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Barwad A, Huang Y, Randhawa P. T-cell Mediated Rejection Associated Microvascular Inflammation in the Allograft Kidney: RNAseq Analysis Using the Banff Human Organ Transplant Gene Panel. Clin Transplant 2024; 38:e15410. [PMID: 39033507 DOI: 10.1111/ctr.15410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/16/2024] [Accepted: 06/30/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Microvascular inflammation (MVI) can occur in biopsies showing T-cell mediated rejection (TCMR), but it is not well established that T-cells can directly mediate microvascular injury (TCMR-MVI). METHODS This was a cross sectional RNAseq based Banff Human Organ Transplant (BHOT) gene expression (GE) analysis. The objective of this study was to probe the molecular signature of TCMR-MVI in comparison with C4d+, DSA+ antibody mediated rejection (ABMR), stable renal function (STA), and TCMR without MVI. Transcriptome analysis utilized CLC genomic workbench and R-studio software. RESULTS No gene set was specific for any diagnostic category, and all were expressed at low levels in STA biopsies. BHOT gene set scores could differentiate ABMR from TCMR and TCMR-MVI, but not TCMR from TCMR-MVI. TCMR-MVI underexpressed several genes associated with ABMR including DSATs, ENDAT, immunoglobulin genes, ADAMDEC1, PECAM1 and NK cell transcripts (MYBL1, GNLY), but overexpressed C3, NKBBIZ, and LTF. On the other hand, there was no significant difference in the expression of these genes in TCMR-MVI versus TCMR. This indicates that the GE profile of TCMR MVI aligns more closely with TCMR than ABMR. The limitations of classifying biopsies using the binary ABMR-TCMR algorithm, and the occurrence of common pathogenesis mechanisms amongst different rejection phenotype was highlighted by the frequent presence of molecular mixed rejection. CONCLUSIONS T-cell mediated mechanisms play a significant role in the pathogenesis of MVI. GE was broadly different between rejection phenotypes, but molecular scores varied substantially between biopsies with the same Banff grade. It was not always possible to achieve precise molecular score-based diagnostic categorization of individual patients.
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Affiliation(s)
- Adarsh Barwad
- Department of Pathology, All India Institute of Medical Science, New Delhi, India
| | - Yuchen Huang
- Department of Pathology, University of Pittsburgh Medical Centre, Pittsburgh, USA
| | - Parmjeet Randhawa
- Department of Pathology, University of Pittsburgh Medical Centre, Pittsburgh, USA
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2
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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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3
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Wang Y, De Labastida Rivera F, Edwards CL, Frame TC, Engel JA, Bukali L, Na J, Ng SS, Corvino D, Montes de Oca M, Bunn PT, Soon MS, Andrew D, Loughland JR, Zhang J, Amante FH, Barber BE, McCarthy JS, Lopez JA, Boyle MJ, Engwerda CR. STING activation promotes autologous type I interferon-dependent development of type 1 regulatory T cells during malaria. J Clin Invest 2023; 133:e169417. [PMID: 37781920 PMCID: PMC10541195 DOI: 10.1172/jci169417] [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: 02/03/2023] [Accepted: 08/08/2023] [Indexed: 10/03/2023] Open
Abstract
The development of highly effective malaria vaccines and improvement of drug-treatment protocols to boost antiparasitic immunity are critical for malaria elimination. However, the rapid establishment of parasite-specific immune regulatory networks following exposure to malaria parasites hampers these efforts. Here, we identified stimulator of interferon genes (STING) as a critical mediator of type I interferon production by CD4+ T cells during blood-stage Plasmodium falciparum infection. The activation of STING in CD4+ T cells by cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) stimulated IFNB gene transcription, which promoted development of IL-10- and IFN-γ-coproducing CD4+ T (type I regulatory [Tr1]) cells. The critical role for type I IFN signaling for Tr1 cell development was confirmed in vivo using a preclinical malaria model. CD4+ T cell sensitivity to STING phosphorylation was increased in healthy volunteers following P. falciparum infection, particularly in Tr1 cells. These findings identified STING expressed by CD4+ T cells as an important mediator of type I IFN production and Tr1 cell development and activation during malaria.
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Affiliation(s)
- Yulin Wang
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Griffith University, School of Environment and Science, Nathan, Australia
| | | | - Chelsea L. Edwards
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | - Teija C.M. Frame
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | | | - Luzia Bukali
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | - Jinrui Na
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | - Susanna S. Ng
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Dillon Corvino
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Marcela Montes de Oca
- York Biomedical Research Institute, Hull York Medical School, University of York, York, United Kingdom
| | - Patrick T. Bunn
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Megan S.F. Soon
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Dean Andrew
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Jia Zhang
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Fiona H. Amante
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - James S. McCarthy
- Victorian Infectious Diseases Services, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - J. Alejandro Lopez
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Griffith University, School of Environment and Science, Nathan, Australia
| | - Michelle J. Boyle
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Life Sciences Division, Burnet Institute, Melbourne, Australia
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Fang R, Mohammed AN, Yadav JS, Wang J. Cytotoxicity and Characterization of Ultrafine Particles from Desktop Three-Dimensional Printers with Multiple Filaments. TOXICS 2023; 11:720. [PMID: 37755731 PMCID: PMC10536656 DOI: 10.3390/toxics11090720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023]
Abstract
Previous research has indicated that ultrafine particles (UFPs, particles less than 100 nm) emitted from desktop three-dimensional (3D) printers exhibit cytotoxicity. However, only a limited number of particles from different filaments and their combinations have been tested for cytotoxicity. This study quantified the emissions of UFPs from a commercially available filament extrusion desktop 3D printer using three different filaments, including acrylonitrile butadiene Styrene (ABS), thermoplastic polyurethane (TPU), and polyethylene terephthalate glycol (PETG). In this study, controlled experiments were conducted where the particles emitted were used to expose cells grown in an air-liquid interface (ALI) system. The ALI exposures were utilized for in vitro characterization of particle mixtures, including UFPs from a 3D printer. Additionally, a lactate dehydrogenase (LDH) assay was used to evaluate the cytotoxic effects of these UFPs. A549 cells were exposed at the ALI to UFPs generated by an operational 3D printer for an average of 45 and 90 min. Twenty-four hours post-exposure, the cells were analyzed for percent cytotoxicity in a 24-well ALI insert (LDH assay). UFP exposure resulted in diminished cell viability, as evidenced by significantly increased LDH levels. The findings demonstrate that ABS has the most significant particle emission. ABS was the only filament that showed a significant difference compared to the high efficiency particulate arrestance (HEPA) following 90 min of exposure (p-value < 0.05). Both ABS and PETG exhibited a significant difference compared to the HEPA control after 45 min of exposure. A preliminary analysis of potential exposure to these products in a typical environment advises caution when operating multiple printer and filament combinations in poorly ventilated spaces or without combined gas and particle filtration systems.
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Affiliation(s)
- Runcheng Fang
- Environmental and Industrial Hygiene, Department of Environmental and Public Health Sciences, College of Medicine University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Afzaal Nadeem Mohammed
- Environmental Genetics and Molecular Toxicology, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (A.N.M.); (J.S.Y.)
| | - Jagjit Singh Yadav
- Environmental Genetics and Molecular Toxicology, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (A.N.M.); (J.S.Y.)
| | - Jun Wang
- Environmental and Industrial Hygiene, Department of Environmental and Public Health Sciences, College of Medicine University of Cincinnati, Cincinnati, OH 45267, USA;
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5
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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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6
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Halloran K, Mackova M, Parkes MD, Hirji A, Weinkauf J, Timofte IL, Snell GI, Westall GP, Lischke R, Zajacova A, Havlin J, Hachem R, Kreisel D, Levine D, Kubisa B, Piotrowska M, Juvet S, Keshavjee S, Jaksch P, Klepetko W, Halloran PF. The molecular features of chronic lung allograft dysfunction in lung transplant airway mucosa. J Heart Lung Transplant 2022; 41:1689-1699. [PMID: 36163162 DOI: 10.1016/j.healun.2022.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/22/2022] [Accepted: 08/17/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Many lung transplants fail due to chronic lung allograft dysfunction (CLAD). We recently showed that transbronchial biopsies (TBBs) from CLAD patients manifest severe parenchymal injury and dedifferentiation, distinct from time-dependent changes. The present study explored time-selective and CLAD-selective transcripts in mucosal biopsies from the third bronchial bifurcation (3BMBs), compared to those in TBBs. METHODS We used genome-wide microarray measurements in 324 3BMBs to identify CLAD-selective changes as well as time-dependent changes and develop a CLAD classifier. CLAD-selective transcripts were identified with linear models for microarray data (limma) and were used to build an ensemble of 12 classifiers to predict CLAD. Hazard models and random forests were then used to predict the risk of graft loss using the CLAD classifier, transcript sets associated with rejection, injury, and time. RESULTS T cell-mediated rejection and donor-specific antibody were increased in CLAD 3BMBs but most had no rejection. Like TBBs, 3BMBs showed a time-dependent increase in transcripts expressed in inflammatory cells that was not associated with CLAD or survival. Also like TBBs, the CLAD-selective transcripts in 3BMBs reflected severe parenchymal injury and dedifferentiation, not inflammation or rejection. While 3BMBs and TBBs did not overlap in their top 20 CLAD-selective transcripts, many CLAD-selective transcripts were significantly increased in both for example LOXL1, an enzyme controlling matrix remodeling. In Cox models for one-year survival, the 3BMB CLAD-selective transcripts and CLAD classifier predicted graft loss and correlated with CLAD stage. Many 3BMB CLAD-selective transcripts were also increased by injury in kidney transplants and correlated with decreased kidney survival, including LOXL1. CONCLUSIONS Mucosal and transbronchial biopsies from CLAD patients reveal a diffuse molecular injury and dedifferentiation state that impacts prognosis and correlates with the physiologic disturbances. CLAD state in lung transplants shares features with failing kidney transplants, indicating elements shared by the injury responses of distressed organs.
