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Kuscu C, Kiran M, Mohammed A, Kuscu C, Satpathy S, Wolen A, Bardhi E, Bajwa A, Eason JD, Maluf D, Mas V, Akalin E. Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy. Int J Mol Sci 2021; 22:ijms22126218. [PMID: 34207555 PMCID: PMC8226568 DOI: 10.3390/ijms22126218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transplant glomerulopathy develops through multiple mechanisms, including donor-specific antibodies, T cells and innate immunity. This study investigates circulating small RNA profiles in serum samples of kidney transplant recipients with biopsy-proven transplant glomerulopathy. Among total small RNA population, miRNAs were the most abundant species in the serum of kidney transplant patients. In addition, fragments arising from mature tRNA and rRNA were detected. Most of the tRNA fragments were generated from 5′ ends of mature tRNA and mainly from two parental tRNAs: tRNA-Gly and tRNA-Glu. Moreover, transplant patients with transplant glomerulopathy displayed a novel tRNA fragments signature. Gene expression analysis from allograft tissues demonstrated changes in canonical pathways related to immune activation such as iCos-iCosL signaling pathway in T helper cells, Th1 and Th2 activation pathway, and dendritic cell maturation. mRNA targets of down-regulated miRNAs such as miR-1224-5p, miR-4508, miR-320, miR-378a from serum were globally upregulated in tissue. Integration of serum miRNA profiles with tissue gene expression showed that changes in serum miRNAs support the role of T-cell mediated mechanisms in ongoing allograft injury.
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Affiliation(s)
- Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
- Correspondence: ; Tel.: +1-901-448-3162
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Akram Mohammed
- Center for Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Sarthak Satpathy
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Aaron Wolen
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Elissa Bardhi
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - James D. Eason
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Daniel Maluf
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Valeria Mas
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Enver Akalin
- Montefiore Medical Center, Abdominal Transplant Program, Albert Einstein College of Medicine, Bronx, NY 10467, USA;
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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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Utilizing Precision Medicine to Estimate Timing for Surgical Closure of Traumatic Extremity Wounds. Ann Surg 2019; 270:535-543. [DOI: 10.1097/sla.0000000000003470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Lubetzky M, Hayde N, Ó Broin P, Ajaimy M, Bao Y, Mohammed O, Schwartz D, Pullman J, Akalin E. Molecular signatures and clinical outcomes of transplant glomerulopathy stratified by microvascular inflammation and donor-specific antibody. Clin Transplant 2019; 33:e13469. [PMID: 30578675 DOI: 10.1111/ctr.13469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 11/15/2018] [Accepted: 11/20/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND We investigated clinical outcomes and molecular signatures of transplant glomerulopathy (TG) stratified by microvascular inflammation (MVI) and donor-specific antibody (DSA) status. METHODS We performed a retrospective review of 749 kidney transplant patients who received a for-cause kidney biopsy from 2009 to 2014. We classified TG as MVI positive (MVI+) or MVI negative (MVI-), and with or without DSA. We obtained gene expression profiles for 44 biopsies by Affymetrix HuGene 1.0 ST expression arrays. RESULTS A total of 100 patients had TG; 49 were MVI+, and 51 were MVI-. After a median post-biopsy follow-up of 2.08 years (range 0.43-4.59), Kaplan-Meier survival analysis demonstrated worse allograft survival in MVI+ TG patients compared with MVI- TG patients (P = 0.01), and time to graft failure was significantly shorter in MVI+ patients (1.08 ± 1.01 years vs 2.3 ± 1.8 years; P = 0.002). DSA status did not affect graft survival within MVI+ or MVI- groups. Analysis of pathogenesis-based transcripts (PBT) showed that MVI+ TG biopsies had increased expression of gamma interferon and rejection (GRIT) and DSA-associated transcripts (DSAST), as observed in antibody-mediated rejection. MVI- TG biopsies had increased expression of cytotoxic and regulatory T cell- and B cell-associated transcripts but not GRIT or DSAST. DSA status had no effect on expression of any PBTs studied in MVI- TG biopsies. CONCLUSIONS Graft survival in TG is significantly worse in the presence of MVI. Gene expression profiles of MVI+ TG resemble antibody-mediated rejection while gene expression profiles of MVI- TG resemble cell-mediated rejection regardless of DSA status.
