1
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Zarinsefat A, Dobi D, Kelly YM, Szabo G, Henrich T, Laszik ZG, Stock PG. An Enhanced Role of Innate Immunity in the Immune Response After Kidney Transplant in People Living With HIV: A Transcriptomic Analysis. Transplantation 2024:00007890-990000000-00785. [PMID: 38867347 DOI: 10.1097/tp.0000000000005096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
BACKGROUND Although kidney transplantation (KT) has become the standard of care for people living with HIV (PLWH) suffering from renal failure, early experiences revealed unanticipated higher rejection rates than those observed in HIV- recipients. The cause of increased acute rejection (AR) in PLWH was assessed by performing a transcriptomic analysis of biopsy specimens, comparing HIV+ to HIV- recipients. METHODS An analysis of 68 (34 HIV+, 34 HIV-) formalin-fixed paraffin-embedded (FFPE) renal biopsies matched for degree of inflammation was performed from KT recipients with acute T cell-mediated rejection (aTCMR), borderline for aTCMR (BL), and normal findings. Gene expression was measured using the NanoString platform on a custom gene panel to assess differential gene expression (DE) and pathway analysis (PA). RESULTS DE analysis revealed multiple genes with significantly increased expression in the HIV+ cohort in aTCMR and BL relative to the HIV- cohort. PA of these genes showed enrichment of various inflammatory pathways, particularly innate immune pathways associated with Toll-like receptors. CONCLUSIONS Upregulation of the innate immune pathways in the biopsies of PLWH with aTCMR and BL is suggestive of a unique immune response that may stem from immune dysregulation related to HIV infection. These findings suggest that these unique HIV-driven pathways may in part be contributory to the increased incidence of allograft rejection after renal transplantation in PLWH.
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Affiliation(s)
- Arya Zarinsefat
- Department of Surgery, University of California, San Francisco, CA
| | - Dejan Dobi
- Department of Pathology, University of California, San Francisco, CA
| | - Yvonne M Kelly
- Department of Surgery, University of California, San Francisco, CA
| | - Gyula Szabo
- Department of Pathology, University of California, San Francisco, CA
| | - Timothy Henrich
- Department of Medicine, University of California, San Francisco, CA
| | - Zoltan G Laszik
- Department of Pathology, University of California, San Francisco, CA
| | - Peter G Stock
- Department of Surgery, University of California, San Francisco, CA
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2
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Alexander MP, Zaidi M, Larson N, Mullan A, Pavelko KD, Stegall MD, Bentall A, Wouters BG, McKee T, Taner T. Exploring the single-cell immune landscape of kidney allograft inflammation using imaging mass cytometry. Am J Transplant 2024; 24:549-563. [PMID: 37979921 DOI: 10.1016/j.ajt.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/01/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Kidney allograft inflammation, mostly attributed to rejection and infection, is an important cause of graft injury and loss. Standard histopathological assessment of allograft inflammation provides limited insights into biological processes and the immune landscape. Here, using imaging mass cytometry with a panel of 28 validated biomarkers, we explored the single-cell landscape of kidney allograft inflammation in 32 kidney transplant biopsies and 247 high-dimensional histopathology images of various phenotypes of allograft inflammation (antibody-mediated rejection, T cell-mediated rejection, BK nephropathy, and chronic pyelonephritis). Using novel analytical tools, for cell segmentation, we segmented over 900 000 cells and developed a tissue-based classifier using over 3000 manually annotated kidney microstructures (glomeruli, tubules, interstitium, and arteries). Using PhenoGraph, we identified 11 immune and 9 nonimmune clusters and found a high prevalence of memory T cell and macrophage-enriched immune populations across phenotypes. Additionally, we trained a machine learning classifier to identify spatial biomarkers that could discriminate between the different allograft inflammatory phenotypes. Further validation of imaging mass cytometry in larger cohorts and with more biomarkers will likely help interrogate kidney allograft inflammation in more depth than has been possible to date.
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Affiliation(s)
- Mariam P Alexander
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, Minnesota, USA.
| | - Mark Zaidi
- Department of Medical Biophysics, University of Toronto, Canada
| | - Nicholas Larson
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Aidan Mullan
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Kevin D Pavelko
- Immune Monitoring Core Laboratory, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark D Stegall
- Departments of Surgery and Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew Bentall
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Bradly G Wouters
- Department of Medical Biophysics, University of Toronto, Canada; Princess Margaret Cancer Center, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Trevor McKee
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Pathomics Inc., Toronto, Ontario, Canada
| | - Timucin Taner
- Departments of Surgery and Immunology, Mayo Clinic, Rochester, Minnesota, USA
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3
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Zhang H, Haun RS, Collin F, Cassol C, Napier JOH, Wilson J, Hassen S, Ararat K, Boils C, Messias N, Caza TN, Cossey LN, Sharma S, Ambruzs JM, Agrawal N, Shekhtman G, Tian W, Srinivas T, Qu K, Woodward RN, Larsen CP, Stone S, Coley SM. Development and Validation of a Multiclass Model Defining Molecular Archetypes of Kidney Transplant Rejection: A Large Cohort Study of the Banff Human Organ Transplant Gene Expression Panel. J Transl Med 2024; 104:100304. [PMID: 38092179 DOI: 10.1016/j.labinv.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/19/2023] [Accepted: 12/06/2023] [Indexed: 01/15/2024] Open
Abstract
Gene expression profiling from formalin-fixed paraffin-embedded (FFPE) renal allograft biopsies is a promising approach for feasibly providing a molecular diagnosis of rejection. However, large-scale studies evaluating the performance of models using NanoString platform data to define molecular archetypes of rejection are lacking. We tested a diverse retrospective cohort of over 1400 FFPE biopsy specimens, rescored according to Banff 2019 criteria and representing 10 of 11 United Network of Organ Sharing regions, using the Banff Human Organ Transplant panel from NanoString and developed a multiclass model from the gene expression data to assign relative probabilities of 4 molecular archetypes: No Rejection, Antibody-Mediated Rejection, T Cell-Mediated Rejection, and Mixed Rejection. Using Least Absolute Shrinkage and Selection Operator regularized regression with 10-fold cross-validation fitted to 1050 biopsies in the discovery cohort and technically validated on an additional 345 biopsies, our model achieved overall accuracy of 85% in the discovery cohort and 80% in the validation cohort, with ≥75% positive predictive value for each class, except for the Mixed Rejection class in the validation cohort (positive predictive value, 53%). This study represents the technical validation of the first model built from a large and diverse sample of diagnostic FFPE biopsy specimens to define and classify molecular archetypes of histologically defined diagnoses as derived from Banff Human Organ Transplant panel gene expression profiling data.
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Affiliation(s)
| | | | | | | | | | - Jon Wilson
- Arkana Laboratories, Little Rock, Arkansas
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4
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Mubarak M, Raza A, Rashid R, Shakeel S. Evolution of human kidney allograft pathology diagnostics through 30 years of the Banff classification process. World J Transplant 2023; 13:221-238. [PMID: 37746037 PMCID: PMC10514746 DOI: 10.5500/wjt.v13.i5.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 09/15/2023] Open
Abstract
The second half of the previous century witnessed a tremendous rise in the number of clinical kidney transplants worldwide. This activity was, however, accompanied by many issues and challenges. An accurate diagnosis and appropriate management of causes of graft dysfunction were and still are, a big challenge. Kidney allograft biopsy played a vital role in addressing the above challenge. However, its interpretation was not standardized for many years until, in 1991, the Banff process was started to fill this void. Thereafter, regular Banff meetings took place every 2 years for the past 30 years. Marked changes have taken place in the interpretation of kidney allograft biopsies, diagnosis, and classification of rejection and other non-rejection pathologies from the original Banff 93 classification. This review attempts to summarize those changes for increasing the awareness and understanding of kidney allograft pathology through the eyes of the Banff process. It will interest the transplant surgeons, physicians, pathologists, and allied professionals associated with the care of kidney transplant patients.
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Affiliation(s)
- Muhammed Mubarak
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Amber Raza
- Department of Nephrology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Rahma Rashid
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Shaheera Shakeel
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
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5
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Beadle J, Papadaki A, Toulza F, Santos E, Willicombe M, McLean A, Peters J, Roufosse C. Application of the Banff Human Organ Transplant Panel to kidney transplant biopsies with features suspicious for antibody-mediated rejection. Kidney Int 2023; 104:526-541. [PMID: 37172690 DOI: 10.1016/j.kint.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
The Banff Classification for Allograft Pathology includes the use of gene expression in the diagnosis of antibody-mediated rejection (AMR) of kidney transplants, but a predictive set of genes for classifying biopsies with 'incomplete' phenotypes has not yet been studied. Here, we developed and assessed a gene score that, when applied to biopsies with features of AMR, would identify cases with a higher risk of allograft loss. To do this, RNA was extracted from a continuous retrospective cohort of 349 biopsies randomized 2:1 to include 220 biopsies in a discovery cohort and 129 biopsies in a validation cohort. The biopsies were divided into three groups: 31 that fulfilled the 2019 Banff Criteria for active AMR, 50 with histological features of AMR but not meeting the full criteria (Suspicious-AMR), and 269 with no features of active AMR (No-AMR). Gene expression analysis using the 770 gene Banff Human Organ Transplant NanoString panel was carried out with LASSO Regression performed to identify a parsimonious set of genes predictive of AMR. We identified a nine gene score that was highly predictive of active AMR (accuracy 0.92 in the validation cohort) and was strongly correlated with histological features of AMR. In biopsies suspicious for AMR, our gene score was strongly associated with risk of allograft loss and independently associated with allograft loss in multivariable analysis. Thus, we show that a gene expression signature in kidney allograft biopsy samples can help classify biopsies with incomplete AMR phenotypes into groups that correlate strongly with histological features and outcomes.
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Affiliation(s)
- Jack Beadle
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College NHS Trust, London, UK.
| | - Artemis Papadaki
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Frederic Toulza
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Eva Santos
- H&I Laboratory, North West London Pathology, London, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Imperial College Renal and Transplant Centre, Imperial College NHS Trust, London, UK
| | - Adam McLean
- Imperial College Renal and Transplant Centre, Imperial College NHS Trust, London, UK
| | - James Peters
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Candice Roufosse
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Department of Cellular Pathology, North West London Pathology, London, UK
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6
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Chancharoenthana W, Traitanon O, Leelahavanichkul A, Tasanarong A. Molecular immune monitoring in kidney transplant rejection: a state-of-the-art review. Front Immunol 2023; 14:1206929. [PMID: 37675106 PMCID: PMC10477600 DOI: 10.3389/fimmu.2023.1206929] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Although current regimens of immunosuppressive drugs are effective in renal transplant recipients, long-term renal allograft outcomes remain suboptimal. For many years, the diagnosis of renal allograft rejection and of several causes of renal allograft dysfunction, such as chronic subclinical inflammation and infection, was mostly based on renal allograft biopsy, which is not only invasive but also possibly performed too late for proper management. In addition, certain allograft dysfunctions are difficult to differentiate from renal histology due to their similar pathogenesis and immune responses. As such, non-invasive assays and biomarkers may be more beneficial than conventional renal biopsy for enhancing graft survival and optimizing immunosuppressive drug regimens during long-term care. This paper discusses recent biomarker candidates, including donor-derived cell-free DNA, transcriptomics, microRNAs, exosomes (or other extracellular vesicles), urine chemokines, and nucleosomes, that show high potential for clinical use in determining the prognosis of long-term outcomes of kidney transplantation, along with their limitations.
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Affiliation(s)
- Wiwat Chancharoenthana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Tropical Immunology and Translational Research Unit (TITRU), Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Opas Traitanon
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Asada Leelahavanichkul
- Center of Excellence on Translational Research in Inflammation and Immunology (CETRII), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Adis Tasanarong
- Thammasat Multi-Organ Transplant Center, Thammasat University Hospital, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
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7
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Masutani K. Progress in Pathological Diagnosis after Kidney Transplantation: Current Trend and Future Perspective. J Atheroscler Thromb 2023; 30:720-732. [PMID: 37245995 PMCID: PMC10322740 DOI: 10.5551/jat.rv22005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023] Open
Abstract
Advances in immunosuppressive therapy; posttransplant management of allograft rejection; and measures against infectious diseases, cardiovascular diseases, and malignancy dramatically improved graft and patient survival after kidney transplantation (KT). Among them, kidney allograft biopsy is an important tool and the gold standard for the diagnosis of various kidney allograft injuries, including allograft rejection, virus-induced nephropathy, calcineurin inhibitor toxicity, and posttransplant glomerular diseases. The Banff Conference on Allograft Pathology has contributed to establishing the diagnostic criteria for kidney allograft rejection and polyomavirus-associated nephropathy that are used as a common standard worldwide. In addition to the for-cause biopsy, many transplant centers perform protocol biopsies in the early and late posttransplant periods to detect and treat allograft injury earlier. Preimplantation biopsy in deceased-donor KT has also been performed, especially in the marginal donor, and attempts have been made to predict the prognosis in combination with clinical information and the renal resistance of hypothermic machine perfusion. Regarding the preimplantation biopsy from a living kidney donor, it can provide useful information on aging and/or early changes in lifestyle diseases, such as glomerulosclerosis, tubulointerstitial changes, and arterial and arteriolar sclerosis, and be used as a reference for the subsequent management of living donors. In this review, morphologic features of important kidney allograft pathology, such as allograft rejection and polyomavirus-associated nephropathy, according to the latest Banff classification and additional information derived from protocol biopsy, and future perspectives with recently developed technologies are discussed.
