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Alam A, Van Zyl J, Paul Milligan G, Michelle McKean S, Patel R, Anne Hall S. Evolving the surveillance and workup of heart transplant rejection: A real-world analysis of the Molecular Microscope Diagnostic System. Am J Transplant 2022; 22:2443-2450. [PMID: 35514138 DOI: 10.1111/ajt.17087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 01/25/2023]
Abstract
The Molecular Microscope Diagnostic System (MMDx) analyzes RNA transcripts of transplanted heart tissue to differentiate among T cell-mediated rejection (TCMR), antibody-mediated rejection (AMR), injury, and healthy tissue. However, little is known about its performance in relation to other modalities in a real-world heart transplant population. We evaluated whether MMDx performs in agreement with other validated modalities. Two hundred and twenty-eight corresponding endomyocardial biopsies (EMBx) and MMDx specimens from 135 adult heart transplant patients were retrospectively reviewed with correlating donor-derived cell-free DNA (dd-cfDNA). Rejection was classified on EMBx in 29 specimens (TCMR ≥ 2R and/or AMR ≥ 1), on MMDx in 56 specimens, and in 74 values with dd-cfDNA ≥0.20%. Despite moderate agreement between EMBx and MMDx (84% agreement, Cohen's kappa, 0.48, p < .001), systematic differences were observed (McNemar's test, p < .001) where MMDx classified 32 of 37 discordant cases as rejection. MMDx and dd-cfDNA demonstrated slight agreement (72% agreement, Cohen's kappa, 0.39, p < .001); however, systematic differences were also apparent where MMDx classified 12 of 50 discordant specimens as rejection when dd-cfDNA was <0.20% (McNemar's test, p < .001). Our findings provide insight on the performance of MMDx relative to other modalities in a heart transplant cohort and have implications on the surveillance and workup of allograft rejection in heart transplantation.
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Affiliation(s)
- Amit Alam
- Division of Advanced Heart Failure, Baylor University Medical Center, Dallas, Texas, USA.,Texas A&M University College of Medicine, Bryan, Texas, USA
| | - Johanna Van Zyl
- Division of Advanced Heart Failure, Baylor University Medical Center, Dallas, Texas, USA.,Texas A&M University College of Medicine, Bryan, Texas, USA
| | - Gregory Paul Milligan
- Division of Advanced Heart Failure, Baylor University Medical Center, Dallas, Texas, USA
| | - Staci Michelle McKean
- Division of Advanced Heart Failure, Baylor University Medical Center, Dallas, Texas, USA
| | - Raksha Patel
- Division of Advanced Heart Failure, Baylor University Medical Center, Dallas, Texas, USA
| | - Shelley Anne Hall
- Division of Advanced Heart Failure, Baylor University Medical Center, Dallas, Texas, USA.,Texas A&M University College of Medicine, Bryan, Texas, USA
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2
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Halloran PF, Madill‐Thomsen KS, Pon S, Sikosana MLN, Böhmig GA, Bromberg J, Einecke G, Eskandary F, Gupta G, Hidalgo LG, Myslak M, Viklicky O, Perkowska‐Ptasinska A. Molecular diagnosis of ABMR with or without donor-specific antibody in kidney transplant biopsies: Differences in timing and intensity but similar mechanisms and outcomes. Am J Transplant 2022; 22:1976-1991. [PMID: 35575435 PMCID: PMC9540308 DOI: 10.1111/ajt.17092] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We studied the clinical, histologic, and molecular features distinguishing DSA-negative from DSA-positive molecularly defined antibody-mediated rejection (mABMR). We analyzed mABMR biopsies with available DSA assessments from the INTERCOMEX study: 148 DSA-negative versus 248 DSA-positive, compared with 864 no rejection (excluding TCMR and Mixed). DSA-positivity varied with mABMR stage: early-stage (EABMR) 56%; fully developed (FABMR) 70%; and late-stage (LABMR) 58%. DSA-negative patients with mABMR were usually sensitized, 60% being HLA antibody-positive. Compared with DSA-positive mABMR, DSA-negative mABMR was more often C4d-negative; earlier by 1.5 years (average 2.4 vs. 3.9 years); and had lower ABMR activity and earlier stage in molecular and histology features. However, the top ABMR-associated transcripts were identical in DSA-negative versus DSA-positive mABMR, for example, NK-associated (e.g., KLRD1 and GZMB) and IFNG-inducible (e.g., PLA1A). Genome-wide class comparison between DSA-negative and DSA-positive mABMR showed no significant differences in transcript expression except those related to lower intensity and earlier time of DSA-negative ABMR. Three-year graft loss in DSA-negative mABMR was the same as DSA-positive mABMR, even after adjusting for ABMR stage. Thus, compared with DSA-positive mABMR, DSA-negative mABMR is on average earlier, less active, and more often C4d-negative but has similar graft loss, and genome-wide analysis suggests that it involves the same mechanisms. SUMMARY SENTENCE: In 398 kidney transplant biopsies with molecular antibody-mediated rejection, the 150 DSA-negative cases are earlier, less intense, and mostly C4d-negative, but use identical molecular mechanisms and have the same risk of graft loss as the 248 DSA-positive cases.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics CentreEdmontonAlbertaCanada,Department of Medicine, Division of Nephrology and Transplant ImmunologyUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Shane Pon
- Alberta Transplant Applied Genomics CentreEdmontonAlbertaCanada
| | | | - Georg A. Böhmig
- Division of Nephrology and Dialysis, Department of Medicine IIIMedical University of ViennaViennaAustria
| | | | - Gunilla Einecke
- Department of NephrologyHannover Medical SchoolHannoverGermany
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine IIIMedical University of ViennaViennaAustria
| | - Gaurav Gupta
- Division of NephrologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | | | - Marek Myslak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation SPWSZ HospitalPomeranian Medical UniversitySzczecinPoland
| | - Ondrej Viklicky
- Department of Nephrology and Transplant CenterInstitute for Clinical and Experimental MedicinePragueCzech Republic
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3
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Greenland JR, McDyer JF. Molecular diagnostics for CLAD: When and where? Am J Transplant 2022; 22:1012-1013. [PMID: 34910363 PMCID: PMC8983448 DOI: 10.1111/ajt.16925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/01/2021] [Accepted: 12/13/2021] [Indexed: 01/25/2023]
Affiliation(s)
- John R Greenland
- University of California, San Francisco, CA; San Francisco VA Health Care System
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4
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Madill-Thomsen KS, Abouljoud M, Bhati C, Ciszek M, Durlik M, Feng S, Foroncewicz B, Francis I, Grąt M, Jurczyk K, Klintmalm G, Krasnodębski M, McCaughan G, Miquel R, Montano-Loza A, Moonka D, Mucha K, Myślak M, Pączek L, Perkowska-Ptasińska A, Piecha G, Reichman T, Sanchez-Fueyo A, Tronina O, Wawrzynowicz-Syczewska M, Więcek A, Zieniewicz K, Halloran PF. The molecular phenotypes of injury, steatohepatitis, and fibrosis in liver transplant biopsies in the INTERLIVER study. Am J Transplant 2022; 22:909-926. [PMID: 34780106 DOI: 10.1111/ajt.16890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 01/25/2023]
Abstract
To extend previous molecular analyses of rejection in liver transplant biopsies in the INTERLIVER study (ClinicalTrials.gov #NCT03193151), the present study aimed to define the gene expression selective for parenchymal injury, fibrosis, and steatohepatitis. We analyzed genome-wide microarray measurements from 337 liver transplant biopsies from 13 centers. We examined expression of genes previously annotated as increased in injury and fibrosis using principal component analysis (PCA). PC1 reflected parenchymal injury and related inflammation in the early posttransplant period, slowly regressing over many months. PC2 separated early injury from late fibrosis. Positive PC3 identified a distinct mildly inflamed state correlating with histologic steatohepatitis. Injury PCs correlated with liver function and histologic abnormalities. A classifier trained on histologic steatohepatitis predicted histologic steatohepatitis with cross-validated AUC = 0.83, and was associated with pathways reflecting metabolic abnormalities distinct from fibrosis. PC2 predicted histologic fibrosis (AUC = 0.80), as did a molecular fibrosis classifier (AUC = 0.74). The fibrosis classifier correlated with matrix remodeling pathways with minimal overlap with those selective for steatohepatitis, although some biopsies had both. Genome-wide assessment of liver transplant biopsies can not only detect molecular changes induced by rejection but also those correlating with parenchymal injury, steatohepatitis, and fibrosis, offering potential insights into disease mechanisms for primary diseases.