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Affiliation(s)
| | | | | | - Alim Hirji
- University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Greg I Snell
- Alfred Hospital Lung Transplant Service, Melbourne, Victoria, Australia
| | - Glen P Westall
- Alfred Hospital Lung Transplant Service, Melbourne, Victoria, Australia
| | | | | | - Jan Havlin
- University Hospital Motol, Prague, Czech Republic
| | - Ramsey Hachem
- Washington University in St Louis, St. Louis, Missouri
| | | | | | | | | | - Stephen Juvet
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
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7
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Duneton C, Winterberg PD, Ford ML. Activation and regulation of alloreactive T cell immunity in solid organ transplantation. Nat Rev Nephrol 2022; 18:663-676. [PMID: 35902775 PMCID: PMC9968399 DOI: 10.1038/s41581-022-00600-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2022] [Indexed: 01/18/2023]
Abstract
Transplantation is the only curative treatment for patients with kidney failure but it poses unique immunological challenges that must be overcome to prevent allograft rejection and ensure long-term graft survival. Alloreactive T cells are important contributors to graft rejection, and a clearer understanding of the mechanisms by which these cells recognize donor antigens - through direct, indirect or semi-direct pathways - will facilitate their therapeutic targeting. Post-T cell priming rejection responses can also be modified by targeting pathways that regulate T cell trafficking, survival cytokines or innate immune activation. Moreover, the quantity and quality of donor-reactive memory T cells crucially shape alloimmune responses. Of note, many fundamental concepts in transplant immunology have been derived from models of infection. However, the programmed differentiation of allograft-specific T cell responses is probably distinct from that of pathogen-elicited responses, owing to the dearth of pathogen-derived innate immune activation in the transplantation setting. Understanding the fundamental (and potentially unique) immunological pathways that lead to allograft rejection is therefore a prerequisite for the rational development of therapeutics that promote transplantation tolerance.
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Affiliation(s)
- Charlotte Duneton
- Paediatric Nephrology, Robert Debré Hospital, Paris, France
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Pamela D Winterberg
- Paediatric Nephrology, Emory University Department of Paediatrics and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Mandy L Ford
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, USA.
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8
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Choi SM, Park HJ, Choi EA, Jung KC, Lee JI. Heterogeneity of circulating CD4 +CD8 + double-positive T cells characterized by scRNA-seq analysis and trajectory inference. Sci Rep 2022; 12:14111. [PMID: 35982155 PMCID: PMC9388645 DOI: 10.1038/s41598-022-18340-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022] Open
Abstract
The frequency of CD4+CD8+ double-positive (DP) T cells is highly associated with a variety of diseases. Recently, we used high-throughput single-cell RNA sequencing to show that circulating DP T cells in cynomolgus monkeys comprise nine heterogeneous populations. To better understand the characteristics of DP T cells, we analyzed 7601 cells from a rhesus monkey and detected 14,459 genes. Rhesus monkey DP T cells comprised heterogeneous populations (naïve, Treg-, Tfh-, CCR9+ Th-, Th17-, Th2-, Eomes+ Tr1-, CTL-, PLZF+ innate- and Eomes+ innate-like cells) with multiple potential functions. We also identified two new subsets using aggregated scRNA-seq datasets from the rhesus and the cynomolgus monkey: CCR9+ Th-like cells expressing ICAM2 and ITGA1, and PLZF+ innate-like cells that display innate-associated gene signatures such as ZBTB16, TYROBP, MAP3K8, and KLRB1. Trajectory inference of cell differentiation status showed that most DP T cells in the rhesus monkey were found in the mid-to-late pseudotime, whereas DP T cells from the cynomolgus monkey were found in early pseudotime. This suggests that DP T cells in rhesus monkeys may exhibit more diverse differentiation states than those in cynomolgus monkeys. Thus, scRNA-seq and trajectory inference identified a more diverse subset of the circulating DP T cells than originally thought.
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Affiliation(s)
- Sung Min Choi
- Graduate Course of Translational Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hi Jung Park
- Graduate Course of Translational Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Eun A Choi
- Graduate Course of Translational Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Kyeong Cheon Jung
- Transplantation Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Pathology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Integrated Major in Innovative Medical Science, Seoul National University Graduate School, Seoul, 03080, Republic of Korea
| | - Jae Il Lee
- Transplantation Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea. .,Department of Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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9
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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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10
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Ba R, Geffard E, Douillard V, Simon F, Mesnard L, Vince N, Gourraud PA, Limou S. Surfing the Big Data Wave: Omics Data Challenges in Transplantation. Transplantation 2022; 106:e114-e125. [PMID: 34889882 DOI: 10.1097/tp.0000000000003992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In both research and care, patients, caregivers, and researchers are facing a leap forward in the quantity of data that are available for analysis and interpretation, marking the daunting "big data era." In the biomedical field, this quantitative shift refers mostly to the -omics that permit measuring and analyzing biological features of the same type as a whole. Omics studies have greatly impacted transplantation research and highlighted their potential to better understand transplant outcomes. Some studies have emphasized the contribution of omics in developing personalized therapies to avoid graft loss. However, integrating omics data remains challenging in terms of analytical processes. These data come from multiple sources. Consequently, they may contain biases and systematic errors that can be mistaken for relevant biological information. Normalization methods and batch effects have been developed to tackle issues related to data quality and homogeneity. In addition, imputation methods handle data missingness. Importantly, the transplantation field represents a unique analytical context as the biological statistical unit is the donor-recipient pair, which brings additional complexity to the omics analyses. Strategies such as combined risk scores between 2 genomes taking into account genetic ancestry are emerging to better understand graft mechanisms and refine biological interpretations. The future omics will be based on integrative biology, considering the analysis of the system as a whole and no longer the study of a single characteristic. In this review, we summarize omics studies advances in transplantation and address the most challenging analytical issues regarding these approaches.
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Affiliation(s)
- Rokhaya Ba
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Département Informatique et Mathématiques, Ecole Centrale de Nantes, Nantes, France
| | - Estelle Geffard
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Venceslas Douillard
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Françoise Simon
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Mount Sinai School of Medicine, New York, NY
| | - Laurent Mesnard
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
- Sorbonne Université, Paris, France
| | - Nicolas Vince
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Pierre-Antoine Gourraud
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Sophie Limou
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Département Informatique et Mathématiques, Ecole Centrale de Nantes, Nantes, France
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11
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Salem FE, Perin L, Sedrakyan S, Angeletti A, Ghiggeri G, Coccia MC, Ross M, Fribourg M, Cravedi P. The spatially resolved transcriptional profile of acute T cell-mediated rejection in a kidney allograft. Kidney Int 2022; 101:131-136. [PMID: 34555393 PMCID: PMC9387544 DOI: 10.1016/j.kint.2021.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 01/03/2023]
Abstract
Analysis of the transcriptional profile of graft biopsies represents a promising strategy to study T cell-mediated-rejection (TCMR), also known as acute cellular rejection. However, bulk RNA sequencing of graft biopsies may not capture the focal nature of acute rejection. Herein, we used the whole exome GeoMX Digital Space Profiling platform to study five tubular and three glomerular regions of interest in the kidney graft biopsy from a patient with a chronic-active TCMR episode and in analogous areas from two different normal kidney control biopsies. All kidney sections were from paraffin blocks. Overall, inflammatory genes were significantly upregulated in the tubular areas of the TCMR biopsy and showed an enrichment for gene-ontology terms associated with T-cell activation, differentiation, and proliferation. Enrichment analysis of the 100 genes with the highest coefficient of variation across the TCMR tubular regions of interest revealed that these highly variable genes are involved in kidney development and injury and interestingly do not associate with the 2019 Banff classification pathology scores within the individual regions of interest. Spatial transcriptomics allowed us to unravel a previously unappreciated variability across different areas of the TCMR biopsy related to the graft response to the alloimmune attack, rather than to the immune cells. Thus, our approach has the potential to decipher clinically relevant, new pathogenic mechanisms, and therapeutic targets in acute cellular rejection and other kidney diseases with a focal nature.
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Affiliation(s)
- Fadi E. Salem
- Department of Pathology & Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Perin
- GOFARR Laboratory for Organ Regenerative Research and Cell Therapeutics in Urology, Saban Research Institute, Division of Urology, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Sargis Sedrakyan
- GOFARR Laboratory for Organ Regenerative Research and Cell Therapeutics in Urology, Saban Research Institute, Division of Urology, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Andrea Angeletti
- Nephrology, Dialysis and Transplantation Unit, Giannina Gaslini Scientific Institute for Research, Hospitalization and Healthcare, Genoa, Italy
| | - GianMarco Ghiggeri
- Nephrology, Dialysis and Transplantation Unit, Giannina Gaslini Scientific Institute for Research, Hospitalization and Healthcare, Genoa, Italy
| | - Maria Cristina Coccia
- Pathological Anatomy Unit, Giannina Gaslini Scientific Institute for Research, Hospitalization and Healthcare, Genoa, Italy
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA, USA
| | - Miguel Fribourg
- Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paolo Cravedi
- Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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12
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Cellular heterogeneity of circulating CD4 +CD8 + double-positive T cells characterized by single-cell RNA sequencing. Sci Rep 2021; 11:23607. [PMID: 34880348 PMCID: PMC8655006 DOI: 10.1038/s41598-021-03013-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Circulating CD4+CD8+ double-positive (DP) T cells are associated with a variety of disease states. However, unlike conventional T cells, the composition of this population is poorly understood. Here, we used single-cell RNA sequencing (scRNA-seq) to analyze the composition and characteristics of the DP T cell population circulating in the peripheral blood of cynomolgus monkeys. We found that circulating DP T cells not only contain a large number of naïve cells, but also comprise a heterogeneous population (CD4 CTL-, Eomes+ Tr1-, Th2-, Th17-, Tfh-, Treg-, CD8 CTL-, and innate-like cells) with multiple potential functions. Flow cytometry analysis revealed that a substantial number of the naïve DP T cells expressed CD8αβ, as well as CD8αα, along with high expression of CD31. Moreover, the CD4hiCD8lo and CD4hiCD8hi populations, which express high levels of the CD4 coreceptor, comprised subsets characterized by helper and regulatory functions, some of which also exhibited cytotoxic functions. By contrast, the CD4loCD8hi population with high CD8 coreceptor expression comprised a subset characterized by CD8 CTL- and innate-like properties. Taken together, the data show that scRNA-seq analysis identified a more diverse subset of the circulating DP cells than is currently known, despite this population being very small.
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13
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Abstract
Involvement of T lymphocytes in kidney transplantation is a well-developed topic; however, most of the scientific interest focused on the different type of CD4+ lymphocyte subpopulations. Few authors, instead, investigated the role of CD8+ T cells in renal transplantation and how deleterious they can be to long-term allograft survival. Recently, there has been a renewed interest in the CD8+ T cells involvement in the transplantation field with the aim to investigate the immunological mechanisms underlying the infiltration of CD8+ T cells and their biological functions in human kidney allografts. The purpose of the present review is to highlight the role of allo-reactive cytotoxic T lymphocytes (CTLs) CD8+ subset in allograft kidney recipients and their related clinical complications.
