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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.
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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
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Assis de Souza A, Stubbs AP, Hesselink DA, Baan CC, Boer K. Cherry on Top or Real Need? A Review of Explainable Machine Learning in Kidney Transplantation. Transplantation 2024:00007890-990000000-00768. [PMID: 38773859 DOI: 10.1097/tp.0000000000005063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Research on solid organ transplantation has taken advantage of the substantial acquisition of medical data and the use of artificial intelligence (AI) and machine learning (ML) to answer diagnostic, prognostic, and therapeutic questions for many years. Nevertheless, despite the question of whether AI models add value to traditional modeling approaches, such as regression models, their "black box" nature is one of the factors that have hindered the translation from research to clinical practice. Several techniques that make such models understandable to humans were developed with the promise of increasing transparency in the support of medical decision-making. These techniques should help AI to close the gap between theory and practice by yielding trust in the model by doctors and patients, allowing model auditing, and facilitating compliance with emergent AI regulations. But is this also happening in the field of kidney transplantation? This review reports the use and explanation of "black box" models to diagnose and predict kidney allograft rejection, delayed graft function, graft failure, and other related outcomes after kidney transplantation. In particular, we emphasize the discussion on the need (or not) to explain ML models for biological discovery and clinical implementation in kidney transplantation. We also discuss promising future research paths for these computational tools.
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Affiliation(s)
- Alvaro Assis de Souza
- Department of Internal Medicine, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Andrew P Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Stubbs Group, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dennis A Hesselink
- Department of Internal Medicine, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Carla C Baan
- Department of Internal Medicine, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Karin Boer
- Department of Internal Medicine, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Poudel S, Gupta S, Saigal S. Basics and Art of Immunosuppression in Liver Transplantation. J Clin Exp Hepatol 2024; 14:101345. [PMID: 38450290 PMCID: PMC10912712 DOI: 10.1016/j.jceh.2024.101345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/09/2024] [Indexed: 03/08/2024] Open
Abstract
Liver transplantation is one of the most challenging areas in the medical field. Despite that, it has already been established as a standard treatment option, especially in decompensated cirrhosis and selected cases of hepatocellular carcinoma and acute liver failure. Complications due to graft rejection, including mortality and morbidity, have greatly improved over time due to better immunosuppressive agents and management protocols. Currently, immunosuppression in liver transplant patients makes use of the best possible combinations of effective agents to achieve optimal immunosuppression for long-term graft survival. Induction agents are no longer used routinely, and the aim is to provide minimal immunosuppression in the maintenance phase. Currently available immunosuppressive agents are mainly classified as biological and pharmacological agents. Though the protocols may vary among the centers and over time, the basics of effective use usually remain similar. Most protocols use the combination of multiple agents with different mechanisms of action to reduce the dose and minimize the side effects. Along with the improvement in operative and perioperative techniques, this art of immunosuppression has contributed to the recent progress made in the outcomes of liver transplants. In this review, we will discuss the various types of immunosuppressive agents currently in use, the different protocols of immunosuppression used, and the art of optimal use for achieving maximum immunosuppression without increasing toxicity. We will also discuss the practical aspects of various immunosuppression regimens, including drug monitoring, and briefly discuss the concepts of immunosuppression minimization and withdrawal.
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Affiliation(s)
- Shekhar Poudel
- Fellow Transplant Hepatology, Centre for Liver and Biliary Sciences, Max Super Specialty Hospital, Saket, New Delhi, India
| | - Subhash Gupta
- Liver Transplant and Gastrointestinal Surgery, Centre for Liver and Biliary Sciences, Max Super Speciality Hospital, Saket, New Delhi, India
| | - Sanjiv Saigal
- Principal Director and Head, Transplant Hepatology, Centre for Liver and Biliary Sciences, Max Super Specialty Hospital, Saket, New Delhi, India
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Gauthier PT, Madill-Thomsen KS, Demko Z, Prewett A, Gauthier P, Halloran PF. Distinct Molecular Processes Mediate Donor-derived Cell-free DNA Release From Kidney Transplants in Different Disease States. Transplantation 2024; 108:898-910. [PMID: 38150492 PMCID: PMC10962427 DOI: 10.1097/tp.0000000000004877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Among all biopsies in the Trifecta-Kidney Study ( ClinicalTrials.gov NCT04239703), elevated plasma donor-derived cell-free DNA (dd-cfDNA) correlated most strongly with molecular antibody-mediated rejection (AMR) but was also elevated in other states: T cell-mediated rejection (TCMR), acute kidney injury (AKI), and some apparently normal biopsies. The present study aimed to define the molecular correlates of plasma dd-cfDNA within specific states. METHODS Dd-cfDNA was measured by the Prospera test. Molecular rejection and injury states were defined using the Molecular Microscope system. We studied the correlation between dd-cfDNA and the expression of genes, transcript sets, and classifier scores within specific disease states, and compared AMR, TCMR, and AKI to biopsies classified as normal and no injury (NRNI). RESULTS In all 604 biopsies, dd-cfDNA was elevated in AMR, TCMR, and AKI. Within AMR biopsies, dd-cfDNA correlated with AMR activity and stage. Within AKI, the correlations reflected acute parenchymal injury, including cell cycling. Within biopsies classified as MMDx Normal and archetypal No injury (NRNI), dd-cfDNA still correlated significantly with rejection- and injury-related genes. TCMR activity (eg, the TCMR Prob classifier) correlated with dd-cfDNA, but within TCMR biopsies, top gene correlations were complex and not the top TCMR-selective genes. CONCLUSIONS In kidney transplants, elevated plasma dd-cfDNA is associated with 3 distinct molecular states in the donor tissue: AMR, recent parenchymal injury (including cell cycling), and TCMR, potentially complicated by parenchymal disruption. Moreover, subtle rejection- and injury-related changes in the donor tissue can contribute to dd-cfDNA elevations in transplants considered to have no rejection or injury.
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Affiliation(s)
- Patrick T. Gauthier
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
- Transcriptome Sciences Inc, Edmonton, AB, Canada
| | - Katelynn S. Madill-Thomsen
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
- Transcriptome Sciences Inc, Edmonton, AB, Canada
| | | | | | | | - Philip F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
- Transcriptome Sciences Inc, Edmonton, AB, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
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Halloran PF, Reeve J, Mackova M, Madill-Thomsen KS, Demko Z, Olymbios M, Campbell P, Melenovsky V, Gong T, Hall S, Stehlik J. Comparing Plasma Donor-derived Cell-free DNA to Gene Expression in Endomyocardial Biopsies in the Trifecta-Heart Study. Transplantation 2024:00007890-990000000-00702. [PMID: 38538559 DOI: 10.1097/tp.0000000000004986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
BACKGROUND Plasma donor-derived cell-free DNA (dd-cfDNA) is used to screen for rejection in heart transplants. We launched the Trifecta-Heart study (ClinicalTrials.gov No. NCT04707872), an investigator-initiated, prospective trial, to examine the correlations between genome-wide molecular changes in endomyocardial biopsies (EMBs) and plasma dd-cfDNA. The present report analyzes the correlation of plasma dd-cfDNA with gene expression in EMBs from 4 vanguard centers and compared these correlations with those in 604 kidney transplant biopsies in the Trifecta-Kidney study (ClinicalTrials.gov No. NCT04239703). METHODS We analyzed 137 consecutive dd-cfDNA-EMB pairs from 70 patients. Plasma %dd-cfDNA was measured by the Prospera test (Natera Inc), and gene expression in EMBs was assessed by Molecular Microscope Diagnostic System using machine-learning algorithms to interpret rejection and injury states. RESULTS Top transcripts correlating with dd-cfDNA were related to genes increased in rejection such as interferon gamma-inducible genes (eg, HLA-DMA ) but also with genes induced by injury and expressed in macrophages (eg, SERPINA1 and HMOX1 ). In gene enrichment analysis, the top dd-cfDNA-correlated genes reflected inflammation and rejection pathways. Dd-cfDNA correlations with rejection genes in EMB were similar to those seen in kidney transplant biopsies, with somewhat stronger correlations for TCMR genes in hearts and ABMR genes in kidneys. However, the correlations with parenchymal injury-induced genes and macrophage genes were much stronger in hearts. CONCLUSIONS In this first analysis of Trifecta-Heart study, dd-cfDNA correlates significantly with molecular rejection but also with injury and macrophage infiltration, reflecting the proinflammatory properties of injured cardiomyocytes. The relationship supports the utility of dd-cfDNA in clinical management of heart transplant recipients.
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Center, Edmonton, AB, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Transcriptome Sciences Inc, Edmonton, AB, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Center, Edmonton, AB, Canada
- Transcriptome Sciences Inc, Edmonton, AB, Canada
| | - Martina Mackova
- Alberta Transplant Applied Genomics Center, Edmonton, AB, Canada
- Transcriptome Sciences Inc, Edmonton, AB, Canada
| | - Katelynn S Madill-Thomsen
- Alberta Transplant Applied Genomics Center, Edmonton, AB, Canada
- Transcriptome Sciences Inc, Edmonton, AB, Canada
| | | | | | | | | | | | | | - Josef Stehlik
- Department of Internal Medicine, University of Utah, Salt Lake City, UT
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Harmacek D, Weidmann L, Castrezana Lopez K, Schmid N, Korach R, Bortel N, von Moos S, Rho E, Helmchen B, Gaspert A, Schachtner T. Molecular diagnosis of antibody-mediated rejection: Evaluating biopsy-based transcript diagnostics in the presence of donor-specific antibodies but without microvascular inflammation, a single-center descriptive analysis. Am J Transplant 2024:S1600-6135(24)00244-2. [PMID: 38548057 DOI: 10.1016/j.ajt.2024.03.034] [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: 10/10/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024]
Abstract
Biopsy-based transcript diagnostics may identify molecular antibody-mediated rejection (AMR) when microvascular inflammation (MVI) is absent. In this single-center cohort, biopsy-based transcript diagnostics were validated in 326 kidney allograft biopsies. A total of 71 histological AMR and 35 T cell-mediated rejection (TCMR) cases were identified as molecular AMR and TCMR in 55% and 63%, respectively. Among 121 cases without MVI (glomerulitis + peritubular capillaritis = 0), 45 (37%) donor-specific antibody (DSA)-positive and 76 (63%) DSA-negative cases were analyzed. Twenty-one out of the 121 (17%) cases showed borderline changes, or TCMR, while BK nephropathy was excluded. None of the 45 DSA-positive patients showed molecular AMR. Among 76 DSA-negative patients, 2 had mixed molecular AMR/TCMR. All-AMR phenotype scores (sum of R4-R6) exhibited median values of 0.13 and 0.12 for DSA-positive and DSA-negative patients, respectively (P = .84). A total of 13% (6/45) DSA-positive and 11% (8/76) DSA-negative patients showed an all-AMR phenotype score > 0.30 (P = .77). Patients with a higher all-AMR phenotype score showed 33% more histologic TCMR (P = .005). The median all-AMR phenotype scores of glomerular basement membrane double contours = 0 and glomerular basement membrane double contours > 0 biopsies were 0.12 and 0.10, respectively (P = .35). Biopsy-based transcript diagnostics did not identify molecular AMR in cases without MVI. Follow-up biopsies and outcome data should evaluate the clinical relevance of subthreshold molecular alterations.
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Affiliation(s)
- Dusan Harmacek
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Lukas Weidmann
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | | | - Nicolas Schmid
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Raphael Korach
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Nicola Bortel
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Seraina von Moos
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Elena Rho
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Birgit Helmchen
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Ariana Gaspert
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland.