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Affiliation(s)
| | | | - Chandra Bhati
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Michał Ciszek
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Durlik
- Department of Transplant Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sandy Feng
- University of California San Francisco, San Francisco, California, USA
| | - Bartosz Foroncewicz
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Michał Grąt
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Jurczyk
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University, Szczecin, Poland
| | | | - Maciej Krasnodębski
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Geoff McCaughan
- Centenary Research Institute, Australian National Liver Transplant Unit, Royal Prince Alfred Hospital, The University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Myślak
- Department of Clinical Interventions, Department of Nephrology and Kidney Transplantation SPWSZ Hospital, Pomeranian Medical University, Szczecin, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Grzegorz Piecha
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, Katowice, Poland
| | | | | | - Olga Tronina
- Department of Transplant Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marta Wawrzynowicz-Syczewska
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University, Szczecin, Poland
| | - Andrzej Więcek
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, Katowice, Poland
| | - Krzysztof Zieniewicz
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
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5
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Li Y, Nieuwenhuis LM, Voskuil MD, Gacesa R, Hu S, Jansen BH, Venema WTU, Hepkema BG, Blokzijl H, Verkade HJ, Lisman T, Weersma RK, Porte RJ, Festen EAM, de Meijer VE. Donor genetic variants as risk factors for thrombosis after liver transplantation: A genome-wide association study. Am J Transplant 2021; 21:3133-3147. [PMID: 33445220 PMCID: PMC8518362 DOI: 10.1111/ajt.16490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 01/25/2023]
Abstract
Thrombosis after liver transplantation substantially impairs graft- and patient survival. Inevitably, heritable disorders of coagulation originating in the donor liver are transmitted by transplantation. We hypothesized that genetic variants in donor thrombophilia genes are associated with increased risk of posttransplant thrombosis. We genotyped 775 donors for adult recipients and 310 donors for pediatric recipients transplanted between 1993 and 2018. We determined the association between known donor thrombophilia gene variants and recipient posttransplant thrombosis. In addition, we performed a genome-wide association study (GWAS) and meta-analyzed 1085 liver transplantations. In our donor cohort, known thrombosis risk loci were not associated with posttransplant thrombosis, suggesting that it is unnecessary to exclude liver donors based on thrombosis-susceptible polymorphisms. By performing a meta-GWAS from children and adults, we identified 280 variants in 55 loci at suggestive genetic significance threshold. Downstream prioritization strategies identified biologically plausible candidate genes, among which were AK4 (rs11208611-T, p = 4.22 × 10-05 ) which encodes a protein that regulates cellular ATP levels and concurrent activation of AMPK and mTOR, and RGS5 (rs10917696-C, p = 2.62 × 10-05 ) which is involved in vascular development. We provide evidence that common genetic variants in the donor, but not previously known thrombophilia-related variants, are associated with increased risk of thrombosis after liver transplantation.
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Affiliation(s)
- Yanni Li
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands,Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Lianne M. Nieuwenhuis
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Michiel D. Voskuil
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Shixian Hu
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Bernadien H. Jansen
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Werna T. U. Venema
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Bouke G. Hepkema
- Department of Laboratory MedicineUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Henkjan J. Verkade
- Department of Pediatric Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Ton Lisman
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Robert J. Porte
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Eleonora A. M. Festen
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands,Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
| | - Vincent E. de Meijer
- Department of SurgerySection of Hepatobiliary Surgery and Liver TransplantationUniversity of GroningenUniversity Medical Center GroningenGroningenthe Netherlands
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6
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Halloran PF, Böhmig GA, Bromberg JS, Budde K, Gupta G, Einecke G, Eskandary F, Madill-Thomsen K, Reeve J. Discovering novel injury features in kidney transplant biopsies associated with TCMR and donor aging. Am J Transplant 2021; 21:1725-1739. [PMID: 33107191 DOI: 10.1111/ajt.16374] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/27/2020] [Accepted: 10/19/2020] [Indexed: 01/25/2023]
Abstract
We previously characterized the molecular changes in acute kidney injury (AKI) and chronic kidney disease (CKD) in kidney transplant biopsies, but parenchymal changes selective for specific types of injury could be missed by such analyses. The present study searched for injury changes beyond AKI and CKD related to specific scenarios, including correlations with donor age. We defined injury using previously defined gene sets and classifiers and used principal component analysis to discover new injury dimensions. As expected, Dimension 1 distinguished normal vs. injury, and Dimension 2 separated early AKI from late CKD, correlating with time posttransplant. However, Dimension 3 was novel, distinguishing a set of genes related to epithelial polarity (e.g., PARD3) that were increased in early AKI and decreased in T cell-mediated rejection (TCMR) but not in antibody-mediated rejection. Dimension 3 was increased in kidneys from older donors and was particularly important in survival of early kidneys. Thus high Dimension 3 scores emerge as a previously unknown element in the kidney response-to-injury that affects epithelial polarity genes and is increased in AKI but depressed in TCMR, indicating that in addition to general injury elements, certain injury elements are selective for specific pathologic mechanisms. (ClinicalTrials.gov NCT01299168).
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada.,Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Klemens Budde
- Charite-Medical University of Berlin, Berlin, Germany
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia
| | | | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
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7
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Guerrero-Miranda CY, Hall SA. Rethinking the future with evolving technology: It's time to empower change in heart transplantation. Am J Transplant 2021; 21:453-455. [PMID: 32717109 DOI: 10.1111/ajt.16221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 01/25/2023]
Affiliation(s)
- Cesar Y Guerrero-Miranda
- Annette C. and Harold C. Simmons Transplant Institute, Baylor Scott & White Research Institute, Dallas, Texas, USA.,Center for Advanced Heart and Lung Disease, Baylor University Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, Texas A&M Health Science Center, Dallas, Texas, USA
| | - Shelley A Hall
- Annette C. and Harold C. Simmons Transplant Institute, Baylor Scott & White Research Institute, Dallas, Texas, USA.,Center for Advanced Heart and Lung Disease, Baylor University Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, Texas A&M Health Science Center, Dallas, Texas, USA
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8
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Halloran PF, Madill-Thomsen KS. The Molecular Microscope ® Diagnostic System meets eminence-based medicine: A clinician's perspective. Am J Transplant 2020; 20:2964-2965. [PMID: 32337824 DOI: 10.1111/ajt.15940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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9
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Zou D, Dai Y, Zhang X, Wang G, Xiao X, Jia P, Li XC, Guo Z, Chen W. T cell exhaustion is associated with antigen abundance and promotes transplant acceptance. Am J Transplant 2020; 20:2540-2550. [PMID: 32185888 PMCID: PMC8000649 DOI: 10.1111/ajt.15870] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/19/2020] [Accepted: 03/05/2020] [Indexed: 01/25/2023]
Abstract
Exhaustion of T cells limits their ability to clear chronic infections or eradicate tumors. Here, in the context of transplant, we investigated whether T cell exhaustion occurs and has a role in determining transplant outcome. A peptide/MHC tetramer-based approach was used to track exhausted CD8+ T cells in a male-to-female skin transplant model. Transplant of large whole-tail skins, but not small tail skins (0.8 cm × 0.8 cm), led to exhaustion of anti-male tetramer+ CD8+ T cells and subsequently the acceptance of skin grafts. To study CD4+ T cell exhaustion, we used the TCR-transgenic B6 TEa cells that recognize a major transplant antigen I-Eα from Balb/c mice. TEa cells were adoptively transferred either into B6 recipients that received Balb/c donor skins or into CB6F1 mice that contained an excessive amount of I-Eα antigen. Adoptively transferred TEa cells in skin-graft recipients were not exhausted. By contrast, virtually all adoptively transferred TEa cells were exhausted in CB6F1 mice. Those exhausted TEa cells lost ability to reject Balb/c skins upon further transfer into lymphopenic B6.Rag1-/- mice. Hence, T cell exhaustion develops in the presence of abundant antigen and promotes transplant acceptance. These findings are essential for better understanding the nature of transplant tolerance.
