1
|
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
|
2
|
Mueller FB, Yang H, Li C, Dadhania DM, Xiang JZ, Salvatore S, Seshan SV, Sharma VK, Suthanthiran M, Muthukumar T. RNA-sequencing of Human Kidney Allografts and Delineation of T-Cell Genes, Gene Sets, and Pathways Associated With Acute T Cell-mediated Rejection. Transplantation 2024; 108:911-922. [PMID: 38291584 PMCID: PMC10963156 DOI: 10.1097/tp.0000000000004896] [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] [Indexed: 02/01/2024]
Abstract
BACKGROUND Delineation of T-cell genes, gene sets, pathways, and T-cell subtypes associated with acute T cell-mediated rejection (TCMR) may improve its management. METHODS We performed bulk RNA-sequencing of 34 kidney allograft biopsies (16 Banff TCMR and 18 no rejection [NR] biopsies) from 34 adult recipients of human kidneys. Computational analysis was performed to determine the differential intragraft expression of T-cell genes at the level of single-gene, gene set, and pathways. RESULTS T-cell signaling pathway gene sets for plenary T-cell activation were overrepresented in TCMR biopsies compared with NR biopsies. Heightened expression of T-cell signaling genes was validated using external TCMR biopsies. Pro- and anti-inflammatory immune gene sets were enriched, and metabolism gene sets were depleted in TCMR biopsies compared with NR biopsies. Gene signatures of regulatory T cells, Th1 cells, Th2 cells, Th17 cells, T follicular helper cells, CD4 tissue-resident memory T cells, and CD8 tissue-resident memory T cells were enriched in TCMR biopsies compared with NR biopsies. T-cell exhaustion and anergy were also molecular attributes of TCMR. Gene sets associated with antigen processing and presentation, and leukocyte transendothelial migration were overexpressed in TCMR biopsies compared with NR biopsies. Cellular deconvolution of graft infiltrating cells by gene expression patterns identified CD8 T cell to be the most abundant T-cell subtype infiltrating the allograft during TCMR. CONCLUSIONS Our delineation of intragraft T-cell gene expression patterns, in addition to yielding new biological insights, may help prioritize T-cell genes and T-cell subtypes for therapeutic targeting.
Collapse
Affiliation(s)
- Franco B. Mueller
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Hua Yang
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Darshana M. Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
- Department of Transplantation Medicine, NewYork Presbyterian Hospital-Weill Cornell Medical College, New York, NY
| | - Jenny Z. Xiang
- Genomics Resources Core Facility, Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY
| | - Steven Salvatore
- Division of Renal Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Surya V. Seshan
- Division of Renal Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Vijay K. Sharma
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
- Department of Transplantation Medicine, NewYork Presbyterian Hospital-Weill Cornell Medical College, New York, NY
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
- Department of Transplantation Medicine, NewYork Presbyterian Hospital-Weill Cornell Medical College, New York, NY
| |
Collapse
|
3
|
Mengel M, Adam BA. Emerging phenotypes in kidney transplant rejection. Curr Opin Organ Transplant 2024; 29:97-103. [PMID: 38032262 DOI: 10.1097/mot.0000000000001130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
PURPOSE OF REVIEW This review focuses on more recently emerging rejection phenotypes in the context of time post transplantation and the resulting differential diagnostic challenges. It also discusses how novel ancillary diagnostic tools can potentially increase the accuracy of biopsy-based rejection diagnosis. RECENT FINDINGS With advances in reducing immunological risk at transplantation and improved immunosuppression treatment renal allograft survival improved. However, allograft rejection remains a major challenge and represent a frequent course for allograft failure. With prolonged allograft survival, novel phenotypes of rejection are emerging, which can show complex overlap and transition between cellular and antibody-mediated rejection mechanisms as well as mixtures of acute/active and chronic diseases. With the emerging complexity in rejection phenotypes, it is crucial to achieve diagnostic accuracy in the individual patient. SUMMARY The prospective validation and adoption of novel molecular and computational diagnostic tools into well defined and appropriate clinical context of uses will improve our ability to accurately diagnose, stage, and grade allograft rejection.
Collapse
Affiliation(s)
- Michael Mengel
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | |
Collapse
|
4
|
Heeger PS, Haro MC, Jordan S. Translating B cell immunology to the treatment of antibody-mediated allograft rejection. Nat Rev Nephrol 2024; 20:218-232. [PMID: 38168662 DOI: 10.1038/s41581-023-00791-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2023] [Indexed: 01/05/2024]
Abstract
Antibody-mediated rejection (AMR), including chronic AMR (cAMR), causes ~50% of kidney allograft losses each year. Despite attempts to develop well-tolerated and effective therapeutics for the management of AMR, to date, none has obtained FDA approval, thereby highlighting an urgent unmet medical need. Discoveries over the past decade from basic, translational and clinical studies of transplant recipients have provided a foundation for developing novel therapeutic approaches to preventing and treating AMR and cAMR. These interventions are aimed at reducing donor-specific antibody levels, decreasing graft injury and fibrosis, and preserving kidney function. Innovative approaches emerging from basic science findings include targeting interactions between alloreactive T cells and B cells, and depleting alloreactive memory B cells, as well as donor-specific antibody-producing plasmablasts and plasma cells. Therapies aimed at reducing the cytotoxic antibody effector functions mediated by natural killer cells and the complement system, and their associated pro-inflammatory cytokines, are also undergoing evaluation. The complexity of the pathogenesis of AMR and cAMR suggest that multiple approaches will probably be required to treat these disease processes effectively. Definitive answers await results from large, double-blind, multicentre, randomized controlled clinical trials.
Collapse
Affiliation(s)
- Peter S Heeger
- Comprehensive Transplant Center, Department of Medicine, Division of Nephrology Cedars-Sinai Medical Center Los Angeles, Los Angeles, CA, USA
| | - Maria Carrera Haro
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA
| | - Stanley Jordan
- Comprehensive Transplant Center, Department of Medicine, Division of Nephrology Cedars-Sinai Medical Center Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
5
|
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
|
6
|
Beadle J, Papadaki A, Toulza F, Santos E, Willicombe M, McLean A, Peters J, Roufosse C. Application of the Banff Human Organ Transplant Panel to kidney transplant biopsies with features suspicious for antibody-mediated rejection. Kidney Int 2023; 104:526-541. [PMID: 37172690 DOI: 10.1016/j.kint.2023.04.015] [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: 10/10/2022] [Revised: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
The Banff Classification for Allograft Pathology includes the use of gene expression in the diagnosis of antibody-mediated rejection (AMR) of kidney transplants, but a predictive set of genes for classifying biopsies with 'incomplete' phenotypes has not yet been studied. Here, we developed and assessed a gene score that, when applied to biopsies with features of AMR, would identify cases with a higher risk of allograft loss. To do this, RNA was extracted from a continuous retrospective cohort of 349 biopsies randomized 2:1 to include 220 biopsies in a discovery cohort and 129 biopsies in a validation cohort. The biopsies were divided into three groups: 31 that fulfilled the 2019 Banff Criteria for active AMR, 50 with histological features of AMR but not meeting the full criteria (Suspicious-AMR), and 269 with no features of active AMR (No-AMR). Gene expression analysis using the 770 gene Banff Human Organ Transplant NanoString panel was carried out with LASSO Regression performed to identify a parsimonious set of genes predictive of AMR. We identified a nine gene score that was highly predictive of active AMR (accuracy 0.92 in the validation cohort) and was strongly correlated with histological features of AMR. In biopsies suspicious for AMR, our gene score was strongly associated with risk of allograft loss and independently associated with allograft loss in multivariable analysis. Thus, we show that a gene expression signature in kidney allograft biopsy samples can help classify biopsies with incomplete AMR phenotypes into groups that correlate strongly with histological features and outcomes.
Collapse
Affiliation(s)
- Jack Beadle
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College NHS Trust, London, UK.
| | - Artemis Papadaki
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Frederic Toulza
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Eva Santos
- H&I Laboratory, North West London Pathology, London, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College NHS Trust, London, UK
| | - Adam McLean
- Imperial College Renal and Transplant Centre, Imperial College NHS Trust, London, UK
| | - James Peters
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Candice Roufosse
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Department of Cellular Pathology, North West London Pathology, London, UK
| |
Collapse
|
7
|
Varol H, van der Elst G, Baan CC, van Baardwijk M, Hesselink DA, Duong van Huyen JP, Kramann R, Rabant M, van den Bosch TP, Clahsen-van Groningen MC. Mast Cells in Kidney Transplant Biopsies With Borderline T Cell-mediated Rejection and Their Relation to Chronicity. Transplant Direct 2023; 9:e1480. [PMID: 37096153 PMCID: PMC10121434 DOI: 10.1097/txd.0000000000001480] [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: 02/13/2023] [Accepted: 03/08/2023] [Indexed: 04/26/2023] Open
Abstract
Mast cells are potential contributors to chronic changes in kidney transplants (KTx). Here, the role of mast cells (MCs) in KTx is investigated in patients with minimal inflammatory lesions. Methods Fourty-seven KTx biopsies (2009-2018) with borderline pathological evidence for T cell-mediated rejection according to the Banff'17 Update were retrospectively included and corresponding clinical data was collected. Immunohistochemistry for tryptase was performed on formalin-fixed paraffin-embedded sections. Cortical MCs were counted and corrected for area (MC/mm²). Interstitial fibrosis was assessed by Sirius Red staining and quantified using digital image analysis (QuPath). Results Increased MC number was correlated to donor age (spearman's r = 0.35, P = 0.022), deceased donor kidneys (mean difference = 0.74, t [32.5] = 2.21, P = 0.035), and delayed graft function (MD = 0.78, t [33.9] = 2.43, P = 0.020). Increased MC number was also correlated to the amount of interstitial fibrosis (r = 0.42, P = 0.003) but did not correlate with transplant function over time (r = -0.14, P = 0.36). Additionally, transplant survival 2 y post-biopsy was not correlated to MC number (mean difference = -0.02, t [15.36] = -0.06, P = 0.96). Conclusions MC number in suspicious (borderline) for acute T cell-mediated rejection is correlated to interstitial fibrosis and time post-transplantation, suggesting MCs to be a marker for cumulative burden of tissue injury. There was no association between MCs and transplant function over time or transplant survival 2 y post-biopsy. It remains unclear whether MCs are just a bystander or have pro-inflammatory or anti-inflammatory effects in the KTx with minimal lesions.