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Affiliation(s)
- Kosuke Masutani
- Division of Nephrology and Rheumatology, Department of Internal Medicine, Faculty of Medicine, Fukuoka University, Fukuoka,
Japan
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8
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Bajema IM, Balow JE, Haas M, Jayne D, Lightstone L, Rovin BH, Seshan SV, Fogo AB. Update on scoring and providing evidence basis for assessing pathology in lupus nephritis. Kidney Int 2023; 103:813-816. [PMID: 37085251 DOI: 10.1016/j.kint.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 04/23/2023]
Affiliation(s)
- Ingeborg M Bajema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
| | - James E Balow
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Mark Haas
- Department of Pathology & Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David Jayne
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Liz Lightstone
- Faculty of Medicine, Imperial College London, London, UK
| | - Brad H Rovin
- Department of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA; Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Surya V Seshan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, New York, USA
| | - Agnes B Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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9
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Smith RN, Rosales IA, Tomaszewski KT, Mahowald GT, Araujo-Medina M, Acheampong E, Bruce A, Rios A, Otsuka T, Tsuji T, Hotta K, Colvin R. Utility of Banff Human Organ Transplant Gene Panel in Human Kidney Transplant Biopsies. Transplantation 2023; 107:1188-1199. [PMID: 36525551 PMCID: PMC10132999 DOI: 10.1097/tp.0000000000004389] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Microarray transcript analysis of human renal transplantation biopsies has successfully identified the many patterns of graft rejection. To evaluate an alternative, this report tests whether gene expression from the Banff Human Organ Transplant (B-HOT) probe set panel, derived from validated microarrays, can identify the relevant allograft diagnoses directly from archival human renal transplant formalin-fixed paraffin-embedded biopsies. To test this hypothesis, principal components (PCs) of gene expressions were used to identify allograft diagnoses, to classify diagnoses, and to determine whether the PC data were rich enough to identify diagnostic subtypes by clustering, which are all needed if the B-HOT panel can substitute for microarrays. METHODS RNA was isolated from routine, archival formalin-fixed paraffin-embedded tissue renal biopsy cores with both rejection and nonrejection diagnoses. The B-HOT panel expression of 770 genes was analyzed by PCs, which were then tested to determine their ability to identify diagnoses. RESULTS PCs of microarray gene sets identified the Banff categories of renal allograft diagnoses, modeled well the aggregate diagnoses, showing a similar correspondence with the pathologic diagnoses as microarrays. Clustering of the PCs identified diagnostic subtypes including non-chronic antibody-mediated rejection with high endothelial expression. PCs of cell types and pathways identified new mechanistic patterns including differential expression of B and plasma cells. CONCLUSIONS Using PCs of gene expression from the B-Hot panel confirms the utility of the B-HOT panel to identify allograft diagnoses and is similar to microarrays. The B-HOT panel will accelerate and expand transcript analysis and will be useful for longitudinal and outcome studies.
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Affiliation(s)
- Rex N Smith
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Ivy A Rosales
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Kristen T Tomaszewski
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Grace T Mahowald
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Milagros Araujo-Medina
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ellen Acheampong
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Amy Bruce
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Andrea Rios
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Takuya Otsuka
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - Takahiro Tsuji
- Department of Pathology, Sapporo City General Hospital, Sapporo, Japan
| | - Kiyohiko Hotta
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan
| | - Robert Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
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10
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de Nattes T, Beadle J, Toulza F, Candon E, Ruminy P, François A, Bertrand D, Guerrot D, Drieux F, Roufosse C, Candon S. A Simple Molecular Tool for the Assessment of Kidney Transplant Biopsies. Clin J Am Soc Nephrol 2023; 18:499-509. [PMID: 36723289 PMCID: PMC10103338 DOI: 10.2215/cjn.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
BACKGROUND The Banff Classification for Allograft Pathology recommendations for the diagnosis of kidney transplant rejection includes molecular assessment of the transplant biopsy. However, implementation of molecular tools in clinical practice is still limited, partly due to the required expertise and financial investment. The reverse transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) assay is a simple, rapid, and inexpensive assay that permits simultaneous evaluation of a restricted gene panel using paraffin-embedded tissue blocks. The aim of this study was to develop and validate a RT-MLPA assay for diagnosis and classification of rejection. METHODS A retrospective cohort of 220 kidney transplant biopsies from two centers, which included 52 antibody-mediated rejection, 51 T-cell-mediated rejection, and 117 no-rejection controls, was assessed. A 17-gene panel was identified on the basis of relevant pathophysiological pathways. A support vector machine classifier was developed. A subset of 109 biopsies was also assessed using the Nanostring Banff Human Organ Transplant panel to compare the two assays. RESULTS The support vector machine classifier train and test accuracy scores were 0.84 and 0.83, respectively. In the test cohort, the F1 score for antibody-mediated rejection, T-cell-mediated rejection, and control were 0.88, 0.86, and 0.69, respectively. Using receiver-operating characteristic curves, the area under the curve for class predictions was 0.96, 0.89, and 0.91, respectively, with a weighted average at 0.94. Classifiers' performances were highest for antibody-mediated rejection diagnosis with 94% correct predictions, compared with 88% correct predictions for control biopsies and 60% for T-cell-mediated rejection biopsies. Gene expression levels assessed by RT-MLPA and Nanostring were correlated: r = 0.68, P < 0.001. Equivalent gene expression profiles were obtained with both assays in 81% of the samples. CONCLUSIONS The 17-gene panel RT-MLPA assay, developed here for formalin-fixed paraffin-embedded kidney transplant biopsies, classified kidney transplant rejection with an overall accurate prediction ratio of 0.83. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/CJASN/2023_04_10_CJN10100822.mp3.
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Affiliation(s)
- Tristan de Nattes
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
- Univ Rouen Normandie, INSERM U1234, Rouen, France
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Jack Beadle
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Frederic Toulza
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Edvin Candon
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Philippe Ruminy
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - Arnaud François
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Dominique Bertrand
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Dominique Guerrot
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Fanny Drieux
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Candice Roufosse
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
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11
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Kawabe M, Yamamoto I. Current Status and Perspectives on Recurrent IgA Nephropathy after Kidney Transplantation. Nephron Clin Pract 2023; 147 Suppl 1:9-13. [PMID: 36966530 DOI: 10.1159/000530341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023] Open
Abstract
IgA nephropathy (IgAN) is the most common form of glomerulonephritis worldwide. IgAN progresses to end-stage kidney disease in 20-40% of patients within 20 years of diagnosis. Kidney transplantation is the most effective option for patients with end-stage kidney disease caused by IgAN, but recurrence can occur in the transplanted kidney. The IgAN recurrence rate varies from 1% to 10% per year and varies according to the follow-up period, diagnostic modality, and biopsy criteria. Of note, studies based on protocol biopsies have reported a higher incidence of recurrence, which also occurred earlier after transplantation. In addition, recent data show that recurrence of IgAN is a more significant cause of allograft failure than previously believed. Little is known about the pathophysiology of IgAN recurrence, but several potential biomarkers have been investigated. Among them, galactose-deficient IgA1 (Gd-IgA1), IgG anti-Gd-IgA1 antibodies, and soluble CD89 could play a pivotal role in disease activity. This review aims to describe the current status of recurrent IgAN, including the incidence, clinical characteristics, risk factors, and future perspectives, with a focus on the available therapeutic approaches.
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Affiliation(s)
- Mayuko Kawabe
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan,
| | - Izumi Yamamoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
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12
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Yamamoto I, Kawabe M, Hayashi A, Kobayashi A, Yamamoto H, Yokoo T. Challenges Posed by the Banff Classification: Diagnosis and Treatment of Chronic Active T-Cell-Mediated Rejection. Nephron Clin Pract 2023; 147 Suppl 1:74-79. [PMID: 36928337 DOI: 10.1159/000530158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
The three primary sites of acute T-cell-mediated rejection (TCMR) in transplanted kidneys are the tubular epithelial cells, interstitium, and the vascular endothelial cells. The pathology of acute lesions is characterized by inflammatory cell infiltration; the final diagnosis suggested by the Banff 2019 classification is guided by grading of tubulitis (the t score), interstitial inflammation (the i score), and endarteritis (the v score). Consistent major issues when using the Banff classification are the etiological classifications of interstitial fibrosis and tubular atrophy (IFTA). From 2015 to 2019, technological advances (i.e., genetic analysis in paraffin sections) increased our understanding of IFTA status in patients with smoldering acute TCMR and the roles played by inflammatory cell infiltration (the i-IFTA score) and tubulitis (the t-IFTA score) in IFTA. These two scores were introduced when establishing the diagnostic criteria for chronic active TCMR. Despite the increase in complexity and the lack of a consensus treatment for chronic active TCMR, the Banff classification may evolve as new techniques (i.e., genetic analysis in paraffin sections and deep learning of renal pathology) are introduced. The Banff conference proceeded as follows. First, lesions were defined. Next, working groups were established to better understand the lesions and to derive better classification methods. Finally, the new Banff classification was developed. This approach will continue to evolve; the Banff classification will become a very useful diagnostic standard. This paper overviews the history of TCMR diagnosis using the Banff classification, and the clinical importance, treatment, and prospects for acute and chronic active TCMR.
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Affiliation(s)
- Izumi Yamamoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Mayuko Kawabe
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Ayaka Hayashi
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Akimitsu Kobayashi
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Hiroyasu Yamamoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Takashi Yokoo
- Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
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13
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Kikić Ž, Adam BA, Porras AB, Lefaucheur C, Loupy A, Regele H, Cejka D, Haas M, Colvin RB, Mengel M. Quantitative scoring of progression in transplant glomerulopathy using digital pathology may be superior to Banff cg scoring. Kidney Int 2023; 103:365-377. [PMID: 36436680 DOI: 10.1016/j.kint.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022]
Abstract
Antibody-mediated rejection (ABMR) is a major cause of kidney allograft failure. Biopsy-based surrogate endpoints reflecting ABMR progression on sequential biopsies that predict long-term outcome offer the potential to make treatment trials for ABMR feasible. However, the Banff transplant glomerulopathy (TG) scoring system (chronic glomerular injury score [cg]) relies on relatively crude and arbitrary ordinal grades and has low inter-observer concordance that currently limits its usefulness as a surrogate endpoint for ABMR progression in clinical drug trials. Here, we describe and validate a novel quantitative method for quantifying progression of TG in ABMR. Using digital pathology in sequential biopsies from 75 patients at various stages of ABMR, we scored all capillaries in the most affected glomeruli for basement membrane duplication that were correlated with allograft function, outcome, Banff lesion scores, and gene expression. Our digital scoring reflected TG progression better than the categorical Banff cg score and correlated with Banff ABMR and chronicity lesions, but not transcript changes. In multivariate analysis, the delta change between biopsies with serum creatinine and mean percent duplicated glomerular basement membranes was significantly associated with graft loss. Neither the delta in any Banff lesion scores (including cg) nor in gene expression was associated with outcome. Receiver operating characteristic curve analysis showed that the digital pathology approach was superior to the conventional score for predicting graft failure. Thus, our digital pathology-based approach for scoring TG accurately assessed progression in TG. However, further validation as a potential surrogate endpoint in clinical trials for the treatment of ABMR is warranted.
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Affiliation(s)
- Željko Kikić
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria; Department of Urology, Medical University Vienna, Vienna, Austria
| | - Benjamin A Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Anna Buxeda Porras
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Heinz Regele
- Institute of Clinical Pathology, Medical University Vienna, Vienna, Austria
| | - Daniel Cejka
- Division of Nephrology and Dialysis, Ordensklinikum Linz-Elisabethinen, Linz, Austria
| | - Mark Haas
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Robert B Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
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14
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El Sabagh A, Mohamed IB, Aloor FZ, Abdelwahab A, Hassan MM, Jalal PK. Current Status of Biomarkers and Molecular Diagnostic Tools for Rejection in Liver Transplantation: Light at the End of the Tunnel? J Clin Exp Hepatol 2023; 13:139-148. [PMID: 36647415 PMCID: PMC9840072 DOI: 10.1016/j.jceh.2022.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/24/2022] [Indexed: 01/19/2023] Open
Abstract
Strategies to minimize immune-suppressive medications after liver transplantation are limited by allograft rejection. Biopsy of liver is the current standard of care in diagnosing rejection. However, it adds to physical and economic burden to the patient and has diagnostic limitations. In this review, we aim to highlight the different biomarkers to predict and diagnose acute rejection. We also aim to explore recent advances in molecular diagnostics to improve the diagnostic yield of liver biopsies.