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Affiliation(s)
- Dawei Zou
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodis Hospital, Houston, Texas,Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Xiaolong Zhang
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodis Hospital, Houston, Texas
| | - Guohua Wang
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodis Hospital, Houston, Texas
| | - Xiang Xiao
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodis Hospital, Houston, Texas
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Xian C. Li
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodis Hospital, Houston, Texas,Department of Surgery, Weill Cornell Medicine, Cornell University, New York, New York
| | - Zhiyong Guo
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenhao Chen
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodis Hospital, Houston, Texas,Department of Surgery, Weill Cornell Medicine, Cornell University, New York, New York
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Madill-Thomsen K, Perkowska-Ptasińska A, Böhmig GA, Eskandary F, Einecke G, Gupta G, Halloran PF. Discrepancy analysis comparing molecular and histology diagnoses in kidney transplant biopsies. Am J Transplant 2020; 20:1341-1350. [PMID: 31846554 DOI: 10.1111/ajt.15752] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 01/25/2023]
Abstract
Discrepancy analysis comparing two diagnostic platforms offers potential insights into both without assuming either is always correct. Having optimized the Molecular Microscope Diagnostic System (MMDx) in renal transplant biopsies, we studied discrepancies within MMDx (reports and sign-out comments) and between MMDx and histology. Interpathologist discrepancies have been documented previously and were not assessed. Discrepancy cases were classified as "clear" (eg, antibody-mediated rejection [ABMR] vs T cell-mediated rejection [TCMR]), "boundary" (eg, ABMR vs possible ABMR), or "mixed" (eg, Mixed vs ABMR). MMDx report scores showed 99% correlations; sign-out interpretations showed 7% variation between observers, all located around boundaries. Histology disagreed with MMDx in 37% of biopsies, including 315 clear discrepancies, all with implications for therapy. Discrepancies were distributed widely in all histology diagnoses but increased in some scenarios; for example, histology TCMR contained 14% MMDx ABMR and 20% MMDx no rejection. MMDx usually gave unambiguous diagnoses in cases with ambiguous histology, for example, borderline and transplant glomerulopathy. Histology lesions or features associated with more frequent discrepancies (eg, tubulitis, arteritis, and polyomavirus nephropathy) were not associated with increased MMDx uncertainty, indicating that MMDx can clarify biopsies with histologic ambiguity. The patterns of histology-MMDx discrepancies highlight specific histology diagnoses in which MMDx assessment should be considered for guiding therapy.
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Affiliation(s)
- Katelynn Madill-Thomsen
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gunilla Einecke
- Department of Nephrology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia
| | - Philip F Halloran
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada.,Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
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12
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Halloran K, Parkes MD, Timofte IL, Snell GI, Westall GP, Hachem R, Kreisel D, Levine D, Juvet S, Keshavjee S, Jaksch P, Klepetko W, Hirji A, Weinkauf J, Halloran PF. Molecular phenotyping of rejection-related changes in mucosal biopsies from lung transplants. Am J Transplant 2020; 20:954-966. [PMID: 31679176 DOI: 10.1111/ajt.15685] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/06/2019] [Accepted: 10/21/2019] [Indexed: 01/25/2023]
Abstract
Diagnosing lung transplant rejection currently depends on histologic assessment of transbronchial biopsies (TBB) with limited reproducibility and considerable risk of complications. Mucosal biopsies are safer but not histologically interpretable. Microarray-based diagnostic systems for TBBs and other transplants suggest such systems could assess mucosal biopsies as well. We studied 243 mucosal biopsies from the third bronchial bifurcation (3BMBs) collected from seven centers and classified them using unsupervised machine learning algorithms. Using the expression of a set of rejection-associated transcripts annotated in kidneys and validated in hearts and lung transplant TBBs, the algorithms identified and scored major rejection and injury-related phenotypes in 3BMBs without need for labeled training data. No rejection or injury, rejection, late inflammation, and recent injury phenotypes were thus scored in new 3BMBs. The rejection phenotype correlated with IFNG-inducible transcripts, the hallmarks of rejection. Progressive atrophy-related changes reflected by the late inflammation phenotype in 3BMBs suggest widespread time-dependent airway deterioration, which was especially pronounced after two years posttransplant. Thus molecular assessment of 3BMBs can detect rejection in a previously unusable biopsy format with potential utility in patients with severe lung dysfunction where TBB is not possible and provide unique insights into airway deterioration. ClinicalTrials.gov NCT02812290.
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Affiliation(s)
- Kieran Halloran
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Michael D Parkes
- Alberta Transplant Applied Genomics Center, Edmonton, Alberta, Canada
| | - Irina L Timofte
- Division of Pulmonary and Critical Care, Department of Medicine, University of Maryland, Baltimore, Maryland
| | - Gregory I Snell
- Lung Transplant Service, Alfred Hospital, Monash University, Melbourne, Victoria, Australia
| | - Glen P Westall
- Lung Transplant Service, Alfred Hospital, Monash University, Melbourne, Victoria, Australia
| | - Ramsey Hachem
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel Kreisel
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | | | - Stephen Juvet
- Toronto Lung Transplant Program, University of Toronto, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Toronto Lung Transplant Program, University of Toronto, Toronto, Ontario, Canada
| | - Peter Jaksch
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Walter Klepetko
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Alim Hirji
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Justin Weinkauf
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Philip F Halloran
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Alberta Transplant Applied Genomics Center, Edmonton, Alberta, Canada
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13
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Ventura CG, Whisenant T, Gelbart T, David DS, Agena F, Salomon DR, David-Neto E, Kurian SM. Discovery and cross-validation of peripheral blood and renal biopsy gene expression signatures from ethnically diverse kidney transplant populations. Am J Transplant 2019; 19:3356-3366. [PMID: 31152474 PMCID: PMC6883121 DOI: 10.1111/ajt.15482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/15/2019] [Accepted: 05/04/2019] [Indexed: 01/25/2023]
Abstract
We determined peripheral blood (PB) and biopsy (Bx) RNA expression signatures in a Brazilian and US cohort of kidney transplant patients. Phenotypes assigned by precise histology were: acute rejection (AR), interstitial fibrosis/tubular atrophy/chronic rejection (CR), excellent functioning transplants (TX), and glomerulonephritis recurrence (GN). Samples were analyzed on microarrays and profiles from each cohort were cross-validated on the other cohort with similar phenotypes. We discovered signatures for each tissue: (1) AR vs TX, (2) CR vs TX, and (3) GN vs TX using the Random Forests algorithm. We validated biopsies signatures of AR vs TX (area under the curve [AUC] 0.97) and CR vs TX (AUC 0.87). We also validated both PB and Bx signatures of AR vs TX and CR vs TX with varying degrees of accuracy. Several biological pathways were shared between AR and CR, suggesting similar rejection mechanisms in these 2 clinical phenotypes. Thus, we identified gene expression signatures for AR and CR in transplant patients and validated them in independent cohorts of significantly different racial/ethnic backgrounds. These results reveal that there are strong unifying immune mechanisms driving transplant diseases and identified in the signatures discovered in each cohort, suggesting that molecular diagnostics across populations are feasible despite ethnic and environmental differences.