Collapse
Affiliation(s)
- Hilal Varol
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Guus van der Elst
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carla C. Baan
- Department of Internal Medicine, Division of Nephrology and Renal Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Myrthe van Baardwijk
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Companion Diagnostics and Personalised Healthcare, Omnigen BV, Delft, Netherlands
| | - Dennis A. Hesselink
- Department of Internal Medicine, Division of Nephrology and Renal Transplantation, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Rafael Kramann
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
- Department of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Marion Rabant
- Department of Pathology, Necker Hospital, APHP, Paris, France
| | - Thierry P.P. van den Bosch
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marian C. Clahsen-van Groningen
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
8
|
Jagannathan G, Weins A, Daniel E, Crew RJ, Swanson SJ, Markowitz GS, D'Agati VD, Andeen NK, Rennke HG, Batal I. The pathologic spectrum of adenovirus nephritis in the kidney allograft. Kidney Int 2023; 103:378-390. [PMID: 36436678 DOI: 10.1016/j.kint.2022.10.025] [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: 06/30/2022] [Revised: 09/16/2022] [Accepted: 10/28/2022] [Indexed: 11/25/2022]
Abstract
Adenovirus nephritis (ADVN) is a rare and understudied complication of kidney transplantation. Unlike BK virus nephropathy (BKVN), our knowledge of clinicopathologic manifestations of ADVN remains rudimentary and essentially limited to case reports. To expand on this, we retrospectively studied 11 kidney transplant recipients with ADVN and compared their allograft biopsies to 33 kidney transplant recipients with BKVN using conventional microscopy and the 770 gene Nanostring Banff Human Organ Transplant Profiling Panel. Patients with ADVN had a median age of 44 years, were predominantly male, and developed ADVN at a median of 31 months post-transplantation. Eight patients presented with fever and ten had hematuria. The most common histologic manifestations included granulomas (82%), tubulocentric inflammation (73%), and tubular degenerative changes consistent with acute tubular necrosis (73%). During a median follow-up of 55 months after biopsy, three patients developed allograft failure from subsequent acute rejection. All seven patients with available follow-up PCR showed resolution of viremia at a median of 30 days after diagnosis. Compared to BKVN, ADVN demonstrated more granulomas and less tubulointerstitial scarring. On follow-up, patients with ADVN had more rapid clearance of viral DNA from plasma. Transcriptomic analyses showed that ADVN had increased expression of several pro-inflammatory transcriptomes, mainly related to innate immunity, was associated with increased expression of transcripts with inhibitory effects on inflammatory response and showed higher enrichment with neutrophils, which can cause aggressive but short-lasting damage. Thus, we demonstrate that, despite its association with aggressive neutrophil-rich inflammation, ADVN does not often lead to allograft failure. Hence, preventing subsequent acute rejection following resolution of ADVN may improve allograft survival.
Collapse
Affiliation(s)
- Geetha Jagannathan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Astrid Weins
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Emily Daniel
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA
| | - Russel J Crew
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA
| | - Sidney J Swanson
- Department of Surgery, Christiana Hospital, Newark, Delaware, USA
| | - Glen S Markowitz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Vivette D D'Agati
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Nicole K Andeen
- Department of Pathology, Oregon Health & Science University, Portland, Oregon, USA
| | - Helmut G Rennke
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ibrahim Batal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA.
| |
Collapse
|
9
|
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
|
10
|
Johnson AC, Silva JAF, Kim SC, Larsen CP. Progress in kidney transplantation: The role for systems immunology. Front Med (Lausanne) 2022; 9:1070385. [PMID: 36590970 PMCID: PMC9800623 DOI: 10.3389/fmed.2022.1070385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
The development of systems biology represents an immense breakthrough in our ability to perform translational research and deliver personalized and precision medicine. A multidisciplinary approach in combination with use of novel techniques allows for the extraction and analysis of vast quantities of data even from the volume and source limited samples that can be obtained from human subjects. Continued advances in microfluidics, scalability and affordability of sequencing technologies, and development of data analysis tools have made the application of a multi-omics, or systems, approach more accessible for use outside of specialized centers. The study of alloimmune and protective immune responses after solid organ transplant offers innumerable opportunities for a multi-omics approach, however, transplant immunology labs are only just beginning to adopt the systems methodology. In this review, we focus on advances in biological techniques and how they are improving our understanding of the immune system and its interactions, highlighting potential applications in transplant immunology. First, we describe the techniques that are available, with emphasis on major advances that allow for increased scalability. Then, we review initial applications in the field of transplantation with a focus on topics that are nearing clinical integration. Finally, we examine major barriers to adapting these methods and discuss potential future developments.
Collapse
|
11
|
Adam BA, Murakami N, Reid G, Du K, Jasim R, Boils CL, Bu L, Hill PD, Murray AG, Renaudin K, Roufosse C, Weins A, Wen K, Riella LV, Mengel M. Gene Expression Profiling in Kidney Transplants with Immune Checkpoint Inhibitor-Associated Adverse Events. Clin J Am Soc Nephrol 2021; 16:1376-1386. [PMID: 34244334 PMCID: PMC8729568 DOI: 10.2215/cjn.00920121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Immune checkpoint inhibitors are increasingly used to treat various malignancies, but their application in patients with kidney transplants is complicated by high allograft rejection rates. Immune checkpoint inhibitor-associated rejection is a novel, poorly understood entity demonstrating overlapping histopathologic features with immune checkpoint inhibitor-associated acute interstitial nephritis, which poses a challenge for diagnosis and clinical management. We sought to improve the understanding of these entities through biopsy-based gene expression analysis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS NanoString was used to measure and compare the expression of 725 immune-related genes in 75 archival kidney biopsies, including a 25-sample discovery cohort comprising pure T cell-mediated rejection and immune checkpoint inhibitor-associated acute interstitial nephritis and an independent 50-sample validation cohort comprising immune checkpoint inhibitor-associated acute interstitial nephritis, immune checkpoint inhibitor-associated T cell-mediated rejection, immune checkpoint inhibitor-associated crescentic GN, drug-induced acute interstitial nephritis, BK virus nephropathy, and normal biopsies. RESULTS Significant molecular overlap was observed between immune checkpoint inhibitor-associated acute interstitial nephritis and T cell-mediated rejection. Nevertheless, IFI27, an IFN-α-induced transcript, was identified and validated as a novel biomarker for differentiating immune checkpoint inhibitor-associated T cell-mediated rejection from immune checkpoint inhibitor-associated acute interstitial nephritis (validation cohort: P<0.001, area under the receiver operating characteristic curve =100%, accuracy =86%). Principal component analysis revealed heterogeneity in inflammatory gene expression patterns within sample groups; however, immune checkpoint inhibitor-associated T cell-mediated rejection and immune checkpoint inhibitor-associated acute interstitial nephritis both demonstrated relatively more molecular overlap with drug-induced acute interstitial nephritis than T cell-mediated rejection, suggesting potential dominance of hypersensitivity mechanisms in these entities. CONCLUSIONS These results indicate that, although there is significant molecular similarity between immune checkpoint inhibitor-associated rejection and acute interstitial nephritis, biopsy-based measurement of IFI27 gene expression represents a potential biomarker for differentiating these entities.
Collapse
Affiliation(s)
- Benjamin A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Naoka Murakami
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Graeme Reid
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Katie Du
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Ruqaya Jasim
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Lihong Bu
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Peter D. Hill
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Allan G. Murray
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karine Renaudin
- Department of Pathology, Nantes University Hospital, Nantes, France
| | - Candice Roufosse
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Astrid Weins
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Kevin Wen
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Leonardo V. Riella
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
12
|
Toulza F, Dominy K, Willicombe M, Beadle J, Santos E, Cook HT, Szydlo RM, McLean A, Roufosse C. Diagnostic application of transcripts associated with antibody-mediated rejection in kidney transplant biopsies. Nephrol Dial Transplant 2021; 37:1576-1584. [PMID: 34320215 PMCID: PMC9317169 DOI: 10.1093/ndt/gfab231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Indexed: 11/22/2022] Open
Abstract
Background The diagnosis of antibody-mediated rejection (AMR) is reached using the Banff Classification for Allograft Pathology, which now includes gene expression analysis. In this study, we investigate the application of ‘increased expression of thoroughly validated gene transcripts/classifiers strongly associated with AMR’ as diagnostic criteria. Method We used quantitative real-time polymerase chain reaction for 10 genes associated with AMR in a retrospective cohort of 297 transplant biopsies, including biopsies that met the full diagnostic criteria for AMR, even without molecular data (AMR, n = 27), biopsies that showed features of AMR, but that would only meet criteria for AMR with increased transcripts [suspicious for AMR (AMRsusp), n = 49] and biopsies that would never meet criteria for AMR (No-AMR, n = 221). Results A 10-gene AMR score trained by a receiver-operating characteristic to identify AMR found 16 cases with a high score among the AMRsusp cases (AMRsusp-high) that had significantly worse graft survival than those with a low score (AMRsusp-low; n = 33). In both univariate and multivariate Cox regression analysis, the AMR 10-gene score was significantly associated with an increased hazard ratio (HR) for graft loss (GL) in the AMRsusp group (HR = 1.109, P = 0.004 and HR = 1.138, P = 0.012, respectively), but not in the whole cohort. Net reclassification index and integrated discrimination improvement analyses demonstrated improved risk classification and superior discrimination, respectively, for GL when considering the gene score in addition to histological and serological data, but only in the AMRsusp group, not the whole cohort. Conclusions This study provides evidence that a gene score strongly associated with AMR helps identify cases at higher risk of GL in biopsies that are suspicious for AMR but do not meet full criteria.