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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.
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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
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Zhang H, Haun RS, Collin F, Cassol C, Napier JOH, Wilson J, Hassen S, Ararat K, Boils C, Messias N, Caza TN, Cossey LN, Sharma S, Ambruzs JM, Agrawal N, Shekhtman G, Tian W, Srinivas T, Qu K, Woodward RN, Larsen CP, Stone S, Coley SM. Development and Validation of a Multiclass Model Defining Molecular Archetypes of Kidney Transplant Rejection: A Large Cohort Study of the Banff Human Organ Transplant Gene Expression Panel. J Transl Med 2024; 104:100304. [PMID: 38092179 DOI: 10.1016/j.labinv.2023.100304] [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: 03/29/2023] [Revised: 11/19/2023] [Accepted: 12/06/2023] [Indexed: 01/15/2024] Open
Abstract
Gene expression profiling from formalin-fixed paraffin-embedded (FFPE) renal allograft biopsies is a promising approach for feasibly providing a molecular diagnosis of rejection. However, large-scale studies evaluating the performance of models using NanoString platform data to define molecular archetypes of rejection are lacking. We tested a diverse retrospective cohort of over 1400 FFPE biopsy specimens, rescored according to Banff 2019 criteria and representing 10 of 11 United Network of Organ Sharing regions, using the Banff Human Organ Transplant panel from NanoString and developed a multiclass model from the gene expression data to assign relative probabilities of 4 molecular archetypes: No Rejection, Antibody-Mediated Rejection, T Cell-Mediated Rejection, and Mixed Rejection. Using Least Absolute Shrinkage and Selection Operator regularized regression with 10-fold cross-validation fitted to 1050 biopsies in the discovery cohort and technically validated on an additional 345 biopsies, our model achieved overall accuracy of 85% in the discovery cohort and 80% in the validation cohort, with ≥75% positive predictive value for each class, except for the Mixed Rejection class in the validation cohort (positive predictive value, 53%). This study represents the technical validation of the first model built from a large and diverse sample of diagnostic FFPE biopsy specimens to define and classify molecular archetypes of histologically defined diagnoses as derived from Banff Human Organ Transplant panel gene expression profiling data.
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Affiliation(s)
| | | | | | | | | | - Jon Wilson
- Arkana Laboratories, Little Rock, Arkansas
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Wu CC, Islam MM, Poly TN, Weng YC. Artificial Intelligence in Kidney Disease: A Comprehensive Study and Directions for Future Research. Diagnostics (Basel) 2024; 14:397. [PMID: 38396436 PMCID: PMC10887584 DOI: 10.3390/diagnostics14040397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Artificial intelligence (AI) has emerged as a promising tool in the field of healthcare, with an increasing number of research articles evaluating its applications in the domain of kidney disease. To comprehend the evolving landscape of AI research in kidney disease, a bibliometric analysis is essential. The purposes of this study are to systematically analyze and quantify the scientific output, research trends, and collaborative networks in the application of AI to kidney disease. This study collected AI-related articles published between 2012 and 20 November 2023 from the Web of Science. Descriptive analyses of research trends in the application of AI in kidney disease were used to determine the growth rate of publications by authors, journals, institutions, and countries. Visualization network maps of country collaborations and author-provided keyword co-occurrences were generated to show the hotspots and research trends in AI research on kidney disease. The initial search yielded 673 articles, of which 631 were included in the analyses. Our findings reveal a noteworthy exponential growth trend in the annual publications of AI applications in kidney disease. Nephrology Dialysis Transplantation emerged as the leading publisher, accounting for 4.12% (26 out of 631 papers), followed by the American Journal of Transplantation at 3.01% (19/631) and Scientific Reports at 2.69% (17/631). The primary contributors were predominantly from the United States (n = 164, 25.99%), followed by China (n = 156, 24.72%) and India (n = 62, 9.83%). In terms of institutions, Mayo Clinic led with 27 contributions (4.27%), while Harvard University (n = 19, 3.01%) and Sun Yat-Sen University (n = 16, 2.53%) secured the second and third positions, respectively. This study summarized AI research trends in the field of kidney disease through statistical analysis and network visualization. The findings show that the field of AI in kidney disease is dynamic and rapidly progressing and provides valuable information for recognizing emerging patterns, technological shifts, and interdisciplinary collaborations that contribute to the advancement of knowledge in this critical domain.
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Affiliation(s)
- Chieh-Chen Wu
- Department of Healthcare Information and Management, School of Health and Medical Engineering, Ming Chuan University, Taipei 111, Taiwan;
| | - Md. Mohaimenul Islam
- Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Tahmina Nasrin Poly
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan;
| | - Yung-Ching Weng
- Department of Healthcare Information and Management, School of Health and Medical Engineering, Ming Chuan University, Taipei 111, Taiwan;
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10
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Sikosana ML, Reeve J, Madill-Thomsen KS, Halloran PF. Using Regression Equations to Enhance Interpretation of Histology Lesions of Kidney Transplant Rejection. Transplantation 2024; 108:445-454. [PMID: 37726883 PMCID: PMC10798587 DOI: 10.1097/tp.0000000000004783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 07/07/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND The Banff system for histologic diagnosis of rejection in kidney transplant biopsies uses guidelines to assess designated features-lesions, donor-specific antibody (DSA), and C4d staining. We explored whether using regression equations to interpret the features as well as current guidelines could establish the relative importance of each feature and improve histologic interpretation. METHODS We developed logistic regression equations using the designated features to predict antibody-mediated rejection (AMR/mixed) and T-cell-mediated rejection (TCMR/mixed) in 1679 indication biopsies from the INTERCOMEX study ( ClinicalTrials.gov NCT01299168). Equations were trained on molecular diagnoses independent of the designated features. RESULTS In regression and random forests, the important features predicting molecular rejection were as follows: for AMR, ptc and g, followed by cg; for TCMR, t > i. V-lesions were relatively unimportant. C4d and DSA were also relatively unimportant for predicting AMR: by AUC, the model excluding them (0.853) was nearly as good as the model including them (0.860). Including time posttransplant slightly but significantly improved all models. By AUC, regression predicted molecular AMR and TCMR better than Banff histologic diagnoses. More importantly, in biopsies called "no rejection" by Banff guidelines, regression equations based on histology features identified histologic and molecular rejection-related changes in some biopsies and improved survival predictions. Thus, regression can screen for missed rejection. CONCLUSIONS Using lesion-based regression equations in addition to Banff histology guidelines defines the relative important of histology features for identifying rejection, allows screening for potential missed diagnoses, and permits early estimates of AMR when C4d and DSA are not available.
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Affiliation(s)
- Majid L.N. Sikosana
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
| | | | - Philip F. Halloran
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
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11
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Mubarak M, Raza A, Rashid R, Shakeel S. Evolution of human kidney allograft pathology diagnostics through 30 years of the Banff classification process. World J Transplant 2023; 13:221-238. [PMID: 37746037 PMCID: PMC10514746 DOI: 10.5500/wjt.v13.i5.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 09/15/2023] Open
Abstract
The second half of the previous century witnessed a tremendous rise in the number of clinical kidney transplants worldwide. This activity was, however, accompanied by many issues and challenges. An accurate diagnosis and appropriate management of causes of graft dysfunction were and still are, a big challenge. Kidney allograft biopsy played a vital role in addressing the above challenge. However, its interpretation was not standardized for many years until, in 1991, the Banff process was started to fill this void. Thereafter, regular Banff meetings took place every 2 years for the past 30 years. Marked changes have taken place in the interpretation of kidney allograft biopsies, diagnosis, and classification of rejection and other non-rejection pathologies from the original Banff 93 classification. This review attempts to summarize those changes for increasing the awareness and understanding of kidney allograft pathology through the eyes of the Banff process. It will interest the transplant surgeons, physicians, pathologists, and allied professionals associated with the care of kidney transplant patients.
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Affiliation(s)
- Muhammed Mubarak
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Amber Raza
- Department of Nephrology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Rahma Rashid
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Shaheera Shakeel
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
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Rizvi A, Faiz S, Thakkar PH, Hussain S, Gamilla-Crudo AN, Kueht M, Mujtaba MA. Kidney Allograft Monitoring by Combining Donor-Derived Cell-Free DNA and Molecular Gene Expression: A Clinical Management Perspective. J Pers Med 2023; 13:1205. [PMID: 37623456 PMCID: PMC10455393 DOI: 10.3390/jpm13081205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Donor-derived cell-free DNA (dd-cfDNA) may safely assess kidney allograft rejection. Molecular Microscope (MMDx®) gene expression may offer increased precision to histology. This single-center retrospective study monitored kidney transplant recipients for rejection at specified time intervals by utilizing creatinine (SCr), proteinuria, donor-specific antibodies (DSAs), and dd-cfDNA. A clinically indicated biopsy sample was sent for histopathology and MMDx®. Patients were categorized into rejection (Rej) and non-rejection (NRej) groups, and further grouped according to antibody-mediated rejection (ABMR) subtypes. Rej and NRej groups included 52 and 37 biopsies, respectively. Median follow-up duration was 506 days. DSAs were positive in 53% and 22% of patients in both groups, respectively (p = 0.01). Among these groups, pre- and post-intervention median SCr, proteinuria, and dd-cfDNA at 1 month, 2 months, and at the last follow-up revealed significant difference for dd-cfDNA (all p = 0.01), however, no difference was found for SCr and proteinuria (p > 0.05). The AUC was 0.80 (95% CI: 0.69-0.91), with an optimal dd-cfDNA criterion of 2.2%. Compared to histology, MMDx® was more likely to diagnose ABMR (79% vs. 100%) with either C4d positivity or negativity and/or DSA positivity or negativity. Hence, a pre- and post-intervention allograft monitoring protocol in combination with dd-cfDNA, MMDx®, and histology has aided in early diagnosis and timely individualized intervention.
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Affiliation(s)
- Asim Rizvi
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Sara Faiz
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Parin H. Thakkar
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Syed Hussain
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Ann N. Gamilla-Crudo
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
| | - Michael Kueht
- Department of Transplant Surgery, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA;
| | - Muhammad A. Mujtaba
- Department of Nephrology, Hypertension and Transplant Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (A.R.); (P.H.T.); (S.H.); (A.N.G.-C.)
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Madill-Thomsen KS, Böhmig GA, Bromberg J, Einecke G, Eskandary F, Gupta G, Myslak M, Viklicky O, Perkowska-Ptasinska A, Solez K, Halloran PF. Relating Molecular T Cell-mediated Rejection Activity in Kidney Transplant Biopsies to Time and to Histologic Tubulitis and Atrophy-fibrosis. Transplantation 2023; 107:1102-1114. [PMID: 36575574 PMCID: PMC10125115 DOI: 10.1097/tp.0000000000004396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/29/2022] [Accepted: 09/12/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND We studied the variation in molecular T cell-mediated rejection (TCMR) activity in kidney transplant indication biopsies and its relationship with histologic lesions (particularly tubulitis and atrophy-fibrosis) and time posttransplant. METHODS We examined 175 kidney transplant biopsies with molecular TCMR as defined by archetypal analysis in the INTERCOMEX study ( ClinicalTrials.gov #NCT01299168). TCMR activity was defined by a molecular classifier. RESULTS Archetypal analysis identified 2 TCMR classes, TCMR1 and TCMR2: TCMR1 had higher TCMR activity and more antibody-mediated rejection ("mixed") activity and arteritis but little hyalinosis, whereas TCMR2 had less TCMR activity but more atrophy-fibrosis. TCMR1 and TCMR2 had similar levels of molecular injury and tubulitis. Both TCMR1 and TCMR2 biopsies were uncommon after 2 y posttransplant and were rare after 10 y, particularly TCMR1. Within late TCMR biopsies, TCMR classifier activity and activity molecules such as IFNG fell progressively with time, but tubulitis and molecular injury were sustained. Atrophy-fibrosis was increased in TCMR biopsies, even in the first year posttransplant, and rose with time posttransplant. TCMR1 and TCMR2 both reduced graft survival, but in random forests, the strongest determinant of survival after biopsies with TCMR was molecular injury, not TCMR activity. CONCLUSIONS TCMR varies in intensity but is always strongly related to molecular injury and atrophy-fibrosis, which ultimately explains its effect on survival. We hypothesize, based on the reciprocal relationship with hyalinosis, that the TCMR1-TCMR2 gradient reflects calcineurin inhibitor drug underexposure, whereas the time-dependent decline in TCMR activity and frequency after the first year reflects T-cell exhaustion.
