits simultaneous evaluation of a restricted gene panel using paraffin-embedded tissue blocks. The aim of this study was to develop and validate a RT-MLPA assay for diagnosis and classification of rejection. METHODS A retrospective cohort of 220 kidney transplant biopsies from two centers, which included 52 antibody-mediated rejection, 51 T-cell-mediated rejection, and 117 no-rejection controls, was assessed. A 17-gene panel was identified on the basis of relevant pathophysiological pathways. A support vector machine classifier was developed. A subset of 109 biopsies was also assessed using the Nanostring Banff Human Organ Transplant panel to compare the two assays. RESULTS The support vector machine classifier train and test accuracy scores were 0.84 and 0.83, respectively. In the test cohort, the F1 score for antibody-mediated rejection, T-cell-mediated rejection, and control were 0.88, 0.86, and 0.69, respectively. Using receiver-operating characteristic curves, the area under the curve for class predictions was 0.96, 0.89, and 0.91, respectively, with a weighted average at 0.94. Classifiers' performances were highest for antibody-mediated rejection diagnosis with 94% correct predictions, compared with 88% correct predictions for control biopsies and 60% for T-cell-mediated rejection biopsies. Gene expression levels assessed by RT-MLPA and Nanostring were correlated: r = 0.68, P < 0.001. Equivalent gene expression profiles were obtained with both assays in 81% of the samples. CONCLUSIONS The 17-gene panel RT-MLPA assay, developed here for formalin-fixed paraffin-embedded kidney transplant biopsies, classified kidney transplant rejection with an overall accurate prediction ratio of 0.83. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/CJASN/2023_04_10_CJN10100822.mp3.
Collapse
Affiliation(s)
- Tristan de Nattes
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
- Univ Rouen Normandie, INSERM U1234, Rouen, France
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Jack Beadle
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Frederic Toulza
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Edvin Candon
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Philippe Ruminy
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - Arnaud François
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Dominique Bertrand
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Dominique Guerrot
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Fanny Drieux
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Candice Roufosse
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | | |
Collapse
|
19
|
Böhmig GA, Halloran PF, Feucht HE. On a Long and Winding Road: Alloantibodies in Organ Transplantation. Transplantation 2023; 107:1027-1041. [PMID: 36944603 DOI: 10.1097/tp.0000000000004550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Today we know that both the humoral and the cellular arm of the immune system are engaged in severe immunological challenges. A close interaction between B and T cells can be observed in most "natural" challenges, including infections, malignancies, and autoimmune diseases. The importance and power of humoral immunity are impressively demonstrated by the current coronavirus disease 2019 pandemic. Organ transplant rejection is a normal immune response to a completely "artificial" challenge. It took a long time before the multifaceted action of different immunological forces was recognized and a unified, generally accepted opinion could be formed. Here, we address prominent paradigms and paradigm shifts in the field of transplantation immunology. We identify several instances in which the transplant community missed a timely paradigm shift because essential, available knowledge was ignored. Moreover, we discuss key findings that critically contributed to our understanding of transplant immunology but sometimes developed with delay and in a roundabout way, as was the case with antibody-mediated rejection-a main focus of this article. These include the discovery of the molecular principles of histocompatibility, the recognition of the microcirculation as a key interface of immune damage, the refinement of alloantibody detection, the description of C4d as a footmark of endothelium-bound antibody, and last but not least, the developments in biopsy-based diagnostics beyond conventional morphology, which only now give us a glimpse of the enormous complexity and pathogenetic diversity of rejection.
Collapse
Affiliation(s)
- Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, ATAGC, University of Alberta, Edmonton, AB, Canada
| | | |
Collapse
|
20
|
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
|
21
|
Miller DV. Response to Manion, et al. Cardiovasc Pathol 2023; 63:107487. [PMID: 36306969 DOI: 10.1016/j.carpath.2022.107487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Dylan V Miller
- University of Utah, Electron Microscopy and Immunostains Lab, Intermountain Central Laboratory, 5252 S Intermountain Drive, Salt Lake City, UT 84157, USA.
| |
Collapse
|
22
|
Manion H, McCloskey C, Ramesh P, Lawrence C. Response to Commentary on development of the "molecular microscope (MMDx) assay for heart transplant rejection surveillance: SCVP journal club". Cardiovasc Pathol 2023; 63:107486. [PMID: 36202192 DOI: 10.1016/j.carpath.2022.107486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heather Manion
- Thermo Fisher Scientific, 22801 Roscoe Blvd, West Hills, CA, 91304
| | - Chris McCloskey
- Thermo Fisher Scientific, 22801 Roscoe Blvd, West Hills, CA, 91304
| | - Pradeep Ramesh
- Sherlock Biosciences, Inc. Watertown, MA 02472; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | | |
Collapse
|
23
|
Jimenez-Coll V, Llorente S, Boix F, Alfaro R, Galián JA, Martinez-Banaclocha H, Botella C, Moya-Quiles MR, Muro-Pérez M, Minguela A, Legaz I, Muro M. Monitoring of Serological, Cellular and Genomic Biomarkers in Transplantation, Computational Prediction Models and Role of Cell-Free DNA in Transplant Outcome. Int J Mol Sci 2023; 24:ijms24043908. [PMID: 36835314 PMCID: PMC9963702 DOI: 10.3390/ijms24043908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023] Open
Abstract
The process and evolution of an organ transplant procedure has evolved in terms of the prevention of immunological rejection with the improvement in the determination of immune response genes. These techniques include considering more important genes, more polymorphism detection, more refinement of the response motifs, as well as the analysis of epitopes and eplets, its capacity to fix complement, the PIRCHE algorithm and post-transplant monitoring with promising new biomarkers that surpass the classic serum markers such as creatine and other similar parameters of renal function. Among these new biomarkers, we analyze new serological, urine, cellular, genomic and transcriptomic biomarkers and computational prediction, with particular attention to the analysis of donor free circulating DNA as an optimal marker of kidney damage.
Collapse
Affiliation(s)
- Víctor Jimenez-Coll
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Santiago Llorente
- Nephrology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Francisco Boix
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Rafael Alfaro
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - José Antonio Galián
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Helios Martinez-Banaclocha
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Carmen Botella
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - María R. Moya-Quiles
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Manuel Muro-Pérez
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Alfredo Minguela
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
| | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain
- Correspondence: (I.L.); (M.M.); Tel.: +34-699986674 (M.M.); Fax: +34-868834307 (M.M.)
| | - Manuel Muro
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain
- Correspondence: (I.L.); (M.M.); Tel.: +34-699986674 (M.M.); Fax: +34-868834307 (M.M.)