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Key Words
- 3BMBs, third bifurcation mucosal endo-bronchial biopsies
- AMR, antibody mediated rejection
- APC, antigen presenting cells
- AR, Acute rejection
- ATCMR, acute T-cell mediated rejection
- ATG, Anti-thymoglobulin
- AUC, area under curve
- AUROC, area under receiver operating characteristic curve
- B-HOT, Banff Human Organ Transplant
- CNI, Calcineurin inhibitors
- DSA, Donor specific antibodies
- FDA, Food and drug administration
- FFPE, formalin fixed paraffin embedded preparation
- GLUT-4, glucose transport-4
- HLA, human leukocyte antigens
- HNMR, high nuclear magnetic resonance
- ILTS, International liver transplantation society
- LT, Liver transplantation
- Liver transplantation
- MDWG, molecular diagnostic work group
- MFI, mean fluorescence intensity
- MHC, major histo–compatibility complex
- MMDX
- MMDX, Molecular microscopic diagnostic system
- MMF, Mycophenolate Mofetil
- MToR, Mechanistic target of Rapamycin
- NPV, Negative predictive value
- PPV, Positive predictive value
- RATs, rejection associated transcripts
- TBB, trans-bronchial biopsies
- UNOS, United network for organ sharing and procurement
- biomarker
- dd cfDNA, donor-derived cell-free DNA
- donor-derived cell-free DNA
- immune-suppression
- mRNA, messenger RNA
- miRNA, micro-RNA
- micro-RNA
- molecular diagnosis
- nano-string
- rejection
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Affiliation(s)
- Ahmed El Sabagh
- Division of Gastroenterology, Baylor College of Medicine, Houston, TX, USA
- Department of Internal Medicine, Gastroenterology & Hepatology, Ain Shams University, Cairo, Egypt
| | - Islam B. Mohamed
- Division of Gastroenterology, Baylor College of Medicine, Houston, TX, USA
- Department of Internal Medicine, Gastroenterology & Hepatology, Ain Shams University, Cairo, Egypt
| | - Fuad Z. Aloor
- Division of Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | - Ahmed Abdelwahab
- Division of Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | - Manal M. Hassan
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Prasun K. Jalal
- Division of Gastroenterology, Baylor College of Medicine, Houston, TX, USA
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15
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Varol H, Ernst A, Cristoferi I, Arns W, Baan CC, van Baardwijk M, van den Bosch T, Eckhoff J, Harth A, Hesselink DA, van Kemenade FJ, de Koning W, Kurschat C, Minnee RC, Mustafa DAM, Reinders MEJ, Shahzad-Arshad SP, Snijders MLH, Stippel D, Stubbs AP, von der Thüsen J, Wirths K, Becker JU, Clahsen-van Groningen MC. Feasibility and Potential of Transcriptomic Analysis Using the NanoString nCounter Technology to Aid the Classification of Rejection in Kidney Transplant Biopsies. Transplantation 2022; 107:903-912. [PMID: 36413151 PMCID: PMC10065817 DOI: 10.1097/tp.0000000000004372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Transcriptome analysis could be an additional diagnostic parameter in diagnosing kidney transplant (KTx) rejection. Here, we assessed feasibility and potential of NanoString nCounter analysis of KTx biopsies to aid the classification of rejection in clinical practice using both the Banff-Human Organ Transplant (B-HOT) panel and a customized antibody-mediated rejection (AMR)-specific NanoString nCounter Elements (Elements) panel. Additionally, we explored the potential for the classification of KTx rejection building and testing a classifier within our dataset. METHODS Ninety-six formalin-fixed paraffin-embedded KTx biopsies were retrieved from the archives of the ErasmusMC Rotterdam and the University Hospital Cologne. Biopsies with AMR, borderline or T cell-mediated rejections (BLorTCMR), and no rejection were compared using the B-HOT and Elements panels. RESULTS High correlation between gene expression levels was found when comparing the 2 chemistries pairwise (r = 0.76-0.88). Differential gene expression (false discovery rate; P < 0.05) was identified in biopsies diagnosed with AMR (B-HOT: 294; Elements: 76) and BLorTCMR (B-HOT: 353; Elements: 57) compared with no rejection. Using the most predictive genes from the B-HOT analysis and the Element analysis, 2 least absolute shrinkage and selection operators-based regression models to classify biopsies as AMR versus no AMR (BLorTCMR or no rejection) were developed achieving an receiver-operating-characteristic curve of 0.994 and 0.894, sensitivity of 0.821 and 0.480, and specificity of 1.00 and 0.979, respectively, during cross-validation. CONCLUSIONS Transcriptomic analysis is feasible on KTx biopsies previously used for diagnostic purposes. The B-HOT panel has the potential to differentiate AMR from BLorTCMR or no rejection and could prove valuable in aiding kidney transplant rejection classification.
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Affiliation(s)
- Hilal Varol
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Angela Ernst
- Institute of Medical Statistics and Computational Biology, University Hospital of Cologne, Cologne, Germany
| | - Iacopo Cristoferi
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Surgery, Division of HPB & Transplant Surgery, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wolfgang Arns
- Cologne Merheim Medical Center, Cologne General Hospital, Cologne, Germany
| | - Carla C Baan
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Myrthe van Baardwijk
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Surgery, Division of HPB & Transplant Surgery, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thierry van den Bosch
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jennifer Eckhoff
- Department of General Visceral Cancer and Transplant Surgery Transplant Center Cologne, University of Cologne Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | - Ana Harth
- Cologne Merheim Medical Center, Cologne General Hospital, Cologne, Germany
| | - Dennis A Hesselink
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Folkert J van Kemenade
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Willem de Koning
- Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christine Kurschat
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Robert C Minnee
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Surgery, Division of HPB & Transplant Surgery, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dana A M Mustafa
- Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marlies E J Reinders
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Nephrology and Transplantation, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Malou L H Snijders
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Dirk Stippel
- Department of General Visceral Cancer and Transplant Surgery Transplant Center Cologne, University of Cologne Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | - Andrew P Stubbs
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Clinical Bioinformatics Unit, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan von der Thüsen
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Katharina Wirths
- Department of Internal Medicine, Faculty of Medicine, University Bonn, Bonn, Germany
| | - Jan U Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Marian C Clahsen-van Groningen
- Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
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16
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Manjunath HS, Al Khulaifi M, Sidahmed H, Ammar A, Vadakekolathu J, Rutella S, Al-Mohannadi MJ, Elawad M, Mifsud W, Charles A, Maccalli C, Tomei S. Gene Expression Profiling of FFPE Samples: A Titration Test. Technol Cancer Res Treat 2022; 21:15330338221129710. [PMID: 36415121 PMCID: PMC9706083 DOI: 10.1177/15330338221129710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/23/2022] [Indexed: 12/23/2023] Open
Abstract
The gene expression analysis of formalin-fixed paraffin-embedded (FFPE) tissues is often hampered by poor RNA quality, which results from the oxidation, cross-linking and other chemical modifications induced by the inclusion in paraffin. Yet, FFPE samples are a valuable source for molecular studies and can provide great insights into disease progression and prognosis. With the advancement of genomic technologies, new methods have been established that offer reliable and accurate gene expression workflows on samples of poor quality. NanoString is a probe-based technology that allows the direct counting of the mRNA transcripts and can be applied to degraded samples. Here, we have tested 2 RNA extraction methods for FFPE samples, and we have performed a titration experiment to evaluate the impact of RNA degradation and RNA input on the gene expression profiles assessed using the NanoString IO360 panel. We have selected FFPE samples of different DV200 values and assessed them on the nCounter platform with 2 different amounts of input RNA. This study concludes that the nCounter is a robust and reliable platform to assess the gene expression of RNA samples with DV200 > 30%; its robustness and ease of use could be of particular benefit to clinical settings.
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Affiliation(s)
| | - Moza Al Khulaifi
- Laboratory of Immune and Biological Therapy, Research Department,
Sidra
Medicine, Doha, Qatar
| | - Heba Sidahmed
- Laboratory of Immune and Biological Therapy, Research Department,
Sidra
Medicine, Doha, Qatar
| | - Adham Ammar
- Department of Pathology, Hamad Medical
Corporation, Doha, Qatar
| | - Jayakumar Vadakekolathu
- John van Geest Cancer Research Centre, School of Science and
Technology, Nottingham
Trent University, Nottingham, UK
| | - Sergio Rutella
- John van Geest Cancer Research Centre, School of Science and
Technology, Nottingham
Trent University, Nottingham, UK
| | | | - Mamoun Elawad
- Department of Gastroenterology, Sidra Medicine,
Doha, Qatar
| | - William Mifsud
- Department of Anatomical Pathology,
Sidra
Medicine, Doha, Qatar
| | - Adrian Charles
- Department of Anatomical Pathology,
Sidra
Medicine, Doha, Qatar
| | - Cristina Maccalli
- Laboratory of Immune and Biological Therapy, Research Department,
Sidra
Medicine, Doha, Qatar
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Research Department,
Sidra
Medicine, Doha, Qatar
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17
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Klomjit N, El Ters M, Adam BA, Sampathkumar P, Razonable RR, Taler SJ, Taner T, Alexander MP. Diffuse C4d staining of peritubular capillaries in renal allograft following bamlanivimab therapy. Am J Transplant 2022; 22:289-293. [PMID: 34358400 DOI: 10.1111/ajt.16783] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 01/25/2023]
Abstract
Neutralizing monoclonal antibodies such as bamlanivimab emerged as promising agents in treating kidney transplant recipients with COVID-19. However, the impact of bamlanivimab on kidney allograft histology remains unknown. We report a case of a kidney transplant recipient who received bamlanivimab for COVID-19 with subsequent histologic findings of diffuse peritubular capillary C4d staining. A 33-year-old man with end-stage kidney disease secondary to hypertension who received an ABO compatible kidney from a living donor, presented for his 4-month protocol visit. He was diagnosed with COVID-19 44 days prior to his visit and had received bamlanivimab with an uneventful recovery. His 4-month surveillance biopsy showed diffuse C4d staining of the peritubular capillaries without other features of antibody-mediated rejection (ABMR). Donor-specific antibodies were negative on repeat evaluations. ABMR gene expression panel was negative. His creatinine was stable at 1.3 mg/dl, without albuminuria. Given the temporal relationship between bamlanivimab and our observations of diffuse C4d staining of the peritubular capillaries, we hypothesize that bamlanivimab might bind to angiotensin-converting enzyme 2, resulting in classical complement pathway and C4d deposition. We elected to closely monitor kidney function which has been stable at 6 months after the biopsy. In conclusion, diffuse C4d may present following bamlanivimab administration without any evidence of ABMR.
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Affiliation(s)
- Nattawat Klomjit
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Mireille El Ters
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Benjamin A Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Sandra J Taler
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Timucin Taner
- Division of Transplant Surgery and Department of Immunology, Mayo Clinic, Rochester, Minnesota
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18
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Loupy A, Mengel M, Haas M. 30 years of the International Banff Classification for Allograft Pathology: The Past, Present and Future of Kidney Transplant Diagnostics. Kidney Int 2021; 101:678-691. [DOI: 10.1016/j.kint.2021.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
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19
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Trailin A, Mrazova P, Hruba P, Voska L, Sticova E, Slavcev A, Novotny M, Kocik M, Viklicky O. Chronic Active Antibody-Mediated Rejection Is Associated With the Upregulation of Interstitial But Not Glomerular Transcripts. Front Immunol 2021; 12:729558. [PMID: 34616398 PMCID: PMC8488163 DOI: 10.3389/fimmu.2021.729558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
Molecular assessment of renal allografts has already been suggested in antibody-mediated rejection (ABMR), but little is known about the gene transcript patterns in particular renal compartments. We used laser capture microdissection coupled with quantitative RT-PCR to distinguish the transcript patterns in the glomeruli and tubulointerstitium of kidney allografts in sensitized retransplant recipients at high risk of ABMR. The expressions of 13 genes were quantified in biopsies with acute active ABMR, chronic active ABMR, acute tubular necrosis (ATN), and normal findings. The transcripts were either compartment specific (TGFB1 in the glomeruli and HAVCR1 and IGHG1 in the tubulointerstitium), ABMR specific (GNLY), or follow-up specific (CXCL10 and CX3CR1). The transcriptional profiles of early acute ABMR shared similarities with ATN. The transcripts of CXCL10 and TGFB1 increased in the glomeruli in both acute ABMR and chronic active ABMR. Chronic active ABMR was associated with the upregulation of most genes (SH2D1B, CX3CR1, IGHG1, MS4A1, C5, CD46, and TGFB1) in the tubulointerstitium. In this study, we show distinct gene expression patterns in specific renal compartments reflecting cellular infiltration observed by conventional histology. In comparison with active ABMR, chronic active ABMR is associated with increased transcripts of tubulointerstitial origin.