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Affiliation(s)
| | - Georg A. Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Gunilla Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Marek Myslak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation SPWSZ Hospital, Pomeranian Medical University, Szczecin, Poland
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | | | - Kim Solez
- Department of Laboratory Medicine and Pathology, Division of Anatomical Pathology, University of Alberta, Edmonton, Canada
| | - Philip F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
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Smith RN, Rosales IA, Tomaszewski KT, Mahowald GT, Araujo-Medina M, Acheampong E, Bruce A, Rios A, Otsuka T, Tsuji T, Hotta K, Colvin R. Utility of Banff Human Organ Transplant Gene Panel in Human Kidney Transplant Biopsies. Transplantation 2023; 107:1188-1199. [PMID: 36525551 PMCID: PMC10132999 DOI: 10.1097/tp.0000000000004389] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Microarray transcript analysis of human renal transplantation biopsies has successfully identified the many patterns of graft rejection. To evaluate an alternative, this report tests whether gene expression from the Banff Human Organ Transplant (B-HOT) probe set panel, derived from validated microarrays, can identify the relevant allograft diagnoses directly from archival human renal transplant formalin-fixed paraffin-embedded biopsies. To test this hypothesis, principal components (PCs) of gene expressions were used to identify allograft diagnoses, to classify diagnoses, and to determine whether the PC data were rich enough to identify diagnostic subtypes by clustering, which are all needed if the B-HOT panel can substitute for microarrays. METHODS RNA was isolated from routine, archival formalin-fixed paraffin-embedded tissue renal biopsy cores with both rejection and nonrejection diagnoses. The B-HOT panel expression of 770 genes was analyzed by PCs, which were then tested to determine their ability to identify diagnoses. RESULTS PCs of microarray gene sets identified the Banff categories of renal allograft diagnoses, modeled well the aggregate diagnoses, showing a similar correspondence with the pathologic diagnoses as microarrays. Clustering of the PCs identified diagnostic subtypes including non-chronic antibody-mediated rejection with high endothelial expression. PCs of cell types and pathways identified new mechanistic patterns including differential expression of B and plasma cells. CONCLUSIONS Using PCs of gene expression from the B-Hot panel confirms the utility of the B-HOT panel to identify allograft diagnoses and is similar to microarrays. The B-HOT panel will accelerate and expand transcript analysis and will be useful for longitudinal and outcome studies.
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Affiliation(s)
- Rex N Smith
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Ivy A Rosales
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Kristen T Tomaszewski
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Grace T Mahowald
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Milagros Araujo-Medina
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ellen Acheampong
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Amy Bruce
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Andrea Rios
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Takuya Otsuka
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - Takahiro Tsuji
- Department of Pathology, Sapporo City General Hospital, Sapporo, Japan
| | - Kiyohiko Hotta
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan
| | - Robert Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
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Scarpa JR, Elemento O. Multi-omic molecular profiling and network biology for precision anaesthesiology: a narrative review. Br J Anaesth 2023:S0007-0912(23)00125-3. [PMID: 37055274 DOI: 10.1016/j.bja.2023.03.006] [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: 11/11/2022] [Revised: 02/21/2023] [Accepted: 03/04/2023] [Indexed: 04/15/2023] Open
Abstract
Technological advancement, data democratisation, and decreasing costs have led to a revolution in molecular biology in which the entire set of DNA, RNA, proteins, and various other molecules - the 'multi-omic' profile - can be measured in humans. Sequencing 1 million bases of human DNA now costs US$0.01, and emerging technologies soon promise to reduce the cost of sequencing the whole genome to US$100. These trends have made it feasible to sample the multi-omic profile of millions of people, much of which is publicly available for medical research. Can anaesthesiologists use these data to improve patient care? This narrative review brings together a rapidly growing literature in multi-omic profiling across numerous fields that points to the future of precision anaesthesiology. Here, we discuss how DNA, RNA, proteins, and other molecules interact in molecular networks that can be used for preoperative risk stratification, intraoperative optimisation, and postoperative monitoring. This literature provides evidence for four fundamental insights: (1) Clinically similar patients have different molecular profiles and, as a consequence, different outcomes. (2) Vast, publicly available, and rapidly growing molecular datasets have been generated in chronic disease patients and can be repurposed to estimate perioperative risk. (3) Multi-omic networks are altered in the perioperative period and influence postoperative outcomes. (4) Multi-omic networks can serve as empirical, molecular measurements of a successful postoperative course. With this burgeoning universe of molecular data, the anaesthesiologist-of-the-future will tailor their clinical management to an individual's multi-omic profile to optimise postoperative outcomes and long-term health.
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Affiliation(s)
- Joseph R Scarpa
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
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Virmani S, Rao A, Menon MC. Allograft tissue under the microscope: only the beginning. Curr Opin Organ Transplant 2023; 28:126-132. [PMID: 36787238 PMCID: PMC10214011 DOI: 10.1097/mot.0000000000001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
PURPOSE OF REVIEW To review novel modalities for interrogating a kidney allograft biopsy to complement the current Banff schema. RECENT FINDINGS Newer approaches of Artificial Intelligence (AI), Machine Learning (ML), digital pathology including Ex Vivo Microscopy, evaluation of the biopsy gene expression using bulk, single cell, and spatial transcriptomics and spatial proteomics are now available for tissue interrogation. SUMMARY Banff Schema of classification of allograft histology has standardized reporting of tissue pathology internationally greatly impacting clinical care and research. Inherent sampling error of biopsies, and lack of automated morphometric analysis with ordinal outputs limit its performance in prognostication of allograft health. Over the last decade, there has been an explosion of newer methods of evaluation of allograft tissue under the microscope. Digital pathology along with the application of AI and ML algorithms could revolutionize histopathological analyses. Novel molecular diagnostics such as spatially resolved single cell transcriptomics are identifying newer mechanisms underlying the pathologic diagnosis to delineate pathways of immunological activation, tissue injury, repair, and regeneration in allograft tissues. While these techniques are the future of tissue analysis, costs and complex logistics currently limit their clinical use.
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Affiliation(s)
- Sarthak Virmani
- Section of Nephrology, Division of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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17
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Halloran PF, Reeve J, Madill-Thomsen KS, Demko Z, Prewett A, Gauthier P, Billings P, Lawrence C, Lowe D, Hidalgo LG. Antibody-mediated Rejection Without Detectable Donor-specific Antibody Releases Donor-derived Cell-free DNA: Results From the Trifecta Study. Transplantation 2023; 107:709-719. [PMID: 36190186 PMCID: PMC9946174 DOI: 10.1097/tp.0000000000004324] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Trifecta (ClinicalTrials.gov #NCT04239703) is a prospective trial defining relationships between donor-derived cell-free DNA (dd-cfDNA), donor-specific antibody (DSA), and molecular findings in kidney transplant biopsies. Previous analyses of double results showed dd-cfDNA was strongly associated with rejection-associated molecules in the biopsy. The present study analyzed the triple results in 280 biopsies, focusing on the question of dd-cfDNA levels in DSA-negative antibody-mediated rejection (AMR). METHODS Molecular Microscope Diagnostic System biopsy testing was performed at Alberta Transplant Applied Genomics Centre, dd-cfDNA testing at Natera, Inc, and central HLA antibody testing at One Lambda Inc. Local DSA and histologic diagnoses were assigned per center standard-of-care. RESULTS DSA was frequently negative in both molecular (56%) and histologic (51%) AMR. DSA-negative AMR had slightly less molecular AMR activity and histologic peritubular capillaritis than DSA-positive AMR. However, all AMRs-DSA-positive or -negative-showed elevated %dd-cfDNA. There was no association between dd-cfDNA and DSA in biopsies without rejection. In AMR, %dd-cfDNA ≥1.0 was more frequent (75%) than DSA positivity (44%). In logistic regression, dd-cfDNA percent (area under the curve [AUC] 0.85) or quantity (AUC 0.86) predicted molecular AMR better than DSA (AUC 0.66). However, the best predictions incorporated both dd-cfDNA and DSA, plus time posttransplant (AUC 0.88). CONCLUSIONS DSA-negative AMR has moderately decreased mean molecular and histologic AMR-associated features compared with DSA-positive AMR, though similarly elevated dd-cfDNA levels. In predicting AMR at the time of indication biopsies in this population, dd-cfDNA is superior to DSA, reflecting the prevalence of DSA-negative AMR, but the optimal predictions incorporated both dd-cfDNA and DSA.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Transcriptome Sciences, Inc, Edmonton, AB, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
| | | | | | | | | | | | | | | | - Luis G. Hidalgo
- Division of Transplantation, Department of Surgery, University of Wisconsin, Madison, WI
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The Molecular Diagnosis Might Be Clinically Useful in Discrepant Kidney Allograft Biopsy Findings: An Analysis of Clinical Outcomes. Transplantation 2023; 107:485-494. [PMID: 36117252 PMCID: PMC9875837 DOI: 10.1097/tp.0000000000004284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND The Molecular Microscope Diagnostic System (MMDx) may overcome histology shortcomings. Previous studies have simply examined discrepant findings but have not attempted to determine clinical endpoints. To measure performance, clinical outcomes are strongly required. METHODS This single-center cohort study described discrepancies between MMDx and histology from 51 kidney transplant recipients (KTRs) and analyzed 72 indication biopsies, including 21 follow-up biopsies. Clinical performance was assessed by a combined endpoint of graft failure, rejection on follow-up biopsy, de novo donor-specific antibody, and improvement of kidney allograft function upon antirejection treatment. RESULTS MMDx agreed in 33 (65%) and differed in 18 (35%) of 51 KTRs. Most discrepancies occurred in biopsies called no rejection by MMDx and rejection by histology (15/24, 63%). In contrast, in biopsies called rejection by MMDx, 3 were classified as no rejection by histology (3/27, 11%). Discrepant findings between MMDx and histology occurred following delayed graft function and MMDx from biopsies with a low percentage of cortex. Among 15 biopsies classified as no rejection by MMDx but rejection by histology, the clinical course suggested no rejection in 9 cases. Six KTRs reached the endpoint, showing predominant t ≥ 2 lesions. CONCLUSIONS The most often occurring discrepancy is rejection by histology but no rejection by MMDx. As more KTRs do not meet the combined endpoint for rejection, MMDx might be clinically useful in these discrepant cases. Although strong histological findings have priority in indicating the treatment, clinical implementation of MMDx could strengthen treatment strategies.