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Affiliation(s)
- Carlucci Gualberto Ventura
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Thomas Whisenant
- University of California, San Diego, School of Medicine, Center for Computational Biology and Bioinformatics, La Jolla, California
| | - Terri Gelbart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | - Daisa S.R. David
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Fabiana Agena
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | - Elias David-Neto
- Renal Transplant Service, Hospital das Clinicas - University of Sao Paulo School of Medicine, Sao Paulo, Brazil
| | - Sunil M. Kurian
- Scripps Center for Organ Transplantation, Scripps Green Hospital, La Jolla, California
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14
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Nakano T, Chen IH, Wang CC, Chen PJ, Tseng HP, Huang KT, Hu TH, Li LC, Goto S, Cheng YF, Lin CC, Chen CL. Circulating exosomal miR-92b: Its role for cancer immunoediting and clinical value for prediction of posttransplant hepatocellular carcinoma recurrence. Am J Transplant 2019; 19:3250-3262. [PMID: 31162867 DOI: 10.1111/ajt.15490] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/08/2019] [Accepted: 05/11/2019] [Indexed: 01/25/2023]
Abstract
A recurrence of hepatocellular carcinoma (HCC) after living donor liver transplantation (LDLT) is one of the major concerns reflecting the higher mortality of HCC. This study aimed to explore the impact of circulating exosomes on HCC development and recurrence. One-shot transfusion of hepatoma serum to naïve rats induced liver cancer development with gradual elevation of alpha-fetoprotein (AFP), but exosome-free hepatoma serum failed to induce AFP elevation. The microarray analysis revealed miR-92b as one of the highly expressing microribonucleic acids in hepatoma serum exosomes. Overexpression of miR-92b enhanced the migration ability of liver cancer cell lines with active release of exosomal miR-92b. The hepatoma-derived exosomal miR-92b transferred to natural killer (NK) cells, resulting in the downregulation of CD69 and NK cell-mediated cytotoxicity. Furthermore, higher expression of miR-92b in serum exosomes was confirmed in HCC patients before LDLT, and its value at 1 month after LDLT was maintained at a higher level in the patients with posttransplant HCC recurrence. In summary, we demonstrated the impact of circulating exosomes on liver cancer development, partly through the suppression of CD69 on NK cells by hepatoma-derived exosomal miR-92b. The value of circulating exosomal miR-92b may predict the risk of posttransplant HCC recurrence.
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Affiliation(s)
- Toshiaki Nakano
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Liver Transplantation Center and Division of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - I-Hsuan Chen
- Liver Transplantation Center and Division of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chih-Chi Wang
- Liver Transplantation Center and Division of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Po-Jung Chen
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Hui-Peng Tseng
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuang-Tzu Huang
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Tsung-Hui Hu
- Liver Transplantation Center and Division of Hepato-Gastroenterology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Lung-Chih Li
- Liver Transplantation Center and Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Shigeru Goto
- Liver Transplantation Center and Division of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Nobeoka Medical Check Center, Fukuoka Institution of Occupational Health, Nobeoka, Miyazaki, Japan.,Faculty of Nursing, Department of Nursing, Josai International University, Togane, Chiba, Japan
| | - Yu-Fan Cheng
- Liver Transplantation Center and Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chih-Che Lin
- Liver Transplantation Center and Division of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chao-Long Chen
- Liver Transplantation Center and Division of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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15
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Reeve J, Böhmig GA, Eskandary F, Einecke G, Gupta G, Madill-Thomsen K, Mackova M, Halloran PF. Generating automated kidney transplant biopsy reports combining molecular measurements with ensembles of machine learning classifiers. Am J Transplant 2019; 19:2719-2731. [PMID: 30868758 DOI: 10.1111/ajt.15351] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/10/2019] [Accepted: 03/03/2019] [Indexed: 01/25/2023]
Abstract
We previously reported a system for assessing rejection in kidney transplant biopsies using microarray-based gene expression data, the Molecular Microscope® Diagnostic System (MMDx). The present study was designed to optimize the accuracy and stability of MMDx diagnoses by replacing single machine learning classifiers with ensembles of diverse classifier methods. We also examined the use of automated report sign-outs and the agreement between multiple human interpreters of the molecular results. Ensembles generated diagnoses that were both more accurate than the best individual classifiers, and nearly as stable as the best, consistent with expectations from the machine learning literature. Human experts had ≈93% agreement (balanced accuracy) signing out the reports, and random forest-based automated sign-outs showed similar levels of agreement with the human experts (92% and 94% for predicting the expert MMDx sign-outs for T cell-mediated (TCMR) and antibody-mediated rejection (ABMR), respectively). In most cases disagreements, whether between experts or between experts and automated sign-outs, were in biopsies near diagnostic thresholds. Considerable disagreement with histology persisted. The balanced accuracies of MMDx sign-outs for histology diagnoses of TCMR and ABMR were 73% and 78%, respectively. Disagreement with histology is largely due to the known noise in histology assessments (ClinicalTrials.gov NCT01299168).
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Affiliation(s)
- Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Alberta, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gunilla Einecke
- Department of Nephrology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, Virginia
| | | | | | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Alberta, Canada.,Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
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16
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Stapleton CP, Heinzel A, Guan W, van der Most PJ, van Setten J, Lord GM, Keating BJ, Israni AK, de Borst MH, Bakker SJ, Snieder H, Weale ME, Delaney F, Hernandez‐Fuentes MP, Reindl-Schwaighofer R, Oberbauer R, Jacobson PA, Mark PB, Chapman FA, Phelan PJ, Kennedy C, Sexton D, Murray S, Jardine A, Traynor JP, McKnight AJ, Maxwell AP, Smyth LJ, Oetting WS, Matas AJ, Mannon RB, Schladt DP, Iklé DN, Cavalleri GL, Conlon PJ. The impact of donor and recipient common clinical and genetic variation on estimated glomerular filtration rate in a European renal transplant population. Am J Transplant 2019; 19:2262-2273. [PMID: 30920136 PMCID: PMC6989089 DOI: 10.1111/ajt.15326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/22/2019] [Accepted: 02/11/2019] [Indexed: 01/25/2023]
Abstract
Genetic variation across the human leukocyte antigen loci is known to influence renal-transplant outcome. However, the impact of genetic variation beyond the human leukocyte antigen loci is less clear. We tested the association of common genetic variation and clinical characteristics, from both the donor and recipient, with posttransplant eGFR at different time-points, out to 5 years posttransplantation. We conducted GWAS meta-analyses across 10 844 donors and recipients from five European ancestry cohorts. We also analyzed the impact of polygenic risk scores (PRS), calculated using genetic variants associated with nontransplant eGFR, on posttransplant eGFR. PRS calculated using the recipient genotype alone, as well as combined donor and recipient genotypes were significantly associated with eGFR at 1-year posttransplant. Thirty-two percent of the variability in eGFR at 1-year posttransplant was explained by our model containing clinical covariates (including weights for death/graft-failure), principal components and combined donor-recipient PRS, with 0.3% contributed by the PRS. No individual genetic variant was significantly associated with eGFR posttransplant in the GWAS. This is the first study to examine PRS, composed of variants that impact kidney function in the general population, in a posttransplant context. Despite PRS being a significant predictor of eGFR posttransplant, the effect size of common genetic factors is limited compared to clinical variables.