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Affiliation(s)
- Andriy Trailin
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Petra Mrazova
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Ludek Voska
- Department of Clinical and Transplant Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Eva Sticova
- Department of Clinical and Transplant Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Antonij Slavcev
- Department of Immunogenetics, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Marek Novotny
- Department of Nephrology, Transplant Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia.,Institute of Physiology, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Matej Kocik
- Transplantation Surgery Department, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia.,Department of Nephrology, Transplant Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
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20
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Alexander MP, Mangalaparthi KK, Madugundu AK, Moyer AM, Adam BA, Mengel M, Singh S, Herrmann SM, Rule AD, Cheek EH, Herrera Hernandez LP, Graham RP, Aleksandar D, Aubry MC, Roden AC, Hagen CE, Quinton RA, Bois MC, Lin PT, Maleszewski JJ, Cornell LD, Sethi S, Pavelko KD, Charlesworth J, Narasimhan R, Larsen CP, Rizza SA, Nasr SH, Grande JP, McKee TD, Badley AD, Pandey A, Taner T. Acute Kidney Injury in Severe COVID-19 Has Similarities to Sepsis-Associated Kidney Injury: A Multi-Omics Study. Mayo Clin Proc 2021; 96:2561-2575. [PMID: 34425963 PMCID: PMC8279954 DOI: 10.1016/j.mayocp.2021.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 01/20/2023]
Abstract
OBJECTIVE To compare coronavirus disease 2019 (COVID-19) acute kidney injury (AKI) to sepsis-AKI (S-AKI). The morphology and transcriptomic and proteomic characteristics of autopsy kidneys were analyzed. PATIENTS AND METHODS Individuals 18 years of age and older who died from COVID-19 and had an autopsy performed at Mayo Clinic between April 2020 to October 2020 were included. Morphological evaluation of the kidneys of 17 individuals with COVID-19 was performed. In a subset of seven COVID-19 cases with postmortem interval of less than or equal to 20 hours, ultrastructural and molecular characteristics (targeted transcriptome and proteomics analyses of tubulointerstitium) were evaluated. Molecular characteristics were compared with archived cases of S-AKI and nonsepsis causes of AKI. RESULTS The spectrum of COVID-19 renal pathology included macrophage-dominant microvascular inflammation (glomerulitis and peritubular capillaritis), vascular dysfunction (peritubular capillary congestion and endothelial injury), and tubular injury with ultrastructural evidence of mitochondrial damage. Investigation of the spatial architecture using a novel imaging mass cytometry revealed enrichment of CD3+CD4+ T cells in close proximity to antigen-presenting cells, and macrophage-enriched glomerular and interstitial infiltrates, suggesting an innate and adaptive immune tissue response. Coronavirus disease 2019 AKI and S-AKI, as compared to nonseptic AKI, had an enrichment of transcriptional pathways involved in inflammation (apoptosis, autophagy, major histocompatibility complex class I and II, and type 1 T helper cell differentiation). Proteomic pathway analysis showed that COVID-19 AKI and to a lesser extent S-AKI were enriched in necroptosis and sirtuin-signaling pathways, both involved in regulatory response to inflammation. Upregulation of the ceramide-signaling pathway and downregulation of oxidative phosphorylation in COVID-19 AKI were noted. CONCLUSION This data highlights the similarities between S-AKI and COVID-19 AKI and suggests that mitochondrial dysfunction may play a pivotal role in COVID-19 AKI. This data may allow the development of novel diagnostic and therapeutic targets.
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Affiliation(s)
- Mariam P Alexander
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Kiran K Mangalaparthi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Institute of Bioinformatics, International Technology Park, Karnataka, India; Amrita School of Biotechnology, Kerala, India
| | - Anil K Madugundu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Institute of Bioinformatics, International Technology Park, Karnataka, India; Manipal Academy of Higher Education, Manipal, Karnataka, India; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Karnataka, India
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin A Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Smrita Singh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Institute of Bioinformatics, International Technology Park, Karnataka, India; Manipal Academy of Higher Education, Manipal, Karnataka, India; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Karnataka, India
| | - Sandra M Herrmann
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Andrew D Rule
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - E Heidi Cheek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Rondell P Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Denic Aleksandar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - Anja C Roden
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Catherine E Hagen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Reade A Quinton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Melanie C Bois
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Peter T Lin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Joseph J Maleszewski
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Lynn D Cornell
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sanjeev Sethi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Jon Charlesworth
- Microscopy and Cell Analysis Core, Mayo Clinic, Rochester, MN, USA
| | | | | | - Stacey A Rizza
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Samih H Nasr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Joseph P Grande
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Trevor D McKee
- STTARR Innovation Core Facility, University Health Network, Toronto, Ontario, Canada
| | - Andrew D Badley
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA; Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Karnataka, India
| | - Timucin Taner
- Department of Surgery (T.T.), Mayo Clinic, Rochester, MN, USA; Department of Immunology (T.T.), Mayo Clinic, Rochester, MN, USA
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21
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Caveolin-1 in Kidney Chronic Antibody-Mediated Rejection: An Integrated Immunohistochemical and Transcriptomic Analysis Based on the Banff Human Organ Transplant (B-HOT) Gene Panel. Biomedicines 2021; 9:biomedicines9101318. [PMID: 34680435 PMCID: PMC8533527 DOI: 10.3390/biomedicines9101318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Caveolin-1 overexpression has previously been reported as a marker of endothelial injury in kidney chronic antibody-mediated rejection (c-ABMR), but conclusive evidence supporting its use for daily diagnostic practice is missing. This study aims to evaluate if Caveolin-1 can be considered an immunohistochemical surrogate marker of c-ABMR. Caveolin-1 expression was analyzed in a selected series of 22 c-ABMR samples and 11 controls. Caveolin-1 immunohistochemistry proved positive in peritubular and glomerular capillaries of c-ABMR specimens, irrespective of C4d status whereas all controls were negative. Multiplex gene expression profiling in c-ABMR cases confirmed Caveolin-1 overexpression and identified additional genes (n = 220) and pathways, including MHC Class II antigen presentation and Type II interferon signaling. No differences in terms of gene expression (including Caveolin-1 gene) were observed according to C4d status. Conversely, immune cell signatures showed a NK-cell prevalence in C4d-negative samples compared with a B-cell predominance in C4d-positive cases, a finding confirmed by immunohistochemical assessment. Finally, differentially expressed genes were observed between c-ABMR and controls in pathways associated with Caveolin-1 functions (angiogenesis, cell metabolism and cell–ECM interaction). Based on our findings, Caveolin-1 resulted as a key player in c-ABMR, supporting its role as a marker of this condition irrespective of C4d status.
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C3 complement inhibition prevents antibody-mediated rejection and prolongs renal allograft survival in sensitized non-human primates. Nat Commun 2021; 12:5456. [PMID: 34526511 PMCID: PMC8443599 DOI: 10.1038/s41467-021-25745-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 08/24/2021] [Indexed: 12/20/2022] Open
Abstract
Sensitized kidney transplant recipients experience high rates of antibody-mediated rejection due to the presence of donor-specific antibodies and immunologic memory. Here we show that transient peri-transplant treatment with the central complement component C3 inhibitor Cp40 significantly prolongs median allograft survival in a sensitized nonhuman primate model. Despite donor-specific antibody levels remaining high, fifty percent of Cp40-treated primates maintain normal kidney function beyond the last day of treatment. Interestingly, presence of antibodies of the IgM class associates with reduced median graft survival (8 vs. 40 days; p = 0.02). Cp40 does not alter lymphocyte depletion by rhesus-specific anti-thymocyte globulin, but inhibits lymphocyte activation and proliferation, resulting in reduced antibody-mediated injury and complement deposition. In summary, Cp40 prevents acute antibody-mediated rejection and prolongs graft survival in primates, and inhibits T and B cell activation and proliferation, suggesting an immunomodulatory effect beyond its direct impact on antibody-mediated injury. Donor-specific antibodies in sensitized recipients may cause kidney transplant rejection. Here the authors show that complement component C3 inhibition prolongs graft survival by inhibiting T and B cell proliferation/activation and hence tissue injury, despite antibody levels remaining unaffected.
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23
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Adam BA, Murakami N, Reid G, Du K, Jasim R, Boils CL, Bu L, Hill PD, Murray AG, Renaudin K, Roufosse C, Weins A, Wen K, Riella LV, Mengel M. Gene Expression Profiling in Kidney Transplants with Immune Checkpoint Inhibitor-Associated Adverse Events. Clin J Am Soc Nephrol 2021; 16:1376-1386. [PMID: 34244334 PMCID: PMC8729568 DOI: 10.2215/cjn.00920121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Immune checkpoint inhibitors are increasingly used to treat various malignancies, but their application in patients with kidney transplants is complicated by high allograft rejection rates. Immune checkpoint inhibitor-associated rejection is a novel, poorly understood entity demonstrating overlapping histopathologic features with immune checkpoint inhibitor-associated acute interstitial nephritis, which poses a challenge for diagnosis and clinical management. We sought to improve the understanding of these entities through biopsy-based gene expression analysis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS NanoString was used to measure and compare the expression of 725 immune-related genes in 75 archival kidney biopsies, including a 25-sample discovery cohort comprising pure T cell-mediated rejection and immune checkpoint inhibitor-associated acute interstitial nephritis and an independent 50-sample validation cohort comprising immune checkpoint inhibitor-associated acute interstitial nephritis, immune checkpoint inhibitor-associated T cell-mediated rejection, immune checkpoint inhibitor-associated crescentic GN, drug-induced acute interstitial nephritis, BK virus nephropathy, and normal biopsies. RESULTS Significant molecular overlap was observed between immune checkpoint inhibitor-associated acute interstitial nephritis and T cell-mediated rejection. Nevertheless, IFI27, an IFN-α-induced transcript, was identified and validated as a novel biomarker for differentiating immune checkpoint inhibitor-associated T cell-mediated rejection from immune checkpoint inhibitor-associated acute interstitial nephritis (validation cohort: P<0.001, area under the receiver operating characteristic curve =100%, accuracy =86%). Principal component analysis revealed heterogeneity in inflammatory gene expression patterns within sample groups; however, immune checkpoint inhibitor-associated T cell-mediated rejection and immune checkpoint inhibitor-associated acute interstitial nephritis both demonstrated relatively more molecular overlap with drug-induced acute interstitial nephritis than T cell-mediated rejection, suggesting potential dominance of hypersensitivity mechanisms in these entities. CONCLUSIONS These results indicate that, although there is significant molecular similarity between immune checkpoint inhibitor-associated rejection and acute interstitial nephritis, biopsy-based measurement of IFI27 gene expression represents a potential biomarker for differentiating these entities.
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Affiliation(s)
- Benjamin A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Naoka Murakami
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Graeme Reid
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Katie Du
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Ruqaya Jasim
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Lihong Bu
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Peter D. Hill
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Allan G. Murray
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karine Renaudin
- Department of Pathology, Nantes University Hospital, Nantes, France
| | - Candice Roufosse
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Astrid Weins
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Kevin Wen
- Division of Nephrology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Leonardo V. Riella
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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24
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Multiplex gene analysis reveals T-cell and antibody-mediated rejection-specific upregulation of complement in renal transplants. Sci Rep 2021; 11:15464. [PMID: 34326417 PMCID: PMC8322413 DOI: 10.1038/s41598-021-94954-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/13/2021] [Indexed: 01/03/2023] Open
Abstract
In renal transplantation, complement is involved in ischemia reperfusion injury, graft rejection and dysfunction. However, it is still unclear how induction of complement and its activation are initiated. Using allograft biopsies of a well-characterized cohort of 28 renal transplant patients with no rejection (Ctrl), delayed graft function (DGF), acute T-cell-mediated (TCMR) or antibody-mediated rejection (ABMR) we analyzed differences in complement reaction. For that mRNA was isolated from FFPE sections, quantified with a multiplex gene expression panel and correlated with transplant conditions and follow-up of patients. Additionally, inflammatory cells were quantified by multiplex immunohistochemistry. In allograft biopsies with TCMR and ABMR gene expression of C1QB was 2-4 fold elevated compared to Ctrl. In TCMR biopsies, mRNA counts of several complement-related genes including C1S, C3, CFB and complement regulators CFH, CR1 and SERPING1 were significantly increased compared to Ctrl. Interestingly, expression levels of about 75% of the analyzed complement related genes correlated with cold ischemia time (CIT) and markers of inflammation. In conclusion, this study suggest an important role of complement in transplant pathology which seems to be at least in part triggered by CIT. Multiplex mRNA analysis might be a useful method to refine diagnosis and explore new pathways involved in rejection.