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Affiliation(s)
- Michelle Lubetzky
- Weill Cornell-NY Presbyterian, Division of Nephrology, New York City, New York
| | - Nicole Hayde
- Montefiore Medical Center Transplant Center, Albert Einstein College of Medicine, New York City, New York
| | - Pilib Ó Broin
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Maria Ajaimy
- Montefiore Medical Center Transplant Center, Albert Einstein College of Medicine, New York City, New York
| | - Yi Bao
- Montefiore Medical Center Transplant Center, Albert Einstein College of Medicine, New York City, New York
| | - Omar Mohammed
- Montefiore Medical Center Transplant Center, Albert Einstein College of Medicine, New York City, New York
| | - Daniel Schwartz
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, New York City, New York
| | - James Pullman
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, New York City, New York
| | - Enver Akalin
- Montefiore Medical Center Transplant Center, Albert Einstein College of Medicine, New York City, New York
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Heinemann FM, Jindra PT, Bockmeyer CL, Zeuschner P, Wittig J, Höflich H, Eßer M, Abbas M, Dieplinger G, Stolle K, Vester U, Hoyer PF, Immenschuh S, Heinold A, Horn PA, Li W, Eisenberger U, Becker JU. Glomerulocapillary miRNA response to HLA-class I antibody in vitro and in vivo. Sci Rep 2017; 7:14554. [PMID: 29109529 PMCID: PMC5673998 DOI: 10.1038/s41598-017-14674-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 10/16/2017] [Indexed: 01/12/2023] Open
Abstract
Changes in miRNA expression glomerular of capillaries during antibody-mediated rejection (ABMR) are poorly understood and could contribute to the deleterious inflammation and fibrosis of ABMR via suppression of target genes. A better understanding could lead to novel diagnostic tools and reveal novel therapeutic targets. We explored deregulated miRNAs in an glomeruloendothelial in vitro model of ABMR due to class I human leukocyte antigen (HLA) with and without complement activation. We studied a set of 16 promising candidate miRNAs in microdissected glomeruli a confirmation set of 20 human transplant biopsies (DSA+) compared to 10 matched controls without evidence for ABMR. Twelve out of these 16 glomerulocapillary miRNAs could successfully be confirmed as dysregulated in vivo with 10 upregulated (let-7c-5p, miR-28-3p, miR-30d-5p, miR-99b-5p, miR-125a-5p, miR-195-5p, miR-374b-3p, miR-484, miR-501-3p, miR-520e) and 2 downregulated (miR29b-3p, miR-885-5p) in DSA+ vs. CONTROLS A random forest analysis based on glomerular miRNAs identified 18/20 DSA+ and 8/10 controls correctly. This glomerulocapillary miRNA signature associated with HLA class I-DSA could improve our understanding of ABMR and be useful for diagnostic or therapeutic purposes.
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Affiliation(s)
- Falko M Heinemann
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Peter T Jindra
- Immune Evaluation Laboratory, Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Clemens L Bockmeyer
- Institute of Pathology, Department of Nephropathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Philip Zeuschner
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Juliane Wittig
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Heike Höflich
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Marc Eßer
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | | | - Georg Dieplinger
- Department of General, Visceral and Cancer Surgery, Transplant Center Cologne, University of Cologne, Cologne, Germany
| | - Katharina Stolle
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Udo Vester
- Children's Hospital, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Peter F Hoyer
- Children's Hospital, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Stephan Immenschuh
- Institute of Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Andreas Heinold
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Wentian Li
- Robert S Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Ute Eisenberger
- Clinic for Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jan U Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany.
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Clinical, Histological, and Molecular Markers Associated With Allograft Loss in Transplant Glomerulopathy Patients. Transplantation 2015; 99:1912-8. [PMID: 25675205 DOI: 10.1097/tp.0000000000000598] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND We aimed to investigate the clinical, histopathological, and molecular factors associated with allograft loss in transplant glomerulopathy (TGP) patients. METHODS Of the 525 patients who underwent clinically indicated kidney biopsies, 52 (10%) had diagnosis of TGP. Gene expression profiles of 28 TGP and 11 normal transplant kidney biopsy samples were analyzed by Affymetrix HuGene 1.0 ST expression arrays. RESULTS Over a median follow up of 23 months (1-46 months) after the diagnosis of TGP by biopsy, 17 patients (32%) lost their allografts at a median of 16 months (1-44 months). There was no difference between the 2 groups in terms of any demographic variables, serum creatinine, panel reactive antibody levels, donor-specific antibody frequency, or mean fluorescence intensity values. Patients who lost their allograft had a significantly higher median spot protein to creatinine ratio 2.81 (1.20-6.00) compared to no graft loss patients 1.16 (0.15-2.53), (P < 0.01), and a trends toward a higher mean chronic glomerulopathy (cg) score (1.65 ± 0.93 vs 1.11 ± 0.93) (P = 0.05). There was also no difference in microvascular inflammation or any other Banff injury scores between the 2 groups. Although 117 gene transcripts were upregulated in both groups, 86 and 57 were upregulated in graft loss and functioning allograft groups, respectively. There were significantly increased levels of intragraft endothelial cell-associated transcripts, gene transcripts associated with complement cascade, interleukins and their receptors and granulysin in graft loss patients compared to patients with a functioning allograft. CONCLUSION Our results demonstrate differential intragraft gene expression profiles in TGP patients with allograft loss.