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14
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Molecular patterns of isolated tubulitis differ from tubulitis with interstitial inflammation in early indication biopsies of kidney allografts. Sci Rep 2020; 10:22220. [PMID: 33335257 PMCID: PMC7746707 DOI: 10.1038/s41598-020-79332-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/02/2020] [Indexed: 11/09/2022] Open
Abstract
The Banff 2019 kidney allograft pathology update excluded isolated tubulitis without interstitial inflammation (ISO-T) from the category of borderline (suspicious) for acute T cell-mediated rejection due to its proposed benign clinical outcome. In this study, we explored the molecular assessment of ISO-T. ISO-T or interstitial inflammation with tubulitis (I + T) was diagnosed in indication biopsies within the first 14 postoperative days. The molecular phenotype of ISO-T was compared to I + T either by using RNA sequencing (n = 16) or by Molecular Microscope Diagnostic System (MMDx, n = 51). RNA sequencing showed lower expression of genes related to interferon-y (p = 1.5 *10-16), cytokine signaling (p = 2.1 *10-20) and inflammatory response (p = 1.0*10-13) in the ISO-T group than in I + T group. Transcripts with increased expression in the I + T group overlapped significantly with previously described pathogenesis-based transcript sets associated with cytotoxic and effector T cell transcripts, and with T cell-mediated rejection (TCMR). MMDx classified 25/32 (78%) ISO-T biopsies and 12/19 (63%) I + T biopsies as no-rejection. ISO-T had significantly lower MMDx scores for interstitial inflammation (p = 0.014), tubulitis (p = 0.035) and TCMR (p = 0.016) compared to I + T. Fewer molecular signals of inflammation in isolated tubulitis suggest that this is also a benign phenotype on a molecular level.
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15
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Madill-Thomsen K, 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 diagnosis of rejection in liver transplant biopsies: First results of the INTERLIVER study. Am J Transplant 2020; 20:2156-2172. [PMID: 32090446 DOI: 10.1111/ajt.15828] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 01/25/2023]
Abstract
Molecular diagnosis of rejection is emerging in kidney, heart, and lung transplant biopsies and could offer insights for liver transplant biopsies. We measured gene expression by microarrays in 235 liver transplant biopsies from 10 centers. Unsupervised archetypal analysis based on expression of previously annotated rejection-related transcripts identified 4 groups: normal "R1normal " (N = 129), T cell-mediated rejection (TCMR) "R2TCMR " (N = 37), early injury "R3injury " (N = 61), and fibrosis "R4late " (N = 8). Groups differed in median time posttransplant, for example, R3injury 99 days vs R4late 3117 days. R2TCMR biopsies expressed typical TCMR-related transcripts, for example, intense IFNG-induced effects. R3injury displayed increased expression of parenchymal injury transcripts (eg, hypoxia-inducible factor EGLN1). R4late biopsies showed immunoglobulin transcripts and injury-related transcripts. R2TCMR correlated with histologic rejection although with many discrepancies, and R4late with fibrosis. R2TCMR , R3injury , and R4late correlated with liver function abnormalities. Supervised classifiers trained on histologic rejection showed less agreement with histology than unsupervised R2TCMR scores. No confirmed cases of clinical antibody-mediated rejection (ABMR) were present in the population, and strategies that previously revealed ABMR in kidney and heart transplants failed to reveal a liver ABMR phenotype. In conclusion, molecular analysis of liver transplant biopsies detects rejection, has the potential to resolve ambiguities, and could assist with immunosuppressive management.
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Affiliation(s)
| | | | - Chandra Bhati
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Michał Ciszek
- Department of Immunology, Transplantology and Internal Diseases, 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 Diseases, 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, NSW, Australia
| | | | | | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, 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 Diseases, 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
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,University of Alberta, Edmonton, Alberta, Canada
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16
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Late Onset Graft Plasmacytoma-Like PTLD Presenting as Acute Hyperglycemia in a Kidney-Pancreas Transplant Recipient. Case Rep Nephrol 2019; 2019:2818074. [PMID: 31236295 PMCID: PMC6545763 DOI: 10.1155/2019/2818074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/12/2019] [Accepted: 04/18/2019] [Indexed: 11/17/2022] Open
Abstract
Allograft infiltration has been described in up to 20% of all patients with posttransplant lymphoproliferative disorder (PTLD), most representing EBV-positive B-cell lymphomas. Plasma cells are often observed in humoral rejection biopsies, but graft infiltration by plasmacytoma-like PTLD is rare. We report the case of a 54-year-old simultaneous pancreas-kidney transplant recipient (immunosuppression: OKT3, methylprednisolone, cyclosporine, and azathioprine), diagnosed with an IgG-kappa monoclonal gammopathy of undetermined significance eighteen years after transplant. Nine months later, pancreas allograft biopsy performed due to new-onset hyperglycemia (HgA1C 8.6%, C-peptide 6.15ng/mL and anti-GAD 0.9UI/mL) revealed a monotypic plasma cell infiltrate, CD19, CD79a, CD138 positive, with IgG-kappa light chain restriction, and EBV negative. PET-scan FDG uptake was limited to pancreas allograft. Tumor origin could not be established (using DNA microsatellite analysis). Despite treatment with bortezomib and dexamethasone, patient eventually died one month later. This is the first report of a late onset extramedullary plasmacytoma involving a pancreas allograft.
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17
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Halloran PF, Matas A, Kasiske BL, Madill-Thomsen KS, Mackova M, Famulski KS. Molecular phenotype of kidney transplant indication biopsies with inflammation in scarred areas. Am J Transplant 2019; 19:1356-1370. [PMID: 30417539 DOI: 10.1111/ajt.15178] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 01/25/2023]
Abstract
In kidney transplant biopsies, inflammation in areas of atrophy-fibrosis (i-IFTA) is associated with increased risk of failure, presumably because inflammation is evoked by recent parenchymal injury from rejection or other insults, but some cases also have rejection. The present study explored the frequency of rejection in i-IFTA, by using histology Banff 2015 and a microarray-based molecular diagnostic system (MMDx). In unselected indication biopsies (108 i-IFTA, 73 uninflamed IFTA [i0-IFTA], and 53 no IFTA), i-IFTA biopsies occurred later, showed more scarring, and had more antibody-mediated rejection (ABMR) based on histology (28%) and MMDx (45%). T cell-mediated rejection (TCMR) was infrequent in i-IFTA based on histology (8%) and MMDx (16%). Twelve i-IFTA biopsies (11%) had molecular TCMR not diagnosed by histology, although 6 were called borderline and almost all had histologic TCMR lesions. The prominent feature of i-IFTA biopsies was molecular injury (eg, acute kidney injury [AKI] transcripts). In multivariate analysis of biopsies >1 year posttransplant, the strongest associations with graft loss were AKI transcripts and histologic atrophy-scarring; i-IFTA was not significant when molecular AKI was included. We conclude that i-IFTA in indication biopsies reflects recent/ongoing parenchymal injury, often with concomitant ABMR but few with TCMR. Thus, the application of Banff i-IFTA in the population of late biopsies needs to be reconsidered.
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Arthur Matas
- Department of Surgery, University of Minnesota at Fairview, Minneapolis, Minnesota
| | | | - Katelynn S Madill-Thomsen
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Martina Mackova
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
| | - Konrad S Famulski
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
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18
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An integrated molecular diagnostic report for heart transplant biopsies using an ensemble of diagnostic algorithms. J Heart Lung Transplant 2019; 38:636-646. [PMID: 30795962 DOI: 10.1016/j.healun.2019.01.1318] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND We previously reported a microarray-based diagnostic system for heart transplant endomyocardial biopsies (EMBs), using either 3-archetype (3AA) or 4-archetype (4AA) unsupervised algorithms to estimate rejection. In the present study we examined the stability of machine-learning algorithms in new biopsies, compared 3AA vs 4AA algorithms, assessed supervised binary classifiers trained on histologic or molecular diagnoses, created a report combining many scores into an ensemble of estimates, and examined possible automated sign-outs. METHODS We studied 889 EMBs from 454 transplant recipients at 8 centers: the initial cohort (N = 331) and a new cohort (N = 558). Published 3AA algorithms derived in Cohort 331 were tested in Cohort 558, the 3AA and 4AA models were compared, and supervised binary classifiers were created. RESULTS A`lgorithms derived in Cohort 331 performed similarly in new biopsies despite differences in case mix. In the combined cohort, the 4AA model, including a parenchymal injury score, retained correlations with histologic rejection and DSA similar to the 3AA model. Supervised molecular classifiers predicted molecular rejection (areas under the curve [AUCs] >0.87) better than histologic rejection (AUCs <0.78), even when trained on histology diagnoses. A report incorporating many AA and binary classifier scores interpreted by 1 expert showed highly significant agreement with histology (p < 0.001), but with many discrepancies, as expected from the known noise in histology. An automated random forest score closely predicted expert diagnoses, confirming potential for automated signouts. CONCLUSIONS Molecular algorithms are stable in new populations and can be assembled into an ensemble that combines many supervised and unsupervised estimates of the molecular disease states.
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19
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Halloran PF, Reeve J, Aliabadi AZ, Cadeiras M, Crespo-Leiro MG, Deng M, Depasquale EC, Goekler J, Jouven X, Kim DH, Kobashigawa J, Loupy A, Macdonald P, Potena L, Zuckermann A, Parkes MD. Exploring the cardiac response to injury in heart transplant biopsies. JCI Insight 2018; 3:123674. [PMID: 30333303 DOI: 10.1172/jci.insight.123674] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Because injury is universal in organ transplantation, heart transplant endomyocardial biopsies present an opportunity to explore response to injury in heart parenchyma. Histology has limited ability to assess injury, potentially confusing it with rejection, whereas molecular changes have potential to distinguish injury from rejection. Building on previous studies of transcripts associated with T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR), we explored transcripts reflecting injury. METHODS Microarray data from 889 prospectively collected endomyocardial biopsies from 454 transplant recipients at 14 centers were subjected to unsupervised principal component analysis and archetypal analysis to detect variation not explained by rejection. The resulting principal component and archetype scores were then examined for their transcript, transcript set, and pathway associations and compared to the histology diagnoses and left ventricular function. RESULTS Rejection was reflected by principal components PC1 and PC2, and by archetype scores S2TCMR, and S3ABMR, with S1normal indicating normalness. PC3 and a new archetype score, S4injury, identified unexplained variation correlating with expression of transcripts inducible in injury models, many expressed in macrophages and associated with inflammation in pathway analysis. S4injury scores were high in recent transplants, reflecting donation-implantation injury, and both S4injury and S2TCMR were associated with reduced left ventricular ejection fraction. CONCLUSION Assessment of injury is necessary for accurate estimates of rejection and for understanding heart transplant phenotypes. Biopsies with molecular injury but no molecular rejection were often misdiagnosed rejection by histology.TRAIL REGISTRATION. ClinicalTrials.gov NCT02670408FUNDING. Roche Organ Transplant Research Foundation, the University of Alberta Hospital Foundation, and Alberta Health Services.