Collapse
Affiliation(s)
- Frederic Toulza
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
| | - Kathy Dominy
- Molecular Pathology Laboratory, North West London Pathology, London, United Kingdom
| | - Michelle Willicombe
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom.,Imperial College Renal and Transplant Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Jack Beadle
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
| | - Eva Santos
- Histocompatibility and Immunogenetics, North West London Pathology, London, United Kingdom
| | - H Terence Cook
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
| | - Richard M Szydlo
- Imperial College, Medical Statistician, Dept Immunology and Inflammation, London, United Kingdom
| | - Adam McLean
- Imperial College Renal and Transplant Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Candice Roufosse
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
| |
Collapse
|
13
|
Impact of Belatacept Conversion on Renal Function, Histology, and Gene Expression in Kidney Transplant Patients With Chronic Active Antibody-mediated Rejection. Transplantation 2021; 105:660-667. [PMID: 32510913 DOI: 10.1097/tp.0000000000003278] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Here, we present our initial experience with a prospective protocol of belatacept conversion in patients with chronic active antibody-mediated rejection (caAMR) and a high degree of chronicity at the time of diagnosis. METHODS We converted 19 patients (mean age, 45 ± 12 y) with biopsy-proven caAMR from tacrolimus to belatacept at a median of 44 months post-kidney transplant. RESULTS At a median of 29 months (interquartile range, 16-46 mo) postconversion, death-censored graft and patient survivals were 89% and 95%, respectively. When compared to a 1:2 propensity-matched control cohort from the INSERM U970 registry maintained on calcineurin inhibitor, the belatacept group had progressive improvement (P = 0.02) in estimated glomerular filtration rate from a mean of 33.9 ± 10 at baseline to 37.8 ± 13 at 6 months and 38.5 ± 12 mL/min/1.73 m2 at 12 months postconversion, as compared to a steady decline noted in the controls (36.2 [baseline] → 33.1 [6 mo] → 32.7 mL/min/1.73 m2 [12 mo] of follow-up). A paired histologic comparison of preconversion and postconversion (performed at median 9.5 mo postconversion) biopsies showed no worsening in microvascular inflammation or chronicity. The paired tissue gene expression analysis showed improved mean total rejection score (0.68 ± 0.26-0.56 ± 0.33; P = 0.02) and a trend toward improved antibody-mediated rejection score (0.64 ± 0.34-0.56 ± 0.39; P = 0.06). CONCLUSIONS Here, we report that in patients diagnosed with caAMR who were not subjected to intensive salvage immunosuppressive therapies, isolated belatacept conversion alone was associated with stabilization in renal function. These results are bolstered by molecular evidence of improved inflammation.
Collapse
|
14
|
Correlation of Donor-Derived Cell-free DNA with Histology and Molecular Diagnoses of Kidney Transplant Biopsies. Transplantation 2021; 106:1061-1070. [PMID: 34075006 DOI: 10.1097/tp.0000000000003838] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Circulating donor-derived cell free DNA (cfDNA), a minimally invasive diagnostic tool for kidney transplant rejection, was validated using traditional histology. The Molecular Microscope (MMDx) tissue gene expression platform may provide increased precision to traditional histology. METHODS In this single-center prospective study of 208 biopsies (median=5.8 months) post-transplant, we report on the calibration of cfDNA with simultaneous biopsy assessments using MMDx and histology by Area under the curve (AUC) analyses for optimal criterion, as well as for, previously published cfDNA cut-offs ≤0.21% to 'rule-out' rejection and ≥1% to 'rule-in' rejection. RESULTS There were significant discrepancies between histology and MMDx, with MMDx identifying more antibody-mediated rejection (65; 31%) than histology (43; 21%); the opposite was true for T-cell mediated rejection [TCMR; histology: 27 (13%) vs MMDx: 13 (6%)]. Most of the TCMR discrepancies were seen for histologic borderline/1A TCMR. AUC Curves for cfDNA and prediction of rejection were slightly better with MMDx (AUC=0.80; 95%CI: 0.74-0.86) vs. histology (AUC=0.75; 95%CI: 0.69-0.81). A cfDNA≤0.21% had similar sensitivity (~91%) to 'rule-out' rejection by histology and MMDx. Specificity was slightly higher with MMDx (92%) compared with histology (85%) to 'rule-in' rejection using cfDNA criterion≥1%. Strong positive quantitative correlations were observed between cfDNA scores and molecular acute kidney injury (AKI) for both 'rejection' and 'nonrejection' biopsies. CONCLUSIONS Molecular diagnostics using tissue gene expression and blood-based donor-derived cell-free DNA may add precision to some cases of traditional histology. The positive correlation of cfDNA with molecular AKI suggests a dose-dependent association with tissue injury irrespective of rejection characteristics.
Collapse
|
15
|
Gupta G, Raynaud M, Kumar D, Sanghi P, Chang J, Kimball P, Kang L, Levy M, Sharma A, Bhati CS, Kamal L, Yakubu I, Massey HD, Kidd C, King AL, Halloran PF. Impact of belatacept conversion on kidney transplant function, histology, and gene expression - a single-center study. Transpl Int 2020; 33:1458-1471. [PMID: 32790889 DOI: 10.1111/tri.13718] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/28/2020] [Accepted: 08/07/2020] [Indexed: 11/28/2022]
Abstract
Prior studies on belatacept conversion from calcineurin inhibitor (CNI) have been limited by an absence of postconversion surveillance biopsies that could underestimate subclinical rejection, or a case-controlled design. A total of 53 adult patients with allograft dysfunction underwent belatacept conversion (median: 6 months) post-transplant. At a median follow-up = 2.5 years, patient survival was 94% with a death-censored graft survival of 85%. Seven (13%) patients had acute rejection (including 3 subclinical) at median 6 months postconversion. Overall, eGFR improved (P = <0.001) from baseline = 31±15 to 40.2 ± 17.6 ml/min/1.73m2 by 6 months postconversion, but then stayed stable. This improvement was also observed (P < 0.001) in comparison with a propensity matched control cohort on CNI, where eGFR stayed stable (mean ~ 32ml/min/1.72m2 ) over 2-year follow-up. Patients converted < 6 months post-transplant were more likely to have a long-term improvement in kidney function. Paired gene expression analysis of 30 (of 53) consecutive pre- and postconversion surveillance biopsies did not reveal changes in inflammation/acute injury; although atrophy-fibrosis score worsened (mean = 0.28 to 0.44; P = 0.005). Thus, improvement in renal function with belatacept conversion occurred early and then sustained in comparison with controls where renal function remained unchanged overtime. We were unable to show molecular signals that could be related to CNI administration and regressed after withdrawal.
Collapse
Affiliation(s)
- Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Dhiren Kumar
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, USA
| | - Pooja Sanghi
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, USA
| | - Jessica Chang
- Alberta Transplant Applied Genomics Center, Edmonton, AB, Canada
| | - Pam Kimball
- Division of Transplant Surgery, Virginia Commonwealth University, Richmond, VA, USA
| | - Le Kang
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Marlon Levy
- Division of Transplant Surgery, Virginia Commonwealth University, Richmond, VA, USA
| | - Amit Sharma
- Division of Transplant Surgery, Virginia Commonwealth University, Richmond, VA, USA
| | - Chandra S Bhati
- Division of Transplant Surgery, Virginia Commonwealth University, Richmond, VA, USA
| | - Layla Kamal
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, USA
| | - Idris Yakubu
- Division of Transplant Surgery, Virginia Commonwealth University, Richmond, VA, USA
| | - Hugh D Massey
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Chelsea Kidd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA
| | - Anne L King
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, USA
| | | |
Collapse
|
16
|
Immunological follow-up of patients with renal transplants: A proposal for clinical practice in Colombia. ACTA ACUST UNITED AC 2020; 40:479-486. [PMID: 33030826 PMCID: PMC7666855 DOI: 10.7705/biomedica.5092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Indexed: 11/21/2022]
Abstract
Graft damage is a process that starts at the moment of transplantation, due to comorbidities of receptor, donor status, ischemia time, ischemia-reperfusion phenomenon, among others, those induce metabolic and immune factors that ultimately trigger clinical manifestations of graft dysfunction. However, the preclinical progression between the time of transplantation and the appearance of signs and symptoms of graft damage can take weeks to years.
Therefore, the implementation of rational monitoring approaches during the post-transplantation period is critical and should include not only the clinical follow-up but also anticipate immunological graft damage. In the present essay, we propose an immunological monitoring algorithm for the post-renal transplantation period.
Collapse
|
17
|
Mengel M, Loupy A, Haas M, Roufosse C, Naesens M, Akalin E, Clahsen‐van Groningen MC, Dagobert J, Demetris AJ, Duong van Huyen J, Gueguen J, Issa F, Robin B, Rosales I, Von der Thüsen JH, Sanchez‐Fueyo A, Smith RN, Wood K, Adam B, Colvin RB. Banff 2019 Meeting Report: Molecular diagnostics in solid organ transplantation-Consensus for the Banff Human Organ Transplant (B-HOT) gene panel and open source multicenter validation. Am J Transplant 2020; 20:2305-2317. [PMID: 32428337 PMCID: PMC7496585 DOI: 10.1111/ajt.16059] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/19/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023]
Abstract
This meeting report from the XV Banff conference describes the creation of a multiorgan transplant gene panel by the Banff Molecular Diagnostics Working Group (MDWG). This Banff Human Organ Transplant (B-HOT) panel is the culmination of previous work by the MDWG to identify a broadly useful gene panel based on whole transcriptome technology. A data-driven process distilled a gene list from peer-reviewed comprehensive microarray studies that discovered and validated their use in kidney, liver, heart, and lung transplant biopsies. These were supplemented by genes that define relevant cellular pathways and cell types plus 12 reference genes used for normalization. The 770 gene B-HOT panel includes the most pertinent genes related to rejection, tolerance, viral infections, and innate and adaptive immune responses. This commercially available panel uses the NanoString platform, which can quantitate transcripts from formalin-fixed paraffin-embedded samples. The B-HOT panel will facilitate multicenter collaborative clinical research using archival samples and permit the development of an open source large database of standardized analyses, thereby expediting clinical validation studies. The MDWG believes that a pathogenesis and pathway based molecular approach will be valuable for investigators and promote therapeutic decision-making and clinical trials.