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Hayde N, Bao Y, Pullman J, Ye B, Calder RB, Chung M, Schwartz D, Lubetzky M, Ajaimy M, de Boccardo G, Akalin E. The clinical and genomic significance of donor-specific antibody-positive/C4d-negative and donor-specific antibody-negative/C4d-negative transplant glomerulopathy. Clin J Am Soc Nephrol 2013; 8:2141-8. [PMID: 24030736 DOI: 10.2215/cjn.04240413] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND This study investigated the mechanisms involved in development of donor-specific antibody (DSA) and/or C4d-negative transplant glomerulopathy (TGP) by allograft gene expression profiles using microarrays. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS This cohort study was conducted in kidney transplant recipients. Patients were eligible for inclusion if they required a clinically indicated biopsy at any time point after their transplant. They were then classified according to their histopathology findings and DSA and C4d results. Eighteen chronic antibody-mediated rejection (CAMR), 14 DSA+/C4d- TGP, 25 DSA-/C4d- TGP, and 47 nonspecific interstitial fibrosis/tubular atrophy (IFTA) biopsy specimens were identified. In a subset of patients from the study population, biopsy specimens in each group and normal transplant kidney specimens were analyzed with Affymetrix Human Gene 1.0 ST Arrays. RESULTS The mean sum score of glomerulitis and peritubular capillaritis increased from 0.28±0.78 in IFTA specimens to 0.75±0.85 in DSA-/C4d- TGP specimens, 1.71±1.49 in DSA+/C4d-/TGP specimens, and 2.11±1.74 in CAMR specimens (P<0.001). During a median follow-up time of 2 (interquartile range, 1.4-2.8) years after biopsy, graft loss was highest in CAMR specimens (27.8%) compared to IFTA specimens (8.5%), DSA+/C4d- TGP specimens (14.3%), and DSA-/C4d- TGP specimens (16%) (P=0.01). With use of microarrays, comparison of the gene expression profiles of DSA-/C4d- TGP specimens with glomerulitis + peritubular capillaritis scores > 0 to normal and IFTA biopsy specimens revealed higher expression of quantitative cytotoxic T cell-associated transcripts (QCAT). However, both CAMR and DSA+/C4d- TGP specimens had higher expression of not only QCAT but also IFN-γ and rejection-induced, constitutive macrophage-associated, natural killer cell-associated, and DSA-selective transcripts. Endothelial cell-associated transcript expression was upregulated only in CAMR biopsy specimens. CONCLUSIONS These results suggested that DSA+/C4d- TGP biopsy specimens may be classified as CAMR. In contrast, DSA-/C4d- TGP specimens showed increased cytotoxic T cell-associated transcripts, suggesting T cell activation as a mechanism of injury.
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Affiliation(s)
- Nicole Hayde
- Division of Pediatric Nephrology,, †Montefiore-Einstein Center for Transplantation,, ‡Department of Pathology,, §Computational Genomics Facility, Department of Genetics, and, ‖Division of Nephrology, Albert Einstein College of Medicine, Bronx, New York
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Husain S, Sis B. Advances in the understanding of transplant glomerulopathy. Am J Kidney Dis 2013; 62:352-63. [PMID: 23313456 DOI: 10.1053/j.ajkd.2012.10.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 10/03/2012] [Indexed: 02/06/2023]
Abstract
Transplant glomerulopathy is a sign of chronic kidney allograft damage. It has poor survival and no effective therapies. This entity develops as a maladaptive repair/remodeling response to sustained endothelial injury and is characterized by duplication/multilamination of capillary basement membranes. This review provides up-to-date information for transplant glomerulopathy, including new insights into underlying causes and mechanisms, and highlights unmet needs in diagnostics. Transplant glomerulopathy is widely accepted as the principal manifestation of chronic antibody-mediated rejection, mostly with HLA antigen class II antibodies. However, recent data suggest that at least in some patients, there also is an association with hepatitis C virus infection, autoimmunity, and late thrombotic microangiopathy. Furthermore, intragraft molecular studies reveal nonresolving inflammation after sustained endothelial injury as a key mechanism and therapeutic target. Unfortunately, current international criteria rely heavily on light microscopy and miss patients at early stages, when they likely are treatable. Therefore, better tools, such as electron microscopy or molecular probes, are needed to detect patients when kidney injury is in an early active phase. Better understanding of causes and effector mechanisms coupled with early diagnosis can lead to the development of new therapeutics for transplant glomerulopathy and improved kidney outcomes.
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Affiliation(s)
- Sufia Husain
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
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Tan RJ, Liu Y. Matrix metalloproteinases in kidney homeostasis and diseases. Am J Physiol Renal Physiol 2012; 302:F1351-61. [PMID: 22492945 DOI: 10.1152/ajprenal.00037.2012] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that have been increasingly linked to both normal physiology and abnormal pathology in the kidney. Collectively able to degrade all components of the extracellular matrix, MMPs were originally thought to antagonize the development of fibrotic diseases solely through digestion of excessive matrix. However, increasing evidence has shown that MMPs play a wide variety of roles in regulating inflammation, epithelial-mesenchymal transition, cell proliferation, angiogenesis, and apoptosis. We now have robust evidence for MMP dysregulation in a multitude of renal diseases including acute kidney injury, diabetic nephropathy, glomerulonephritis, inherited kidney disease, and chronic allograft nephropathy. The goal of this review is to summarize current findings regarding the role of MMPs in kidney diseases as well as the mechanisms of action of this family of proteases.
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Affiliation(s)
- Roderick J Tan
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15261, USA
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