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The Molecular Microscope Diagnostic System: Assessment of Rejection and Injury in Heart Transplant Biopsies. Transplantation 2023; 107:27-44. [PMID: 36508644 DOI: 10.1097/tp.0000000000004323] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review describes the development of the Molecular Microscope Diagnostic System (MMDx) for heart transplant endomyocardial biopsies (EMBs). MMDx-Heart uses microarrays to measure biopsy-based gene expression and ensembles of machine learning algorithms to interpret the results and compare each new biopsy to a large reference set of earlier biopsies. MMDx assesses T cell-mediated rejection (TCMR), antibody-mediated rejection (AMR), recent parenchymal injury, and atrophy-fibrosis, continually "learning" from new biopsies. Rejection-associated transcripts mapped in kidney transplants and experimental systems were used to identify TCMR, AMR, and recent injury-induced inflammation. Rejection and injury emerged as gradients of intensity, rather than binary classes. AMR was one-third donor-specific antibody (DSA)-negative, and many EMBs first considered to have no rejection displayed minor AMR-like changes, with increased probability of DSA positivity and subtle inflammation. Rejection-associated transcript-based algorithms now classify EMBs as "Normal," "Minor AMR changes," "AMR," "possible AMR," "TCMR," "possible TCMR," and "recent injury." Additionally, MMDx uses injury-associated transcript sets to assess the degree of parenchymal injury and atrophy-fibrosis in every biopsy and study the effect of rejection on the parenchyma. TCMR directly injures the parenchyma whereas AMR usually induces microcirculation stress but relatively little initial parenchymal damage, although slowly inducing parenchymal atrophy-fibrosis. Function (left ventricular ejection fraction) and short-term risk of failure are strongly determined by parenchymal injury. These discoveries can guide molecular diagnostic applications, either as a central MMDx system or adapted to other platforms. MMDx can also help calibrate noninvasive blood-based biomarkers to avoid unnecessary biopsies and monitor response to therapy.
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Barbetta A, Rocque B, Sarode D, Bartlett JA, Emamaullee J. Revisiting transplant immunology through the lens of single-cell technologies. Semin Immunopathol 2023; 45:91-109. [PMID: 35980400 PMCID: PMC9386203 DOI: 10.1007/s00281-022-00958-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
Abstract
Solid organ transplantation (SOT) is the standard of care for end-stage organ disease. The most frequent complication of SOT involves allograft rejection, which may occur via T cell- and/or antibody-mediated mechanisms. Diagnosis of rejection in the clinical setting requires an invasive biopsy as there are currently no reliable biomarkers to detect rejection episodes. Likewise, it is virtually impossible to identify patients who exhibit operational tolerance and may be candidates for reduced or complete withdrawal of immunosuppression. Emerging single-cell technologies, including cytometry by time-of-flight (CyTOF), imaging mass cytometry, and single-cell RNA sequencing, represent a new opportunity for deep characterization of pathogenic immune populations involved in both allograft rejection and tolerance in clinical samples. These techniques enable examination of both individual cellular phenotypes and cell-to-cell interactions, ultimately providing new insights into the complex pathophysiology of allograft rejection. However, working with these large, highly dimensional datasets requires expertise in advanced data processing and analysis using computational biology techniques. Machine learning algorithms represent an optimal strategy to analyze and create predictive models using these complex datasets and will likely be essential for future clinical application of patient level results based on single-cell data. Herein, we review the existing literature on single-cell techniques in the context of SOT.
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Affiliation(s)
- Arianna Barbetta
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA
- University of Southern California, Los Angeles, CA, USA
| | - Brittany Rocque
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA
- University of Southern California, Los Angeles, CA, USA
| | - Deepika Sarode
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA
- University of Southern California, Los Angeles, CA, USA
| | - Johanna Ascher Bartlett
- Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Juliet Emamaullee
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA.
- University of Southern California, Los Angeles, CA, USA.
- Division of Hepatobiliary and Abdominal Organ Transplantation Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.
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The Histological Spectrum and Clinical Significance of T Cell-mediated Rejection of Kidney Allografts. Transplantation 2022; 107:1042-1055. [PMID: 36584369 DOI: 10.1097/tp.0000000000004438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
T cell-mediated rejection (TCMR) remains a significant cause of long-term kidney allograft loss, either indirectly through induction of donor-specific anti-HLA alloantibodies or directly through chronic active TCMR. Whether found by indication or protocol biopsy, Banff defined acute TCMR should be treated with antirejection therapy and maximized maintenance immunosuppression. Neither isolated interstitial inflammation in the absence of tubulitis nor isolated tubulitis in the absence of interstitial inflammation results in adverse outcomes, and neither requires antirejection treatment. RNA gene expression analysis of biopsy material may supplement conventional histology, especially in ambiguous cases. Lesser degrees of tubular and interstitial inflammation (Banff borderline) may portend adverse outcomes and should be treated when found on an indication biopsy. Borderline lesions on protocol biopsies may resolve spontaneously but require close follow-up if untreated. Following antirejection therapy of acute TCMR, surveillance protocol biopsies should be considered. Minimally invasive blood-borne assays (donor-derived cell-free DNA and gene expression profiling) are being increasingly studied as a means of following stable patients in lieu of biopsy. The clinical benefit and cost-effectiveness require confirmation in randomized controlled trials. Treatment of acute TCMR is not standardized but involves bolus corticosteroids with lymphocyte depleting antibodies for severe, refractory, or relapsing cases. Arteritis may be found with acute TCMR, active antibody-mediated rejection, or mixed rejections and should be treated accordingly. The optimal treatment ofchronic active TCMR is uncertain. Randomized controlled trials are necessary to optimally define therapy.
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22
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Halloran PF, Reeve J, Madill-Thomsen KS, Kaur N, Ahmed E, Cantos C, Al Haj Baddar N, Demko Z, Liang N, Swenerton RK, Zimmermann BG, Van Hummelen P, Prewett A, Rabinowitz M, Tabriziani H, Gauthier P, Billings P. Combining Donor-derived Cell-free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology as Confirmation. Transplantation 2022; 106:2435-2442. [PMID: 35765145 PMCID: PMC9698190 DOI: 10.1097/tp.0000000000004212] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/14/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) fraction and quantity have both been shown to be associated with allograft rejection. The present study compared the relative predictive power of each of these variables to the combination of the two, and developed an algorithm incorporating both variables to detect active rejection in renal allograft biopsies. METHODS The first 426 sequential indication biopsy samples collected from the Trifecta study ( ClinicalTrials.gov # NCT04239703) with microarray-derived gene expression and dd-cfDNA results were included. After exclusions to simulate intended clinical use, 367 samples were analyzed. Biopsies were assessed using the molecular microscope diagnostic system and histology (Banff 2019). Logistic regression analysis examined whether combining dd-cfDNA fraction and quantity adds predictive value to either alone. The first 149 sequential samples were used to develop a two-threshold algorithm and the next 218 to validate the algorithm. RESULTS In regression, the combination of dd-cfDNA fraction and quantity was found to be significantly more predictive than either variable alone ( P = 0.009 and P < 0.0001). In the test set, the area under the receiver operating characteristic curve of the two-variable system was 0.88, and performance of the two-threshold algorithm showed a sensitivity of 83.1% and specificity of 81.0% for molecular diagnoses and a sensitivity of 73.5% and specificity of 80.8% for histology diagnoses. CONCLUSIONS This prospective, biopsy-matched, multisite dd-cfDNA study in kidney transplant patients found that the combination of dd-cfDNA fraction and quantity was more powerful than either dd-cfDNA fraction or quantity alone and validated a novel two-threshold algorithm incorporating both variables.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - the Trifecta Investigators*
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
- Natera Inc, San Carlos, CA
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23
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Pang Q, Chen H, Wu H, Wang Y, An C, Lai S, Xu J, Wang R, Zhou J, Xiao H. N6-methyladenosine regulators-related immune genes enable predict graft loss and discriminate T-cell mediate rejection in kidney transplantation biopsies for cause. Front Immunol 2022; 13:1039013. [PMID: 36483557 PMCID: PMC9722771 DOI: 10.3389/fimmu.2022.1039013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Objective The role of m6A modification in kidney transplant-associated immunity, especially in alloimmunity, still remains unknown. This study aims to explore the potential value of m6A-related immune genes in predicting graft loss and diagnosing T cell mediated rejection (TCMR), as well as the possible role they play in renal graft dysfunction. Methods Renal transplant-related cohorts and transcript expression data were obtained from the GEO database. First, we conducted correlation analysis in the discovery cohort to identify the m6A-related immune genes. Then, lasso regression and random forest were used respectively to build prediction models in the prognosis and diagnosis cohort, to predict graft loss and discriminate TCMR in dysfunctional renal grafts. Connectivity map (CMap) analysis was applied to identify potential therapeutic compounds for TCMR. Results The prognostic prediction model effectively predicts the prognosis and survival of renal grafts with clinical indications (P< 0.001) and applies to both rejection and non-rejection situations. The diagnostic prediction model discriminates TCMR in dysfunctional renal grafts with high accuracy (area under curve = 0.891). Meanwhile, the classifier score of the diagnostic model, as a continuity index, is positively correlated with the severity of main pathological injuries of TCMR. Furthermore, it is found that METTL3, FTO, WATP, and RBM15 are likely to play a pivotal part in the regulation of immune response in TCMR. By CMap analysis, several small molecular compounds are found to be able to reverse TCMR including fenoldopam, dextromethorphan, and so on. Conclusions Together, our findings explore the value of m6A-related immune genes in predicting the prognosis of renal grafts and diagnosis of TCMR.
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Affiliation(s)
- Qidan Pang
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Chen
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Hang Wu
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Wang
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Changyong An
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Suhe Lai
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Jia Xu
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Ruiqiong Wang
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Zhou
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Hanyu Xiao, ; Juan Zhou,
| | - Hanyu Xiao
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Hanyu Xiao, ; Juan Zhou,
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24
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Liu X, Liu D, Zhou S, Jiang W, Zhang J, Hu J, Liao G, Liao J, Guo Z, Li Y, Yang S, Li S, Chen H, Guo Y, Li M, Fan L, Li L, Zhao M, Liu Y. CARARIME: Interactive web server for comprehensive analysis of renal allograft rejection in immune microenvironment. Front Immunol 2022; 13:1026280. [DOI: 10.3389/fimmu.2022.1026280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
BackgroundRenal transplantation is a very effective treatment for renal failure patients following kidney transplant. However, the clinical benefit is restricted by the high incidence of organ rejection. Therefore, there exists a wealth of literature regarding the mechanism of renal transplant rejection, including a large library of expression data. In recent years, research has shown the immune microenvironment to play an important role in renal transplant rejection. Nephrology web analysis tools currently exist to address chronic nephropathy, renal tumors and children’s kidneys, but no such tool exists that analyses the impact of immune microenvironment in renal transplantation rejection.MethodsTo fill this gap, we have developed a web page analysis tool called Comprehensive Analysis of Renal Allograft Rerejction in Immune Microenvironment (CARARIME).ResultsCARARIME analyzes the gene expression and immune microenvironment of published renal transplant rejection cohorts, including differential analysis (gene expression and immune cells), prognosis analysis (logistics regression, Univariable Cox Regression and Kaplan Meier), correlation analysis, enrichment analysis (GSEA and ssGSEA), and ROC analysis.ConclusionsUsing this tool, researchers can easily analyze the immune microenvironment in the context of renal transplant rejection by clicking on the available options, helping to further the development of approaches to renal transplant rejection in the immune microenvironment field. CARARIME can be found in http://www.cararime.com.