Collapse
Affiliation(s)
- Michael Mengel
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonCanada
| | - Alexandre Loupy
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Mark Haas
- Department of Pathology and Laboratory MedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Candice Roufosse
- Department of Immunology and InflammationImperial College London and North West London PathologyLondonUK
| | - Maarten Naesens
- Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium,Department of NephrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Enver Akalin
- Montefiore‐Einstein Center for TransplantationMontefiore Medical CenterBronxNew YorkUSA
| | | | - Jessy Dagobert
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Anthony J. Demetris
- Department of PathologyUniversity of Pittsburgh Medical CenterMontefiore, PittsburghPennsylvaniaUSA
| | - Jean‐Paul Duong van Huyen
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Juliette Gueguen
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Fadi Issa
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Blaise Robin
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Ivy Rosales
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | | | | | - Rex N. Smith
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Kathryn Wood
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Benjamin Adam
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonCanada
| | - Robert B. Colvin
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| |
Collapse
|
18
|
Enhancing the Value of Histopathological Assessment of Allograft Biopsy Monitoring. Transplantation 2020; 103:1306-1322. [PMID: 30768568 DOI: 10.1097/tp.0000000000002656] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Traditional histopathological allograft biopsy evaluation provides, within hours, diagnoses, prognostic information, and mechanistic insights into disease processes. However, proponents of an array of alternative monitoring platforms, broadly classified as "invasive" or "noninvasive" depending on whether allograft tissue is needed, question the value proposition of tissue histopathology. The authors explore the pros and cons of current analytical methods relative to the value of traditional and illustrate advancements of next-generation histopathological evaluation of tissue biopsies. We describe the continuing value of traditional histopathological tissue assessment and "next-generation pathology (NGP)," broadly defined as staining/labeling techniques coupled with digital imaging and automated image analysis. Noninvasive imaging and fluid (blood and urine) analyses promote low-risk, global organ assessment, and "molecular" data output, respectively; invasive alternatives promote objective, "mechanistic" insights by creating gene lists with variably increased/decreased expression compared with steady state/baseline. Proponents of alternative approaches contrast their preferred methods with traditional histopathology and: (1) fail to cite the main value of traditional and NGP-retention of spatial and inferred temporal context available for innumerable objective analyses and (2) belie an unfamiliarity with the impact of advances in imaging and software-guided analytics on emerging histopathology practices. Illustrative NGP examples demonstrate the value of multidimensional data that preserve tissue-based spatial and temporal contexts. We outline a path forward for clinical NGP implementation where "software-assisted sign-out" will enable pathologists to conduct objective analyses that can be incorporated into their final reports and improve patient care.
Collapse
|
19
|
Sánchez-Pla A, Salicrú M, Ocaña J. An equivalence approach to the integrative analysis of feature lists. BMC Bioinformatics 2019; 20:441. [PMID: 31455218 PMCID: PMC6712676 DOI: 10.1186/s12859-019-3008-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/29/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting lists of genes into predefined levels of the Gene Ontology, in such a way that a multinomial model can be used for estimation and testing. Of particular interest is the fact that it may be used for proving equivalence (in the sense of "enough similarity") between two lists, instead of proving differences between them, which seems conceptually better suited to the end goal of establishing similarity among gene lists. An equivalence method has been derived that uses a distance-based approach and the confidence interval inclusion principle. Equivalence is declared if the upper limit of a one-sided confidence interval for the distance between two profiles is below a pre-established equivalence limit. RESULTS In this work, this method is extended to establish the equivalence of any number of gene lists. Additionally, an algorithm to obtain the smallest equivalence limit that would allow equivalence between two or more lists to be declared is presented. This algorithm is at the base of an iterative method of graphic visualization to represent the most to least equivalent gene lists. These methods deal adequately with the problem of adjusting for multiple testing. The applicability of these techniques is illustrated in two typical situations: (i) a collection of cancer-related gene lists, suggesting which of them are more reasonable to combine -as claimed by the authors- and (ii) a collection of pathogenesis-based transcript sets, showing which of these are more closely related. The methods developed are available in the goProfiles Bioconductor package. CONCLUSIONS The method provides a simple yet powerful and statistically well-grounded way to classify a set of genes or other feature lists by establishing their equivalence at a given equivalence threshold. The classification results can be viewed using standard visualization methods. This may be applied to a variety of problems, from deciding whether a series of datasets generating the lists can be combined to the simplification of groups of lists.
Collapse
Affiliation(s)
- Alex Sánchez-Pla
- Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Avinguda Diagonal, 648, Barcelona, 08028 Spain
| | - Miquel Salicrú
- Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Avinguda Diagonal, 648, Barcelona, 08028 Spain
| | - Jordi Ocaña
- Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Avinguda Diagonal, 648, Barcelona, 08028 Spain
| |
Collapse
|
20
|
Barner M, DeKoning J, Kashi Z, Halloran P. Recent Advancements in the Assessment of Renal Transplant Dysfunction with an Emphasis on Microarray Molecular Diagnostics. Clin Lab Med 2018; 38:623-635. [PMID: 30420057 DOI: 10.1016/j.cll.2018.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conventional assessment of renal transplant rejection and injury through use of histology, C4d staining, and HLA antibody testing, has been the standard approach to transplant management. By many measures, these methods of conventional assessment may be considered flawed, particularly with the subjective nature of histologic diagnoses. The Alberta Transplant Applied Genomics Center has developed the Molecular Microscope diagnostic system, which uses microarrays to measure gene expression. These data are analyzed using classifiers (weighted equations) that compare the tested biopsy to a proprietary reference set of biopsies to provide objective measures of the status of the renal transplant.
Collapse
Affiliation(s)
- Meagan Barner
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA
| | - Jenefer DeKoning
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA
| | - Zahra Kashi
- Kashi Clinical Laboratories, 10101 Southwest Barbur Boulevard Suite 200, Portland, OR 97219, USA.
| | - Phillip Halloran
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Alberta Transplant Applied Genomics Center, 250 Heritage Medical Research Centre, Edmonton, Alberta T6G 2S2, Canada; Transcriptome Sciences Inc, Edmonton, Alberta, Canada
| |
Collapse
|
21
|
Kumar D, Yakubu I, Cooke RH, Halloran PF, Gupta G. Belatacept rescue for delayed kidney allograft function in a patient with previous combined heart-liver transplant. Am J Transplant 2018; 18:2613-2614. [PMID: 29981184 DOI: 10.1111/ajt.15003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Dhiren Kumar
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, USA
| | - Idris Yakubu
- Department of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Richard H Cooke
- Division of Cardiology, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, USA
| |
Collapse
|
22
|
Molecular Assessment of C4d-Positive Renal Transplant Biopsies Without Evidence of Rejection. Kidney Int Rep 2018; 4:148-158. [PMID: 30596178 PMCID: PMC6308373 DOI: 10.1016/j.ekir.2018.09.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/17/2018] [Accepted: 09/10/2018] [Indexed: 12/28/2022] Open
Abstract
Introduction Immunohistochemical staining for C4d in peritubular capillaries has been part of antibody-mediated rejection (AbMR) definition in the Banff Classification for Allograft Pathology since 2003. However, it has limited sensitivity and specificity, therefore the clinical significance of C4d-positive biopsies without evidence of rejection (C4d+ WER) is unknown. We investigated the transcript levels of genes associated with AbMR in C4d+ WER biopsies from both ABO-compatible and incompatible renal transplant patients. Methods RNA was extracted from formalin-fixed paraffin-embedded renal transplant biopsies (n = 125) and gene expression analysis of 35 AbMR-associated transcripts carried out using the NanoString nCounter system. Results AbMR-associated transcripts were significantly increased in samples with AbMR or suspicious AbMR. A subgroup of 17 of 35 transcripts that best distinguished AbMR from C4d-negative biopsies without evidence of rejection was used to study C4d+ WER samples. There was no differential expression between C4d-negative and C4d+ WER from both ABO-incompatible and -compatible transplants. The geometric mean of 17 differentially expressed genes was used to assign the C4d+ WER biopsies a high- or low-AbMR transcript score. Follow-up biopsies showed AbMR within 1 year of initial biopsy in 5 of 7 high-AbMR transcript patients but only 2 of 46 low-AbMR transcript patients. In multivariate logistic regression analysis, elevated transcript levels in a C4d+ WER biopsy were associated with increased odds for biopsy-proven AbMR on follow-up (P = 0.032, odds ratio 16.318), whereas factors including donor-specific antibody (DSA) status and time since transplantation were not. Conclusion Gene expression analysis in C4d+ WER samples has the potential to identify patients at higher risk of developing AbMR.
Collapse
|
23
|
Eikrem Ø, Walther TC, Flatberg A, Beisvag V, Strauss P, Farstad M, Beisland C, Koch E, Mueller TF, Marti HP. Fine needle aspirates of kidneys: a promising tool for RNA sequencing in native and transplanted kidneys. BMC Nephrol 2018; 19:221. [PMID: 30185151 PMCID: PMC6126030 DOI: 10.1186/s12882-018-1012-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/23/2018] [Indexed: 01/17/2023] Open
Abstract
Background Transcriptome analysis is emerging as emerging as a promising tool to enhance precision of diagnosis and monitoring in solid organ transplantation. Clinical progress has however been hampered by the current reliance on samples from core needle biopsies. This proof-of-principle study examined whether fine needle aspirates, being less invasive, permit the ascertainment of the identical molecular information as core biopsies. Methods We collected fine needles aspirates from various needle sizes (G19, 21, 23, 25) and the corresponding core biopsies (G16 needle) of non-tumor tissue of full nephrectomy specimens from patients suffering from clear cell renal cell carcinoma (n = 11). RNA expression patterns of two gene sets (156 genes) were executed using targeted RNA sequencing in samples from fine needle vs. core needle samples. A subgroup of kidneys (n = 6) also underwent whole transcriptome RNA sequencing from core biopsies of tumor and peri-tumoral normal tissue (Tru Seq RNA Access, Illumina). Results Samples from all needle sizes except two G25 aspirates yielded RNA potentially suitable for sequencing of both gene sets. The mRNA expression patterns of the two gene sets were highly correlated between fine needle aspirates (G23) and corresponding (G16) core biopsies (r = 0.985 and 0.982, respectively). This close correlation was further documented by heat map, Principal Component Analyses (PCA) and whole transcription RNA sequencing. The similarity between fine neddle aspirates and core needle biopsies was additionally confirmed in the subgroup with complete RNA sequencing. Conclusions Fine needle biopsies yield similar genomic information to core needle biopsies. The less invasive nature of fine needle biopsies may therefore permit more frequent molecular monitoring and a more targeted use of core needle biopsies in native and especially in transplanted kidneys.