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25
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Toulza F, Dominy K, Willicombe M, Beadle J, Santos E, Cook HT, Szydlo RM, McLean A, Roufosse C. Diagnostic application of transcripts associated with antibody-mediated rejection in kidney transplant biopsies. Nephrol Dial Transplant 2021; 37:1576-1584. [PMID: 34320215 PMCID: PMC9317169 DOI: 10.1093/ndt/gfab231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Indexed: 11/22/2022] Open
Abstract
Background The diagnosis of antibody-mediated rejection (AMR) is reached using the Banff Classification for Allograft Pathology, which now includes gene expression analysis. In this study, we investigate the application of ‘increased expression of thoroughly validated gene transcripts/classifiers strongly associated with AMR’ as diagnostic criteria. Method We used quantitative real-time polymerase chain reaction for 10 genes associated with AMR in a retrospective cohort of 297 transplant biopsies, including biopsies that met the full diagnostic criteria for AMR, even without molecular data (AMR, n = 27), biopsies that showed features of AMR, but that would only meet criteria for AMR with increased transcripts [suspicious for AMR (AMRsusp), n = 49] and biopsies that would never meet criteria for AMR (No-AMR, n = 221). Results A 10-gene AMR score trained by a receiver-operating characteristic to identify AMR found 16 cases with a high score among the AMRsusp cases (AMRsusp-high) that had significantly worse graft survival than those with a low score (AMRsusp-low; n = 33). In both univariate and multivariate Cox regression analysis, the AMR 10-gene score was significantly associated with an increased hazard ratio (HR) for graft loss (GL) in the AMRsusp group (HR = 1.109, P = 0.004 and HR = 1.138, P = 0.012, respectively), but not in the whole cohort. Net reclassification index and integrated discrimination improvement analyses demonstrated improved risk classification and superior discrimination, respectively, for GL when considering the gene score in addition to histological and serological data, but only in the AMRsusp group, not the whole cohort. Conclusions This study provides evidence that a gene score strongly associated with AMR helps identify cases at higher risk of GL in biopsies that are suspicious for AMR but do not meet full criteria.
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Affiliation(s)
- Frederic Toulza
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
| | - Kathy Dominy
- Molecular Pathology Laboratory, North West London Pathology, London, United Kingdom
| | - Michelle Willicombe
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom.,Imperial College Renal and Transplant Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Jack Beadle
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
| | - Eva Santos
- Histocompatibility and Immunogenetics, North West London Pathology, London, United Kingdom
| | - H Terence Cook
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
| | - Richard M Szydlo
- Imperial College, Medical Statistician, Dept Immunology and Inflammation, London, United Kingdom
| | - Adam McLean
- Imperial College Renal and Transplant Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Candice Roufosse
- Imperial College, Centre for Inflammatory Disease, Dept Immunology and Inflammation, London, United Kingdom
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26
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Robin B, Dagobert J, Isnard P, Rabant M, Duong-Van-Huyen JP. [New technologies for renal pathology: Transcriptomics on paraffin-embedded fixed tissue]. Nephrol Ther 2021; 17S:S54-S59. [PMID: 33910699 DOI: 10.1016/j.nephro.2020.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/01/2020] [Indexed: 11/19/2022]
Abstract
The development of new high-throughput technologies in genomics and then in transcriptomics has modified clinical approach in nephrology. At the interface between high-throughput technologies (microarray, new generation sequencing «NGS») and few mRNA analysis (reverse transcriptase quantitative PCR [RT-qPCR]), the nCounter® of NanoString® offers a new and complementary approach. Capable of analyzing formalin-fixed paraffin-embedded samples, this technology is a credible candidate for implanting transcriptomics in clinical routine.
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Affiliation(s)
- Blaise Robin
- Paris Translational Research Center for Organ Transplantation, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 56, rue Leblanc, 75015 Paris, France; Inserm U970, 56, rue Leblanc, 75015 Paris, France.
| | - Jessy Dagobert
- Paris Translational Research Center for Organ Transplantation, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 56, rue Leblanc, 75015 Paris, France; Inserm U970, 56, rue Leblanc, 75015 Paris, France
| | - Pierre Isnard
- Service d'anatomie pathologique, hôpital Necker-Enfants-Malades, 149, rue de Sèvres, 75015 Paris, France
| | - Marion Rabant
- Service d'anatomie pathologique, hôpital Necker-Enfants-Malades, 149, rue de Sèvres, 75015 Paris, France
| | - Jean-Paul Duong-Van-Huyen
- Paris Translational Research Center for Organ Transplantation, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 56, rue Leblanc, 75015 Paris, France; Inserm U970, 56, rue Leblanc, 75015 Paris, France; Service d'anatomie pathologique, hôpital Necker-Enfants-Malades, 149, rue de Sèvres, 75015 Paris, France
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27
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Molecular Analysis of Renal Allograft Biopsies: Where Do We Stand and Where Are We Going? Transplantation 2021; 104:2478-2486. [PMID: 32150035 DOI: 10.1097/tp.0000000000003220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A renal core biopsy for histological evaluation is the gold standard for diagnosing renal transplant pathology. However, renal biopsy interpretation is subjective and can render insufficient precision, making it difficult to apply a targeted therapeutic regimen for the individual patient. This warrants a need for additional methods assessing disease state in the renal transplant. Significant research activity has been focused on the role of molecular analysis in the diagnosis of renal allograft rejection. The identification of specific molecular expression patterns in allograft biopsies related to different types of allograft injury could provide valuable information about the processes underlying renal transplant dysfunction and can be used for the development of molecular classifier scores, which could improve our diagnostic and prognostic ability and could guide treatment. Molecular profiling has the potential to be more precise and objective than histological evaluation and may identify injury even before it becomes visible on histology, making it possible to start treatment at the earliest time possible. Combining conventional diagnostics (histology, serology, and clinical data) and molecular evaluation will most likely offer the best diagnostic approach. We believe that the use of state-of-the-art molecular analysis will have a significant impact in diagnostics after renal transplantation. In this review, we elaborate on the molecular phenotype of both acute and chronic T cell-mediated rejection and antibody-mediated rejection and discuss the additive value of molecular profiling in the setting of diagnosing renal allograft rejection and how this will improve transplant patient care.
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28
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Adam BA, Kikic Z, Wagner S, Bouatou Y, Gueguen J, Drieux F, Reid G, Du K, Bräsen JH, D'Agati VD, Drachenberg CB, Farkash EA, Brad Farris A, Geldenhuys L, Loupy A, Nickeleit V, Rabant M, Randhawa P, Regele H, Mengel M. Intragraft gene expression in native kidney BK virus nephropathy versus T cell-mediated rejection: Prospects for molecular diagnosis and risk prediction. Am J Transplant 2020; 20:3486-3501. [PMID: 32372431 DOI: 10.1111/ajt.15980] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/03/2020] [Accepted: 04/25/2020] [Indexed: 01/25/2023]
Abstract
Novel tools are needed to improve diagnostic accuracy and risk prediction in BK virus nephropathy (BKVN). We assessed the utility of intragraft gene expression testing for these purposes. Eight hundred genes were measured in 110 archival samples, including a discovery cohort of native kidney BKVN (n = 5) vs pure T cell-mediated rejection (TCMR; n = 10). Five polyomavirus genes and seven immune-related genes (five associated with BKVN and two associated with TCMR) were significantly differentially expressed between these entities (FDR < 0.05). These three sets of genes were further evaluated in samples representing a spectrum of BK infection (n = 25), followed by a multicenter validation cohort of allograft BKVN (n = 60) vs TCMR (n = 10). Polyomavirus 5-gene set expression reliably distinguished BKVN from TCMR (validation cohort AUC = 0.992), but the immune gene sets demonstrated suboptimal diagnostic performance (AUC ≤ 0.720). Within the validation cohort, no significant differences in index biopsy gene expression were identified between BKVN patients demonstrating resolution (n = 35), persistent infection (n = 14) or de novo rejection (n = 11) 6 months following a standardized reduction in immunosuppression. These results suggest that, while intragraft polyomavirus gene expression may be useful as an ancillary diagnostic for BKVN, assessment for concurrent TCMR and prediction of clinical outcome may not be feasible with current molecular tools.
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Affiliation(s)
- Benjamin A Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Zeljko Kikic
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Siegfried Wagner
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Yassine Bouatou
- Paris Translational Research Center for Organ Transplantation, Paris, France
| | - Juliette Gueguen
- Paris Translational Research Center for Organ Transplantation, Paris, France
| | - Fanny Drieux
- Department of Pathology, Necker Hospital, Paris, France
| | - Graeme Reid
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Katie Du
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Jan H Bräsen
- Nephropathology Unit, Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Vivette D D'Agati
- Department of Pathology, Columbia University Medical Center, New York, New York, USA
| | - Cinthia B Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Evan A Farkash
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Alexandre Loupy
- Paris Translational Research Center for Organ Transplantation, Paris, France
| | - Volker Nickeleit
- Division of Nephropathology, Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Marion Rabant
- Department of Pathology, Necker Hospital, Paris, France
| | - Parmjeet Randhawa
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Heinz Regele
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
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29
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Jantuan E, Chiu B, Chiu B, Shen F, Oudit GY, Sergi C. The tumor microenvironment may trigger lymphoproliferation in cardiac myxoma. Transl Oncol 2020; 14:100911. [PMID: 33129111 PMCID: PMC7586245 DOI: 10.1016/j.tranon.2020.100911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
Lymphoproliferative disorders (LPD) in cardiac myxomas (CM) has been occasionally reported, and chronic inflammation in response to viral infection may be the key. CM can upregulate autophagy, creating a favorable environment for Epstein Barr Virus (EBV)-driven oncogenesis. P62 accumulates when autophagy is inhibited, and aberrant excessive p62 may result from autophagy defect, causing oxidative stress and tumorigenesis. NanoString technology is a relatively new method for capturing tumor-immune signaling in tissues exploring how the signaling axis is associated with inflammation.
Cardiac myxomas (CM) and primary cardiac lymphoproliferative disorders (LPD) are rare primary cardiac neoplasms. The composite occurrence of LPD in CM has been occasionally reported, and chronic inflammation in response to viral infection has been suggested to be at the basis of oncogenesis. Cancers can upregulate autophagy to endure microenvironmental stress and to increase local growth and aggressiveness. CM exhibit a dichotomous separation in low and high inflammatory grades (LIG vs. HIG). We studied 23 CMs using autophagy-related proteins and NanoString technology for gene expression. Autophagy-related proteins (Beclin-1, LAMP-1, LC3, and p62) were demonstrated in both tumor and stromal cells. ATG genes showed a progression of involvement in CM using an 8-gene signature. They were associated with Epstein-Barr virus (EBV) encoded latent membrane protein 1 (EBV LMP1) activation. We suggest that CM can upregulate autophagy, creating a favorable environment for EBV-driven oncogenesis. To the best of our knowledge, the present study is the first to report on the TME using the expression of autophagy-related genes and proteins in CM. The microenvironment of CM is dynamic, with a variety of cell types and different molecular pathways at play, and this study may clearly warrant further investigation.
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Affiliation(s)
- Eugeniu Jantuan
- Department of Laboratory Medicine and Pathology, University of Alberta Hospital, 8440-112 Street, Edmonton T6G 2B7, Alberta, Canada
| | - Brian Chiu
- Department of Laboratory Medicine and Pathology, University of Alberta Hospital, 8440-112 Street, Edmonton T6G 2B7, Alberta, Canada
| | - Bonnie Chiu
- Department of Laboratory Medicine and Pathology, University of Alberta Hospital, 8440-112 Street, Edmonton T6G 2B7, Alberta, Canada
| | - Fan Shen
- Department of Laboratory Medicine and Pathology, University of Alberta Hospital, 8440-112 Street, Edmonton T6G 2B7, Alberta, Canada
| | - Gavin Y Oudit
- Department of Medicine, Division of Cardiology, Mazankowski Alberta Heart Institute, Edmonton, AB, Canada
| | - Consolato Sergi
- Department of Laboratory Medicine and Pathology, University of Alberta Hospital, 8440-112 Street, Edmonton T6G 2B7, Alberta, Canada; Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; National "111″ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China; Tianyou Hospital, Wuhan University of Science and Technology, Wuhan, Hubei, China.
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30
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Toulza F, Dominy K, Cook T, Galliford J, Beadle J, McLean A, Roufosse C. Technical considerations when designing a gene expression panel for renal transplant diagnosis. Sci Rep 2020; 10:17909. [PMID: 33087822 PMCID: PMC7578804 DOI: 10.1038/s41598-020-74794-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Gene expression analysis is emerging as a new diagnostic tool in transplant pathology, in particular for the diagnosis of antibody-mediated rejection. Diagnostic gene expression panels are defined on the basis of their pathophysiological relevance, but also need to be tested for their robustness across different preservatives and analysis platforms. The aim of this study is the investigate the effect of tissue sampling and preservation on candidate genes included in a renal transplant diagnostic panel. Using the NanoString platform, we compared the expression of 219 genes in 51 samples, split for formalin-fixation and paraffin-embedding (FFPE) and RNAlater preservation (RNAlater). We found that overall, gene expression significantly correlated between FFPE and RNAlater samples. However, at the individual gene level, 46 of the 219 genes did not correlate across the 51 matched FFPE and RNAlater samples. Comparing gene expression results using NanoString and qRT-PCR for 18 genes in the same pool of RNA (RNAlater), we found a significant correlation in 17/18 genes. Our study indicates that, in samples from the same routine diagnostic renal transplant biopsy procedure split for FFPE and RNAlater, 21% of 219 genes of potential biological significance do not correlate in expression. Whether this is due to fixatives or tissue sampling, selection of gene panels for routine diagnosis should take this information into consideration.