| |
Collapse
|
24
|
Benincasa G, Viglietti M, Coscioni E, Napoli C. "Transplantomics" for predicting allograft rejection: real-life applications and new strategies from Network Medicine. Hum Immunol 2023; 84:89-97. [PMID: 36424231 DOI: 10.1016/j.humimm.2022.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/23/2022]
Abstract
Although decades of the reductionist approach achieved great milestones in optimizing the immunosuppression therapy, traditional clinical parameters still fail in predicting both acute and chronic (mainly) rejection events leading to higher rates across all solid organ transplants. To clarify the underlying immune-related cellular and molecular mechanisms, current biomedical research is increasingly focusing on "transplantomics" which relies on a huge quantity of big data deriving from genomics, transcriptomics, epigenomics, proteomics, and metabolomics platforms. The AlloMap (gene expression) and the AlloSure (donor-derived cell-free DNA) tests represent two successful examples of how omics and liquid biopsy can really improve the precision medicine of heart and kidney transplantation. One of the major challenges in translating big data in clinically useful biomarkers is the integration and interpretation of the different layers of omics datasets. Network Medicine offers advanced bioinformatic-molecular strategies which were widely used to integrate large omics datasets and clinical information in end-stage patients to prioritize potential biomarkers and drug targets. The application of network-oriented approaches to clarify the complex nature of graft rejection is still in its infancy. Here, we briefly discuss the real-life clinical applications derived from omics datasets as well as novel opportunities for establishing predictive tests in solid organ transplantation. Also, we provide an original "graft rejection interactome" and propose network-oriented strategies which can be useful to improve precision medicine of solid organ transplantation.
Collapse
Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Mario Viglietti
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Enrico Coscioni
- Division of Cardiac Surgery, AOU San Giovanni di Dio e Ruggi d'Aragona, 84131, Salerno, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy; U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania "Luigi Vanvitelli", Naples, Italy
| |
Collapse
|
25
|
The Molecular Diagnosis Might Be Clinically Useful in Discrepant Kidney Allograft Biopsy Findings: An Analysis of Clinical Outcomes. Transplantation 2023; 107:485-494. [PMID: 36117252 PMCID: PMC9875837 DOI: 10.1097/tp.0000000000004284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND The Molecular Microscope Diagnostic System (MMDx) may overcome histology shortcomings. Previous studies have simply examined discrepant findings but have not attempted to determine clinical endpoints. To measure performance, clinical outcomes are strongly required. METHODS This single-center cohort study described discrepancies between MMDx and histology from 51 kidney transplant recipients (KTRs) and analyzed 72 indication biopsies, including 21 follow-up biopsies. Clinical performance was assessed by a combined endpoint of graft failure, rejection on follow-up biopsy, de novo donor-specific antibody, and improvement of kidney allograft function upon antirejection treatment. RESULTS MMDx agreed in 33 (65%) and differed in 18 (35%) of 51 KTRs. Most discrepancies occurred in biopsies called no rejection by MMDx and rejection by histology (15/24, 63%). In contrast, in biopsies called rejection by MMDx, 3 were classified as no rejection by histology (3/27, 11%). Discrepant findings between MMDx and histology occurred following delayed graft function and MMDx from biopsies with a low percentage of cortex. Among 15 biopsies classified as no rejection by MMDx but rejection by histology, the clinical course suggested no rejection in 9 cases. Six KTRs reached the endpoint, showing predominant t ≥ 2 lesions. CONCLUSIONS The most often occurring discrepancy is rejection by histology but no rejection by MMDx. As more KTRs do not meet the combined endpoint for rejection, MMDx might be clinically useful in these discrepant cases. Although strong histological findings have priority in indicating the treatment, clinical implementation of MMDx could strengthen treatment strategies.
Collapse
|
26
|
Yeh H. Applications of Transcriptomics in the Research of Antibody-Mediated Rejection in Kidney Transplantation: Progress and Perspectives. Organogenesis 2022; 18:2131357. [PMID: 36259540 PMCID: PMC9586696 DOI: 10.1080/15476278.2022.2131357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Antibody-mediated rejection (ABMR) is the major cause of chronic allograft dysfunction and loss in kidney transplantation. The immunological mechanisms of ABMR that have been featured in the latest studies indicate a highly complex interplay between various immune and nonimmune cell types. Clinical diagnostic standards have long been criticized for being arbitrary and the lack of accuracy. Transcriptomic approaches, including microarray and RNA sequencing of allograft biopsies, enable the identification of differential gene expression and the continuous improvement of diagnostics. Given that conventional bulk transcriptomic approaches only reflect the average gene expression but not the status at the single-cell level, thereby ignoring the heterogeneity of the transcriptome across individual cells, single-cell RNA sequencing is rising as a powerful tool to provide a high-resolution transcriptome map of immune cells, which allows the elucidation of the pathogenesis and may facilitate the development of novel strategies for clinical treatment of ABMR.
Collapse
Affiliation(s)
- Hsuan Yeh
- Division of Renal-Electrolyte, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,CONTACT Hsuan Yeh S976 Scaife Hall 3550 Terrace Street Pittsburgh, PA 15261
| |
Collapse
|
27
|
Halloran PF, Reeve J, Madill-Thomsen KS, Kaur N, Ahmed E, Cantos C, Al Haj Baddar N, Demko Z, Liang N, Swenerton RK, Zimmermann BG, Van Hummelen P, Prewett A, Rabinowitz M, Tabriziani H, Gauthier P, Billings P. Combining Donor-derived Cell-free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology as Confirmation. Transplantation 2022; 106:2435-2442. [PMID: 35765145 PMCID: PMC9698190 DOI: 10.1097/tp.0000000000004212] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/14/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) fraction and quantity have both been shown to be associated with allograft rejection. The present study compared the relative predictive power of each of these variables to the combination of the two, and developed an algorithm incorporating both variables to detect active rejection in renal allograft biopsies. METHODS The first 426 sequential indication biopsy samples collected from the Trifecta study ( ClinicalTrials.gov # NCT04239703) with microarray-derived gene expression and dd-cfDNA results were included. After exclusions to simulate intended clinical use, 367 samples were analyzed. Biopsies were assessed using the molecular microscope diagnostic system and histology (Banff 2019). Logistic regression analysis examined whether combining dd-cfDNA fraction and quantity adds predictive value to either alone. The first 149 sequential samples were used to develop a two-threshold algorithm and the next 218 to validate the algorithm. RESULTS In regression, the combination of dd-cfDNA fraction and quantity was found to be significantly more predictive than either variable alone ( P = 0.009 and P < 0.0001). In the test set, the area under the receiver operating characteristic curve of the two-variable system was 0.88, and performance of the two-threshold algorithm showed a sensitivity of 83.1% and specificity of 81.0% for molecular diagnoses and a sensitivity of 73.5% and specificity of 80.8% for histology diagnoses. CONCLUSIONS This prospective, biopsy-matched, multisite dd-cfDNA study in kidney transplant patients found that the combination of dd-cfDNA fraction and quantity was more powerful than either dd-cfDNA fraction or quantity alone and validated a novel two-threshold algorithm incorporating both variables.