Collapse
Affiliation(s)
- Øystein Eikrem
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tedd C Walther
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vidar Beisvag
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Magnus Farstad
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Christian Beisland
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway.,Department of Urology, Haukeland University Hospital, Bergen, Norway
| | - Even Koch
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Thomas F Mueller
- Division of Nephrology, Department of Medicine, University Hospital of Zurich, Zurich, Switzerland
| | - Hans-Peter Marti
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway. .,Department of Medicine, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
24
|
Agbor-Enoh S, Jackson AM, Tunc I, Berry GJ, Cochrane A, Grimm D, Davis A, Shah P, Brown AW, Wang Y, Timofte I, Shah P, Gorham S, Wylie J, Goodwin N, Jang MK, Marishta A, Bhatti K, Fideli U, Yang Y, Luikart H, Cao Z, Pirooznia M, Zhu J, Marboe C, Iacono A, Nathan SD, Orens J, Valantine HA, Khush K. Late manifestation of alloantibody-associated injury and clinical pulmonary antibody-mediated rejection: Evidence from cell-free DNA analysis. J Heart Lung Transplant 2018; 37:925-932. [DOI: 10.1016/j.healun.2018.01.1305] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 10/24/2022] Open
|
25
|
Agniel D, Hejblum BP. Variance component score test for time-course gene set analysis of longitudinal RNA-seq data. Biostatistics 2018; 18:589-604. [PMID: 28334305 DOI: 10.1093/biostatistics/kxx005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/04/2017] [Indexed: 01/28/2023] Open
Abstract
As gene expression measurement technology is shifting from microarrays to sequencing, the statistical tools available for their analysis must be adapted since RNA-seq data are measured as counts. It has been proposed to model RNA-seq counts as continuous variables using nonparametric regression to account for their inherent heteroscedasticity. In this vein, we propose tcgsaseq, a principled, model-free, and efficient method for detecting longitudinal changes in RNA-seq gene sets defined a priori. The method identifies those gene sets whose expression varies over time, based on an original variance component score test accounting for both covariates and heteroscedasticity without assuming any specific parametric distribution for the (transformed) counts. We demonstrate that despite the presence of a nonparametric component, our test statistic has a simple form and limiting distribution, and both may be computed quickly. A permutation version of the test is additionally proposed for very small sample sizes. Applied to both simulated data and two real datasets, tcgsaseq is shown to exhibit very good statistical properties, with an increase in stability and power when compared to state-of-the-art methods ROAST (rotation gene set testing), edgeR, and DESeq2, which can fail to control the type I error under certain realistic settings. We have made the method available for the community in the R package tcgsaseq.
Collapse
Affiliation(s)
- Denis Agniel
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA 02115, USA
| | - Boris P Hejblum
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA University of Bordeaux, ISPED, INSERM U1219, INRIA SISTM, 146 rue Léo Saignat, 33076 Bordeaux, FRANCE Vaccine Research Institute, Créteil, FRANCE
| |
Collapse
|
26
|
Smith RN, Matsunami M, Adam BA, Rosales IA, Oura T, Cosimi AB, Kawai T, Mengel M, Colvin RB. RNA expression profiling of nonhuman primate renal allograft rejection identifies tolerance. Am J Transplant 2018; 18:1328-1339. [PMID: 29288556 PMCID: PMC6021122 DOI: 10.1111/ajt.14637] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023]
Abstract
Tolerance induction to prevent allograft rejection is a long-standing clinical goal. However, convincing and dependable tolerance identification remains elusive. Hypothesizing that intragraft RNA expression is informative in both rejection and tolerance, we profile intrarenal allograft RNA expression in a mixed chimerism renal allograft model of cynomolgus monkeys and identify biologically significant tolerance. Analysis of 67 genes identified 3 dominant factors, each with a different pattern of gene expressions, relating to T cell-mediated rejection (TCMR), chronic antibody-mediated rejection (CAMR), or Tolerance. Clustering these 3 factors created 9 groups. One of the 9 clustered groups, the Tolerance cluster, showed the lowest probability of terminal rejection, the longest duration of allograft survival, and the lowest relative risk of terminal rejection. The Tolerance factor consists of a novel set of gene expressions including cytokine and immunoregulatory genes adding mechanistic insights into tolerance. The Tolerance factor could not be identified within current pathologic diagnostic categories. The TCMR and CAMR factors are dominant to the Tolerance factor, causing rejection even if the Tolerance factor is present. These 3 factors determine the probability of terminal rejection or tolerance. This novel a posteriori approach permits identification of pathways of rejection, including tolerance.
Collapse
Affiliation(s)
- R. N. Smith
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - M. Matsunami
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - B. A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - I. A. Rosales
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - T. Oura
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - A. B. Cosimi
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - T. Kawai
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - M. Mengel
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - R. B. Colvin
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| |
Collapse
|
27
|
Smith R, Adam B, Rosales I, Matsunami M, Oura T, Cosimi A, Kawai T, Mengel M, Colvin R. RNA expression profiling of renal allografts in a nonhuman primate identifies variation in NK and endothelial gene expression. Am J Transplant 2018; 18:1340-1350. [PMID: 29286578 PMCID: PMC5992005 DOI: 10.1111/ajt.14639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 12/12/2017] [Indexed: 01/25/2023]
Abstract
RNA transcript expression estimates are a promising method to study the mechanisms and classification of renal allograft rejections. Here we use the Nanostring platform to profile RNA expression in renal allografts in a nonhuman primate (NHP), the Cynomolgus monkey. We analyzed protocol and indication 278 archival renal allograft samples, both protocol and indication from 76 animals with diagnoses of chronic antibody-mediated rejection (CAMR), acute cellular rejection (TCMR), and MIXED (both CAMR and TCMR), plus normals and samples with no pathological rejection using a Cynomolgus-specific probe set of 67 genes. Analysis identified RNA expression heterogeneity of endothelial and NK genes within CAMR and TCMR, including the stages of CAMR. Three factors were partitioned into additional groups. One group with the longest allograft survival time is pure CAMR without NK or CD3. Three mixed groups show variation in NK and CD3. TCMR was split into 2 groups with variation in NK genes. Additional validation of the complete gene-set correlated many of the genes with diagnoses of CAMR, MIXED, and TCMR rejections and with Banff histologic criteria defined in human subjects. These NHP data demonstrate the utility of RNA expression profiling to identify additional heterogeneity of endothelial and NK RNA gene expressions.
Collapse
Affiliation(s)
- R.N. Smith
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - B.A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - I.A. Rosales
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - M. Matsunami
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - T. Oura
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - A.B. Cosimi
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - T. Kawai
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - M. Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - R.B. Colvin
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| |
Collapse
|
28
|
Eskandary F, Jilma B, Mühlbacher J, Wahrmann M, Regele H, Kozakowski N, Firbas C, Panicker S, Parry GC, Gilbert JC, Halloran PF, Böhmig GA. Anti-C1s monoclonal antibody BIVV009 in late antibody-mediated kidney allograft rejection-results from a first-in-patient phase 1 trial. Am J Transplant 2018; 18:916-926. [PMID: 28980446 DOI: 10.1111/ajt.14528] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 09/03/2017] [Accepted: 09/24/2017] [Indexed: 01/25/2023]
Abstract
The classical pathway (CP) of complement may contribute to the pathogenesis of antibody-mediated rejection (ABMR). Selective CP blockade may be a promising strategy to counteract rejection. The objective of this first-in-patient phase 1b trial was to evaluate the safety/tolerability and CP-blocking potential of 4 weekly doses (60 mg/kg) of the anti-C1s antibody BIVV009 in complement-mediated disorders. Here we describe the results in a cohort of 10 stable kidney transplant recipients (median of 4.3 years posttransplantation) with late active ABMR and features of CP activation, such as capillary C4d or complement-fixing donor-specific antibodies (DSA). During 7 weeks follow-up, no severe adverse events were reported, and BIVV009 profoundly inhibited overall and DSA-triggered CP activation in serum. Five of 8 C4d-positive recipients turned C4d-negative in 5-week follow-up biopsies, while another 2 recipients showed a substantial decrease in C4d scores. There was, however, no change in microcirculation inflammation, gene expression patterns, DSA levels, or kidney function. In conclusion, we demonstrate that BIVV009 effectively blocks alloantibody-triggered CP activation, even though short-course treatment had no effect on indices of activity in late ABMR. This initial trial provides a valuable basis for future studies designed to clarify the therapeutic value of CP blockade in transplantation. ClinicalTrials.gov NCT#02502903.
Collapse
Affiliation(s)
- F Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - B Jilma
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - J Mühlbacher
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - M Wahrmann
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - H Regele
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - N Kozakowski
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - C Firbas
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - S Panicker
- Bioverativ Therapeutics, Inc, South San Francisco, CA, USA
| | - G C Parry
- Bioverativ Therapeutics, Inc, South San Francisco, CA, USA
| | - J C Gilbert
- True North Therapeutics, Inc, South San Francisco, CA, USA
| | - P F Halloran
- Alberta Transplant Applied Genomics Centre, ATAGC, University of Alberta, Edmonton, AB, Canada
| | - G A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
29
|
Antlanger M, Domenig O, Kovarik JJ, Kaltenecker CC, Kopecky C, Poglitsch M, Säemann MD. Molecular remodeling of the renin-angiotensin system after kidney transplantation. J Renin Angiotensin Aldosterone Syst 2018; 18:1470320317705232. [PMID: 28490223 PMCID: PMC5843863 DOI: 10.1177/1470320317705232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Objective: We aimed at assessing the molecular adaptation of the renin-angiotensin system (RAS) after successful kidney transplantation (KTX). Materials and methods: In this prospective, exploratory study we analyzed 12 hemodialysis (HD) patients, who received a KTX and had excellent graft function six to 12 months thereafter. The concentrations of plasma Angiotensin (Ang) peptides (Ang I, Ang II, Ang-(1–7), Ang-(1–5), Ang-(2–8), Ang-(3–8)) were simultaneously quantified with a novel mass spectrometry-based method. Further, renin and aldosterone concentrations were determined by standard immunoassays. Results: Ang values showed a strong inter-individual variability among HD patients. Yet, despite a continued broad dispersion of Ang values after KTX, a substantial improvement of the renin/Ang II correlation was observed in patients without RAS blockade or on angiotensin receptor blocker (HD: renin/Ang II R2 = 0.660, KTX: renin/Ang II R2 = 0.918). Ang-(1–7) representing the alternative RAS axis was only marginally detectable both on HD and after KTX. Conclusions: Following KTX, renin-dependent Ang II formation adapts in non-ACE inhibitor-treated patients. Thus, a largely normal RAS regulation is reconstituted after successful KTX. However, individual Ang concentration variations and a lack of potentially beneficial alternative peptides after KTX call for individualized treatment. The long-term post-transplant RAS regulation remains to be determined.