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Randhawa P. The MMDx ® diagnostic system: A critical re-appraisal of its knowledge gaps and a call for rigorous validation studies. Clin Transplant 2022; 36:e14747. [PMID: 35678044 DOI: 10.1111/ctr.14747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 12/15/2022]
Abstract
Transcriptomics generates pathogenetic insights not obtainable by histology, but translation of these insights into diagnostic tests is not a trivial task. This opinion-piece critically appraises declarative MMDx statements, such as the infallibility of machine learning algorithms, measurements of gene expression with >99% precision, and "unambiguous reclassifications" of contentious biopsies such as those with borderline change, polyomavirus nephropathy, chronic active T-cell or mixed rejection, isolated intimal arteritis, and renal medullary pathology. It is shown that molecular diagnoses that do not agree with histology cannot be attributed primarily to pathology reading errors. Neither can all molecular calls derived from arbitrary binary thresholds be automatically accepted as the ground truth. Important other sources of discrepancies between clinico-pathologic and molecular calls include: (a) organ being studied, (b) disease definition, (c) clinical histologic, and gene expression heterogeneity within the same diagnostic label, (d) size and composition of comparator groups, (e) molecular noise, (f) variability in output of different machine learning algorithms, and (g) the nonavailability of a molecular classifier for chronic active TCMR. Carefully designed clinical trials are needed to determine which of the proposed indications of MMDx provide incremental value over existing standard of care protocols.
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Affiliation(s)
- Parmjeet Randhawa
- Division of Transplantation Pathology, Department of Pathology, The Thomas E Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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26
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Kherabi Y, Messika J, Peiffer‐Smadja N. Machine learning, antimicrobial stewardship, and solid organ transplantation: Is this the future? Transpl Infect Dis 2022; 24:e13957. [DOI: 10.1111/tid.13957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Yousra Kherabi
- Infectious and Tropical Diseases Department Bichat‐Claude Bernard Hospital Assistance Publique‐Hôpitaux de Paris Paris France
| | - Jonathan Messika
- Université Paris Cité AP‐HP Bichat‐Claude Bernard Hospital Pneumologie B et Transplantation Pulmonaire Paris France
| | - Nathan Peiffer‐Smadja
- Infectious and Tropical Diseases Department Bichat‐Claude Bernard Hospital Assistance Publique‐Hôpitaux de Paris Paris France
- Université Paris Cité and Université Sorbonne Paris Nord Inserm IAME Paris France
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27
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Peloso A, Moeckli B, Delaune V, Oldani G, Andres A, Compagnon P. Artificial Intelligence: Present and Future Potential for Solid Organ Transplantation. Transpl Int 2022; 35:10640. [PMID: 35859667 PMCID: PMC9290190 DOI: 10.3389/ti.2022.10640] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/13/2022] [Indexed: 12/12/2022]
Abstract
Artificial intelligence (AI) refers to computer algorithms used to complete tasks that usually require human intelligence. Typical examples include complex decision-making and- image or speech analysis. AI application in healthcare is rapidly evolving and it undoubtedly holds an enormous potential for the field of solid organ transplantation. In this review, we provide an overview of AI-based approaches in solid organ transplantation. Particularly, we identified four key areas of transplantation which could be facilitated by AI: organ allocation and donor-recipient pairing, transplant oncology, real-time immunosuppression regimes, and precision transplant pathology. The potential implementations are vast—from improved allocation algorithms, smart donor-recipient matching and dynamic adaptation of immunosuppression to automated analysis of transplant pathology. We are convinced that we are at the beginning of a new digital era in transplantation, and that AI has the potential to improve graft and patient survival. This manuscript provides a glimpse into how AI innovations could shape an exciting future for the transplantation community.
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Affiliation(s)
- Andrea Peloso
- Department of General Surgery, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
- Department of Transplantation, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
- *Correspondence: Andrea Peloso,
| | - Beat Moeckli
- Department of General Surgery, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
- Department of Transplantation, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
| | - Vaihere Delaune
- Department of General Surgery, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
| | - Graziano Oldani
- Department of General Surgery, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
- Department of Transplantation, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
| | - Axel Andres
- Department of General Surgery, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
- Department of Transplantation, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
| | - Philippe Compagnon
- Department of Transplantation, University of Geneva Hospitals, University of Geneva, Geneva, Switzerland
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28
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McCloskey C, Zubrycki M, Lawrence C. The Molecular Microscope Diagnostic System (MMDx) interpretation of solid organ allograft biopsies: Restoring the perspective. Clin Transplant 2022; 36:e14711. [PMID: 35668041 DOI: 10.1111/ctr.14711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/02/2022] [Accepted: 05/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Chris McCloskey
- Transplant Diagnostics Division, Thermo Fisher Scientific, West Hills, California, USA
| | - Michelle Zubrycki
- Transplant Diagnostics Division, Thermo Fisher Scientific, West Hills, California, USA
| | - Christopher Lawrence
- Transplant Diagnostics Division, Thermo Fisher Scientific, West Hills, California, USA
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29
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Steggerda JA, Pizzo H, Garrison J, Zhang X, Haas M, Kim IK, Jordan SC, Puliyanda DP. Use of a donor-derived cell-free DNA assay to monitor treatment response in pediatric renal transplant recipients with allograft rejection. Pediatr Transplant 2022; 26:e14258. [PMID: 35340104 DOI: 10.1111/petr.14258] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/09/2022] [Accepted: 02/08/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND Detection of donor-derived cell-free DNA (dd-cfDNA) reliably identifies allograft rejection in pediatric and adult kidney transplant (KT) recipients. Here, we evaluate the utility of dd-cfDNA for monitoring response to treatment among pediatric renal transplant recipients suffering graft rejection. METHODS 58 pediatric transplant recipients were enrolled between April 2018 and March 2020 and underwent initial dd-cfDNA testing to monitor for rejection. Allograft biopsy was performed for dd-cfDNA scores >1.0%. Patients with histologically proven rejection formed the study cohort and underwent appropriate treatment. Results of dd-cfDNA, serum creatinine (SCr), biopsy findings, and treatment outcomes were evaluated. Standard statistical analyses were applied. RESULTS Nineteen of 58 (31%) patients had dd-cfDNA score >1.0%, of which 18 (94.7%) had biopsy-proven rejection. Median dd-cfDNA value was 1.90% (interquartile range 1.43%-3.23%), and biopsy results showed 11 patients (61.1%) with antibody-mediated rejection (AMR), 2 patients (11.1%) with T-cell mediated rejection (TCMR), and 5 patients (27.7%) with mixed AMR/TCMR. SCr at time of biopsy was 1.28 ± 1.09 mg/dl. Following treatment, dd-cfDNA scores decreased for all types of rejection but still remained >1.0% in both AMR (1.50% [0.90%-3.10%]) and mixed (1.40% [0.95%-4.15%]) groups. Repeat dd-cfDNA values were <1.0% for patients with TCMR (0.20%-0.28%). SCr showed minimal change from pre-treatment levels regardless of rejection subtype. CONCLUSIONS Patients with TCMR may be reliably followed by dd-cfDNA; however, it remains unclear whether persistently elevated dd-cfDNA levels in AMR is a reflection of ongoing subclinical rejection or an inherent limitation of the assay's utility.
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Affiliation(s)
- Justin A Steggerda
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
| | - Helen Pizzo
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
| | - Jonathan Garrison
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
| | - Xiaohai Zhang
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
| | - Mark Haas
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
| | - Irene K Kim
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
| | - Stanley C Jordan
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
| | - Dechu P Puliyanda
- Cedars Sinai Medical Center, Pediatric Nephrology, Los Angeles, California, USA
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30
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Halloran PF, Böhmig GA, Bromberg J, Einecke G, Eskandary FA, Gupta G, Myslak M, Viklicky O, Perkowska-Ptasinska A, Madill-Thomsen KS. Archetypal Analysis of Injury in Kidney Transplant Biopsies Identifies Two Classes of Early AKI. Front Med (Lausanne) 2022; 9:817324. [PMID: 35463013 PMCID: PMC9021747 DOI: 10.3389/fmed.2022.817324] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/07/2022] [Indexed: 01/07/2023] Open
Abstract
All transplanted kidneys are subjected to some degree of injury as a result of the donation-implantation process and various post-transplant stresses such as rejection. Because transplants are frequently biopsied, they present an opportunity to explore the full spectrum of kidney response-to-wounding from all causes. Defining parenchymal damage in transplanted organs is important for clinical management because it determines function and survival. In this study, we classified the scenarios associated with parenchymal injury in genome-wide microarray results from 1,526 kidney transplant indication biopsies collected during the INTERCOMEX study. We defined injury groups by using archetypal analysis (AA) of scores for gene sets and classifiers previously identified in various injury states. Six groups and their characteristics were defined in this population: No injury, minor injury, two classes of acute kidney injury ("AKI," AKI1, and AKI2), chronic kidney disease (CKD), and CKD combined with AKI. We compared the two classes of AKI, namely, AKI1 and AKI2. AKI1 had a poor function and increased parenchymal dedifferentiation but minimal response-to-injury and inflammation, instead having increased expression of PARD3, a gene previously characterized as being related to epithelial polarity and adherens junctions. In contrast, AKI2 had a poor function and increased response-to-injury, significant inflammation, and increased macrophage activity. In random forest analysis, the most important predictors of function (estimated glomerular filtration rate) and graft loss were injury-based molecular scores, not rejection scores. AKI1 and AKI2 differed in 3-year graft survival, with better survival in the AKI2 group. Thus, injury archetype analysis of injury-induced gene expression shows new heterogeneity in kidney response-to-wounding, revealing AKI1, a class of early transplants with a poor function but minimal inflammation or response to injury, a deviant response characterized as PC3, and an increased risk of failure. Given the relationship between parenchymal injury and kidney survival, further characterization of the injury phenotypes in kidney transplants will be important for an improved understanding that could have implications for understanding native kidney diseases (ClinicalTrials.gov #NCT01299168).
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada.,Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Jonathan Bromberg
- Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Gunilla Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Farsad A Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA, United States
| | - Marek Myslak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation Samodzielny Publiczny Wojewódzki Szpital Zespolony (SPWSZ) Hospital, Pomeranian Medical University, Szczecin, Poland
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Agnieszka Perkowska-Ptasinska
- Department of Transplantation Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
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31
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Parkes MD, Halloran K, Hirji A, Pon S, Weinkauf J, Timofte IL, Snell GI, Westall GP, Havlin J, Lischke R, Zajacová A, Hachem R, Kreisel D, Levine D, Kubisa B, Piotrowska M, Juvet S, Keshavjee S, Jaksch P, Klepetko W, Halloran PF. Transcripts associated with chronic lung allograft dysfunction in transbronchial biopsies of lung transplants. Am J Transplant 2022; 22:1054-1072. [PMID: 34850543 DOI: 10.1111/ajt.16895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/14/2021] [Accepted: 11/07/2021] [Indexed: 01/25/2023]
Abstract
Transplanted lungs suffer worse outcomes than other organ transplants with many developing chronic lung allograft dysfunction (CLAD), diagnosed by physiologic changes. Histology of transbronchial biopsies (TBB) yields little insight, and the molecular basis of CLAD is not defined. We hypothesized that gene expression in TBBs would reveal the nature of CLAD and distinguish CLAD from changes due simply to time posttransplant. Whole-genome mRNA profiling was performed with microarrays in 498 prospectively collected TBBs from the INTERLUNG study, 90 diagnosed as CLAD. Time was associated with increased expression of inflammation genes, for example, CD1E and immunoglobulins. After correcting for time, CLAD manifested not as inflammation but as parenchymal response-to-wounding, with increased expression of genes such as HIF1A, SERPINE2, and IGF1 that are increased in many injury and disease states and cancers, associated with development, angiogenesis, and epithelial response-to-wounding in pathway analysis. Fibrillar collagen genes were increased in CLAD, indicating matrix changes, and normal transcripts were decreased-dedifferentiation. Gene-based classifiers predicted CLAD with AUC 0.70 (no time-correction) and 0.87 (time-corrected). CLAD related gene sets and classifiers were strongly prognostic for graft failure and correlated with CLAD stage. Thus, in TBBs, molecular changes indicate that CLAD primarily reflects severe parenchymal injury-induced changes and dedifferentiation.