Collapse
Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - the Trifecta Investigators*
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
- Natera Inc, San Carlos, CA
| |
Collapse
|
28
|
Morath C, Schmitt A, Schmitt M, Wang L, Kleist C, Opelz G, Süsal C, Tran TH, Scherer S, Schwenger V, Kemmner S, Fischereder M, Stangl M, Hauser IA, Sommerer C, Nusshag C, Kälble F, Speer C, Benning L, Bischofs C, Sauer S, Schubert ML, Kunz A, Hückelhoven-Krauss A, Neuber B, Mehrabi A, Schwab C, Waldherr R, Sander A, Büsch C, Czock D, Böhmig GA, Reiser J, Roers A, Müller-Tidow C, Terness P, Zeier M, Daniel V, Schaier M. Individualised immunosuppression with intravenously administered donor-derived modified immune cells compared with standard of care in living donor kidney transplantation (TOL-2 Study): protocol for a multicentre, open-label, phase II, randomised controlled trial. BMJ Open 2022; 12:e066128. [PMID: 36368749 PMCID: PMC9660568 DOI: 10.1136/bmjopen-2022-066128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Donor-derived modified immune cells (MIC) induced long-term specific immunosuppression against the allogeneic donor in preclinical models of transplantation. In a phase I clinical trial (TOL-1 Study), MIC treatment resulted in a cellular phenotype that was directly and indirectly suppressive to the recipient's immune system allowing for reduction of conventional immunosuppressive therapy. Here, we describe a protocol for a randomised controlled, multicentre phase-IIb clinical trial of individualised immunosuppression with intravenously administered donor MIC compared with standard-of-care (SoC) in living donor kidney transplantation (TOL-2 Study). METHODS AND ANALYSIS Sixty-three living donor kidney transplant recipients from six German transplant centres are randomised 2:1 to treatment with MIC (MIC group, N=42) or no treatment with MIC (control arm, N=21). MIC are manufactured from donor peripheral blood mononuclear cells under Good Manufacturing Practice conditions. The primary objective of this trial is to determine the efficacy of MIC treatment together with reduced conventional immunosuppressive therapy in terms of achieving an operational tolerance-like phenotype compared with SoC 12 months after MIC administration. Key secondary endpoints are the number of patient-relevant infections as well as a composite of biopsy-proven acute rejection, graft loss, graft dysfunction or death. Immunosuppressive therapy of MIC-treated patients is reduced during follow-up under an extended immunological monitoring including human leucocyte antigen-antibody testing, and determination of lymphocyte subsets, for example, regulatory B lymphocytes (Breg) and antidonor T cell response. A Data Safety Monitoring Board has been established to allow an independent assessment of safety and efficacy. ETHICS AND DISSEMINATION Ethical approval has been provided by the Ethics Committee of the Medical Faculty of the University of Heidelberg, Heidelberg, Germany (AFmu-580/2021, 17 March 2022) and from the Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Institute, Langen, Germany (Vorlage-Nr. 4586/02, 21 March 2022). Written informed consent will be obtained from all patients and respective donors prior to enrolment in the study. The results from the TOL-2 Study will be published in peer-reviewed medical journals and will be presented at symposia and scientific meetings. TRIAL REGISTRATION NUMBER NCT05365672.
Collapse
Affiliation(s)
- Christian Morath
- TolerogenixX GmbH, Heidelberg, Germany
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research, DZIF, TTU-IICH, Partner site Heidelberg, Heidelberg, Germany
| | - Anita Schmitt
- TolerogenixX GmbH, Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Schmitt
- TolerogenixX GmbH, Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Lei Wang
- TolerogenixX GmbH, Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Kleist
- TolerogenixX GmbH, Heidelberg, Germany
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Gerhard Opelz
- TolerogenixX GmbH, Heidelberg, Germany
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Caner Süsal
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Transplant Immunology Research Center of Excellence, Koç University, Istanbul, Turkey
| | - T Hien Tran
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sabine Scherer
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Vedat Schwenger
- Department of Nephrology, Transplant Center, Klinikum der Landeshauptstadt Stuttgart, Stuttgart, Germany
| | - Stephan Kemmner
- Transplant Center, University Hospital Munich, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Michael Fischereder
- Division of Nephrology, Department of Internal Medicine IV, University Hospital Munich, Ludwig-Maximilians University Munich (LMU), Munich, Germany
| | - Manfred Stangl
- Department of General, Visceral, and Transplant Surgery, University Hospital Munich, Ludwig-Maximilians University Munich (LMU), Munich, Germany
| | - Ingeborg A Hauser
- Department of Nephrology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Claudia Sommerer
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research, DZIF, TTU-IICH, Partner site Heidelberg, Heidelberg, Germany
| | - Christian Nusshag
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Kälble
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Claudius Speer
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Louise Benning
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Bischofs
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sandra Sauer
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Maria-Luisa Schubert
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Alexander Kunz
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Angela Hückelhoven-Krauss
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Brigitte Neuber
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Arianeb Mehrabi
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Constantin Schwab
- Institut of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rüdiger Waldherr
- Institut of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anja Sander
- Institut of Medical Biometry, Heidelberg University Hospital, Heidelberg, Germany
| | - Christopher Büsch
- Institut of Medical Biometry, Heidelberg University Hospital, Heidelberg, Germany
| | - David Czock
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Jochen Reiser
- Department of Medicine, Rush University, Chicago, Illinois, USA
| | - Axel Roers
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Terness
- TolerogenixX GmbH, Heidelberg, Germany
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Zeier
- TolerogenixX GmbH, Heidelberg, Germany
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Volker Daniel
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias Schaier
- TolerogenixX GmbH, Heidelberg, Germany
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
29
|
Varol H, Ernst A, Cristoferi I, Arns W, Baan CC, van Baardwijk M, van den Bosch T, Eckhoff J, Harth A, Hesselink DA, van Kemenade FJ, de Koning W, Kurschat C, Minnee RC, Mustafa DAM, Reinders MEJ, Shahzad-Arshad SP, Snijders MLH, Stippel D, Stubbs AP, von der Thüsen J, Wirths K, Becker JU, Clahsen-van Groningen MC. Feasibility and Potential of Transcriptomic Analysis Using the NanoString nCounter Technology to Aid the Classification of Rejection in Kidney Transplant Biopsies. Transplantation 2022; 107:903-912. [PMID: 36413151 PMCID: PMC10065817 DOI: 10.1097/tp.0000000000004372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Transcriptome analysis could be an additional diagnostic parameter in diagnosing kidney transplant (KTx) rejection. Here, we assessed feasibility and potential of NanoString nCounter analysis of KTx biopsies to aid the classification of rejection in clinical practice using both the Banff-Human Organ Transplant (B-HOT) panel and a customized antibody-mediated rejection (AMR)-specific NanoString nCounter Elements (Elements) panel. Additionally, we explored the potential for the classification of KTx rejection building and testing a classifier within our dataset. METHODS Ninety-six formalin-fixed paraffin-embedded KTx biopsies were retrieved from the archives of the ErasmusMC Rotterdam and the University Hospital Cologne. Biopsies with AMR, borderline or T cell-mediated rejections (BLorTCMR), and no rejection were compared using the B-HOT and Elements panels. RESULTS High correlation between gene expression levels was found when comparing the 2 chemistries pairwise (r = 0.76-0.88). Differential gene expression (false discovery rate; P < 0.05) was identified in biopsies diagnosed with AMR (B-HOT: 294; Elements: 76) and BLorTCMR (B-HOT: 353; Elements: 57) compared with no rejection. Using the most predictive genes from the B-HOT analysis and the Element analysis, 2 least absolute shrinkage and selection operators-based regression models to classify biopsies as AMR versus no AMR (BLorTCMR or no rejection) were developed achieving an receiver-operating-characteristic curve of 0.994 and 0.894, sensitivity of 0.821 and 0.480, and specificity of 1.00 and 0.979, respectively, during cross-validation. CONCLUSIONS Transcriptomic analysis is feasible on KTx biopsies previously used for diagnostic purposes. The B-HOT panel has the potential to differentiate AMR from BLorTCMR or no rejection and could prove valuable in aiding kidney transplant rejection classification.