Collapse
Affiliation(s)
- Marlies Antlanger
- 1 Medical University of Vienna, Department of Internal Medicine III, Clinical Division of Nephrology and Dialysis, Austria
| | - Oliver Domenig
- 1 Medical University of Vienna, Department of Internal Medicine III, Clinical Division of Nephrology and Dialysis, Austria
| | - Johannes J Kovarik
- 1 Medical University of Vienna, Department of Internal Medicine III, Clinical Division of Nephrology and Dialysis, Austria
| | - Christopher C Kaltenecker
- 1 Medical University of Vienna, Department of Internal Medicine III, Clinical Division of Nephrology and Dialysis, Austria
| | - Chantal Kopecky
- 1 Medical University of Vienna, Department of Internal Medicine III, Clinical Division of Nephrology and Dialysis, Austria
| | | | - Marcus D Säemann
- 1 Medical University of Vienna, Department of Internal Medicine III, Clinical Division of Nephrology and Dialysis, Austria
| |
Collapse
|
30
|
An integrated view of immune monitoring in vascularized composite allotransplantation. Curr Opin Organ Transplant 2017; 21:516-22. [PMID: 27517506 DOI: 10.1097/mot.0000000000000354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Vascularized composite allotransplantation (VCA) has several immunological peculiarities that imply a specific immune monitoring. Here, we provide an integrated view of current procedures of immune monitoring in VCA and potential complementary approaches learned from organ transplantation. RECENT FINDINGS Because the skin is highly immunogenic and is the main target of the alloimmune response, immune monitoring in VCA essentially relies on visual inspection and pathological examination of for-causes and protocol skin biopsies. Light microscopical and immunohistochemical analyses enable us to identify skin lesions that are characteristic, but not specific, of allograft rejection. Complementary approaches of immunological assessment may assist in reinforcing the diagnosis of rejection and preventing over-immunosuppression or under-immunosuppression. Such approaches can inform either on the patient's global immune status or more specifically on the B-cell-mediated or T-cell-mediated immune responses against donor antigens. SUMMARY Strategies that integrate both the current 'gold standards' of monitoring in VCA and a complementary multilayer immunological assessment are likely to provide the highest precision for the personalized determination of the recipients' immunological status. The objective is a tailored adaptation of immunosuppressive treatment.
Collapse
|
31
|
Dorr CR, Oetting WS, Jacobson PA, Israni AK. Genetics of acute rejection after kidney transplantation. Transpl Int 2017; 31:263-277. [PMID: 29030886 DOI: 10.1111/tri.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/07/2017] [Accepted: 10/09/2017] [Indexed: 01/02/2023]
Abstract
Treatment of acute rejection (AR) following kidney transplantation has improved in recent years, but there are still limitations to successful outcomes. This review article covers literature in regard to recipient and donor genetics of AR kidney and secondarily of liver allografts. Many candidate gene and some genome-wide association studies (GWASs) have been conducted for AR in kidney transplantation. Genetic associations with AR in kidney and liver are mostly weak, and in most cases, the associations have not been reproducible. A limitation in the study of AR is the lack of sufficiently large populations that account for population stratification to study the AR phenotype which in this era occurs in <10% of transplants. Furthermore, the AR phenotype has been difficult to define and the definitions of classifications have evolved over time. Literature related to the pharmacogenomics of tacrolimus is robust and has been validated in many studies. Associations between gene expression and AR are emerging as markers of outcomes and AR classification. In the future, combinations of pretransplant genotype for AR risk prediction, genotype-based immune suppressant dosing, and pharmacogenomic markers to select AR maintenance or treatment and expression markers from biopsies may provide valuable clinical tools for guiding treatment.
Collapse
Affiliation(s)
- Casey R Dorr
- Department of Nephrology, Minneapolis Medical Research Foundation, Minneapolis, MN, USA.,Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Ajay K Israni
- Department of Nephrology, Minneapolis Medical Research Foundation, Minneapolis, MN, USA.,Department of Medicine, University of Minnesota, Minneapolis, MN, USA.,Department of Medicine, Hennepin County Medical Center, Minneapolis, MN, USA
| |
Collapse
|
32
|
Adam B, Smith R, Rosales I, Matsunami M, Afzali B, Oura T, Cosimi A, Kawai T, Colvin R, Mengel M. Chronic Antibody-Mediated Rejection in Nonhuman Primate Renal Allografts: Validation of Human Histological and Molecular Phenotypes. Am J Transplant 2017; 17:2841-2850. [PMID: 28444814 PMCID: PMC5658276 DOI: 10.1111/ajt.14327] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/19/2017] [Accepted: 04/19/2017] [Indexed: 01/25/2023]
Abstract
Molecular testing represents a promising adjunct for the diagnosis of antibody-mediated rejection (AMR). Here, we apply a novel gene expression platform in sequential formalin-fixed paraffin-embedded samples from nonhuman primate (NHP) renal transplants. We analyzed 34 previously described gene transcripts related to AMR in humans in 197 archival NHP samples, including 102 from recipients that developed chronic AMR, 80 from recipients without AMR, and 15 normal native nephrectomies. Three endothelial genes (VWF, DARC, and CAV1), derived from 10-fold cross-validation receiver operating characteristic curve analysis, demonstrated excellent discrimination between AMR and non-AMR samples (area under the curve = 0.92). This three-gene set correlated with classic features of AMR, including glomerulitis, capillaritis, glomerulopathy, C4d deposition, and DSAs (r = 0.39-0.63, p < 0.001). Principal component analysis confirmed the association between three-gene set expression and AMR and highlighted the ambiguity of v lesions and ptc lesions between AMR and T cell-mediated rejection (TCMR). Elevated three-gene set expression corresponded with the development of immunopathological evidence of rejection and often preceded it. Many recipients demonstrated mixed AMR and TCMR, suggesting that this represents the natural pattern of rejection. These data provide NHP animal model validation of recent updates to the Banff classification including the assessment of molecular markers for diagnosing AMR.
Collapse
Affiliation(s)
- B.A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - R.N. Smith
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - I.A. Rosales
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - M. Matsunami
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - B. Afzali
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - T. Oura
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - A.B. Cosimi
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - T. Kawai
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - R.B. Colvin
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - M. Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| |
Collapse
|
33
|
Drachenberg CB, Papadimitriou JC, Chaudhry MR, Ugarte R, Mavanur M, Thomas B, Cangro C, Costa N, Ramos E, Weir MR, Haririan A. Histological Evolution of BK Virus-Associated Nephropathy: Importance of Integrating Clinical and Pathological Findings. Am J Transplant 2017; 17:2078-2091. [PMID: 28422412 DOI: 10.1111/ajt.14314] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 01/25/2023]
Abstract
Long-term clinicopathological studies of BK-associated nephropathy (PyVAN) are not available. We studied 206 biopsies (71 patients), followed 3.09 ± 1.46 years after immunosuppression reduction. The biopsy features (% immunostain for PyV large T ag + staining and inflammation ± acute rejection) were correlated with viral load dynamics and serum creatinine to define the clinicopathological status (PyVCPS). Incidence of acute rejection was 28% in the second biopsy and 50% subsequently (25% mixed T cell-mediated allograft rejection (TCMR) + antibody-mediated allograft rejection (AMR); rejection overall affected 38% of patients (>50% AMR). Graft loss was 15.4% (0.8-5.3 years after PyVAN); 76% had complete viral clearance (mean 28 weeks). The only predictors of graft loss were acute rejection (TCMR p = 0.008, any type p = 0.07), and increased "t" and "ci" in the second biopsy (p = 0.006 and 0.048). Higher peak viremia correlated with poorer viral clearance (p = 0.002). Presumptive and proven PyVAN had similar presentation, evolution, and outcome. Late PyVAN (>2 years, 9.8%) justifies BK viremia evaluation at any point with graft dysfunction and/or biopsy evaluation. This study describes the histological evolution of PyVAN and corresponding clinicopathological correlations. Although the pathological features overall reflect the viral and immunological interactions, the PyVAN course remains difficult to predict based on any single feature. Appropriate clinical management requires repeat biopsies and determination of the PyVCPS at relevant time points, for corresponding personalized immunosuppression adjustment.
Collapse
Affiliation(s)
- C B Drachenberg
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - J C Papadimitriou
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - M R Chaudhry
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - R Ugarte
- Departments of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - M Mavanur
- Departments of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - B Thomas
- Departments of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - C Cangro
- Departments of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - N Costa
- Departments of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - E Ramos
- Department of Medicine, Division of Nephrology, Erie County Medical Center, Buffalo, NY
| | - M R Weir
- Departments of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - A Haririan
- Departments of Medicine, University of Maryland School of Medicine, Baltimore, MD
| |
Collapse
|
34
|
Acute and Chronic Micro- and Macrovascular Lesions in Pancreas Transplants: Implications for the Diagnosis of T Cell-Mediated and Antibody-Mediated Allograft Rejection. CURRENT TRANSPLANTATION REPORTS 2017. [DOI: 10.1007/s40472-017-0143-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
35
|
Agbor-Enoh S, Tunc I, De Vlaminck I, Fideli U, Davis A, Cuttin K, Bhatti K, Marishta A, Solomon MA, Jackson A, Graninger G, Harper B, Luikart H, Wylie J, Wang X, Berry G, Marboe C, Khush K, Zhu J, Valantine H. Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation. J Heart Lung Transplant 2017. [PMID: 28624139 DOI: 10.1016/j.healun.2017.05.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Use of new genomic techniques in clinical settings requires that such methods are rigorous and reproducible. Previous studies have shown that quantitation of donor-derived cell-free DNA (%ddcfDNA) by unbiased shotgun sequencing is a sensitive, non-invasive marker of acute rejection after heart transplantation. The primary goal of this study was to assess the reproducibility of %ddcfDNA measurements across technical replicates, manual vs automated platforms, and rejection phenotypes in distinct patient cohorts. METHODS After developing and validating the %ddcfDNA assay, we subjected the method to a rigorous test of its reproducibility. We measured %ddcfDNA in technical replicates performed by 2 independent laboratories and verified the reproducibility of %ddcfDNA patterns of 2 rejection phenotypes: acute cellular rejection and antibody-mediated rejection in distinct patient cohorts. RESULTS We observed strong concordance of technical-replicate %ddcfDNA measurements across 2 independent laboratories (slope = 1.02, R2 > 0.99, p < 10-6), as well as across manual and automated platforms (slope = 0.80, R2 = 0.92, p < 0.001). The %ddcfDNA measurements in distinct heart transplant cohorts had similar baselines and error rates. The %ddcfDNA temporal patterns associated with rejection phenotypes were similar in both patient cohorts; however, the quantity of ddcfDNA was significantly higher in samples with severe vs mild histologic rejection grade (2.73% vs 0.14%, respectively; p < 0.001). CONCLUSIONS The %ddcfDNA assay is precise and reproducible across laboratories and in samples from 2 distinct types of heart transplant rejection. These findings pave the way for larger studies to assess the clinical utility of %ddcfDNA as a marker of acute rejection after heart transplantation.