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Martin Cadeiras
- Ronald Reagan UCLA Medical Center, Los Angeles, California, USA
| | | | - Mario Deng
- Ronald Reagan UCLA Medical Center, Los Angeles, California, USA
| | | | | | | | - Daniel H Kim
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Peter Macdonald
- The Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Luciano Potena
- Cardiovascular Department, University of Bologna, Bologna, Italy
| | | | - Michael D Parkes
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
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20
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Einecke G, Reeve J, Halloran PF. A molecular biopsy test based on arteriolar under-hyalinosis reflects increased probability of rejection related to under-immunosuppression. Am J Transplant 2018; 18:821-831. [PMID: 28985016 DOI: 10.1111/ajt.14532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 01/25/2023]
Abstract
Calcineurin inhibitor immunosuppressive drugs induce changes such as arteriolar hyalinosis (ah) in kidney transplants, raising the possibility that molecular changes in biopsies related to histologic ah can provide information about drug exposure. We hypothesized that molecular changes associated with less-than-expected hyalinosis might highlight a subpopulation of patients with under-immunosuppression/nonadherence at intermediate times of biopsy posttransplant (TxBx). Using gene expression data from 562 indication biopsies, we developed a molecular classifier for predicting the expected ah lesions (Mah ) at a particular TxBx. Mah -scores increased linearly with log(TxBx), but some biopsies had lower scores than expected for TxBx. The deviation of individual Mah -scores below the predicted regression line of Mah -scores vs TxBx is defined as "low hyalinosis index." Low hyalinosis indices were frequent in biopsies between 3 months and 3 years posttransplant, particularly among biopsies lacking histologic hyalinosis (ah0), and were associated with T cell-mediated rejection and a subset of recent-onset antibody-mediated rejection without glomerular double contours. In patients with medical records available for review, low hyalinosis indices were frequently associated with physician-recorded concerns about nonadherence (suspected or proven). We conclude that the Mah classifier and hyalinosis index identify indication biopsies with rejection for which the possibility of patient nonadherence should be considered.
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Affiliation(s)
- Gunilla Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre Edmonton, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre Edmonton, Edmonton, AB, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, AB, Canada
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21
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Polyomavirus BK Nephropathy-Associated Transcriptomic Signatures: A Critical Reevaluation. Transplant Direct 2018; 4:e339. [PMID: 29464200 PMCID: PMC5811268 DOI: 10.1097/txd.0000000000000752] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/07/2017] [Indexed: 12/29/2022] Open
Abstract
Background Recent work using DNA microarrays has suggested that genes related to DNA replication, RNA polymerase assembly, and pathogen recognition receptors can serve as surrogate tissue biomarkers for polyomavirus BK nephropathy (BKPyVN). Methods We have examined this premise by looking for differential regulation of these genes using a different technology platform (RNA-seq) and an independent set 25 biopsies covering a wide spectrum of diagnoses. Results RNA-seq could discriminate T cell–mediated rejection from other common lesions seen in formalin fixed biopsy material. However, overlapping RNA-seq signatures were found among all disease processes investigated. Specifically, genes previously reported as being specific for the diagnosis of BKPyVN were found to be significantly upregulated in T cell–mediated rejection, inflamed areas of fibrosis/tubular atrophy, as well as acute tubular injury. Conclusions In conclusion, the search for virus specific molecular signatures is confounded by substantial overlap in pathogenetic mechanisms between BKPyVN and nonviral forms of allograft injury. Clinical heterogeneity, overlapping exposures, and different morphologic patterns and stage of disease are a source of substantial variability in “Omics” experiments. These variables should be better controlled in future biomarker studies on BKPyVN, T cell–mediated rejection, and other forms of allograft injury, before widespread implementation of these tests in the transplant clinic.
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22
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Salcido-Ochoa F, Hue SSS, Peng S, Fan Z, Li RL, Iqbal J, Allen Jr JC, Loh AHL. Histopathological analysis of infiltrating T cell subsets in acute T cell-mediated rejection in the kidney transplant. World J Transplant 2017; 7:222-234. [PMID: 28900605 PMCID: PMC5573898 DOI: 10.5500/wjt.v7.i4.222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 05/21/2017] [Accepted: 07/03/2017] [Indexed: 02/05/2023] Open
Abstract
AIM To compare the differential immune T cell subset composition in patients with acute T cell-mediated rejection in the kidney transplant with subset composition in the absence of rejection, and to explore the association of their respective immune profiles with kidney transplant outcomes.
METHODS A pilot cross-sectional histopathological analysis of the immune infiltrate was performed using immunohistochemistry in a cohort of 14 patients with acute T cell-mediated rejection in the kidney transplant and 7 kidney transplant patients with no rejection subjected to biopsy to investigate acute kidney transplant dysfunction. All patients were recruited consecutively from 2012 to 2014 at the Singapore General Hospital. Association of the immune infiltrates with kidney transplant outcomes at up to 54 mo of follow up was also explored prospectively.
RESULTS In comparison to the absence of rejection, acute T cell-mediated rejection in the kidney transplant was characterised by numerical dominance of cytotoxic T lymphocytes over Foxp3+ regulatory T cells, but did not reach statistical significance owing to the small sample size in our pilot study. There was no obvious difference in absolute numbers of infiltrating cytotoxic T lymphocytes, Foxp3+ regulatory T cells and Th17 cells between the two patient groups when quantified separately. Our exploratory analysis on associations of T cell subset quantifications with kidney transplant outcomes revealed that the degree of Th17 cell infiltration was significantly associated with shorter time to doubling of creatinine and shorter time to transplant loss.
CONCLUSION Although this was a small pilot study, results support our suspicion that in kidney transplant patients the immune balance in acute T cell-mediated rejection is tilted towards the pro-rejection forces and prompt larger and more sophisticated studies.
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Affiliation(s)
- Francisco Salcido-Ochoa
- Tregs and HLA Research Force and Renal Medicine Department, Singapore General Hospital, Singapore 169856, Singapore
| | - Susan Swee-Shan Hue
- Tregs and HLA Research Force and Department of Pathology, National University Hospital, Singapore 119074, Singapore
| | - Siyu Peng
- Tregs and HLA Research Force and Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Zhaoxiang Fan
- Tregs and HLA Research Force and Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Reiko Lixiang Li
- Department of Pathology and Laboratory Medicine, KK Women’s and Children’s Hospital, Singapore 229899, Singapore
| | - Jabed Iqbal
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore,
| | - John Carson Allen Jr
- Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, Singapore 169856, Singapore
| | - Alwin Hwai Liang Loh
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore,
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Sugimoto C, Fujita H, Wakao H. Mucosal-associated invariant T cells from induced pluripotent stem cells: A novel approach for modeling human diseases. World J Stem Cells 2016; 8:158-169. [PMID: 27114747 PMCID: PMC4835674 DOI: 10.4252/wjsc.v8.i4.158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/17/2015] [Accepted: 02/16/2016] [Indexed: 02/06/2023] Open
Abstract
Mice have frequently been used to model human diseases involving immune dysregulation such as autoimmune and inflammatory diseases. These models help elucidate the mechanisms underlying the disease and in the development of novel therapies. However, if mice are deficient in certain cells and/or effectors associated with human diseases, how can their functions be investigated in this species? Mucosal-associated invariant T (MAIT) cells, a novel innate-like T cell family member, are a good example. MAIT cells are abundant in humans but scarce in laboratory mice. MAIT cells harbor an invariant T cell receptor and recognize nonpeptidic antigens vitamin B2 metabolites from bacteria and yeasts. Recent studies have shown that MAIT cells play a pivotal role in human diseases such as bacterial infections and autoimmune and inflammatory diseases. MAIT cells possess granulysin, a human-specific effector molecule, but granulysin and its homologue are absent in mice. Furthermore, MAIT cells show poor proliferation in vitro. To overcome these problems and further our knowledge of MAIT cells, we have established a method to expand MAIT cells via induced pluripotent stem cells (iPSCs). In this review, we describe recent advances in the field of MAIT cell research and our approach for human disease modeling with iPSC-derived MAIT cells.
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Bonaccorsi-Riani E, Pennycuick A, Londoño MC, Lozano JJ, Benítez C, Sawitzki B, Martínez-Picola M, Bohne F, Martínez-Llordella M, Miquel R, Rimola A, Sánchez-Fueyo A. Molecular Characterization of Acute Cellular Rejection Occurring During Intentional Immunosuppression Withdrawal in Liver Transplantation. Am J Transplant 2016; 16:484-96. [PMID: 26517400 DOI: 10.1111/ajt.13488] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/26/2015] [Accepted: 08/02/2015] [Indexed: 01/25/2023]
Abstract
Acute cellular rejection occurs frequently during the first few weeks following liver transplantation. During this period, its molecular phenotype is confounded by peri- and postoperative proinflammatory events. To unambiguously define the molecular profile associated with rejection, we collected sequential biological specimens from 55 patients at least 3 years after liver transplantation who developed rejection during trials of intentional immunosuppression withdrawal. We analyzed liver tissue and blood samples obtained before initiation of drug withdrawal and at rejection, alongside blood samples collected during the weaning process. Gene expression profiling was conducted using whole-genome microarrays and real-time polymerase chain reaction. Rejection resulted in distinct blood and liver tissue transcriptional changes in patients who were either positive or negative for hepatitis C virus (HCV). Gene expression changes were mostly independent from pharmacological immunosuppression, and their magnitude correlated with severity of histological damage. Differential expression of a subset of genes overlapped across all conditions. These were used to define a blood predictive model that accurately identified rejection in HCV-negative, but not HCV-positive, patients. Changes were detectable 1-2 mo before rejection was diagnosed. Our results provide insight into the molecular processes underlying acute cellular rejection in liver transplantation and help clarify the potential utility and limitations of transcriptional biomarkers in this setting.