Collapse
Affiliation(s)
- Hilal Varol
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Angela Ernst
- Institute of Medical Statistics and Computational Biology, University Hospital of Cologne, Cologne, Germany
| | - Iacopo Cristoferi
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Surgery, Division of HPB & Transplant Surgery, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wolfgang Arns
- Cologne Merheim Medical Center, Cologne General Hospital, Cologne, Germany
| | - Carla C Baan
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Myrthe van Baardwijk
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Surgery, Division of HPB & Transplant Surgery, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thierry van den Bosch
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jennifer Eckhoff
- Department of General Visceral Cancer and Transplant Surgery Transplant Center Cologne, University of Cologne Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | - Ana Harth
- Cologne Merheim Medical Center, Cologne General Hospital, Cologne, Germany
| | - Dennis A Hesselink
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Folkert J van Kemenade
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Willem de Koning
- Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christine Kurschat
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Robert C Minnee
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Surgery, Division of HPB & Transplant Surgery, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dana A M Mustafa
- Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marlies E J Reinders
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Malou L H Snijders
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Dirk Stippel
- Department of General Visceral Cancer and Transplant Surgery Transplant Center Cologne, University of Cologne Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | - Andrew P Stubbs
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan von der Thüsen
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Katharina Wirths
- Department of Internal Medicine, Faculty of Medicine, University Bonn, Bonn, Germany
| | - Jan U Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Marian C Clahsen-van Groningen
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
30
|
Taner T, Bruner J, Emaumaullee J, Bonaccorsi-Riani E, Zarrinpar A. New Approaches to the Diagnosis of Rejection and Prediction of Tolerance in Liver Transplantation. Transplantation 2022; 106:1952-1962. [PMID: 35594482 PMCID: PMC9529763 DOI: 10.1097/tp.0000000000004160] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Immunosuppression after liver transplantation is essential for preventing allograft rejection. However, long-term drug toxicity and associated complications necessitate investigation of immunosuppression minimization and withdrawal protocols. Development of such protocols is hindered by reliance on current paradigms for monitoring allograft function and rejection status. The current standard of care for diagnosis of rejection is histopathologic assessment and grading of liver biopsies in accordance with the Banff Rejection Activity Index. However, this method is limited by cost, sampling variability, and interobserver variation. Moreover, the invasive nature of biopsy increases the risk of patient complications. Incorporating noninvasive techniques may supplement existing methods through improved understanding of rejection causes, hepatic spatial architecture, and the role of idiopathic fibroinflammatory regions. These techniques may also aid in quantification and help integrate emerging -omics analyses with current assessments. Alternatively, emerging noninvasive methods show potential to detect and distinguish between different types of rejection while minimizing risk of adverse advents. Although biomarkers have yet to replace biopsy, preliminary studies suggest that several classes of analytes may be used to detect rejection with greater sensitivity and in earlier stages than traditional methods, possibly when coupled with artificial intelligence. Here, we provide an overview of the latest efforts in optimizing the diagnosis of rejection in liver transplantation.
Collapse
Affiliation(s)
- Timucin Taner
- Departments of Surgery & Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Julia Bruner
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Juliet Emaumaullee
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eliano Bonaccorsi-Riani
- Abdominal Transplant Unit, Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Ali Zarrinpar
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
| |
Collapse
|
31
|
The Role of Complement Split-products as Biomarkers for Acute Antibody-mediated Rejection of Kidney Allografts. Transplant Direct 2022; 8:e1366. [PMID: 35935026 PMCID: PMC9355106 DOI: 10.1097/txd.0000000000001366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022] Open
Abstract
Acute antibody-mediated rejection (AMR) is mediated by the activation of the classical complement system in addition to noncomplement-dependent inflammatory pathways. Complement fixation by donor-specific antibodies leads to cleavage of the complement proteins C4, C3, and C5 to produce multiple complement split-products (CSP) and the end-effector membrane attack complex, C5b-9. In this study, we investigate CSP as potential biomarkers for AMR.
Collapse
|
32
|
Assessing the Relationship Between Molecular Rejection and Parenchymal Injury in Heart Transplant Biopsies. Transplantation 2022; 106:2205-2216. [PMID: 35968995 DOI: 10.1097/tp.0000000000004231] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND The INTERHEART study (ClinicalTrials.gov #NCT02670408) used genome-wide microarrays to detect rejection in endomyocardial biopsies; however, many heart transplants with no rejection have late dysfunction and impaired survival. We used the microarray measurements to develop a molecular classification of parenchymal injury. METHODS In 1320 endomyocardial biopsies from 645 patients previously studied for rejection-associated transcripts, we measured the expression of 10 injury-induced transcript sets: 5 induced by recent injury; 2 reflecting macrophage infiltration; 2 normal heart transcript sets; and immunoglobulin transcripts, which correlate with time. We used archetypal clustering to assign injury groups. RESULTS Injury transcript sets correlated with impaired function. Archetypal clustering based on the expression of injury transcript sets assigned each biopsy to 1 of 5 injury groups: 87 Severe-injury, 221 Late-injury, and 3 with lesser degrees of injury, 376 No-injury, 526 Mild-injury, and 110 Moderate-injury. Severe-injury had extensive loss of normal transcripts (dedifferentiation) and increase in macrophage and injury-induced transcripts. Late-injury was characterized by high immunoglobulin transcript expression. In Severe- and Late-injury, function was depressed, and short-term graft failure was increased, even in hearts with no rejection. T cell-mediated rejection almost always had parenchymal injury, and 85% had Severe- or Late-injury. In contrast, early antibody-mediated rejection (ABMR) had little injury, but late ABMR often had the Late-injury state. CONCLUSION Characterizing heart transplants for their injury state provides new understanding of dysfunction and outcomes and demonstrates the differential impact of T cell-mediated rejection versus ABMR on the parenchyma. Slow deterioration from ABMR emerges as a major contributor to late dysfunction.