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Affiliation(s)
- Caragh P. Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Weihua Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Peter J. van der Most
- Departments of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Graham M. Lord
- King’s College London, MRC Centre for Transplantation, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
| | - Brendan J. Keating
- Department of Surgery, Penn Transplant Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ajay K. Israni
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Martin H. de Borst
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Stephan J.L. Bakker
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Departments of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael E. Weale
- Division of Genetics & Molecular Medicine, King’s College London, London, UK
| | - Florence Delaney
- King’s College London, MRC Centre for Transplantation, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
| | | | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Patrick B. Mark
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Fiona A. Chapman
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Paul J. Phelan
- Department of Nephrology, Royal Infirmary of Edinburgh, NHS Lothian, UK
| | - Claire Kennedy
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Donal Sexton
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Susan Murray
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Alan Jardine
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Jamie P. Traynor
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | | | | | - Laura J. Smyth
- Centre for Public Health, Queen’s University of Belfast, Belfast, UK
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Arthur J. Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Roslyn B. Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | | | | | | | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter J. Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
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17
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Roux A, Levine DJ, Zeevi A, Hachem R, Halloran K, Halloran PF, Gibault L, Taupin JL, Neil DAH, Loupy A, Adam BA, Mengel M, Hwang DM, Calabrese F, Berry G, Pavlisko EN. Banff Lung Report: Current knowledge and future research perspectives for diagnosis and treatment of pulmonary antibody-mediated rejection (AMR). Am J Transplant 2019; 19:21-31. [PMID: 29956477 DOI: 10.1111/ajt.14990] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 01/25/2023]
Abstract
The Lung session of the 2017 14th Banff Foundation for Allograft Pathology Conference, Barcelona focused on the multiple aspects of antibody-mediated rejection (AMR) in lung transplantation. Multidimensional approaches for AMR diagnosis, including classification, histological and immunohistochemical analysis, and donor- specific antibody (DSA) characterization with their current strengths and limitations were reviewed in view of recent research. The group also discussed the role of tissue gene expression analysis in the context of unmet needs in lung transplantation. The current best practice for monitoring of AMR and the therapeutic approach are summarized and highlighted in this report. The working group reached consensus of the major gaps in current knowledge and focused on the unanswered questions regarding pulmonary AMR. An important outcome of the meeting was agreement on the need for future collaborative research projects to address these gaps in the field of lung transplantation.
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Affiliation(s)
- A Roux
- Pneumology, Adult CF Center and Lung Transplantation Department, Foch Hospital, Suresnes, France.,Paris Translational Research Center for Organ Transplantation, French National institute of Health and Medical Research (INSERM). Unit UMR S970, Paris, France.,Versailles Saint-Quentin-en-Yvelines University, UPRES EA 220, Suresnes, France
| | - D J Levine
- Division of Pulmonary and Critical Care Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX, USA
| | - A Zeevi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - R Hachem
- Washington University, School of Medicine Division of Pulmonary & Critical Care, St. Louis, MO, USA
| | - K Halloran
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - P F Halloran
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, Alberta, Canada
| | - L Gibault
- Department of Pathology, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - J L Taupin
- Department of Immunology and Histocompatibility, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - D A H Neil
- Department of Pathology, Queen Elizabeth Hospital, Birmingham, UK
| | - A Loupy
- Paris Translational Research Center for Organ Transplantation, French National institute of Health and Medical Research (INSERM). Unit UMR S970, Paris, France
| | - B A Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - M Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - D M Hwang
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Ontario, Canada
| | - F Calabrese
- Department of Cardio-Thoracic and Vascular Sciences, Pathology Section, University of Padova, Italy
| | - G Berry
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - E N Pavlisko
- Department of Pathology, Duke University Hospital, Durham, NC, USA
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18
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Parkes MD, Halloran PF, Hidalgo LG. Mechanistic Sharing Between NK Cells in ABMR and Effector T Cells in TCMR. Am J Transplant 2018; 18:63-73. [PMID: 28654216 DOI: 10.1111/ajt.14410] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/02/2017] [Accepted: 06/20/2017] [Indexed: 01/25/2023]
Abstract
Human organ allograft rejection depends on effector lymphocytes: NK cells in antibody-mediated rejection (ABMR) and effector T cells in T cell-mediated rejection (TCMR). We hypothesized that NK cell CD16a stimulation and CD8 T cell TCR/CD3 stimulation represent highly similar effector systems, and should lead to shared molecular changes between ABMR and TCMR. We studied similarity between soluble proteins and the transcripts induced in CD16a stimulated NK cells and TCR/CD3-stimulated T cells in vitro. Of 30 soluble mediators tested, CD16a-activated NK cells and CD3/TCR activated T cells produced the same limited set of five mediators-CCL3, CCL4, CSF2, IFNG, and TNF-and failed to produce 25 others. Many transcripts increased in stimulated NK cells were also increased in CD3-stimulated CD8 T cells (FDR < 0.05), including IFNG, CSF2, CCL3, CCL4, and XCL1. We hypothesized that shared transcripts not produced by other cell types should be expressed both in ABMR and TCMR kidney transplant biopsies. CD160, XCL1, TNFRSF9, and IFNG were selective for TCR/CD3-activated T cells and CD16a-NK cells and all were strongly increased in ABMR and TCMR. The molecules such as CD160 and XCL1 shared between NK cells in ABMR and effector T cells in TCMR may hold insights into important rejection mechanisms.
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Affiliation(s)
- M D Parkes
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
| | - P F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada.,Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - L G Hidalgo
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada.,Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB, Canada
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19
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Halloran PF, Reeve J, Akalin E, Aubert O, Bohmig GA, Brennan D, Bromberg J, Einecke G, Eskandary F, Gosset C, Duong Van Huyen JP, Gupta G, Lefaucheur C, Malone A, Mannon RB, Seron D, Sellares J, Weir M, Loupy A. Real Time Central Assessment of Kidney Transplant Indication Biopsies by Microarrays: The INTERCOMEX Study. Am J Transplant 2017; 17:2851-2862. [PMID: 28449409 DOI: 10.1111/ajt.14329] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 01/25/2023]
Abstract
The authors conducted a prospective trial to assess the feasibility of real time central molecular assessment of kidney transplant biopsy samples from 10 North American or European centers. Biopsy samples taken 1 day to 34 years posttransplantation were stabilized in RNAlater, sent via courier overnight at ambient temperature to the central laboratory, and processed (29 h workflow) using microarrays to assess T cell- and antibody-mediated rejection (TCMR and ABMR, respectively). Of 538 biopsy samples submitted, 519 (96%) were sufficient for microarray analysis (average length, 3 mm). Automated reports were generated without knowledge of histology and HLA antibody, with diagnoses assigned based on Molecular Microscope Diagnostic System (MMDx) classifier algorithms and signed out by one observer. Agreement between MMDx and histology (balanced accuracy) was 77% for TCMR, 77% for ABMR, and 76% for no rejection. A classification tree derived to provide automated sign-outs predicted the observer sign-outs with >90% accuracy. In 451 biopsy samples where feedback was obtained, clinicians indicated that MMDx more frequently agreed with clinical judgment (87%) than did histology (80%) (p = 0.0042). In 81% of feedback forms, clinicians reported that MMDx increased confidence in management compared with conventional assessment alone. The authors conclude that real time central molecular assessment is feasible and offers a useful new dimension in biopsy interpretation. ClinicalTrials.gov NCT#01299168.