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Affiliation(s)
- E Bonaccorsi-Riani
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - A Pennycuick
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - M-C Londoño
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - J-J Lozano
- Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - C Benítez
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - B Sawitzki
- AG Transplantationstoleranz, Charite Universitätsmedizin, Institut für Med. Immunologie, Berlin, Germany
| | - M Martínez-Picola
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - F Bohne
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - M Martínez-Llordella
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - R Miquel
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK
| | - A Rimola
- Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
| | - A Sánchez-Fueyo
- Department of Liver Studies, Division of Transplantation Immunology and Mucosal Biology, Medical Research Council Centre for Transplantation, Faculty of Life Sciences and Medicine, King's College London University, King's College Hospital, Denmark Hill, London, UK.,Liver Unit, Hospital Clinic Barcelona, Institut d' Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Networked Biomedical Research Centre of Hepatic and Digestive Diseases (CIBERehd), University of Barcelona, Barcelona, Spain
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25
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Abstract
Despite its long-standing status as the diagnostic "gold standard", the renal transplant biopsy is limited by a fundamental dependence on descriptive, empirically-derived consensus classification. The recent shift towards personalized medicine has resulted in an increased demand for precise, mechanism-based diagnoses, which is not fully met by the contemporary transplantation pathology standard of care. The expectation is that molecular techniques will provide novel pathogenetic insights that will allow for the identification of more accurate diagnostic, prognostic, and therapeutic targets. Here we review the current state of molecular renal transplantation pathology. Despite significant research activity and progress within the field, routine adoption of clinical molecular testing has not yet been achieved. The recent development of novel molecular platforms suitable for use with formalin-fixed paraffin-embedded tissue will offer potential solution for the major barriers to implementation. The recent incorporation of molecular diagnostic criteria into the 2013 Banff classification is a reflection of progress made and future directions in the area of molecular transplantation pathology. Transcripts related to endothelial injury and NK cell activation have consistently been shown to be associated with antibody-mediated rejection. Prospective multicenter validation and implementation of molecular diagnostics for major entities remains an unmet clinical need in transplantation. It is expected that an integrated system of transplantation pathology diagnosis comprising molecular, morphological, serological, and clinical variables will ultimately provide the greatest diagnostic precision.
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26
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Dorr C, Wu B, Guan W, Muthusamy A, Sanghavi K, Schladt DP, Maltzman JS, Scherer SE, Brott MJ, Matas AJ, Jacobson PA, Oetting WS, Israni AK. Differentially expressed gene transcripts using RNA sequencing from the blood of immunosuppressed kidney allograft recipients. PLoS One 2015; 10:e0125045. [PMID: 25946140 PMCID: PMC4422721 DOI: 10.1371/journal.pone.0125045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/09/2015] [Indexed: 02/05/2023] Open
Abstract
We performed RNA sequencing (RNAseq) on peripheral blood mononuclear cells (PBMCs) to identify differentially expressed gene transcripts (DEGs) after kidney transplantation and after the start of immunosuppressive drugs. RNAseq is superior to microarray to determine DEGs because it’s not limited to available probes, has increased sensitivity, and detects alternative and previously unknown transcripts. DEGs were determined in 32 adult kidney recipients, without clinical acute rejection (AR), treated with antibody induction, calcineurin inhibitor, mycophenolate, with and without steroids. Blood was obtained pre-transplant (baseline), week 1, months 3 and 6 post-transplant. PBMCs were isolated, RNA extracted and gene expression measured using RNAseq. Principal components (PCs) were computed using a surrogate variable approach. DEGs post-transplant were identified by controlling false discovery rate (FDR) at < 0.01 with at least a 2 fold change in expression from pre-transplant. The top 5 DEGs with higher levels of transcripts in blood at week 1 were TOMM40L, TMEM205, OLFM4, MMP8, and OSBPL9 compared to baseline. The top 5 DEGs with lower levels at week 1 post-transplant were IL7R, KLRC3, CD3E, CD3D, and KLRC2 (Striking Image) compared to baseline. The top pathways from genes with lower levels at 1 week post-transplant compared to baseline, were T cell receptor signaling and iCOS-iCOSL signaling while the top pathways from genes with higher levels than baseline were axonal guidance signaling and LXR/RXR activation. Gene expression signatures at month 3 were similar to week 1. DEGs at 6 months post-transplant create a different gene signature than week 1 or month 3 post-transplant. RNAseq analysis identified more DEGs with lower than higher levels in blood compared to baseline at week 1 and month 3. The number of DEGs decreased with time post-transplant. Further investigations to determine the specific lymphocyte(s) responsible for differential gene expression may be important in selecting and personalizing immune suppressant drugs and may lead to targeted therapies.
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Affiliation(s)
- Casey Dorr
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Baolin Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Weihua Guan
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Amutha Muthusamy
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
| | - Kinjal Sanghavi
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David P. Schladt
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
| | - Jonathan S. Maltzman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Steven E. Scherer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Dallas, Texas, United States of America
| | - Marcia J. Brott
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Arthur J. Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Pamala A. Jacobson
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William S. Oetting
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ajay K. Israni
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Epidemiology and Community Health, University of Minnesota School of Medicine, Minneapolis, Minnesota, United States of America
- * E-mail:
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Halloran B, Chang J, Shih DQ, McGovern D, Famulski K, Evaschesen C, Fedorak RN, Thiesen A, Targan S, Halloran PF. Molecular patterns in human ulcerative colitis and correlation with response to infliximab. Inflamm Bowel Dis 2014; 20:2353-63. [PMID: 25397893 PMCID: PMC4985265 DOI: 10.1097/mib.0000000000000239] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND As a T cell-mediated disease of the colonic epithelium, ulcerative colitis (UC) is likely to share pathogenic elements with other T cell-mediated inflammatory diseases. Recently, microarray analysis revealed large-scale molecular changes in T cell-mediated rejection of kidney and heart transplants. We hypothesized that similar disturbances might be operating in UC and could provide insights into responsiveness to therapy. METHODS We studied 56 colon biopsies from patients with colitis characterizing the clinical and histological features and using microarrays to define the messenger RNA phenotype. We expressed the microarray results using previously defined pathogenesis-based transcript sets. We also studied 48 published microarray files from human colon biopsies downloaded from the Gene Expression Omnibus database, classified by response to infliximab therapy, to examine whether the molecular measurements derived from our studies correlated with nonresponsiveness to treatment. RESULTS UC biopsies manifested coordinate transcript changes resembling rejecting transplants, with effector T cell, IFNG-induced, macrophage, and injury transcripts increasing while parenchymal transcripts decreased. The disturbance in gene expression, summarized as principal component 1 (PC1), correlated with conventional clinical and histologic assessments. When assessed in microarray results from published studies, the disturbance (PC1) predicted response to infliximab: patients with intense disturbance did not achieve clinical response, although quantitative improvement was seen even in many clinical nonresponders. Similar changes were seen in Crohn's colitis. CONCLUSIONS The molecular phenotype of UC manifests a large-scale coordinate disturbance reflecting changes in inflammatory cells and parenchymal elements that correlates with conventional features and predicts response to infliximab.
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Affiliation(s)
- Brendan Halloran
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | | | - David Q. Shih
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dermot McGovern
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Konrad Famulski
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Chad Evaschesen
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Richard N Fedorak
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Aducio Thiesen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Stephan Targan
- F. Widjaja Foundation, Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Philip F. Halloran
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, AB, Canada
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28
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Mengel M. Renalomics: Molecular Pathology in Kidney Biopsies. Surg Pathol Clin 2014; 7:443-55. [PMID: 26837449 DOI: 10.1016/j.path.2014.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this article, various omics technologies and their applications in renal pathology (native and transplant biopsies) are reviewed and discussed. Despite significant progress and novel insights derived from these applications, extensive adoption of molecular diagnostics in renal pathology has not been accomplished. Further validation of specific applications leading to increased diagnostic precision in a clinically relevant way is ongoing.
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Affiliation(s)
- Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta Hospital, 4B1.18 Walter Mackenzie Center, 8440-112 Street, Edmonton T6G2S2, Canada.
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29
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Elevation of CD4+ differentiated memory T cells is associated with acute cellular and antibody-mediated rejection after liver transplantation. Transplantation 2013; 95:1512-20. [PMID: 23619734 DOI: 10.1097/tp.0b013e318290de18] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND It is now well known that the outcome after allogeneic transplantation, such as incidence of acute rejections, very much depends on the individual's immune reactivity status. There is also increasing evidence that the presence of preexisting memory T cells can affect antigraft immune responses. METHODS In a prospective study, we monitored peripheral CD4 and CD8 central memory, effector memory, and terminal differentiated effector memory (TEMRA) T cells in 55 patients who underwent deceased liver transplantation and received conventional immunosuppressive treatment with or without basiliximab induction. The primary endpoint of the study was acute allograft rejection during a 1-year follow-up period. RESULTS We observed significantly increased proportions of CD4 and CD8 TEMRA cells in patients before transplantation compared with healthy controls (P=0.006 and 0.009, respectively). This characteristic was independent of the underlying disease. In patients with no signs of acute rejection, we observed an immediate reduction of CD4 TEMRA cells. In contrast, patients who experienced acute cellular rejection, and especially antibody-mediated rejection, displayed persistent elevated TEMRA cells (P=0.017 and 0.027, respectively). Basiliximab induction therapy did not influence CD4 and CD8 TEMRA numbers. CONCLUSIONS Conventional immunosuppressive or basiliximab treatment cannot control the persistence of TEMRA T cells, which may contribute to acute cellular rejection and antibody-mediated rejection after liver transplantation. In the future, specific targeting of TEMRA cells in selected patients may prevent the occurrence of difficult to treat steroid-resistant rejections, thereby leading to improved patient outcome.
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30
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Molecular transplantation pathology: the interface between molecules and histopathology. Curr Opin Organ Transplant 2013; 18:354-62. [PMID: 23619514 DOI: 10.1097/mot.0b013e3283614c90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW In the last decade, high-throughput molecular screening methods have revolutionized the transplantation research. This article reviews the new knowledge that has emerged from transplant patient sample-derived 'omics data by examining the interface between molecular signals and allograft pathology. RECENT FINDINGS State-of-the-art molecular studies have shed light on the biology of organ transplant diseases and provided several potential molecular tests with diagnostic, prognostic, and theranostic applications for the implementation of personalized medicine in transplantation. By comprehensive molecular profiling of patient samples, we have learned numerous new insights into the effector mechanisms and parenchymal response during allograft diseases. It has become evident that molecular profiles are coordinated and move in patterns similar to histopathology lesions, and therefore lack qualitative specificity. However, molecular tests can empower precision diagnosis and prognostication through their objective and quantitative manner when they are integrated in a holistic approach with histopathology and clinical factors of patients. SUMMARY Despite clever science and large amounts of public money invested in transplant 'omics studies, multiparametric molecular testing has not yet been translated to patient care. There are serious challenges in the implementation of transplant molecular diagnostics that have increased frustration in transplant community. We appeal for a full collaboration between pathologists and researchers to accelerate transition from research to clinical practice in transplantation.