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Affiliation(s)
| | | | - Alim Hirji
- University of Alberta, Edmonton, Alberta, Canada
| | - Shane Pon
- University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Greg I Snell
- Alfred Hospital Lung Transplant Service, Melbourne, Australia
| | - Glen P Westall
- Alfred Hospital Lung Transplant Service, Melbourne, Australia
| | - Jan Havlin
- University Hospital Motol, Prague, Czech Republic
| | | | | | - Ramsey Hachem
- Washington University in St Louis, St. Louis, Missouri, USA
| | - Daniel Kreisel
- Washington University in St Louis, St. Louis, Missouri, USA
| | - Deborah Levine
- University of Texas San Antonio, San Antonio, Texas, USA
| | - Bartosz Kubisa
- Pomeranian Medical University of Szczecin, Szczecin, Poland
| | | | - Stephen Juvet
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
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32
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Zhou XJ, Zhong XH, Duan LX. Integration of Artificial Intelligence And Multi-omics in Kidney Diseases. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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33
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Zhou H, Lu H, Sun L, Wang Z, Zheng M, Hang Z, Zhang D, Tan R, Gu M. Diagnostic Biomarkers and Immune Infiltration in Patients With T Cell-Mediated Rejection After Kidney Transplantation. Front Immunol 2022; 12:774321. [PMID: 35058922 PMCID: PMC8764245 DOI: 10.3389/fimmu.2021.774321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
T cell-mediated rejection (TCMR) is an important rejection type in kidney transplantation, characterized by T cells and macrophages infiltration. The application of bioinformatic analysis in genomic research has been widely used. In the present study, Microarray data was analyzed to identify the potential diagnostic markers of TCMR in kidney transplantation. Cell-type identification by estimating relative subsets of RNA transcript (CIBERSORT) was performed to determine the distribution of immune cell infiltration in the pathology. Totally 129 upregulated differently expressed genes (DEGs) and 378 downregulated DEGs were identified. The GO and KEGG results demonstrated that DEGs were mainly associated with pathways and diseases involved in immune response. The intersection of the two algorithms (PPI network and LASSO) contains three overlapping genes (CXCR6, CXCL13 and FCGR1A). After verification in GSE69677, only CXCR6 and CXCL13 were selected. Immune cells Infiltration analysis demonstrated that CXCR6 and CXCL13 were positively correlated with gamma delta T cells (p < 0.001), CD4+ memory activated T cells (p < 0.001), CD8+ T cells (p < 0.001) and M1 macrophages (p = 0.006), and negatively correlated with M2 macrophages (p < 0.001) and regulatory T cells (p < 0.001). Immunohistochemical staining and image analysis confirmed the overexpression of CXCR6 and CXCL13 in human allograft TCMR samples. CXCR6 and CXCL13 could be diagnostic biomarkers of TCMR and potential targets for immunotherapy in patients with TCMR.
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Affiliation(s)
- Hai Zhou
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongcheng Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Zheng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhou Hang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Dongliang Zhang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Gu
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Madill-Thomsen KS, Abouljoud M, Bhati C, Ciszek M, Durlik M, Feng S, Foroncewicz B, Francis I, Grąt M, Jurczyk K, Klintmalm G, Krasnodębski M, McCaughan G, Miquel R, Montano-Loza A, Moonka D, Mucha K, Myślak M, Pączek L, Perkowska-Ptasińska A, Piecha G, Reichman T, Sanchez-Fueyo A, Tronina O, Wawrzynowicz-Syczewska M, Więcek A, Zieniewicz K, Halloran PF. The molecular phenotypes of injury, steatohepatitis, and fibrosis in liver transplant biopsies in the INTERLIVER study. Am J Transplant 2022; 22:909-926. [PMID: 34780106 DOI: 10.1111/ajt.16890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 01/25/2023]
Abstract
To extend previous molecular analyses of rejection in liver transplant biopsies in the INTERLIVER study (ClinicalTrials.gov #NCT03193151), the present study aimed to define the gene expression selective for parenchymal injury, fibrosis, and steatohepatitis. We analyzed genome-wide microarray measurements from 337 liver transplant biopsies from 13 centers. We examined expression of genes previously annotated as increased in injury and fibrosis using principal component analysis (PCA). PC1 reflected parenchymal injury and related inflammation in the early posttransplant period, slowly regressing over many months. PC2 separated early injury from late fibrosis. Positive PC3 identified a distinct mildly inflamed state correlating with histologic steatohepatitis. Injury PCs correlated with liver function and histologic abnormalities. A classifier trained on histologic steatohepatitis predicted histologic steatohepatitis with cross-validated AUC = 0.83, and was associated with pathways reflecting metabolic abnormalities distinct from fibrosis. PC2 predicted histologic fibrosis (AUC = 0.80), as did a molecular fibrosis classifier (AUC = 0.74). The fibrosis classifier correlated with matrix remodeling pathways with minimal overlap with those selective for steatohepatitis, although some biopsies had both. Genome-wide assessment of liver transplant biopsies can not only detect molecular changes induced by rejection but also those correlating with parenchymal injury, steatohepatitis, and fibrosis, offering potential insights into disease mechanisms for primary diseases.
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Affiliation(s)
| | | | - Chandra Bhati
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Michał Ciszek
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Durlik
- Department of Transplant Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sandy Feng
- University of California San Francisco, San Francisco, California, USA
| | - Bartosz Foroncewicz
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Michał Grąt
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Jurczyk
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University, Szczecin, Poland
| | | | - Maciej Krasnodębski
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Geoff McCaughan
- Centenary Research Institute, Australian National Liver Transplant Unit, Royal Prince Alfred Hospital, The University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Myślak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation SPWSZ Hospital, Pomeranian Medical University, Szczecin, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Grzegorz Piecha
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, Katowice, Poland
| | | | | | - Olga Tronina
- Department of Transplant Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marta Wawrzynowicz-Syczewska
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University, Szczecin, Poland
| | - Andrzej Więcek
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, Katowice, Poland
| | - Krzysztof Zieniewicz
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
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Halloran PF, Reeve J, Madill-Thomsen KS, Demko Z, Prewett A, Billings P. The Trifecta Study: Comparing Plasma Levels of Donor-derived Cell-Free DNA with the Molecular Phenotype of Kidney Transplant Biopsies. J Am Soc Nephrol 2022; 33:387-400. [PMID: 35058354 PMCID: PMC8819982 DOI: 10.1681/asn.2021091191] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The relationship between the donor-derived cell-free DNA fraction (dd-cfDNA[%]) in plasma in kidney transplant recipients at time of indication biopsy and gene expression in the biopsied allograft has not been defined. METHODS In the prospective, multicenter Trifecta study, we collected tissue from 300 biopsies from 289 kidney transplant recipients to compare genome-wide gene expression in biopsies with dd-cfDNA(%) in corresponding plasma samples drawn just before biopsy. Rejection was assessed with the microarray-based Molecular Microscope Diagnostic System using automatically assigned rejection archetypes and molecular report sign-outs, and histology assessments that followed Banff guidelines. RESULTS The median time of biopsy post-transplantation was 455 days (5 days to 32 years), with a case mix similar to that of previous studies: 180 (60%) no rejection, 89 (30%) antibody-mediated rejection (ABMR), and 31 (10%) T cell-mediated rejection (TCMR) and mixed. In genome-wide mRNA measurements, all 20 top probe sets correlating with dd-cfDNA(%) were previously annotated for association with ABMR and all types of rejection, either natural killer (NK) cell-expressed (e.g., GNLY, CCL4, TRDC, and S1PR5) or IFN-γ-inducible (e.g., PLA1A, IDO1, CXCL11, and WARS). Among gene set and classifier scores, dd-cfDNA(%) correlated very strongly with ABMR and all types of rejection, reasonably strongly with active TCMR, and weakly with inactive TCMR, kidney injury, and atrophy fibrosis. Active ABMR, mixed, and active TCMR had the highest dd-cfDNA(%), whereas dd-cfDNA(%) was lower in late-stage ABMR and less-active TCMR. By multivariate random forests and logistic regression, molecular rejection variables predicted dd-cfDNA(%) better than histologic variables. CONCLUSIONS The dd-cfDNA(%) at time of indication biopsy strongly correlates with active molecular rejection and has the potential to reduce unnecessary biopsies. CLINICAL TRIAL REGISTRATION NUMBER NCT04239703.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Center, Edmonton, Canada,Department of Medicine, University of Alberta, Edmonton, Canada,Transcriptome Sciences Inc., Edmonton, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Center, Edmonton, Canada
| | - Katelynn S. Madill-Thomsen
- Alberta Transplant Applied Genomics Center, Edmonton, Canada,Transcriptome Sciences Inc., Edmonton, Canada
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36
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Fusfeld L, Menon S, Gupta G, Lawrence C, Masud SF, Goss TF. US payer budget impact of a microarray assay with machine learning to evaluate kidney transplant rejection in for-cause biopsies. J Med Econ 2022; 25:515-523. [PMID: 35345966 DOI: 10.1080/13696998.2022.2059221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AIM This study evaluates the economic impact to US commercial payers of MMDx-Kidney used in conjunction with histologic evaluation of for-cause kidney transplant biopsies. MATERIALS AND METHODS An Excel-based model was developed to assess the cost impact of histology plus MMDx-Kidney versus histology alone for the evaluation of potential rejection in kidney transplant patients who receive a for-cause biopsy. Different model time periods were assessed, ranging from 1 to 5 years post-biopsy. A targeted literature review was used to identify parameter estimates, validated by two external clinicians with expertise in managing kidney transplant rejection. A sensitivity analysis was conducted to evaluate the relative impact of key clinical and cost parameters. In particular, the model identified the magnitude of MMDx-Kidney's impact on graft failure from rejection that would be required for MMDx-Kidney to be cost-neutral. RESULTS By more accurately characterizing rejection, MMDx-Kidney is estimated to increase antirejection treatment costs by $1,126 per test. Nevertheless, a break-even analysis shows that the costs of MMDx-Kidney and anti-rejection medication, as well as the costs associated with an increase in the number of patients with functioning transplants, may be offset by reductions in costs associated with graft failure (i.e. costs of hospitalizations, dialysis, and repeat transplants) over 5 years, assuming MMDx-Kidney reduces annual graft failure from rejection by at least 5%. For the base case, with a 25% relative reduction in annual rate of graft failures from rejection, MMDx-Kidney increases overall costs incurred in the first year of the model but starts generating savings by the second year of the model. CONCLUSIONS Compared with histologic evaluation of for-cause kidney transplant biopsies alone, the use of MMDx-Kidney in conjunction with histologic evaluation improves the diagnoses of graft dysfunction and may have the potential to generate overall savings from reductions in rejection-related graft failure.