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Affiliation(s)
- P F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada.,Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - J Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
| | - E Akalin
- Montefiore Medical Center, Bronx, NY
| | - O Aubert
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France
| | - G A Bohmig
- Medizinische Universität Wien, Vienna, Austria
| | - D Brennan
- Washington University at St. Louis, St. Louis, MO
| | - J Bromberg
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - G Einecke
- Medizinische Hochschule Hannover, Hannover, Germany
| | - F Eskandary
- Medizinische Universität Wien, Vienna, Austria
| | - C Gosset
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France.,Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - J-P Duong Van Huyen
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France
| | - G Gupta
- Virginia Commonwealth University, Richmond, VA
| | - C Lefaucheur
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France.,Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - A Malone
- Washington University at St. Louis, St. Louis, MO
| | - R B Mannon
- University of Alabama at Birmingham, Birmingham, AL
| | - D Seron
- Hospital Universitari Vall D'Hebron, Barcelona, Spain
| | - J Sellares
- Hospital Universitari Vall D'Hebron, Barcelona, Spain
| | - M Weir
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - A Loupy
- Paris Translational Research Center for Organ Transplantation, INSERM, Uss-S970, Paris, France.,Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
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20
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Kurian S, Velazquez E, Thompson R, Whisenant T, Rose S, Riley N, Harrison F, Gelbart T, Friedewald J, charrette J, Brietigam S, Peysakhovich J, First M, Abecassis M, Salomon D. Orthogonal Comparison of Molecular Signatures of Kidney Transplants With Subclinical and Clinical Acute Rejection: Equivalent Performance Is Agnostic to Both Technology and Platform. Am J Transplant 2017; 17:2103-2116. [PMID: 28188669 PMCID: PMC5519433 DOI: 10.1111/ajt.14224] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/06/2017] [Accepted: 01/20/2017] [Indexed: 01/25/2023]
Abstract
We performed orthogonal technology comparisons of concurrent peripheral blood and biopsy tissue samples from 69 kidney transplant recipients who underwent comprehensive algorithm-driven clinical phenotyping. The sample cohort included patients with normal protocol biopsies and stable transplant (sTx) function (n = 25), subclinical acute rejection (subAR, n = 23), and clinical acute rejection (cAR, n = 21). Comparisons between microarray and RNA sequencing (RNA-seq) signatures were performed and demonstrated a strong correlation between the blood and tissue compartments for both technology platforms. A number of shared differentially expressed genes and pathways between subAR and cAR in both platforms strongly suggest that these two clinical phenotypes form a continuum of alloimmune activation. SubAR is associated with fewer or less expressed genes than cAR in blood, whereas in biopsy tissues, this clinical phenotype demonstrates a more robust molecular signature for both platforms. The discovery work done in this study confirms a clear ability to detect gene expression profiles for sTx, subAR, and cAR in both blood and biopsy tissue, yielding equivalent predictive performance that is agnostic to both technology and platform. Our data also provide strong biological insights into the molecular mechanisms underlying these signatures, underscoring their logistical potential as molecular diagnostics to improve clinical outcomes following kidney transplantation.
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Affiliation(s)
- S.M. Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - E. Velazquez
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - R. Thompson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - T. Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - S. Rose
- Transplant Genomics Inc., Mansfield, MA
| | - N. Riley
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - F. Harrison
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - T. Gelbart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - J.J. Friedewald
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - j. charrette
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - S. Brietigam
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - J. Peysakhovich
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - M.R. First
- Transplant Genomics Inc., Mansfield, MA,Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - M.M. Abecassis
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - D.R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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21
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Madill-Thomsen KS, Wiggins RC, Eskandary F, Böhmig GA, Halloran PF. The Effect of Cortex/Medulla Proportions on Molecular Diagnoses in Kidney Transplant Biopsies: Rejection and Injury Can Be Assessed in Medulla. Am J Transplant 2017; 17:2117-2128. [PMID: 28226404 PMCID: PMC5550741 DOI: 10.1111/ajt.14233] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/10/2017] [Accepted: 02/12/2017] [Indexed: 01/25/2023]
Abstract
Histologic assessment of kidney transplant biopsies relies on cortex rather than medulla, but for microarray studies, the proportion cortex in a biopsy is typically unknown and could affect the molecular readings. The present study aimed to develop a molecular estimate of proportion cortex in biopsies and examine its effect on molecular diagnoses. Microarrays from 26 kidney transplant biopsies divided into cortex and medulla components and processed separately showed that many of the most significant differences were in glomerular genes (e.g. NPHS2, NPHS1, CLIC5, PTPRO, PLA2R1, PLCE1, PODXL, and REN). Using NPHS2 (podocin) to estimate proportion cortex, we examined whether proportion cortex influenced molecular assessment in the molecular microscope diagnostic system. In 1190 unselected kidney transplant indication biopsies (Clinicaltrials.govNCT01299168), only 11% had <50% cortex. Molecular scores for antibody-mediated rejection, T cell-mediated rejection, and injury were independent of proportion cortex. Rejection was diagnosed in many biopsies that were mostly or all medulla. Agreement in molecular diagnoses in paired cortex/medulla samples (23/26) was similar to biological replicates (32/37). We conclude that NPHS2 expression can estimate proportion cortex; that proportion cortex has little influence on molecular diagnosis of rejection; and that, although histology cannot assess medulla, rejection does occur in medulla as well as cortex.
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Affiliation(s)
| | - R. C. Wiggins
- Nephrology Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - F. Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - G. A. Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - P. F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada,Department of Medicine, University of Alberta, Edmonton, AB, Canada,Corresponding author: Philip F. Halloran,
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22
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Einecke G, Reeve J, Halloran PF. Hyalinosis Lesions in Renal Transplant Biopsies: Time-Dependent Complexity of Interpretation. Am J Transplant 2017; 17:1346-1357. [PMID: 27873464 DOI: 10.1111/ajt.14136] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/28/2016] [Indexed: 01/25/2023]
Abstract
Because calcineurin inhibitor (CNI) immunosuppressive drugs induce arteriolar hyalinosis (ah) in kidney transplants, ah lesions can potentially provide information about drug exposure. We studied the relationship of ah lesions to findings and outcomes in 562 indication biopsies taken 3 days to 35 years after transplant. Prevalence of ah lesions increased with time of biopsy after transplant (TxBx). The ah scores correlated with arterial intimal thickening and atrophy-fibrosis but, unlike atrophy-fibrosis, did not increase until after 500 days because of a background of ah1 lesions in early biopsies reflecting donor aging. Correlation of ah scores with other features varied with TxBx-in early biopsies, donor age and related changes, and in very late biopsies, chronic antibody-mediated rejection and glomerulonephritis and associated lesions. After correction for TxBx, ah0 in intermediate time periods was associated with increased risk of T cell-mediated rejection and graft loss, probably because of underimmunosuppression and nonadherence. Thus, ah lesions in indication biopsies have multiple associations: donor age (early, usually ah1), chronic glomerular diseases (late, often ah2/3), and adequate exposure to CNIs at intermediate times. This threefold TxBx-dependent complexity must be considered when interpreting indication biopsies: ah lesions often indicate adequate CNI exposure, not toxicity, and unexpected ah0 should increase vigilance for nonadherence and underimmunosuppression.
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Affiliation(s)
- G Einecke
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - J Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - P F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.,Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
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23
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Affiliation(s)
- D R Kuypers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - T Vanhove
- Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
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24
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Oetting WS, Jacobson PA, Israni AK. Validation Is Critical for Genome-Wide Association Study-Based Associations. Am J Transplant 2017; 17:318-319. [PMID: 27640398 PMCID: PMC5266629 DOI: 10.1111/ajt.14051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 01/25/2023]
Affiliation(s)
- William S. Oetting
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN,Corresponding author: William S. Oetting,
| | - Pamala A. Jacobson
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - Ajay K. Israni
- Minneapolis Medical Research Foundation, Minneapolis, MN,University of Minnesota, Department of Medicine, Hennepin County Medical Center, Minneapolis, MN,University of Minnesota, Department of Epidemiology & Community Health, Minneapolis MN
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25
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Ling Q, Xie H, Li J, Liu J, Cao J, Yang F, Wang C, Hu Q, Xu X, Zheng S. Donor Graft MicroRNAs: A Newly Identified Player in the Development of New-onset Diabetes After Liver Transplantation. Am J Transplant 2017; 17:255-264. [PMID: 27458792 PMCID: PMC5215980 DOI: 10.1111/ajt.13984] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 01/25/2023]
Abstract
New-onset diabetes after liver transplantation (NODALT) is a frequent complication with an unfavorable outcome. We previously demonstrated a crucial link between donor graft genetics and the risk of NODALT. We selected 15 matched pairs of NODALT and non-NODALT liver recipients using propensity score matching analysis. The donor liver tissues were tested for the expression of 10 microRNAs (miRNAs) regulating human hepatic glucose homeostasis. The biological functions of potential target genes were predicted using gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Both miR-103 and miR-181a were significantly highly expressed in the NODALT group as compared to the non-NODALT group. The predicted target genes (e.g. Irs2, Pik3r1, Akt2, and Gsk3b) were involved in glucose import and the insulin signaling pathway. We also observed dysregulation of miRNAs (e.g. let-7, miR-26b, miR-145, and miR-183) in cultured human hepatocytes treated with tacrolimus or high glucose, the two independent risk factors of NODALT identified in this cohort. The hepatic miRNA profiles altered by tacrolimus or hyperglycemia were associated with insulin resistance and glucose homeostatic imbalance as revealed by enrichment analysis. The disease susceptibility miRNA expressive pattern could be imported directly from the donor and consolidated by the transplant factors.