Collapse
|
33
|
Eller K, Böhmig GA, Banas MC, Viklicky O. Editorial: Advances in the diagnosis and treatment in kidney transplantation. Front Med (Lausanne) 2022; 9:967749. [PMID: 35991631 PMCID: PMC9382307 DOI: 10.3389/fmed.2022.967749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Kathrin Eller
- Division of Nephrology, Medical University of Graz, Graz, Austria
- *Correspondence: Kathrin Eller
| | - Georg A. Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Miriam C. Banas
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Ondrej Viklicky
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czechia
| |
Collapse
|
34
|
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
|
35
|
Zamir MR, Shahi A, Salehi S, Amirzargar A. Natural killer cells and killer cell immunoglobulin-like receptors in solid organ transplantation: Protectors or opponents? Transplant Rev (Orlando) 2022; 36:100723. [DOI: 10.1016/j.trre.2022.100723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
|
36
|
McCloskey C, Zubrycki M, Lawrence C. The Molecular Microscope Diagnostic System (MMDx) interpretation of solid organ allograft biopsies: Restoring the perspective. Clin Transplant 2022; 36:e14711. [PMID: 35668041 DOI: 10.1111/ctr.14711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/02/2022] [Accepted: 05/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Chris McCloskey
- Transplant Diagnostics Division, Thermo Fisher Scientific, West Hills, California, USA
| | - Michelle Zubrycki
- Transplant Diagnostics Division, Thermo Fisher Scientific, West Hills, California, USA
| | - Christopher Lawrence
- Transplant Diagnostics Division, Thermo Fisher Scientific, West Hills, California, USA
| |
Collapse
|
37
|
van Baardwijk M, Cristoferi I, Ju J, Varol H, Minnee RC, Reinders MEJ, Li Y, Stubbs AP, Clahsen-van Groningen MC. A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel. Front Immunol 2022; 13:841519. [PMID: 35619722 PMCID: PMC9128066 DOI: 10.3389/fimmu.2022.841519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/11/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction A decentralized and multi-platform-compatible molecular diagnostic tool for kidney transplant biopsies could improve the dissemination and exploitation of this technology, increasing its clinical impact. As a first step towards this molecular diagnostic tool, we developed and validated a classifier using the genes of the Banff-Human Organ Transplant (B-HOT) panel extracted from a historical Molecular Microscope® Diagnostic system microarray dataset. Furthermore, we evaluated the discriminative power of the B-HOT panel in a clinical scenario. Materials and Methods Gene expression data from 1,181 kidney transplant biopsies were used as training data for three random forest models to predict kidney transplant biopsy Banff categories, including non-rejection (NR), antibody-mediated rejection (ABMR), and T-cell-mediated rejection (TCMR). Performance was evaluated using nested cross-validation. The three models used different sets of input features: the first model (B-HOT Model) was trained on only the genes included in the B-HOT panel, the second model (Feature Selection Model) was based on sequential forward feature selection from all available genes, and the third model (B-HOT+ Model) was based on the combination of the two models, i.e. B-HOT panel genes plus highly predictive genes from the sequential forward feature selection. After performance assessment on cross-validation, the best-performing model was validated on an external independent dataset based on a different microarray version. Results The best performances were achieved by the B-HOT+ Model, a multilabel random forest model trained on B-HOT panel genes with the addition of the 6 most predictive genes of the Feature Selection Model (ST7, KLRC4-KLRK1, TRBC1, TRBV6-5, TRBV19, and ZFX), with a mean accuracy of 92.1% during cross-validation. On the validation set, the same model achieved Area Under the ROC Curve (AUC) of 0.965 and 0.982 for NR and ABMR respectively. Discussion This kidney transplant biopsy classifier is one step closer to the development of a decentralized kidney transplant biopsy classifier that is effective on data derived from different gene expression platforms. The B-HOT panel proved to be a reliable highly-predictive panel for kidney transplant rejection classification. Furthermore, we propose to include the aforementioned 6 genes in the B-HOT panel for further optimization of this commercially available panel.
Collapse
Affiliation(s)
- Myrthe van Baardwijk
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Companion Diagnostics and Personalised Healthcare, Omnigen BV, Delft, Netherlands
| | - Iacopo Cristoferi
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jie Ju
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Hilal Varol
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Robert C Minnee
- Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marlies E J Reinders
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Yunlei Li
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Andrew P Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marian C Clahsen-van Groningen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Institute of Experimental Medicine and Systems Biology, Rheinish-Westphalian Technical University Aachen University (RWTH), Aachen, Germany
| |
Collapse
|
38
|
Becker JU, Seron D, Rabant M, Roufosse C, Naesens M. Evolution of the Definition of Rejection in Kidney Transplantation and Its Use as an Endpoint in Clinical Trials. Transpl Int 2022; 35:10141. [PMID: 35669978 PMCID: PMC9163319 DOI: 10.3389/ti.2022.10141] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022]
Abstract
This article outlines the evolving definition of rejection following kidney transplantation. The viewpoints and evidence presented were included in documentation prepared for a Broad Scientific Advice request to the European Medicines Agency (EMA), relating to clinical trial endpoints in kidney transplantation. This request was initiated by the European Society for Organ Transplantation (ESOT) in 2016 and finalized following discussions between the EMA and ESOT in 2020. In ESOT’s opinion, the use of “biopsy-proven acute rejection” as an endpoint for clinical trials in kidney transplantation is no longer accurate, although it is still the approved histopathological endpoint. The spectrum of rejection is now divided into the phenotypes of borderline changes, T cell-mediated rejection, and antibody-mediated rejection, with the latter two phenotypes having further subclassifications. Rejection is also described in relation to graft (dys)function, diagnosed because of protocol (surveillance) or indication (for-cause) biopsies. The ongoing use of outdated terminology has become a potential barrier to clinical research in kidney transplantation. This article presents these perspectives and issues, and provides a foundation on which subsequent articles within this Special Issue of Transplant International build.
Collapse
Affiliation(s)
- Jan Ulrich Becker
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Daniel Seron
- Department of Nephrology and Kidney Transplantation, Vall d’Hebrón University Hospital, Barcelona, Spain
| | - Marion Rabant
- Department of Pathology, Hôpital Necker–Enfants Malades, Paris, France
| | - Candice Roufosse
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- *Correspondence: Maarten Naesens,
| |
Collapse
|
39
|
Halloran PF, Böhmig GA, Bromberg J, Einecke G, Eskandary FA, Gupta G, Myslak M, Viklicky O, Perkowska-Ptasinska A, Madill-Thomsen KS. Archetypal Analysis of Injury in Kidney Transplant Biopsies Identifies Two Classes of Early AKI. Front Med (Lausanne) 2022; 9:817324. [PMID: 35463013 PMCID: PMC9021747 DOI: 10.3389/fmed.2022.817324] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/07/2022] [Indexed: 01/07/2023] Open
Abstract
All transplanted kidneys are subjected to some degree of injury as a result of the donation-implantation process and various post-transplant stresses such as rejection. Because transplants are frequently biopsied, they present an opportunity to explore the full spectrum of kidney response-to-wounding from all causes. Defining parenchymal damage in transplanted organs is important for clinical management because it determines function and survival. In this study, we classified the scenarios associated with parenchymal injury in genome-wide microarray results from 1,526 kidney transplant indication biopsies collected during the INTERCOMEX study. We defined injury groups by using archetypal analysis (AA) of scores for gene sets and classifiers previously identified in various injury states. Six groups and their characteristics were defined in this population: No injury, minor injury, two classes of acute kidney injury ("AKI," AKI1, and AKI2), chronic kidney disease (CKD), and CKD combined with AKI. We compared the two classes of AKI, namely, AKI1 and AKI2. AKI1 had a poor function and increased parenchymal dedifferentiation but minimal response-to-injury and inflammation, instead having increased expression of PARD3, a gene previously characterized as being related to epithelial polarity and adherens junctions. In contrast, AKI2 had a poor function and increased response-to-injury, significant inflammation, and increased macrophage activity. In random forest analysis, the most important predictors of function (estimated glomerular filtration rate) and graft loss were injury-based molecular scores, not rejection scores. AKI1 and AKI2 differed in 3-year graft survival, with better survival in the AKI2 group. Thus, injury archetype analysis of injury-induced gene expression shows new heterogeneity in kidney response-to-wounding, revealing AKI1, a class of early transplants with a poor function but minimal inflammation or response to injury, a deviant response characterized as PC3, and an increased risk of failure. Given the relationship between parenchymal injury and kidney survival, further characterization of the injury phenotypes in kidney transplants will be important for an improved understanding that could have implications for understanding native kidney diseases (ClinicalTrials.gov #NCT01299168).