Collapse
Affiliation(s)
- Sean Agbor-Enoh
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Ilker Tunc
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Iwijn De Vlaminck
- Department of Bioengineering, Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Ulgen Fideli
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Andrew Davis
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Karen Cuttin
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Kenneth Bhatti
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Argit Marishta
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Michael A Solomon
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Annette Jackson
- Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Grace Graninger
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Bonnie Harper
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Helen Luikart
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Jennifer Wylie
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Xujing Wang
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Gerald Berry
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Charles Marboe
- Department of Medicine, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Kiran Khush
- Department of Medicine, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Jun Zhu
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Hannah Valantine
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland.
| |
Collapse
|
36
|
Antibody-mediated rejection in the cardiac allograft: diagnosis, treatment and future considerations. Curr Opin Cardiol 2017; 32:326-335. [PMID: 28212151 DOI: 10.1097/hco.0000000000000390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW This review summarizes the latest publications dealing with antibody-mediated rejection (AMR) and defines areas of controversy and future steps that may improve the outcome for patients with this virulent form of rejection. RECENT FINDINGS Recent progress includes publication of standardized pathologic criteria for acute AMR by the International Society for Heart and Lung Transplantation (ISHLT) and guidelines for treatment of acute AMR by the American Heart Association, endorsed by ISHLT as well. Recently published review articles emphasize the important role of innate immune mechanisms, clarify the role of viral infection and provide insights into vascular biology and the role of innate effector populations, macrophages and dendritic cells. SUMMARY Strategies for future studies are discussed in the context of these new findings and similar efforts undertaken by renal and liver allograft investigators.
Collapse
|
37
|
Afzali B, Chapman E, Racapé M, Adam B, Bruneval P, Gil F, Kim D, Hidalgo L, Campbell P, Sis B, Duong Van Huyen JP, Mengel M. Molecular Assessment of Microcirculation Injury in Formalin-Fixed Human Cardiac Allograft Biopsies With Antibody-Mediated Rejection. Am J Transplant 2017; 17:496-505. [PMID: 27401781 DOI: 10.1111/ajt.13956] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/06/2016] [Accepted: 06/26/2016] [Indexed: 01/25/2023]
Abstract
Precise diagnosis of antibody-mediated rejection (AMR) in cardiac allograft endomyocardial biopsies (EMBs) remains challenging. This study assessed molecular diagnostics in human EMBs with AMR. A set of 34 endothelial, natural killer cell and inflammatory genes was quantified in 106 formalin-fixed, paraffin-embedded EMBs classified according to 2013 International Society for Heart and Lung Transplantation (ISHLT) criteria. The gene set expression was compared between ISHLT diagnoses and correlated with donor-specific antibody (DSA), endothelial injury by electron microscopy (EM) and prognosis. Findings were validated in an independent set of 57 EMBs. In the training set (n = 106), AMR cases (n = 70) showed higher gene set expression than acute cellular rejection (ACR; n = 21, p < 0.001) and controls (n = 15, p < 0.0001). Anti-HLA DSA positivity was associated with higher gene set expression (p = 0.01). Endothelial injury by electron microscopy strongly correlated with gene set expression, specifically in AMR cases (r = 0.62, p = 0.002). Receiver operating characteristic curve analysis for diagnosing AMR showed greater accuracy with gene set expression (area under the curve [AUC] = 79.88) than with DSA (AUC = 70.47) and C4d (AUC = 70.71). In AMR patients (n = 17) with sequential biopsies, increasing gene set expression was associated with inferior prognosis (p = 0.034). These findings were confirmed in the validation set. In conclusion, biopsy-based molecular assessment of antibody-mediated microcirculation injury has the potential to improve diagnosis of AMR in human cardiac transplants.
Collapse
Affiliation(s)
- B Afzali
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.,Institute for Pathology, University of Duisburg-Essen, Essen, Germany
| | - E Chapman
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - M Racapé
- Paris Translational Research Centre for Organ Transplantation, Paris Descartes University, Paris, France
| | - B Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - P Bruneval
- Paris Translational Research Centre for Organ Transplantation, Paris Descartes University, Paris, France
| | - F Gil
- Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada
| | - D Kim
- Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada
| | - L Hidalgo
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - P Campbell
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - B Sis
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - J P Duong Van Huyen
- Paris Translational Research Centre for Organ Transplantation, Paris Descartes University, Paris, France
| | - M Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
38
|
Ochando J, Kwan WH, Ginhoux F, Hutchinson JA, Hashimoto D, Collin M. The Mononuclear Phagocyte System in Organ Transplantation. Am J Transplant 2016; 16:1053-69. [PMID: 26602545 DOI: 10.1111/ajt.13627] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/04/2015] [Accepted: 11/08/2015] [Indexed: 01/25/2023]
Abstract
The mononuclear phagocyte system (MPS) comprises monocytes, macrophages and dendritic cells (DCs). Over the past few decades, classification of the cells of the MPS has generated considerable controversy. Recent studies into the origin, developmental requirements and function of MPS cells are beginning to solve this problem in an objective manner. Using high-resolution genetic analyses and fate-mapping studies, three main mononuclear phagocyte lineages have been defined, namely, macrophage populations established during embryogenesis, monocyte-derived cells that develop during adult life and DCs. These subsets and their diverse subsets have specialized functions that are largely conserved between species, justifying the introduction of a new, universal scheme of nomenclature and providing the framework for therapeutic manipulation of immune responses in the clinic. In this review, we have commented on the implications of this novel MPS classification in solid organ transplantation.
Collapse
Affiliation(s)
- J Ochando
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - W-H Kwan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - F Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Singapore, Singapore
| | - J A Hutchinson
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - D Hashimoto
- Department of Hematology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - M Collin
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| |
Collapse
|
39
|
Adam B, Afzali B, Dominy KM, Chapman E, Gill R, Hidalgo LG, Roufosse C, Sis B, Mengel M. Multiplexed color-coded probe-based gene expression assessment for clinical molecular diagnostics in formalin-fixed paraffin-embedded human renal allograft tissue. Clin Transplant 2016; 30:295-305. [DOI: 10.1111/ctr.12689] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Benjamin Adam
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton AB Canada
| | - Bahman Afzali
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton AB Canada
- Institute of Pathology; University of Duisburg−Essen; Essen Germany
| | - Katherine M. Dominy
- Division of Immunology and Inflammation; Department of Medicine; Centre for Complement and Inflammation Research; Imperial College; London UK
| | - Erin Chapman
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton AB Canada
| | - Reeda Gill
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton AB Canada
| | - Luis G. Hidalgo
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton AB Canada
| | - Candice Roufosse
- Division of Immunology and Inflammation; Department of Medicine; Centre for Complement and Inflammation Research; Imperial College; London UK
- Department of Cellular Pathology; Hammersmith Hospital; London UK
| | - Banu Sis
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton AB Canada
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology; University of Alberta; Edmonton AB Canada
| |
Collapse
|
40
|
Bonaccorsi-Riani E, Pennycuick A, Londoño MC, Lozano JJ, Benítez C, Sawitzki B, Martínez-Picola M, Bohne F, Martínez-Llordella M, Miquel R, Rimola A, Sánchez-Fueyo A. Molecular Characterization of Acute Cellular Rejection Occurring During Intentional Immunosuppression Withdrawal in Liver Transplantation. Am J Transplant 2016; 16:484-96. [PMID: 26517400 DOI: 10.1111/ajt.13488] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/26/2015] [Accepted: 08/02/2015] [Indexed: 01/25/2023]
Abstract
Acute cellular rejection occurs frequently during the first few weeks following liver transplantation. During this period, its molecular phenotype is confounded by peri- and postoperative proinflammatory events. To unambiguously define the molecular profile associated with rejection, we collected sequential biological specimens from 55 patients at least 3 years after liver transplantation who developed rejection during trials of intentional immunosuppression withdrawal. We analyzed liver tissue and blood samples obtained before initiation of drug withdrawal and at rejection, alongside blood samples collected during the weaning process. Gene expression profiling was conducted using whole-genome microarrays and real-time polymerase chain reaction. Rejection resulted in distinct blood and liver tissue transcriptional changes in patients who were either positive or negative for hepatitis C virus (HCV). Gene expression changes were mostly independent from pharmacological immunosuppression, and their magnitude correlated with severity of histological damage. Differential expression of a subset of genes overlapped across all conditions. These were used to define a blood predictive model that accurately identified rejection in HCV-negative, but not HCV-positive, patients. Changes were detectable 1-2 mo before rejection was diagnosed. Our results provide insight into the molecular processes underlying acute cellular rejection in liver transplantation and help clarify the potential utility and limitations of transcriptional biomarkers in this setting.