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Affiliation(s)
- Q. Ling
- Department of SurgeryCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesFirst Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina,Key Lab of Combined Multi‐Organ TransplantationMinistry of Public HealthHangzhouChina
| | - H. Xie
- Key Lab of Combined Multi‐Organ TransplantationMinistry of Public HealthHangzhouChina
| | - J. Li
- Department of SurgeryCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesFirst Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina
| | - J. Liu
- Department of SurgeryCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesFirst Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina,Department of Pathology and Molecular MedicineFaculty of Health SciencesMcMaster UniversityHamiltonOntarioCanada
| | - J. Cao
- Key Lab of Combined Multi‐Organ TransplantationMinistry of Public HealthHangzhouChina
| | - F. Yang
- Department of SurgeryCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesFirst Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina
| | - C. Wang
- Department of SurgeryCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesFirst Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina
| | - Q. Hu
- Key Lab of Combined Multi‐Organ TransplantationMinistry of Public HealthHangzhouChina
| | - X. Xu
- Department of SurgeryCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesFirst Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina,Key Lab of Combined Multi‐Organ TransplantationMinistry of Public HealthHangzhouChina
| | - S. Zheng
- Department of SurgeryCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesFirst Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina,Key Lab of Combined Multi‐Organ TransplantationMinistry of Public HealthHangzhouChina
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26
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Ghisdal L, Baron C, Lebranchu Y, Viklický O, Konarikova A, Naesens M, Kuypers D, Dinic M, Alamartine E, Touchard G, Antoine T, Essig M, Rerolle JP, Merville P, Taupin JL, Le Meur Y, Grall‐Jezequel A, Glowacki F, Noël C, Legendre C, Anglicheau D, Broeders N, Coppieters W, Docampo E, Georges M, Ajarchouh Z, Massart A, Racapé J, Abramowicz D, Abramowicz M. Genome-Wide Association Study of Acute Renal Graft Rejection. Am J Transplant 2017; 17:201-209. [PMID: 27272414 PMCID: PMC5215306 DOI: 10.1111/ajt.13912] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 01/25/2023]
Abstract
Acute renal rejection is a major risk factor for chronic allograft dysfunction and long-term graft loss. We performed a genome-wide association study to detect loci associated with biopsy-proven acute T cell-mediated rejection occurring in the first year after renal transplantation. In a discovery cohort of 4127 European renal allograft recipients transplanted in eight European centers, we used a DNA pooling approach to compare 275 cases and 503 controls. In an independent replication cohort of 2765 patients transplanted in two European countries, we identified 313 cases and 531 controls, in whom we genotyped individually the most significant single nucleotide polymorphisms (SNPs) from the discovery cohort. In the discovery cohort, we found five candidate loci tagged by a number of contiguous SNPs (more than five) that was never reached in iterative in silico permutations of our experimental data. In the replication cohort, two loci remained significantly associated with acute rejection in both univariate and multivariate analysis. One locus encompasses PTPRO, coding for a receptor-type tyrosine kinase essential for B cell receptor signaling. The other locus involves ciliary gene CCDC67, in line with the emerging concept of a shared building design between the immune synapse and the primary cilium.
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Affiliation(s)
- L. Ghisdal
- Department of Nephrology, Dialysis, and TransplantationHôpital Erasme (Université Libre de Bruxelles)BrusselsBelgium,Present address: Department of NephrologyCentre Hospitalier EpiCURABaudourBelgium
| | - C. Baron
- Department of NephrologyCentre Hospitalier Régional Universitaire de ToursToursFrance
| | - Y. Lebranchu
- Department of NephrologyCentre Hospitalier Régional Universitaire de ToursToursFrance
| | - O. Viklický
- Department of NephrologyTransplant CentreInstitute for Clinical and Experimental MedicinePragueCzech Republic
| | - A. Konarikova
- Department of NephrologyTransplant CentreInstitute for Clinical and Experimental MedicinePragueCzech Republic
| | - M. Naesens
- Department of Microbiology and ImmunologyKU LeuvenUniversity of LeuvenLeuvenBelgium,Department of NephrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - D. Kuypers
- Department of Microbiology and ImmunologyKU LeuvenUniversity of LeuvenLeuvenBelgium,Department of NephrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - M. Dinic
- Department of NephrologyCentre Hospitalier Universitaire de Saint‐EtienneSaint‐EtienneFrance
| | - E. Alamartine
- Department of NephrologyCentre Hospitalier Universitaire de Saint‐EtienneSaint‐EtienneFrance
| | - G. Touchard
- Department of NephrologyCentre Hospitalier Universitaire de PoitiersPoitiersFrance
| | - T. Antoine
- Department of NephrologyCentre Hospitalier Universitaire de PoitiersPoitiersFrance
| | - M. Essig
- Department of Nephrology, Dialysis, TransplantationCentre Hospitalier Universitaire de Limoges and INSERM UMR 850 (Université de Limoges)LimogesFrance
| | - J. P. Rerolle
- Department of Nephrology, Dialysis, TransplantationCentre Hospitalier Universitaire de Limoges and INSERM UMR 850 (Université de Limoges)LimogesFrance
| | - P. Merville
- Department of NephrologyCentre Hospitalier Universitaire de BordeauxBordeauxFrance
| | - J. L. Taupin
- Department of Immunology and HistocompatibilityHôpital Saint‐LouisParisFrance
| | - Y. Le Meur
- Department of NephrologyCentre Hospitalier Universitaire la Cavale blancheBrestFrance
| | - A. Grall‐Jezequel
- Department of NephrologyCentre Hospitalier Universitaire la Cavale blancheBrestFrance
| | - F. Glowacki
- Department of NephrologyCentre Régional Hospitalier Universitaire de LilleLilleFrance
| | - C. Noël
- Department of NephrologyCentre Régional Hospitalier Universitaire de LilleLilleFrance
| | - C. Legendre
- Department of Renal TransplantationUniversité Paris Descartes and Hôpital NeckerAssistance Publique‐Hôpitaux de ParisParisFrance
| | - D. Anglicheau
- Department of Renal TransplantationUniversité Paris Descartes and Hôpital NeckerAssistance Publique‐Hôpitaux de ParisParisFrance
| | - N. Broeders
- Department of Nephrology, Dialysis, and TransplantationHôpital Erasme (Université Libre de Bruxelles)BrusselsBelgium
| | - W. Coppieters
- Unit of Animal GenomicsGroupe Interdisciplinaire de Génoprotéomique Appliquée‐Research (GIGA‐R)University of LiègeLiègeBelgium
| | - E. Docampo
- Unit of Animal GenomicsGroupe Interdisciplinaire de Génoprotéomique Appliquée‐Research (GIGA‐R)University of LiègeLiègeBelgium
| | - M. Georges
- Unit of Animal GenomicsGroupe Interdisciplinaire de Génoprotéomique Appliquée‐Research (GIGA‐R)University of LiègeLiègeBelgium
| | - Z. Ajarchouh
- Institute of Interdisciplinary Research in Molecular and Human biology (IRIBHM)Université Libre de BruxellesBrusselsBelgium
| | - A. Massart
- Department of Nephrology, Dialysis, and TransplantationHôpital Erasme (Université Libre de Bruxelles)BrusselsBelgium,Institute of Interdisciplinary Research in Molecular and Human biology (IRIBHM)Université Libre de BruxellesBrusselsBelgium
| | - J. Racapé
- Centre of EpidemiologyBiostatistic and Clinical ResearchSchool of Public Health (Université Libre de Bruxelles)BrusselsBelgium
| | - D. Abramowicz
- Department of Nephrology, Dialysis, and TransplantationHôpital Erasme (Université Libre de Bruxelles)BrusselsBelgium,Department of NephrologyAntwerp University HospitalAntwerpenBelgium