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Affiliation(s)
- Lauren Fusfeld
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
| | - Sreeranjani Menon
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
| | - Gaurav Gupta
- Division of Nephrology, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Salwa F Masud
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
| | - Thomas F Goss
- Boston Healthcare Associates, Inc. (now a Veranex company), Boston, MA, USA
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37
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Loupy A, Mengel M, Haas M. 30 years of the International Banff Classification for Allograft Pathology: The Past, Present and Future of Kidney Transplant Diagnostics. Kidney Int 2021; 101:678-691. [DOI: 10.1016/j.kint.2021.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
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38
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Madill-Thomsen KS, Böhmig GA, Bromberg J, Einecke G, Eskandary F, Gupta G, Hidalgo LG, Myslak M, Viklicky O, Perkowska-Ptasinska A, Halloran PF. Donor-Specific Antibody Is Associated with Increased Expression of Rejection Transcripts in Renal Transplant Biopsies Classified as No Rejection. J Am Soc Nephrol 2021; 32:2743-2758. [PMID: 34253587 PMCID: PMC8806080 DOI: 10.1681/asn.2021040433] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/20/2021] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Donor -specific HLA antibody (DSA) is present in many kidney transplant patients whose biopsies are classified as no rejection (NR). We explored whether in some NR kidneys DSA has subtle effects not currently being recognized. METHODS We used microarrays to examine the relationship between standard-of-care DSA and rejection-related transcript increases in 1679 kidney transplant indication biopsies in the INTERCOMEX study (ClinicalTrials.gov NCT01299168), focusing on biopsies classified as NR by automatically assigned archetypal clustering. DSA testing results were available for 835 NR biopsies and were positive in 271 (32%). RESULTS DSA positivity in NR biopsies was associated with mildly increased expression of antibody-mediated rejection (ABMR)-related transcripts, particularly IFNG-inducible and NK cell transcripts. We developed a machine learning DSA probability (DSAProb) classifier based on transcript expression in biopsies from DSA-positive versus DSA-negative patients, assigning scores using 10-fold cross-validation. This DSAProb classifier was very similar to a previously described "ABMR probability" classifier trained on histologic ABMR in transcript associations and prediction of molecular or histologic ABMR. Plotting the biopsies using Uniform Manifold Approximation and Projection revealed a gradient of increasing molecular ABMR-like transcript expression in NR biopsies, associated with increased DSA (P<2 × 10-16). In biopsies with no molecular or histologic rejection, increased DSAProb or ABMR probability scores were associated with increased risk of kidney failure over 3 years. CONCLUSIONS Many biopsies currently considered to have no molecular or histologic rejection have mild increases in expression of ABMR-related transcripts, associated with increasing frequency of DSA. Thus, mild molecular ABMR-related pathology is more common than previously realized.
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Affiliation(s)
| | - Georg A. Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Jonathan Bromberg
- Departments of Surgery and Microbiology and Immunology, University of Maryland, Baltimore, Maryland
| | - Gunilla Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia
| | - Luis G. Hidalgo
- Department of Surgery, University of Wisconsin, Madison, Wisconsin
| | - Marek Myslak
- Pomeranian Medical University, Department of Clinical Interventions and Department of Nephrology and Kidney Transplantation, Samodzielny Publiczny Wojewodzki Szpital Zespolony, Szczecin, Poland
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | | | - Philip F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada,Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
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39
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Halloran PF, Madill-Thomsen KS, Böhmig GA, Myslak M, Gupta G, Kumar D, Viklicky O, Perkowska-Ptasinska A, Famulski KS. A 2-fold Approach to Polyoma Virus (BK) Nephropathy in Kidney Transplants: Distinguishing Direct Virus Effects From Cognate T Cell-mediated Inflammation. Transplantation 2021; 105:2374-2384. [PMID: 34310102 DOI: 10.1097/tp.0000000000003884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND BK nephropathy (BKN) in kidney transplants diagnosed by histology is challenging because it involves damage from both virus activity and cognate T cell-mediated inflammation, directed against alloantigens (rejection) or viral antigens. The present study of indication biopsies from the Integrated Diagnostic System in the International Collaborative Microarray Study Extension study measured major capsid viral protein 2 (VP2) mRNA to assess virus activity and a T cell-mediated rejection (TCMR) classifier to assess cognate T cell-mediated inflammation. METHODS Biopsies were assessed by local standard-of-care histology and by genome-wide microarrays and Molecular Microscope Diagnostic System (MMDx) algorithms to detect rejection and injury. In a subset of 102 biopsies (50 BKN and 52 BKN-negative biopsies with various abnormalities), we measured VP2 transcripts by real-time polymerase chain reaction. RESULTS BKN was diagnosed in 55 of 1679 biopsies; 30 had cognate T cell-mediated activity assessed by by MMDx and TCMR lesions, but only 3 of 30 were histologically diagnosed as TCMR. We developed a BKN probability classifier that predicted histologic BKN (area under the curve = 0.82). Virus activity (VP2 expression) was highly selective for BKN (area under the curve = 0.94) and correlated with acute injury, atrophy-fibrosis, macrophage activation, and the BKN classifier, but not with the TCMR classifier. BKN with molecular TCMR had more tubulitis and inflammation than BKN without molecular TCMR. In 5 BKN cases with second biopsies, VP2 mRNA decreased in second biopsies, whereas in 4 of 5 TCMR classifiers, scores increased. Genes and pathways associated with BKN and VP2 mRNA were similar, reflecting injury, inflammation, and macrophage activation but none was selective for BKN. CONCLUSIONS Risk-benefit decisions in BKN may be assisted by quantitative assessment of the 2 major pathologic processes, virus activity and cognate T cell-mediated inflammation.
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, AB, Canada
| | | | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Marek Myslak
- Department of Nephrology and Kidney Transplantation, SPWSZ Hospital in Szczecin, Pomeranian Medical University, Szczecin, Poland
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Dhiren Kumar
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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40
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Balch JA, Delitto D, Tighe PJ, Zarrinpar A, Efron PA, Rashidi P, Upchurch GR, Bihorac A, Loftus TJ. Machine Learning Applications in Solid Organ Transplantation and Related Complications. Front Immunol 2021; 12:739728. [PMID: 34603324 PMCID: PMC8481939 DOI: 10.3389/fimmu.2021.739728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
The complexity of transplant medicine pushes the boundaries of innate, human reasoning. From networks of immune modulators to dynamic pharmacokinetics to variable postoperative graft survival to equitable allocation of scarce organs, machine learning promises to inform clinical decision making by deciphering prodigious amounts of available data. This paper reviews current research describing how algorithms have the potential to augment clinical practice in solid organ transplantation. We provide a general introduction to different machine learning techniques, describing their strengths, limitations, and barriers to clinical implementation. We summarize emerging evidence that recent advances that allow machine learning algorithms to predict acute post-surgical and long-term outcomes, classify biopsy and radiographic data, augment pharmacologic decision making, and accurately represent the complexity of host immune response. Yet, many of these applications exist in pre-clinical form only, supported primarily by evidence of single-center, retrospective studies. Prospective investigation of these technologies has the potential to unlock the potential of machine learning to augment solid organ transplantation clinical care and health care delivery systems.
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Affiliation(s)
- Jeremy A Balch
- Department of Surgery, University of Florida Health, Gainesville, FL, United States
| | - Daniel Delitto
- Department of Surgery, Johns Hopkins University, Baltimore, MD, United States
| | - Patrick J Tighe
- Department of Anesthesiology, University of Florida Health, Gainesville, FL, United States.,Department of Orthopedics, University of Florida Health, Gainesville, FL, United States.,Department of Information Systems/Operations Management, University of Florida Health, Gainesville, FL, United States
| | - Ali Zarrinpar
- Department of Surgery, University of Florida Health, Gainesville, FL, United States
| | - Philip A Efron
- Department of Surgery, University of Florida Health, Gainesville, FL, United States
| | - Parisa Rashidi
- Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States.,Department of Computer and Information Science and Engineering University of Florida, Gainesville, FL, United States.,Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, United States.,Precision and Intelligent Systems in Medicine (PrismaP), University of Florida, Gainesville, FL, United States
| | - Gilbert R Upchurch
- Department of Surgery, University of Florida Health, Gainesville, FL, United States
| | - Azra Bihorac
- Precision and Intelligent Systems in Medicine (PrismaP), University of Florida, Gainesville, FL, United States.,Department of Medicine, University of Florida Health, Gainesville, FL, United States
| | - Tyler J Loftus
- Department of Surgery, University of Florida Health, Gainesville, FL, United States.,Precision and Intelligent Systems in Medicine (PrismaP), University of Florida, Gainesville, FL, United States
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41
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Affiliation(s)
- Sundaram Hariharan
- From the University of Pittsburgh Medical Center, Pittsburgh (S.H.); Hennepin Healthcare, the University of Minnesota, and the Scientific Registry of Transplant Recipients - all in Minneapolis (A.K.I.); and the University of California, Los Angeles, Los Angeles (G.D.)
| | - Ajay K Israni
- From the University of Pittsburgh Medical Center, Pittsburgh (S.H.); Hennepin Healthcare, the University of Minnesota, and the Scientific Registry of Transplant Recipients - all in Minneapolis (A.K.I.); and the University of California, Los Angeles, Los Angeles (G.D.)
| | - Gabriel Danovitch
- From the University of Pittsburgh Medical Center, Pittsburgh (S.H.); Hennepin Healthcare, the University of Minnesota, and the Scientific Registry of Transplant Recipients - all in Minneapolis (A.K.I.); and the University of California, Los Angeles, Los Angeles (G.D.)
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42
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Schwantes IR, Axelrod DA. Technology-Enabled Care and Artificial Intelligence in Kidney Transplantation. CURRENT TRANSPLANTATION REPORTS 2021; 8:235-240. [PMID: 34341714 PMCID: PMC8317681 DOI: 10.1007/s40472-021-00336-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2021] [Indexed: 01/24/2023]
Abstract
Purpose of Review Artificial intelligence (AI), machine learning, and technology-enabled remote patient care have evolved rapidly and have now been incorporated into many aspects of medical care. Transplantation is fortunate to have large data sets upon which machine learning algorithms can be constructed. AI are now available to improve pretransplant management, donor selection, and post-operative management of transplant patients. Recent Findings Changes in patient and donor characteristics warrant new approaches to listing and organ acceptance practices. Machine learning has been employed to optimize donor selection to identify patients likely to benefit from transplantation of higher risk organs, increasing organ discard and reducing waitlist mortality. These models have greater precisions and predictive ability than currently employed metrics including the Kidney Donor Profile Index and the expected posttransplant survival models. After transplant, AI tools have been developed to optimize immunosuppression management, track patients adherence, and assess graft survival. Summary AI and technology-enabled management tools are now available throughout the transplant journey. Unfortunately, those are frequently not available at the point of decision (patient listing, organ acceptance, posttransplant clinic), limiting utilization. Incorporation of these tools into the EMR, the Donor Net® organ offer system, and mobile devices is vital to ensure widespread adoption.
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Affiliation(s)
- Issac R Schwantes
- Department of Surgery, Oregon Health & Science University, Portland, OR USA
| | - David A Axelrod
- Organ Transplant Center, University of Iowa, 200 Hawkins Dr, Iowa City, LA 52240 USA
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43
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Seyahi N, Ozcan SG. Artificial intelligence and kidney transplantation. World J Transplant 2021; 11:277-289. [PMID: 34316452 PMCID: PMC8290997 DOI: 10.5500/wjt.v11.i7.277] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/17/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Artificial intelligence and its primary subfield, machine learning, have started to gain widespread use in medicine, including the field of kidney transplantation. We made a review of the literature that used artificial intelligence techniques in kidney transplantation. We located six main areas of kidney transplantation that artificial intelligence studies are focused on: Radiological evaluation of the allograft, pathological evaluation including molecular evaluation of the tissue, prediction of graft survival, optimizing the dose of immunosuppression, diagnosis of rejection, and prediction of early graft function. Machine learning techniques provide increased automation leading to faster evaluation and standardization, and show better performance compared to traditional statistical analysis. Artificial intelligence leads to improved computer-aided diagnostics and quantifiable personalized predictions that will improve personalized patient care.