Collapse
Affiliation(s)
- E Bonaccorsi-Riani
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - A Pennycuick
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - M-C Londoño
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - J-J Lozano
- Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - C Benítez
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - B Sawitzki
- AG Transplantationstoleranz, Charite Universitätsmedizin, Institut für Med. Immunologie, Berlin, Germany
| | - M Martínez-Picola
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - F Bohne
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - M Martínez-Llordella
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - R Miquel
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - A Rimola
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - A Sánchez-Fueyo
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK.,Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| |
Collapse
|
41
|
Ochando J, Kwan WH, Ginhoux F, Hutchinson JA, Hashimoto D, Collin M. The Mononuclear Phagocyte System in Organ Transplantation. Am J Transplant 2016. [DOI: 10.1111/ajt.13627 and 21=21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J. Ochando
- Department of Oncological Sciences; Icahn School of Medicine at Mount Sinai; New York NY
| | - W.-H. Kwan
- Department of Microbiology; Icahn School of Medicine at Mount Sinai; New York NY
| | - F. Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove; Singapore Singapore
| | - J. A. Hutchinson
- Department of Surgery; University Hospital Regensburg; Regensburg Germany
| | - D. Hashimoto
- Department of Hematology; Hokkaido University Graduate School of Medicine; Sapporo Japan
| | - M. Collin
- Institute of Cellular Medicine; Newcastle University; Newcastle UK
| |
Collapse
|
42
|
Current status of the evaluation and management of antibody-mediated rejection in kidney transplantation. Curr Opin Nephrol Hypertens 2015; 24:576-81. [DOI: 10.1097/mnh.0000000000000167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
43
|
Halloran PF, Kreepala C, Einecke G, Loupy A, Sellarés J. Therapeutic approaches to organ transplantation. Transpl Immunol 2015. [DOI: 10.1002/9781119072997.ch10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
44
|
Expression of decoy receptor 3 in kidneys is associated with allograft survival after kidney transplant rejection. Sci Rep 2015; 5:12769. [PMID: 26335204 PMCID: PMC4558610 DOI: 10.1038/srep12769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/07/2015] [Indexed: 11/08/2022] Open
Abstract
Decoy receptor 3 (DcR3) expression in kidneys has been shown to predict progression of chronic kidney disease. We prospectively investigated a cohort comprising 96 renal transplant recipients (RTRs) undergoing graft kidney biopsies. Computer-assisted quantitative immunohistochemical staining value of DcR3 in renal tubular epithelial cells (RTECs) was used to determine the predictive role of DcR3 in kidney disease progression. The primary end point was doubling of serum creatinine and/or graft failure. A multivariate Cox proportional hazards model was used to assess the risk of DcR3 expression in rejected kidney grafts toward the renal end point. In total, RTRs with kidney allograft rejection were evaluated and the median follow-up was 30.9 months. The greater expression of DcR3 immunoreactivity in RTECs was correlated with a higher rate of the histopathological concordance of acute T cell-mediated rejection. Compared with 65 non-progressors, 31 progressors had higher DcR3 expression (HDE) regardless of the traditional risk factors. Cox regression analysis showed HDE was significantly associated with the risk of renal end point with a hazard ratio of 3.19 (95% confidence interval, 1.40 to 7.27; P = 0.006) after adjusting for other variables. In repetitive biopsies, HDE in tissue showed rapid kidney disease progression due to persistent inflammation.
Collapse
|
45
|
Abstract
Despite its long-standing status as the diagnostic "gold standard", the renal transplant biopsy is limited by a fundamental dependence on descriptive, empirically-derived consensus classification. The recent shift towards personalized medicine has resulted in an increased demand for precise, mechanism-based diagnoses, which is not fully met by the contemporary transplantation pathology standard of care. The expectation is that molecular techniques will provide novel pathogenetic insights that will allow for the identification of more accurate diagnostic, prognostic, and therapeutic targets. Here we review the current state of molecular renal transplantation pathology. Despite significant research activity and progress within the field, routine adoption of clinical molecular testing has not yet been achieved. The recent development of novel molecular platforms suitable for use with formalin-fixed paraffin-embedded tissue will offer potential solution for the major barriers to implementation. The recent incorporation of molecular diagnostic criteria into the 2013 Banff classification is a reflection of progress made and future directions in the area of molecular transplantation pathology. Transcripts related to endothelial injury and NK cell activation have consistently been shown to be associated with antibody-mediated rejection. Prospective multicenter validation and implementation of molecular diagnostics for major entities remains an unmet clinical need in transplantation. It is expected that an integrated system of transplantation pathology diagnosis comprising molecular, morphological, serological, and clinical variables will ultimately provide the greatest diagnostic precision.
Collapse
|
46
|
|
47
|
Adam B, Mengel M. Molecular nephropathology: ready for prime time? Am J Physiol Renal Physiol 2015; 309:F185-8. [PMID: 26017976 DOI: 10.1152/ajprenal.00153.2015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/20/2015] [Indexed: 11/22/2022] Open
Abstract
In the current era of precision medicine, the existing nephropathology paradigm of light microscopy, immunofluorescence, and electron microscopy will become increasingly insufficient. There will be an expectation to supplement these traditional diagnostic tools with patient-specific information related to a growing understanding of molecular pathophysiology. Next generation sequencing technologies are expected to play a key role in the future of nephropathology, but transcriptomics is poised to represent the first major foray into routine molecular testing. The introduction of molecular techniques into clinical nephropathology has been hindered in part by the reliance of existing platforms on fresh tissue samples. The NanoString gene expression system works with formalin-fixed paraffin-embedded tissue and thus represents a promising solution to this technical barrier that may finally allow for the translation of recent transcriptomics discoveries into the enhancement of patient care. Widespread adoption of this new diagnostic dimension will require ongoing multidisciplinary cooperation between pathologists and clinicians, including molecular testing consensus generation and rigorous multicenter validation.
Collapse
Affiliation(s)
- Benjamin Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
48
|
Boor P, Floege J. Renal allograft fibrosis: biology and therapeutic targets. Am J Transplant 2015; 15:863-86. [PMID: 25691290 DOI: 10.1111/ajt.13180] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/30/2014] [Accepted: 12/19/2014] [Indexed: 01/25/2023]
Abstract
Renal tubulointerstitial fibrosis is the final common pathway of progressive renal diseases. In allografts, it is assessed with tubular atrophy as interstitial fibrosis/tubular atrophy (IF/TA). IF/TA occurs in about 40% of kidney allografts at 3-6 months after transplantation, increasing to 65% at 2 years. The origin of renal fibrosis in the allograft is complex and includes donor-related factors, in particular in case of expanded criteria donors, ischemia-reperfusion injury, immune-mediated damage, recurrence of underlying diseases, hypertensive damage, nephrotoxicity of immunosuppressants, recurrent graft infections, postrenal obstruction, etc. Based largely on studies in the non-transplant setting, there is a large body of literature on the role of different cell types, be it intrinsic to the kidney or bone marrow derived, in mediating renal fibrosis, and the number of mediator systems contributing to fibrotic changes is growing steadily. Here we review the most important cellular processes and mediators involved in the progress of renal fibrosis, with a focus on the allograft situation, and discuss some of the challenges in translating experimental insights into clinical trials, in particular fibrosis biomarkers or imaging modalities.
Collapse
Affiliation(s)
- P Boor
- Division of Nephrology and Clinical Immunology, RWTH University of Aachen, Aachen, Germany; Department of Pathology, RWTH University of Aachen, Aachen, Germany; Institute of Molecular Biomedicine, Bratislava, Slovakia
| | | |
Collapse
|
49
|
Girmanova E, Hruba P, Viklicky O. Circulating biomarkers of tolerance. Transplant Rev (Orlando) 2015; 29:68-72. [PMID: 25636718 DOI: 10.1016/j.trre.2015.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 02/01/2023]
Abstract
On the basis of reviewed literature here we describe models of tolerance and summarize the evidence of circulating biomarkers suitable for the assessment of immunological risk in organ transplantation. We focused on results of evaluation of specific peripheral immune cell populations and transcripts in peripheral blood of operationally tolerant liver and kidney transplant recipients. Validation of described markers to define potentially tolerant patients before their use in clinical trials is critical.
Collapse
Affiliation(s)
- Eva Girmanova
- Transplant Laboratory, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Petra Hruba
- Transplant Laboratory, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ondrej Viklicky
- Department of Nephrology, Transplant Laboratory, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic.
| |
Collapse
|
50
|
Halloran B, Chang J, Shih DQ, McGovern D, Famulski K, Evaschesen C, Fedorak RN, Thiesen A, Targan S, Halloran PF. Molecular patterns in human ulcerative colitis and correlation with response to infliximab. Inflamm Bowel Dis 2014; 20:2353-63. [PMID: 25397893 PMCID: PMC4985265 DOI: 10.1097/mib.0000000000000239] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND As a T cell-mediated disease of the colonic epithelium, ulcerative colitis (UC) is likely to share pathogenic elements with other T cell-mediated inflammatory diseases. Recently, microarray analysis revealed large-scale molecular changes in T cell-mediated rejection of kidney and heart transplants. We hypothesized that similar disturbances might be operating in UC and could provide insights into responsiveness to therapy. METHODS We studied 56 colon biopsies from patients with colitis characterizing the clinical and histological features and using microarrays to define the messenger RNA phenotype. We expressed the microarray results using previously defined pathogenesis-based transcript sets. We also studied 48 published microarray files from human colon biopsies downloaded from the Gene Expression Omnibus database, classified by response to infliximab therapy, to examine whether the molecular measurements derived from our studies correlated with nonresponsiveness to treatment. RESULTS UC biopsies manifested coordinate transcript changes resembling rejecting transplants, with effector T cell, IFNG-induced, macrophage, and injury transcripts increasing while parenchymal transcripts decreased. The disturbance in gene expression, summarized as principal component 1 (PC1), correlated with conventional clinical and histologic assessments. When assessed in microarray results from published studies, the disturbance (PC1) predicted response to infliximab: patients with intense disturbance did not achieve clinical response, although quantitative improvement was seen even in many clinical nonresponders. Similar changes were seen in Crohn's colitis. CONCLUSIONS The molecular phenotype of UC manifests a large-scale coordinate disturbance reflecting changes in inflammatory cells and parenchymal elements that correlates with conventional features and predicts response to infliximab.
Collapse
Affiliation(s)
- Brendan Halloran
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | | | - David Q. Shih
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dermot McGovern
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Konrad Famulski
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Chad Evaschesen
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Richard N Fedorak
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Aducio Thiesen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Stephan Targan
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Philip F. Halloran
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|