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31
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Giaretta F, Bussolino S, Beltramo S, Fop F, Rossetti M, Messina M, Cantaluppi V, Ranghino A, Basso E, Camussi G, Segoloni GP, Biancone L. Different regulatory and cytotoxic CD4+ T lymphocyte profiles in renal transplants with antibody-mediated chronic rejection or long-term good graft function. Transpl Immunol 2012. [PMID: 23178518 DOI: 10.1016/j.trim.2012.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Comparative analysis of the different subsets of CD4(+) T-lymphocytes may provide hints on the immunologic mechanisms operating in the long-term fate of a kidney transplant. We analyzed peripheral regulatory CD4(+) T cells (Tregs) and CD4(+) cytotoxic T lymphocytes (CTLs) in antibody-mediated chronic rejection (AMCR), in middle-term kidney transplants (2-4 years, MTKT) with good graft function and rejection-free history, in long-term kidney transplants (>15 years, LTKT) and in normal healthy subjects (NHS). Transplant groups with good prognosis (MTKT and LTKT) displayed a significant lower amount of CD4(+)CD25(high) T lymphocytes than NHS, with a trend of a higher percentage in AMCR than in MTKT and LTKT. However, CD4(+)CD25(high) Foxp3(+) cells were significantly higher in LTKT and MTKT than AMCR. Characterization of CD4(+)CD25(high) T cells showed a marked increase of intracellular CTLA-4 in the AMCR group in respect to the other transplant groups, while the expression of the surface molecule seemed to follow a reverse trend. In addition, CD27, a costimulatory receptor involved in long-term T cell survival and prevention of immune tolerance, is significantly reduced in CD4(+)CD25(high) and CD4(+)Foxp3(+) T cells in the LTKT in respect to the other transplant groups. CD4(+)CD25(high)CD45RO(+) and CD4(+)Foxp3(+)CD45RO(+) regulatory T cells with memory function were increased in LTKT compared to NHS and for the latter also in AMCR group. Finally, CD4(+)CTLs that were quantified on the basis of granzyme A expression, were more represented in AMCR patients in comparison to the other groups. Strikingly, CD27 in the CD4(+)CTLs was suppressed in LTKT and MTKT and markedly expressed in AMCR group. No significant differences in the expression of CD28 were observed among different groups. In conclusion, different profiles of Tregs and CD4(+)CTL populations correlate with different long-term conditions of kidney-transplanted patients, suggesting their role in the development of immunologic events in kidney transplantation.
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Affiliation(s)
- Fulvia Giaretta
- Department of Internal Medicine, University of Torino and San Giovanni Battista Hospital, Corso Dogliotti 14, Torino 10126, Italy
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Hidalgo LG, Sellares J, Sis B, Mengel M, Chang J, Halloran PF. Interpreting NK cell transcripts versus T cell transcripts in renal transplant biopsies. Am J Transplant 2012; 12:1180-91. [PMID: 22390872 DOI: 10.1111/j.1600-6143.2011.03970.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
NK cell transcripts are increased in biopsies with antibody-mediated rejection, whereas T cell transcripts are increased in T cell-mediated rejection. However, NK and T cells share many features, creating potential ambiguity. Therefore to estimate the NK- versus T cell transcript burdens separately, we defined nonoverlapping transcripts selective for NK cells (N = 4) or T cells (N = 5). We compared NK- versus T cell transcript burdens in microarrays from 403 kidney transplant biopsies (182 early, 221 late). In late biopsies, high NK-cell transcript expression was associated with antibody-mediated rejection, correlating with microvascular inflammation and donor specific HLA antibody. However, some early biopsies with T cell-mediated rejection had high NK-cell transcript expression, as well as T cell transcripts, without evidence of antibody-mediated rejection or DSA, correlating with interstitial inflammation and tubulitis. Both NK-cell and T cell transcripts were moderately increased in many kidneys with inflammation secondary to injury or atrophy scarring. These results support the distinct role of NK cells in late antibody-mediated rejection, but indicate a role for NK-transcript expressing cells (NK cells or T cells with NK features) both in T cell-mediated rejection and in inflammation associated with injury and atrophy scarring.
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Affiliation(s)
- L G Hidalgo
- Department of Laboratory Medicine and Pathology, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
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33
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de Freitas DG, Sellarés J, Mengel M, Chang J, Hidalgo LG, Famulski KS, Sis B, Einecke G, Halloran PF. The nature of biopsies with "borderline rejection" and prospects for eliminating this category. Am J Transplant 2012; 12:191-201. [PMID: 21992503 DOI: 10.1111/j.1600-6143.2011.03784.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In kidney transplantation, many inflamed biopsies with changes insufficient to be called T-cell-mediated rejection (TCMR) are labeled "borderline", leaving management uncertain. This study examined the nature of borderline biopsies as a step toward eventual elimination of this category. We compared 40 borderline, 35 TCMR and 116 nonrejection biopsies. TCMR biopsies had more inflammation than borderline but similar degrees of tubulitis and scarring. Surprisingly, recovery of function after biopsy was similar in all categories, indicating that response to treatment is unreliable for defining TCMR. We studied the molecular changes in TCMR, borderline and nonrejection using microarrays, measuring four published features: T-cell burden; a rejection classifier; a canonical TCMR classifier; and risk score. These reassigned borderline biopsies as TCMR-like 13/40 (33%) or nonrejection-like 27/40 (67%). A major reason that histology diagnosed molecularly defined TCMR as borderline was atrophy-scarring, which interfered with assessment of inflammation and tubulitis. Decision tree analysis showed that i-total >27% and tubulitis extent >3% match the molecular diagnosis of TCMR in 85% of cases. In summary, most cases designated borderline by histopathology are found to be nonrejection by molecular phenotyping. Both molecular measurements and histopathology offer opportunities for more precise assignment of these cases after clinical validation.
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Affiliation(s)
- D G de Freitas
- Alberta Transplant Applied Genomics Centre, University of Alberta, Edmonton, Canada
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34
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Spivey TL, Uccellini L, Ascierto ML, Zoppoli G, De Giorgi V, Delogu LG, Engle AM, Thomas JM, Wang E, Marincola FM, Bedognetti D. Gene expression profiling in acute allograft rejection: challenging the immunologic constant of rejection hypothesis. J Transl Med 2011; 9:174. [PMID: 21992116 PMCID: PMC3213224 DOI: 10.1186/1479-5876-9-174] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 10/12/2011] [Indexed: 02/06/2023] Open
Abstract
In humans, the role and relationship between molecular pathways that lead to tissue destruction during acute allograft rejection are not fully understood. Based on studies conducted in humans, we recently hypothesized that different immune-mediated tissue destruction processes (i.e. cancer, infection, autoimmunity) share common convergent final mechanisms. We called this phenomenon the "Immunologic Constant of Rejection (ICR)." The elements of the ICR include molecular pathways that are consistently described through different immune-mediated tissue destruction processes and demonstrate the activation of interferon-stimulated genes (ISGs), the recruitment of cytotoxic immune cells (primarily through CXCR3/CCR5 ligand pathways), and the activation of immune effector function genes (IEF genes; granzymes A/B, perforin, etc.). Here, we challenge the ICR hypothesis by using a meta-analytical approach and systematically reviewing microarray studies evaluating gene expression on tissue biopsies during acute allograft rejection. We found the pillars of the ICR consistently present among the studies reviewed, despite implicit heterogeneity. Additionally, we provide a descriptive mechanistic overview of acute allograft rejection by describing those molecular pathways most frequently encountered and thereby thought to be most significant. The biological role of the following molecular pathways is described: IFN-γ, CXCR3/CCR5 ligand, IEF genes, TNF-α, IL-10, IRF-1/STAT-1, and complement pathways. The role of NK cell, B cell and T-regulatory cell signatures are also addressed.
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Affiliation(s)
- Tara L Spivey
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, Maryland 20892, USA
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35
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Tomlinson GS, Cashmore TJ, Elkington PTG, Yates J, Lehloenya RJ, Tsang J, Brown M, Miller RF, Dheda K, Katz DR, Chain BM, Noursadeghi M. Transcriptional profiling of innate and adaptive human immune responses to mycobacteria in the tuberculin skin test. Eur J Immunol 2011; 41:3253-60. [PMID: 21805471 PMCID: PMC3258543 DOI: 10.1002/eji.201141841] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/06/2011] [Accepted: 07/25/2011] [Indexed: 12/24/2022]
Abstract
The tuberculin skin test (TST) is a model of integrated innate and adaptive human immune responses to Mycobacterium tuberculosis, but the component processes that are involved in this model have not previously been defined in vivo. We used transcriptional profiling to study these responses within the TST at molecular and system levels. Skin biopsies from TST injection sites were examined in subjects classified as TST+ or TST− by clinical and histological criteria. Genome-wide expression arrays showed evolution of immune responses reflecting T-cell activation and recruitment with uniquely Th1-polarized responses and cytotoxic T cells (CTLs). In addition, distinct innate immune and IFN-γ-stimulated gene expression signatures were identified, under the regulation of NF-κB and STAT1 transcriptional control. These were highly enriched for chemokines and MHC class II molecules providing a potential mechanism for paracrine amplification of inflammatory responses in the TST, by supporting cellular recruitment and enhancing antigen presentation. The same repertoire of innate and adaptive immune responses was evident in TST+ and TST− subjects alike, clinically positive TSTs being distinguished only by quantitatively greater differences. These data provide new insights into complex multifaceted responses within the TST, with much greater sensitivity than previous clinical or histological assessments.