Collapse
Affiliation(s)
- Philip 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
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Jonathan Bromberg
- Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Gunilla Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Farsad A Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, United States
| | - Marek Myslak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation Samodzielny Publiczny Wojewódzki Szpital Zespolony (SPWSZ) Hospital, Pomeranian Medical University, Szczecin, Poland
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Agnieszka Perkowska-Ptasinska
- Department of Transplantation Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | | |
Collapse
|
40
|
Madill-Thomsen KS, Abouljoud M, Bhati C, Ciszek M, Durlik M, Feng S, Foroncewicz B, Francis I, Grąt M, Jurczyk K, Klintmalm G, Krasnodębski M, McCaughan G, Miquel R, Montano-Loza A, Moonka D, Mucha K, Myślak M, Pączek L, Perkowska-Ptasińska A, Piecha G, Reichman T, Sanchez-Fueyo A, Tronina O, Wawrzynowicz-Syczewska M, Więcek A, Zieniewicz K, Halloran PF. The molecular phenotypes of injury, steatohepatitis, and fibrosis in liver transplant biopsies in the INTERLIVER study. Am J Transplant 2022; 22:909-926. [PMID: 34780106 DOI: 10.1111/ajt.16890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 01/25/2023]
Abstract
To extend previous molecular analyses of rejection in liver transplant biopsies in the INTERLIVER study (ClinicalTrials.gov #NCT03193151), the present study aimed to define the gene expression selective for parenchymal injury, fibrosis, and steatohepatitis. We analyzed genome-wide microarray measurements from 337 liver transplant biopsies from 13 centers. We examined expression of genes previously annotated as increased in injury and fibrosis using principal component analysis (PCA). PC1 reflected parenchymal injury and related inflammation in the early posttransplant period, slowly regressing over many months. PC2 separated early injury from late fibrosis. Positive PC3 identified a distinct mildly inflamed state correlating with histologic steatohepatitis. Injury PCs correlated with liver function and histologic abnormalities. A classifier trained on histologic steatohepatitis predicted histologic steatohepatitis with cross-validated AUC = 0.83, and was associated with pathways reflecting metabolic abnormalities distinct from fibrosis. PC2 predicted histologic fibrosis (AUC = 0.80), as did a molecular fibrosis classifier (AUC = 0.74). The fibrosis classifier correlated with matrix remodeling pathways with minimal overlap with those selective for steatohepatitis, although some biopsies had both. Genome-wide assessment of liver transplant biopsies can not only detect molecular changes induced by rejection but also those correlating with parenchymal injury, steatohepatitis, and fibrosis, offering potential insights into disease mechanisms for primary diseases.
Collapse
Affiliation(s)
| | | | - Chandra Bhati
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Michał Ciszek
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Durlik
- Department of Transplant Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sandy Feng
- University of California San Francisco, San Francisco, California, USA
| | - Bartosz Foroncewicz
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Michał Grąt
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Jurczyk
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University, Szczecin, Poland
| | | | - Maciej Krasnodębski
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Geoff McCaughan
- Centenary Research Institute, Australian National Liver Transplant Unit, Royal Prince Alfred Hospital, The University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Myślak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation SPWSZ Hospital, Pomeranian Medical University, Szczecin, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Grzegorz Piecha
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, Katowice, Poland
| | | | | | - Olga Tronina
- Department of Transplant Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marta Wawrzynowicz-Syczewska
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University, Szczecin, Poland
| | - Andrzej Więcek
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, Katowice, Poland
| | - Krzysztof Zieniewicz
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | | |
Collapse
|
41
|
Lezoeva E, Nilsson J, Wüthrich R, Mueller TF, Schachtner T. High PIRCHE Scores May Allow Risk Stratification of Borderline Rejection in Kidney Transplant Recipients. Front Immunol 2022; 13:788818. [PMID: 35250973 PMCID: PMC8894244 DOI: 10.3389/fimmu.2022.788818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Background The diagnosis of borderline rejection (BLR) ranges from mild inflammation to clinically significant TCMR and is associated with an increased risk of allograft dysfunction. Currently, there is no consensus regarding its treatment due in part to a lack of biomarkers to identify cases with increased risk for immune-mediated injury. Methods We identified 60 of 924 kidney transplant recipients (KTRs) with isolated and untreated BLR. We analyzed the impact of predicted indirectly recognizable HLA epitopes (PIRCHE) score on future rejection, de novo DSA development, and recovery to baseline allograft function. Additionally, we compared the outcomes of different Banff rejection phenotypes. Results Total PIRCHE scores were significantly higher in KTRs with BLR compared to the entire study population (p=0.016). Among KTRs with BLR total PIRCHE scores were significantly higher in KTRs who developed TCMR/ABMR in follow-up biopsies (p=0.029). Notably, the most significant difference was found in PIRCHE scores for the HLA-A locus (p=0.010). PIRCHE scores were not associated with the development of de novo DSA or recovery to baseline allograft function among KTRs with BLR (p>0.05). However, KTRs under cyclosporine-based immunosuppression were more likely to develop de novo DSA (p=0.033) than those with tacrolimus, whereas KTRs undergoing retransplantation were less likely to recover to baseline allograft function (p=0.003). Conclusions High PIRCHE scores put KTRs with BLR at an increased risk for future TCMR/ABMR and contribute to improved immunological risk stratification. The benefit of anti-rejection treatment, however, needs to be evaluated in future studies.
Collapse
Affiliation(s)
- Ekaterina Lezoeva
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Rudolf Wüthrich
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas F. Mueller
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Schachtner
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
- *Correspondence: Thomas Schachtner, ; orcid.org/0000-0001-5549-4798
| |
Collapse
|
42
|
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.