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Affiliation(s)
- Nurhan Seyahi
- Department of Nephrology, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul 34098, Fatih, Turkey
| | - Seyda Gul Ozcan
- Department of Internal Medicine, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul 34098, Fatih, Turkey
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44
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Kläger J, Eskandary F, Böhmig GA, Kozakowski N, Kainz A, Colin Aronovicz Y, Cartron JP, Segerer S, Regele H. Renal allograft DARCness in subclinical acute and chronic active ABMR. Transpl Int 2021; 34:1494-1505. [PMID: 33983671 PMCID: PMC8453966 DOI: 10.1111/tri.13904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
Gene expression profiling of renal allograft biopsies revealed the Duffy antigen receptor for chemokines (DARC) as being strikingly upregulated in antibody‐mediated rejection (ABMR). DARC has previously been shown to be associated with endothelial injury. This study aimed at assessing the value of DARC immunohistochemistry as diagnostic marker in ABMR. The study was performed on 82 prospectively collected biopsies of a clinically well‐defined population (BORTEJECT trial, NCT01873157) of DSA‐positive patients with gene expression data available for all biopsies. Diagnostic histologic assessment of biopsies was performed according to the Banff diagnostic scheme. DARC expression was focally accentuated, on peritubular capillaries (PTC) mostly in areas of interstitial fibrosis and/or inflammation. DARC positivity was associated with diagnosis of ABMR and correlated with DARC gene expression levels detected by microarray analysis. Still, as previously described, a substantial number of biopsies without signs of rejection showed DARC‐positive PTC. We did not observe significantly reduced graft survival in cases showing histologic signs of ABMR and being DARC‐positive, as compared to DARC‐negative ABMR. In summary, the upregulation of DARC, detected by immunohistochemistry, is associated with but not specific for ABMR. We did not observe reduced graft survival in DARC‐positive patients.
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Affiliation(s)
- Johannes Kläger
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | | | - Alexander Kainz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Yves Colin Aronovicz
- Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France
| | - Jean-Pierre Cartron
- Université Sorbonne Paris Cité, Université Paris Diderot, Inserm U1134, Institut National de la Transfusion Sanguine, Unité Biologie Intégrée du Globule Rouge, Paris, France
| | - Stephan Segerer
- Division of Nephrology, Dialysis and Transplantation, Kantonsspital Aarau, Aarau, Switzerland
| | - Heinz Regele
- Department of Pathology, Medical University Vienna, Vienna, Austria
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45
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Rosenkranz AR, Tesar V. Lupus nephritis and ANCA-associated vasculitis: towards precision medicine? Nephrol Dial Transplant 2021; 36:37-43. [PMID: 34153980 DOI: 10.1093/ndt/gfab166] [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: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
Historically the treatment of lupus nephritis (LN) and anti-neutrophil cytoplasmic antibody (ANCA) vasculitis was 'one size fits all'; however, with the emergence of precision medicine initiatives, the field is moving towards more personalized treatment approaches. The recent development of a more accurate and reproducible histopathological classification system for LN could lead to better disease categorization and therefore more targeted therapies. A better understanding of the pathophysiology of LN has provided evidence that not only T but also B cells play an important role, opening new opportunities for individualized treatment approaches. Recent trials have shown calcineurin inhibitors and the anti-CD20 antibodies rituximab and ofatumumab to be effective in the treatment of LN, adding new treatment options. State-of-the-art targeted therapy in ANCA-associated vasculitis (AAV) takes interindividual heterogeneity in disease severity, type of ANCA antibody [myeloperoxidase versus proteinase 3 (PR3)] and the risk for side effects of therapy into consideration. In addition, within an individual, induction therapy differs from maintenance therapy, the same holding true in incident and relapsing disease. Rituximab is now widely used in AAV and it has become clear that prolonged B cell depletion, as in LN, must be achieved to obtain a long-lasting clinical response, especially in anti-PR3-associated disease. Still, despite these advances, molecular and genetic markers are rarely incorporated into diagnostic and treatment algorithms and true precision medicine remains an aspiration that hopefully can be achieved.
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Affiliation(s)
- Alexander R Rosenkranz
- Department of Internal Medicine, Clinical Division of Nephrology, Medical University of Graz, Graz, Austria
| | - Vladimir Tesar
- Department of Nephrology, 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
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46
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Clement J, Maldonado AQ. Augmenting the Transplant Team With Artificial Intelligence: Toward Meaningful AI Use in Solid Organ Transplant. Front Immunol 2021; 12:694222. [PMID: 34177958 PMCID: PMC8226178 DOI: 10.3389/fimmu.2021.694222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 11/19/2022] Open
Abstract
Advances in systems immunology, such as new biomarkers, offer the potential for highly personalized immunosuppression regimens that could improve patient outcomes. In the future, integrating all of this information with other patient history data will likely have to rely on artificial intelligence (AI). AI agents can help augment transplant decision making by discovering patterns and making predictions for specific patients that are not covered in the literature or in ways that are impossible for humans to anticipate by integrating vast amounts of data (e.g. trending across numerous biomarkers). Similar to other clinical decision support systems, AI may help overcome human biases or judgment errors. However, AI is not widely utilized in transplant to date. In this rapid review, we survey the methods employed in recent research in transplant-related AI applications and identify concerns related to implementing these tools. We identify three key challenges (bias/accuracy, clinical decision process/AI explainability, AI acceptability criteria) holding back AI in transplant. We also identify steps that can be taken in the near term to help advance meaningful use of AI in transplant (forming a Transplant AI Team at each center, establishing clinical and ethical acceptability criteria, and incorporating AI into the Shared Decision Making Model).
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Affiliation(s)
- Jeffrey Clement
- Information and Decision Sciences, Carlson School of Management, University of Minnesota, Minneapolis, MN, United States
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47
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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.
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Halloran PF, Böhmig GA, Bromberg JS, Budde K, Gupta G, Einecke G, Eskandary F, Madill-Thomsen K, Reeve J. Discovering novel injury features in kidney transplant biopsies associated with TCMR and donor aging. Am J Transplant 2021; 21:1725-1739. [PMID: 33107191 DOI: 10.1111/ajt.16374] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/27/2020] [Accepted: 10/19/2020] [Indexed: 01/25/2023]
Abstract
We previously characterized the molecular changes in acute kidney injury (AKI) and chronic kidney disease (CKD) in kidney transplant biopsies, but parenchymal changes selective for specific types of injury could be missed by such analyses. The present study searched for injury changes beyond AKI and CKD related to specific scenarios, including correlations with donor age. We defined injury using previously defined gene sets and classifiers and used principal component analysis to discover new injury dimensions. As expected, Dimension 1 distinguished normal vs. injury, and Dimension 2 separated early AKI from late CKD, correlating with time posttransplant. However, Dimension 3 was novel, distinguishing a set of genes related to epithelial polarity (e.g., PARD3) that were increased in early AKI and decreased in T cell-mediated rejection (TCMR) but not in antibody-mediated rejection. Dimension 3 was increased in kidneys from older donors and was particularly important in survival of early kidneys. Thus high Dimension 3 scores emerge as a previously unknown element in the kidney response-to-injury that affects epithelial polarity genes and is increased in AKI but depressed in TCMR, indicating that in addition to general injury elements, certain injury elements are selective for specific pathologic mechanisms. (ClinicalTrials.gov NCT01299168).
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Klemens Budde
- Charite-Medical University of Berlin, Berlin, Germany
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia
| | | | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
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Bülow RD, Dimitrov D, Boor P, Saez-Rodriguez J. How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade? Semin Immunopathol 2021; 43:739-752. [PMID: 33835214 PMCID: PMC8551101 DOI: 10.1007/s00281-021-00847-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/17/2021] [Indexed: 01/16/2023]
Abstract
IgA nephropathy (IgAN) is the most common glomerulonephritis. It is characterized by the deposition of immune complexes containing immunoglobulin A (IgA) in the kidney’s glomeruli, triggering an inflammatory process. In many patients, the disease has a progressive course, eventually leading to end-stage kidney disease. The current understanding of IgAN’s pathophysiology is incomplete, with the involvement of several potential players, including the mucosal immune system, the complement system, and the microbiome. Dissecting this complex pathophysiology requires an integrated analysis across molecular, cellular, and organ scales. Such data can be obtained by employing emerging technologies, including single-cell sequencing, next-generation sequencing, proteomics, and complex imaging approaches. These techniques generate complex “big data,” requiring advanced computational methods for their analyses and interpretation. Here, we introduce such methods, focusing on the broad areas of bioinformatics and artificial intelligence and discuss how they can advance our understanding of IgAN and ultimately improve patient care. The close integration of advanced experimental and computational technologies with medical and clinical expertise is essential to improve our understanding of human diseases. We argue that IgAN is a paradigmatic disease to demonstrate the value of such a multidisciplinary approach.
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Affiliation(s)
- Roman David Bülow
- University Hospital RWTH Aachen, Institute of Pathology, Aachen, Germany
| | - Daniel Dimitrov
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Institute for Computational Biomedicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Peter Boor
- University Hospital RWTH Aachen, Institute of Pathology, Aachen, Germany.
- Department of Nephrology and Immunology, University Hospital RWTH Aachen, Aachen, Germany.
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany.
- Institute for Computational Biomedicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074, RWTH Aachen University, Aachen, Germany.
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany.
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50
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Einecke G, Reeve J, Gupta G, Böhmig GA, Eskandary F, Bromberg JS, Budde K, Halloran PF. Factors associated with kidney graft survival in pure antibody-mediated rejection at the time of indication biopsy: Importance of parenchymal injury but not disease activity. Am J Transplant 2021; 21:1391-1401. [PMID: 32594646 DOI: 10.1111/ajt.16161] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/28/2020] [Accepted: 06/15/2020] [Indexed: 01/25/2023]
Abstract
We studied the relative association of clinical, histologic, and molecular variables with risk of kidney transplant failure after an indication biopsy, both in all kidneys and in kidneys with pure antibody-mediated rejection (ABMR). From a prospective study of 1679 biopsies with histologic and molecular testing, we selected one random biopsy per patient (N = 1120), including 321 with pure molecular ABMR. Diagnoses were associated with actuarial survival differences but not good predictions. Therefore we concentrated on clinical (estimated GFR [eGFR], proteinuria, time posttransplant, donor-specific antibody [DSA]) and molecular and histologic features reflecting injury (acute kidney injury [AKI] and atrophy-fibrosis [chronic kidney disease (CKD)] and rejection. For all biopsies, univariate analysis found that failure was strongly associated with low eGFR, AKI, CKD, and glomerular deterioration, but not with rejection activity. In molecular ABMR, the findings were similar: Molecular and histologic activity and DSA were not important compared with injury. Survival in DSA-negative and DSA-positive molecular ABMR was similar. Multivariate survival analysis confirmed the dominance of molecular AKI, CKD, and eGFR. Thus, at indication biopsy, the dominant predictors of failure, both in all kidneys and in ABMR, were related to molecular AKI and CKD and to eGFR, not rejection activity, presumably because rejection confers risk via injury.
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Affiliation(s)
- Gunilla Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité-University Hospital Berlin, Berlin, Germany
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,Department of Medicine, Division of Nephrology, University of Alberta, Edmonton, Alberta, Canada
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