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Affiliation(s)
- F Toulza
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK
| | - K Dominy
- Molecular Pathology Laboratory, North West London Pathology, London, UK
| | - T Cook
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK
| | - J Galliford
- Imperial Kidney and Transplant Centre, London, UK
| | - J Beadle
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK
| | - A McLean
- Imperial Kidney and Transplant Centre, London, UK
| | - C Roufosse
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK.
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31
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Bozso SJ, Kang JJH, Basu R, Adam B, Dyck JRB, Oudit GY, Moon MC, Freed DH, Nagendran J, Nagendran J. Structural Valve Deterioration Is Linked to Increased Immune Infiltrate and Chemokine Expression. J Cardiovasc Transl Res 2020; 14:503-512. [PMID: 33089488 DOI: 10.1007/s12265-020-10080-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/15/2020] [Indexed: 01/04/2023]
Abstract
We aim to investigate whether structural valve deterioration (SVD) of bioprosthetic xenogenic tissue heart valves (XTHVs) is associated with increased immune cell infiltration and whether co-expression of several chemokines correlates with this increase in immune infiltrate. Explanted XTHVs from patients undergoing redo valve replacement for SVD were obtained. Immunohistochemical, microscopic, and gene expression analysis approaches were used. XTHVs (n = 37) were obtained from 32 patients (mean 67.7 years) after a mean time of 11.6 years post-implantation. Significantly increased immune cellular infiltration was observed in the explanted SVD valves for all immune cell types examined, including T cells, macrophages, B cells, neutrophils, and plasma cells, compared to non-SVD controls. Furthermore, a significantly increased chemokine gradient in explanted SVD valves accompanied immune cell infiltration. These data suggest the development of SVD is associated with a significantly increased burden of immune cellular infiltrate correlated to the induction of a chemokine gradient around the XHTV, representing chronic immune rejection.Graphical abstract Proposed interaction between innate and adaptive immunity leading to the development of structural valve deterioration in xenogenic tissue heart valves.
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Affiliation(s)
- Sabin J Bozso
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Jimmy J H Kang
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Ratnadeep Basu
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Benjamin Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Jason R B Dyck
- Cardiovascular Research Centre, Division of Pediatrics, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Gavin Y Oudit
- Cardiovascular Research Centre, Division of Cardiology, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Michael C Moon
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Darren H Freed
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Jayan Nagendran
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Jeevan Nagendran
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, AB, T6G 2R3, Canada.
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32
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Dobi D, Vincenti F, Chandran S, Greenland JR, Bowman C, Chen A, Junger H, Laszik ZG. The impact of belatacept on the phenotypic heterogeneity of renal T cell-mediated alloimmune response: The critical role of maintenance treatment and inflammatory load. Clin Transplant 2020; 34:e14084. [PMID: 32939817 DOI: 10.1111/ctr.14084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 07/30/2020] [Accepted: 08/21/2020] [Indexed: 11/30/2022]
Abstract
Belatacept offers superior long-term outcome relative to calcineurin inhibitor (CNI)-based immunosuppression. However, the higher frequency of early T cell-mediated rejection (TCMR) in belatacept-treated patients hampered the widespread adoption of costimulation blockade. Here, we applied gene expression analysis and whole-slide inflammatory cell quantification to assess the impact of belatacept on intragraft immune signature. We studied formalin-fixed, paraffin-embedded renal biopsies from 92 patients stratified by histopathologic diagnosis (TCMR, borderline changes, or normal) and immunosuppression regimen (belatacept, CNI). An interaction model was built to explore maintenance treatment-dependent expression level changes of immune response-related genes across diagnostic categories of normal, borderline changes, and TCMR. Ninety-one percent of genes overexpressed in TCMR showed significant correlation with whole section inflammatory load. There were 27 genes that had a positive association with belatacept treatment. These were mostly related to myeloid cells and innate immunity. Genes negatively associated with costimulation blockade (n = 14) could be linked to B-cell differentiation and proliferation. We concluded that expression levels of genes characteristic of TCMR are strongly interconnected with quantitative changes of the biopsy inflammatory load. Our results might suggest differential involvement of the innate immune system, and an altered B-cell engagement during TCMR in belatacept-treated patients relative to CNI-treated referents.
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Affiliation(s)
- Dejan Dobi
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Flavio Vincenti
- Department of Medicine, University of California, San Francisco, CA, USA.,Department of Surgery, University of California, San Francisco, CA, USA
| | - Sindhu Chandran
- Department of Medicine, University of California, San Francisco, CA, USA
| | - John R Greenland
- Department of Medicine, University of California, San Francisco, CA, USA.,Medical Service, Veterans Affairs Health Care System, San Francisco, CA, USA
| | - Christopher Bowman
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Adeline Chen
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Henrik Junger
- Department of Surgery, University of California, San Francisco, CA, USA
| | - Zoltan G Laszik
- Department of Pathology, University of California, San Francisco, CA, USA
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33
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Loupy A, Haas M, Roufosse C, Naesens M, Adam B, Afrouzian M, Akalin E, Alachkar N, Bagnasco S, Becker JU, Cornell LD, Clahsen‐van Groningen MC, Demetris AJ, Dragun D, Duong van Huyen J, Farris AB, Fogo AB, Gibson IW, Glotz D, Gueguen J, Kikic Z, Kozakowski N, Kraus E, Lefaucheur C, Liapis H, Mannon RB, Montgomery RA, Nankivell BJ, Nickeleit V, Nickerson P, Rabant M, Racusen L, Randhawa P, Robin B, Rosales IA, Sapir‐Pichhadze R, Schinstock CA, Seron D, Singh HK, Smith RN, Stegall MD, Zeevi A, Solez K, Colvin RB, Mengel M. The Banff 2019 Kidney Meeting Report (I): Updates on and clarification of criteria for T cell- and antibody-mediated rejection. Am J Transplant 2020; 20:2318-2331. [PMID: 32463180 PMCID: PMC7496245 DOI: 10.1111/ajt.15898] [Citation(s) in RCA: 426] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/24/2020] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
Abstract
The XV. Banff conference for allograft pathology was held in conjunction with the annual meeting of the American Society for Histocompatibility and Immunogenetics in Pittsburgh, PA (USA) and focused on refining recent updates to the classification, advances from the Banff working groups, and standardization of molecular diagnostics. This report on kidney transplant pathology details clarifications and refinements to the criteria for chronic active (CA) T cell-mediated rejection (TCMR), borderline, and antibody-mediated rejection (ABMR). The main focus of kidney sessions was on how to address biopsies meeting criteria for CA TCMR plus borderline or acute TCMR. Recent studies on the clinical impact of borderline infiltrates were also presented to clarify whether the threshold for interstitial inflammation in diagnosis of borderline should be i0 or i1. Sessions on ABMR focused on biopsies showing microvascular inflammation in the absence of C4d staining or detectable donor-specific antibodies; the potential value of molecular diagnostics in such cases and recommendations for use of the latter in the setting of solid organ transplantation are presented in the accompanying meeting report. Finally, several speakers discussed the capabilities of artificial intelligence and the potential for use of machine learning algorithms in diagnosis and personalized therapeutics in solid organ transplantation.
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Mengel M, Loupy A, Haas M, Roufosse C, Naesens M, Akalin E, Clahsen‐van Groningen MC, Dagobert J, Demetris AJ, Duong van Huyen J, Gueguen J, Issa F, Robin B, Rosales I, Von der Thüsen JH, Sanchez‐Fueyo A, Smith RN, Wood K, Adam B, Colvin RB. Banff 2019 Meeting Report: Molecular diagnostics in solid organ transplantation-Consensus for the Banff Human Organ Transplant (B-HOT) gene panel and open source multicenter validation. Am J Transplant 2020; 20:2305-2317. [PMID: 32428337 PMCID: PMC7496585 DOI: 10.1111/ajt.16059] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/19/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023]
Abstract
This meeting report from the XV Banff conference describes the creation of a multiorgan transplant gene panel by the Banff Molecular Diagnostics Working Group (MDWG). This Banff Human Organ Transplant (B-HOT) panel is the culmination of previous work by the MDWG to identify a broadly useful gene panel based on whole transcriptome technology. A data-driven process distilled a gene list from peer-reviewed comprehensive microarray studies that discovered and validated their use in kidney, liver, heart, and lung transplant biopsies. These were supplemented by genes that define relevant cellular pathways and cell types plus 12 reference genes used for normalization. The 770 gene B-HOT panel includes the most pertinent genes related to rejection, tolerance, viral infections, and innate and adaptive immune responses. This commercially available panel uses the NanoString platform, which can quantitate transcripts from formalin-fixed paraffin-embedded samples. The B-HOT panel will facilitate multicenter collaborative clinical research using archival samples and permit the development of an open source large database of standardized analyses, thereby expediting clinical validation studies. The MDWG believes that a pathogenesis and pathway based molecular approach will be valuable for investigators and promote therapeutic decision-making and clinical trials.
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Affiliation(s)
- Michael Mengel
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonCanada
| | - Alexandre Loupy
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Mark Haas
- Department of Pathology and Laboratory MedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Candice Roufosse
- Department of Immunology and InflammationImperial College London and North West London PathologyLondonUK
| | - Maarten Naesens
- Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium,Department of NephrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Enver Akalin
- Montefiore‐Einstein Center for TransplantationMontefiore Medical CenterBronxNew YorkUSA
| | | | - Jessy Dagobert
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Anthony J. Demetris
- Department of PathologyUniversity of Pittsburgh Medical CenterMontefiore, PittsburghPennsylvaniaUSA
| | - Jean‐Paul Duong van Huyen
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Juliette Gueguen
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Fadi Issa
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Blaise Robin
- Paris Translational Research Center for Organ TransplantationINSERM U970 and Necker HospitalUniversity of ParisParisFrance
| | - Ivy Rosales
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | | | | | - Rex N. Smith
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Kathryn Wood
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Benjamin Adam
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonCanada
| | - Robert B. Colvin
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
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35
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Roufosse C, Drachenberg C, Renaudin K, Willicombe M, Toulza F, Dominy K, McLean A, Simmonds N, de Kort H, Cantarovitch D, Scalea J, Mengel M, Adam B. Molecular assessment of antibody-mediated rejection in human pancreas allograft biopsies. Clin Transplant 2020; 34:e14065. [PMID: 32805760 DOI: 10.1111/ctr.14065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/30/2020] [Accepted: 08/11/2020] [Indexed: 01/09/2023]
Abstract
Pancreas transplant longevity is limited by immune rejection, which is diagnosed by graft biopsy using the Banff Classification. The histological criteria for antibody-mediated rejection (AMR) are poorly reproducible and inconsistently associated with outcome. We hypothesized that a 34-gene set associated with antibody-mediated rejection in other solid organ transplants could improve diagnosis in pancreas grafts. The AMR 34-gene set, comprising endothelial, natural killer cell and inflammatory genes, was quantified using the NanoString platform in 52 formalin-fixed, paraffin-embedded pancreas transplant biopsies from 41 patients: 15 with pure AMR or mixed rejection, 22 with T cell-mediated rejection/borderline and 15 without rejection. The AMR 34-gene set was significantly increased in pure AMR and mixed rejection (P = .001) vs no rejection. The gene set predicted histological AMR with an area under the receiver operating characteristic curve (ROC AUC) of 0.714 (P = .004). The AMR 34-gene set was the only biopsy feature significantly predictive of allograft failure in univariate analysis (P = .048). Adding gene expression to DSA and histology increased ROC AUC for the prediction of failure from 0.736 to 0.770, but this difference did not meet statistical significance. In conclusion, assessment of transcripts has the potential to improve diagnosis and outcome prediction in pancreas graft biopsies.