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Mengel M, Chang J, Kayser D, Gwinner W, Schwarz A, Einecke G, Broecker V, Famulski K, de Freitas DG, Guembes-Hidalgo L, Sis B, Haller H, Halloran PF. The molecular phenotype of 6-week protocol biopsies from human renal allografts: reflections of prior injury but not future course. Am J Transplant 2011; 11:708-18. [PMID: 21114657 DOI: 10.1111/j.1600-6143.2010.03339.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We assessed the molecular phenotype of 107 6-week protocol biopsies from human renal allografts, using Affymetrix microarrays. Transcript changes were summarized as nonoverlapping pathogenesis-based transcript sets (PBTs) reflecting inflammation (T cells, macrophages, IFNG effects) and the injury-repair response of the parenchyma, stroma and microcirculation-increased ('injury-up') and decreased ('injury-down') transcripts. The molecular changes were highly correlated with each other, even when all rejection and borderline cases were excluded. Inflammation and injury-down PBTs correlated with histologic inflammation and tubulitis, and the inflammation transcripts were greater in kidneys diagnosed as T cell-mediated or borderline rejection. Injury-up PBTs did not correlate with histopathology but did correlate with kidney function: thus functional disturbances are represented in transcript changes but not in histopathology. PBT changes correlated with prior delayed graft function. However, there was little difference between live donor kidneys and deceased donor kidneys that had not shown delayed graft function. Molecular changes did not predict future biopsies for clinical indications, rejection episodes, functional deterioration or allograft loss. Thus while detecting T cell-mediated inflammation, the molecular phenotype of early protocol biopsies mostly reflects the injury-repair response to implantation stresses, and has little relationship to future events and outcomes.
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Affiliation(s)
- M Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada.
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37
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Perkins D, Verma M, Park KJ. Advances of genomic science and systems biology in renal transplantation: a review. Semin Immunopathol 2011; 33:211-8. [PMID: 21318414 PMCID: PMC3082700 DOI: 10.1007/s00281-011-0243-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 01/07/2011] [Indexed: 12/24/2022]
Abstract
The diagnosis of rejection in kidney transplant patients is based on histologic classification of a graft biopsy. The current “gold standard” is the Banff 97 criteria; however, there are several limitations in classifying rejection based on biopsy samples. First, a biopsy involves an invasive procedure. Second, there is significant variance among blinded pathologists in the interpretation of a biopsy. And third, there is also variance between the histology and the molecular profiles of a biopsy. To increase the positive predictive value of classifiers of rejection, a Banff committee is developing criteria that integrate histologic and molecular data into a unified classifier that could diagnose and prognose rejection. To develop the most appropriate molecular criteria, there have been studies by multiple groups applying omics technologies in attempts to identify biomarkers of rejection. In this review, we discuss studies using genome-wide data sets of the transcriptome and proteome to investigate acute rejection, chronic allograft dysfunction, and tolerance. We also discuss studies which focus on genetic biomarkers in urine and peripheral blood, which will provide clinicians with minimally invasive methods for monitoring transplant patients. We also discuss emerging technologies, including whole-exome sequencing and RNA-Seq and new bioinformatic and systems biology approaches, which should increase the ability to develop both biomarkers and mechanistic understanding of the rejection process.
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Affiliation(s)
- David Perkins
- Division of Nephrology, Department of Medicine, University of California San Diego, San Diego, CA, USA.
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Halloran PF, de Freitas DG, Einecke G, Famulski KS, Hidalgo LG, Mengel M, Reeve J, Sellares J, Sis B. The molecular phenotype of kidney transplants. Am J Transplant 2010; 10:2215-22. [PMID: 20931695 DOI: 10.1111/j.1600-6143.2010.03267.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microarray studies of kidney transplant biopsies provide an opportunity to define the molecular phenotype. To facilitate this process, we used experimental systems to annotate transcripts as members of pathogenesis-based transcript sets (PBTs) representing biological processes in injured or diseased tissue. Applying this annotation to microarray results revealed that changes in single molecules and PBTs reflected a large-scale coordinate disturbance, stereotyped across various diseases and injuries, without absolute specificity of individual molecules or PBTs for rejection. Nevertheless, expression of molecules and PBTs was quantitatively specific: IFNG effects for rejection; T cell and macrophage transcripts for T cell-mediated rejection; endothelial and NK transcripts for antibody-mediated rejection. Various diseases and injuries induced the same injury-repair response, undetectable by histopathology, involving epithelium, stroma and endothelium, with increased expression of developmental, cell cycle and apoptosis genes and decreased expression of differentiated epithelial features. Transcripts reflecting this injury-repair response were the best correlates of functional disturbance and risk of future graft loss. Late biopsies with atrophy-fibrosis, reflecting their cumulative burden of injury, displayed more transcripts for B cells, plasma cells and mast cells. Thus the molecular phenotype is best described in terms of three elements: specific diseases, including rejection; the injury-repair response and the cumulative burden of injury.
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Affiliation(s)
- P F Halloran
- Department of Medicine, Division of Nephrology & Immunology, University of Alberta, Edmonton, Canada.
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39
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Park WD, Griffin MD, Cornell LD, Cosio FG, Stegall MD. Fibrosis with inflammation at one year predicts transplant functional decline. J Am Soc Nephrol 2010; 21:1987-97. [PMID: 20813870 DOI: 10.1681/asn.2010010049] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Lack of knowledge regarding specific causes for late loss of kidney transplants hampers improvements in long-term allograft survival. Kidney transplants with both interstitial fibrosis and subclinical inflammation but not fibrosis alone after 1 year have reduced survival. This study tested whether fibrosis with inflammation at 1 year associates with decline of renal function in a low-risk cohort and characterized the nature of the inflammation. We studied 151 living-donor, tacrolimus/mycophenolate-treated recipients without overt risk factors for reduced graft survival. Transplants with normal histology (n = 86) or fibrosis alone (n = 45) on 1-year protocol biopsy had stable renal function between 1 and 5 years, whereas those with both fibrosis and inflammation (n = 20) exhibited a decline in GFR and reduced graft survival. Immunohistochemistry confirmed increased interstitial T cells and macrophages/dendritic cells in the group with both fibrosis and inflammation, and there was increased expression of transcripts related to innate and cognate immunity. Pathway- and pathologic process-specific analyses of microarray profiles revealed that potentially damaging immunologic activities were enriched among the overexpressed transcripts (e.g., Toll-like receptor signaling, antigen presentation/dendritic cell maturation, IFN-γ-inducible response, cytotoxic T lymphocyte-associated and acute rejection-associated genes). Therefore, the combination of fibrosis and inflammation in 1-year protocol biopsies associates with reduced graft function and survival as well as a rejection-like gene expression signature, even among recipients with no clinical risk factors for poor outcomes. Early interventions aimed at altering rejection-like inflammation may improve long-term survival of kidney allografts.
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Affiliation(s)
- Walter D Park
- Department of Surgery, Division of Transplantation Surgery, Mayo Clinic, Rochester, Minnesota, USA
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40
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Mengel M, Sis B, Kim D, Chang J, Famulski KS, Hidalgo LG, Einecke G, de Freitas DG, Tymchak W, Burton J, Halloran PF. The molecular phenotype of heart transplant biopsies: relationship to histopathological and clinical variables. Am J Transplant 2010; 10:2105-15. [PMID: 20883545 DOI: 10.1111/j.1600-6143.2010.03182.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Histopathology of endomyocardial biopsies (EMB) is the standard rejection surveillance for heart transplants. However, ISHLT consensus criteria for interpreting biopsies are arbitrarily defined. Gene expression offers an independent re-evaluation of existing diagnostic systems. We performed histologic and microarray analysis on 105 EMB from 45 heart allograft recipients. Histologic lesions, diagnosis and transcripts were compared to one another, time posttransplantation, indication for biopsy and left ventricular ejection fraction (LVEF). Histologic lesions presented in two groups: myocyte-interstitial and microcirculation lesions. Expression of transcript sets reflecting T cell and macrophage infiltration, and γ-interferon effects correlated strongly with each other and with transcripts indicating tissue/myocardium injury. This molecular phenotype correlated with Quilty (p < 0.005), microcirculation lesions (p < 0.05) and decreased LVEF (p < 0.007), but not with the histologic diagnosis of rejection. In multivariate analysis, LVEF was associated (p < 0.03) with γ-interferon inducible transcripts, time posttransplantation, ischemic injury and clinically indicated biopsies, but not the diagnosis of rejection. The results indicate that (a) the current ISHLT system for diagnosing rejection does not reflect the molecular phenotype in EMB and lacks clinical relevance; (b) the interpretation of Quilty lesions has to be revisited; (c) the assessment of molecules in heart biopsy can guide improvements of current diagnostics.
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Affiliation(s)
- M Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
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41
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Bosco A, Ehteshami S, Stern DA, Martinez FD. Decreased activation of inflammatory networks during acute asthma exacerbations is associated with chronic airflow obstruction. Mucosal Immunol 2010; 3:399-409. [PMID: 20336062 PMCID: PMC2891355 DOI: 10.1038/mi.2010.13] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Asthma exacerbations are associated with subsequent deficits in lung function. Here, we tested the hypothesis that a specific pattern of inflammatory responses during acute exacerbations may be associated with chronic airway obstruction. Gene coexpression networks were characterized in induced sputum obtained during an acute exacerbation, from asthmatic children with or without chronic airflow limitation. The data showed that activation of Th1-like/cytotoxic and interferon signaling pathways during acute exacerbations was decreased in asthmatic children with deficits in baseline lung function. These associations were independent of the identification of picornaviruses in nasal secretions or the use of medications at the time of the exacerbation. Th2-related pathways were also detected in the responses, but variations in these pathways were not related to chronic airways obstruction. Our findings show that decreased activation of Th1-like/cytotoxic and interferon pathways is a hallmark of acute exacerbation responses in asthmatic children with evidence of chronic airways obstruction.
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Affiliation(s)
- Anthony Bosco
- Arizona Respiratory Center, College of Medicine, and BIO5 Institute, University of Arizona
| | - Samira Ehteshami
- Arizona Respiratory Center, College of Medicine, and BIO5 Institute, University of Arizona
| | - Debra A. Stern
- Arizona Respiratory Center, College of Medicine, and BIO5 Institute, University of Arizona
| | - Fernando D. Martinez
- Arizona Respiratory Center, College of Medicine, and BIO5 Institute, University of Arizona
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42
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Einecke G, Reeve J, Sis B, Mengel M, Hidalgo L, Famulski KS, Matas A, Kasiske B, Kaplan B, Halloran PF. A molecular classifier for predicting future graft loss in late kidney transplant biopsies. J Clin Invest 2010; 120:1862-72. [PMID: 20501945 DOI: 10.1172/jci41789] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 04/26/2010] [Indexed: 01/05/2023] Open
Abstract
Kidney transplant recipients that develop signs of renal dysfunction or proteinuria one or more years after transplantation are at considerable risk for progression to renal failure. To assess the kidney at this time, a "for-cause" biopsy is performed, but this provides little indication as to which recipients will go on to organ failure. In an attempt to identify molecules that could provide this information, we used microarrays to analyze gene expression in 105 for-cause biopsies taken between 1 and 31 years after transplantation. Using supervised principal components analysis, we derived a molecular classifier to predict graft loss. The genes associated with graft failure were related to tissue injury, epithelial dedifferentiation, matrix remodeling, and TGF-beta effects and showed little overlap with rejection-associated genes. We assigned a prognostic molecular risk score to each patient, identifying those at high or low risk for graft loss. The molecular risk score was correlated with interstitial fibrosis, tubular atrophy, tubulitis, interstitial inflammation, proteinuria, and glomerular filtration rate. In multivariate analysis, molecular risk score, peritubular capillary basement membrane multilayering, arteriolar hyalinosis, and proteinuria were independent predictors of graft loss. In an independent validation set, the molecular risk score was the only predictor of graft loss. Thus, the molecular risk score reflects active injury and is superior to either scarring or function in predicting graft failure.