Collapse
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
| | | | | | | | | |
Collapse
|
43
|
Fehr T, Hübel K, de Rougemont O, Abela I, Gaspert A, Güngör T, Hauri M, Helmchen B, Linsenmeier C, Müller T, Nilsson J, Riesterer O, Scandling JD, Schanz U, Cippà PE. Successful Induction of Specific Immunological Tolerance by Combined Kidney and Hematopoietic Stem Cell Transplantation in HLA-Identical Siblings. Front Immunol 2022; 13:796456. [PMID: 35173720 PMCID: PMC8841472 DOI: 10.3389/fimmu.2022.796456] [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: 10/16/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022] Open
Abstract
Induction of immunological tolerance has been the holy grail of transplantation immunology for decades. The only successful approach to achieve it in patients has been a combined kidney and hematopoietic stem cell transplantation from an HLA-matched or -mismatched living donor. Here, we report the first three patients in Europe included in a clinical trial aiming at the induction of tolerance by mixed lymphohematopoietic chimerism after kidney transplantation. Two female and one male patient were transplanted with a kidney and peripherally mobilized hematopoietic stem cells from their HLA-identical sibling donor. The protocol followed previous studies at Stanford University: kidney transplantation was performed on day 0 including induction with anti-thymocyte globulin followed by conditioning with 10x 1.2 Gy total lymphoid irradiation and the transfusion of CD34+ cells together with a body weight-adjusted dose of donor T cells on day 11. Immunosuppression consisted of cyclosporine A and steroids for 10 days, cyclosporine A and mycophenolate mofetil for 1 month, and then cyclosporine A monotherapy with tapering over 9–20 months. The 3 patients have been off immunosuppression for 4 years, 19 months and 8 months, respectively. No rejection or graft-versus-host disease occurred. Hematological donor chimerism was stable in the first, but slowly declining in the other two patients. A molecular microscope analysis in patient 2 revealed the genetic profile of a normal kidney. No relevant infections were observed, and the quality of life in all three patients is excellent. During the SARS-CoV-2 pandemic, all three patients were vaccinated with the mRNA vaccine BNT162b2 (Comirnaty®), and they showed excellent humoral and in 2 out 3 patients also cellular SARS-CoV-2-specific immunity. Thus, combined kidney and hematopoietic stem cell transplantation is a feasible and successful approach to induce specific immunological tolerance in the setting of HLA-matched sibling living kidney donation while maintaining immune responsiveness to an mRNA vaccine (ClinicalTrials.gov: NCT00365846).
Collapse
Affiliation(s)
- Thomas Fehr
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Department of Internal Medicine, Cantonal Hospital Graubuenden, Chur, Switzerland
- *Correspondence: Thomas Fehr,
| | - Kerstin Hübel
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Olivier de Rougemont
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Irene Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Ariana Gaspert
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Tayfun Güngör
- Division of Stem Cell Transplantation, University Children’s Hospital Zurich – Eleonore Foundation & Children`s Research Center (CRC), Zurich, Switzerland
| | - Mathias Hauri
- Division of Stem Cell Transplantation, University Children’s Hospital Zurich – Eleonore Foundation & Children`s Research Center (CRC), Zurich, Switzerland
| | - Birgit Helmchen
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Claudia Linsenmeier
- Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Müller
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Laboratory for Transplantation Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Riesterer
- Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - John D. Scandling
- Division of Nephrology, Stanford University School of Medicine, Stanford, CA, United States
| | - Urs Schanz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Pietro E. Cippà
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| |
Collapse
|
44
|
Fusfeld L, Menon S, Gupta G, Lawrence C, Masud SF, Goss TF. US payer budget impact of a microarray assay with machine learning to evaluate kidney transplant rejection in for-cause biopsies. J Med Econ 2022; 25:515-523. [PMID: 35345966 DOI: 10.1080/13696998.2022.2059221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AIM This study evaluates the economic impact to US commercial payers of MMDx-Kidney used in conjunction with histologic evaluation of for-cause kidney transplant biopsies. MATERIALS AND METHODS An Excel-based model was developed to assess the cost impact of histology plus MMDx-Kidney versus histology alone for the evaluation of potential rejection in kidney transplant patients who receive a for-cause biopsy. Different model time periods were assessed, ranging from 1 to 5 years post-biopsy. A targeted literature review was used to identify parameter estimates, validated by two external clinicians with expertise in managing kidney transplant rejection. A sensitivity analysis was conducted to evaluate the relative impact of key clinical and cost parameters. In particular, the model identified the magnitude of MMDx-Kidney's impact on graft failure from rejection that would be required for MMDx-Kidney to be cost-neutral. RESULTS By more accurately characterizing rejection, MMDx-Kidney is estimated to increase antirejection treatment costs by $1,126 per test. Nevertheless, a break-even analysis shows that the costs of MMDx-Kidney and anti-rejection medication, as well as the costs associated with an increase in the number of patients with functioning transplants, may be offset by reductions in costs associated with graft failure (i.e. costs of hospitalizations, dialysis, and repeat transplants) over 5 years, assuming MMDx-Kidney reduces annual graft failure from rejection by at least 5%. For the base case, with a 25% relative reduction in annual rate of graft failures from rejection, MMDx-Kidney increases overall costs incurred in the first year of the model but starts generating savings by the second year of the model. CONCLUSIONS Compared with histologic evaluation of for-cause kidney transplant biopsies alone, the use of MMDx-Kidney in conjunction with histologic evaluation improves the diagnoses of graft dysfunction and may have the potential to generate overall savings from reductions in rejection-related graft failure.
Collapse
Affiliation(s)
- Lauren Fusfeld
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
| | - Sreeranjani Menon
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
| | - Gaurav Gupta
- Division of Nephrology, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Salwa F Masud
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
| | - Thomas F Goss
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
| |
Collapse
|
45
|
Deville KA, Seifert ME. Biomarkers of alloimmune events in pediatric kidney transplantation. Front Pediatr 2022; 10:1087841. [PMID: 36741087 PMCID: PMC9895094 DOI: 10.3389/fped.2022.1087841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023] Open
Abstract
Alloimmune events such as the development of de novo donor-specific antibody (dnDSA), T cell-mediated rejection (TCMR), and antibody-mediated rejection (ABMR) are the primary contributors to kidney transplant failure in children. For decades, a creatinine-based estimated glomerular filtration rate (eGFR) has been the non-invasive gold standard biomarker for detecting clinically significant alloimmune events, but it suffers from low sensitivity and specificity, especially in smaller children and older allografts. Many clinically "stable" children (based on creatinine) will have alloimmune events known as "subclinical acute rejection" (based on biopsy) that merely reflect the inadequacy of creatinine-based estimates for alloimmune injury rather than a distinct phenotype from clinical rejection with allograft dysfunction. The poor biomarker performance of creatinine leads to many unnecessary surveillance and for-cause biopsies that could be avoided by integrating non-invasive biomarkers with superior sensitivity and specificity into current clinical paradigms. In this review article, we will present and appraise the current state-of-the-art in monitoring for alloimmune events in pediatric kidney transplantation. We will first discuss the current clinical standards for assessing the presence of alloimmune injury and predicting long-term outcomes. We will review principles of biomarker medicine and the application of comprehensive metrics to assess the performance of a given biomarker against the current gold standard. We will then highlight novel blood- and urine-based biomarkers (with special emphasis on pediatric biomarker studies) that have shown superior diagnostic and prognostic performance to the current clinical standards including creatinine-based eGFR. Finally, we will review some of the barriers to translating this research and implementing emerging biomarkers into common clinical practice, and present a transformative approach to using multiple biomarker platforms at different times to optimize the detection and management of critical alloimmune events in pediatric kidney transplant recipients.