| | - M. Abramowicz
- Institute of Interdisciplinary Research in Molecular and Human biology (IRIBHM)Université Libre de BruxellesBrusselsBelgium,Medical Genetics DepartmentHôpital Erasme (Université Libre de Bruxelles)BrusselsBelgium
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27
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Oetting WS, Schladt DP, Guan W, Miller MB, Remmel RP, Dorr C, Sanghavi K, Mannon RB, Herrera B, Matas AJ, Salomon DR, Kwok PY, Keating BJ, Israni AK, Jacobson PA. Genomewide Association Study of Tacrolimus Concentrations in African American Kidney Transplant Recipients Identifies Multiple CYP3A5 Alleles. Am J Transplant 2016; 16:574-82. [PMID: 26485092 PMCID: PMC4733408 DOI: 10.1111/ajt.13495] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 08/15/2015] [Indexed: 01/25/2023]
Abstract
We previously reported that tacrolimus (TAC) trough blood concentrations for African American (AA) kidney allograft recipients were lower than those observed in white patients. Subtherapeutic TAC troughs may be associated with acute rejection (AR) and AR-associated allograft failure. This variation in TAC troughs is due, in part, to differences in the frequency of the cytochrome P450 CYP3A5*3 allele (rs776746, expresses nonfunctional enzyme) between white and AA recipients; however, even after accounting for this variant, variability in AA-associated troughs is significant. We conducted a genomewide association study of TAC troughs in AA kidney allograft recipients to search for additional genetic variation. We identified two additional CYP3A5 variants in AA recipients independently associated with TAC troughs: CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343). All three variants and clinical factors account for 53.9% of the observed variance in troughs, with 19.8% of the variance coming from demographic and clinical factors including recipient age, glomerular filtration rate, anticytomegalovirus drug use, simultaneous pancreas-kidney transplant and antibody induction. There was no evidence of common genetic variants in AA recipients significantly influencing TAC troughs aside from the CYP3A gene. These results reveal that additional and possibly rare functional variants exist that account for the additional variation.
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Affiliation(s)
- W. S. Oetting
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN,Corresponding author: William S. Oetting,
| | - D. P. Schladt
- Minneapolis Medical Research Foundation, Minneapolis, MN
| | - W. Guan
- University of Minnesota, Department of Biostatistics, Minneapolis, MN
| | - M. B. Miller
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - R. P. Remmel
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - C. Dorr
- Minneapolis Medical Research Foundation, Minneapolis, MN
| | - K. Sanghavi
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - R. B. Mannon
- University of Alabama, Division of Nephrology, Birmingham, AL
| | - B. Herrera
- University of California, San Francisco, CA
| | - A. J. Matas
- University of Minnesota, Department of Surgery, Minneapolis, MN
| | | | - P.-Y. Kwok
- University of California, San Francisco, CA
| | - B. J. Keating
- Children's Hospital of Philadelphia, Philadelphia, PA
| | - A. K. Israni
- Minneapolis Medical Research Foundation, Minneapolis, MN,University of Minnesota, Department of Medicine, Hennepin County Medical Center, Minneapolis, MN,University of Minnesota, Department of Epidemiology and Community Health, Minneapolis, MN
| | - P. A. Jacobson
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
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28
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Van Aelst LNL, Summer G, Li S, Gupta SK, Heggermont W, De Vusser K, Carai P, Naesens M, Van Cleemput J, Van de Werf F, Vanhaecke J, Thum T, Waer M, Papageorgiou A, Schroen B, Heymans S. RNA Profiling in Human and Murine Transplanted Hearts: Identification and Validation of Therapeutic Targets for Acute Cardiac and Renal Allograft Rejection. Am J Transplant 2016; 16:99-110. [PMID: 26249758 PMCID: PMC5054886 DOI: 10.1111/ajt.13421] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 05/22/2015] [Accepted: 06/11/2015] [Indexed: 01/25/2023]
Abstract
Acute cellular rejection (ACR) is the adverse response of the recipient's immune system against the allogeneic graft. Using human surveillance endomyocardial biopsies (EMBs) manifesting ACR and murine allogeneic grafts, we profiled implicated microRNAs (miRs) and mRNAs. MiR profiling showed that miR-21, -142-3p, -142-5p, -146a, -146b, -155, -222, -223, and -494 increased during ACR in humans and mice, whereas miR-149-5p decreased. mRNA profiling revealed 70 common differentially regulated transcripts, all involved in immune signaling and immune-related diseases. Interestingly, 33 of 70 transcripts function downstream of IL-6 and its transcription factor spleen focus forming virus proviral integration oncogene (SPI1), an established target of miR-155, the most upregulated miR in human EMBs manifesting rejection. In a mouse model of cardiac transplantation, miR-155 absence and pharmacological inhibition attenuated ACR, demonstrating the causal involvement and therapeutic potential of miRs. Finally, we corroborated our miR signature in acute cellular renal allograft rejection, suggesting a nonorgan specific signature of acute rejection. We concluded that miR and mRNA profiling in human and murine ACR revealed the shared significant dysregulation of immune genes. Inflammatory miRs, for example miR-155, and transcripts, in particular those related to the IL-6 pathway, are promising therapeutic targets to prevent acute allograft rejection.
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Affiliation(s)
| | - G. Summer
- Center for Heart Failure ResearchCardiovascular Research Institute Maastricht (CARIM)University Hospital MaastrichtMaastrichtthe Netherlands
| | - S. Li
- Laboratory of Experimental TransplantationUniversity of LeuvenLeuvenBelgium
| | - S. K. Gupta
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS)Hannover Medical SchoolHannoverGermany
| | - W. Heggermont
- Department of Cardiovascular SciencesUniversity of LeuvenLeuvenBelgium
| | - K. De Vusser
- Department of Nephrology and Renal TransplantationUniversity Hospitals LeuvenLeuvenBelgium
| | - P. Carai
- Department of Cardiovascular SciencesUniversity of LeuvenLeuvenBelgium,Center for Heart Failure ResearchCardiovascular Research Institute Maastricht (CARIM)University Hospital MaastrichtMaastrichtthe Netherlands
| | - M. Naesens
- Department of Nephrology and Renal TransplantationUniversity Hospitals LeuvenLeuvenBelgium
| | - J. Van Cleemput
- Department of Cardiovascular SciencesUniversity of LeuvenLeuvenBelgium
| | - F. Van de Werf
- Department of Cardiovascular SciencesUniversity of LeuvenLeuvenBelgium
| | - J. Vanhaecke
- Department of Cardiovascular SciencesUniversity of LeuvenLeuvenBelgium
| | - T. Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS)Hannover Medical SchoolHannoverGermany
| | - M. Waer
- Laboratory of Experimental TransplantationUniversity of LeuvenLeuvenBelgium
| | - A.‐P. Papageorgiou
- Department of Cardiovascular SciencesUniversity of LeuvenLeuvenBelgium,Center for Heart Failure ResearchCardiovascular Research Institute Maastricht (CARIM)University Hospital MaastrichtMaastrichtthe Netherlands
| | - B. Schroen
- Center for Heart Failure ResearchCardiovascular Research Institute Maastricht (CARIM)University Hospital MaastrichtMaastrichtthe Netherlands
| | - S. Heymans
- Department of Cardiovascular SciencesUniversity of LeuvenLeuvenBelgium,Center for Heart Failure ResearchCardiovascular Research Institute Maastricht (CARIM)University Hospital MaastrichtMaastrichtthe Netherlands,ICIN‐Netherlands Heart InstituteUtrechtthe Netherlands
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