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Affiliation(s)
- Candice Roufosse
- Centre for Inflammatory Disease, Dept Immunology and Inflammation, Faculty of Medicine, Imperial College, London, UK
| | - Cinthia Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Michelle Willicombe
- Centre for Inflammatory Disease, Dept Immunology and Inflammation, Faculty of Medicine, Imperial College, London, UK
| | - Frederic Toulza
- Centre for Inflammatory Disease, Dept Immunology and Inflammation, Faculty of Medicine, Imperial College, London, UK
| | - Kathy Dominy
- Molecular Pathology, Imperial College Healthcare NHS Trust, London, UK
| | - Adam McLean
- Imperial Renal and Transplant Centre, London, UK
| | - Naomi Simmonds
- Dept Cellular Pathology, Guys' and St Thomas' NHS Trust, London, UK
| | | | - Diego Cantarovitch
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Joseph Scalea
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Benjamin Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
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36
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Masoud AG, Lin J, Azad AK, Farhan MA, Fischer C, Zhu LF, Zhang H, Sis B, Kassiri Z, Moore RB, Kim D, Anderson CC, Vederas JC, Adam BA, Oudit GY, Murray AG. Apelin directs endothelial cell differentiation and vascular repair following immune-mediated injury. J Clin Invest 2020; 130:94-107. [PMID: 31738185 DOI: 10.1172/jci128469] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/18/2019] [Indexed: 01/06/2023] Open
Abstract
Sustained, indolent immune injury of the vasculature of a heart transplant limits long-term graft and recipient survival. This injury is mitigated by a poorly characterized, maladaptive repair response. Vascular endothelial cells respond to proangiogenic cues in the embryo by differentiation to specialized phenotypes, associated with expression of apelin. In the adult, the role of developmental proangiogenic cues in repair of the established vasculature is largely unknown. We found that human and minor histocompatibility-mismatched donor mouse heart allografts with alloimmune-mediated vasculopathy upregulated expression of apelin in arteries and myocardial microvessels. In vivo, loss of donor heart expression of apelin facilitated graft immune cell infiltration, blunted vascular repair, and worsened occlusive vasculopathy in mice. In vitro, an apelin receptor agonist analog elicited endothelial nitric oxide synthase activation to promote endothelial monolayer wound repair and reduce immune cell adhesion. Thus, apelin acted as an autocrine growth cue to sustain vascular repair and mitigate the effects of immune injury. Treatment with an apelin receptor agonist after vasculopathy was established markedly reduced progression of arterial occlusion in mice. Together, these initial data identify proangiogenic apelin as a key mediator of coronary vascular repair and a pharmacotherapeutic target for immune-mediated injury of the coronary vasculature.
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Affiliation(s)
| | - Jiaxin Lin
- Department of Surgery.,Department of Medical Microbiology and Immunology, and
| | | | | | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Hao Zhang
- Department of Medicine.,Mazankowski Heart Institute, Edmonton, Alberta, Canada
| | - Banu Sis
- Department of Laboratory Medicine and Pathology and
| | - Zamaneh Kassiri
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Colin C Anderson
- Department of Surgery.,Department of Medical Microbiology and Immunology, and
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Gavin Y Oudit
- Department of Medicine.,Mazankowski Heart Institute, Edmonton, Alberta, Canada
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37
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Adam N, Coutance G, Viailly PJ, Drieux F, Ruminy P, Sater AA, Toquet C, Rouvier P, François A, Chenard MP, Epailly E, Guillemain R, Pattier S, Gay A, Varnous S, Taupin JL, Rabant M, Loupy A, Bruneval P, Duong Van Huyen JP. Reverse transcriptase multiplex ligation-dependent probe amplification in endomyocardial biopsies for the diagnosis of cardiac allograft rejection. J Heart Lung Transplant 2020; 39:115-124. [DOI: 10.1016/j.healun.2019.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/29/2022] Open
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38
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Multi-gene technical assessment of qPCR and NanoString n-Counter analysis platforms in cynomolgus monkey cardiac allograft recipients. Cell Immunol 2019; 347:104019. [PMID: 31744596 DOI: 10.1016/j.cellimm.2019.104019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/17/2022]
Abstract
Quantitative gene expression profiling of cardiac allografts characterizes the phenotype of the alloimmune response, yields information regarding differential effects that may be associated with various anti-rejection drug regimens, and generates testable hypotheses regarding the pathogenesis of the chronic rejection lesions typically observed in non-human primate heart transplant models. The goal of this study was to assess interplatform performance and variability between the relatively novel NanoString nCounter Analysis System, ΔΔCT (relative) RT-qPCR, and standard curve (absolute) RT-qPCR utilizing cynomolgus monkey cardiac allografts. Methods for RNA isolation and preamplification were also systematically evaluated and effective methods are proposed. In this study, we demonstrate strong correlation between the two RT-qPCR methods, but variable and, at times, weak correlation between RT-qPCR and NanoString. NanoString fold change results demonstrate less sensitivity to small changes in gene expression than RT-qPCR. These findings appear to be driven by technical aspects of each platform that influence the conditions under which each technique is ideal. Collectively, our data contribute to the general effort to optimally utilize gene expression profiling techniques, not only for transplanted tissues, but for many other applications where accurate rank-order of gene expression versus precise quantification of absolute gene transcript number may be relatively valuable.
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39
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Matsunami M, Rosales IA, Adam BA, Oura T, Mengel M, Smith RN, Lee H, Cosimi AB, Colvin RB, Kawai T. Long-term Kinetics of Intragraft Gene Signatures in Renal Allograft Tolerance Induced by Transient Mixed Chimerism. Transplantation 2019; 103:e334-e344. [PMID: 31397805 PMCID: PMC6814550 DOI: 10.1097/tp.0000000000002911] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Renal allograft tolerance (TOL) has been successfully induced in nonhuman primates (NHPs) and humans through the induction of transient mixed chimerism. To elucidate the mechanisms of TOL, we compared local immunologic responses in renal allografts with those in T-cell-mediated rejection (TCMR) and chronic antibody-mediated rejection (CAMR) in NHPs. METHODS Using the NanoString nCounter platform, we retrospectively studied 52 mRNAs in 256 kidney allograft samples taken from NHP kidney recipients of donor BMT. No immunosuppression was given after 1-month post-donor BMT. Recipients who achieved TOL (n = 13) survived for >1840 ± 1724 days with normal kidney function, while recipients with CAMR (n = 13) survived for 899 ± 550 days with compromised graft function, and recipients with TCMR (n = 15) achieved only short-term survival (132 ± 69 days). RESULTS The most prominent difference between the groups was FOXP3, which was significantly higher in TOL than in CAMR and TCMR, both early (<1 y, P < 0.01) and late (≥1 y, P < 0.05) after transplant. Other mRNAs related to regulatory T cells (Treg), such as IL10, TGFB, and GATA3, were also high in TOL. In contrast, transcripts of inflammatory cytokines were higher in TCMR, while activated endothelium-associated transcripts were higher in CAMR than in TOL. The receiver operating characteristic analyses revealed that intragraft FOXP3 and CAV1 can reliably distinguish TOL from CAMR. CONCLUSIONS High FOXP3 and other Treg-related mRNAs together with suppressed inflammatory responses and endothelial activation in renal allografts suggest that intragraft enrichment of Treg is a critical mechanism of renal allograft TOL induced by transient mixed chimerism.
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Affiliation(s)
- Masatoshi Matsunami
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ivy A. Rosales
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Benjamin A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Tetsu Oura
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Rex-Neal Smith
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Hang Lee
- Department of Biostatistics, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - A. Benedict Cosimi
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Robert B. Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Tatsuo Kawai
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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40
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Sigdel T, Nguyen M, Liberto J, Dobi D, Junger H, Vincenti F, Laszik Z, Sarwal MM. Assessment of 19 Genes and Validation of CRM Gene Panel for Quantitative Transcriptional Analysis of Molecular Rejection and Inflammation in Archival Kidney Transplant Biopsies. Front Med (Lausanne) 2019; 6:213. [PMID: 31632976 PMCID: PMC6781675 DOI: 10.3389/fmed.2019.00213] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023] Open
Abstract
Background: There is an urgent need to develop and implement low cost, high-throughput standardized methods for routine molecular assessment of transplant biopsies. Given the vast archive of formalin-fixed and paraffin-embedded (FFPE) tissue blocks in transplant centers, a reliable protocol for utilizing this tissue bank for clinical validation of target molecules as predictors of graft outcome over time, would be of great value. Methods: We designed and optimized assays to quantify 19 target genes, including previously reported set of tissue common rejection module (tCRM) genes. We interrogated their performance for their clinical utility for detection of graft rejection and inflammation by analyzing gene expression microarrays analysis of 163 renal allograft biopsies, and subsequently validated in 40 independent FFPE archived kidney transplant biopsies at a single center. Results: A QPCR (Fluidigm) and a barcoded oligo-based (NanoString) gene expression platform were compared for evaluation of amplification of gene expression signal for 19 genes from degraded RNA extracted from FFPE biopsy sections by a set protocol. Increased expression of the selected 19 genes, that reflect a combination of specific cellular infiltrates (8/19 genes) and a graft inflammation score (11/19 genes which computes the tCRM score allowed for segregation of kidney transplant biopsies with stable allograft function and normal histology from those with histologically confirmed acute rejection (AR; p = 0.0022, QPCR; p = 0.0036, barcoded assay) and many cases of histological borderline inflammation (BL). Serial biopsy shaves used for gene expression were also processed for in-situ hybridization (ISH) for a subset of genes. ISH confirmed a high degree of correlation of signal amplification and tissue localization. Conclusions: Target gene expression amplification across a custom set of genes can identify AR independent of histology, and quantify inflammation from archival kidney transplant biopsy tissue, providing a new tool for clinical correlation and outcome analysis of kidney allografts, without the need for prospective kidney biopsy biobanking efforts.
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Affiliation(s)
- Tara Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Mark Nguyen
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Juliane Liberto
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Dejan Dobi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Henrik Junger
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Flavio Vincenti
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Zoltan Laszik
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
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41
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Seifert ME, Gaut JP, Guo B, Jain S, Malone AF, Geraghty F, Manna DD, Yang ES, Yi N, Brennan DC, Mannon RB. WNT pathway signaling is associated with microvascular injury and predicts kidney transplant failure. Am J Transplant 2019; 19:2833-2845. [PMID: 30916889 PMCID: PMC6763350 DOI: 10.1111/ajt.15372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 01/25/2023]
Abstract
Microvascular injury is associated with accelerated kidney transplant dysfunction and allograft failure. Molecular pathology can identify new mechanisms of microvascular injury while improving on the diagnostic and prognostic capabilities of traditional histology. We conducted a case-control study of archived kidney biopsy specimens stored up to 10 years with microvascular injury (n = 50) compared with biopsy specimens without histologic injury (n = 45) from patients of similar age, race, and sex. We measured WNT gene expression with a multiplex quantification platform by using digital barcoding, given the importance of WNT reactivation to the response to wounding in the kidney microvasculature and other compartments. Of 210 genes from a commercial WNT panel, 71 were associated with microvascular injury and 79 were associated with allograft failure, with considerable overlap of genes between each set. Molecular pathology identified 46 biopsy specimens with molecular evidence of microvascular injury; 18 (39%) were either C4d negative, donor-specific antibody negative, or had no microvascular injury by histology. The majority of cases with molecular evidence of microvascular injury had poor long-term outcomes. We identified novel WNT pathway genes associated with microvascular injury and allograft failure in residual clinical biopsy specimens obtained up to 10 years earlier. Further mechanistic studies may identify the WNT pathway as a new diagnostic and therapeutic target.
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Affiliation(s)
- Michael E. Seifert
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL
| | - Joseph P. Gaut
- Department of Pathology, Washington University, St. Louis, Missouri
| | - Boyi Guo
- Department of Biostatistics, School of Public Health, University of Alabama, Birmingham, Alabama
| | - Sanjay Jain
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri
| | - Andrew F. Malone
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri
| | - Feargal Geraghty
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri
| | - Deborah Della Manna
- UAB NanoString Laboratory, Department of Radiation Oncology, University of Alabama School of Medicine, Birmingham, Alabama
| | - Eddy S. Yang
- UAB NanoString Laboratory, Department of Radiation Oncology, University of Alabama School of Medicine, Birmingham, Alabama
| | - Nengjun Yi
- Department of Biostatistics, School of Public Health, University of Alabama, Birmingham, Alabama
| | - Daniel C. Brennan
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri,Comprehensive Transplant Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Roslyn B. Mannon
- Department of Medicine, University of Alabama School of Medicine, Birmingham, Alabama,Comprehensive Transplant Institute, University of Alabama School of Medicine, Birmingham, Alabama
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Dromparis P, Aboelnazar NS, Wagner S, Himmat S, White CW, Hatami S, Luc JGY, Rotich S, Freed DH, Nagendran J, Mengel M, Adam BA. Ex vivo perfusion induces a time- and perfusate-dependent molecular repair response in explanted porcine lungs. Am J Transplant 2019; 19:1024-1036. [PMID: 30230229 DOI: 10.1111/ajt.15123] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/25/2023]
Abstract
Ex vivo lung perfusion (EVLP) shows promise in ameliorating pretransplant acute lung injury (ALI) and expanding the donor organ pool, but the mechanisms of ex vivo repair remain poorly understood. We aimed to assess the utility of gene expression for characterizing ALI during EVLP. One hundred sixty-nine porcine lung samples were collected in vivo (n = 25), after 0 (n = 11) and 12 (n = 11) hours of cold static preservation (CSP), and after 0 (n = 57), 6 (n = 8), and 12 (n = 57) hours of EVLP, utilizing various ventilation and perfusate strategies. The expression of 53 previously described ALI-related genes was measured and correlated with function and histology. Twenty-eight genes were significantly upregulated and 6 genes downregulated after 12 hours of EVLP. Aggregate gene sets demonstrated differential expression with EVLP (P < .001) but not CSP. Upregulated 28-gene set expression peaked after 6 hours of EVLP, whereas downregulated 6-gene set expression continued to decline after 12 hours. Cellular perfusates demonstrated a greater reduction in downregulated 6-gene set expression vs acellular perfusate (P < .038). Gene set expression correlated with relevant functional and histologic parameters, including P/F ratio (P < .001) and interstitial inflammation (P < .005). Further studies with posttransplant results are warranted to evaluate the clinical significance of this novel molecular approach for assessing organ quality during EVLP.