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Affiliation(s)
- Gunilla Einecke
- Alberta Transplant Applied Genomics Centre, University of Alberta, Edmonton, Alberta, Canada
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43
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Abstract
In kidney allografts, T cell mediated rejection (TCMR) is characterized by infiltration of the interstitium by T cells and macrophages, intense IFNG and TGFB effects, and epithelial deterioration. Recent experimental and clinical studies provide the basis for a provisional model for TCMR. The model proposes that the major unit of cognate recognition in TCMR is effector T cells engaging donor antigen on macrophages. This event creates the inflammatory compartment that recruits effector and effector memory CD4 and CD8 T cells, both cognate and noncognate, and macrophage precursors. Cognate T cells cross the donor microcirculation to enter the interstitium but spare the microcirculation. Local inflammation triggers dedifferentiation of the adjacent epithelium (e.g. loss of transporters and expression of embryonic genes) rather than cell death, via mechanisms that do not require known T-cell cytotoxic mechanisms or direct contact of T cells with the epithelium. Local epithelial changes trigger a response of the entire nephron and a second wave of dedifferentiation. The dedifferentiated epithelium is unable to exclude T cells, which enter to produce tubulitis lesions. Thus TCMR is a cognate recognition-based process that creates local inflammation and epithelial dedifferentiation, stereotyped nephron responses, and tubulitis, and if untreated causes irreversible nephron loss.
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Affiliation(s)
- P F Halloran
- Department of Medicine, Division of Nephrology and Immunology, Alberta Transplant Applied Genomics Centre, University of Alberta, Edmonton, Canada.
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44
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Famulski KS, Einecke G, Sis B, Mengel M, Hidalgo LG, Kaplan B, Halloran PF. Defining the canonical form of T-cell-mediated rejection in human kidney transplants. Am J Transplant 2010; 10:810-820. [PMID: 20132168 DOI: 10.1111/j.1600-6143.2009.03007.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Banff defines T-cell-mediated rejection (TCMR) using nonspecific lesions and arbitrary cutoffs, with no external gold standard. We reexamined features of TCMR using exclusively molecular definition independent of histopathology. The definition was derived from mouse kidney transplants with fully developed TCMR, and is based on high expression of transcripts reflecting IFNG effects and alternative macrophage activation. In 234 human kidney transplant biopsies for cause phenotyped by microarrays, we identified 26 biopsies meeting these criteria. After excluding three biopsies with unrelated diseases, all 23 biopsies had typical Banff lesions of TCMR (inflammation, tubulitis), with v lesions in 10/23. Banff histopathology diagnosed 18 as TCMR, 1 as mixed and 4 as borderline. Despite marked changes in transcriptome indicating tissue injury and dedifferentiation, all kidneys with molecularly defined TCMR, even with v lesions or late rejection, demonstrated excellent recovery of function at 6 months with no graft loss (mean follow-up 2.5 years). Thus TCMR defined exclusively by molecules manifests TCMR-related lesions and function impairment, but good recovery and survival, even with late rejection or arteritis. This combination of pathologic, clinical and molecular features constitutes the typical or canonical T-cell-mediated rejection.
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Affiliation(s)
- K S Famulski
- Alberta Transplant Applied Genomics Centre, Division of Nephrology and Transplant Immunology, Department of Medicine.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - G Einecke
- Alberta Transplant Applied Genomics Centre, Division of Nephrology and Transplant Immunology, Department of Medicine.,Department of Nephrology, Hannover Medical School, Germany
| | - B Sis
- Alberta Transplant Applied Genomics Centre, Division of Nephrology and Transplant Immunology, Department of Medicine.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - M Mengel
- Alberta Transplant Applied Genomics Centre, Division of Nephrology and Transplant Immunology, Department of Medicine.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - L G Hidalgo
- Alberta Transplant Applied Genomics Centre, Division of Nephrology and Transplant Immunology, Department of Medicine.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - B Kaplan
- Department of Pharmacology, University of Arizona, Tucson, AZ
| | - P F Halloran
- Alberta Transplant Applied Genomics Centre, Division of Nephrology and Transplant Immunology, Department of Medicine
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Juan Alberto Fierro C. Monitoreo inmunológico: el comienzo de una nueva era en trasplantes. REVISTA MÉDICA CLÍNICA LAS CONDES 2010. [DOI: 10.1016/s0716-8640(10)70529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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46
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Endothelial transcripts uncover a previously unknown phenotype: C4d-negative antibody-mediated rejection. Curr Opin Organ Transplant 2010; 15:42-8. [DOI: 10.1097/mot.0b013e3283352a50] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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47
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48
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Sis B, Jhangri GS, Bunnag S, Allanach K, Kaplan B, Halloran PF. Endothelial gene expression in kidney transplants with alloantibody indicates antibody-mediated damage despite lack of C4d staining. Am J Transplant 2009; 9:2312-23. [PMID: 19681822 DOI: 10.1111/j.1600-6143.2009.02761.x] [Citation(s) in RCA: 366] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Anti-HLA alloantibody is a risk factor for graft loss, but does not indicate which kidneys are experiencing antibody-mediated rejection (ABMR). C4d staining in biopsies is specific for ABMR but insensitive. We hypothesized that altered expression of endothelial genes due to alloantibody acting on the microcirculation would be sensitive indicator of ABMR. We identified 119 endothelial-associated transcripts (ENDATs) from literature, and studied their expression by microarrays in 173 renal allograft biopsies for cause. Mean ENDAT expression was increased in all rejection but was higher in ABMR than in T-cell-mediated rejection and correlated with histopathologic lesions of ABMR, and alloantibody. Many individual ENDATs were increased in ABMR and predicted graft loss. Kidneys with high ENDATs and antibody showed increased lesions of ABMR and worse prognosis in comparison to controls. Only 40% of kidneys with high ENDAT expression and chronic ABMR or graft loss were diagnosed by C4d positivity. High ENDAT expression with antibody predicts graft loss with higher sensitivity (77% vs. 31%) and slightly lower specificity (71% vs. 94%) than C4d. The results were validated in independent set of 82 kidneys. High renal endothelial transcript expression in patients with alloantibody is indicator of active antibody-mediated allograft damage and poor graft outcome.
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Affiliation(s)
- Banu Sis
- Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
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49
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Mengel M, Reeve J, Bunnag S, Einecke G, Jhangri GS, Sis B, Famulski K, Guembes-Hidalgo L, Halloran PF. Scoring total inflammation is superior to the current Banff inflammation score in predicting outcome and the degree of molecular disturbance in renal allografts. Am J Transplant 2009; 9:1859-67. [PMID: 19563338 DOI: 10.1111/j.1600-6143.2009.02727.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Emerging molecular analysis can be used as an objective and independent assessment of histopathological scoring systems. We compared the existing Banff i-score to the total inflammation (total i-) score for assessing the molecular phenotype in 129 renal allograft biopsies for cause. The total i-score showed stronger correlations with microarray-based gene sets representing major biological processes during allograft rejection. Receiver operating characteristic curves showed that total-i was superior (areas under the curves 0.85 vs. 0.73 for Banff i-score, p = 0.012) at assessing an abnormal cytotoxic T-cell burden, because it identified molecular disturbances in biopsies with advanced scarring. The total-i score was also a better predictor of graft survival than the Banff i-score and essentially all current diagnostic Banff categories. The exception was antibody-mediated rejection which is able to predict graft loss with greater specificity (96%) but at low sensitivity (38%) due to the fact that it only applies to cases with this diagnosis. The total i-score is able to achieve moderate sensitivities (60-80%) with losses in specificity (60-80%) across the whole population. Thus, the total i-score is superior to the current Banff i-score and most diagnostic Banff categories in predicting outcome and assessing the molecular phenotype of renal allografts.
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Affiliation(s)
- M Mengel
- Department of Laboratory Medicine and Pathology, Alberta Transplant Applied Genomics Centre, Canada.
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50
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Reeve J, Einecke G, Mengel M, Sis B, Kayser N, Kaplan B, Halloran PF. Diagnosing rejection in renal transplants: a comparison of molecular- and histopathology-based approaches. Am J Transplant 2009; 9:1802-10. [PMID: 19519809 DOI: 10.1111/j.1600-6143.2009.02694.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The transcriptome has considerable potential for improving biopsy diagnoses. However, to realize this potential the relationship between the molecular phenotype of disease and histopathology must be established. We assessed 186 consecutive clinically indicated kidney transplant biopsies using microarrays, and built a classifier to distinguish rejection from nonrejection using predictive analysis of microarrays (PAM). Most genes selected by PAM were interferon-gamma-inducible or cytotoxic T-cell associated, for example, CXCL9, CXCL11, GBP1 and INDO. We then compared the PAM diagnoses to those from histopathology, which are based on the Banff diagnostic criteria. Disagreement occurred in approximately 20% of diagnoses, principally because of idiosyncratic limitations in the histopathology scoring system. The problematic diagnosis of 'borderline rejection' was resolved by PAM into two distinct classes, rejection and nonrejection. The diagnostic discrepancies between Banff and PAM in these cases were largely due to the Banff system's requirement for a tubulitis threshold in defining rejection. By examining the discrepancies between gene expression and histopathology, we provide external validation of the main features of the histopathology diagnostic criteria (the Banff consensus system), recommend improvements and outline a pathway for introducing molecular measurements.
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Affiliation(s)
- J Reeve
- Department of Laboratory Medicine and Pathology, Arizona Health Science Centre, University of Arizona, Tucson, AZ, USA
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