Collapse
Affiliation(s)
- Kyle A Deville
- Division of Pediatric Nephrology, Department of Pediatrics, University of Alabama Heersink School of Medicine, Birmingham, AL, United States
| | - Michael E Seifert
- Division of Pediatric Nephrology, Department of Pediatrics, University of Alabama Heersink School of Medicine, Birmingham, AL, United States
| |
Collapse
|
46
|
Yatim KM, Azzi JR. Novel Biomarkers in Kidney Transplantation. Semin Nephrol 2022; 42:2-13. [DOI: 10.1016/j.semnephrol.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
47
|
Novotný M, Kment M, Viklický O. Adipose tissue macrophages and atherogenesis – a synergy with cholesterolaemia. Physiol Res 2021. [DOI: 10.33549//physiolres.934801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Antibody-mediated rejection (ABMR) is a major obstacle to the long-term success in kidney transplantation. Diagnosis of ABMR is determined according to the internationally recognized Banff criteria. However, a significant proportion of patients does not meet all the defined criteria, and the outcome of such cases remains poorly understood. The histology of ABMR frequently lacks sensitivity and specificity. More importantly, mixed forms of ABMR and T cell-mediated rejection as well as findings of nonspecific injury are common in clinical settings. Donor-specific anti-HLA antibodies (DSA) are detectable only in half of the ABMR cases by histology. Prognostic role of non-HLA antibodies against various endothelial proteins has been discussed. Antibody independent NK cell activation reflecting killer-cells’ inhibitory receptor incompatibility is suggested in microvascular inflammation in DSA negative patients. Molecular assessment of ABMR has been prioritized to overcome high interobserver variability and improve diagnostics in mixed forms of rejections and in DSA negative cases. Finally, donor-derived cell-free DNA detected in a recipient’s peripheral blood sample has been proposed as a noninvasive marker for diagnosis of graft rejection, and thus might serve as a liquid biopsy in the near future. Despite all achievements, diagnosing ABMR in kidney allografts remains to be a challenge in a significant number of cases.
Collapse
Affiliation(s)
| | | | - O Viklický
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic.
| |
Collapse
|
48
|
Callemeyn J, Lamarthée B, Koenig A, Koshy P, Thaunat O, Naesens M. Allorecognition and the spectrum of kidney transplant rejection. Kidney Int 2021; 101:692-710. [PMID: 34915041 DOI: 10.1016/j.kint.2021.11.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/05/2021] [Accepted: 11/08/2021] [Indexed: 12/18/2022]
Abstract
Detection of mismatched human leukocyte antigens by adaptive immune cells is considered as the main cause of transplant rejection, leading to either T-cell mediated rejection or antibody-mediated rejection. This canonical view guided the successful development of immunosuppressive therapies and shaped the diagnostic Banff classification for kidney transplant rejection that is used in clinics worldwide. However, several observations have recently emerged that question this dichotomization between T-cell mediated rejection and antibody-mediated rejection, related to heterogeneity in the serology, histology, and prognosis of the rejection phenotypes. In parallel, novel insights were obtained concerning the dynamics of donor-specific anti-human leukocyte antigen antibodies, the immunogenicity of donor-recipient non-human leukocyte antigen mismatches, and the autoreactivity against self-antigens. Moreover, the potential of innate allorecognition was uncovered, as exemplified by natural killer cell-mediated microvascular inflammation through missing self, and by the emerging evidence on monocyte-driven allorecognition. In this review, we highlight the gaps in the current classification of rejection, provide an overview of the expanding insights into the mechanisms of allorecognition, and critically appraise how these could improve our understanding and clinical approach to kidney transplant rejection. We argue that consideration of the complex interplay of various allorecognition mechanisms can foster a more integrated view of kidney transplant rejection and can lead to improved risk stratification, targeted therapies, and better outcome after kidney transplantation.
Collapse
Affiliation(s)
- Jasper Callemeyn
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Baptiste Lamarthée
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Necker-Enfants Malades Institute, French National Institute of Health and Medical Research (INSERM) Unit 1151, Paris, France
| | - Alice Koenig
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University Lyon, Lyon, France; Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France; Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Priyanka Koshy
- Department of Morphology and Molecular Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Olivier Thaunat
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University Lyon, Lyon, France; Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France; Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Maarten Naesens
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium.
| |
Collapse
|
49
|
Loupy A, Mengel M, Haas M. 30 years of the International Banff Classification for Allograft Pathology: The Past, Present and Future of Kidney Transplant Diagnostics. Kidney Int 2021; 101:678-691. [DOI: 10.1016/j.kint.2021.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
|
50
|
Shi T, Roskin K, Baker BM, Woodle ES, Hildeman D. Advanced Genomics-Based Approaches for Defining Allograft Rejection With Single Cell Resolution. Front Immunol 2021; 12:750754. [PMID: 34721421 PMCID: PMC8551864 DOI: 10.3389/fimmu.2021.750754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Solid organ transplant recipients require long-term immunosuppression for prevention of rejection. Calcineurin inhibitor (CNI)-based immunosuppressive regimens have remained the primary means for immunosuppression for four decades now, yet little is known about their effects on graft resident and infiltrating immune cell populations. Similarly, the understanding of rejection biology under specific types of immunosuppression remains to be defined. Furthermore, development of innovative, rationally designed targeted therapeutics for mitigating or preventing rejection requires a fundamental understanding of the immunobiology that underlies the rejection process. The established use of microarray technologies in transplantation has provided great insight into gene transcripts associated with allograft rejection but does not characterize rejection on a single cell level. Therefore, the development of novel genomics tools, such as single cell sequencing techniques, combined with powerful bioinformatics approaches, has enabled characterization of immune processes at the single cell level. This can provide profound insights into the rejection process, including identification of resident and infiltrating cell transcriptomes, cell-cell interactions, and T cell receptor α/β repertoires. In this review, we discuss genomic analysis techniques, including microarray, bulk RNAseq (bulkSeq), single-cell RNAseq (scRNAseq), and spatial transcriptomic (ST) techniques, including considerations of their benefits and limitations. Further, other techniques, such as chromatin analysis via assay for transposase-accessible chromatin sequencing (ATACseq), bioinformatic regulatory network analyses, and protein-based approaches are also examined. Application of these tools will play a crucial role in redefining transplant rejection with single cell resolution and likely aid in the development of future immunomodulatory therapies in solid organ transplantation.
Collapse
Affiliation(s)
- Tiffany Shi
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Krishna Roskin
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - E Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - David Hildeman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| |
Collapse
|