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Affiliation(s)
- Peter Dromparis
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Nader S Aboelnazar
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Siegfried Wagner
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sayed Himmat
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Christopher W White
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Sanaz Hatami
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Jessica G Y Luc
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Silas Rotich
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Darren H Freed
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Jayan Nagendran
- Division of Cardiac Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Benjamin A Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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43
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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] [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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44
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Immunomics of Renal Allograft Acute T Cell-Mediated Rejection Biopsies of Tacrolimus- and Belatacept-Treated Patients. Transplant Direct 2018; 5:e418. [PMID: 30656216 PMCID: PMC6324913 DOI: 10.1097/txd.0000000000000857] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/02/2018] [Accepted: 11/10/2018] [Indexed: 12/14/2022] Open
Abstract
Supplemental digital content is available in the text. Background Belatacept-based therapy in kidney transplant recipient has been shown to increase long-term renal allograft and patient survival compared with calcineurin inhibitor–based therapy, however, with an increased risk of acute T cell-mediated rejection (aTCMR). An improved understanding of costimulation blockade-resistant rejections could lead to a more personalized approach to belatacept therapy. Here, immunomic profiles of aTCMR biopsies of patients treated with either tacrolimus or belatacept were compared. Methods Formalin-fixed paraffin-embedded renal transplant biopsies were used for immunohistochemistry and gene expression analysis using the innovative NanoString technique. To validate NanoString, transcriptomic profiles of patients with and without biopsy-proven aTCMR were compared. Biopsies from 31 patients were studied: 14 tacrolimus-treated patients with aTCMR, 11 belatacept-treated patients with aTCMR, and 6 controls without rejection. Results A distinct pattern was seen in biopsies with aTCMR compared to negative controls: 78 genes had a higher expression in the aTCMR group (false discovery rate P value <.05 to 1.42e–05). The most significant were T cell-associated genes (CD3, CD8, and CD4; P < 1.98e-04), γ-interferon-inducible genes (CCL5, CXCL9, CXCL11, CXCL10, TBX21; P < 1.33e-04) plus effector genes (GNLY, GZMB, ITGAX; P < 2.82e-03). Immunophenotypical analysis of the classic immune markers of the innate and adaptive immune system was comparable between patients treated with either tacrolimus or belatacept. In addition, the transcriptome of both groups was not significantly different. Conclusions In this small pilot study, no difference was found in immunomics of aTCMR biopsies of tacrolimus- and belatacept-treated patients. This suggests that clinically diagnosed aTCMR reflects a final common pathway of allorecognition which is unaffected by the type of immunosuppressive therapy.
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45
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Bagnasco SM. Beyond the microscope: interpreting renal biopsy findings in the era of precision medicine. Am J Physiol Renal Physiol 2018; 315:F1652-F1655. [PMID: 30280602 DOI: 10.1152/ajprenal.00407.2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
As rapid progress in science and biotechnology is affecting the practice of renal medicine, increasingly precise diagnostic assessment is needed to select the most effective therapeutic approach for individual patients. The kidney biopsy remains the gold standard for the diagnosis of renal disease, but the field of renal pathology is evolving, classification of renal parenchyma lesions and histopathological diagnostic criteria are undergoing more validation and updates, and new technologies and assays are sought to improve efficiency and accuracy of the diagnostic process. How new knowledge and scientific advances may potentially affect renal pathology is discussed.
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Affiliation(s)
- Serena M Bagnasco
- Department of Pathology, Johns Hopkins School of Medicine , Baltimore, Maryland
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46
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Liu P, Tseng G, Wang Z, Huang Y, Randhawa P. Diagnosis of T-cell-mediated kidney rejection in formalin-fixed, paraffin-embedded tissues using RNA-Seq-based machine learning algorithms. Hum Pathol 2018; 84:283-290. [PMID: 30296518 DOI: 10.1016/j.humpath.2018.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/21/2018] [Accepted: 09/29/2018] [Indexed: 12/26/2022]
Abstract
Molecular diagnosis is being increasingly used in transplant pathology to render more objective and quantitative determinations that also provide mechanistic and prognostic insights. This study performed RNA-Seq on biopsies from kidneys with stable function (STA) and biopsies with classical findings of T-cell-mediated rejection (TCMR). Machine learning tools were used to develop prediction models for distinguishing TCMR and STA samples using the top genes identified by DSeq2. The prediction models were tested on 703 biopsies with Affymetrix chip gene expression profiles available in the public domain. Linear discriminant analysis predicted TCMR in 55 of 67 biopsies labeled TCMR, and 65 of 105 biopsies designated as antibody-mediated rejection. The random forest and support vector machine models showed comparable performance. These data illustrate the feasibility of using RNA-Seq for molecular diagnosis of TCMR in formalin-fixed tissue. Application of the derived diagnostic algorithms to publicly available data sets demonstrates frequent coexistence of TCMR in biopsies designated as antibody-mediated rejection. This underrecognition of TCMR in renal allograft biopsies has significant implications with respect to patient care.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - George Tseng
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Zijie Wang
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Yuchen Huang
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Parmjeet Randhawa
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.
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47
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Smith RN, Matsunami M, Adam BA, Rosales IA, Oura T, Cosimi AB, Kawai T, Mengel M, Colvin RB. RNA expression profiling of nonhuman primate renal allograft rejection identifies tolerance. Am J Transplant 2018; 18:1328-1339. [PMID: 29288556 PMCID: PMC6021122 DOI: 10.1111/ajt.14637] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023]
Abstract
Tolerance induction to prevent allograft rejection is a long-standing clinical goal. However, convincing and dependable tolerance identification remains elusive. Hypothesizing that intragraft RNA expression is informative in both rejection and tolerance, we profile intrarenal allograft RNA expression in a mixed chimerism renal allograft model of cynomolgus monkeys and identify biologically significant tolerance. Analysis of 67 genes identified 3 dominant factors, each with a different pattern of gene expressions, relating to T cell-mediated rejection (TCMR), chronic antibody-mediated rejection (CAMR), or Tolerance. Clustering these 3 factors created 9 groups. One of the 9 clustered groups, the Tolerance cluster, showed the lowest probability of terminal rejection, the longest duration of allograft survival, and the lowest relative risk of terminal rejection. The Tolerance factor consists of a novel set of gene expressions including cytokine and immunoregulatory genes adding mechanistic insights into tolerance. The Tolerance factor could not be identified within current pathologic diagnostic categories. The TCMR and CAMR factors are dominant to the Tolerance factor, causing rejection even if the Tolerance factor is present. These 3 factors determine the probability of terminal rejection or tolerance. This novel a posteriori approach permits identification of pathways of rejection, including tolerance.
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Affiliation(s)
- R. N. Smith
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - M. Matsunami
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - B. A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - I. A. Rosales
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - T. Oura
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - A. B. Cosimi
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - T. Kawai
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - M. Mengel
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - R. B. Colvin
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
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48
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Smith R, Adam B, Rosales I, Matsunami M, Oura T, Cosimi A, Kawai T, Mengel M, Colvin R. RNA expression profiling of renal allografts in a nonhuman primate identifies variation in NK and endothelial gene expression. Am J Transplant 2018; 18:1340-1350. [PMID: 29286578 PMCID: PMC5992005 DOI: 10.1111/ajt.14639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 12/12/2017] [Indexed: 01/25/2023]
Abstract
RNA transcript expression estimates are a promising method to study the mechanisms and classification of renal allograft rejections. Here we use the Nanostring platform to profile RNA expression in renal allografts in a nonhuman primate (NHP), the Cynomolgus monkey. We analyzed protocol and indication 278 archival renal allograft samples, both protocol and indication from 76 animals with diagnoses of chronic antibody-mediated rejection (CAMR), acute cellular rejection (TCMR), and MIXED (both CAMR and TCMR), plus normals and samples with no pathological rejection using a Cynomolgus-specific probe set of 67 genes. Analysis identified RNA expression heterogeneity of endothelial and NK genes within CAMR and TCMR, including the stages of CAMR. Three factors were partitioned into additional groups. One group with the longest allograft survival time is pure CAMR without NK or CD3. Three mixed groups show variation in NK and CD3. TCMR was split into 2 groups with variation in NK genes. Additional validation of the complete gene-set correlated many of the genes with diagnoses of CAMR, MIXED, and TCMR rejections and with Banff histologic criteria defined in human subjects. These NHP data demonstrate the utility of RNA expression profiling to identify additional heterogeneity of endothelial and NK RNA gene expressions.
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Affiliation(s)
- R.N. Smith
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - B.A. Adam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - I.A. Rosales
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - M. Matsunami
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - T. Oura
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - A.B. Cosimi
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - T. Kawai
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, USA
| | - M. Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - R.B. Colvin
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, USA
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49
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Targeted Transcriptional Profiling of Kidney Transplant Biopsies. Kidney Int Rep 2018; 3:722-731. [PMID: 29854981 PMCID: PMC5976814 DOI: 10.1016/j.ekir.2018.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023] Open
Abstract
Introduction Studies are needed to assess the quality of transcriptome analysis in paired human tissue samples preserved by different methods and different gene amplification platforms to enable data comparisons across experimenters. Methods RNA was extracted from kidney biopsies, either submerged in RNA-stabilizing solution (RSS) or stored in formalin-fixed, paraffin-embedded (FFPE) blocks. RNA quality and integrity were compared. Gene expression of the common rejection module and other immune cell genes were quantified for both tissue preservation methods in the same sample using conventional quantitative polymerase chain reaction (QPCR) by 2 different commercial platforms, (fluidigm [FD]) or barcoded-oligos (nanostring [NS]). Results RNA quality was inferior in FFPE tissues. Despite this, gene expression for 19 measured genes on the same sample, stored in FFPE or RSS, were strongly correlated on the FD (r = 0.81) or NS platforms (r = 0.82). For the same samples, interplatform gene expression correlations were excellent (r = 0.80) for RSS and moderate (r = 0.66) for FFPE. Significant differences in gene expression were confirmed on both platforms (FD: P = 1.1E-03; NS: P = 2.5E-04) for biopsy-confirmed acute rejection. Conclusion Our study provided supportive evidence that despite a low RNA quality of archival FFPE kidney transplantation tissue, small quantities of this tissue can be obtained from existing paraffin blocks to provide a viable and rich biospecimen source for focused gene expression assays. In addition, reliable and reproducible gene expression evaluation can be performed on these FFPE tissues using either a QPCR-based or a barcoded-oligo approach, which provides opportunities for collaborative analytics.
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50
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Polyomavirus BK Nephropathy-Associated Transcriptomic Signatures: A Critical Reevaluation. Transplant Direct 2018; 4:e339. [PMID: 29464200 PMCID: PMC5811268 DOI: 10.1097/txd.0000000000000752] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/07/2017] [Indexed: 12/29/2022] Open
Abstract
Background Recent work using DNA microarrays has suggested that genes related to DNA replication, RNA polymerase assembly, and pathogen recognition receptors can serve as surrogate tissue biomarkers for polyomavirus BK nephropathy (BKPyVN). Methods We have examined this premise by looking for differential regulation of these genes using a different technology platform (RNA-seq) and an independent set 25 biopsies covering a wide spectrum of diagnoses. Results RNA-seq could discriminate T cell–mediated rejection from other common lesions seen in formalin fixed biopsy material. However, overlapping RNA-seq signatures were found among all disease processes investigated. Specifically, genes previously reported as being specific for the diagnosis of BKPyVN were found to be significantly upregulated in T cell–mediated rejection, inflamed areas of fibrosis/tubular atrophy, as well as acute tubular injury. Conclusions In conclusion, the search for virus specific molecular signatures is confounded by substantial overlap in pathogenetic mechanisms between BKPyVN and nonviral forms of allograft injury. Clinical heterogeneity, overlapping exposures, and different morphologic patterns and stage of disease are a source of substantial variability in “Omics” experiments. These variables should be better controlled in future biomarker studies on BKPyVN, T cell–mediated rejection, and other forms of allograft injury, before widespread implementation of these tests in the transplant clinic.
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